From d576f75438a1df605da93f134485e0271312d444 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Thu, 5 Sep 2024 16:47:46 -0300 Subject: [PATCH 001/486] update mirtrace (#6593) --- modules/nf-core/mirtrace/qc/main.nf | 3 +- .../nf-core/mirtrace/qc/tests/main.nf.test | 3 +- .../mirtrace/qc/tests/main.nf.test.snap | 30 ++++++++----------- 3 files changed, 14 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/mirtrace/qc/main.nf b/modules/nf-core/mirtrace/qc/main.nf index ac9575bb35c2..9d047a7a1e36 100644 --- a/modules/nf-core/mirtrace/qc/main.nf +++ b/modules/nf-core/mirtrace/qc/main.nf @@ -25,7 +25,6 @@ process MIRTRACE_QC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def file_list = reads.collect { it.toString() } """ mirtrace qc \\ @@ -33,7 +32,7 @@ process MIRTRACE_QC { --write-fasta \\ --output-dir . \\ --force \\ - ${file_list.join(' ')} + ${reads} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test b/modules/nf-core/mirtrace/qc/tests/main.nf.test index ea2f99fbf2f4..9ce14fd468c3 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test @@ -17,8 +17,7 @@ nextflow_process { input[0] = [ [ id:'test', single_end:false ], // meta map [ - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) ] ] input[1] = "hsa" diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap index 7f7f3742e298..22efdd9e9b9b 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap @@ -7,10 +7,7 @@ "id": "test", "single_end": false }, - [ - "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560", - "test_rnaseq_2.fasta:md5,302d432f8b5cbf6556e1143679c42847" - ] + "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560" ] ] ], @@ -18,7 +15,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.226466479" + "timestamp": "2024-09-05T18:05:42.043272808" }, "versions": { "content": [ @@ -41,13 +38,13 @@ "single_end": false }, [ - "mirtrace-stats-contamination_basic.tsv:md5,b668899b3ad2f006e073474122103b7a", - "mirtrace-stats-contamination_detailed.tsv:md5,84437ccb74715e956fab549f0567c5c9", - "mirtrace-stats-length.tsv:md5,37a0d254fdb800a0467c8fba7215d724", - "mirtrace-stats-mirna-complexity.tsv:md5,12cebc277d1d7873e4cb707291a82dd2", - "mirtrace-stats-phred.tsv:md5,118bbdc67433ce6fd38c74c37b0fcd3b", - "mirtrace-stats-qcstatus.tsv:md5,6bf4bf54faca386a74bb92592ae4f8ba", - "mirtrace-stats-rnatype.tsv:md5,10ec4e1ad0837efeecc97913cbab5d0f" + "mirtrace-stats-contamination_basic.tsv:md5,ac69ca6d2a709854f1048b635d06e927", + "mirtrace-stats-contamination_detailed.tsv:md5,ef80997ac12662c64cbcf5fe9851e786", + "mirtrace-stats-length.tsv:md5,54ecc0698e8e83d5b1c979b2ee3b1512", + "mirtrace-stats-mirna-complexity.tsv:md5,ab2a7600a2daa5c1797eea13d0abc2f0", + "mirtrace-stats-phred.tsv:md5,44eaeae26ec629e71fb31e56bfb5a548", + "mirtrace-stats-qcstatus.tsv:md5,623cf3a0c5e363488966844feb0dd978", + "mirtrace-stats-rnatype.tsv:md5,ed8d3a76247a1432a365def87c3f4c67" ] ] ] @@ -56,7 +53,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.194166262" + "timestamp": "2024-09-05T18:05:41.888457948" }, "human - fastq - stub": { "content": [ @@ -173,10 +170,7 @@ "id": "test", "single_end": false }, - [ - "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560", - "test_rnaseq_2.fasta:md5,302d432f8b5cbf6556e1143679c42847" - ] + "test_rnaseq_1.fasta:md5,0181296141177654088bbc2a96b29560" ] ] ], @@ -184,6 +178,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-02T13:42:28.208336131" + "timestamp": "2024-09-05T18:05:41.978281344" } } \ No newline at end of file From b5c4f7b5988ce59f1d2d15b8294e819de9414f20 Mon Sep 17 00:00:00 2001 From: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com> Date: Thu, 5 Sep 2024 23:10:01 +0100 Subject: [PATCH 002/486] Orthofinder (#6288) * working with orthofinder continue feature * Working resume test * With existing data from datasets and chose stable expected outputs. * updated snap shot (sorted) * fix test to have untar-ed workdir dir input * Fix folder direction * Add new output inputs to yml * fix tag * working conda on gitpod * force diamond install to 2.1.9 * Removed defaults --------- Co-authored-by: Usman Rashid --- modules/nf-core/orthofinder/environment.yml | 8 +- modules/nf-core/orthofinder/main.nf | 33 +- modules/nf-core/orthofinder/meta.yml | 12 + .../nf-core/orthofinder/tests/main.nf.test | 73 +++- .../orthofinder/tests/main.nf.test.snap | 353 +++--------------- 5 files changed, 149 insertions(+), 330 deletions(-) diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml index f93b9bb0e885..4239c4c18154 100644 --- a/modules/nf-core/orthofinder/environment.yml +++ b/modules/nf-core/orthofinder/environment.yml @@ -1,9 +1,7 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "orthofinder" +name: orthofinder channels: - conda-forge - bioconda - - defaults dependencies: - - "bioconda::orthofinder=2.5.5" + - bioconda::diamond=2.1.9 + - bioconda::orthofinder=2.5.5 diff --git a/modules/nf-core/orthofinder/main.nf b/modules/nf-core/orthofinder/main.nf index 2971fc0acf8b..a47c4dea36c2 100644 --- a/modules/nf-core/orthofinder/main.nf +++ b/modules/nf-core/orthofinder/main.nf @@ -9,31 +9,40 @@ process ORTHOFINDER { input: tuple val(meta), path(fastas, stageAs: 'input/') + tuple val(meta2), path(prior_run) output: - tuple val(meta), path("$prefix") , emit: orthofinder - path "versions.yml" , emit: versions + tuple val(meta), path("$prefix") , emit: orthofinder + tuple val(meta), path("$prefix/WorkingDirectory") , emit: working + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def include_command = prior_run ? "-b $prior_run" : '' + """ mkdir temp_pickle orthofinder \\ - $args \\ -t $task.cpus \\ -a $task.cpus \\ -p temp_pickle \\ -f input \\ - -n $prefix + -n $prefix \\ + $include_command \\ + $args + + if [ -e input/OrthoFinder/Results_$prefix ]; then + mv input/OrthoFinder/Results_$prefix $prefix + fi - mv \\ - input/OrthoFinder/Results_$prefix \\ - $prefix + if [ -e ${prior_run}/OrthoFinder/Results_$prefix ]; then + mv ${prior_run}/OrthoFinder/Results_$prefix $prefix + fi cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -42,8 +51,10 @@ process ORTHOFINDER { """ stub: - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def include_command = prior_run ? "-b $prior_run" : '' + """ mkdir -p $prefix/Comparative_Genomics_Statistics mkdir $prefix/Gene_Duplication_Events diff --git a/modules/nf-core/orthofinder/meta.yml b/modules/nf-core/orthofinder/meta.yml index 23cc5320bcb3..8c7689b3e86d 100644 --- a/modules/nf-core/orthofinder/meta.yml +++ b/modules/nf-core/orthofinder/meta.yml @@ -29,6 +29,15 @@ input: type: list description: Input fasta files pattern: "*.{fa,faa,fasta,fas,pep}" + - meta2: + type: map + description: | + Groovy Map containing a name + e.g. `[ id:'folder1' ]` + - prior_run: + type: directory + description: | + A folder container containing a previous WorkingDirectory from Orthofinder. output: - meta: @@ -43,6 +52,9 @@ output: - orthofinder: type: directory description: Orthofinder output directory + - working: + type: directory + description: Orthofinder output WorkingDirectory (used for the orthofinder resume function) authors: - "@GallVp" diff --git a/modules/nf-core/orthofinder/tests/main.nf.test b/modules/nf-core/orthofinder/tests/main.nf.test index 2d648004b063..aa68d1d21abb 100644 --- a/modules/nf-core/orthofinder/tests/main.nf.test +++ b/modules/nf-core/orthofinder/tests/main.nf.test @@ -9,6 +9,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "orthofinder" + tag "untar" test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome") { @@ -28,6 +29,10 @@ nextflow_process { [ id:'test', single_end:false ], [ file_a, file_b ] ] + input[1] = [ + [], + [] + ] """ } } @@ -41,8 +46,6 @@ nextflow_process { all_files << file } - def all_file_names = all_files.collect { it.name }.sort(false) - def stable_file_names = [ 'Statistics_PerSpecies.tsv', 'SpeciesTree_Gene_Duplications_0.5_Support.txt', @@ -52,8 +55,66 @@ nextflow_process { def stable_files = all_files.findAll { it.name in stable_file_names } assert snapshot( - all_file_names, - stable_files, + stable_files.toSorted(), + process.out.versions[0] + ).match() + } + + } + + + test("sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume") { + + + setup { + run("UNTAR") { + script "../../untar/main.nf" + process { + """ + input[0] = [ [ id:'test1' ], // meta map + file(params.modules_testdata_base_path + 'delete_me/orthofinder/WorkingDirectory.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true) + .copyTo("${workDir}/sarscov2.fasta") + + def file_a = file("https://raw.githubusercontent.com/nf-core/test-datasets/proteinfold/testdata/sequences/H1065.fasta") + def file_c = UNTAR.out.untar + input[0] = [ + [ id:'test_2', single_end:false ], + [ file_a ] + ] + input[1] = UNTAR.out.untar + """ + } + } + + then { + assert process.success + + def all_files = [] + + file(process.out.orthofinder[0][1]).eachFileRecurse (FileType.FILES) { file -> + all_files << file + } + + def stable_file_names = [ + 'Statistics_PerSpecies.tsv', + 'OrthologuesStats_Totals.tsv', + 'Duplications_per_Species_Tree_Node.tsv' + ] + + def stable_files = all_files.findAll { it.name in stable_file_names } + + assert snapshot( + stable_files.toSorted(), process.out.versions[0] ).match() } @@ -80,6 +141,10 @@ nextflow_process { [ id:'test', single_end:false ], [ file_a, file_b ] ] + input[1] = [ + [], + [] + ] """ } } diff --git a/modules/nf-core/orthofinder/tests/main.nf.test.snap b/modules/nf-core/orthofinder/tests/main.nf.test.snap index 8b621c052b57..f2c7b9168146 100644 --- a/modules/nf-core/orthofinder/tests/main.nf.test.snap +++ b/modules/nf-core/orthofinder/tests/main.nf.test.snap @@ -1,310 +1,6 @@ { "sarscov2 - candidatus_portiera_aleyrodidarum - proteome": { "content": [ - [ - "Blast0_0.txt.gz", - "Blast0_1.txt.gz", - "Blast1_0.txt.gz", - "Blast1_1.txt.gz", - "Citation.txt", - "Duplications.tsv", - "Duplications_per_Orthogroup.tsv", - "Duplications_per_Species_Tree_Node.tsv", - "Log.txt", - "N0.tsv", - "OG0000000.fa", - "OG0000000_tree.txt", - "OG0000000_tree.txt", - "OG0000000_tree_id.txt", - "OG0000001.fa", - "OG0000001_tree.txt", - "OG0000001_tree.txt", - "OG0000001_tree_id.txt", - "OG0000002.fa", - "OG0000003.fa", - "OG0000004.fa", - "OG0000005.fa", - "OG0000006.fa", - "OG0000007.fa", - "OG0000008.fa", - "OG0000009.fa", - "OG0000010.fa", - "OG0000011.fa", - "OG0000012.fa", - "OG0000013.fa", - "OG0000014.fa", - "OG0000015.fa", - "OG0000016.fa", - "OG0000017.fa", - "OG0000018.fa", - "OG0000019.fa", - "OG0000020.fa", - "OG0000021.fa", - "OG0000022.fa", - "OG0000023.fa", - "OG0000024.fa", - "OG0000025.fa", - "OG0000026.fa", - "OG0000027.fa", - "OG0000028.fa", - "OG0000029.fa", - "OG0000030.fa", - "OG0000031.fa", - "OG0000032.fa", - "OG0000033.fa", - "OG0000034.fa", - "OG0000035.fa", - "OG0000036.fa", - "OG0000037.fa", - "OG0000038.fa", - "OG0000039.fa", - "OG0000040.fa", - "OG0000041.fa", - "OG0000042.fa", - "OG0000043.fa", - "OG0000044.fa", - "OG0000045.fa", - "OG0000046.fa", - "OG0000047.fa", - "OG0000048.fa", - "OG0000049.fa", - "OG0000050.fa", - "OG0000051.fa", - "OG0000052.fa", - "OG0000053.fa", - "OG0000054.fa", - "OG0000055.fa", - "OG0000056.fa", - "OG0000057.fa", - "OG0000058.fa", - "OG0000059.fa", - "OG0000060.fa", - "OG0000061.fa", - "OG0000062.fa", - "OG0000063.fa", - "OG0000064.fa", - "OG0000065.fa", - "OG0000066.fa", - "OG0000067.fa", - "OG0000068.fa", - "OG0000069.fa", - "OG0000070.fa", - "OG0000071.fa", - "OG0000072.fa", - "OG0000073.fa", - "OG0000074.fa", - "OG0000075.fa", - "OG0000076.fa", - "OG0000077.fa", - "OG0000078.fa", - "OG0000079.fa", - "OG0000080.fa", - "OG0000081.fa", - "OG0000082.fa", - "OG0000083.fa", - "OG0000084.fa", - "OG0000085.fa", - "OG0000086.fa", - "OG0000087.fa", - "OG0000088.fa", - "OG0000089.fa", - "OG0000090.fa", - "OG0000091.fa", - "OG0000092.fa", - "OG0000093.fa", - "OG0000094.fa", - "OG0000095.fa", - "OG0000096.fa", - "OG0000097.fa", - "OG0000098.fa", - "OG0000099.fa", - "OG0000100.fa", - "OG0000101.fa", - "OG0000102.fa", - "OG0000103.fa", - "OG0000104.fa", - "OG0000105.fa", - "OG0000106.fa", - "OG0000107.fa", - "OG0000108.fa", - "OG0000109.fa", - "OG0000110.fa", - "OG0000111.fa", - "OG0000112.fa", - "OG0000113.fa", - "OG0000114.fa", - "OG0000115.fa", - "OG0000116.fa", - "OG0000117.fa", - "OG0000118.fa", - "OG0000119.fa", - "OG0000120.fa", - "OG0000121.fa", - "OG0000122.fa", - "OG0000123.fa", - "OG0000124.fa", - "OG0000125.fa", - "OG0000126.fa", - "OG0000127.fa", - "OG0000128.fa", - "OG0000129.fa", - "OG0000130.fa", - "OG0000131.fa", - "OG0000132.fa", - "OG0000133.fa", - "OG0000134.fa", - "OG0000135.fa", - "OG0000136.fa", - "OG0000137.fa", - "OG0000138.fa", - "OG0000139.fa", - "OG0000140.fa", - "OG0000141.fa", - "OG0000142.fa", - "OG0000143.fa", - "OG0000144.fa", - "OG0000145.fa", - "OG0000146.fa", - "OG0000147.fa", - "OG0000148.fa", - "OG0000149.fa", - "OG0000150.fa", - "OG0000151.fa", - "OG0000152.fa", - "OG0000153.fa", - "OG0000154.fa", - "OG0000155.fa", - "OG0000156.fa", - "OG0000157.fa", - "OG0000158.fa", - "OG0000159.fa", - "OG0000160.fa", - "OG0000161.fa", - "OG0000162.fa", - "OG0000163.fa", - "OG0000164.fa", - "OG0000165.fa", - "OG0000166.fa", - "OG0000167.fa", - "OG0000168.fa", - "OG0000169.fa", - "OG0000170.fa", - "OG0000171.fa", - "OG0000172.fa", - "OG0000173.fa", - "OG0000174.fa", - "OG0000175.fa", - "OG0000176.fa", - "OG0000177.fa", - "OG0000178.fa", - "OG0000179.fa", - "OG0000180.fa", - "OG0000181.fa", - "OG0000182.fa", - "OG0000183.fa", - "OG0000184.fa", - "OG0000185.fa", - "OG0000186.fa", - "OG0000187.fa", - "OG0000188.fa", - "OG0000189.fa", - "OG0000190.fa", - "OG0000191.fa", - "OG0000192.fa", - "OG0000193.fa", - "OG0000194.fa", - "OG0000195.fa", - "OG0000196.fa", - "OG0000197.fa", - "OG0000198.fa", - "OG0000199.fa", - "OG0000200.fa", - "OG0000201.fa", - "OG0000202.fa", - "OG0000203.fa", - "OG0000204.fa", - "OG0000205.fa", - "OG0000206.fa", - "OG0000207.fa", - "OG0000208.fa", - "OG0000209.fa", - "OG0000210.fa", - "OG0000211.fa", - "OG0000212.fa", - "OG0000213.fa", - "OG0000214.fa", - "OG0000215.fa", - "OG0000216.fa", - "OG0000217.fa", - "OG0000218.fa", - "OG0000219.fa", - "OG0000220.fa", - "OG0000221.fa", - "OG0000222.fa", - "OG0000223.fa", - "OG0000224.fa", - "OG0000225.fa", - "OG0000226.fa", - "OG0000227.fa", - "OG0000228.fa", - "OG0000229.fa", - "OG0000230.fa", - "OG0000231.fa", - "OG0000232.fa", - "OG0000233.fa", - "OG0000234.fa", - "OG0000235.fa", - "OG0000236.fa", - "OG0000237.fa", - "OG0000238.fa", - "OG0000239.fa", - "OG0000240.fa", - "OG0000241.fa", - "OG0000242.fa", - "OG0000243.fa", - "OG0000244.fa", - "OG0000245.fa", - "OrthoFinder_graph.txt", - "Orthogroups.GeneCount.tsv", - "Orthogroups.tsv", - "Orthogroups.txt", - "Orthogroups_SingleCopyOrthologues.txt", - "Orthogroups_SpeciesOverlaps.tsv", - "Orthogroups_UnassignedGenes.tsv", - "OrthologuesStats_Totals.tsv", - "OrthologuesStats_many-to-many.tsv", - "OrthologuesStats_many-to-one.tsv", - "OrthologuesStats_one-to-many.tsv", - "OrthologuesStats_one-to-one.tsv", - "SequenceIDs.txt", - "SimpleTest.phy", - "SimpleTest.phy_fastme_stat.txt", - "SimpleTest.tre", - "Species0.fa", - "Species0.fa", - "Species1.fa", - "SpeciesIDs.txt", - "SpeciesTree_Gene_Duplications_0.5_Support.txt", - "SpeciesTree_rooted.txt", - "SpeciesTree_rooted_ids.txt", - "SpeciesTree_rooted_node_labels.txt", - "SpeciesTree_unrooted.txt", - "SpeciesTree_unrooted_ids.txt", - "Statistics_Overall.tsv", - "Statistics_PerSpecies.tsv", - "candidatus_portiera_aleyrodidarum.tsv", - "candidatus_portiera_aleyrodidarum.tsv", - "candidatus_portiera_aleyrodidarum__v__sarscov2.tsv", - "clusters_OrthoFinder_I1.5.txt", - "clusters_OrthoFinder_I1.5.txt_id_pairs.txt", - "diamondDBSpecies0.dmnd", - "diamondDBSpecies0.dmnd", - "diamondDBSpecies1.dmnd", - "sarscov2.tsv", - "sarscov2.tsv", - "sarscov2__v__candidatus_portiera_aleyrodidarum.tsv", - "test_search_results.txt.gz" - ], [ "Statistics_PerSpecies.tsv:md5,984b5011a34d54527fe17896bfa36a2d", "SpeciesTree_Gene_Duplications_0.5_Support.txt:md5,8b7a673e2e8b6d1aeb697f2bb88afa18", @@ -313,10 +9,10 @@ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-07T21:33:50.902329" + "timestamp": "2024-09-03T10:59:02.895708598" }, "sarscov2 - candidatus_portiera_aleyrodidarum - proteome - stub": { "content": [ @@ -372,6 +68,17 @@ ] ], "1": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] + ], + "2": [ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" ], "orthofinder": [ @@ -426,13 +133,39 @@ ], "versions": [ "versions.yml:md5,86b472c85626aac1840eec0769016f5c" + ], + "working": [ + [ + { + "id": "test", + "single_end": false + }, + [ + + ] + ] ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T11:07:31.319665056" + }, + "sarscov2 - candidatus_portiera_aleyrodidarum - proteome - resume": { + "content": [ + [ + "Duplications_per_Species_Tree_Node.tsv:md5,addc6f5ceec40bd82b00038d1872a27c", + "OrthologuesStats_Totals.tsv:md5,20d243abef226051a43cb37e922fc3eb", + "Statistics_PerSpecies.tsv:md5,83174c383b6c6828d1cc9b3be1679890" + ], + "versions.yml:md5,86b472c85626aac1840eec0769016f5c" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-07T16:00:56.530716" + "timestamp": "2024-09-03T11:04:10.916947006" } } \ No newline at end of file From 449e04b5f180aef9c22ff63c2bb9bc8a6cf21e16 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:27:03 +1200 Subject: [PATCH 003/486] Added nf-test for homer/annotatepeaks (#6573) * Added nf-test for homer/annotatepeaks * Removed defaults --- .../homer/annotatepeaks/environment.yml | 1 - modules/nf-core/homer/annotatepeaks/main.nf | 12 ++++ .../homer/annotatepeaks/tests/main.nf.test | 68 +++++++++++++++++++ .../annotatepeaks/tests/main.nf.test.snap | 62 +++++++++++++++++ .../homer/annotatepeaks/tests/nextflow.config | 3 + tests/config/pytest_modules.yml | 3 - .../nf-core/homer/annotatepeaks/main.nf | 14 ---- .../homer/annotatepeaks/nextflow.config | 6 -- .../nf-core/homer/annotatepeaks/test.yml | 8 --- 9 files changed, 145 insertions(+), 32 deletions(-) create mode 100644 modules/nf-core/homer/annotatepeaks/tests/main.nf.test create mode 100644 modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap create mode 100644 modules/nf-core/homer/annotatepeaks/tests/nextflow.config delete mode 100644 tests/modules/nf-core/homer/annotatepeaks/main.nf delete mode 100644 tests/modules/nf-core/homer/annotatepeaks/nextflow.config delete mode 100644 tests/modules/nf-core/homer/annotatepeaks/test.yml diff --git a/modules/nf-core/homer/annotatepeaks/environment.yml b/modules/nf-core/homer/annotatepeaks/environment.yml index aef00e188a90..f6522d695038 100644 --- a/modules/nf-core/homer/annotatepeaks/environment.yml +++ b/modules/nf-core/homer/annotatepeaks/environment.yml @@ -2,6 +2,5 @@ name: homer_annotatepeaks channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11 diff --git a/modules/nf-core/homer/annotatepeaks/main.nf b/modules/nf-core/homer/annotatepeaks/main.nf index 32478df4124c..d3d752c8302e 100644 --- a/modules/nf-core/homer/annotatepeaks/main.nf +++ b/modules/nf-core/homer/annotatepeaks/main.nf @@ -39,4 +39,16 @@ process HOMER_ANNOTATEPEAKS { homer: $VERSION END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.annotatePeaks.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + homer: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test new file mode 100644 index 000000000000..e54c4b907681 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test @@ -0,0 +1,68 @@ + +nextflow_process { + + name "Test Process HOMER_ANNOTATEPEAKS" + script "../main.nf" + process "HOMER_ANNOTATEPEAKS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "homer" + tag "homer/annotatepeaks" + + test("test-homer-annotatepeaks") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.txt[0][1]).name, // unstable + process.out.stats, + process.out.versions + ).match() + } + ) + } + } + + test("test-homer-annotatepeaks-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap new file mode 100644 index 000000000000..0d6c813b2b13 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "test-homer-annotatepeaks-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ], + "stats": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.annotatePeaks.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:21:30.264399" + }, + "test-homer-annotatepeaks": { + "content": [ + "test.annotatePeaks.txt", + [ + [ + { + "id": "test" + }, + "test.annStats.txt:md5,eba336bce28fb5ec5d4ea3215b502dc5" + ] + ], + [ + "versions.yml:md5,d109521b6e43672cf246fd269b3833c8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:28:26.487711" + } +} \ No newline at end of file diff --git a/modules/nf-core/homer/annotatepeaks/tests/nextflow.config b/modules/nf-core/homer/annotatepeaks/tests/nextflow.config new file mode 100644 index 000000000000..309aac551b00 --- /dev/null +++ b/modules/nf-core/homer/annotatepeaks/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = {"-annStats ${meta.id}.annStats.txt"} +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 6cec5cab4082..d3187a9dfa57 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -356,9 +356,6 @@ hmmer/hmmbuild: hmtnote/annotate: - modules/nf-core/hmtnote/annotate/** - tests/modules/nf-core/hmtnote/annotate/** -homer/annotatepeaks: - - modules/nf-core/homer/annotatepeaks/** - - tests/modules/nf-core/homer/annotatepeaks/** homer/makeucscfile: - modules/nf-core/homer/makeucscfile/** - tests/modules/nf-core/homer/makeucscfile/** diff --git a/tests/modules/nf-core/homer/annotatepeaks/main.nf b/tests/modules/nf-core/homer/annotatepeaks/main.nf deleted file mode 100644 index cfd52c1ba494..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HOMER_ANNOTATEPEAKS } from '../../../../../modules/nf-core/homer/annotatepeaks/main.nf' - -workflow test_homer_annotatepeaks { - input = [ [ id:'test'], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - HOMER_ANNOTATEPEAKS ( input, fasta, gtf ) -} diff --git a/tests/modules/nf-core/homer/annotatepeaks/nextflow.config b/tests/modules/nf-core/homer/annotatepeaks/nextflow.config deleted file mode 100644 index 86470e916848..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/nextflow.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - ext.args = {"-annStats ${meta.id}.annStats.txt"} - -} diff --git a/tests/modules/nf-core/homer/annotatepeaks/test.yml b/tests/modules/nf-core/homer/annotatepeaks/test.yml deleted file mode 100644 index 9a07bc5d597e..000000000000 --- a/tests/modules/nf-core/homer/annotatepeaks/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: homer annotatepeaks test_homer_annotatepeaks - command: nextflow run ./tests/modules/nf-core/homer/annotatepeaks -entry test_homer_annotatepeaks -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/homer/annotatepeaks/nextflow.config - tags: - - homer - - homer/annotatepeaks - files: - - path: output/homer/test.annotatePeaks.txt - - path: output/homer/test.annStats.txt From b8717ccb7d673ffb95c7a9db7abab70c78966874 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:28:21 +1200 Subject: [PATCH 004/486] Added nf-test for emboss/revseq (#6581) * Added nf-test for emboss/revseq * Removed defaults --- modules/nf-core/emboss/revseq/environment.yml | 1 - .../nf-core/emboss/revseq/tests/main.nf.test | 57 +++++++++++++++ .../emboss/revseq/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/emboss/revseq/main.nf | 15 ---- .../nf-core/emboss/revseq/nextflow.config | 5 -- tests/modules/nf-core/emboss/revseq/test.yml | 9 --- 7 files changed, 129 insertions(+), 33 deletions(-) create mode 100644 modules/nf-core/emboss/revseq/tests/main.nf.test create mode 100644 modules/nf-core/emboss/revseq/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/emboss/revseq/main.nf delete mode 100644 tests/modules/nf-core/emboss/revseq/nextflow.config delete mode 100644 tests/modules/nf-core/emboss/revseq/test.yml diff --git a/modules/nf-core/emboss/revseq/environment.yml b/modules/nf-core/emboss/revseq/environment.yml index cc8acbdfe674..5e2d20e5b7cf 100644 --- a/modules/nf-core/emboss/revseq/environment.yml +++ b/modules/nf-core/emboss/revseq/environment.yml @@ -2,6 +2,5 @@ name: emboss_revseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::emboss=6.6.0 diff --git a/modules/nf-core/emboss/revseq/tests/main.nf.test b/modules/nf-core/emboss/revseq/tests/main.nf.test new file mode 100644 index 000000000000..b8f980ea6db2 --- /dev/null +++ b/modules/nf-core/emboss/revseq/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process EMBOSS_REVSEQ" + script "../main.nf" + process "EMBOSS_REVSEQ" + + tag "modules" + tag "modules_nfcore" + tag "emboss" + tag "emboss/revseq" + + test("test-emboss-revseq") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-emboss-revseq-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/emboss/revseq/tests/main.nf.test.snap b/modules/nf-core/emboss/revseq/tests/main.nf.test.snap new file mode 100644 index 000000000000..cf064fbebb51 --- /dev/null +++ b/modules/nf-core/emboss/revseq/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-emboss-revseq-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ], + "revseq": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:23:57.293555" + }, + "test-emboss-revseq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,78a4b77f08b5c95ab24e592f543f679c" + ] + ], + "1": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ], + "revseq": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rev.fasta:md5,78a4b77f08b5c95ab24e592f543f679c" + ] + ], + "versions": [ + "versions.yml:md5,6036bdf4f510114f18e8304e88b7c453" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:23:52.761673" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index d3187a9dfa57..53c4bc67d97e 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -169,9 +169,6 @@ elprep/filter: elprep/merge: - modules/nf-core/elprep/merge/** - tests/modules/nf-core/elprep/merge/** -emboss/revseq: - - modules/nf-core/emboss/revseq/** - - tests/modules/nf-core/emboss/revseq/** emboss/seqret: - modules/nf-core/emboss/seqret/** - tests/modules/nf-core/emboss/seqret/** diff --git a/tests/modules/nf-core/emboss/revseq/main.nf b/tests/modules/nf-core/emboss/revseq/main.nf deleted file mode 100644 index f6a5cf1e684e..000000000000 --- a/tests/modules/nf-core/emboss/revseq/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { EMBOSS_REVSEQ } from '../../../../../modules/nf-core/emboss/revseq/main.nf' - -workflow test_emboss_revseq { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - EMBOSS_REVSEQ ( input ) -} diff --git a/tests/modules/nf-core/emboss/revseq/nextflow.config b/tests/modules/nf-core/emboss/revseq/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/emboss/revseq/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/emboss/revseq/test.yml b/tests/modules/nf-core/emboss/revseq/test.yml deleted file mode 100644 index 5cbc7e368f78..000000000000 --- a/tests/modules/nf-core/emboss/revseq/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: emboss revseq test_emboss_revseq - command: nextflow run ./tests/modules/nf-core/emboss/revseq -entry test_emboss_revseq -c ./tests/config/nextflow.config - tags: - - emboss/revseq - - emboss - files: - - path: output/emboss/test.rev.fasta - md5sum: 78a4b77f08b5c95ab24e592f543f679c - - path: output/emboss/versions.yml From c1b71e1acbea37b87cf9685518243b0ae71df013 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:29:07 +1200 Subject: [PATCH 005/486] Added nf-test for hapibd (#6575) * Added nf-test for hapibd * Removed defaults --- modules/nf-core/hapibd/environment.yml | 1 - modules/nf-core/hapibd/main.nf | 21 ++++ modules/nf-core/hapibd/meta.yml | 2 +- modules/nf-core/hapibd/tests/main.nf.test | 99 +++++++++++++++++ .../nf-core/hapibd/tests/main.nf.test.snap | 103 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/hapibd/main.nf | 28 ----- tests/modules/nf-core/hapibd/nextflow.config | 5 - tests/modules/nf-core/hapibd/test.yml | 21 ---- 9 files changed, 224 insertions(+), 59 deletions(-) create mode 100644 modules/nf-core/hapibd/tests/main.nf.test create mode 100644 modules/nf-core/hapibd/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/hapibd/main.nf delete mode 100644 tests/modules/nf-core/hapibd/nextflow.config delete mode 100644 tests/modules/nf-core/hapibd/test.yml diff --git a/modules/nf-core/hapibd/environment.yml b/modules/nf-core/hapibd/environment.yml index 2902e831e196..4c2f52d3d384 100644 --- a/modules/nf-core/hapibd/environment.yml +++ b/modules/nf-core/hapibd/environment.yml @@ -2,6 +2,5 @@ name: hapibd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hap-ibd=1.0.rev20May22.818 diff --git a/modules/nf-core/hapibd/main.nf b/modules/nf-core/hapibd/main.nf index cd920ca29a18..92c355b65e74 100644 --- a/modules/nf-core/hapibd/main.nf +++ b/modules/nf-core/hapibd/main.nf @@ -47,4 +47,25 @@ process HAPIBD { hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar \\[ version //; s/, /rev/; s/ \\]//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[hapibd] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + + """ + touch ${prefix}.log + echo | gzip > ${prefix}.hbd.gz + echo | gzip > ${prefix}.ibd.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hapibd: \$(hap-ibd 2>&1 |head -n1 | sed 's/^hap-ibd.jar \\[ version //; s/, /rev/; s/ \\]//') + END_VERSIONS + """ } diff --git a/modules/nf-core/hapibd/meta.yml b/modules/nf-core/hapibd/meta.yml index 686ae88bf22d..8def0c8d6625 100644 --- a/modules/nf-core/hapibd/meta.yml +++ b/modules/nf-core/hapibd/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" doi: "10.1016/j.ajhg.2020.02.010" - licence: "['Apache-2.0']" + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/nf-core/hapibd/tests/main.nf.test b/modules/nf-core/hapibd/tests/main.nf.test new file mode 100644 index 000000000000..85d14460690e --- /dev/null +++ b/modules/nf-core/hapibd/tests/main.nf.test @@ -0,0 +1,99 @@ + +nextflow_process { + + name "Test Process HAPIBD" + script "../main.nf" + process "HAPIBD" + + tag "modules" + tag "modules_nfcore" + tag "hapibd" + + test("test-hapibd") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('End Time') }, + { assert snapshot( + file(process.out.hbd[0][1]).name, // empty + file(process.out.ibd[0][1]).name, // unstable + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-hapibd-excludesamples") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.log[0][1]).text.contains('End Time') }, + { assert snapshot( + file(process.out.hbd[0][1]).name, // empty + file(process.out.ibd[0][1]).name, // unstable + file(process.out.log[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-hapibd-excludesamples-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) + ] + input[1] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) + input[2] = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hapibd/tests/main.nf.test.snap b/modules/nf-core/hapibd/tests/main.nf.test.snap new file mode 100644 index 000000000000..b5a5951f27f5 --- /dev/null +++ b/modules/nf-core/hapibd/tests/main.nf.test.snap @@ -0,0 +1,103 @@ +{ + "test-hapibd": { + "content": [ + "test.hbd.gz", + "test.ibd.gz", + "test.log", + [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:50:07.8312" + }, + "test-hapibd-excludesamples": { + "content": [ + "test.hbd.gz", + "test.ibd.gz", + "test.log", + [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:50:29.730739" + }, + "test-hapibd-excludesamples-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ], + "hbd": [ + [ + { + "id": "test", + "single_end": false + }, + "test.hbd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "ibd": [ + [ + { + "id": "test", + "single_end": false + }, + "test.ibd.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "log": [ + [ + { + "id": "test", + "single_end": false + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,27c1ec7c19884a358c01031f02604c2a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:40:49.71258" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 53c4bc67d97e..57288b26ea92 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -323,9 +323,6 @@ gunc/mergecheckm: gunc/run: - modules/nf-core/gunc/run/** - tests/modules/nf-core/gunc/run/** -hapibd: - - modules/nf-core/hapibd/** - - tests/modules/nf-core/hapibd/** hicexplorer/hicpca: - modules/nf-core/hicexplorer/hicpca/** - tests/modules/nf-core/hicexplorer/hicpca/** diff --git a/tests/modules/nf-core/hapibd/main.nf b/tests/modules/nf-core/hapibd/main.nf deleted file mode 100644 index 3a7a0deb4da6..000000000000 --- a/tests/modules/nf-core/hapibd/main.nf +++ /dev/null @@ -1,28 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HAPIBD } from '../../../../modules/nf-core/hapibd/main.nf' - -workflow test_hapibd { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) - ] - map = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) - - HAPIBD ( input, map, [] ) -} - -workflow test_hapibd_excludesamples { - - input = [ - [ id:'test', single_end:false ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.truth.vcf.gz", checkIfExists: true) - ] - map = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/target.map", checkIfExists: true) - exclude = file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hapibd/excludeSamples.txt", checkIfExists: true) - - HAPIBD ( input, map, exclude ) -} diff --git a/tests/modules/nf-core/hapibd/nextflow.config b/tests/modules/nf-core/hapibd/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/hapibd/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/hapibd/test.yml b/tests/modules/nf-core/hapibd/test.yml deleted file mode 100644 index 12f5192db221..000000000000 --- a/tests/modules/nf-core/hapibd/test.yml +++ /dev/null @@ -1,21 +0,0 @@ -- name: hapibd test_hapibd - command: nextflow run ./tests/modules/nf-core/hapibd -entry test_hapibd -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hapibd/nextflow.config - tags: - - hapibd - files: - - path: output/hapibd/test.hbd.gz # this is an empty file for this test example - - path: output/hapibd/test.ibd.gz - contains: ["I3019"] - - path: output/hapibd/test.log - contains: ["hap-ibd.jar"] - -- name: hapibd test_hapibd_excludesamples - command: nextflow run ./tests/modules/nf-core/hapibd -entry test_hapibd_excludesamples -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hapibd/nextflow.config - tags: - - hapibd - files: - - path: output/hapibd/test.hbd.gz # this is an empty file for this test example - - path: output/hapibd/test.ibd.gz - contains: ["I3019"] - - path: output/hapibd/test.log - contains: ["hap-ibd.jar"] From 04d7c5945837365cc63f2309c9e48e50943f212c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:41:06 +1200 Subject: [PATCH 006/486] Added nf-test for hypo (#6571) * Added nf-test for hypo * Removed defaults --- modules/nf-core/hypo/environment.yml | 1 - modules/nf-core/hypo/meta.yml | 2 +- modules/nf-core/hypo/tests/main.nf.test | 76 ++++++++++++++++++++ modules/nf-core/hypo/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/hypo/main.nf | 24 ------- tests/modules/nf-core/hypo/nextflow.config | 5 -- tests/modules/nf-core/hypo/test.yml | 9 --- 8 files changed, 149 insertions(+), 43 deletions(-) create mode 100644 modules/nf-core/hypo/tests/main.nf.test create mode 100644 modules/nf-core/hypo/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/hypo/main.nf delete mode 100644 tests/modules/nf-core/hypo/nextflow.config delete mode 100644 tests/modules/nf-core/hypo/test.yml diff --git a/modules/nf-core/hypo/environment.yml b/modules/nf-core/hypo/environment.yml index dd2c6e25118b..70e432fada78 100644 --- a/modules/nf-core/hypo/environment.yml +++ b/modules/nf-core/hypo/environment.yml @@ -2,6 +2,5 @@ name: hypo channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hypo=1.0.3 diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml index 36a7e714f752..002b418f5c8c 100644 --- a/modules/nf-core/hypo/meta.yml +++ b/modules/nf-core/hypo/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/kensung-lab/hypo/blob/master/README.md" tool_dev_url: "https://github.com/kensung-lab/hypo" doi: "10.1101/2019.12.19.882506" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/hypo/tests/main.nf.test b/modules/nf-core/hypo/tests/main.nf.test new file mode 100644 index 000000000000..06fb15906f07 --- /dev/null +++ b/modules/nf-core/hypo/tests/main.nf.test @@ -0,0 +1,76 @@ + +nextflow_process { + + name "Test Process HYPO" + script "../main.nf" + process "HYPO" + + tag "modules" + tag "modules_nfcore" + tag "hypo" + + test("test-hypo") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = 29903 + input[4] = 5 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-hypo-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + ] + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = 29903 + input[4] = 5 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hypo/tests/main.nf.test.snap b/modules/nf-core/hypo/tests/main.nf.test.snap new file mode 100644 index 000000000000..999ec08c13df --- /dev/null +++ b/modules/nf-core/hypo/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-hypo-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:15:49.822312" + }, + "test-hypo": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad" + ] + ], + "1": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ], + "fasta": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fasta:md5,d326ff4fc91e25617c43d678f68187ad" + ] + ], + "versions": [ + "versions.yml:md5,9529d9976a97d2d8e2d1cc00035906c9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:15:37.149543" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 57288b26ea92..b3f44e9f2940 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -353,9 +353,6 @@ hmtnote/annotate: homer/makeucscfile: - modules/nf-core/homer/makeucscfile/** - tests/modules/nf-core/homer/makeucscfile/** -hypo: - - modules/nf-core/hypo/** - - tests/modules/nf-core/hypo/** icountmini/metagene: - modules/nf-core/icountmini/metagene/** - tests/modules/nf-core/icountmini/metagene/** diff --git a/tests/modules/nf-core/hypo/main.nf b/tests/modules/nf-core/hypo/main.nf deleted file mode 100644 index 89b169fc58eb..000000000000 --- a/tests/modules/nf-core/hypo/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HYPO } from '../../../../modules/nf-core/hypo/main.nf' - -workflow test_hypo { - - bam_sr = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - reads = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) - ] - ] - draft = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - genome_size = 29903 - reads_coverage = 5 - HYPO ( bam_sr, reads, draft, genome_size, reads_coverage ) -} diff --git a/tests/modules/nf-core/hypo/nextflow.config b/tests/modules/nf-core/hypo/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/hypo/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/hypo/test.yml b/tests/modules/nf-core/hypo/test.yml deleted file mode 100644 index f298d04ea897..000000000000 --- a/tests/modules/nf-core/hypo/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: "hypo" - command: nextflow run ./tests/modules/nf-core/hypo -entry test_hypo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hypo/nextflow.config - tags: - - "hypo" - files: - - path: "output/hypo/test.fasta" - md5sum: d326ff4fc91e25617c43d678f68187ad - - path: "output/hypo/versions.yml" - md5sum: 34233e4c5530683bf3c9e890e2b20e91 From 73694be9f7c2673f07af77664648b02783da8bb0 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:41:25 +1200 Subject: [PATCH 007/486] Added nf-test for hmmer/hmmbuild (#6576) * Added nf-test for hmmer/hmmbuild * Removed defaults --- .../nf-core/hmmer/hmmbuild/environment.yml | 1 - modules/nf-core/hmmer/hmmbuild/main.nf | 12 ++++ modules/nf-core/hmmer/hmmbuild/meta.yml | 2 +- .../nf-core/hmmer/hmmbuild/tests/main.nf.test | 66 +++++++++++++++++++ .../hmmer/hmmbuild/tests/main.nf.test.snap | 55 ++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/hmmer/hmmbuild/main.nf | 15 ----- .../nf-core/hmmer/hmmbuild/nextflow.config | 5 -- tests/modules/nf-core/hmmer/hmmbuild/test.yml | 12 ---- 9 files changed, 134 insertions(+), 37 deletions(-) create mode 100644 modules/nf-core/hmmer/hmmbuild/tests/main.nf.test create mode 100644 modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/hmmer/hmmbuild/main.nf delete mode 100644 tests/modules/nf-core/hmmer/hmmbuild/nextflow.config delete mode 100644 tests/modules/nf-core/hmmer/hmmbuild/test.yml diff --git a/modules/nf-core/hmmer/hmmbuild/environment.yml b/modules/nf-core/hmmer/hmmbuild/environment.yml index 1957ad5c63aa..5eb083ed9ed9 100644 --- a/modules/nf-core/hmmer/hmmbuild/environment.yml +++ b/modules/nf-core/hmmer/hmmbuild/environment.yml @@ -2,6 +2,5 @@ name: hmmer_hmmbuild channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmbuild/main.nf b/modules/nf-core/hmmer/hmmbuild/main.nf index 3e3022fe643a..b4629cb47a65 100644 --- a/modules/nf-core/hmmer/hmmbuild/main.nf +++ b/modules/nf-core/hmmer/hmmbuild/main.nf @@ -41,4 +41,16 @@ process HMMER_HMMBUILD { hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo | gzip > ${prefix}.hmm.gz + touch ${prefix}.hmmbuild.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + hmmer: \$(echo \$(hmmbuild -h | grep HMMER | sed 's/# HMMER //' | sed 's/ .*//' 2>&1)) + END_VERSIONS + """ } diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index 4bf6b1cfee90..fb9d50830016 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "http://hmmer.org/documentation.html" tool_dev_url: "https://github.com/EddyRivasLab/hmmer" doi: "10.1371/journal.pcbi.1002195" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test new file mode 100644 index 000000000000..d7c058255eaa --- /dev/null +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test @@ -0,0 +1,66 @@ + +nextflow_process { + + name "Test Process HMMER_HMMBUILD" + script "../main.nf" + process "HMMER_HMMBUILD" + + tag "modules" + tag "modules_nfcore" + tag "hmmer" + tag "hmmer/hmmbuild" + + test("test-hmmer-hmmbuild") { + + when { + process { + """ + input[0] = [ + [ id: 'PF14720' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.hmmbuildout[0]).text.contains('CPU time:') }, + { assert snapshot( + file(process.out.hmm[0][1]).name, // unstable + file(process.out.hmmbuildout[0]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-hmmer-hmmbuild-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'PF14720' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) + ] + input[1] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap new file mode 100644 index 000000000000..8cdff17c1420 --- /dev/null +++ b/modules/nf-core/hmmer/hmmbuild/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "test-hmmer-hmmbuild-stub": { + "content": [ + { + "0": [ + [ + { + "id": "PF14720" + }, + "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ], + "hmm": [ + [ + { + "id": "PF14720" + }, + "PF14720.hmm.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "hmmbuildout": [ + "PF14720.hmmbuild.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:38:44.751216" + }, + "test-hmmer-hmmbuild": { + "content": [ + "PF14720.hmm.gz", + "PF14720.hmmbuild.txt", + [ + "versions.yml:md5,6f4796b714cb0d5981cd12d9e89cb599" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:49:25.772308" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b3f44e9f2940..7f7f1e143484 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -344,9 +344,6 @@ hmmer/eslreformat: hmmer/hmmalign: - modules/nf-core/hmmer/hmmalign/** - tests/modules/nf-core/hmmer/hmmalign/** -hmmer/hmmbuild: - - modules/nf-core/hmmer/hmmbuild/** - - tests/modules/nf-core/hmmer/hmmbuild/** hmtnote/annotate: - modules/nf-core/hmtnote/annotate/** - tests/modules/nf-core/hmtnote/annotate/** diff --git a/tests/modules/nf-core/hmmer/hmmbuild/main.nf b/tests/modules/nf-core/hmmer/hmmbuild/main.nf deleted file mode 100644 index 7bd3a4b3a5f9..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HMMER_HMMBUILD } from '../../../../../modules/nf-core/hmmer/hmmbuild/main.nf' - -workflow test_hmmer_hmmbuild { - - input = [ - [ id: 'PF14720' ], // meta map - file('https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/hmmer/PF14720_seed.alnfaa.gz', checkIfExists: true) - ] - - HMMER_HMMBUILD ( input, [] ) -} diff --git a/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config b/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/hmmer/hmmbuild/test.yml b/tests/modules/nf-core/hmmer/hmmbuild/test.yml deleted file mode 100644 index be321bf489a1..000000000000 --- a/tests/modules/nf-core/hmmer/hmmbuild/test.yml +++ /dev/null @@ -1,12 +0,0 @@ -- name: hmmer hmmbuild test_hmmer_hmmbuild - command: nextflow run ./tests/modules/nf-core/hmmer/hmmbuild -entry test_hmmer_hmmbuild -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/hmmer/hmmbuild/nextflow.config - tags: - - hmmer - - hmmer/hmmbuild - files: - - path: output/hmmer/PF14720.hmm.gz - contains: - - "LENG 80" - - path: output/hmmer/versions.yml - contains: - - "hmmer:" From 50b3cbc6167e6e17c5322a9d13f4f8997f98c457 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:45:15 +1200 Subject: [PATCH 008/486] Added nf-test for legsta (#6566) * Added nf-test for legsta * Removed defaults --- modules/nf-core/legsta/environment.yml | 1 - modules/nf-core/legsta/main.nf | 11 +++ modules/nf-core/legsta/meta.yml | 2 + modules/nf-core/legsta/tests/main.nf.test | 57 +++++++++++++++ .../nf-core/legsta/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/legsta/main.nf | 15 ---- tests/modules/nf-core/legsta/nextflow.config | 5 -- tests/modules/nf-core/legsta/test.yml | 9 --- 9 files changed, 142 insertions(+), 33 deletions(-) create mode 100644 modules/nf-core/legsta/tests/main.nf.test create mode 100644 modules/nf-core/legsta/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/legsta/main.nf delete mode 100644 tests/modules/nf-core/legsta/nextflow.config delete mode 100644 tests/modules/nf-core/legsta/test.yml diff --git a/modules/nf-core/legsta/environment.yml b/modules/nf-core/legsta/environment.yml index 34d11fcfbe37..ae157ec4a905 100644 --- a/modules/nf-core/legsta/environment.yml +++ b/modules/nf-core/legsta/environment.yml @@ -2,6 +2,5 @@ name: legsta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::legsta=0.5.1 diff --git a/modules/nf-core/legsta/main.nf b/modules/nf-core/legsta/main.nf index d28d01bbb3e2..d776d64153f1 100644 --- a/modules/nf-core/legsta/main.nf +++ b/modules/nf-core/legsta/main.nf @@ -30,4 +30,15 @@ process LEGSTA { legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + legsta: \$(echo \$(legsta --version 2>&1) | sed 's/^.*legsta //; s/ .*\$//;') + END_VERSIONS + """ } diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml index 399438332392..734498e06126 100644 --- a/modules/nf-core/legsta/meta.yml +++ b/modules/nf-core/legsta/meta.yml @@ -3,6 +3,8 @@ description: Typing of clinical and environmental isolates of Legionella pneumop keywords: - bacteria - legionella + - clinical + - pneumophila tools: - legsta: description: In silico Legionella pneumophila Sequence Based Typing diff --git a/modules/nf-core/legsta/tests/main.nf.test b/modules/nf-core/legsta/tests/main.nf.test new file mode 100644 index 000000000000..bed639db0a6b --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test @@ -0,0 +1,57 @@ + +nextflow_process { + + name "Test Process LEGSTA" + script "../main.nf" + process "LEGSTA" + + tag "modules" + tag "modules_nfcore" + tag "legsta" + + test("test-legsta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-legsta-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/legsta/tests/main.nf.test.snap b/modules/nf-core/legsta/tests/main.nf.test.snap new file mode 100644 index 000000000000..54adc1906f77 --- /dev/null +++ b/modules/nf-core/legsta/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-legsta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,c493bdd19335de4828aa8b4e3ce7e1f8" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:21.017956" + }, + "test-legsta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,a853be87d21977365afe63ef07450a44" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:09:26.594828" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 7f7f1e143484..1854ac037dca 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -428,9 +428,6 @@ krona/ktupdatetaxonomy: leehom: - modules/nf-core/leehom/** - tests/modules/nf-core/leehom/** -legsta: - - modules/nf-core/legsta/** - - tests/modules/nf-core/legsta/** limma/differential: - modules/nf-core/limma/differential/** - tests/modules/nf-core/limma/differential/** diff --git a/tests/modules/nf-core/legsta/main.nf b/tests/modules/nf-core/legsta/main.nf deleted file mode 100644 index b74a9cf278a6..000000000000 --- a/tests/modules/nf-core/legsta/main.nf +++ /dev/null @@ -1,15 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { LEGSTA } from '../../../../modules/nf-core/legsta/main.nf' - -workflow test_legsta { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - LEGSTA ( input ) -} diff --git a/tests/modules/nf-core/legsta/nextflow.config b/tests/modules/nf-core/legsta/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/legsta/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/legsta/test.yml b/tests/modules/nf-core/legsta/test.yml deleted file mode 100644 index 6d193422d341..000000000000 --- a/tests/modules/nf-core/legsta/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: legsta test_legsta - command: nextflow run ./tests/modules/nf-core/legsta -entry test_legsta -c ./tests/config/nextflow.config - tags: - - legsta - files: - - path: output/legsta/test.tsv - md5sum: c493bdd19335de4828aa8b4e3ce7e1f8 - - path: output/legsta/versions.yml - md5sum: d16c5f6fd68d2bcc2c71954e3342aabe From bf39676ede488ab5ef5deeded118c88ac92a072c Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 10:50:43 +1200 Subject: [PATCH 009/486] Added nf-test for cnvkit/call (#6582) * Added nf-test for cnvkit/call * Removed defaults --- modules/nf-core/cnvkit/call/environment.yml | 1 - modules/nf-core/cnvkit/call/main.nf | 11 ++ .../nf-core/cnvkit/call/tests/main.nf.test | 83 ++++++++++++++ .../cnvkit/call/tests/main.nf.test.snap | 107 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/cnvkit/call/main.nf | 27 ----- .../nf-core/cnvkit/call/nextflow.config | 5 - tests/modules/nf-core/cnvkit/call/test.yml | 19 ---- 8 files changed, 201 insertions(+), 55 deletions(-) create mode 100644 modules/nf-core/cnvkit/call/tests/main.nf.test create mode 100644 modules/nf-core/cnvkit/call/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/cnvkit/call/main.nf delete mode 100644 tests/modules/nf-core/cnvkit/call/nextflow.config delete mode 100644 tests/modules/nf-core/cnvkit/call/test.yml diff --git a/modules/nf-core/cnvkit/call/environment.yml b/modules/nf-core/cnvkit/call/environment.yml index 3b96de7008ff..4aaf29c04f0e 100644 --- a/modules/nf-core/cnvkit/call/environment.yml +++ b/modules/nf-core/cnvkit/call/environment.yml @@ -2,6 +2,5 @@ name: cnvkit_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/call/main.nf b/modules/nf-core/cnvkit/call/main.nf index fade6df0fd1e..06d51e857ecd 100644 --- a/modules/nf-core/cnvkit/call/main.nf +++ b/modules/nf-core/cnvkit/call/main.nf @@ -33,4 +33,15 @@ process CNVKIT_CALL { cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.cns + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cnvkit: \$(cnvkit.py version | sed -e 's/cnvkit v//g') + END_VERSIONS + """ } diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test b/modules/nf-core/cnvkit/call/tests/main.nf.test new file mode 100644 index 000000000000..6012ef137f71 --- /dev/null +++ b/modules/nf-core/cnvkit/call/tests/main.nf.test @@ -0,0 +1,83 @@ + +nextflow_process { + + name "Test Process CNVKIT_CALL" + script "../main.nf" + process "CNVKIT_CALL" + + tag "modules" + tag "modules_nfcore" + tag "cnvkit" + tag "cnvkit/call" + + test("test-cnvkit-call") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-cnvkit-call-with-vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-cnvkit-call-with-vcf-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file('https://raw.githubusercontent.com/etal/cnvkit/v0.9.9/test/formats/amplicon.cns', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/cnvkit/call/tests/main.nf.test.snap b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap new file mode 100644 index 000000000000..844a415ecf6b --- /dev/null +++ b/modules/nf-core/cnvkit/call/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "test-cnvkit-call": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,7746029caf9ecc134a075a2d50be269f" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,7746029caf9ecc134a075a2d50be269f" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:41.048386" + }, + "test-cnvkit-call-with-vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,2a4b3da8a8131a4ed4ae902a9f96a405" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:50.134984" + }, + "test-cnvkit-call-with-vcf-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ], + "cns": [ + [ + { + "id": "test", + "single_end": false + }, + "test.cns:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f47253e21b991f72a741d6b5c9a351a5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T22:24:56.743954" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 1854ac037dca..5866c9d4e292 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -94,9 +94,6 @@ circexplorer2/parse: clippy: - modules/nf-core/clippy/** - tests/modules/nf-core/clippy/** -cnvkit/call: - - modules/nf-core/cnvkit/call/** - - tests/modules/nf-core/cnvkit/call/** cnvkit/export: - modules/nf-core/cnvkit/export/** - tests/modules/nf-core/cnvkit/export/** diff --git a/tests/modules/nf-core/cnvkit/call/main.nf b/tests/modules/nf-core/cnvkit/call/main.nf deleted file mode 100644 index 17a88db14776..000000000000 --- a/tests/modules/nf-core/cnvkit/call/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { CNVKIT_CALL } from '../../../../../modules/nf-core/cnvkit/call/main.nf' - -workflow test_cnvkit_call { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['cnvkit']['amplicon_cns'], checkIfExists: true), - [] - ] - - CNVKIT_CALL ( input ) -} - -workflow test_cnvkit_call_with_vcf { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['cnvkit']['amplicon_cns'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true) - ] - - CNVKIT_CALL ( input ) -} \ No newline at end of file diff --git a/tests/modules/nf-core/cnvkit/call/nextflow.config b/tests/modules/nf-core/cnvkit/call/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/cnvkit/call/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/cnvkit/call/test.yml b/tests/modules/nf-core/cnvkit/call/test.yml deleted file mode 100644 index 261c77ae4c46..000000000000 --- a/tests/modules/nf-core/cnvkit/call/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: cnvkit call test_cnvkit_call - command: nextflow run ./tests/modules/nf-core/cnvkit/call -entry test_cnvkit_call -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/call/nextflow.config - tags: - - cnvkit/call - - cnvkit - files: - - path: output/cnvkit/test.cns - md5sum: 7746029caf9ecc134a075a2d50be269f - - path: output/cnvkit/versions.yml - -- name: cnvkit call test_cnvkit_call_with_vcf - command: nextflow run ./tests/modules/nf-core/cnvkit/call -entry test_cnvkit_call_with_vcf -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/cnvkit/call/nextflow.config - tags: - - cnvkit/call - - cnvkit - files: - - path: output/cnvkit/test.cns - md5sum: 2a4b3da8a8131a4ed4ae902a9f96a405 - - path: output/cnvkit/versions.yml From 2ae4d69365d1e7772fcbce368733f978767eb3e0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 5 Sep 2024 22:51:20 +0000 Subject: [PATCH 010/486] Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.4 (#6592) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 907cd28dc28d..efc08e8cf7a5 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.3 + rev: v0.6.4 hooks: - id: ruff files: \.py$ From 51ba46d1299847eeec811ac7ba9b612125cf38df Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 16:19:34 +1200 Subject: [PATCH 011/486] Added nf-test for gubbins (#6598) * Added nf-test for gubbins * Version bump * Updated test names --- modules/nf-core/gubbins/environment.yml | 3 +- modules/nf-core/gubbins/main.nf | 29 ++++- modules/nf-core/gubbins/meta.yml | 1 + modules/nf-core/gubbins/tests/main.nf.test | 63 ++++++++++ .../nf-core/gubbins/tests/main.nf.test.snap | 113 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/gubbins/main.nf | 11 -- tests/modules/nf-core/gubbins/nextflow.config | 5 - tests/modules/nf-core/gubbins/test.yml | 23 ---- 9 files changed, 205 insertions(+), 46 deletions(-) create mode 100644 modules/nf-core/gubbins/tests/main.nf.test create mode 100644 modules/nf-core/gubbins/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gubbins/main.nf delete mode 100644 tests/modules/nf-core/gubbins/nextflow.config delete mode 100644 tests/modules/nf-core/gubbins/test.yml diff --git a/modules/nf-core/gubbins/environment.yml b/modules/nf-core/gubbins/environment.yml index 915378223606..0e8285b41c2d 100644 --- a/modules/nf-core/gubbins/environment.yml +++ b/modules/nf-core/gubbins/environment.yml @@ -2,6 +2,5 @@ name: gubbins channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gubbins=3.0.0 + - bioconda::gubbins=3.3.5 diff --git a/modules/nf-core/gubbins/main.nf b/modules/nf-core/gubbins/main.nf index a934f1dd629e..2d91dfc0009a 100644 --- a/modules/nf-core/gubbins/main.nf +++ b/modules/nf-core/gubbins/main.nf @@ -3,8 +3,8 @@ process GUBBINS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gubbins:3.0.0--py39h5bf99c6_0' : - 'biocontainers/gubbins:3.0.0--py39h5bf99c6_0' }" + 'https://depot.galaxyproject.org/singularity/gubbins:3.3.5--py39pl5321he4a0461_0' : + 'biocontainers/gubbins:3.3.5--py39pl5321he4a0461_0' }" input: path alignment @@ -27,6 +27,9 @@ process GUBBINS { script: def args = task.ext.args ?: '' """ + mkdir numba_cache_dir + export NUMBA_CACHE_DIR='./numba_cache_dir' + run_gubbins.py \\ --threads $task.cpus \\ $args \\ @@ -36,4 +39,26 @@ process GUBBINS { gubbins: \$(run_gubbins.py --version 2>&1) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + """ + mkdir numba_cache_dir + export NUMBA_CACHE_DIR='./numba_cache_dir' + + touch ${alignment.baseName}.fasta + touch ${alignment.baseName}.gff + touch ${alignment.baseName}.vcf + touch ${alignment.baseName}.csv + touch ${alignment.baseName}.phylip + touch ${alignment.baseName}.recombination_predictions.embl + touch ${alignment.baseName}.branch_base_reconstruction.embl + touch ${alignment.baseName}.final_tree.tre + touch ${alignment.baseName}.node_labelled.final_tree.tre + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gubbins: \$(run_gubbins.py --version 2>&1) + END_VERSIONS + """ } diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml index 30f6bd7f4327..191660b82ae8 100644 --- a/modules/nf-core/gubbins/meta.yml +++ b/modules/nf-core/gubbins/meta.yml @@ -4,6 +4,7 @@ licence: ["GPL-2.0-only"] keywords: - recombination - alignment + - phylogeny tools: - gubbins: description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. diff --git a/modules/nf-core/gubbins/tests/main.nf.test b/modules/nf-core/gubbins/tests/main.nf.test new file mode 100644 index 000000000000..357d3d71d063 --- /dev/null +++ b/modules/nf-core/gubbins/tests/main.nf.test @@ -0,0 +1,63 @@ + +nextflow_process { + + name "Test Process GUBBINS" + script "../main.nf" + process "GUBBINS" + + tag "modules" + tag "modules_nfcore" + tag "gubbins" + + test("sarscov2-alignment") { + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + process.out.gff, + path(process.out.vcf[0]).vcf.variantsMD5, + process.out.stats, + process.out.phylip, + file(process.out.embl_predicted[0]).name, // empty + process.out.embl_branch, + process.out.tree[0].collect { file(it).name }, // unstable + file(process.out.tree_labelled[0]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("sarscov2-alignment-stub") { + options '-stub' + + when { + process { + """ + input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/all_sites.fas', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gubbins/tests/main.nf.test.snap b/modules/nf-core/gubbins/tests/main.nf.test.snap new file mode 100644 index 000000000000..33f66d8c9416 --- /dev/null +++ b/modules/nf-core/gubbins/tests/main.nf.test.snap @@ -0,0 +1,113 @@ +{ + "sarscov2-alignment-stub": { + "content": [ + { + "0": [ + "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "3": [ + "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "4": [ + "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "5": [ + "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "6": [ + "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "7": [ + [ + "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "9": [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ], + "embl_branch": [ + "all_sites.branch_base_reconstruction.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "embl_predicted": [ + "all_sites.recombination_predictions.embl:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "fasta": [ + "all_sites.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "gff": [ + "all_sites.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "phylip": [ + "all_sites.phylip:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "stats": [ + "all_sites.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "tree": [ + [ + "all_sites.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e", + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tree_labelled": [ + "all_sites.node_labelled.final_tree.tre:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "vcf": [ + "all_sites.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:20:39.212181" + }, + "sarscov2-alignment": { + "content": [ + [ + "all_sites.filtered_polymorphic_sites.fasta:md5,0f945512f071fd1599bb7455492e31bc" + ], + [ + "all_sites.recombination_predictions.gff:md5,7605a21ad8812866adbdb5cada8a59d4" + ], + "d314daa06c635c0b31b132a1092ee4e3", + [ + "all_sites.per_branch_statistics.csv:md5,8012a76a2486a8b3dfe78d6902b56ed4" + ], + [ + "all_sites.filtered_polymorphic_sites.phylip:md5,d28da2dd14d08bbb996756064516aee1" + ], + "all_sites.recombination_predictions.embl", + [ + "all_sites.branch_base_reconstruction.embl:md5,9dfd7e411404360ce4a7938aab8db701" + ], + [ + "all_sites.final_tree.tre", + "all_sites.node_labelled.final_tree.tre" + ], + "all_sites.node_labelled.final_tree.tre", + [ + "versions.yml:md5,42d794e45e0374e029afdbfbc585cc76" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:16:35.669362" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 5866c9d4e292..41a01d0afded 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -308,9 +308,6 @@ gridss/gridssgenerateponbedpe: gsea/gsea: - modules/nf-core/gsea/gsea/** - tests/modules/nf-core/gsea/gsea/** -gubbins: - - modules/nf-core/gubbins/** - - tests/modules/nf-core/gubbins/** gunc/downloaddb: - modules/nf-core/gunc/downloaddb/** - tests/modules/nf-core/gunc/downloaddb/** diff --git a/tests/modules/nf-core/gubbins/main.nf b/tests/modules/nf-core/gubbins/main.nf deleted file mode 100644 index f65460d821ea..000000000000 --- a/tests/modules/nf-core/gubbins/main.nf +++ /dev/null @@ -1,11 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GUBBINS } from '../../../../modules/nf-core/gubbins/main.nf' - -workflow test_gubbins { - input = file(params.test_data['sarscov2']['genome']['all_sites_fas'], checkIfExists: true) - - GUBBINS ( input ) -} diff --git a/tests/modules/nf-core/gubbins/nextflow.config b/tests/modules/nf-core/gubbins/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/gubbins/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gubbins/test.yml b/tests/modules/nf-core/gubbins/test.yml deleted file mode 100644 index 39b9d738cf26..000000000000 --- a/tests/modules/nf-core/gubbins/test.yml +++ /dev/null @@ -1,23 +0,0 @@ -- name: gubbins - command: nextflow run ./tests/modules/nf-core/gubbins -entry test_gubbins -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gubbins/nextflow.config - tags: - - gubbins - files: - - path: output/gubbins/all_sites.filtered_polymorphic_sites.fasta - md5sum: 4cbfd93868d8ed7d4d8b099eba137134 - - path: output/gubbins/all_sites.recombination_predictions.embl - md5sum: d41d8cd98f00b204e9800998ecf8427e - - path: output/gubbins/all_sites.recombination_predictions.gff - md5sum: f95871e79968340cb82532e2c9b0c92b - - path: output/gubbins/all_sites.branch_base_reconstruction.embl - md5sum: 9e051646d630f528fff58f1f73286006 - - path: output/gubbins/all_sites.summary_of_snp_distribution.vcf - md5sum: 276e62e888ea811577c8ffb2da0b3aff - - path: output/gubbins/all_sites.per_branch_statistics.csv - md5sum: 25e4fdb6681c3709a9add1d5632bbf3e - - path: output/gubbins/all_sites.filtered_polymorphic_sites.phylip - md5sum: 0a77f397a7797c5c3386832745b0c97a - - path: output/gubbins/all_sites.final_tree.tre - md5sum: 6cb251b58307aab11cb4b48792d6cda1 - - path: output/gubbins/all_sites.node_labelled.final_tree.tre - md5sum: e01f965a15924b4f97603b8011c8d3f7 From 8291e7e35cf305b26433cb9c255d49f7d559aa97 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:22:50 +1200 Subject: [PATCH 012/486] Added nf-test for goleft/indexsplit (#6595) --- .../nf-core/goleft/indexsplit/environment.yml | 1 - modules/nf-core/goleft/indexsplit/meta.yml | 2 +- .../goleft/indexsplit/tests/main.nf.test | 68 ++++++++++++++++++ .../goleft/indexsplit/tests/main.nf.test.snap | 72 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - .../modules/nf-core/goleft/indexsplit/main.nf | 21 ------ .../nf-core/goleft/indexsplit/nextflow.config | 5 -- .../nf-core/goleft/indexsplit/test.yml | 9 --- 8 files changed, 141 insertions(+), 40 deletions(-) create mode 100644 modules/nf-core/goleft/indexsplit/tests/main.nf.test create mode 100644 modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/goleft/indexsplit/main.nf delete mode 100644 tests/modules/nf-core/goleft/indexsplit/nextflow.config delete mode 100644 tests/modules/nf-core/goleft/indexsplit/test.yml diff --git a/modules/nf-core/goleft/indexsplit/environment.yml b/modules/nf-core/goleft/indexsplit/environment.yml index d8c37692adc2..192482ae4576 100644 --- a/modules/nf-core/goleft/indexsplit/environment.yml +++ b/modules/nf-core/goleft/indexsplit/environment.yml @@ -2,6 +2,5 @@ name: goleft_indexsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::goleft=0.2.4 diff --git a/modules/nf-core/goleft/indexsplit/meta.yml b/modules/nf-core/goleft/indexsplit/meta.yml index 023a25a4ce3c..49ee3b4f4ebd 100644 --- a/modules/nf-core/goleft/indexsplit/meta.yml +++ b/modules/nf-core/goleft/indexsplit/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/goleft/indexsplit/tests/main.nf.test b/modules/nf-core/goleft/indexsplit/tests/main.nf.test new file mode 100644 index 000000000000..9469e402f78d --- /dev/null +++ b/modules/nf-core/goleft/indexsplit/tests/main.nf.test @@ -0,0 +1,68 @@ + +nextflow_process { + + name "Test Process GOLEFT_INDEXSPLIT" + script "../main.nf" + process "GOLEFT_INDEXSPLIT" + + tag "modules" + tag "modules_nfcore" + tag "goleft" + tag "goleft/indexsplit" + + test("test-goleft-indexsplit") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'sarscov2'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + + ] + input[2] = 10 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-goleft-indexsplit-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ + [ id:'sarscov2'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + ] + input[2] = 10 + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap b/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap new file mode 100644 index 000000000000..d8c7963eb10c --- /dev/null +++ b/modules/nf-core/goleft/indexsplit/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-goleft-indexsplit": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9" + ] + ], + "1": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,6158ae22773bda2b1380c1f7e324d7a9" + ] + ], + "versions": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:39:21.842028" + }, + "test-goleft-indexsplit-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ], + "bed": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f71bc54dc512c7e78b0cf5fe7d3f0b05" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:39:26.342137" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 41a01d0afded..6943f7e3d724 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -284,9 +284,6 @@ glimpse2/concordance: glnexus: - modules/nf-core/glnexus/** - tests/modules/nf-core/glnexus/** -goleft/indexsplit: - - modules/nf-core/goleft/indexsplit/** - - tests/modules/nf-core/goleft/indexsplit/** gprofiler2/gost: - modules/nf-core/gprofiler2/gost/** - tests/modules/nf-core/gprofiler2/gost/** diff --git a/tests/modules/nf-core/goleft/indexsplit/main.nf b/tests/modules/nf-core/goleft/indexsplit/main.nf deleted file mode 100644 index 30df3304d63f..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/main.nf +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GOLEFT_INDEXSPLIT } from '../../../../../modules/nf-core/goleft/indexsplit/main.nf' - -workflow test_goleft_indexsplit { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam_bai'], checkIfExists: true) - ] - - fai = [ - [ id:'sarscov2'], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - - ] - - GOLEFT_INDEXSPLIT ( input, fai, 10 ) -} diff --git a/tests/modules/nf-core/goleft/indexsplit/nextflow.config b/tests/modules/nf-core/goleft/indexsplit/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/goleft/indexsplit/test.yml b/tests/modules/nf-core/goleft/indexsplit/test.yml deleted file mode 100644 index e089286a9323..000000000000 --- a/tests/modules/nf-core/goleft/indexsplit/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: goleft indexsplit test_goleft_indexsplit - command: nextflow run ./tests/modules/nf-core/goleft/indexsplit -entry test_goleft_indexsplit -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/goleft/indexsplit/nextflow.config - tags: - - goleft - - goleft/indexsplit - files: - - path: output/goleft/test.bed - md5sum: 6158ae22773bda2b1380c1f7e324d7a9 - - path: output/goleft/versions.yml From 9d7e0d655ae401df16ec4b897eed7af5998dd98b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:23:21 +1200 Subject: [PATCH 013/486] Added nf-test for graphtyper/vcfconcatenate (#6596) --- .../graphtyper/vcfconcatenate/environment.yml | 1 - .../nf-core/graphtyper/vcfconcatenate/main.nf | 15 ++++ .../graphtyper/vcfconcatenate/meta.yml | 2 +- .../vcfconcatenate/tests/main.nf.test | 70 +++++++++++++++++++ .../vcfconcatenate/tests/main.nf.test.snap | 69 ++++++++++++++++++ .../vcfconcatenate/tests/nextflow.config | 5 ++ tests/config/pytest_modules.yml | 3 - .../nf-core/graphtyper/vcfconcatenate/main.nf | 18 ----- .../graphtyper/vcfconcatenate/nextflow.config | 8 --- .../graphtyper/vcfconcatenate/test.yml | 10 --- 10 files changed, 160 insertions(+), 41 deletions(-) create mode 100644 modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test create mode 100644 modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap create mode 100644 modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config delete mode 100644 tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf delete mode 100644 tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config delete mode 100644 tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml diff --git a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml index 0bba162dfadb..0f22a4f9d518 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml @@ -2,6 +2,5 @@ name: graphtyper_vcfconcatenate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::graphtyper=2.7.2 diff --git a/modules/nf-core/graphtyper/vcfconcatenate/main.nf b/modules/nf-core/graphtyper/vcfconcatenate/main.nf index efd0dbbf2d35..cf0ae5dbc31f 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/main.nf +++ b/modules/nf-core/graphtyper/vcfconcatenate/main.nf @@ -36,4 +36,19 @@ process GRAPHTYPER_VCFCONCATENATE { graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$vcf" == "${prefix}.vcf.gz") { + error "Input and output names are the same, set prefix in module configuration to disambiguate!" + } + """ + echo | gzip > ${prefix}.vcf.gz + touch ${prefix}.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + graphtyper: \$(graphtyper --help | tail -n 1 | sed 's/^ //') + END_VERSIONS + """ } diff --git a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml index 92ec7981fddf..a34a83e83fc3 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test new file mode 100644 index 000000000000..a596539386b6 --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test @@ -0,0 +1,70 @@ + +nextflow_process { + + name "Test Process GRAPHTYPER_VCFCONCATENATE" + script "../main.nf" + process "GRAPHTYPER_VCFCONCATENATE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "graphtyper" + tag "graphtyper/vcfconcatenate" + + test("test-graphtyper-vcfconcatenate") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + file(process.out.tbi[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-graphtyper-vcfconcatenate-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap new file mode 100644 index 000000000000..ab8947ec4adb --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "test-graphtyper-vcfconcatenate-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ], + "tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "prefix.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:42:58.201156" + }, + "test-graphtyper-vcfconcatenate": { + "content": [ + "ff00185efbeeac85dbe22d3b63466f71", + "prefix.vcf.gz.tbi", + [ + "versions.yml:md5,da65963fb13e605b770c500fcddca43f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T08:42:53.20738" + } +} \ No newline at end of file diff --git a/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config b/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config new file mode 100644 index 000000000000..31dce6d2949e --- /dev/null +++ b/modules/nf-core/graphtyper/vcfconcatenate/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GRAPHTYPER_VCFCONCATENATE { + ext.prefix = "prefix" + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 6943f7e3d724..b467564348bf 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -293,9 +293,6 @@ graphmap2/align: graphtyper/genotype: - modules/nf-core/graphtyper/genotype/** - tests/modules/nf-core/graphtyper/genotype/** -graphtyper/vcfconcatenate: - - modules/nf-core/graphtyper/vcfconcatenate/** - - tests/modules/nf-core/graphtyper/vcfconcatenate/** grids/gridsssomaticfilter: - modules/nf-core/grids/gridsssomaticfilter/** - tests/modules/nf-core/grids/gridsssomaticfilter/** diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf b/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf deleted file mode 100644 index a5fe35ca6a92..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/main.nf +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GRAPHTYPER_VCFCONCATENATE } from '../../../../../modules/nf-core/graphtyper/vcfconcatenate/main.nf' - -workflow test_graphtyper_vcfconcatenate { - - input = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true) - ] - ] - - GRAPHTYPER_VCFCONCATENATE ( input ) -} diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config b/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config deleted file mode 100644 index c7cbbe669b98..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: GRAPHTYPER_VCFCONCATENATE { - ext.prefix = "prefix" - } -} diff --git a/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml b/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml deleted file mode 100644 index 08964bc36800..000000000000 --- a/tests/modules/nf-core/graphtyper/vcfconcatenate/test.yml +++ /dev/null @@ -1,10 +0,0 @@ -- name: graphtyper vcfconcatenate test_graphtyper_vcfconcatenate - command: nextflow run ./tests/modules/nf-core/graphtyper/vcfconcatenate -entry test_graphtyper_vcfconcatenate -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/graphtyper/vcfconcatenate/nextflow.config - tags: - - graphtyper - - graphtyper/vcfconcatenate - files: - - path: output/graphtyper/prefix.vcf.gz - contains: ["FORMAT data/genomics/sarscov2/bam/test_paired_end.sorted.bam"] - - path: output/graphtyper/prefix.vcf.gz.tbi - - path: output/graphtyper/versions.yml From a2d3dc49d25bbfd1c158bdaff859602bd86a6310 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:23:55 +1200 Subject: [PATCH 014/486] Added nf-test for geoquery/getgeo (#6594) * Added nf-test for geoquery/getgeo * Version bump and stub * Added versions trap * Locked r-base version * Updated power assertions --- .../nf-core/geoquery/getgeo/environment.yml | 4 +- modules/nf-core/geoquery/getgeo/main.nf | 18 ++- modules/nf-core/geoquery/getgeo/meta.yml | 2 +- .../geoquery/getgeo/tests/main.nf.test | 94 ++++++++++++++ .../geoquery/getgeo/tests/main.nf.test.snap | 116 ++++++++++++++++++ .../geoquery/getgeo/tests/nextflow.config | 6 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/geoquery/getgeo/main.nf | 23 ---- .../nf-core/geoquery/getgeo/nextflow.config | 10 -- .../modules/nf-core/geoquery/getgeo/test.yml | 25 ---- 10 files changed, 235 insertions(+), 66 deletions(-) create mode 100644 modules/nf-core/geoquery/getgeo/tests/main.nf.test create mode 100644 modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap create mode 100644 modules/nf-core/geoquery/getgeo/tests/nextflow.config delete mode 100644 tests/modules/nf-core/geoquery/getgeo/main.nf delete mode 100644 tests/modules/nf-core/geoquery/getgeo/nextflow.config delete mode 100644 tests/modules/nf-core/geoquery/getgeo/test.yml diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml index bfbf8a2df29b..3385fdc5e478 100644 --- a/modules/nf-core/geoquery/getgeo/environment.yml +++ b/modules/nf-core/geoquery/getgeo/environment.yml @@ -2,6 +2,6 @@ name: geoquery_getgeo channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::bioconductor-geoquery=2.66.0 + - bioconda::bioconductor-geoquery=2.70.0 + - conda-forge::r-base=4.3.2 # Locked with container diff --git a/modules/nf-core/geoquery/getgeo/main.nf b/modules/nf-core/geoquery/getgeo/main.nf index c66aca93ff76..ec32b43d5cf2 100644 --- a/modules/nf-core/geoquery/getgeo/main.nf +++ b/modules/nf-core/geoquery/getgeo/main.nf @@ -4,8 +4,8 @@ process GEOQUERY_GETGEO { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.66.0--r42hdfd78af_0' : - 'biocontainers/bioconductor-geoquery:2.66.0--r42hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bioconductor-geoquery:2.70.0--r43hdfd78af_0' : + 'biocontainers/bioconductor-geoquery:2.70.0--r43hdfd78af_0' }" input: tuple val(meta), val(querygse) @@ -21,4 +21,18 @@ process GEOQUERY_GETGEO { script: template 'getgeo.R' + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.rds + touch ${prefix}.matrix.tsv + touch ${prefix}.annotation.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + r-base: \$(Rscript -e 'R.Version()\$version.string' | sed -n 's|\\[1\\] "R version \\(.*\\) (.*|\\1|p') + bioconductor-geoquery: \$(Rscript -e 'packageVersion("GEOquery")' | sed -n 's|\\[1\\] ‘\\(.*\\)’|\\1|p') + END_VERSIONS + """ } diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml index ca0074c7a533..b8000288415f 100644 --- a/modules/nf-core/geoquery/getgeo/meta.yml +++ b/modules/nf-core/geoquery/getgeo/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://bioconductor.org/packages/release/bioc/vignettes/GEOquery/inst/doc/GEOquery.html" tool_dev_url: "https://github.com/seandavi/GEOquery" doi: "10.1093/bioinformatics/btm254" - licence: "MIT" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/geoquery/getgeo/tests/main.nf.test b/modules/nf-core/geoquery/getgeo/tests/main.nf.test new file mode 100644 index 000000000000..7debd2c0b12c --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/main.nf.test @@ -0,0 +1,94 @@ + +nextflow_process { + + name "Test Process GEOQUERY_GETGEO" + script "../main.nf" + process "GEOQUERY_GETGEO" + + tag "modules" + tag "modules_nfcore" + tag "geoquery" + tag "geoquery/getgeo" + + test("test-geoquery-getgeo") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.rds[0][1]).name, + file(process.out.expression[0][1]).name, // unstable + process.out.annotation, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches + ).match() + } + ) + } + } + + test("test-geoquery-getgeo-with-metacols") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.rds[0][1]).name, + file(process.out.expression[0][1]).name, // unstable + process.out.annotation, + process.out.versions + ).match() + } + ) + } + } + + test("test-geoquery-getgeo-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + 'GSE50790' + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap b/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap new file mode 100644 index 000000000000..c80986d960f2 --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/main.nf.test.snap @@ -0,0 +1,116 @@ +{ + "test-geoquery-getgeo-with-metacols": { + "content": [ + "test.eset.rds", + "test.matrix.tsv", + [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,40300ae222ae35fa54daf10a1b86e830" + ] + ], + [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:41:39.616967" + }, + "test-geoquery-getgeo-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.matrix.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ], + "annotation": [ + [ + { + "id": "test" + }, + "test.annotation.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "expression": [ + [ + { + "id": "test" + }, + "test.matrix.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "rds": [ + [ + { + "id": "test" + }, + "test.rds:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:50:33.782155" + }, + "test-geoquery-getgeo": { + "content": [ + "eset.rds", + "matrix.tsv", + [ + [ + { + "id": "test" + }, + "annotation.tsv:md5,4dbb874b49a11dff13557f58da643ee0" + ] + ], + [ + "versions.yml:md5,6364f5393cdbde3b4c7c92aac6f70dd0" + ], + [ + "\"GEOQUERY_GETGEO\":", + "r-base: 4.3.2", + "bioconductor-geoquery: 2.70.0" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:41:16.597153" + } +} \ No newline at end of file diff --git a/modules/nf-core/geoquery/getgeo/tests/nextflow.config b/modules/nf-core/geoquery/getgeo/tests/nextflow.config new file mode 100644 index 000000000000..9b3028d7bbd7 --- /dev/null +++ b/modules/nf-core/geoquery/getgeo/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: 'GEOQUERY_GETGEO' { + ext.args = { "--metacols \"ID,ENTREZ_GENE_ID,Gene Symbol,Sequence Type\"" } + ext.prefix = { "${meta.id}." } + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b467564348bf..c96ba47f1668 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -266,9 +266,6 @@ genotyphi/parse: genrich: - modules/nf-core/genrich/** - tests/modules/nf-core/genrich/** -geoquery/getgeo: - - modules/nf-core/geoquery/getgeo/** - - tests/modules/nf-core/geoquery/getgeo/** gfaffix: - modules/nf-core/gfaffix/** - tests/modules/nf-core/gfaffix/** diff --git a/tests/modules/nf-core/geoquery/getgeo/main.nf b/tests/modules/nf-core/geoquery/getgeo/main.nf deleted file mode 100644 index 1f40aa6c5534..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GEOQUERY_GETGEO } from '../../../../../modules/nf-core/geoquery/getgeo/main.nf' - -workflow test_geoquery_getgeo { - - input = [[ id:'test' ], // meta map - 'GSE50790' - ] - - GEOQUERY_GETGEO ( input ) -} - -workflow test_geoquery_getgeo_with_metacols { - - input = [[ id:'test' ], // meta map - 'GSE50790' - ] - - GEOQUERY_GETGEO ( input ) -} diff --git a/tests/modules/nf-core/geoquery/getgeo/nextflow.config b/tests/modules/nf-core/geoquery/getgeo/nextflow.config deleted file mode 100644 index a191b883efc4..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/nextflow.config +++ /dev/null @@ -1,10 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: 'test_geoquery_getgeo_with_metacols:GEOQUERY_GETGEO' { - ext.args = { "--metacols \"ID,ENTREZ_GENE_ID,Gene Symbol,Sequence Type\"" } - ext.prefix = { "${meta.id}." } - } - -} diff --git a/tests/modules/nf-core/geoquery/getgeo/test.yml b/tests/modules/nf-core/geoquery/getgeo/test.yml deleted file mode 100644 index 1f13db5c22de..000000000000 --- a/tests/modules/nf-core/geoquery/getgeo/test.yml +++ /dev/null @@ -1,25 +0,0 @@ -- name: geoquery getgeo test_geoquery_getgeo - command: nextflow run ./tests/modules/nf-core/geoquery/getgeo -entry test_geoquery_getgeo -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/geoquery/getgeo/nextflow.config - tags: - - geoquery/getgeo - - geoquery - files: - - path: output/geoquery/annotation.tsv - md5sum: 4dbb874b49a11dff13557f58da643ee0 - - path: output/geoquery/eset.rds - - path: output/geoquery/matrix.tsv - md5sum: 230f87f91c0c1a7e2ab354200c4b978c - - path: output/geoquery/versions.yml - -- name: geoquery getgeo test_geoquery_getgeo_with_metacols - command: nextflow run ./tests/modules/nf-core/geoquery/getgeo -entry test_geoquery_getgeo_with_metacols -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/geoquery/getgeo/nextflow.config - tags: - - geoquery/getgeo - - geoquery - files: - - path: output/geoquery/test.annotation.tsv - md5sum: 40300ae222ae35fa54daf10a1b86e830 - - path: output/geoquery/test.eset.rds - - path: output/geoquery/test.matrix.tsv - md5sum: 230f87f91c0c1a7e2ab354200c4b978c - - path: output/geoquery/versions.yml From 99a7e61b359f7b7b379cee49259879942d2d2533 Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Fri, 6 Sep 2024 07:25:22 +0200 Subject: [PATCH 015/486] Fix bcftools merge for one sample (#6591) --- modules/nf-core/bcftools/merge/main.nf | 3 +- .../nf-core/bcftools/merge/tests/main.nf.test | 71 +++++++++++++++++++ .../bcftools/merge/tests/main.nf.test.snap | 52 ++++++++++++++ .../bcftools/merge/tests/nextflow.config | 2 +- 4 files changed, 126 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/bcftools/merge/main.nf b/modules/nf-core/bcftools/merge/main.nf index 1afe2fa9b4cb..facb14ea1316 100644 --- a/modules/nf-core/bcftools/merge/main.nf +++ b/modules/nf-core/bcftools/merge/main.nf @@ -24,7 +24,8 @@ process BCFTOOLS_MERGE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = vcfs.sort{ it.name } + + def input = (vcfs.collect().size() > 1) ? vcfs.sort{ it.name } : vcfs def regions = bed ? "--regions-file $bed" : "" def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test b/modules/nf-core/bcftools/merge/tests/main.nf.test index 1cde9998de32..3995fc1a91bb 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test @@ -244,6 +244,7 @@ nextflow_process { config "./vcf_gz_index_csi.config" when { + process { """ input[0] = [ @@ -363,6 +364,7 @@ nextflow_process { test("homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output") { config "./nextflow.gvcf.config" + when { process { """ @@ -406,6 +408,41 @@ nextflow_process { } + test("sarscov2 - [vcf, tbi], [], [], [] - one sample") { + + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot( + path(process.out.vcf.get(0).get(1)).md5, + process.out.versions, + ).match() } + ) + } + + } + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { options "-stub" @@ -779,4 +816,38 @@ nextflow_process { } } + + test("sarscov2 - [vcf, tbi], [], [], [] - one sample - stub") { + + options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true) + ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true) + ] + ] + input[1] = [[],[]] + input[2] = [[],[]] + input[3] = [[],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf.get(0).get(1).endsWith("vcf") }, + { assert snapshot(process.out).match() } + ) + } + + } } diff --git a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap index 963cfc1379fe..b3b62556313f 100644 --- a/modules/nf-core/bcftools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/merge/tests/main.nf.test.snap @@ -372,6 +372,45 @@ }, "timestamp": "2024-09-05T13:17:47.356328326" }, + "sarscov2 - [vcf, tbi], [], [], [] - one sample - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ], + "index": [ + + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T15:13:18.708495878" + }, "homo_sapiens - [vcf, tbi], fasta, fai, bed - vcf.gz output - stub": { "content": [ { @@ -438,6 +477,19 @@ }, "timestamp": "2024-09-05T13:55:44.299812124" }, + "sarscov2 - [vcf, tbi], [], [], [] - one sample": { + "content": [ + "2a374cf02f0c32cf607646167e7f153b", + [ + "versions.yml:md5,d2c0a30d9a4cc6df89a464ae82e0c38a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T15:37:38.491844702" + }, "sarscov2 - [vcf, tbi], [], [], [] - stub": { "content": [ { diff --git a/modules/nf-core/bcftools/merge/tests/nextflow.config b/modules/nf-core/bcftools/merge/tests/nextflow.config index 80491d4e579b..c3f0b7159956 100644 --- a/modules/nf-core/bcftools/merge/tests/nextflow.config +++ b/modules/nf-core/bcftools/merge/tests/nextflow.config @@ -1,5 +1,5 @@ process { withName: BCFTOOLS_MERGE { - ext.args = '--force-samples --no-version' + ext.args = '--force-samples --force-single --no-version' } } From 5cc90b8bc2e2a579f49b2f6ac3112efd1989a1a9 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:30:15 +1200 Subject: [PATCH 016/486] Added nf-test for ivar/consensus (#6568) * Added nf-test for ivar/consensus * Verion bump --- .../nf-core/ivar/consensus/environment.yml | 3 +- modules/nf-core/ivar/consensus/main.nf | 18 ++- .../nf-core/ivar/consensus/tests/main.nf.test | 100 +++++++++++++++ .../ivar/consensus/tests/main.nf.test.snap | 117 ++++++++++++++++++ .../ivar/consensus/tests/nextflow.config | 5 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/ivar/consensus/main.nf | 29 ----- .../nf-core/ivar/consensus/nextflow.config | 9 -- tests/modules/nf-core/ivar/consensus/test.yml | 22 ---- 9 files changed, 239 insertions(+), 67 deletions(-) create mode 100644 modules/nf-core/ivar/consensus/tests/main.nf.test create mode 100644 modules/nf-core/ivar/consensus/tests/main.nf.test.snap create mode 100644 modules/nf-core/ivar/consensus/tests/nextflow.config delete mode 100644 tests/modules/nf-core/ivar/consensus/main.nf delete mode 100644 tests/modules/nf-core/ivar/consensus/nextflow.config delete mode 100644 tests/modules/nf-core/ivar/consensus/test.yml diff --git a/modules/nf-core/ivar/consensus/environment.yml b/modules/nf-core/ivar/consensus/environment.yml index c7b87d024807..75e6ef41745f 100644 --- a/modules/nf-core/ivar/consensus/environment.yml +++ b/modules/nf-core/ivar/consensus/environment.yml @@ -2,6 +2,5 @@ name: ivar_consensus channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ivar=1.4 + - bioconda::ivar=1.4.3 diff --git a/modules/nf-core/ivar/consensus/main.nf b/modules/nf-core/ivar/consensus/main.nf index 9786200e94c9..d57d17642a9b 100644 --- a/modules/nf-core/ivar/consensus/main.nf +++ b/modules/nf-core/ivar/consensus/main.nf @@ -4,8 +4,8 @@ process IVAR_CONSENSUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'biocontainers/ivar:1.4--h6b7c446_1' }" + 'https://depot.galaxyproject.org/singularity/ivar:1.4.3--h43eeafb_0' : + 'biocontainers/ivar:1.4.3--h43eeafb_0' }" input: tuple val(meta), path(bam) @@ -43,4 +43,18 @@ process IVAR_CONSENSUS { ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def touch_mpileup = save_mpileup ? "touch ${prefix}.mpileup" : '' + """ + touch ${prefix}.fa + touch ${prefix}.qual.txt + $touch_mpileup + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/ivar/consensus/tests/main.nf.test b/modules/nf-core/ivar/consensus/tests/main.nf.test new file mode 100644 index 000000000000..9255bed082e6 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/main.nf.test @@ -0,0 +1,100 @@ + +nextflow_process { + + name "Test Process IVAR_CONSENSUS" + script "../main.nf" + process "IVAR_CONSENSUS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "ivar" + tag "ivar/consensus" + + test("test-ivar-consensus") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = false + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + file(process.out.qual[0][1]).name, // empty + process.out.mpileup, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() } // Trap to catch conda version mismatches + ).match() + } + ) + } + } + + test("test-ivar-consensus-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.fasta, + file(process.out.qual[0][1]).name, // empty + file(process.out.mpileup[0][1]).name, // empty + process.out.versions + ).match() + } + ) + } + } + + test("test-ivar-consensus-mpileup-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/ivar/consensus/tests/main.nf.test.snap b/modules/nf-core/ivar/consensus/tests/main.nf.test.snap new file mode 100644 index 000000000000..e220ecabb5e6 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/main.nf.test.snap @@ -0,0 +1,117 @@ +{ + "test-ivar-consensus-mpileup-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "qual": [ + [ + { + "id": "test" + }, + "test.qual.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:57.447441" + }, + "test-ivar-consensus-mpileup": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8" + ] + ], + "test.qual.txt", + "test.mpileup", + [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:52.938906" + }, + "test-ivar-consensus": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.fa:md5,9e21a64818f4302b4dece5480fa5e8b8" + ] + ], + "test.qual.txt", + [ + + ], + [ + "versions.yml:md5,e652db2cbd4a8cd9b7482a01abe5e6b3" + ], + [ + "\"IVAR_CONSENSUS\":", + "ivar: 1.4.3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:58:48.289344" + } +} \ No newline at end of file diff --git a/modules/nf-core/ivar/consensus/tests/nextflow.config b/modules/nf-core/ivar/consensus/tests/nextflow.config new file mode 100644 index 000000000000..e34c650406f9 --- /dev/null +++ b/modules/nf-core/ivar/consensus/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: IVAR_CONSENSUS { + ext.args2 = '-aa -A -d 0 -Q 0' + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c96ba47f1668..cb964a336982 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -365,9 +365,6 @@ iphop/download: iphop/predict: - modules/nf-core/iphop/predict/** - tests/modules/nf-core/iphop/predict/** -ivar/consensus: - - modules/nf-core/ivar/consensus/** - - tests/modules/nf-core/ivar/consensus/** ivar/variants: - modules/nf-core/ivar/variants/** - tests/modules/nf-core/ivar/variants/** diff --git a/tests/modules/nf-core/ivar/consensus/main.nf b/tests/modules/nf-core/ivar/consensus/main.nf deleted file mode 100644 index 37ce0f8f17ec..000000000000 --- a/tests/modules/nf-core/ivar/consensus/main.nf +++ /dev/null @@ -1,29 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IVAR_CONSENSUS } from '../../../../../modules/nf-core/ivar/consensus/main.nf' - -workflow test_ivar_consensus { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - save_mpileup = false - - IVAR_CONSENSUS ( input, fasta, save_mpileup) -} - -workflow test_ivar_consensus_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - save_mpileup = true - - IVAR_CONSENSUS ( input, fasta, save_mpileup) -} diff --git a/tests/modules/nf-core/ivar/consensus/nextflow.config b/tests/modules/nf-core/ivar/consensus/nextflow.config deleted file mode 100644 index 7407619ad579..000000000000 --- a/tests/modules/nf-core/ivar/consensus/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: IVAR_CONSENSUS { - ext.args2 = '-aa -A -d 0 -Q 0' - } - -} diff --git a/tests/modules/nf-core/ivar/consensus/test.yml b/tests/modules/nf-core/ivar/consensus/test.yml deleted file mode 100644 index b676caf11e19..000000000000 --- a/tests/modules/nf-core/ivar/consensus/test.yml +++ /dev/null @@ -1,22 +0,0 @@ -- name: ivar consensus test_ivar_consensus - command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config - tags: - - ivar - - ivar/consensus - files: - - path: output/ivar/test.fa - md5sum: 9e21a64818f4302b4dece5480fa5e8b8 - - path: output/ivar/test.qual.txt - md5sum: 68b329da9893e34099c7d8ad5cb9c940 - -- name: ivar consensus test_ivar_consensus_mpileup - command: nextflow run ./tests/modules/nf-core/ivar/consensus -entry test_ivar_consensus_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/consensus/nextflow.config - tags: - - ivar - - ivar/consensus - files: - - path: output/ivar/test.fa - md5sum: 9e21a64818f4302b4dece5480fa5e8b8 - - path: output/ivar/test.qual.txt - md5sum: 68b329da9893e34099c7d8ad5cb9c940 - - path: output/ivar/test.mpileup From 5479d8df0003f9e8d30c4e466ef642e4a0a59a20 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:31:26 +1200 Subject: [PATCH 017/486] Added nf-test for circexplorer2/parse (#6577) * Added nf-test for circexplorer2/parse * Updated power assertion --- .../circexplorer2/parse/environment.yml | 1 - modules/nf-core/circexplorer2/parse/meta.yml | 2 +- .../circexplorer2/parse/tests/main.nf.test | 62 +++++++++++++++++++ .../parse/tests/main.nf.test.snap | 48 ++++++++++++++ tests/config/pytest_modules.yml | 3 - .../nf-core/circexplorer2/parse/main.nf | 16 ----- .../circexplorer2/parse/nextflow.config | 5 -- .../nf-core/circexplorer2/parse/test.yml | 16 ----- 8 files changed, 111 insertions(+), 42 deletions(-) create mode 100644 modules/nf-core/circexplorer2/parse/tests/main.nf.test create mode 100644 modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/circexplorer2/parse/main.nf delete mode 100644 tests/modules/nf-core/circexplorer2/parse/nextflow.config delete mode 100644 tests/modules/nf-core/circexplorer2/parse/test.yml diff --git a/modules/nf-core/circexplorer2/parse/environment.yml b/modules/nf-core/circexplorer2/parse/environment.yml index 52e172e7edd1..17613a2a1914 100644 --- a/modules/nf-core/circexplorer2/parse/environment.yml +++ b/modules/nf-core/circexplorer2/parse/environment.yml @@ -2,6 +2,5 @@ name: circexplorer2_parse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::circexplorer2=2.3.8 diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml index ef3ebf856437..83e6e9d35b4e 100644 --- a/modules/nf-core/circexplorer2/parse/meta.yml +++ b/modules/nf-core/circexplorer2/parse/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/YangLab/CIRCexplorer2/" documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" - licence: "['MIT License']" + licence: ["MIT License"] input: - meta: type: map diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test b/modules/nf-core/circexplorer2/parse/tests/main.nf.test new file mode 100644 index 000000000000..4768ab5ddbce --- /dev/null +++ b/modules/nf-core/circexplorer2/parse/tests/main.nf.test @@ -0,0 +1,62 @@ + +nextflow_process { + + name "Test Process CIRCEXPLORER2_PARSE" + script "../main.nf" + process "CIRCEXPLORER2_PARSE" + + tag "modules" + tag "modules_nfcore" + tag "circexplorer2" + tag "circexplorer2/parse" + + test("test-circexplorer2-parse") { + + when { + process { + """ + input[0] = [ + [ id:'fust1_3' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.junction[0][1]).text.contains('FUSIONJUNC') }, + { assert snapshot( + file(process.out.junction[0][1]).name, // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-circexplorer2-parse-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [ id:'fust1_3' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap b/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap new file mode 100644 index 000000000000..f9b6869f7719 --- /dev/null +++ b/modules/nf-core/circexplorer2/parse/tests/main.nf.test.snap @@ -0,0 +1,48 @@ +{ + "test-circexplorer2-parse-stub": { + "content": [ + { + "0": [ + [ + { + "id": "fust1_3" + }, + "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ], + "junction": [ + [ + { + "id": "fust1_3" + }, + "fust1_3.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:58:38.034614" + }, + "test-circexplorer2-parse": { + "content": [ + "fust1_3.bed", + [ + "versions.yml:md5,6490a204cc08154871418e5fbb3aff17" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:53:55.470118" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index cb964a336982..5138b502d5ec 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -88,9 +88,6 @@ cellrangeratac/mkref: checkm/qa: - modules/nf-core/checkm/qa/** - tests/modules/nf-core/checkm/qa/** -circexplorer2/parse: - - modules/nf-core/circexplorer2/parse/** - - tests/modules/nf-core/circexplorer2/parse/** clippy: - modules/nf-core/clippy/** - tests/modules/nf-core/clippy/** diff --git a/tests/modules/nf-core/circexplorer2/parse/main.nf b/tests/modules/nf-core/circexplorer2/parse/main.nf deleted file mode 100644 index 52918ea39cc0..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/main.nf +++ /dev/null @@ -1,16 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { CIRCEXPLORER2_PARSE } from '../../../../../modules/nf-core/circexplorer2/parse/main.nf' - -workflow test_circexplorer2_parse { - - input = [ - [ id:'fust1_3' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/circrna/circexplorer2/fust1_3.Chimeric.out.junction") - ] - - CIRCEXPLORER2_PARSE ( input ) - -} diff --git a/tests/modules/nf-core/circexplorer2/parse/nextflow.config b/tests/modules/nf-core/circexplorer2/parse/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/circexplorer2/parse/test.yml b/tests/modules/nf-core/circexplorer2/parse/test.yml deleted file mode 100644 index 0b7a4a2e7290..000000000000 --- a/tests/modules/nf-core/circexplorer2/parse/test.yml +++ /dev/null @@ -1,16 +0,0 @@ -- name: circexplorer2 parse test_circexplorer2_parse - command: nextflow run ./tests/modules/nf-core/circexplorer2/parse -entry test_circexplorer2_parse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/circexplorer2/parse/nextflow.config - tags: - - circexplorer2/parse - - circexplorer2 - files: - - path: output/circexplorer2/fust1_3.bed - md5sum: 592e0594c4d588a055f36fb1c3d04729 - -- name: circexplorer2 parse test_circexplorer2_parse_stub - command: nextflow run ./tests/modules/nf-core/circexplorer2/parse -entry test_circexplorer2_parse -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/circexplorer2/parse/nextflow.config -stub - tags: - - circexplorer2/parse - - circexplorer2 - files: - - path: output/circexplorer2/fust1_3.bed From b442ecd232af325b41553ab7afb64a3c85b3ceed Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 17:32:21 +1200 Subject: [PATCH 018/486] Added nf-test for mmseqs/databases (#6563) * Added nf-test for mmseqs/databases * Updated power assertion * Removed defaults * Now sorting list --- .../nf-core/mmseqs/createtsv/environment.yml | 1 - .../nf-core/mmseqs/databases/environment.yml | 1 - modules/nf-core/mmseqs/databases/main.nf | 4 +- .../mmseqs/databases/tests/main.nf.test | 55 ++++++++++++++ .../mmseqs/databases/tests/main.nf.test.snap | 74 +++++++++++++++++++ .../nf-core/mmseqs/taxonomy/environment.yml | 1 - tests/config/pytest_modules.yml | 3 - .../modules/nf-core/mmseqs/databases/main.nf | 12 --- .../nf-core/mmseqs/databases/nextflow.config | 5 -- .../modules/nf-core/mmseqs/databases/test.yml | 18 ----- 10 files changed, 131 insertions(+), 43 deletions(-) create mode 100644 modules/nf-core/mmseqs/databases/tests/main.nf.test create mode 100644 modules/nf-core/mmseqs/databases/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/mmseqs/databases/main.nf delete mode 100644 tests/modules/nf-core/mmseqs/databases/nextflow.config delete mode 100644 tests/modules/nf-core/mmseqs/databases/test.yml diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index 4840fc02945a..6f1bd86b3120 100644 --- a/modules/nf-core/mmseqs/createtsv/environment.yml +++ b/modules/nf-core/mmseqs/createtsv/environment.yml @@ -2,6 +2,5 @@ name: mmseqs_createtsv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index 3bf8437d228f..cad92fadd85f 100644 --- a/modules/nf-core/mmseqs/databases/environment.yml +++ b/modules/nf-core/mmseqs/databases/environment.yml @@ -2,6 +2,5 @@ name: mmseqs_databases channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/databases/main.nf b/modules/nf-core/mmseqs/databases/main.nf index 3e228b29d511..d43681cea94d 100644 --- a/modules/nf-core/mmseqs/databases/main.nf +++ b/modules/nf-core/mmseqs/databases/main.nf @@ -11,8 +11,8 @@ process MMSEQS_DATABASES { val database output: - path "${prefix}/" , emit: database - path "versions.yml" , emit: versions + path "${prefix}/" , emit: database + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test b/modules/nf-core/mmseqs/databases/tests/main.nf.test new file mode 100644 index 000000000000..3fe5d20069de --- /dev/null +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test @@ -0,0 +1,55 @@ + +nextflow_process { + + name "Test Process MMSEQS_DATABASES" + script "../main.nf" + process "MMSEQS_DATABASES" + + tag "modules" + tag "modules_nfcore" + tag "mmseqs" + tag "mmseqs/databases" + + test("test-mmseqs-databases") { + + when { + process { + """ + input[0] = "SILVA" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.database[0]).listFiles().collect { it.name }.toSorted(), // unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-mmseqs-databases-stub") { + options '-stub' + when { + process { + """ + input[0] = "SILVA" + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap new file mode 100644 index 000000000000..00d3003ebbcb --- /dev/null +++ b/modules/nf-core/mmseqs/databases/tests/main.nf.test.snap @@ -0,0 +1,74 @@ +{ + "test-mmseqs-databases": { + "content": [ + [ + "database", + "database.dbtype", + "database.index", + "database.lookup", + "database.source", + "database.version", + "database_h", + "database_h.dbtype", + "database_h.index", + "database_mapping", + "database_taxonomy" + ], + [ + "versions.yml:md5,b038db45e5934b8f0f743449bbac01b4" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:43:58.454012" + }, + "test-mmseqs-databases-stub": { + "content": [ + { + "0": [ + [ + "database:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.source:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.version:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3" + ], + "database": [ + [ + "database:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.lookup:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.source:md5,d41d8cd98f00b204e9800998ecf8427e", + "database.version:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.dbtype:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_h.index:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_mapping:md5,d41d8cd98f00b204e9800998ecf8427e", + "database_taxonomy:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,49082428ec974e4ddb09a6ca2e9f21b3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T17:00:20.527628" + } +} \ No newline at end of file diff --git a/modules/nf-core/mmseqs/taxonomy/environment.yml b/modules/nf-core/mmseqs/taxonomy/environment.yml index fa40c2770e1f..89bc7c503d60 100644 --- a/modules/nf-core/mmseqs/taxonomy/environment.yml +++ b/modules/nf-core/mmseqs/taxonomy/environment.yml @@ -4,6 +4,5 @@ name: "mmseqs_taxonomy" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::mmseqs2=15.6f452" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 5138b502d5ec..4eb6450e873d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -455,9 +455,6 @@ mitohifi/mitohifi: mmseqs/cluster: - modules/nf-core/mmseqs/cluster/** - tests/modules/nf-core/mmseqs/cluster/** -mmseqs/databases: - - modules/nf-core/mmseqs/databases/** - - tests/modules/nf-core/mmseqs/databases/** mmseqs/easysearch: - modules/nf-core/mmseqs/easysearch/** - tests/modules/nf-core/mmseqs/easysearch/** diff --git a/tests/modules/nf-core/mmseqs/databases/main.nf b/tests/modules/nf-core/mmseqs/databases/main.nf deleted file mode 100644 index bd0bb9d4eb60..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/main.nf +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MMSEQS_DATABASES } from '../../../../../modules/nf-core/mmseqs/databases/main.nf' - -workflow test_mmseqs_databases { - - input = "SILVA" - - MMSEQS_DATABASES ( input ) -} diff --git a/tests/modules/nf-core/mmseqs/databases/nextflow.config b/tests/modules/nf-core/mmseqs/databases/nextflow.config deleted file mode 100644 index 50f50a7a3579..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/mmseqs/databases/test.yml b/tests/modules/nf-core/mmseqs/databases/test.yml deleted file mode 100644 index dee34721b304..000000000000 --- a/tests/modules/nf-core/mmseqs/databases/test.yml +++ /dev/null @@ -1,18 +0,0 @@ -- name: mmseqs databases test_mmseqs_databases - command: nextflow run ./tests/modules/nf-core/mmseqs/databases -entry test_mmseqs_databases -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/mmseqs/databases/nextflow.config - tags: - - mmseqs - - mmseqs/databases - files: - - path: output/mmseqs/mmseqs_database/database - - path: output/mmseqs/mmseqs_database/database.dbtype - - path: output/mmseqs/mmseqs_database/database.index - - path: output/mmseqs/mmseqs_database/database.lookup - - path: output/mmseqs/mmseqs_database/database.source - - path: output/mmseqs/mmseqs_database/database.version - - path: output/mmseqs/mmseqs_database/database_h - - path: output/mmseqs/mmseqs_database/database_h.dbtype - - path: output/mmseqs/mmseqs_database/database_h.index - - path: output/mmseqs/mmseqs_database/database_mapping - - path: output/mmseqs/mmseqs_database/database_taxonomy - - path: output/mmseqs/versions.yml From 2e7a85b0afa0f811d6e47c32085eda1de865339d Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Fri, 6 Sep 2024 08:49:59 +0200 Subject: [PATCH 019/486] Bgzip and tabix paraphase (#6543) * Bgzip and tabix paraphase * Fixed snapshot size and added threads * remove defaults channel * fix tests --- modules/nf-core/paraphase/environment.yml | 1 - modules/nf-core/paraphase/main.nf | 32 +- modules/nf-core/paraphase/meta.yml | 8 +- modules/nf-core/paraphase/tests/main.nf.test | 104 +- .../nf-core/paraphase/tests/main.nf.test.snap | 2173 ++--------------- .../paraphase/tests/nextflow.csi_index.config | 6 + 6 files changed, 350 insertions(+), 1974 deletions(-) create mode 100644 modules/nf-core/paraphase/tests/nextflow.csi_index.config diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml index 3c9f5526bc48..64b4a9172dcc 100644 --- a/modules/nf-core/paraphase/environment.yml +++ b/modules/nf-core/paraphase/environment.yml @@ -3,7 +3,6 @@ name: paraphase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.28 diff --git a/modules/nf-core/paraphase/main.nf b/modules/nf-core/paraphase/main.nf index ddaa33ec04d5..8474427e66c0 100644 --- a/modules/nf-core/paraphase/main.nf +++ b/modules/nf-core/paraphase/main.nf @@ -14,17 +14,20 @@ process PARAPHASE { tuple val(meta3), path(config) output: - tuple val(meta), path("*.paraphase.json") , emit: json - tuple val(meta), path("*.paraphase.bam") , emit: bam - tuple val(meta), path("*.paraphase.bam.bai") , emit: bai - tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf"), emit: vcf, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.paraphase.json") , emit: json + tuple val(meta), path("*.paraphase.bam") , emit: bam + tuple val(meta), path("*.paraphase.bam.bai") , emit: bai + tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz") , emit: vcf , optional: true + tuple val(meta), path("${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}"), emit: vcf_index, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' prefix = task.ext.prefix ?: "${meta.id}" def config_file = config ? "--config $config" : "" """ @@ -37,6 +40,18 @@ process PARAPHASE { $config_file \\ --out . + for vcf in ${prefix}_paraphase_vcfs/*.vcf; + do + bgzip \\ + $args2 \\ + --threads $task.cpus \\ + \$vcf; + tabix \\ + $args3 \\ + --threads $task.cpus \\ + \$vcf.gz; + done + cat <<-END_VERSIONS > versions.yml "${task.process}": minimap2: \$(minimap2 --version 2>&1) @@ -46,15 +61,18 @@ process PARAPHASE { """ stub: - def args = task.ext.args ?: '' + def args3 = task.ext.args3 ?: '' prefix = task.ext.prefix ?: "${meta.id}" + + def index = args3.contains('--csi') ? 'csi' : 'tbi' """ mkdir ${prefix}_paraphase_vcfs touch ${prefix}.paraphase.json touch ${prefix}.paraphase.bam touch ${prefix}.paraphase.bam.bai - touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf + echo '' | gzip > ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz + touch ${prefix}_paraphase_vcfs/${prefix}_stub.vcf.gz.${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index 4dae0dd8b4b2..e6cc6d635780 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -74,8 +74,12 @@ output: pattern: "*.paraphase.json" - vcf: type: file - description: VCF file(s) per gene - pattern: "*.vcf" + description: compressed VCF file(s) per gene + pattern: "*.vcf.gz" + - vcf_index: + type: file + description: compressed VCF file index + pattern: "*.vcf.gz.{tbi,csi}" authors: - "@fellen31" diff --git a/modules/nf-core/paraphase/tests/main.nf.test b/modules/nf-core/paraphase/tests/main.nf.test index ff35588f932a..e34d66991477 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test +++ b/modules/nf-core/paraphase/tests/main.nf.test @@ -3,7 +3,6 @@ nextflow_process { name "Test Process PARAPHASE" script "../main.nf" process "PARAPHASE" - config "./nextflow.config" tag "modules" tag "modules_nfcore" @@ -25,6 +24,9 @@ nextflow_process { } test("homo_sapiens - [ bam, bai ], []") { + + config "./nextflow.config" + when { process { """ @@ -45,16 +47,16 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") }, { assert snapshot( file(process.out.json.get(0).get(1)).readLines()[0..39], - process.out.versions, - file(process.out.vcf.get(0).get(1)).readLines()[0..962], - process.out.bam ==~ "test.paraphase.bam", - process.out.bai ==~ "test.paraphase.bam.bai", + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions ).match() - }, - { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" }, - { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" }, + } ) } @@ -62,6 +64,46 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], config") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true), + ] + input[1] = TABIX_BGZIP.out.output + input[2] = [ + [ id:'test_config' ], + file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("tbi") }, + { assert snapshot( + file(process.out.json.get(0).get(1)).readLines()[0..39], + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions + ).match() + } + ) + } + } + + test("homo_sapiens - [ bam, bai ], config - csi_index") { + + config "./nextflow.csi_index.config" + when { process { """ @@ -82,16 +124,16 @@ nextflow_process { then { assertAll( { assert process.success }, + { assert process.out.vcf_index.get(0).get(1).endsWith("csi") }, { assert snapshot( file(process.out.json.get(0).get(1)).readLines()[0..39], - process.out.versions, - file(process.out.vcf.get(0).get(1)).readLines()[0..962], - process.out.bam ==~ "test.paraphase.bam", - process.out.bai ==~ "test.paraphase.bam.bai", + path(process.out.vcf.get(0).get(1)).linesGzip[10], + bam(process.out.bam.get(0).get(1)).getReadsMD5(), + file(process.out.bai.get(0).get(1)).name, + file(process.out.vcf_index.get(0).get(1)).name, + process.out.versions ).match() - }, - { assert process.out.bam.get(0).get(1) =~ "test.paraphase.bam" }, - { assert process.out.bai.get(0).get(1) =~ "test.paraphase.bam.bai" }, + } ) } } @@ -99,6 +141,7 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], [] - stub") { options "-stub" + config "./nextflow.config" when { process { @@ -128,6 +171,37 @@ nextflow_process { test("homo_sapiens - [ bam, bai ], config - stub") { options "-stub" + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/bam/test.sorted.bam.bai', checkIfExists: true), + ] + input[1] = TABIX_BGZIP.out.output + input[2] = [ + [ id:'test_config' ], + file(params.modules_testdata_base_path + 'generic/config/paraphase_config.yaml', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [ bam, bai ], config - stub - csi_index") { + + options "-stub" + config "./nextflow.csi_index.config" when { process { diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap index 32242c1ca13a..b80a34434a61 100644 --- a/modules/nf-core/paraphase/tests/main.nf.test.snap +++ b/modules/nf-core/paraphase/tests/main.nf.test.snap @@ -43,982 +43,19 @@ " \"unique_supporting_reads\": {", " \"12222212222111211221\": [" ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.tbi", [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" - ], - [ - "##fileformat=VCFv4.2", - "##FILTER=", - "##INFO=", - "##FORMAT=", - "##FORMAT=", - "##FORMAT=", - "##contig=", - "##paraphase_version=3.1.1", - "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --out .", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2", - "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", - "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6", - "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3", - "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1", - "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7", - "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7", - "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3", - "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4", - "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912326\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912327\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912328\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912329\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912330\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912331\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912332\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912333\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912334\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912335\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912336\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912337\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912338\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912339\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912340\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912341\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912342\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912343\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912344\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912345\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912346\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912347\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:4:0,3", - "chr22\t18912348\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912349\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912350\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912351\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912352\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2", - "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4", - "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912407\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912408\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912409\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912410\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912411\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912412\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912413\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912414\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912415\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912416\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912417\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912418\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912419\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912420\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912421\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912422\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912423\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912424\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912425\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912426\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912427\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912428\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912429\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912430\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912431\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912432\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912433\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912434\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912435\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912436\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912437\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912438\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912439\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912440\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912441\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912442\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912443\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912444\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912445\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912446\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912447\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912448\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912449\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912450\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912451\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912452\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912453\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912454\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912455\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912456\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912457\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912458\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3", - "chr22\t18912459\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912460\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912461\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912462\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912463\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912464\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912465\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912466\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912467\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912468\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912469\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912497\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912498\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912499\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912500\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912501\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912502\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912503\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912504\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912505\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912506\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2", - "chr22\t18912507\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912508\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912509\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912510\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912511\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912512\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912513\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912514\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912515\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912516\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912517\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912518\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912519\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912520\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912521\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912522\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912523\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912524\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912525\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912526\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912527\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912528\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,4", - "chr22\t18912529\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2", - "chr22\t18912530\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912531\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912532\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912533\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912534\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912535\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912536\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912537\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912538\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912539\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912540\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912541\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912542\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912543\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912544\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912545\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912546\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912547\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912548\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912549\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912550\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912551\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912552\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912553\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912554\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912555\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912556\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912557\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912558\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,5", - "chr22\t18912559\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t.:4:0,2", - "chr22\t18912560\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912561\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912562\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912563\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912564\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912565\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912566\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912567\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912568\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912596\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912597\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912598\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912599\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912600\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912601\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912602\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912603\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912604\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912605\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912606\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912607\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912608\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912609\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912610\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912611\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912612\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912613\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6", - "chr22\t18912614\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912615\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912616\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:2:0,2", - "chr22\t18912617\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912618\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912619\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912620\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:6:0,6", - "chr22\t18912621\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912622\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912623\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912624\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912625\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912626\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912627\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912628\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912629\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912630\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912631\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912632\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912633\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912634\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912635\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912636\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912637\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912638\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912639\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912640\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912641\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912642\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912643\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912644\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912645\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912646\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912647\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912648\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912649\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912650\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912651\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912652\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912653\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912654\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912655\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912656\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912657\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912658\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912659\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912660\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,6", - "chr22\t18912661\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18912662\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912663\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912664\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912665\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912666\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912667\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912668\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912669\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912670\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912671\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912672\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912673\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912674\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912675\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912676\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912686\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912687\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912688\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912689\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912690\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912691\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912692\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912693\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912694\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912695\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6", - "chr22\t18912696\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912697\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912698\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912699\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912700\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912701\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912702\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912703\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912704\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912705\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912706\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912707\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912708\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912709\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912710\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912711\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912712\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912713\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912714\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,6", - "chr22\t18912715\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912716\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912717\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912718\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912719\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912720\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912721\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912722\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912723\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912724\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912725\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912726\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912727\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912728\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912729\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912730\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,3", - "chr22\t18912731\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912732\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912733\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912734\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912735\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912736\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912737\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912738\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912739\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912740\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912741\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912742\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912743\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912744\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912745\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912746\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912747\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912748\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912749\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912750\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912751\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912752\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912753\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912754\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912755\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912756\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912757\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912758\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912759\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912760\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912761\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912762\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912763\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:4:0,4", - "chr22\t18912764\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912765\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912766\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912785\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912786\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912787\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912788\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912789\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912790\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912791\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912792\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912793\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912803\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912804\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912805\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912806\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912807\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912808\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912809\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912810\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912811\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912812\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912813\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912814\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18912815\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t1:4:0,4", - "chr22\t18912816\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912817\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912818\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912819\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912820\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912821\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912822\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912823\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912824\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912825\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912826\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912827\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912828\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912829\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912830\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912831\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912832\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912833\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912834\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,3", - "chr22\t18912835\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912836\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912837\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912838\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912839\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912840\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,2", - "chr22\t18912841\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912842\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912843\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912844\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912845\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912846\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912847\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2", - "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912911\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912912\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912913\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912914\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912915\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912916\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912917\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912918\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t.:2:0,2", - "chr22\t18912919\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912920\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912921\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912922\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6", - "chr22\t18912923\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912924\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912925\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912926\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912927\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912928\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912929\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912930\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,3", - "chr22\t18912931\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912932\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912933\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912934\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912935\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912936\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912937\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912938\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912939\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912940\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912941\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912942\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912943\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912944\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912945\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912946\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6", - "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4", - "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18913010\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913011\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913012\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913013\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913014\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913015\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913016\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913017\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913018\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913019\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913020\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913021\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913022\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913023\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913024\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913025\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913026\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913027\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913028\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913029\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18913030\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913031\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913032\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913033\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18913034\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913035\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913036\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913100\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3", - "chr22\t18913101\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913102\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913103\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5", - "chr22\t18913104\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5", - "chr22\t18913105\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913106\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913107\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913108\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913109\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913110\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913111\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913112\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913113\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913114\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913115\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913116\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913117\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913118\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913119\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913120\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913121\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913122\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913123\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913124\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913125\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913126\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913127\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913128\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913129\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913130\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913131\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913132\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6", - "chr22\t18913133\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:3:0,2", - "chr22\t18913134\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913135\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913136\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913137\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913138\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,5", - "chr22\t18913139\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,1", - "chr22\t18913140\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913141\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913142\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913143\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913144\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913154\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913155\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913156\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913157\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913158\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:2:0,2", - "chr22\t18913159\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913160\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18913161\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913162\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913199\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913200\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913201\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913202\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913203\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18913204\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18913205\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913206\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913207\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18913208\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913209\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913210\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913211\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913212\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913213\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913214\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913215\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913216\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5" - ], - false, - false + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T15:14:21.054789211" + "timestamp": "2024-09-06T06:20:55.135067843" }, "homo_sapiens - [ bam, bai ], config - stub": { "content": [ @@ -1056,10 +93,19 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" ], "bai": [ @@ -1095,7 +141,16 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -1105,9 +160,67 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T17:44:03.275093922" + "timestamp": "2024-09-03T12:04:30.019868621" + }, + "homo_sapiens - [ bam, bai ], config - csi_index": { + "content": [ + [ + "{", + " \"PRODH\": {", + " \"total_cn\": 2,", + " \"gene_cn\": null,", + " \"final_haplotypes\": {", + " \"12222212222111211221\": \"PRODH_hap1\",", + " \"21111121111222122112\": \"PRODH_hap2\"", + " },", + " \"two_copy_haplotypes\": [],", + " \"alleles_final\": [],", + " \"hap_links\": {},", + " \"highest_total_cn\": 2,", + " \"assembled_haplotypes\": [", + " \"12222212222111211221\",", + " \"21111121111222122112\"", + " ],", + " \"sites_for_phasing\": [", + " \"18913237_G_A\",", + " \"18917224_G_A\",", + " \"18917246_A_C\",", + " \"18917262_G_A\",", + " \"18917266_T_C\",", + " \"18917362_C_A\",", + " \"18918010_C_T\",", + " \"18918465_G_A\",", + " \"18918847_T_C\",", + " \"18919892_G_T\",", + " \"18920342_G_A\",", + " \"18920484_C_T\",", + " \"18921128_C_T\",", + " \"18921213_T_C\",", + " \"18921638_T_G\",", + " \"18921763_T_C\",", + " \"18922744_C_T\",", + " \"18923032_C_T\",", + " \"18923315_T_G\",", + " \"18923644_G_A\"", + " ],", + " \"unique_supporting_reads\": {", + " \"12222212222111211221\": [" + ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.csi", + [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T06:24:48.142490096" }, "homo_sapiens - [ bam, bai ], [] - stub": { "content": [ @@ -1145,10 +258,19 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" ], "bai": [ @@ -1184,7 +306,16 @@ "id": "test", "single_end": true }, - "test_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -1194,9 +325,9 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T17:43:56.008820548" + "timestamp": "2024-09-03T12:04:14.370756094" }, "homo_sapiens - [ bam, bai ], config": { "content": [ @@ -1242,981 +373,125 @@ " \"unique_supporting_reads\": {", " \"12222212222111211221\": [" ], + "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", + "add24d02bf7f37b3ca30771c44ab4ee2", + "test.paraphase.bam.bai", + "test_PRODH.vcf.gz.tbi", [ "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" - ], - [ - "##fileformat=VCFv4.2", - "##FILTER=", - "##INFO=", - "##FORMAT=", - "##FORMAT=", - "##FORMAT=", - "##contig=", - "##paraphase_version=3.1.1", - "##paraphase_command=paraphase --gene PRODH --threads 2 --bam test.sorted.bam --reference test_ref.fa --prefix test --config paraphase_config.yaml --out .", - "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\tPRODH_hap1\tPRODH_hap2", - "chr22\t18912284\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:5:0,5", - "chr22\t18912285\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912286\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912287\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912288\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912289\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912290\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912291\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912292\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912293\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912294\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:6:0,6", - "chr22\t18912295\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:3:0,3", - "chr22\t18912296\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912297\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912298\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912299\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:5:0,5\t.:3:0,1", - "chr22\t18912300\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912301\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912302\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912303\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:7:0,7", - "chr22\t18912304\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912305\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912306\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912307\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912308\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912309\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912310\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,9\t1:7:0,7", - "chr22\t18912311\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,7\t.:3:0,3", - "chr22\t18912312\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912313\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912314\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912315\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912316\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:6:0,4", - "chr22\t18912317\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912318\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912319\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912320\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912321\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912322\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912323\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912324\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912325\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912326\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912327\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912328\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912329\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912330\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912331\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912332\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912333\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912334\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912335\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912336\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912337\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912338\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912339\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912340\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912341\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912342\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912343\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912344\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912345\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912346\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912347\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:4:0,3", - "chr22\t18912348\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912349\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912350\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912351\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912352\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18912353\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:2:0,2", - "chr22\t18912354\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912355\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912356\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912357\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912358\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912359\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912360\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912361\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912362\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912363\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912364\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912365\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912366\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912367\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912368\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912369\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912370\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912371\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912372\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912373\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912374\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912375\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912376\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912377\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912378\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912379\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912380\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,4", - "chr22\t18912381\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912382\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912383\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912384\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912385\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912386\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912387\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912388\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912389\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912390\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912391\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912392\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912393\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912394\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912395\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912396\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912397\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912398\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912399\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912400\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912401\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912402\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912403\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912404\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912405\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912406\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912407\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912408\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912409\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912410\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912411\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912412\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912413\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912414\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912415\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912416\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912417\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912418\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912419\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912420\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912421\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912422\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912423\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912424\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912425\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912426\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912427\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912428\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912429\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912430\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912431\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912432\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912433\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912434\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912435\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912436\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912437\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912438\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912439\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912440\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912441\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912442\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912443\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912444\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912445\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912446\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912447\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912448\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912449\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912450\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912451\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912452\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912453\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912454\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912455\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912456\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912457\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912458\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3", - "chr22\t18912459\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912460\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912461\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912462\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912463\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912464\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912465\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912466\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912467\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912468\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912469\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912470\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912471\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912472\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912473\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912474\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912475\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912476\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912477\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912478\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912479\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912480\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912481\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912482\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912483\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912484\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912485\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912486\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912487\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912488\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912489\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912490\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912491\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912492\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912493\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912494\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912495\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912496\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912497\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912498\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912499\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912500\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912501\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912502\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912503\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912504\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912505\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912506\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2", - "chr22\t18912507\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912508\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912509\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912510\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912511\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912512\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912513\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912514\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912515\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912516\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912517\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912518\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912519\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912520\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912521\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912522\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912523\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912524\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912525\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912526\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912527\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912528\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,4", - "chr22\t18912529\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:2:0,2", - "chr22\t18912530\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912531\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912532\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912533\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912534\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912535\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912536\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912537\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912538\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912539\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912540\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912541\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912542\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912543\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912544\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912545\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912546\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912547\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912548\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912549\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912550\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912551\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912552\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912553\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912554\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912555\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912556\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912557\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912558\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,5", - "chr22\t18912559\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t.:4:0,2", - "chr22\t18912560\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912561\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912562\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912563\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912564\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912565\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912566\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912567\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912568\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912569\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912570\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912571\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912572\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912573\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912574\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912575\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912576\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,4", - "chr22\t18912577\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912578\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912579\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912580\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912581\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912582\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912583\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912584\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912585\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912586\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912587\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912588\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912589\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912590\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912591\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912592\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912593\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912594\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912595\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912596\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912597\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912598\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912599\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912600\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912601\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912602\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912603\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912604\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912605\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912606\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912607\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912608\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912609\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912610\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912611\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912612\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912613\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6", - "chr22\t18912614\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912615\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912616\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:2:0,2", - "chr22\t18912617\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912618\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912619\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912620\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t1:6:0,6", - "chr22\t18912621\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912622\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912623\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912624\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912625\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912626\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912627\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912628\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912629\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912630\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912631\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912632\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912633\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912634\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912635\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912636\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912637\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912638\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912639\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912640\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912641\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912642\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912643\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912644\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912645\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912646\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912647\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912648\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912649\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912650\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912651\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912652\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912653\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,3", - "chr22\t18912654\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912655\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912656\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912657\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912658\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912659\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912660\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,6", - "chr22\t18912661\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18912662\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912663\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912664\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912665\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912666\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912667\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912668\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912669\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912670\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912671\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912672\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912673\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912674\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912675\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912676\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912677\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912678\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912679\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912680\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912681\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912682\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912683\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912684\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912685\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912686\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912687\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912688\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912689\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912690\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912691\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912692\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912693\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18912694\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912695\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6", - "chr22\t18912696\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912697\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912698\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912699\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912700\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912701\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912702\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912703\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912704\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912705\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912706\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912707\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912708\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912709\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912710\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912711\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912712\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912713\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912714\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,6", - "chr22\t18912715\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912716\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912717\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912718\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912719\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912720\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912721\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912722\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912723\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912724\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912725\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912726\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912727\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912728\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912729\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912730\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,3", - "chr22\t18912731\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912732\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912733\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912734\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912735\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912736\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912737\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912738\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912739\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912740\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912741\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912742\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912743\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912744\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912745\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912746\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912747\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912748\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912749\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912750\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912751\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912752\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912753\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912754\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912755\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912756\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912757\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912758\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912759\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912760\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912761\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912762\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912763\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:4:0,4", - "chr22\t18912764\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912765\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912766\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912767\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912768\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912769\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912770\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18912771\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912772\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912773\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912774\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912775\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912776\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912777\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912778\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912779\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912780\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912781\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912782\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912783\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912784\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912785\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912786\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912787\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912788\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912789\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912790\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912791\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912792\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912793\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912794\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912795\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18912796\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912797\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912798\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912799\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912800\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912801\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912802\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912803\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912804\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912805\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912806\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912807\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912808\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912809\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912810\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912811\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912812\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912813\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912814\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18912815\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t1:4:0,4", - "chr22\t18912816\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912817\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912818\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912819\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912820\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912821\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912822\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912823\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912824\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912825\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912826\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912827\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912828\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912829\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912830\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912831\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912832\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912833\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912834\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,3", - "chr22\t18912835\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912836\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912837\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912838\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,10\t1:7:0,7", - "chr22\t18912839\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912840\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t.:3:0,2", - "chr22\t18912841\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912842\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912843\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912844\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912845\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912846\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,5", - "chr22\t18912847\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912848\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912849\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912850\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912851\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912852\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912853\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912854\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912855\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912856\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912857\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912858\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912859\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912860\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912861\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912862\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912863\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912864\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912865\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912866\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912867\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t.:3:0,3", - "chr22\t18912868\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912869\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912870\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912871\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912872\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912873\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912874\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912875\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912876\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912877\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912878\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912879\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912880\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,6", - "chr22\t18912881\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:4:0,4", - "chr22\t18912882\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912883\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912884\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912885\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912886\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912887\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912888\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912889\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912890\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912891\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912892\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912893\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:4:0,4", - "chr22\t18912894\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912895\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912896\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18912897\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,5", - "chr22\t18912898\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912899\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912900\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912901\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912902\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18912903\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,2", - "chr22\t18912904\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912905\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912906\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912907\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912908\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912909\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912910\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912911\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912912\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912913\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912914\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912915\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912916\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912917\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,10\t1:7:0,7", - "chr22\t18912918\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,6\t.:2:0,2", - "chr22\t18912919\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912920\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912921\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912922\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:6:0,6", - "chr22\t18912923\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912924\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912925\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912926\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912927\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18912928\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912929\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912930\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,3", - "chr22\t18912931\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912932\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:6:0,6", - "chr22\t18912933\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912934\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912935\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912936\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912937\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18912938\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18912939\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912940\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912941\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912942\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912943\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912944\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912945\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912946\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912947\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912948\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912949\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912950\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912951\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18912952\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912953\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:6:0,6", - "chr22\t18912954\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,8\t1:4:0,4", - "chr22\t18912955\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912956\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912957\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912958\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912959\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912960\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912961\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912962\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912963\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912964\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912965\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912966\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18912967\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912968\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912969\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912970\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912971\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912972\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912973\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18912974\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912975\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912976\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912977\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18912978\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912979\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912980\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912981\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912982\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912983\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912984\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912985\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18912986\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912987\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912988\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18912989\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912990\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912991\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912992\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18912993\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18912994\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18912995\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:4:0,4", - "chr22\t18912996\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912997\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18912998\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18912999\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913000\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913001\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913002\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913003\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913004\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913005\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913006\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913007\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913008\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913009\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t.:3:0,3", - "chr22\t18913010\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913011\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913012\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913013\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913014\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913015\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913016\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913017\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913018\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913019\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913020\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913021\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913022\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913023\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913024\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913025\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913026\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913027\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913028\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913029\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18913030\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913031\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913032\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913033\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:4:0,4", - "chr22\t18913034\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913035\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913036\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913037\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913038\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913039\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913040\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913041\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913042\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913043\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913044\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913045\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913046\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913047\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913048\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913049\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913050\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913051\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913052\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913053\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913054\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913055\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913056\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913057\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913058\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913059\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913060\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913061\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913062\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913063\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913064\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913065\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913066\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913067\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913068\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,7", - "chr22\t18913069\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,7\t.:2:0,2", - "chr22\t18913070\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913071\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913072\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913073\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,6", - "chr22\t18913074\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913075\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913076\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913077\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913078\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913079\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913080\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913081\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913082\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913083\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913084\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913085\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913086\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913087\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913088\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913089\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913090\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913091\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913092\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913093\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913094\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913095\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913096\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913097\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913098\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913099\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913100\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:3:0,3", - "chr22\t18913101\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913102\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913103\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5", - "chr22\t18913104\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t1:5:0,5", - "chr22\t18913105\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913106\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913107\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913108\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913109\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913110\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913111\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913112\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913113\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913114\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913115\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913116\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913117\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913118\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:5:0,5", - "chr22\t18913119\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913120\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913121\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913122\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913123\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913124\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913125\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913126\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913127\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913128\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913129\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913130\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913131\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913132\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:7:0,6", - "chr22\t18913133\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:6:0,5\t.:3:0,2", - "chr22\t18913134\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913135\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913136\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913137\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913138\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,5", - "chr22\t18913139\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:7:0,7\t.:3:0,1", - "chr22\t18913140\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913141\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913142\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913143\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913144\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913145\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913146\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913147\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913148\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913149\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913150\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913151\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913152\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913153\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913154\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913155\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913156\t.\ta\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913157\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913158\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:8:0,8\t.:2:0,2", - "chr22\t18913159\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913160\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:7:0,7", - "chr22\t18913161\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913162\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913163\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913164\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913165\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913166\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913167\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913168\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913169\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913170\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913171\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913172\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:5:0,5", - "chr22\t18913173\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913174\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913175\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913176\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913177\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913178\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913179\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913180\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913181\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913182\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:9:0,9\t1:4:0,4", - "chr22\t18913183\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913184\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913185\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913186\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913187\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913188\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913189\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913190\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913191\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913192\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913193\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913194\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,11\t1:6:0,6", - "chr22\t18913195\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913196\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913197\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913198\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913199\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913200\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913201\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:6:0,6", - "chr22\t18913202\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913203\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,6", - "chr22\t18913204\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,5", - "chr22\t18913205\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913206\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913207\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t.:3:0,3", - "chr22\t18913208\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913209\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913210\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913211\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5", - "chr22\t18913212\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913213\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913214\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913215\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913216\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913217\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913218\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:6:0,6", - "chr22\t18913219\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913220\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:6:0,6", - "chr22\t18913221\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913222\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913223\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913224\t.\tt\tT\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913225\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:5:0,5", - "chr22\t18913226\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913227\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913228\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913229\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913230\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913231\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:10:0,10\t1:7:0,7", - "chr22\t18913232\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:11:0,11\t1:7:0,7", - "chr22\t18913233\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913234\t.\tg\tG\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913235\t.\tc\tC\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:7:0,7", - "chr22\t18913236\t.\ta\tA\t.\tPASS\tHPBOUND=18912283-18936792,18912283-18936792\tGT:DP:AD\t1:12:0,12\t1:5:0,5" - ], - false, - false + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T06:24:34.443854854" + }, + "homo_sapiens - [ bam, bai ], config - stub - csi_index": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ], + "bai": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "json": [ + [ + { + "id": "test", + "single_end": true + }, + "test.paraphase.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_index": [ + [ + { + "id": "test", + "single_end": true + }, + "test_stub.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,9162c83cfe9e915e8743a1c9d64d64eb" + ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-05-29T15:14:33.451355236" + "timestamp": "2024-09-03T12:10:23.256066977" } } \ No newline at end of file diff --git a/modules/nf-core/paraphase/tests/nextflow.csi_index.config b/modules/nf-core/paraphase/tests/nextflow.csi_index.config new file mode 100644 index 000000000000..df8ee6c39bca --- /dev/null +++ b/modules/nf-core/paraphase/tests/nextflow.csi_index.config @@ -0,0 +1,6 @@ +process { + withName: 'PARAPHASE' { + ext.args = '--gene PRODH' + ext.args3 = '--csi' + } +} From 6f2dfbf6bbdf4d0fc056cca15b28c998fdaac86e Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 19:10:46 +1200 Subject: [PATCH 020/486] Added nf-test for ivar/variants (#6567) * Added nf-test for ivar/variants * Simplified version extraction * Version bump --------- Co-authored-by: Joon Klaps --- modules/nf-core/ivar/variants/environment.yml | 3 +- modules/nf-core/ivar/variants/main.nf | 19 +- .../nf-core/ivar/variants/tests/main.nf.test | 118 +++++++++++ .../ivar/variants/tests/main.nf.test.snap | 188 ++++++++++++++++++ tests/config/pytest_modules.yml | 6 +- tests/modules/nf-core/ivar/variants/main.nf | 47 ----- .../nf-core/ivar/variants/nextflow.config | 5 - tests/modules/nf-core/ivar/variants/test.yml | 30 --- 8 files changed, 326 insertions(+), 90 deletions(-) create mode 100644 modules/nf-core/ivar/variants/tests/main.nf.test create mode 100644 modules/nf-core/ivar/variants/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/ivar/variants/main.nf delete mode 100644 tests/modules/nf-core/ivar/variants/nextflow.config delete mode 100644 tests/modules/nf-core/ivar/variants/test.yml diff --git a/modules/nf-core/ivar/variants/environment.yml b/modules/nf-core/ivar/variants/environment.yml index 7431cac4ff1a..6b1443eb15ff 100644 --- a/modules/nf-core/ivar/variants/environment.yml +++ b/modules/nf-core/ivar/variants/environment.yml @@ -2,6 +2,5 @@ name: ivar_variants channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::ivar=1.4 + - bioconda::ivar=1.4.3 diff --git a/modules/nf-core/ivar/variants/main.nf b/modules/nf-core/ivar/variants/main.nf index 189696aaf6a5..e8831ba937f7 100644 --- a/modules/nf-core/ivar/variants/main.nf +++ b/modules/nf-core/ivar/variants/main.nf @@ -4,8 +4,8 @@ process IVAR_VARIANTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ivar:1.4--h6b7c446_1' : - 'biocontainers/ivar:1.4--h6b7c446_1' }" + 'https://depot.galaxyproject.org/singularity/ivar:1.4.3--h43eeafb_0' : + 'biocontainers/ivar:1.4.3--h43eeafb_0' }" input: tuple val(meta), path(bam) @@ -44,7 +44,20 @@ process IVAR_VARIANTS { cat <<-END_VERSIONS > versions.yml "${task.process}": - ivar: \$(echo \$(ivar version 2>&1) | sed 's/^.*iVar version //; s/ .*\$//') + ivar: \$(ivar version | sed 's/^.*iVar version //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def touch_mpileup = save_mpileup ? "touch ${prefix}.mpileup" : '' + """ + touch ${prefix}.tsv + $touch_mpileup + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ivar: \$(ivar version | sed 's/^.*iVar version //; s/ .*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/ivar/variants/tests/main.nf.test b/modules/nf-core/ivar/variants/tests/main.nf.test new file mode 100644 index 000000000000..35a440bf5a0e --- /dev/null +++ b/modules/nf-core/ivar/variants/tests/main.nf.test @@ -0,0 +1,118 @@ + +nextflow_process { + + name "Test Process IVAR_VARIANTS" + script "../main.nf" + process "IVAR_VARIANTS" + + tag "modules" + tag "modules_nfcore" + tag "ivar" + tag "ivar/variants" + + test("test-ivar-variants-no-gff-no-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = [] + input[4] = false + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-no-gff-with-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = [] + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-with-gff-with-mpileup") { + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-ivar-variants-with-gff-with-mpileup-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + input[4] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/ivar/variants/tests/main.nf.test.snap b/modules/nf-core/ivar/variants/tests/main.nf.test.snap new file mode 100644 index 000000000000..75ab31634cb7 --- /dev/null +++ b/modules/nf-core/ivar/variants/tests/main.nf.test.snap @@ -0,0 +1,188 @@ +{ + "test-ivar-variants-no-gff-no-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:35.649607" + }, + "test-ivar-variants-with-gff-with-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,2cf6c48b55e0e81155ff310d48de94df" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,2cf6c48b55e0e81155ff310d48de94df" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:48.194076" + }, + "test-ivar-variants-with-gff-with-mpileup-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:52.839222" + }, + "test-ivar-variants-no-gff-with-mpileup": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "2": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ], + "mpileup": [ + [ + { + "id": "test" + }, + "test.mpileup:md5,958e6bead4103d72026f80153b6b5150" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,76c93420121bb891fa275f716142a157" + ] + ], + "versions": [ + "versions.yml:md5,5b456a9f7e77f16a46a5bd1546b3c83a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:00:41.680848" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4eb6450e873d..514df925847f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -362,9 +362,9 @@ iphop/download: iphop/predict: - modules/nf-core/iphop/predict/** - tests/modules/nf-core/iphop/predict/** -ivar/variants: - - modules/nf-core/ivar/variants/** - - tests/modules/nf-core/ivar/variants/** +ivar/consensus: + - modules/nf-core/ivar/consensus/** + - tests/modules/nf-core/ivar/consensus/** jupyternotebook: - modules/nf-core/jupyternotebook/** - tests/modules/nf-core/jupyternotebook/** diff --git a/tests/modules/nf-core/ivar/variants/main.nf b/tests/modules/nf-core/ivar/variants/main.nf deleted file mode 100644 index b8dd56b5ba38..000000000000 --- a/tests/modules/nf-core/ivar/variants/main.nf +++ /dev/null @@ -1,47 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IVAR_VARIANTS } from '../../../../../modules/nf-core/ivar/variants/main.nf' - -workflow test_ivar_variants_no_gff_no_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = [] - save_mpileup = false - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} - -workflow test_ivar_variants_no_gff_with_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = [] - save_mpileup = true - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} - -workflow test_ivar_variants_with_gff_with_mpileup { - - input = [ - [ id:'test'], - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - gff = file(params.test_data['sarscov2']['genome']['genome_gff3'], checkIfExists: true) - save_mpileup = true - - IVAR_VARIANTS ( input, fasta, fai, gff, save_mpileup ) -} diff --git a/tests/modules/nf-core/ivar/variants/nextflow.config b/tests/modules/nf-core/ivar/variants/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/ivar/variants/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/ivar/variants/test.yml b/tests/modules/nf-core/ivar/variants/test.yml deleted file mode 100644 index 9fc3506f6e92..000000000000 --- a/tests/modules/nf-core/ivar/variants/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: ivar variants no gff no mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_no_mpileup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 76c93420121bb891fa275f716142a157 - -- name: ivar variants no gff with mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_no_gff_with_mpileup -c ./tests/config/nextflow.config --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 76c93420121bb891fa275f716142a157 - - path: output/ivar/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 - -- name: ivar variants with gff with mpileup - command: nextflow run ./tests/modules/nf-core/ivar/variants -entry test_ivar_variants_with_gff_with_mpileup -c ./tests/config/nextflow.config --gff tests/data/gff/sarscov2/MN908947.3.gff3 --save_mpileup -c ./tests/modules/nf-core/ivar/variants/nextflow.config - tags: - - ivar - - ivar/variants - files: - - path: output/ivar/test.tsv - md5sum: 2cf6c48b55e0e81155ff310d48de94df - - path: output/ivar/test.mpileup - md5sum: 958e6bead4103d72026f80153b6b5150 From be7165fc271340f401b25d5780de7973e1e045a4 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 19:32:45 +1200 Subject: [PATCH 021/486] Added nf-test for gfaffix (#6597) * Added nf-test for gfaffix * Version bump * Fixed linting * Fixed versions * version fix --- modules/nf-core/gfaffix/environment.yml | 3 +- modules/nf-core/gfaffix/main.nf | 14 +++- modules/nf-core/gfaffix/tests/main.nf.test | 63 ++++++++++++++ .../nf-core/gfaffix/tests/main.nf.test.snap | 83 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/gfaffix/main.nf | 13 --- tests/modules/nf-core/gfaffix/nextflow.config | 5 -- tests/modules/nf-core/gfaffix/test.yml | 9 -- 8 files changed, 160 insertions(+), 33 deletions(-) create mode 100644 modules/nf-core/gfaffix/tests/main.nf.test create mode 100644 modules/nf-core/gfaffix/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gfaffix/main.nf delete mode 100644 tests/modules/nf-core/gfaffix/nextflow.config delete mode 100644 tests/modules/nf-core/gfaffix/test.yml diff --git a/modules/nf-core/gfaffix/environment.yml b/modules/nf-core/gfaffix/environment.yml index 09e63d2483eb..77262a47394c 100644 --- a/modules/nf-core/gfaffix/environment.yml +++ b/modules/nf-core/gfaffix/environment.yml @@ -2,6 +2,5 @@ name: gfaffix channels: - conda-forge - bioconda - - defaults dependencies: - - bioconda::gfaffix=0.1.5 + - bioconda::gfaffix=0.1.5b diff --git a/modules/nf-core/gfaffix/main.nf b/modules/nf-core/gfaffix/main.nf index efbfe28ffa19..2abdd634a59a 100644 --- a/modules/nf-core/gfaffix/main.nf +++ b/modules/nf-core/gfaffix/main.nf @@ -30,7 +30,19 @@ process GFAFFIX { cat <<-END_VERSIONS > versions.yml "${task.process}": - gfaffix: \$(gfaffix --version 2>&1 | grep -o 'gfaffix .*' | cut -f2 -d ' ') + gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.gfaffix.gfa + touch ${prefix}.affixes.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gfaffix: \$(gfaffix --version | grep -o 'gfaffix .*' | cut -f2 -d ' ') END_VERSIONS """ } diff --git a/modules/nf-core/gfaffix/tests/main.nf.test b/modules/nf-core/gfaffix/tests/main.nf.test new file mode 100644 index 000000000000..41fca58b64e7 --- /dev/null +++ b/modules/nf-core/gfaffix/tests/main.nf.test @@ -0,0 +1,63 @@ + +nextflow_process { + + name "Test Process GFAFFIX" + script "../main.nf" + process "GFAFFIX" + + tag "modules" + tag "modules_nfcore" + tag "gfaffix" + + test("test-gfaffix") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.gfa, + process.out.affixes, + process.out.versions, + file(process.out.versions[0]).readLines().collect { it.trim() }, // Trap for conda version mismatches + ).match() + } + ) + } + } + + test("test-gfaffix-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gfa/assembly.gfa', checkIfExists: true) ] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gfaffix/tests/main.nf.test.snap b/modules/nf-core/gfaffix/tests/main.nf.test.snap new file mode 100644 index 000000000000..6ff3e8df4387 --- /dev/null +++ b/modules/nf-core/gfaffix/tests/main.nf.test.snap @@ -0,0 +1,83 @@ +{ + "test-gfaffix": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,30d7a68fc07623779dbb3d708320c844" + ] + ], + [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,c3540baa386462552d7ebe4e4b7eda6a" + ] + ], + [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ], + [ + "\"GFAFFIX\":", + "gfaffix: 0.1.5b" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:14:01.340269" + }, + "test-gfaffix-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ], + "affixes": [ + [ + { + "id": "test" + }, + "test.affixes.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gfa": [ + [ + { + "id": "test" + }, + "test.gfaffix.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3ec7c6a9cbafbb8131f4e325e140aa80" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T14:36:34.068923" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 514df925847f..58a1759f46f8 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -263,9 +263,6 @@ genotyphi/parse: genrich: - modules/nf-core/genrich/** - tests/modules/nf-core/genrich/** -gfaffix: - - modules/nf-core/gfaffix/** - - tests/modules/nf-core/gfaffix/** gfastats: - modules/nf-core/gfastats/** - tests/modules/nf-core/gfastats/** diff --git a/tests/modules/nf-core/gfaffix/main.nf b/tests/modules/nf-core/gfaffix/main.nf deleted file mode 100644 index 712f7dca3e16..000000000000 --- a/tests/modules/nf-core/gfaffix/main.nf +++ /dev/null @@ -1,13 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GFAFFIX } from '../../../../modules/nf-core/gfaffix/main.nf' - -workflow test_gfaffix { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['assembly_gfa'], checkIfExists: true)] - ] - - GFAFFIX ( input ) -} diff --git a/tests/modules/nf-core/gfaffix/nextflow.config b/tests/modules/nf-core/gfaffix/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/gfaffix/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gfaffix/test.yml b/tests/modules/nf-core/gfaffix/test.yml deleted file mode 100644 index 4c47c0ab78f0..000000000000 --- a/tests/modules/nf-core/gfaffix/test.yml +++ /dev/null @@ -1,9 +0,0 @@ -- name: gfaffix - command: nextflow run ./tests/modules/nf-core/gfaffix -entry test_gfaffix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gfaffix/nextflow.config - tags: - - gfaffix - files: - - path: output/gfaffix/test.gfaffix.gfa - md5sum: 30d7a68fc07623779dbb3d708320c844 - - path: output/gfaffix/test.affixes.txt - md5sum: c3540baa386462552d7ebe4e4b7eda6a From cba25d76a16d44f4823ba5f5a2beb136da60c46a Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 19:37:39 +1200 Subject: [PATCH 022/486] Added nf-test for idr (#6570) * Added nf-test for idr * removed defaults --- modules/nf-core/idr/environment.yml | 1 - modules/nf-core/idr/main.nf | 19 +++ modules/nf-core/idr/meta.yml | 6 +- modules/nf-core/idr/tests/main.nf.test | 127 ++++++++++++++++++++ modules/nf-core/idr/tests/main.nf.test.snap | 88 ++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/idr/main.nf | 35 ------ tests/modules/nf-core/idr/nextflow.config | 5 - tests/modules/nf-core/idr/test.yml | 35 ------ 9 files changed, 237 insertions(+), 82 deletions(-) create mode 100644 modules/nf-core/idr/tests/main.nf.test create mode 100644 modules/nf-core/idr/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/idr/main.nf delete mode 100644 tests/modules/nf-core/idr/nextflow.config delete mode 100644 tests/modules/nf-core/idr/test.yml diff --git a/modules/nf-core/idr/environment.yml b/modules/nf-core/idr/environment.yml index 51378273997f..2790cc3fa4af 100644 --- a/modules/nf-core/idr/environment.yml +++ b/modules/nf-core/idr/environment.yml @@ -2,6 +2,5 @@ name: idr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::idr=2.0.4.2 diff --git a/modules/nf-core/idr/main.nf b/modules/nf-core/idr/main.nf index f27c85917d8d..037435186465 100644 --- a/modules/nf-core/idr/main.nf +++ b/modules/nf-core/idr/main.nf @@ -46,4 +46,23 @@ process IDR { idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//') END_VERSIONS """ + + stub: + if (peaks.toList().size < 2) { + log.error "[ERROR] idr needs at least two replicates only one provided." + } + def peak_types = ['narrowPeak', 'broadPeak', 'bed'] + if (!peak_types.contains(peak_type)) { + log.error "[ERROR] Invalid option: '${peak_type}'. Valid options for 'peak_type': ${peak_types.join(', ')}." + } + """ + touch "${prefix}.idrValues.txt" + touch "${prefix}.log.txt" + touch "${prefix}.png" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + idr: \$(echo \$(idr --version 2>&1) | sed 's/^.*IDR //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/idr/meta.yml b/modules/nf-core/idr/meta.yml index fb7c6944a4c5..5f2ab1109e38 100644 --- a/modules/nf-core/idr/meta.yml +++ b/modules/nf-core/idr/meta.yml @@ -17,15 +17,15 @@ tools: licence: ["GPL v2"] input: - peaks: - type: tuple of two files + type: list description: BED, narrowPeak or broadPeak files of replicates pattern: "*" - peak_type: - type: value + type: string description: Type of peak file pattern: "{narrowPeak,broadPeak,bed}" - prefix: - type: value + type: string description: Prefix for output files output: - versions: diff --git a/modules/nf-core/idr/tests/main.nf.test b/modules/nf-core/idr/tests/main.nf.test new file mode 100644 index 000000000000..7005be87dc40 --- /dev/null +++ b/modules/nf-core/idr/tests/main.nf.test @@ -0,0 +1,127 @@ + +nextflow_process { + + name "Test Process IDR" + script "../main.nf" + process "IDR" + + tag "modules" + tag "modules_nfcore" + tag "idr" + + test("test-idr-narrowpeak") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-broadpeak") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test.broadPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak', checkIfExists: true) + ] + input[1] = 'broadPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-noprefix") { + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.idr, + file(process.out.log[0]).name, + file(process.out.png[0]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-idr-noprefix-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test.narrowPeak', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/narrowpeak/test2.narrowPeak', checkIfExists: true) + ] + input[1] = 'narrowPeak' + input[2] = 'test' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/idr/tests/main.nf.test.snap b/modules/nf-core/idr/tests/main.nf.test.snap new file mode 100644 index 000000000000..26b208ee17ef --- /dev/null +++ b/modules/nf-core/idr/tests/main.nf.test.snap @@ -0,0 +1,88 @@ +{ + "test-idr-noprefix": { + "content": [ + [ + "test.idrValues.txt:md5,09be837cc6abbc3eb5958b74802eea55" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:49.519754" + }, + "test-idr-broadpeak": { + "content": [ + [ + "test.idrValues.txt:md5,387441c716815e4caec3e70a2cc11a4a" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:30.946638" + }, + "test-idr-narrowpeak": { + "content": [ + [ + "test.idrValues.txt:md5,09be837cc6abbc3eb5958b74802eea55" + ], + "test.log.txt", + "test.idrValues.txt.png", + [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T21:09:14.769217" + }, + "test-idr-noprefix-stub": { + "content": [ + { + "0": [ + "test.idrValues.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "test.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "2": [ + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "3": [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ], + "idr": [ + "test.idrValues.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "log": [ + "test.log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "png": [ + "test.png:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,05518207e778f0165930a770902284e3" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:55:35.671555" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 58a1759f46f8..d7cba60d5092 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -341,9 +341,6 @@ icountmini/sigxls: icountmini/summary: - modules/nf-core/icountmini/summary/** - tests/modules/nf-core/icountmini/summary/** -idr: - - modules/nf-core/idr/** - - tests/modules/nf-core/idr/** ilastik/multicut: - modules/nf-core/ilastik/multicut/** - tests/modules/nf-core/ilastik/multicut/** diff --git a/tests/modules/nf-core/idr/main.nf b/tests/modules/nf-core/idr/main.nf deleted file mode 100644 index f532e8f59943..000000000000 --- a/tests/modules/nf-core/idr/main.nf +++ /dev/null @@ -1,35 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { IDR } from '../../../../modules/nf-core/idr/main.nf' - -workflow test_idr_narrowpeak { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true) - ] - - IDR ( input, 'narrowPeak', 'test' ) -} - -workflow test_idr_broadpeak { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_broadpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_broadpeak'], checkIfExists: true) - ] - - IDR ( input, 'broadPeak', 'test' ) -} - -workflow test_idr_noprefix { - - input = [ - file(params.test_data['homo_sapiens']['illumina']['test_narrowpeak'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_narrowpeak'], checkIfExists: true) - ] - - IDR ( input, 'narrowPeak', '' ) -} diff --git a/tests/modules/nf-core/idr/nextflow.config b/tests/modules/nf-core/idr/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/idr/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/idr/test.yml b/tests/modules/nf-core/idr/test.yml deleted file mode 100644 index 42a4b1bda5ae..000000000000 --- a/tests/modules/nf-core/idr/test.yml +++ /dev/null @@ -1,35 +0,0 @@ -- name: idr test_idr_narrowpeak - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_narrowpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/test.idrValues.txt - md5sum: 09be837cc6abbc3eb5958b74802eea55 - - path: output/idr/test.idrValues.txt.png - md5sum: 4a7143ccc0ccadb37c2317bf626e6d96 - - path: output/idr/test.log.txt - md5sum: 6443507ac66b9d3b64bc56b78328083e - -- name: idr test_idr_broadpeak - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_broadpeak -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/test.idrValues.txt - md5sum: 387441c716815e4caec3e70a2cc11a4a - - path: output/idr/test.idrValues.txt.png - md5sum: 7204083ca5b920b4215a5991c12cb4e7 - - path: output/idr/test.log.txt - md5sum: e6917133112b5cec135c182ffac19237 - -- name: idr test_idr_noprefix - command: nextflow run ./tests/modules/nf-core/idr -entry test_idr_noprefix -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/idr/nextflow.config - tags: - - idr - files: - - path: output/idr/idrValues.txt - md5sum: 09be837cc6abbc3eb5958b74802eea55 - - path: output/idr/idrValues.txt.png - md5sum: 4a7143ccc0ccadb37c2317bf626e6d96 - - path: output/idr/log.txt - md5sum: 6443507ac66b9d3b64bc56b78328083e From 5d1979fdbad4444a7d11448db8a20780bf2eeaec Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 19:43:48 +1200 Subject: [PATCH 023/486] Added nf-test for gunc/downloaddb (#6599) --- .../nf-core/gunc/downloaddb/environment.yml | 1 - modules/nf-core/gunc/downloaddb/main.nf | 11 ++++ .../gunc/downloaddb/tests/main.nf.test | 56 +++++++++++++++++++ .../gunc/downloaddb/tests/main.nf.test.snap | 38 +++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/gunc/downloaddb/main.nf | 12 ---- .../nf-core/gunc/downloaddb/nextflow.config | 5 -- .../modules/nf-core/gunc/downloaddb/test.yml | 8 --- 8 files changed, 105 insertions(+), 29 deletions(-) create mode 100644 modules/nf-core/gunc/downloaddb/tests/main.nf.test create mode 100644 modules/nf-core/gunc/downloaddb/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/gunc/downloaddb/main.nf delete mode 100644 tests/modules/nf-core/gunc/downloaddb/nextflow.config delete mode 100644 tests/modules/nf-core/gunc/downloaddb/test.yml diff --git a/modules/nf-core/gunc/downloaddb/environment.yml b/modules/nf-core/gunc/downloaddb/environment.yml index 737b6261125a..25540dddd2fe 100644 --- a/modules/nf-core/gunc/downloaddb/environment.yml +++ b/modules/nf-core/gunc/downloaddb/environment.yml @@ -2,6 +2,5 @@ name: gunc_downloaddb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gunc=1.0.5 diff --git a/modules/nf-core/gunc/downloaddb/main.nf b/modules/nf-core/gunc/downloaddb/main.nf index 2646536bfceb..be43affaaa8c 100644 --- a/modules/nf-core/gunc/downloaddb/main.nf +++ b/modules/nf-core/gunc/downloaddb/main.nf @@ -27,4 +27,15 @@ process GUNC_DOWNLOADDB { gunc: \$( gunc --version ) END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + """ + touch ${db_name}.dmnd + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gunc: \$( gunc --version ) + END_VERSIONS + """ } diff --git a/modules/nf-core/gunc/downloaddb/tests/main.nf.test b/modules/nf-core/gunc/downloaddb/tests/main.nf.test new file mode 100644 index 000000000000..b719ab26f1ef --- /dev/null +++ b/modules/nf-core/gunc/downloaddb/tests/main.nf.test @@ -0,0 +1,56 @@ + +nextflow_process { + + name "Test Process GUNC_DOWNLOADDB" + script "../main.nf" + process "GUNC_DOWNLOADDB" + + tag "modules" + tag "modules_nfcore" + tag "gunc" + tag "gunc/downloaddb" + + test("test-gunc-downloaddb") { + + when { + process { + """ + input[0] = 'progenomes' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.db[0]).name, // ~ 12 GB file + process.out.versions + ).match() + } + ) + } + } + + test("test-gunc-downloaddb-stub") { + options '-stub' + + when { + process { + """ + input[0] = 'progenomes' + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/gunc/downloaddb/tests/main.nf.test.snap b/modules/nf-core/gunc/downloaddb/tests/main.nf.test.snap new file mode 100644 index 000000000000..d2af3a2ee70f --- /dev/null +++ b/modules/nf-core/gunc/downloaddb/tests/main.nf.test.snap @@ -0,0 +1,38 @@ +{ + "test-gunc-downloaddb": { + "content": [ + "gunc_db_progenomes2.1.dmnd", + [ + "versions.yml:md5,ab391d00f34801f2caa143c4c05eba56" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T10:25:14.217951" + }, + "test-gunc-downloaddb-stub": { + "content": [ + { + "0": [ + "progenomes.dmnd:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "versions.yml:md5,ab391d00f34801f2caa143c4c05eba56" + ], + "db": [ + "progenomes.dmnd:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,ab391d00f34801f2caa143c4c05eba56" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T10:25:20.120206" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index d7cba60d5092..647fdb0f4c1a 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -293,9 +293,6 @@ gridss/gridssgenerateponbedpe: gsea/gsea: - modules/nf-core/gsea/gsea/** - tests/modules/nf-core/gsea/gsea/** -gunc/downloaddb: - - modules/nf-core/gunc/downloaddb/** - - tests/modules/nf-core/gunc/downloaddb/** gunc/mergecheckm: - modules/nf-core/gunc/mergecheckm/** - tests/modules/nf-core/gunc/mergecheckm/** diff --git a/tests/modules/nf-core/gunc/downloaddb/main.nf b/tests/modules/nf-core/gunc/downloaddb/main.nf deleted file mode 100644 index a708f54e6ff9..000000000000 --- a/tests/modules/nf-core/gunc/downloaddb/main.nf +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { GUNC_DOWNLOADDB } from '../../../../../modules/nf-core/gunc/downloaddb/main.nf' - -workflow test_gunc_downloaddb { - - input = 'progenomes' - - GUNC_DOWNLOADDB ( input ) -} diff --git a/tests/modules/nf-core/gunc/downloaddb/nextflow.config b/tests/modules/nf-core/gunc/downloaddb/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/gunc/downloaddb/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/gunc/downloaddb/test.yml b/tests/modules/nf-core/gunc/downloaddb/test.yml deleted file mode 100644 index 9f0e52b55b6f..000000000000 --- a/tests/modules/nf-core/gunc/downloaddb/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: gunc downloaddb - command: nextflow run ./tests/modules/nf-core/gunc/downloaddb -entry test_gunc_downloaddb -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/gunc/downloaddb/nextflow.config - tags: - - gunc - - gunc/downloaddb - files: - - path: output/gunc/gunc_db_progenomes2.1.dmnd - md5sum: 447c9330056b02f29f30fe81fe4af4eb From 054b9383de171aaffcabae40b3f7162c88d37642 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 20:01:52 +1200 Subject: [PATCH 024/486] Added nf-test for metabat2/jgisummarizebamcontigdepths (#6565) * Added nf-test for metabat2/jgisummarizebamcontigdepths * Removed defaults --- .../environment.yml | 1 - .../jgisummarizebamcontigdepths/main.nf | 11 +++ .../tests/main.nf.test | 60 ++++++++++++++++ .../tests/main.nf.test.snap | 68 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - .../jgisummarizebamcontigdepths/main.nf | 14 ---- .../nextflow.config | 5 -- .../jgisummarizebamcontigdepths/test.yml | 8 --- 8 files changed, 139 insertions(+), 31 deletions(-) create mode 100644 modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test create mode 100644 modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf delete mode 100644 tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config delete mode 100644 tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml index 3140be6a47b3..887fc413fd69 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml @@ -2,6 +2,5 @@ name: metabat2_jgisummarizebamcontigdepths channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metabat2=2.15 diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf index 60b38e0e71b1..df3971fc3fb5 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf @@ -35,4 +35,15 @@ process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS { metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo | gzip > ${prefix}.txt.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + metabat2: \$( metabat2 --help 2>&1 | head -n 2 | tail -n 1| sed 's/.*\\:\\([0-9]*\\.[0-9]*\\).*/\\1/' ) + END_VERSIONS + """ } diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test new file mode 100644 index 000000000000..d4852ba5b064 --- /dev/null +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test @@ -0,0 +1,60 @@ + +nextflow_process { + + name "Test Process METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS" + script "../main.nf" + process "METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS" + + tag "modules" + tag "modules_nfcore" + tag "metabat2" + tag "metabat2/jgisummarizebamcontigdepths" + + test("test-metabat2-jgisummarizebamcontigdepths") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-metabat2-jgisummarizebamcontigdepths-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test.snap b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test.snap new file mode 100644 index 000000000000..29e60c37deee --- /dev/null +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test-metabat2-jgisummarizebamcontigdepths": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,c7448ff92b336561540717e7b0ca0702" + ] + ], + "1": [ + "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5" + ], + "depth": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,c7448ff92b336561540717e7b0ca0702" + ] + ], + "versions": [ + "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:02:46.985235" + }, + "test-metabat2-jgisummarizebamcontigdepths-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5" + ], + "depth": [ + [ + { + "id": "test" + }, + "test.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,2884d72385b65d0737899da5cb9e89d5" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:01:24.531629" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 647fdb0f4c1a..3031d41c39d3 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -419,9 +419,6 @@ merquryfk/katgc: merquryfk/ploidyplot: - modules/nf-core/merquryfk/ploidyplot/** - tests/modules/nf-core/merquryfk/ploidyplot/** -metabat2/jgisummarizebamcontigdepths: - - modules/nf-core/metabat2/jgisummarizebamcontigdepths/** - - tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/** metabat2/metabat2: - modules/nf-core/metabat2/metabat2/** - tests/modules/nf-core/metabat2/metabat2/** diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf deleted file mode 100644 index 861e0cb5f740..000000000000 --- a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf +++ /dev/null @@ -1,14 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS } from '../../../../../modules/nf-core/metabat2/jgisummarizebamcontigdepths/main.nf' - -workflow test_metabat2_jgisummarizebamcontigdepths { - - input = [ [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - - METABAT2_JGISUMMARIZEBAMCONTIGDEPTHS ( input ) -} diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml b/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml deleted file mode 100644 index c68fac757b79..000000000000 --- a/tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: metabat2 jgisummarizebamcontigdepths test_metabat2_jgisummarizebamcontigdepths - command: nextflow run ./tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths -entry test_metabat2_jgisummarizebamcontigdepths -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/metabat2/jgisummarizebamcontigdepths/nextflow.config - tags: - - metabat2/jgisummarizebamcontigdepths - - metabat2 - files: - - path: output/metabat2/test.txt.gz - md5sum: 8f735aa408d6c90e5a0310e06ace7a9a From cbb5173183476e0ae672d3ff094a731c57584a05 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Fri, 6 Sep 2024 20:25:09 +1200 Subject: [PATCH 025/486] Added nf-test for krona/ktupdatetaxonomy (#6569) * Added nf-test for krona/ktupdatetaxonomy * Removed defaults * Updated power assertion --- .../krona/ktupdatetaxonomy/environment.yml | 1 - .../nf-core/krona/ktupdatetaxonomy/main.nf | 14 +++++ .../krona/ktupdatetaxonomy/tests/main.nf.test | 54 +++++++++++++++++++ .../ktupdatetaxonomy/tests/main.nf.test.snap | 38 +++++++++++++ tests/config/pytest_modules.yml | 3 -- .../nf-core/krona/ktupdatetaxonomy/main.nf | 9 ---- .../krona/ktupdatetaxonomy/nextflow.config | 5 -- .../nf-core/krona/ktupdatetaxonomy/test.yml | 7 --- 8 files changed, 106 insertions(+), 25 deletions(-) create mode 100644 modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test create mode 100644 modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf delete mode 100644 tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config delete mode 100644 tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml diff --git a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml index a2a912962b22..ba3c11062b68 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml +++ b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml @@ -2,6 +2,5 @@ name: krona_ktupdatetaxonomy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krona=2.7.1 diff --git a/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/modules/nf-core/krona/ktupdatetaxonomy/main.nf index 4d5149220f4c..2586f9ce59ba 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ b/modules/nf-core/krona/ktupdatetaxonomy/main.nf @@ -8,6 +8,8 @@ process KRONA_KTUPDATETAXONOMY { 'https://depot.galaxyproject.org/singularity/krona:2.7.1--pl526_5' : 'biocontainers/krona:2.7.1--pl526_5' }" + input: + output: path 'taxonomy/taxonomy.tab', emit: db path "versions.yml" , emit: versions @@ -27,4 +29,16 @@ process KRONA_KTUPDATETAXONOMY { krona: $VERSION END_VERSIONS """ + + stub: + """ + mkdir taxonomy + + touch taxonomy/taxonomy.tab + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + krona: $VERSION + END_VERSIONS + """ } diff --git a/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test new file mode 100644 index 000000000000..672e82d833d8 --- /dev/null +++ b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test @@ -0,0 +1,54 @@ + +nextflow_process { + + name "Test Process KRONA_KTUPDATETAXONOMY" + script "../main.nf" + process "KRONA_KTUPDATETAXONOMY" + + tag "modules" + tag "modules_nfcore" + tag "krona" + tag "krona/ktupdatetaxonomy" + + test("test-krona-ktupdatetaxonomy") { + + when { + process { + """ + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.db[0]).name, //unstable + process.out.versions + ).match() + } + ) + } + } + + test("test-krona-ktupdatetaxonomy-stub") { + options '-stub' + + when { + process { + """ + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test.snap b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test.snap new file mode 100644 index 000000000000..fba939229faa --- /dev/null +++ b/modules/nf-core/krona/ktupdatetaxonomy/tests/main.nf.test.snap @@ -0,0 +1,38 @@ +{ + "test-krona-ktupdatetaxonomy": { + "content": [ + "taxonomy.tab", + [ + "versions.yml:md5,a0e095fdd3ba80fcc62188c4c1f38ff7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T20:17:37.154632" + }, + "test-krona-ktupdatetaxonomy-stub": { + "content": [ + { + "0": [ + "taxonomy.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "1": [ + "versions.yml:md5,a0e095fdd3ba80fcc62188c4c1f38ff7" + ], + "db": [ + "taxonomy.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,a0e095fdd3ba80fcc62188c4c1f38ff7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T20:15:46.959212" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 3031d41c39d3..63f10b608ab0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -392,9 +392,6 @@ krona/ktimporttaxonomy: krona/ktimporttext: - modules/nf-core/krona/ktimporttext/** - tests/modules/nf-core/krona/ktimporttext/** -krona/ktupdatetaxonomy: - - modules/nf-core/krona/ktupdatetaxonomy/** - - tests/modules/nf-core/krona/ktupdatetaxonomy/** leehom: - modules/nf-core/leehom/** - tests/modules/nf-core/leehom/** diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf b/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf deleted file mode 100644 index 2323ba7d8119..000000000000 --- a/tests/modules/nf-core/krona/ktupdatetaxonomy/main.nf +++ /dev/null @@ -1,9 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { KRONA_KTUPDATETAXONOMY } from '../../../../../modules/nf-core/krona/ktupdatetaxonomy/main.nf' - -workflow test_krona_ktupdatetaxonomy { - KRONA_KTUPDATETAXONOMY ( ) -} diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config b/tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml b/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml deleted file mode 100644 index ae94a2ad3eac..000000000000 --- a/tests/modules/nf-core/krona/ktupdatetaxonomy/test.yml +++ /dev/null @@ -1,7 +0,0 @@ -- name: krona ktupdatetaxonomy test_krona_ktupdatetaxonomy - command: nextflow run ./tests/modules/nf-core/krona/ktupdatetaxonomy -entry test_krona_ktupdatetaxonomy -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/krona/ktupdatetaxonomy/nextflow.config - tags: - - krona - - krona/ktupdatetaxonomy - files: - - path: output/krona/taxonomy/taxonomy.tab From 06c8865e36741e05ad32ef70ab3fac127486af48 Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 6 Sep 2024 10:47:36 +0200 Subject: [PATCH 026/486] Mega conda environment update: Remove `name` and `defaults` (#6600) * Remove defaults channel from all modules * Remove 'name' from conda environment files * Update conda environment schema * Remove defaults from env template and GHA CI * Update Prettier in GHA test.yml workflow to match pre-commit version * Remove whitespace from environment.yml files --- .github/env-template.yml | 1 - .github/workflows/test.yml | 6 +++--- modules/environment-schema.json | 7 ++----- modules/nf-core/abacas/environment.yml | 2 -- modules/nf-core/abricate/run/environment.yml | 2 -- modules/nf-core/abricate/summary/environment.yml | 2 -- modules/nf-core/abritamr/run/environment.yml | 2 -- modules/nf-core/adapterremoval/environment.yml | 2 -- modules/nf-core/adapterremovalfixprefix/environment.yml | 2 -- modules/nf-core/admixture/environment.yml | 2 -- modules/nf-core/affy/justrma/environment.yml | 2 -- modules/nf-core/agat/convertspgff2gtf/environment.yml | 2 -- modules/nf-core/agat/convertspgff2tsv/environment.yml | 2 -- modules/nf-core/agat/convertspgxf2gxf/environment.yml | 2 -- modules/nf-core/agat/spaddintrons/environment.yml | 2 -- .../agat/spfilterfeaturefromkilllist/environment.yml | 2 -- modules/nf-core/agat/spmergeannotations/environment.yml | 2 -- modules/nf-core/agat/spstatistics/environment.yml | 2 -- modules/nf-core/agat/sqstatbasic/environment.yml | 2 -- modules/nf-core/agrvate/environment.yml | 2 -- modules/nf-core/ale/environment.yml | 2 -- modules/nf-core/allelecounter/environment.yml | 2 -- modules/nf-core/ampcombi/environment.yml | 2 -- modules/nf-core/ampcombi2/cluster/environment.yml | 2 -- modules/nf-core/ampcombi2/complete/environment.yml | 2 -- modules/nf-core/ampcombi2/parsetables/environment.yml | 2 -- modules/nf-core/ampir/environment.yml | 2 -- modules/nf-core/amplify/predict/environment.yml | 2 -- modules/nf-core/amps/environment.yml | 2 -- modules/nf-core/amrfinderplus/run/environment.yml | 2 -- modules/nf-core/amrfinderplus/update/environment.yml | 2 -- modules/nf-core/angsd/contamination/environment.yml | 2 -- modules/nf-core/angsd/docounts/environment.yml | 2 -- modules/nf-core/angsd/gl/environment.yml | 2 -- modules/nf-core/annotsv/annotsv/environment.yml | 2 -- modules/nf-core/annotsv/installannotations/environment.yml | 2 -- modules/nf-core/anota2seq/anota2seqrun/environment.yml | 2 -- modules/nf-core/antismash/antismashlite/environment.yml | 2 -- .../antismashlitedownloaddatabases/environment.yml | 2 -- modules/nf-core/arcashla/extract/environment.yml | 2 -- modules/nf-core/argnorm/environment.yml | 2 -- modules/nf-core/aria2/environment.yml | 2 -- modules/nf-core/ariba/getref/environment.yml | 2 -- modules/nf-core/ariba/run/environment.yml | 2 -- modules/nf-core/arriba/arriba/environment.yml | 2 -- modules/nf-core/arriba/download/environment.yml | 2 -- modules/nf-core/art/illumina/environment.yml | 2 -- modules/nf-core/artic/guppyplex/environment.yml | 2 -- modules/nf-core/artic/minion/environment.yml | 2 -- modules/nf-core/ascat/environment.yml | 2 -- modules/nf-core/ashlar/environment.yml | 2 -- modules/nf-core/assemblyscan/environment.yml | 2 -- modules/nf-core/ataqv/ataqv/environment.yml | 2 -- modules/nf-core/ataqv/mkarv/environment.yml | 2 -- modules/nf-core/atlas/call/environment.yml | 2 -- modules/nf-core/atlas/pmd/environment.yml | 2 -- modules/nf-core/atlas/recal/environment.yml | 2 -- modules/nf-core/atlas/splitmerge/environment.yml | 2 -- .../gtf2featureannotation/environment.yml | 2 -- modules/nf-core/authentict/deam2cont/environment.yml | 2 -- modules/nf-core/bacphlip/environment.yml | 3 --- modules/nf-core/bakta/bakta/environment.yml | 2 -- modules/nf-core/bakta/baktadbdownload/environment.yml | 2 -- modules/nf-core/bam2fastx/bam2fastq/environment.yml | 2 -- modules/nf-core/bamaligncleaner/environment.yml | 2 -- modules/nf-core/bamclipper/environment.yml | 2 -- modules/nf-core/bamcmp/environment.yml | 2 -- modules/nf-core/bamstats/generalstats/environment.yml | 2 -- modules/nf-core/bamtofastq10x/environment.yml | 2 -- modules/nf-core/bamtools/convert/environment.yml | 2 -- modules/nf-core/bamtools/split/environment.yml | 2 -- modules/nf-core/bamtools/stats/environment.yml | 2 -- modules/nf-core/bamutil/trimbam/environment.yml | 2 -- modules/nf-core/bandage/image/environment.yml | 2 -- modules/nf-core/barrnap/environment.yml | 2 -- modules/nf-core/basicpy/environment.yml | 2 -- modules/nf-core/bbmap/align/environment.yml | 2 -- modules/nf-core/bbmap/bbduk/environment.yml | 2 -- modules/nf-core/bbmap/bbmerge/environment.yml | 2 -- modules/nf-core/bbmap/bbnorm/environment.yml | 2 -- modules/nf-core/bbmap/bbsplit/environment.yml | 2 -- modules/nf-core/bbmap/clumpify/environment.yml | 2 -- modules/nf-core/bbmap/filterbyname/environment.yml | 2 -- modules/nf-core/bbmap/index/environment.yml | 2 -- modules/nf-core/bbmap/pileup/environment.yml | 2 -- modules/nf-core/bbmap/sendsketch/environment.yml | 2 -- modules/nf-core/bcftools/annotate/environment.yml | 2 -- modules/nf-core/bcftools/call/environment.yml | 2 -- modules/nf-core/bcftools/concat/environment.yml | 2 -- modules/nf-core/bcftools/consensus/environment.yml | 2 -- modules/nf-core/bcftools/convert/environment.yml | 2 -- modules/nf-core/bcftools/filter/environment.yml | 2 -- modules/nf-core/bcftools/index/environment.yml | 2 -- modules/nf-core/bcftools/isec/environment.yml | 2 -- modules/nf-core/bcftools/merge/environment.yml | 1 - modules/nf-core/bcftools/mpileup/environment.yml | 2 -- modules/nf-core/bcftools/norm/environment.yml | 2 -- modules/nf-core/bcftools/pluginscatter/environment.yml | 2 -- modules/nf-core/bcftools/pluginsplit/environment.yml | 2 -- modules/nf-core/bcftools/plugintag2tag/environment.yml | 1 - modules/nf-core/bcftools/query/environment.yml | 2 -- modules/nf-core/bcftools/reheader/environment.yml | 2 -- modules/nf-core/bcftools/roh/environment.yml | 2 -- modules/nf-core/bcftools/sort/environment.yml | 2 -- modules/nf-core/bcftools/split/environment.yml | 2 -- modules/nf-core/bcftools/stats/environment.yml | 2 -- modules/nf-core/bcftools/view/environment.yml | 2 -- modules/nf-core/beagle5/beagle/environment.yml | 2 -- modules/nf-core/bedgovcf/environment.yml | 2 -- modules/nf-core/bedops/convert2bed/environment.yml | 2 -- modules/nf-core/bedops/gtf2bed/environment.yml | 2 -- modules/nf-core/bedtools/bamtobed/environment.yml | 2 -- modules/nf-core/bedtools/closest/environment.yml | 2 -- modules/nf-core/bedtools/complement/environment.yml | 2 -- modules/nf-core/bedtools/coverage/environment.yml | 2 -- modules/nf-core/bedtools/genomecov/environment.yml | 2 -- modules/nf-core/bedtools/getfasta/environment.yml | 2 -- modules/nf-core/bedtools/groupby/environment.yml | 2 -- modules/nf-core/bedtools/intersect/environment.yml | 2 -- modules/nf-core/bedtools/jaccard/environment.yml | 2 -- modules/nf-core/bedtools/makewindows/environment.yml | 2 -- modules/nf-core/bedtools/map/environment.yml | 2 -- modules/nf-core/bedtools/maskfasta/environment.yml | 2 -- modules/nf-core/bedtools/merge/environment.yml | 2 -- modules/nf-core/bedtools/multiinter/environment.yml | 2 -- modules/nf-core/bedtools/shift/environment.yml | 2 -- modules/nf-core/bedtools/slop/environment.yml | 2 -- modules/nf-core/bedtools/sort/environment.yml | 2 -- modules/nf-core/bedtools/split/environment.yml | 2 -- modules/nf-core/bedtools/subtract/environment.yml | 2 -- modules/nf-core/bedtools/unionbedg/environment.yml | 2 -- modules/nf-core/bioawk/environment.yml | 2 -- .../nf-core/biobambam/bammarkduplicates2/environment.yml | 2 -- modules/nf-core/biobambam/bammerge/environment.yml | 2 -- modules/nf-core/biobambam/bamsormadup/environment.yml | 2 -- modules/nf-core/biohansel/environment.yml | 2 -- modules/nf-core/biscuit/align/environment.yml | 2 -- modules/nf-core/biscuit/biscuitblaster/environment.yml | 2 -- modules/nf-core/biscuit/bsconv/environment.yml | 2 -- modules/nf-core/biscuit/epiread/environment.yml | 2 -- modules/nf-core/biscuit/index/environment.yml | 2 -- modules/nf-core/biscuit/mergecg/environment.yml | 2 -- modules/nf-core/biscuit/pileup/environment.yml | 2 -- modules/nf-core/biscuit/qc/environment.yml | 2 -- modules/nf-core/biscuit/vcf2bed/environment.yml | 2 -- modules/nf-core/bismark/align/environment.yml | 2 -- modules/nf-core/bismark/coverage2cytosine/environment.yml | 2 -- modules/nf-core/bismark/deduplicate/environment.yml | 2 -- modules/nf-core/bismark/genomepreparation/environment.yml | 2 -- .../nf-core/bismark/methylationextractor/environment.yml | 2 -- modules/nf-core/bismark/report/environment.yml | 2 -- modules/nf-core/bismark/summary/environment.yml | 2 -- modules/nf-core/blast/blastdbcmd/environment.yml | 2 -- modules/nf-core/blast/blastn/environment.yml | 2 -- modules/nf-core/blast/blastp/environment.yml | 2 -- modules/nf-core/blast/makeblastdb/environment.yml | 2 -- modules/nf-core/blast/tblastn/environment.yml | 2 -- modules/nf-core/blast/updateblastdb/environment.yml | 2 -- modules/nf-core/blat/environment.yml | 2 -- modules/nf-core/bowtie/align/environment.yml | 2 -- modules/nf-core/bowtie/build/environment.yml | 2 -- modules/nf-core/bowtie2/align/environment.yml | 2 -- modules/nf-core/bowtie2/build/environment.yml | 2 -- modules/nf-core/bracken/bracken/environment.yml | 2 -- modules/nf-core/bracken/build/environment.yml | 2 -- .../nf-core/bracken/combinebrackenoutputs/environment.yml | 2 -- modules/nf-core/busco/busco/environment.yml | 2 -- modules/nf-core/busco/generateplot/environment.yml | 2 -- modules/nf-core/bwa/aln/environment.yml | 2 -- modules/nf-core/bwa/index/environment.yml | 2 -- modules/nf-core/bwa/mem/environment.yml | 2 -- modules/nf-core/bwa/sampe/environment.yml | 3 --- modules/nf-core/bwa/samse/environment.yml | 3 --- modules/nf-core/bwamem2/index/environment.yml | 2 -- modules/nf-core/bwamem2/mem/environment.yml | 2 -- modules/nf-core/bwameme/index/environment.yml | 2 -- modules/nf-core/bwameme/mem/environment.yml | 2 -- modules/nf-core/bwameth/align/environment.yml | 2 -- modules/nf-core/bwameth/index/environment.yml | 2 -- modules/nf-core/cadd/environment.yml | 2 -- modules/nf-core/cafe/environment.yml | 2 -- modules/nf-core/calder2/environment.yml | 2 -- modules/nf-core/canu/environment.yml | 2 -- modules/nf-core/cat/cat/environment.yml | 2 -- modules/nf-core/cat/fastq/environment.yml | 2 -- modules/nf-core/cdhit/cdhit/environment.yml | 2 -- modules/nf-core/cdhit/cdhitest/environment.yml | 2 -- modules/nf-core/cellbender/merge/environment.yml | 2 -- .../nf-core/cellbender/removebackground/environment.yml | 2 -- modules/nf-core/cellrangeratac/count/environment.yml | 2 -- modules/nf-core/cellrangeratac/mkfastq/environment.yml | 2 -- modules/nf-core/cellrangeratac/mkref/environment.yml | 2 -- modules/nf-core/cellsnp/modea/environment.yml | 2 -- modules/nf-core/centrifuge/build/environment.yml | 2 -- modules/nf-core/centrifuge/centrifuge/environment.yml | 2 -- modules/nf-core/centrifuge/kreport/environment.yml | 2 -- modules/nf-core/checkm/lineagewf/environment.yml | 2 -- modules/nf-core/checkm/qa/environment.yml | 2 -- modules/nf-core/checkm2/databasedownload/environment.yml | 2 -- modules/nf-core/checkm2/predict/environment.yml | 2 -- modules/nf-core/checkqc/environment.yml | 2 -- modules/nf-core/checkv/downloaddatabase/environment.yml | 2 -- modules/nf-core/checkv/endtoend/environment.yml | 2 -- modules/nf-core/checkv/updatedatabase/environment.yml | 2 -- modules/nf-core/chewbbaca/createschema/environment.yml | 3 --- modules/nf-core/chopper/environment.yml | 2 -- modules/nf-core/chromap/chromap/environment.yml | 2 -- modules/nf-core/chromap/index/environment.yml | 2 -- modules/nf-core/chromograph/environment.yml | 2 -- modules/nf-core/circexplorer2/annotate/environment.yml | 2 -- modules/nf-core/circexplorer2/parse/environment.yml | 1 - .../circularmapper/circulargenerator/environment.yml | 2 -- .../nf-core/circularmapper/realignsamfile/environment.yml | 2 -- modules/nf-core/clame/environment.yml | 2 -- modules/nf-core/clippy/environment.yml | 2 -- modules/nf-core/clonalframeml/environment.yml | 2 -- modules/nf-core/clustalo/align/environment.yml | 2 -- modules/nf-core/clustalo/guidetree/environment.yml | 2 -- modules/nf-core/cmseq/polymut/environment.yml | 2 -- modules/nf-core/cnvkit/access/environment.yml | 2 -- modules/nf-core/cnvkit/antitarget/environment.yml | 2 -- modules/nf-core/cnvkit/batch/environment.yml | 3 --- modules/nf-core/cnvkit/call/environment.yml | 1 - modules/nf-core/cnvkit/export/environment.yml | 2 -- modules/nf-core/cnvkit/genemetrics/environment.yml | 2 -- modules/nf-core/cnvkit/reference/environment.yml | 2 -- modules/nf-core/cnvkit/target/environment.yml | 2 -- modules/nf-core/cnvnator/cnvnator/environment.yml | 2 -- modules/nf-core/cnvnator/convert2vcf/environment.yml | 2 -- modules/nf-core/cnvpytor/callcnvs/environment.yml | 2 -- modules/nf-core/cnvpytor/histogram/environment.yml | 2 -- modules/nf-core/cnvpytor/importreaddepth/environment.yml | 2 -- modules/nf-core/cnvpytor/partition/environment.yml | 2 -- modules/nf-core/cnvpytor/view/environment.yml | 2 -- modules/nf-core/cobrameta/environment.yml | 2 -- modules/nf-core/cobs/classicconstruct/environment.yml | 2 -- modules/nf-core/cobs/compactconstruct/environment.yml | 2 -- modules/nf-core/concoct/concoct/environment.yml | 2 -- .../nf-core/concoct/concoctcoveragetable/environment.yml | 2 -- modules/nf-core/concoct/cutupfasta/environment.yml | 2 -- modules/nf-core/concoct/extractfastabins/environment.yml | 2 -- .../nf-core/concoct/mergecutupclustering/environment.yml | 2 -- modules/nf-core/conifer/environment.yml | 2 -- .../controlfreec/assesssignificance/environment.yml | 2 -- modules/nf-core/controlfreec/freec/environment.yml | 2 -- modules/nf-core/controlfreec/freec2bed/environment.yml | 2 -- modules/nf-core/controlfreec/freec2circos/environment.yml | 2 -- modules/nf-core/controlfreec/makegraph/environment.yml | 2 -- modules/nf-core/controlfreec/makegraph2/environment.yml | 2 -- modules/nf-core/cooler/balance/environment.yml | 2 -- modules/nf-core/cooler/cload/environment.yml | 2 -- modules/nf-core/cooler/digest/environment.yml | 2 -- modules/nf-core/cooler/dump/environment.yml | 2 -- modules/nf-core/cooler/makebins/environment.yml | 2 -- modules/nf-core/cooler/merge/environment.yml | 2 -- modules/nf-core/cooler/zoomify/environment.yml | 2 -- modules/nf-core/coreograph/environment.yml | 2 -- modules/nf-core/crabz/compress/environment.yml | 2 -- modules/nf-core/crabz/decompress/environment.yml | 2 -- modules/nf-core/crisprcleanr/normalize/environment.yml | 2 -- modules/nf-core/crumble/environment.yml | 2 -- modules/nf-core/csvtk/concat/environment.yml | 2 -- modules/nf-core/csvtk/join/environment.yml | 2 -- modules/nf-core/csvtk/split/environment.yml | 2 -- modules/nf-core/custom/catadditionalfasta/environment.yml | 2 -- .../nf-core/custom/dumpsoftwareversions/environment.yml | 2 -- modules/nf-core/custom/getchromsizes/environment.yml | 2 -- modules/nf-core/custom/gtffilter/environment.yml | 2 -- modules/nf-core/custom/matrixfilter/environment.yml | 2 -- .../nf-core/custom/sratoolsncbisettings/environment.yml | 2 -- modules/nf-core/custom/tabulartogseacls/environment.yml | 2 -- modules/nf-core/custom/tabulartogseagct/environment.yml | 2 -- modules/nf-core/custom/tx2gene/environment.yml | 2 -- modules/nf-core/cutadapt/environment.yml | 2 -- modules/nf-core/cutesv/environment.yml | 2 -- modules/nf-core/damageprofiler/environment.yml | 2 -- modules/nf-core/dastool/dastool/environment.yml | 2 -- modules/nf-core/dastool/fastatocontig2bin/environment.yml | 2 -- modules/nf-core/dastool/scaffolds2bin/environment.yml | 2 -- modules/nf-core/datavzrd/environment.yml | 2 -- modules/nf-core/dedup/environment.yml | 2 -- modules/nf-core/deeparg/downloaddata/environment.yml | 2 -- modules/nf-core/deeparg/predict/environment.yml | 2 -- modules/nf-core/deepbgc/download/environment.yml | 2 -- modules/nf-core/deepbgc/pipeline/environment.yml | 2 -- modules/nf-core/deeptmhmm/environment.yml | 2 -- modules/nf-core/deeptools/bamcoverage/environment.yml | 2 -- modules/nf-core/deeptools/computematrix/environment.yml | 2 -- modules/nf-core/deeptools/multibamsummary/environment.yml | 2 -- modules/nf-core/deeptools/plotcorrelation/environment.yml | 2 -- modules/nf-core/deeptools/plotfingerprint/environment.yml | 2 -- modules/nf-core/deeptools/plotheatmap/environment.yml | 2 -- modules/nf-core/deeptools/plotpca/environment.yml | 2 -- modules/nf-core/deeptools/plotprofile/environment.yml | 2 -- modules/nf-core/delly/call/environment.yml | 2 -- modules/nf-core/demuxem/environment.yml | 2 -- modules/nf-core/deseq2/differential/environment.yml | 2 -- modules/nf-core/diamond/blastp/environment.yml | 2 -- modules/nf-core/diamond/blastx/environment.yml | 2 -- modules/nf-core/diamond/cluster/environment.yml | 2 -- modules/nf-core/diamond/makedb/environment.yml | 2 -- modules/nf-core/dragmap/align/environment.yml | 2 -- modules/nf-core/dragmap/hashtable/environment.yml | 2 -- modules/nf-core/dragonflye/environment.yml | 2 -- modules/nf-core/dshbio/exportsegments/environment.yml | 2 -- modules/nf-core/dshbio/filterbed/environment.yml | 2 -- modules/nf-core/dshbio/filtergff3/environment.yml | 2 -- modules/nf-core/dshbio/splitbed/environment.yml | 2 -- modules/nf-core/dshbio/splitgff3/environment.yml | 2 -- modules/nf-core/duphold/environment.yml | 2 -- modules/nf-core/dupradar/environment.yml | 2 -- modules/nf-core/dysgu/environment.yml | 2 -- modules/nf-core/ectyper/environment.yml | 2 -- modules/nf-core/eggnogmapper/environment.yml | 2 -- modules/nf-core/eido/convert/environment.yml | 1 - modules/nf-core/eido/validate/environment.yml | 2 -- .../eigenstratsnpcoverage/environment.yml | 2 -- modules/nf-core/eklipse/environment.yml | 2 -- modules/nf-core/elprep/filter/environment.yml | 2 -- modules/nf-core/elprep/merge/environment.yml | 2 -- modules/nf-core/elprep/split/environment.yml | 2 -- modules/nf-core/emboss/cons/environment.yml | 2 -- modules/nf-core/emboss/revseq/environment.yml | 1 - modules/nf-core/emboss/seqret/environment.yml | 2 -- modules/nf-core/emmtyper/environment.yml | 2 -- modules/nf-core/endorspy/environment.yml | 2 -- modules/nf-core/ensemblvep/download/environment.yml | 2 -- modules/nf-core/ensemblvep/environment.yml | 2 -- modules/nf-core/ensemblvep/filtervep/environment.yml | 2 -- modules/nf-core/ensemblvep/vep/environment.yml | 2 -- modules/nf-core/entrezdirect/esearch/environment.yml | 2 -- modules/nf-core/entrezdirect/esummary/environment.yml | 2 -- modules/nf-core/entrezdirect/xtract/environment.yml | 2 -- modules/nf-core/epang/place/environment.yml | 2 -- modules/nf-core/epang/split/environment.yml | 2 -- modules/nf-core/estsfs/environment.yml | 1 - modules/nf-core/evigene/tr2aacds/environment.yml | 2 -- modules/nf-core/expansionhunter/environment.yml | 3 --- .../nf-core/expansionhunterdenovo/merge/environment.yml | 2 -- .../nf-core/expansionhunterdenovo/profile/environment.yml | 2 -- modules/nf-core/falco/environment.yml | 2 -- modules/nf-core/famsa/align/environment.yml | 2 -- modules/nf-core/famsa/guidetree/environment.yml | 2 -- modules/nf-core/faqcs/environment.yml | 2 -- modules/nf-core/fargene/environment.yml | 2 -- modules/nf-core/fastani/environment.yml | 2 -- modules/nf-core/fastavalidator/environment.yml | 2 -- modules/nf-core/fastawindows/environment.yml | 2 -- modules/nf-core/fastk/fastk/environment.yml | 2 -- modules/nf-core/fastk/histex/environment.yml | 2 -- modules/nf-core/fastk/merge/environment.yml | 2 -- modules/nf-core/fastme/environment.yml | 2 -- modules/nf-core/fastp/environment.yml | 2 -- modules/nf-core/fastqc/environment.yml | 2 -- modules/nf-core/fastqscan/environment.yml | 2 -- modules/nf-core/fastqscreen/buildfromindex/environment.yml | 2 -- modules/nf-core/fastqscreen/fastqscreen/environment.yml | 2 -- modules/nf-core/fasttree/environment.yml | 2 -- modules/nf-core/fastx/collapser/environment.yml | 2 -- modules/nf-core/fcs/fcsadaptor/environment.yml | 2 -- modules/nf-core/fcs/fcsgx/environment.yml | 2 -- modules/nf-core/ffq/environment.yml | 2 -- .../nf-core/fgbio/callduplexconsensusreads/environment.yml | 2 -- .../fgbio/callmolecularconsensusreads/environment.yml | 2 -- .../nf-core/fgbio/collectduplexseqmetrics/environment.yml | 2 -- modules/nf-core/fgbio/fastqtobam/environment.yml | 2 -- modules/nf-core/fgbio/filterconsensusreads/environment.yml | 2 -- modules/nf-core/fgbio/groupreadsbyumi/environment.yml | 2 -- modules/nf-core/fgbio/sortbam/environment.yml | 2 -- modules/nf-core/fgbio/zipperbams/environment.yml | 2 -- modules/nf-core/filtlong/environment.yml | 2 -- modules/nf-core/flash/environment.yml | 2 -- modules/nf-core/flye/environment.yml | 2 -- modules/nf-core/foldcomp/compress/environment.yml | 2 -- modules/nf-core/foldcomp/decompress/environment.yml | 2 -- modules/nf-core/foldmason/easymsa/environment.yml | 2 -- modules/nf-core/foldseek/createdb/environment.yml | 2 -- modules/nf-core/foldseek/easysearch/environment.yml | 2 -- modules/nf-core/fq/generate/environment.yml | 2 -- modules/nf-core/fq/lint/environment.yml | 2 -- modules/nf-core/fq/subsample/environment.yml | 2 -- modules/nf-core/fqtk/environment.yml | 2 -- modules/nf-core/freebayes/environment.yml | 2 -- modules/nf-core/freyja/boot/environment.yml | 2 -- modules/nf-core/freyja/demix/environment.yml | 2 -- modules/nf-core/freyja/update/environment.yml | 2 -- modules/nf-core/freyja/variants/environment.yml | 2 -- modules/nf-core/galah/environment.yml | 2 -- modules/nf-core/gamma/gamma/environment.yml | 2 -- modules/nf-core/gangstr/environment.yml | 2 -- modules/nf-core/ganon/buildcustom/environment.yml | 2 -- modules/nf-core/ganon/classify/environment.yml | 2 -- modules/nf-core/ganon/report/environment.yml | 2 -- modules/nf-core/ganon/table/environment.yml | 2 -- modules/nf-core/gappa/examineassign/environment.yml | 2 -- modules/nf-core/gappa/examinegraft/environment.yml | 2 -- modules/nf-core/gappa/examineheattree/environment.yml | 2 -- modules/nf-core/gatk/indelrealigner/environment.yml | 2 -- .../nf-core/gatk/realignertargetcreator/environment.yml | 2 -- modules/nf-core/gatk/unifiedgenotyper/environment.yml | 2 -- .../nf-core/gatk4/addorreplacereadgroups/environment.yml | 2 -- modules/nf-core/gatk4/annotateintervals/environment.yml | 2 -- modules/nf-core/gatk4/applybqsr/environment.yml | 2 -- modules/nf-core/gatk4/applyvqsr/environment.yml | 2 -- modules/nf-core/gatk4/asereadcounter/environment.yml | 2 -- modules/nf-core/gatk4/baserecalibrator/environment.yml | 2 -- modules/nf-core/gatk4/bedtointervallist/environment.yml | 2 -- .../nf-core/gatk4/calculatecontamination/environment.yml | 2 -- .../nf-core/gatk4/calibratedragstrmodel/environment.yml | 2 -- modules/nf-core/gatk4/collectreadcounts/environment.yml | 2 -- modules/nf-core/gatk4/collectsvevidence/environment.yml | 2 -- modules/nf-core/gatk4/combinegvcfs/environment.yml | 2 -- modules/nf-core/gatk4/composestrtablefile/environment.yml | 2 -- .../nf-core/gatk4/condensedepthevidence/environment.yml | 2 -- .../gatk4/createreadcountpanelofnormals/environment.yml | 2 -- .../nf-core/gatk4/createsequencedictionary/environment.yml | 2 -- .../gatk4/createsomaticpanelofnormals/environment.yml | 2 -- modules/nf-core/gatk4/denoisereadcounts/environment.yml | 2 -- .../gatk4/estimatelibrarycomplexity/environment.yml | 2 -- modules/nf-core/gatk4/fastqtosam/environment.yml | 2 -- modules/nf-core/gatk4/filterintervals/environment.yml | 2 -- modules/nf-core/gatk4/filtermutectcalls/environment.yml | 2 -- .../nf-core/gatk4/filtervarianttranches/environment.yml | 2 -- modules/nf-core/gatk4/gatherbqsrreports/environment.yml | 2 -- .../nf-core/gatk4/gatherpileupsummaries/environment.yml | 2 -- modules/nf-core/gatk4/genomicsdbimport/environment.yml | 2 -- modules/nf-core/gatk4/genotypegvcfs/environment.yml | 2 -- modules/nf-core/gatk4/getpileupsummaries/environment.yml | 2 -- modules/nf-core/gatk4/haplotypecaller/environment.yml | 2 -- modules/nf-core/gatk4/indexfeaturefile/environment.yml | 2 -- modules/nf-core/gatk4/intervallisttobed/environment.yml | 2 -- modules/nf-core/gatk4/intervallisttools/environment.yml | 2 -- .../gatk4/learnreadorientationmodel/environment.yml | 2 -- .../nf-core/gatk4/leftalignandtrimvariants/environment.yml | 2 -- modules/nf-core/gatk4/markduplicates/environment.yml | 2 -- modules/nf-core/gatk4/mergebamalignment/environment.yml | 2 -- modules/nf-core/gatk4/mergemutectstats/environment.yml | 2 -- modules/nf-core/gatk4/mergevcfs/environment.yml | 2 -- modules/nf-core/gatk4/mutect2/environment.yml | 2 -- modules/nf-core/gatk4/preprocessintervals/environment.yml | 2 -- modules/nf-core/gatk4/printreads/environment.yml | 2 -- modules/nf-core/gatk4/printsvevidence/environment.yml | 2 -- modules/nf-core/gatk4/reblockgvcf/environment.yml | 2 -- modules/nf-core/gatk4/revertsam/environment.yml | 2 -- modules/nf-core/gatk4/samtofastq/environment.yml | 2 -- modules/nf-core/gatk4/selectvariants/environment.yml | 2 -- modules/nf-core/gatk4/shiftfasta/environment.yml | 2 -- modules/nf-core/gatk4/sitedepthtobaf/environment.yml | 2 -- modules/nf-core/gatk4/splitcram/environment.yml | 2 -- modules/nf-core/gatk4/splitintervals/environment.yml | 2 -- modules/nf-core/gatk4/splitncigarreads/environment.yml | 2 -- modules/nf-core/gatk4/svannotate/environment.yml | 2 -- modules/nf-core/gatk4/svcluster/environment.yml | 2 -- modules/nf-core/gatk4/variantfiltration/environment.yml | 2 -- modules/nf-core/gatk4/variantrecalibrator/environment.yml | 2 -- modules/nf-core/gatk4spark/applybqsr/environment.yml | 2 -- .../nf-core/gatk4spark/baserecalibrator/environment.yml | 2 -- modules/nf-core/gatk4spark/markduplicates/environment.yml | 2 -- modules/nf-core/gawk/environment.yml | 2 -- modules/nf-core/gecco/run/environment.yml | 2 -- modules/nf-core/gem2/gem2bedmappability/environment.yml | 2 -- modules/nf-core/gem2/gemindexer/environment.yml | 2 -- modules/nf-core/gem2/gemmappability/environment.yml | 2 -- modules/nf-core/gem3/gem3indexer/environment.yml | 2 -- modules/nf-core/gem3/gem3mapper/environment.yml | 2 -- modules/nf-core/genescopefk/environment.yml | 2 -- modules/nf-core/genmap/index/environment.yml | 2 -- modules/nf-core/genmap/map/environment.yml | 2 -- modules/nf-core/genmod/annotate/environment.yml | 2 -- modules/nf-core/genmod/compound/environment.yml | 2 -- modules/nf-core/genmod/models/environment.yml | 2 -- modules/nf-core/genmod/score/environment.yml | 2 -- modules/nf-core/genomad/download/environment.yml | 2 -- modules/nf-core/genomad/endtoend/environment.yml | 2 -- modules/nf-core/genomescope2/environment.yml | 2 -- modules/nf-core/genotyphi/parse/environment.yml | 2 -- modules/nf-core/genrich/environment.yml | 2 -- modules/nf-core/geofetch/environment.yml | 2 -- modules/nf-core/geoquery/getgeo/environment.yml | 1 - modules/nf-core/getorganelle/config/environment.yml | 1 - modules/nf-core/gfaffix/environment.yml | 1 - modules/nf-core/gfastats/environment.yml | 2 -- modules/nf-core/gfatools/gfa2fa/environment.yml | 2 -- modules/nf-core/gfatools/stat/environment.yml | 2 -- modules/nf-core/gffcompare/environment.yml | 2 -- modules/nf-core/gffread/environment.yml | 2 -- modules/nf-core/gget/gget/environment.yml | 2 -- modules/nf-core/glimpse/chunk/environment.yml | 2 -- modules/nf-core/glimpse/concordance/environment.yml | 2 -- modules/nf-core/glimpse/ligate/environment.yml | 2 -- modules/nf-core/glimpse/phase/environment.yml | 2 -- modules/nf-core/glimpse/sample/environment.yml | 2 -- modules/nf-core/glimpse2/chunk/environment.yml | 2 -- modules/nf-core/glimpse2/concordance/environment.yml | 2 -- modules/nf-core/glimpse2/ligate/environment.yml | 2 -- modules/nf-core/glimpse2/phase/environment.yml | 2 -- modules/nf-core/glimpse2/splitreference/environment.yml | 2 -- modules/nf-core/glnexus/environment.yml | 2 -- modules/nf-core/gmmdemux/environment.yml | 2 -- modules/nf-core/gnu/sort/environment.yml | 2 -- modules/nf-core/gnu/split/environment.yml | 2 -- modules/nf-core/goat/taxonsearch/environment.yml | 2 -- modules/nf-core/goleft/indexcov/environment.yml | 2 -- modules/nf-core/goleft/indexsplit/environment.yml | 1 - modules/nf-core/gprofiler2/gost/environment.yml | 2 -- modules/nf-core/grabix/check/environment.yml | 2 -- modules/nf-core/graphmap2/align/environment.yml | 2 -- modules/nf-core/graphmap2/index/environment.yml | 2 -- modules/nf-core/graphtyper/genotype/environment.yml | 2 -- modules/nf-core/graphtyper/vcfconcatenate/environment.yml | 1 - modules/nf-core/gridss/gridss/environment.yml | 2 -- modules/nf-core/gsea/gsea/environment.yml | 2 -- modules/nf-core/gstama/collapse/environment.yml | 2 -- modules/nf-core/gstama/merge/environment.yml | 2 -- modules/nf-core/gstama/polyacleanup/environment.yml | 2 -- modules/nf-core/gt/gff3/environment.yml | 2 -- modules/nf-core/gt/gff3validator/environment.yml | 2 -- modules/nf-core/gt/ltrharvest/environment.yml | 2 -- modules/nf-core/gt/stat/environment.yml | 2 -- modules/nf-core/gt/suffixerator/environment.yml | 2 -- modules/nf-core/gtdbtk/classifywf/environment.yml | 2 -- modules/nf-core/gtfsort/environment.yml | 2 -- modules/nf-core/gubbins/environment.yml | 1 - modules/nf-core/gunc/downloaddb/environment.yml | 1 - modules/nf-core/gunc/mergecheckm/environment.yml | 2 -- modules/nf-core/gunc/run/environment.yml | 2 -- modules/nf-core/gunzip/environment.yml | 2 -- modules/nf-core/gvcftools/extractvariants/environment.yml | 2 -- modules/nf-core/hamronization/abricate/environment.yml | 2 -- .../nf-core/hamronization/amrfinderplus/environment.yml | 2 -- modules/nf-core/hamronization/deeparg/environment.yml | 2 -- modules/nf-core/hamronization/fargene/environment.yml | 2 -- modules/nf-core/hamronization/rgi/environment.yml | 2 -- modules/nf-core/hamronization/summarize/environment.yml | 2 -- modules/nf-core/hapibd/environment.yml | 1 - modules/nf-core/haplocheck/environment.yml | 2 -- modules/nf-core/haplogrep2/classify/environment.yml | 2 -- modules/nf-core/happy/ftxpy/environment.yml | 2 -- modules/nf-core/happy/happy/environment.yml | 2 -- modules/nf-core/happy/prepy/environment.yml | 2 -- modules/nf-core/happy/sompy/environment.yml | 2 -- modules/nf-core/hicap/environment.yml | 2 -- modules/nf-core/hicexplorer/hicpca/environment.yml | 2 -- modules/nf-core/hifiasm/environment.yml | 2 -- modules/nf-core/hisat2/align/environment.yml | 2 -- modules/nf-core/hisat2/build/environment.yml | 2 -- modules/nf-core/hisat2/extractsplicesites/environment.yml | 2 -- modules/nf-core/hlala/preparegraph/environment.yml | 2 -- modules/nf-core/hlala/typing/environment.yml | 2 -- modules/nf-core/hmmcopy/gccounter/environment.yml | 2 -- modules/nf-core/hmmcopy/generatemap/environment.yml | 2 -- modules/nf-core/hmmcopy/mapcounter/environment.yml | 2 -- modules/nf-core/hmmcopy/readcounter/environment.yml | 2 -- modules/nf-core/hmmer/eslalimask/environment.yml | 2 -- modules/nf-core/hmmer/eslreformat/environment.yml | 2 -- modules/nf-core/hmmer/hmmalign/environment.yml | 2 -- modules/nf-core/hmmer/hmmbuild/environment.yml | 1 - modules/nf-core/hmmer/hmmfetch/environment.yml | 2 -- modules/nf-core/hmmer/hmmrank/environment.yml | 3 --- modules/nf-core/hmmer/hmmsearch/environment.yml | 2 -- modules/nf-core/hmtnote/annotate/environment.yml | 2 -- modules/nf-core/homer/annotatepeaks/environment.yml | 1 - modules/nf-core/homer/findpeaks/environment.yml | 2 -- modules/nf-core/homer/maketagdirectory/environment.yml | 2 -- modules/nf-core/homer/makeucscfile/environment.yml | 2 -- modules/nf-core/homer/pos2bed/environment.yml | 2 -- modules/nf-core/hpsuissero/environment.yml | 2 -- modules/nf-core/htseq/count/environment.yml | 2 -- modules/nf-core/htsnimtools/vcfcheck/environment.yml | 2 -- modules/nf-core/humid/environment.yml | 2 -- modules/nf-core/hypo/environment.yml | 1 - modules/nf-core/ichorcna/createpon/environment.yml | 2 -- modules/nf-core/ichorcna/run/environment.yml | 2 -- modules/nf-core/icountmini/metagene/environment.yml | 2 -- modules/nf-core/icountmini/peaks/environment.yml | 2 -- modules/nf-core/icountmini/segment/environment.yml | 2 -- modules/nf-core/icountmini/sigxls/environment.yml | 2 -- modules/nf-core/icountmini/summary/environment.yml | 2 -- modules/nf-core/idemux/environment.yml | 2 -- modules/nf-core/idr/environment.yml | 1 - modules/nf-core/igv/js/environment.yml | 2 -- modules/nf-core/igvreports/environment.yml | 2 -- modules/nf-core/ilastik/multicut/environment.yml | 2 -- .../nf-core/ilastik/pixelclassification/environment.yml | 2 -- modules/nf-core/instrain/compare/environment.yml | 2 -- modules/nf-core/instrain/profile/environment.yml | 2 -- modules/nf-core/interproscan/environment.yml | 2 -- modules/nf-core/iphop/download/environment.yml | 2 -- modules/nf-core/iphop/predict/environment.yml | 2 -- modules/nf-core/iqtree/environment.yml | 2 -- modules/nf-core/islandpath/environment.yml | 2 -- modules/nf-core/ismapper/environment.yml | 2 -- modules/nf-core/isoseq/cluster/environment.yml | 2 -- modules/nf-core/isoseq/refine/environment.yml | 2 -- modules/nf-core/isoseq3/tag/environment.yml | 2 -- modules/nf-core/ivar/consensus/environment.yml | 1 - modules/nf-core/ivar/trim/environment.yml | 2 -- modules/nf-core/ivar/variants/environment.yml | 1 - modules/nf-core/jasminesv/environment.yml | 2 -- modules/nf-core/jupyternotebook/environment.yml | 2 -- modules/nf-core/jvarkit/vcfpolyx/environment.yml | 1 - modules/nf-core/kaiju/kaiju/environment.yml | 2 -- modules/nf-core/kaiju/kaiju2krona/environment.yml | 2 -- modules/nf-core/kaiju/kaiju2table/environment.yml | 2 -- modules/nf-core/kaiju/mergeoutputs/environment.yml | 2 -- modules/nf-core/kaiju/mkfmi/environment.yml | 2 -- modules/nf-core/kalign/align/environment.yml | 2 -- modules/nf-core/kallisto/index/environment.yml | 2 -- modules/nf-core/kallisto/quant/environment.yml | 2 -- modules/nf-core/kallistobustools/count/environment.yml | 2 -- modules/nf-core/kallistobustools/ref/environment.yml | 2 -- modules/nf-core/kat/hist/environment.yml | 2 -- modules/nf-core/khmer/normalizebymedian/environment.yml | 2 -- modules/nf-core/khmer/uniquekmers/environment.yml | 2 -- modules/nf-core/kleborate/environment.yml | 2 -- modules/nf-core/kmcp/compute/environment.yml | 2 -- modules/nf-core/kmcp/index/environment.yml | 2 -- modules/nf-core/kmcp/merge/environment.yml | 2 -- modules/nf-core/kmcp/profile/environment.yml | 2 -- modules/nf-core/kmcp/search/environment.yml | 2 -- modules/nf-core/kofamscan/environment.yml | 2 -- modules/nf-core/kraken2/add/environment.yml | 2 -- modules/nf-core/kraken2/build/environment.yml | 2 -- modules/nf-core/kraken2/buildstandard/environment.yml | 2 -- modules/nf-core/kraken2/kraken2/environment.yml | 2 -- .../nf-core/krakentools/combinekreports/environment.yml | 2 -- .../nf-core/krakentools/extractkrakenreads/environment.yml | 2 -- modules/nf-core/krakentools/kreport2krona/environment.yml | 2 -- modules/nf-core/krakenuniq/build/environment.yml | 2 -- modules/nf-core/krakenuniq/download/environment.yml | 2 -- .../nf-core/krakenuniq/preloadedkrakenuniq/environment.yml | 2 -- modules/nf-core/krona/kronadb/environment.yml | 2 -- modules/nf-core/krona/ktimporttaxonomy/environment.yml | 2 -- modules/nf-core/krona/ktimporttext/environment.yml | 2 -- modules/nf-core/krona/ktupdatetaxonomy/environment.yml | 1 - modules/nf-core/last/dotplot/environment.yml | 2 -- modules/nf-core/last/lastal/environment.yml | 2 -- modules/nf-core/last/lastdb/environment.yml | 2 -- modules/nf-core/last/mafconvert/environment.yml | 2 -- modules/nf-core/last/mafswap/environment.yml | 2 -- modules/nf-core/last/postmask/environment.yml | 2 -- modules/nf-core/last/split/environment.yml | 2 -- modules/nf-core/last/train/environment.yml | 2 -- modules/nf-core/learnmsa/align/environment.yml | 2 -- modules/nf-core/leehom/environment.yml | 2 -- modules/nf-core/legsta/environment.yml | 1 - modules/nf-core/leviosam2/index/environment.yml | 2 -- modules/nf-core/leviosam2/lift/environment.yml | 2 -- modules/nf-core/liftoff/environment.yml | 3 --- modules/nf-core/lima/environment.yml | 2 -- modules/nf-core/limma/differential/environment.yml | 2 -- modules/nf-core/lissero/environment.yml | 2 -- modules/nf-core/lofreq/alnqual/environment.yml | 2 -- modules/nf-core/lofreq/call/environment.yml | 2 -- modules/nf-core/lofreq/callparallel/environment.yml | 2 -- modules/nf-core/lofreq/filter/environment.yml | 2 -- modules/nf-core/lofreq/indelqual/environment.yml | 2 -- modules/nf-core/lofreq/somatic/environment.yml | 2 -- modules/nf-core/lofreq/viterbi/environment.yml | 2 -- modules/nf-core/longphase/haplotag/environment.yml | 2 -- modules/nf-core/longphase/phase/environment.yml | 2 -- modules/nf-core/ltrfinder/environment.yml | 2 -- modules/nf-core/ltrharvest/environment.yml | 2 -- modules/nf-core/ltrretriever/lai/environment.yml | 2 -- modules/nf-core/ltrretriever/ltrretriever/environment.yml | 2 -- modules/nf-core/macrel/contigs/environment.yml | 2 -- modules/nf-core/macs2/callpeak/environment.yml | 2 -- modules/nf-core/macs3/callpeak/environment.yml | 2 -- modules/nf-core/mafft/environment.yml | 2 -- modules/nf-core/mageck/count/environment.yml | 2 -- modules/nf-core/mageck/mle/environment.yml | 2 -- modules/nf-core/mageck/test/environment.yml | 2 -- modules/nf-core/magus/align/environment.yml | 2 -- modules/nf-core/magus/guidetree/environment.yml | 2 -- modules/nf-core/malt/build/environment.yml | 2 -- modules/nf-core/malt/run/environment.yml | 2 -- modules/nf-core/maltextract/environment.yml | 2 -- modules/nf-core/manta/convertinversion/environment.yml | 2 -- modules/nf-core/manta/germline/environment.yml | 2 -- modules/nf-core/manta/somatic/environment.yml | 2 -- modules/nf-core/manta/tumoronly/environment.yml | 2 -- modules/nf-core/mapad/index/environment.yml | 2 -- modules/nf-core/mapad/map/environment.yml | 2 -- modules/nf-core/mapdamage2/environment.yml | 2 -- modules/nf-core/mash/dist/environment.yml | 2 -- modules/nf-core/mash/screen/environment.yml | 2 -- modules/nf-core/mash/sketch/environment.yml | 2 -- modules/nf-core/mashmap/environment.yml | 2 -- modules/nf-core/mashtree/environment.yml | 2 -- modules/nf-core/maxbin2/environment.yml | 2 -- modules/nf-core/maxquant/lfq/environment.yml | 2 -- modules/nf-core/mcroni/environment.yml | 2 -- modules/nf-core/mcstaging/imc2mc/environment.yml | 2 -- modules/nf-core/md5sum/environment.yml | 2 -- modules/nf-core/medaka/environment.yml | 2 -- modules/nf-core/megahit/environment.yml | 2 -- modules/nf-core/megan/daa2info/environment.yml | 2 -- modules/nf-core/megan/rma2info/environment.yml | 2 -- modules/nf-core/meningotype/environment.yml | 2 -- modules/nf-core/merfin/hist/environment.yml | 2 -- modules/nf-core/merqury/hapmers/environment.yml | 2 -- modules/nf-core/merqury/merqury/environment.yml | 2 -- modules/nf-core/merquryfk/katcomp/environment.yml | 2 -- modules/nf-core/merquryfk/katgc/environment.yml | 2 -- modules/nf-core/meryl/count/environment.yml | 2 -- modules/nf-core/meryl/histogram/environment.yml | 2 -- modules/nf-core/meryl/unionsum/environment.yml | 2 -- .../metabat2/jgisummarizebamcontigdepths/environment.yml | 1 - modules/nf-core/metabat2/metabat2/environment.yml | 2 -- modules/nf-core/metaeuk/easypredict/environment.yml | 2 -- modules/nf-core/metamaps/classify/environment.yml | 2 -- modules/nf-core/metamaps/mapdirectly/environment.yml | 2 -- modules/nf-core/metaphlan/makedb/environment.yml | 2 -- .../nf-core/metaphlan/mergemetaphlantables/environment.yml | 2 -- modules/nf-core/metaphlan/metaphlan/environment.yml | 2 -- .../metaphlan3/mergemetaphlantables/environment.yml | 2 -- modules/nf-core/metaphlan3/metaphlan3/environment.yml | 2 -- modules/nf-core/methyldackel/extract/environment.yml | 2 -- modules/nf-core/methyldackel/mbias/environment.yml | 2 -- modules/nf-core/midas/run/environment.yml | 2 -- modules/nf-core/mindagap/duplicatefinder/environment.yml | 2 -- modules/nf-core/mindagap/mindagap/environment.yml | 2 -- modules/nf-core/minia/environment.yml | 2 -- modules/nf-core/miniasm/environment.yml | 2 -- modules/nf-core/minimap2/align/environment.yml | 3 --- modules/nf-core/minimap2/index/environment.yml | 2 -- modules/nf-core/miniprot/align/environment.yml | 2 -- modules/nf-core/miniprot/index/environment.yml | 2 -- modules/nf-core/miranda/environment.yml | 2 -- modules/nf-core/mirtrace/qc/environment.yml | 1 - modules/nf-core/mlst/environment.yml | 2 -- modules/nf-core/mmseqs/cluster/environment.yml | 2 -- modules/nf-core/mmseqs/createdb/environment.yml | 2 -- modules/nf-core/mmseqs/createindex/environment.yml | 2 -- modules/nf-core/mmseqs/createtsv/environment.yml | 1 - modules/nf-core/mmseqs/databases/environment.yml | 1 - modules/nf-core/mmseqs/easysearch/environment.yml | 2 -- modules/nf-core/mmseqs/linclust/environment.yml | 2 -- modules/nf-core/mmseqs/search/environment.yml | 2 -- modules/nf-core/mmseqs/taxonomy/environment.yml | 1 - modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml | 2 -- modules/nf-core/mobsuite/recon/environment.yml | 2 -- modules/nf-core/modkit/pileup/environment.yml | 2 -- modules/nf-core/mosdepth/environment.yml | 2 -- modules/nf-core/motus/downloaddb/environment.yml | 2 -- modules/nf-core/motus/merge/environment.yml | 2 -- modules/nf-core/motus/profile/environment.yml | 2 -- modules/nf-core/msisensor/msi/environment.yml | 2 -- modules/nf-core/msisensor/scan/environment.yml | 2 -- modules/nf-core/msisensor2/msi/environment.yml | 2 -- modules/nf-core/msisensor2/scan/environment.yml | 2 -- modules/nf-core/msisensorpro/msisomatic/environment.yml | 2 -- modules/nf-core/msisensorpro/scan/environment.yml | 2 -- modules/nf-core/mtmalign/align/environment.yml | 2 -- modules/nf-core/mtnucratio/environment.yml | 2 -- modules/nf-core/mudskipper/bulk/environment.yml | 2 -- modules/nf-core/mudskipper/index/environment.yml | 2 -- modules/nf-core/multiqc/environment.yml | 2 -- modules/nf-core/multivcfanalyzer/environment.yml | 2 -- modules/nf-core/mummer/environment.yml | 2 -- modules/nf-core/muscle/environment.yml | 2 -- modules/nf-core/muscle5/super5/environment.yml | 2 -- modules/nf-core/mygene/environment.yml | 2 -- modules/nf-core/mykrobe/predict/environment.yml | 2 -- modules/nf-core/nanocomp/environment.yml | 2 -- modules/nf-core/nanofilt/environment.yml | 2 -- modules/nf-core/nanolyse/environment.yml | 2 -- modules/nf-core/nanomonsv/parse/environment.yml | 2 -- modules/nf-core/nanoplot/environment.yml | 2 -- modules/nf-core/nanoq/environment.yml | 2 -- modules/nf-core/narfmap/align/environment.yml | 2 -- modules/nf-core/narfmap/hashtable/environment.yml | 2 -- modules/nf-core/ncbigenomedownload/environment.yml | 2 -- modules/nf-core/nextclade/datasetget/environment.yml | 2 -- modules/nf-core/nextclade/run/environment.yml | 2 -- modules/nf-core/nextgenmap/environment.yml | 2 -- modules/nf-core/ngmaster/environment.yml | 2 -- modules/nf-core/ngmerge/environment.yml | 2 -- modules/nf-core/ngsbits/samplegender/environment.yml | 2 -- modules/nf-core/ngscheckmate/fastq/environment.yml | 2 -- modules/nf-core/ngscheckmate/ncm/environment.yml | 2 -- .../nf-core/ngscheckmate/patterngenerator/environment.yml | 2 -- modules/nf-core/ngscheckmate/vafncm/environment.yml | 2 -- modules/nf-core/nonpareil/curve/environment.yml | 2 -- modules/nf-core/nonpareil/nonpareil/environment.yml | 2 -- modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml | 2 -- modules/nf-core/nonpareil/set/environment.yml | 2 -- modules/nf-core/nucmer/environment.yml | 2 -- modules/nf-core/oatk/environment.yml | 2 -- modules/nf-core/odgi/build/environment.yml | 2 -- modules/nf-core/odgi/draw/environment.yml | 2 -- modules/nf-core/odgi/layout/environment.yml | 2 -- modules/nf-core/odgi/sort/environment.yml | 2 -- modules/nf-core/odgi/squeeze/environment.yml | 2 -- modules/nf-core/odgi/stats/environment.yml | 2 -- modules/nf-core/odgi/unchop/environment.yml | 2 -- modules/nf-core/odgi/view/environment.yml | 2 -- modules/nf-core/odgi/viz/environment.yml | 2 -- modules/nf-core/oncocnv/environment.yml | 2 -- modules/nf-core/openms/decoydatabase/environment.yml | 2 -- modules/nf-core/openms/idfilter/environment.yml | 2 -- modules/nf-core/openms/idmerger/environment.yml | 2 -- modules/nf-core/openms/idripper/environment.yml | 2 -- modules/nf-core/openms/idscoreswitcher/environment.yml | 2 -- modules/nf-core/openms/peakpickerhires/environment.yml | 2 -- modules/nf-core/openms/peptideindexer/environment.yml | 2 -- modules/nf-core/optitype/environment.yml | 2 -- modules/nf-core/orthofinder/environment.yml | 1 - modules/nf-core/paftools/sam2paf/environment.yml | 2 -- modules/nf-core/pairix/environment.yml | 2 -- modules/nf-core/pairtools/dedup/environment.yml | 2 -- modules/nf-core/pairtools/flip/environment.yml | 2 -- modules/nf-core/pairtools/merge/environment.yml | 2 -- modules/nf-core/pairtools/parse/environment.yml | 2 -- modules/nf-core/pairtools/restrict/environment.yml | 2 -- modules/nf-core/pairtools/select/environment.yml | 2 -- modules/nf-core/pairtools/sort/environment.yml | 2 -- modules/nf-core/pairtools/split/environment.yml | 2 -- modules/nf-core/pairtools/stats/environment.yml | 2 -- modules/nf-core/panacus/histgrowth/environment.yml | 2 -- modules/nf-core/panacus/visualize/environment.yml | 2 -- modules/nf-core/panaroo/run/environment.yml | 2 -- modules/nf-core/pangolin/environment.yml | 2 -- modules/nf-core/parabricks/applybqsr/environment.yml | 2 -- modules/nf-core/paraclu/environment.yml | 2 -- modules/nf-core/paragraph/idxdepth/environment.yml | 2 -- modules/nf-core/paragraph/multigrmpy/environment.yml | 2 -- modules/nf-core/paragraph/vcf2paragraph/environment.yml | 3 --- modules/nf-core/paraphase/environment.yml | 2 -- modules/nf-core/pasty/environment.yml | 2 -- modules/nf-core/pbbam/pbmerge/environment.yml | 2 -- modules/nf-core/pbccs/environment.yml | 2 -- modules/nf-core/pbptyper/environment.yml | 2 -- modules/nf-core/pbtk/bam2fastq/environment.yml | 2 -- modules/nf-core/pbtk/pbindex/environment.yml | 2 -- modules/nf-core/pear/environment.yml | 2 -- modules/nf-core/peddy/environment.yml | 2 -- modules/nf-core/peka/environment.yml | 2 -- modules/nf-core/phantompeakqualtools/environment.yml | 2 -- modules/nf-core/pharokka/installdatabases/environment.yml | 2 -- modules/nf-core/pharokka/pharokka/environment.yml | 2 -- modules/nf-core/phispy/environment.yml | 2 -- modules/nf-core/phyloflash/environment.yml | 2 -- .../nf-core/picard/addorreplacereadgroups/environment.yml | 2 -- modules/nf-core/picard/bedtointervallist/environment.yml | 2 -- modules/nf-core/picard/cleansam/environment.yml | 2 -- modules/nf-core/picard/collecthsmetrics/environment.yml | 2 -- .../picard/collectinsertsizemetrics/environment.yml | 2 -- .../nf-core/picard/collectmultiplemetrics/environment.yml | 2 -- .../nf-core/picard/collectrnaseqmetrics/environment.yml | 2 -- modules/nf-core/picard/collectwgsmetrics/environment.yml | 2 -- .../picard/createsequencedictionary/environment.yml | 2 -- .../nf-core/picard/crosscheckfingerprints/environment.yml | 2 -- modules/nf-core/picard/extractfingerprint/environment.yml | 2 -- modules/nf-core/picard/fastqtosam/environment.yml | 2 -- modules/nf-core/picard/filtersamreads/environment.yml | 2 -- modules/nf-core/picard/fixmateinformation/environment.yml | 2 -- modules/nf-core/picard/liftovervcf/environment.yml | 2 -- modules/nf-core/picard/markduplicates/environment.yml | 2 -- modules/nf-core/picard/mergesamfiles/environment.yml | 2 -- .../picard/positionbaseddownsamplesam/environment.yml | 2 -- modules/nf-core/picard/renamesampleinvcf/environment.yml | 2 -- .../nf-core/picard/scatterintervalsbyns/environment.yml | 2 -- modules/nf-core/picard/sortsam/environment.yml | 2 -- modules/nf-core/picard/sortvcf/environment.yml | 2 -- modules/nf-core/pigz/compress/environment.yml | 2 -- modules/nf-core/pilon/environment.yml | 2 -- modules/nf-core/pindel/pindel/environment.yml | 2 -- modules/nf-core/pints/caller/environment.yml | 2 -- modules/nf-core/pirate/environment.yml | 3 --- modules/nf-core/plasmidfinder/environment.yml | 2 -- modules/nf-core/plasmidid/environment.yml | 2 -- modules/nf-core/platypus/environment.yml | 2 -- modules/nf-core/plink/bcf/environment.yml | 2 -- modules/nf-core/plink/epistasis/environment.yml | 2 -- modules/nf-core/plink/exclude/environment.yml | 2 -- modules/nf-core/plink/extract/environment.yml | 2 -- modules/nf-core/plink/fastepistasis/environment.yml | 2 -- modules/nf-core/plink/gwas/environment.yml | 2 -- modules/nf-core/plink/hwe/environment.yml | 2 -- modules/nf-core/plink/indep/environment.yml | 2 -- modules/nf-core/plink/indeppairwise/environment.yml | 2 -- modules/nf-core/plink/ld/environment.yml | 2 -- modules/nf-core/plink/recode/environment.yml | 2 -- modules/nf-core/plink/vcf/environment.yml | 2 -- modules/nf-core/plink2/extract/environment.yml | 2 -- modules/nf-core/plink2/score/environment.yml | 2 -- modules/nf-core/plink2/vcf/environment.yml | 2 -- modules/nf-core/pmdtools/filter/environment.yml | 2 -- modules/nf-core/pneumocat/environment.yml | 2 -- modules/nf-core/poolsnp/environment.yml | 2 -- modules/nf-core/popscle/demuxlet/environment.yml | 2 -- modules/nf-core/popscle/dscpileup/environment.yml | 2 -- modules/nf-core/popscle/freemuxlet/environment.yml | 2 -- modules/nf-core/porechop/abi/environment.yml | 2 -- modules/nf-core/porechop/porechop/environment.yml | 2 -- modules/nf-core/preseq/ccurve/environment.yml | 2 -- modules/nf-core/preseq/lcextrap/environment.yml | 2 -- modules/nf-core/president/environment.yml | 2 -- modules/nf-core/presto/filterseq/environment.yml | 2 -- modules/nf-core/pretextmap/environment.yml | 2 -- modules/nf-core/pretextsnapshot/environment.yml | 2 -- modules/nf-core/prinseqplusplus/environment.yml | 2 -- modules/nf-core/prodigal/environment.yml | 2 -- modules/nf-core/prokka/environment.yml | 2 -- modules/nf-core/propr/grea/environment.yml | 2 -- modules/nf-core/propr/logratio/environment.yml | 2 -- modules/nf-core/propr/propd/environment.yml | 2 -- modules/nf-core/propr/propr/environment.yml | 2 -- modules/nf-core/proteinortho/environment.yml | 2 -- modules/nf-core/proteus/readproteingroups/environment.yml | 2 -- modules/nf-core/pureclip/environment.yml | 2 -- modules/nf-core/purecn/coverage/environment.yml | 2 -- modules/nf-core/purecn/intervalfile/environment.yml | 3 --- modules/nf-core/purecn/normaldb/environment.yml | 3 --- modules/nf-core/purecn/run/environment.yml | 2 -- modules/nf-core/purgedups/calcuts/environment.yml | 2 -- modules/nf-core/purgedups/getseqs/environment.yml | 2 -- modules/nf-core/purgedups/histplot/environment.yml | 2 -- modules/nf-core/purgedups/pbcstat/environment.yml | 2 -- modules/nf-core/purgedups/purgedups/environment.yml | 2 -- modules/nf-core/purgedups/splitfa/environment.yml | 2 -- modules/nf-core/pycoqc/environment.yml | 2 -- modules/nf-core/pydamage/analyze/environment.yml | 2 -- modules/nf-core/pydamage/filter/environment.yml | 2 -- modules/nf-core/pyrodigal/environment.yml | 2 -- modules/nf-core/qcat/environment.yml | 2 -- modules/nf-core/qualimap/bamqc/environment.yml | 2 -- modules/nf-core/qualimap/bamqccram/environment.yml | 2 -- modules/nf-core/qualimap/rnaseq/environment.yml | 2 -- modules/nf-core/quartonotebook/environment.yml | 3 --- modules/nf-core/quast/environment.yml | 2 -- modules/nf-core/quilt/quilt/environment.yml | 2 -- modules/nf-core/racon/environment.yml | 2 -- modules/nf-core/rapidnj/environment.yml | 2 -- modules/nf-core/rasusa/environment.yml | 2 -- modules/nf-core/raven/environment.yml | 2 -- modules/nf-core/raxmlng/environment.yml | 2 -- .../nf-core/repeatmodeler/builddatabase/environment.yml | 2 -- .../nf-core/repeatmodeler/repeatmodeler/environment.yml | 2 -- modules/nf-core/resfinder/run/environment.yml | 2 -- modules/nf-core/rgi/cardannotation/environment.yml | 2 -- modules/nf-core/rgi/main/environment.yml | 2 -- modules/nf-core/rhocall/annotate/environment.yml | 2 -- modules/nf-core/rhocall/viz/environment.yml | 2 -- modules/nf-core/ribotish/predict/environment.yml | 2 -- modules/nf-core/ribotish/quality/environment.yml | 2 -- modules/nf-core/ribotricer/detectorfs/environment.yml | 2 -- modules/nf-core/ribotricer/prepareorfs/environment.yml | 2 -- modules/nf-core/ribowaltz/environment.yml | 2 -- modules/nf-core/rmarkdownnotebook/environment.yml | 2 -- modules/nf-core/roary/environment.yml | 2 -- modules/nf-core/rrnatranscripts/environment.yml | 2 -- modules/nf-core/rsem/calculateexpression/environment.yml | 2 -- modules/nf-core/rsem/preparereference/environment.yml | 2 -- modules/nf-core/rseqc/bamstat/environment.yml | 2 -- modules/nf-core/rseqc/inferexperiment/environment.yml | 2 -- modules/nf-core/rseqc/innerdistance/environment.yml | 2 -- modules/nf-core/rseqc/junctionannotation/environment.yml | 2 -- modules/nf-core/rseqc/junctionsaturation/environment.yml | 2 -- modules/nf-core/rseqc/readdistribution/environment.yml | 2 -- modules/nf-core/rseqc/readduplication/environment.yml | 2 -- modules/nf-core/rseqc/tin/environment.yml | 2 -- modules/nf-core/rtgtools/format/environment.yml | 2 -- modules/nf-core/rtgtools/pedfilter/environment.yml | 2 -- modules/nf-core/rtgtools/rocplot/environment.yml | 2 -- modules/nf-core/rtgtools/vcfeval/environment.yml | 2 -- modules/nf-core/rtn/tni/environment.yml | 2 -- modules/nf-core/sageproteomics/sage/environment.yml | 2 -- modules/nf-core/salmon/index/environment.yml | 2 -- modules/nf-core/salmon/quant/environment.yml | 2 -- modules/nf-core/salsa2/environment.yml | 2 -- modules/nf-core/sam2lca/analyze/environment.yml | 2 -- modules/nf-core/sambamba/flagstat/environment.yml | 2 -- modules/nf-core/sambamba/markdup/environment.yml | 2 -- modules/nf-core/samblaster/environment.yml | 3 --- modules/nf-core/samtools/ampliconclip/environment.yml | 2 -- modules/nf-core/samtools/bam2fq/environment.yml | 2 -- modules/nf-core/samtools/calmd/environment.yml | 2 -- modules/nf-core/samtools/cat/environment.yml | 2 -- modules/nf-core/samtools/collate/environment.yml | 2 -- modules/nf-core/samtools/collatefastq/environment.yml | 3 --- modules/nf-core/samtools/consensus/environment.yml | 2 -- modules/nf-core/samtools/convert/environment.yml | 2 -- modules/nf-core/samtools/coverage/environment.yml | 2 -- modules/nf-core/samtools/cramsize/environment.yml | 3 --- modules/nf-core/samtools/depth/environment.yml | 3 --- modules/nf-core/samtools/dict/environment.yml | 2 -- modules/nf-core/samtools/faidx/environment.yml | 3 --- modules/nf-core/samtools/fasta/environment.yml | 3 --- modules/nf-core/samtools/fastq/environment.yml | 2 -- modules/nf-core/samtools/fixmate/environment.yml | 2 -- modules/nf-core/samtools/flagstat/environment.yml | 2 -- modules/nf-core/samtools/getrg/environment.yml | 3 --- modules/nf-core/samtools/idxstats/environment.yml | 2 -- modules/nf-core/samtools/import/environment.yml | 3 --- modules/nf-core/samtools/index/environment.yml | 2 -- modules/nf-core/samtools/markdup/environment.yml | 2 -- modules/nf-core/samtools/merge/environment.yml | 2 -- modules/nf-core/samtools/mpileup/environment.yml | 2 -- modules/nf-core/samtools/reheader/environment.yml | 2 -- modules/nf-core/samtools/sormadup/environment.yml | 2 -- modules/nf-core/samtools/sort/environment.yml | 2 -- modules/nf-core/samtools/stats/environment.yml | 2 -- modules/nf-core/samtools/view/environment.yml | 2 -- modules/nf-core/scoary/environment.yml | 2 -- modules/nf-core/scramble/clusteranalysis/environment.yml | 2 -- modules/nf-core/scramble/clusteridentifier/environment.yml | 2 -- modules/nf-core/seacr/callpeak/environment.yml | 3 --- modules/nf-core/segemehl/align/environment.yml | 2 -- modules/nf-core/segemehl/index/environment.yml | 2 -- modules/nf-core/semibin/singleeasybin/environment.yml | 2 -- modules/nf-core/sentieon/applyvarcal/environment.yml | 2 -- modules/nf-core/sentieon/bwaindex/environment.yml | 2 -- modules/nf-core/sentieon/bwamem/environment.yml | 2 -- modules/nf-core/sentieon/collectvcmetrics/environment.yml | 2 -- modules/nf-core/sentieon/coveragemetrics/environment.yml | 2 -- modules/nf-core/sentieon/datametrics/environment.yml | 2 -- modules/nf-core/sentieon/dedup/environment.yml | 2 -- modules/nf-core/sentieon/dnamodelapply/environment.yml | 2 -- modules/nf-core/sentieon/dnascope/environment.yml | 2 -- modules/nf-core/sentieon/gvcftyper/environment.yml | 2 -- modules/nf-core/sentieon/haplotyper/environment.yml | 2 -- modules/nf-core/sentieon/qualcal/environment.yml | 2 -- modules/nf-core/sentieon/readwriter/environment.yml | 2 -- modules/nf-core/sentieon/tnfilter/environment.yml | 2 -- modules/nf-core/sentieon/tnhaplotyper2/environment.yml | 2 -- modules/nf-core/sentieon/tnscope/environment.yml | 2 -- modules/nf-core/sentieon/varcal/environment.yml | 2 -- modules/nf-core/sentieon/wgsmetrics/environment.yml | 2 -- modules/nf-core/seqfu/derep/environment.yml | 2 -- modules/nf-core/seqfu/stats/environment.yml | 2 -- modules/nf-core/seqkit/concat/environment.yml | 2 -- modules/nf-core/seqkit/fq2fa/environment.yml | 2 -- modules/nf-core/seqkit/fx2tab/environment.yml | 2 -- modules/nf-core/seqkit/grep/environment.yml | 2 -- modules/nf-core/seqkit/pair/environment.yml | 2 -- modules/nf-core/seqkit/replace/environment.yml | 2 -- modules/nf-core/seqkit/rmdup/environment.yml | 2 -- modules/nf-core/seqkit/seq/environment.yml | 2 -- modules/nf-core/seqkit/sliding/environment.yml | 2 -- modules/nf-core/seqkit/sort/environment.yml | 2 -- modules/nf-core/seqkit/split2/environment.yml | 2 -- modules/nf-core/seqkit/stats/environment.yml | 2 -- modules/nf-core/seqkit/tab2fx/environment.yml | 2 -- modules/nf-core/seqsero2/environment.yml | 2 -- modules/nf-core/seqtk/cutn/environment.yml | 2 -- modules/nf-core/seqtk/mergepe/environment.yml | 2 -- modules/nf-core/seqtk/rename/environment.yml | 2 -- modules/nf-core/seqtk/sample/environment.yml | 2 -- modules/nf-core/seqtk/seq/environment.yml | 2 -- modules/nf-core/seqtk/subseq/environment.yml | 2 -- modules/nf-core/seqtk/trim/environment.yml | 2 -- modules/nf-core/sequencetools/pileupcaller/environment.yml | 2 -- modules/nf-core/sequenzautils/bam2seqz/environment.yml | 2 -- modules/nf-core/sequenzautils/gcwiggle/environment.yml | 2 -- modules/nf-core/seqwish/induce/environment.yml | 2 -- modules/nf-core/seroba/run/environment.yml | 2 -- modules/nf-core/severus/environment.yml | 2 -- modules/nf-core/sexdeterrmine/environment.yml | 2 -- modules/nf-core/sgdemux/environment.yml | 2 -- modules/nf-core/shapeit5/ligate/environment.yml | 2 -- modules/nf-core/shapeit5/phasecommon/environment.yml | 2 -- modules/nf-core/shapeit5/phaserare/environment.yml | 2 -- modules/nf-core/shapeit5/switch/environment.yml | 2 -- modules/nf-core/shasta/environment.yml | 2 -- modules/nf-core/shasum/environment.yml | 2 -- modules/nf-core/shigatyper/environment.yml | 2 -- modules/nf-core/shigeifinder/environment.yml | 2 -- modules/nf-core/shinyngs/app/environment.yml | 2 -- .../nf-core/shinyngs/staticdifferential/environment.yml | 2 -- modules/nf-core/shinyngs/staticexploratory/environment.yml | 2 -- .../nf-core/shinyngs/validatefomcomponents/environment.yml | 2 -- modules/nf-core/shovill/environment.yml | 2 -- modules/nf-core/sickle/environment.yml | 2 -- modules/nf-core/simpleaf/index/environment.yml | 3 --- modules/nf-core/simpleaf/quant/environment.yml | 3 --- modules/nf-core/sistr/environment.yml | 2 -- modules/nf-core/slimfastq/environment.yml | 2 -- modules/nf-core/smncopynumbercaller/environment.yml | 2 -- modules/nf-core/smoothxg/environment.yml | 2 -- modules/nf-core/smoove/call/environment.yml | 2 -- modules/nf-core/snakemake/environment.yml | 2 -- modules/nf-core/snapaligner/align/environment.yml | 2 -- modules/nf-core/snapaligner/index/environment.yml | 2 -- modules/nf-core/sniffles/environment.yml | 2 -- modules/nf-core/snippy/core/environment.yml | 2 -- modules/nf-core/snippy/run/environment.yml | 2 -- modules/nf-core/snpdists/environment.yml | 2 -- modules/nf-core/snpeff/download/environment.yml | 2 -- modules/nf-core/snpeff/environment.yml | 2 -- modules/nf-core/snpeff/snpeff/environment.yml | 2 -- modules/nf-core/snpsift/annotate/environment.yml | 2 -- modules/nf-core/snpsift/dbnsfp/environment.yml | 2 -- modules/nf-core/snpsift/split/environment.yml | 2 -- modules/nf-core/snpsites/environment.yml | 2 -- modules/nf-core/somalier/ancestry/environment.yml | 2 -- modules/nf-core/somalier/extract/environment.yml | 2 -- modules/nf-core/somalier/relate/environment.yml | 2 -- modules/nf-core/sortmerna/environment.yml | 2 -- modules/nf-core/sourmash/compare/environment.yml | 2 -- modules/nf-core/sourmash/gather/environment.yml | 2 -- modules/nf-core/sourmash/index/environment.yml | 2 -- modules/nf-core/sourmash/sketch/environment.yml | 2 -- modules/nf-core/sourmash/taxannotate/environment.yml | 2 -- modules/nf-core/spades/environment.yml | 2 -- modules/nf-core/spatyper/environment.yml | 2 -- modules/nf-core/splitubam/environment.yml | 2 -- modules/nf-core/spotiflow/environment.yml | 1 - modules/nf-core/spring/compress/environment.yml | 2 -- modules/nf-core/spring/decompress/environment.yml | 2 -- modules/nf-core/sratools/fasterqdump/environment.yml | 2 -- modules/nf-core/sratools/prefetch/environment.yml | 2 -- modules/nf-core/srst2/srst2/environment.yml | 2 -- modules/nf-core/ssuissero/environment.yml | 2 -- modules/nf-core/stadeniolib/scramble/environment.yml | 2 -- modules/nf-core/staphopiasccmec/environment.yml | 2 -- modules/nf-core/star/align/environment.yml | 2 -- modules/nf-core/star/genomegenerate/environment.yml | 2 -- modules/nf-core/star/starsolo/environment.yml | 2 -- modules/nf-core/staramr/search/environment.yml | 3 --- modules/nf-core/stardist/environment.yml | 3 --- modules/nf-core/stecfinder/environment.yml | 2 -- modules/nf-core/stitch/environment.yml | 2 -- modules/nf-core/stranger/environment.yml | 2 -- modules/nf-core/strelka/germline/environment.yml | 2 -- modules/nf-core/strelka/somatic/environment.yml | 2 -- modules/nf-core/stringtie/merge/environment.yml | 2 -- modules/nf-core/stringtie/stringtie/environment.yml | 2 -- modules/nf-core/subread/featurecounts/environment.yml | 2 -- .../summarizedexperiment/environment.yml | 2 -- modules/nf-core/survivor/bedpetovcf/environment.yml | 2 -- modules/nf-core/survivor/filter/environment.yml | 2 -- modules/nf-core/survivor/merge/environment.yml | 2 -- modules/nf-core/survivor/simsv/environment.yml | 2 -- modules/nf-core/survivor/stats/environment.yml | 2 -- modules/nf-core/svaba/environment.yml | 2 -- modules/nf-core/svanalyzer/svbenchmark/environment.yml | 3 --- modules/nf-core/svdb/merge/environment.yml | 2 -- modules/nf-core/svdb/query/environment.yml | 2 -- modules/nf-core/svtk/baftest/environment.yml | 2 -- modules/nf-core/svtk/countsvtypes/environment.yml | 2 -- modules/nf-core/svtk/rdtest2vcf/environment.yml | 2 -- modules/nf-core/svtk/standardize/environment.yml | 2 -- modules/nf-core/svtk/vcf2bed/environment.yml | 2 -- modules/nf-core/svtyper/svtyper/environment.yml | 2 -- modules/nf-core/svtyper/svtypersso/environment.yml | 2 -- modules/nf-core/svync/environment.yml | 2 -- modules/nf-core/tabix/bgzip/environment.yml | 2 -- modules/nf-core/tabix/bgziptabix/environment.yml | 2 -- modules/nf-core/tabix/tabix/environment.yml | 3 --- modules/nf-core/tailfindr/environment.yml | 2 -- modules/nf-core/taxonkit/name2taxid/environment.yml | 2 -- modules/nf-core/taxpasta/merge/environment.yml | 2 -- modules/nf-core/taxpasta/standardise/environment.yml | 2 -- modules/nf-core/tbprofiler/profile/environment.yml | 2 -- modules/nf-core/tcoffee/align/environment.yml | 2 -- modules/nf-core/tcoffee/alncompare/environment.yml | 2 -- modules/nf-core/tcoffee/consensus/environment.yml | 2 -- modules/nf-core/tcoffee/irmsd/environment.yml | 2 -- modules/nf-core/tcoffee/seqreformat/environment.yml | 2 -- modules/nf-core/tcoffee/tcs/environment.yml | 2 -- modules/nf-core/thermorawfileparser/environment.yml | 2 -- modules/nf-core/tiara/tiara/environment.yml | 2 -- modules/nf-core/tiddit/cov/environment.yml | 2 -- modules/nf-core/tiddit/sv/environment.yml | 2 -- modules/nf-core/tidk/explore/environment.yml | 2 -- modules/nf-core/tidk/plot/environment.yml | 2 -- modules/nf-core/tidk/search/environment.yml | 2 -- modules/nf-core/topas/gencons/environment.yml | 2 -- modules/nf-core/toulligqc/environment.yml | 2 -- modules/nf-core/transdecoder/longorf/environment.yml | 2 -- modules/nf-core/transdecoder/predict/environment.yml | 2 -- modules/nf-core/trimgalore/environment.yml | 3 --- modules/nf-core/trimmomatic/environment.yml | 2 -- modules/nf-core/trinity/environment.yml | 2 -- modules/nf-core/trust4/environment.yml | 2 -- modules/nf-core/truvari/bench/environment.yml | 2 -- modules/nf-core/truvari/consistency/environment.yml | 2 -- modules/nf-core/truvari/segment/environment.yml | 2 -- modules/nf-core/trycycler/cluster/environment.yml | 2 -- modules/nf-core/trycycler/subsample/environment.yml | 2 -- modules/nf-core/tsebra/environment.yml | 2 -- modules/nf-core/tximeta/tximport/environment.yml | 2 -- modules/nf-core/ucsc/bedclip/environment.yml | 2 -- modules/nf-core/ucsc/bedgraphtobigwig/environment.yml | 2 -- modules/nf-core/ucsc/bedtobigbed/environment.yml | 2 -- modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml | 2 -- modules/nf-core/ucsc/gtftogenepred/environment.yml | 2 -- modules/nf-core/ucsc/liftover/environment.yml | 2 -- modules/nf-core/ucsc/wigtobigwig/environment.yml | 2 -- modules/nf-core/ultra/align/environment.yml | 2 -- modules/nf-core/ultra/index/environment.yml | 2 -- modules/nf-core/ultra/pipeline/environment.yml | 2 -- modules/nf-core/ultraplex/environment.yml | 2 -- modules/nf-core/umicollapse/environment.yml | 2 -- modules/nf-core/umitools/dedup/environment.yml | 2 -- modules/nf-core/umitools/extract/environment.yml | 2 -- modules/nf-core/umitools/group/environment.yml | 2 -- modules/nf-core/umitools/prepareforrsem/environment.yml | 2 -- modules/nf-core/unicycler/environment.yml | 2 -- modules/nf-core/universc/environment.yml | 2 -- modules/nf-core/untar/environment.yml | 2 -- modules/nf-core/untarfiles/environment.yml | 3 --- modules/nf-core/unzip/environment.yml | 2 -- modules/nf-core/unzipfiles/environment.yml | 2 -- modules/nf-core/upd/environment.yml | 2 -- modules/nf-core/vardictjava/environment.yml | 2 -- modules/nf-core/variantbam/environment.yml | 2 -- modules/nf-core/varlociraptor/callvariants/environment.yml | 2 -- .../estimatealignmentproperties/environment.yml | 2 -- modules/nf-core/varlociraptor/preprocess/environment.yml | 2 -- modules/nf-core/vcf2cytosure/environment.yml | 2 -- modules/nf-core/vcf2db/environment.yml | 2 -- modules/nf-core/vcf2maf/environment.yml | 2 -- modules/nf-core/vcfanno/environment.yml | 2 -- modules/nf-core/vcflib/vcfbreakmulti/environment.yml | 2 -- modules/nf-core/vcflib/vcffilter/environment.yml | 2 -- modules/nf-core/vcflib/vcffixup/environment.yml | 2 -- modules/nf-core/vcflib/vcfuniq/environment.yml | 2 -- modules/nf-core/vcftools/environment.yml | 2 -- modules/nf-core/velocyto/environment.yml | 2 -- modules/nf-core/verifybamid/verifybamid/environment.yml | 2 -- modules/nf-core/verifybamid/verifybamid2/environment.yml | 2 -- modules/nf-core/vg/construct/environment.yml | 2 -- modules/nf-core/vg/deconstruct/environment.yml | 2 -- modules/nf-core/vg/index/environment.yml | 2 -- modules/nf-core/viennarna/rnacofold/environment.yml | 2 -- modules/nf-core/viennarna/rnafold/environment.yml | 2 -- modules/nf-core/viennarna/rnalfold/environment.yml | 2 -- modules/nf-core/vireo/environment.yml | 2 -- modules/nf-core/vrhyme/extractunbinned/environment.yml | 2 -- modules/nf-core/vrhyme/linkbins/environment.yml | 2 -- modules/nf-core/vrhyme/vrhyme/environment.yml | 1 - modules/nf-core/vsearch/cluster/environment.yml | 3 --- modules/nf-core/vsearch/dereplicate/environment.yml | 2 -- modules/nf-core/vsearch/fastqfilter/environment.yml | 2 -- modules/nf-core/vsearch/sintax/environment.yml | 2 -- modules/nf-core/vsearch/sort/environment.yml | 2 -- modules/nf-core/vsearch/usearchglobal/environment.yml | 2 -- modules/nf-core/vt/decompose/environment.yml | 2 -- modules/nf-core/vt/normalize/environment.yml | 2 -- modules/nf-core/wfmash/environment.yml | 2 -- modules/nf-core/wgsim/environment.yml | 2 -- modules/nf-core/whamg/environment.yml | 3 --- modules/nf-core/windowmasker/convert/environment.yml | 2 -- modules/nf-core/windowmasker/mkcounts/environment.yml | 2 -- modules/nf-core/windowmasker/ustat/environment.yml | 2 -- modules/nf-core/wisecondorx/convert/environment.yml | 2 -- modules/nf-core/wisecondorx/gender/environment.yml | 2 -- modules/nf-core/wisecondorx/newref/environment.yml | 2 -- modules/nf-core/wisecondorx/predict/environment.yml | 2 -- modules/nf-core/wittyer/environment.yml | 2 -- modules/nf-core/xengsort/index/environment.yml | 2 -- modules/nf-core/xz/compress/environment.yml | 2 -- modules/nf-core/xz/decompress/environment.yml | 2 -- modules/nf-core/yahs/environment.yml | 2 -- modules/nf-core/yak/count/environment.yml | 2 -- modules/nf-core/yara/index/environment.yml | 2 -- modules/nf-core/yara/mapper/environment.yml | 3 --- modules/nf-core/zip/environment.yml | 2 -- 1261 files changed, 5 insertions(+), 2527 deletions(-) diff --git a/.github/env-template.yml b/.github/env-template.yml index bcd3a8b1c632..3cebeff05bfc 100644 --- a/.github/env-template.yml +++ b/.github/env-template.yml @@ -1,4 +1,3 @@ channels: - conda-forge - bioconda - - defaults diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8bea345e76e2..72d7594e7c38 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -50,7 +50,7 @@ jobs: node-version: "20" - name: Install Prettier - run: npm install -g prettier@3.1.0 + run: npm install -g prettier@3.2.5 - name: Run Prettier --check run: prettier --check . @@ -439,7 +439,7 @@ jobs: uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 with: miniconda-version: "latest" - channels: conda-forge,bioconda,defaults + channels: conda-forge,bioconda python-version: ${{ matrix.python-version }} - name: Conda setup @@ -687,7 +687,7 @@ jobs: with: miniconda-version: "latest" auto-update-conda: true - channels: conda-forge,bioconda,defaults + channels: conda-forge,bioconda - name: Conda setup if: matrix.profile == 'conda' diff --git a/modules/environment-schema.json b/modules/environment-schema.json index f8107cf09969..48382b080872 100644 --- a/modules/environment-schema.json +++ b/modules/environment-schema.json @@ -4,10 +4,6 @@ "description": "Validate the environment.yml file for an nf-core module", "type": "object", "properties": { - "name": { - "type": "string", - "description": "The name of the component, same as in the meta.yml" - }, "channels": { "type": "array", "items": { @@ -22,5 +18,6 @@ } } }, - "required": ["name", "channels", "dependencies"] + "required": ["channels", "dependencies"], + "not": { "required": ["name"] } } diff --git a/modules/nf-core/abacas/environment.yml b/modules/nf-core/abacas/environment.yml index c13791900c5d..a3e0eb8d415c 100644 --- a/modules/nf-core/abacas/environment.yml +++ b/modules/nf-core/abacas/environment.yml @@ -1,7 +1,5 @@ -name: abacas channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::abacas=1.3.1 diff --git a/modules/nf-core/abricate/run/environment.yml b/modules/nf-core/abricate/run/environment.yml index 4b2a1d2a75f4..c7a7d19971ff 100644 --- a/modules/nf-core/abricate/run/environment.yml +++ b/modules/nf-core/abricate/run/environment.yml @@ -1,7 +1,5 @@ -name: abricate_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::abricate=1.0.1 diff --git a/modules/nf-core/abricate/summary/environment.yml b/modules/nf-core/abricate/summary/environment.yml index 8b1e520887e1..c7a7d19971ff 100644 --- a/modules/nf-core/abricate/summary/environment.yml +++ b/modules/nf-core/abricate/summary/environment.yml @@ -1,7 +1,5 @@ -name: abricate_summary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::abricate=1.0.1 diff --git a/modules/nf-core/abritamr/run/environment.yml b/modules/nf-core/abritamr/run/environment.yml index 674740eb7a88..a7c8d047fd19 100644 --- a/modules/nf-core/abritamr/run/environment.yml +++ b/modules/nf-core/abritamr/run/environment.yml @@ -1,7 +1,5 @@ -name: abritamr_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::abritamr=1.0.14 diff --git a/modules/nf-core/adapterremoval/environment.yml b/modules/nf-core/adapterremoval/environment.yml index 1737b14b816c..0e089bfb3052 100644 --- a/modules/nf-core/adapterremoval/environment.yml +++ b/modules/nf-core/adapterremoval/environment.yml @@ -1,7 +1,5 @@ -name: adapterremoval channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::adapterremoval=2.3.2 diff --git a/modules/nf-core/adapterremovalfixprefix/environment.yml b/modules/nf-core/adapterremovalfixprefix/environment.yml index 807fe64b52e8..b682ca4baa70 100644 --- a/modules/nf-core/adapterremovalfixprefix/environment.yml +++ b/modules/nf-core/adapterremovalfixprefix/environment.yml @@ -1,7 +1,5 @@ -name: adapterremovalfixprefix channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::adapterremovalfixprefix=0.0.5 diff --git a/modules/nf-core/admixture/environment.yml b/modules/nf-core/admixture/environment.yml index ba57cac30114..30cac0d6b095 100644 --- a/modules/nf-core/admixture/environment.yml +++ b/modules/nf-core/admixture/environment.yml @@ -1,7 +1,5 @@ -name: admixture channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::admixture=1.3.0 diff --git a/modules/nf-core/affy/justrma/environment.yml b/modules/nf-core/affy/justrma/environment.yml index 8e3978c8fbce..6f25cb2ae1ce 100644 --- a/modules/nf-core/affy/justrma/environment.yml +++ b/modules/nf-core/affy/justrma/environment.yml @@ -1,8 +1,6 @@ -name: affy_justrma channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-affy=1.78.0 - conda-forge::r-base=4.3.1 diff --git a/modules/nf-core/agat/convertspgff2gtf/environment.yml b/modules/nf-core/agat/convertspgff2gtf/environment.yml index 67473316dfb7..0410ee765ea9 100644 --- a/modules/nf-core/agat/convertspgff2gtf/environment.yml +++ b/modules/nf-core/agat/convertspgff2gtf/environment.yml @@ -1,7 +1,5 @@ -name: agat_convertspgff2gtf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agat=1.4.0 diff --git a/modules/nf-core/agat/convertspgff2tsv/environment.yml b/modules/nf-core/agat/convertspgff2tsv/environment.yml index 690f50ae5bef..0410ee765ea9 100644 --- a/modules/nf-core/agat/convertspgff2tsv/environment.yml +++ b/modules/nf-core/agat/convertspgff2tsv/environment.yml @@ -1,7 +1,5 @@ -name: agat_convertspgff2tsv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agat=1.4.0 diff --git a/modules/nf-core/agat/convertspgxf2gxf/environment.yml b/modules/nf-core/agat/convertspgxf2gxf/environment.yml index 6ed34fab062e..0410ee765ea9 100644 --- a/modules/nf-core/agat/convertspgxf2gxf/environment.yml +++ b/modules/nf-core/agat/convertspgxf2gxf/environment.yml @@ -1,7 +1,5 @@ -name: agat_convertspgxf2gxf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agat=1.4.0 diff --git a/modules/nf-core/agat/spaddintrons/environment.yml b/modules/nf-core/agat/spaddintrons/environment.yml index b303241cc958..dabc642a1b48 100644 --- a/modules/nf-core/agat/spaddintrons/environment.yml +++ b/modules/nf-core/agat/spaddintrons/environment.yml @@ -1,7 +1,5 @@ -name: agat_spaddintrons channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::agat=1.4.0" diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml index fb2df4893d70..a6b5f2b9aa1f 100644 --- a/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml +++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "agat_spfilterfeaturefromkilllist" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::agat=1.4.0" diff --git a/modules/nf-core/agat/spmergeannotations/environment.yml b/modules/nf-core/agat/spmergeannotations/environment.yml index 5644e08e07d8..a6b5f2b9aa1f 100644 --- a/modules/nf-core/agat/spmergeannotations/environment.yml +++ b/modules/nf-core/agat/spmergeannotations/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "agat_spmergeannotations" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::agat=1.4.0" diff --git a/modules/nf-core/agat/spstatistics/environment.yml b/modules/nf-core/agat/spstatistics/environment.yml index c868b7b8e098..0410ee765ea9 100644 --- a/modules/nf-core/agat/spstatistics/environment.yml +++ b/modules/nf-core/agat/spstatistics/environment.yml @@ -1,7 +1,5 @@ -name: agat_spstatistics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agat=1.4.0 diff --git a/modules/nf-core/agat/sqstatbasic/environment.yml b/modules/nf-core/agat/sqstatbasic/environment.yml index 58b04205eec7..0410ee765ea9 100644 --- a/modules/nf-core/agat/sqstatbasic/environment.yml +++ b/modules/nf-core/agat/sqstatbasic/environment.yml @@ -1,7 +1,5 @@ -name: agat_sqstatbasic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agat=1.4.0 diff --git a/modules/nf-core/agrvate/environment.yml b/modules/nf-core/agrvate/environment.yml index 4e43c3385233..bfdd71d2968f 100644 --- a/modules/nf-core/agrvate/environment.yml +++ b/modules/nf-core/agrvate/environment.yml @@ -1,7 +1,5 @@ -name: agrvate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::agrvate=1.0.2 diff --git a/modules/nf-core/ale/environment.yml b/modules/nf-core/ale/environment.yml index c6e2efc2dbab..8993eb2a3991 100644 --- a/modules/nf-core/ale/environment.yml +++ b/modules/nf-core/ale/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ale" channels: - conda-forge - bioconda - - defaults - tanghaibao dependencies: - "bioconda::ale=20180904" diff --git a/modules/nf-core/allelecounter/environment.yml b/modules/nf-core/allelecounter/environment.yml index b503525445c5..69179cbf949e 100644 --- a/modules/nf-core/allelecounter/environment.yml +++ b/modules/nf-core/allelecounter/environment.yml @@ -1,7 +1,5 @@ -name: allelecounter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cancerit-allelecount=4.3.0 diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml index 0305a5f7097e..21ec05e613ea 100644 --- a/modules/nf-core/ampcombi/environment.yml +++ b/modules/nf-core/ampcombi/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ampcombi" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ampcombi=0.1.7 - python=3.11 diff --git a/modules/nf-core/ampcombi2/cluster/environment.yml b/modules/nf-core/ampcombi2/cluster/environment.yml index aa5e5fe44d1f..420c955bfd29 100644 --- a/modules/nf-core/ampcombi2/cluster/environment.yml +++ b/modules/nf-core/ampcombi2/cluster/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ampcombi2_cluster" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ampcombi=0.2.2" diff --git a/modules/nf-core/ampcombi2/complete/environment.yml b/modules/nf-core/ampcombi2/complete/environment.yml index fa640b771196..420c955bfd29 100644 --- a/modules/nf-core/ampcombi2/complete/environment.yml +++ b/modules/nf-core/ampcombi2/complete/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ampcombi2_complete" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ampcombi=0.2.2" diff --git a/modules/nf-core/ampcombi2/parsetables/environment.yml b/modules/nf-core/ampcombi2/parsetables/environment.yml index 7a4b37ab7021..420c955bfd29 100644 --- a/modules/nf-core/ampcombi2/parsetables/environment.yml +++ b/modules/nf-core/ampcombi2/parsetables/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ampcombi2_parsetables" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ampcombi=0.2.2" diff --git a/modules/nf-core/ampir/environment.yml b/modules/nf-core/ampir/environment.yml index 8cb475d101f3..359e426c5088 100644 --- a/modules/nf-core/ampir/environment.yml +++ b/modules/nf-core/ampir/environment.yml @@ -1,7 +1,5 @@ -name: ampir channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-ampir=1.1.0 diff --git a/modules/nf-core/amplify/predict/environment.yml b/modules/nf-core/amplify/predict/environment.yml index c980cf5e1407..e1cb57035ec4 100644 --- a/modules/nf-core/amplify/predict/environment.yml +++ b/modules/nf-core/amplify/predict/environment.yml @@ -1,7 +1,5 @@ -name: amplify_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::amplify=2.0.0 diff --git a/modules/nf-core/amps/environment.yml b/modules/nf-core/amps/environment.yml index 4cd154761744..d78219cbe01e 100644 --- a/modules/nf-core/amps/environment.yml +++ b/modules/nf-core/amps/environment.yml @@ -1,7 +1,5 @@ -name: amps channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hops=0.35 diff --git a/modules/nf-core/amrfinderplus/run/environment.yml b/modules/nf-core/amrfinderplus/run/environment.yml index 214f44f49576..2744ce544202 100644 --- a/modules/nf-core/amrfinderplus/run/environment.yml +++ b/modules/nf-core/amrfinderplus/run/environment.yml @@ -1,7 +1,5 @@ -name: amrfinderplus_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ncbi-amrfinderplus=3.12.8 diff --git a/modules/nf-core/amrfinderplus/update/environment.yml b/modules/nf-core/amrfinderplus/update/environment.yml index d08f0725ee7d..2744ce544202 100644 --- a/modules/nf-core/amrfinderplus/update/environment.yml +++ b/modules/nf-core/amrfinderplus/update/environment.yml @@ -1,7 +1,5 @@ -name: amrfinderplus_update channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ncbi-amrfinderplus=3.12.8 diff --git a/modules/nf-core/angsd/contamination/environment.yml b/modules/nf-core/angsd/contamination/environment.yml index 57a57276118b..f2f4e7d3d777 100644 --- a/modules/nf-core/angsd/contamination/environment.yml +++ b/modules/nf-core/angsd/contamination/environment.yml @@ -1,7 +1,5 @@ -name: angsd_contamination channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::angsd=0.940 diff --git a/modules/nf-core/angsd/docounts/environment.yml b/modules/nf-core/angsd/docounts/environment.yml index ebaa9ed2ca65..3f1bb661cf2c 100644 --- a/modules/nf-core/angsd/docounts/environment.yml +++ b/modules/nf-core/angsd/docounts/environment.yml @@ -1,7 +1,5 @@ -name: angsd_docounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::angsd=0.939 diff --git a/modules/nf-core/angsd/gl/environment.yml b/modules/nf-core/angsd/gl/environment.yml index aac5db41f82d..6e7fda79f94b 100644 --- a/modules/nf-core/angsd/gl/environment.yml +++ b/modules/nf-core/angsd/gl/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "angsd_gl" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::angsd=0.940" - "bioconda::htslib=1.17" diff --git a/modules/nf-core/annotsv/annotsv/environment.yml b/modules/nf-core/annotsv/annotsv/environment.yml index e5f4a3e4aacd..6b6608d440b7 100644 --- a/modules/nf-core/annotsv/annotsv/environment.yml +++ b/modules/nf-core/annotsv/annotsv/environment.yml @@ -1,7 +1,5 @@ -name: annotsv_annotsv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::annotsv=3.4.2 diff --git a/modules/nf-core/annotsv/installannotations/environment.yml b/modules/nf-core/annotsv/installannotations/environment.yml index b759f91d3224..6b6608d440b7 100644 --- a/modules/nf-core/annotsv/installannotations/environment.yml +++ b/modules/nf-core/annotsv/installannotations/environment.yml @@ -1,7 +1,5 @@ -name: annotsv_installannotations channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::annotsv=3.4.2 diff --git a/modules/nf-core/anota2seq/anota2seqrun/environment.yml b/modules/nf-core/anota2seq/anota2seqrun/environment.yml index 31c82193d125..a0b0b3180f83 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/environment.yml +++ b/modules/nf-core/anota2seq/anota2seqrun/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "anota2seq_anota2seqrun" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-anota2seq=1.24.0" diff --git a/modules/nf-core/antismash/antismashlite/environment.yml b/modules/nf-core/antismash/antismashlite/environment.yml index 227b52645caf..ce4491dc556e 100644 --- a/modules/nf-core/antismash/antismashlite/environment.yml +++ b/modules/nf-core/antismash/antismashlite/environment.yml @@ -1,7 +1,5 @@ -name: antismash_antismashlite channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::antismash-lite=7.1.0 diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml index b9323a931fd8..ce4491dc556e 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/environment.yml @@ -1,7 +1,5 @@ -name: antismash_antismashlitedownloaddatabases channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::antismash-lite=7.1.0 diff --git a/modules/nf-core/arcashla/extract/environment.yml b/modules/nf-core/arcashla/extract/environment.yml index b5789655ec87..f5cd15eabc1f 100644 --- a/modules/nf-core/arcashla/extract/environment.yml +++ b/modules/nf-core/arcashla/extract/environment.yml @@ -1,7 +1,5 @@ -name: arcashla_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::arcas-hla=0.5.0 diff --git a/modules/nf-core/argnorm/environment.yml b/modules/nf-core/argnorm/environment.yml index 771b87c9f08a..783995f288cd 100644 --- a/modules/nf-core/argnorm/environment.yml +++ b/modules/nf-core/argnorm/environment.yml @@ -1,7 +1,5 @@ -name: "argnorm" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::argnorm=0.5.0" diff --git a/modules/nf-core/aria2/environment.yml b/modules/nf-core/aria2/environment.yml index 5dc58a07208e..52d11ba96bab 100644 --- a/modules/nf-core/aria2/environment.yml +++ b/modules/nf-core/aria2/environment.yml @@ -1,7 +1,5 @@ -name: aria2 channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::aria2=1.36.0 diff --git a/modules/nf-core/ariba/getref/environment.yml b/modules/nf-core/ariba/getref/environment.yml index cc886d28876f..49af201aa815 100644 --- a/modules/nf-core/ariba/getref/environment.yml +++ b/modules/nf-core/ariba/getref/environment.yml @@ -1,7 +1,5 @@ -name: ariba_getref channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ariba=2.14.6 diff --git a/modules/nf-core/ariba/run/environment.yml b/modules/nf-core/ariba/run/environment.yml index f161a2be9b6b..49af201aa815 100644 --- a/modules/nf-core/ariba/run/environment.yml +++ b/modules/nf-core/ariba/run/environment.yml @@ -1,7 +1,5 @@ -name: ariba_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ariba=2.14.6 diff --git a/modules/nf-core/arriba/arriba/environment.yml b/modules/nf-core/arriba/arriba/environment.yml index 8494c8c03d6d..d0883a0d2059 100644 --- a/modules/nf-core/arriba/arriba/environment.yml +++ b/modules/nf-core/arriba/arriba/environment.yml @@ -1,7 +1,5 @@ -name: arriba_arriba channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::arriba=2.4.0 diff --git a/modules/nf-core/arriba/download/environment.yml b/modules/nf-core/arriba/download/environment.yml index dc7d3bf9960a..d0883a0d2059 100644 --- a/modules/nf-core/arriba/download/environment.yml +++ b/modules/nf-core/arriba/download/environment.yml @@ -1,7 +1,5 @@ -name: arriba_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::arriba=2.4.0 diff --git a/modules/nf-core/art/illumina/environment.yml b/modules/nf-core/art/illumina/environment.yml index bf446862493a..eedc114c6621 100644 --- a/modules/nf-core/art/illumina/environment.yml +++ b/modules/nf-core/art/illumina/environment.yml @@ -1,7 +1,5 @@ -name: art_illumina channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::art=2016.06.05 diff --git a/modules/nf-core/artic/guppyplex/environment.yml b/modules/nf-core/artic/guppyplex/environment.yml index 19176850c7e6..cf5ae4cf5c51 100644 --- a/modules/nf-core/artic/guppyplex/environment.yml +++ b/modules/nf-core/artic/guppyplex/environment.yml @@ -1,7 +1,5 @@ -name: artic_guppyplex channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::artic=1.2.3 diff --git a/modules/nf-core/artic/minion/environment.yml b/modules/nf-core/artic/minion/environment.yml index 5123f82c1e76..cf5ae4cf5c51 100644 --- a/modules/nf-core/artic/minion/environment.yml +++ b/modules/nf-core/artic/minion/environment.yml @@ -1,7 +1,5 @@ -name: artic_minion channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::artic=1.2.3 diff --git a/modules/nf-core/ascat/environment.yml b/modules/nf-core/ascat/environment.yml index 52935f097824..63d87708d6ad 100644 --- a/modules/nf-core/ascat/environment.yml +++ b/modules/nf-core/ascat/environment.yml @@ -1,8 +1,6 @@ -name: ascat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ascat=3.1.1 - bioconda::cancerit-allelecount=4.3.0 diff --git a/modules/nf-core/ashlar/environment.yml b/modules/nf-core/ashlar/environment.yml index ecfe440a4b1f..8b3e771ac01a 100644 --- a/modules/nf-core/ashlar/environment.yml +++ b/modules/nf-core/ashlar/environment.yml @@ -1,7 +1,5 @@ -name: ashlar channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ashlar=1.18.0 diff --git a/modules/nf-core/assemblyscan/environment.yml b/modules/nf-core/assemblyscan/environment.yml index 34a02bc79340..3751ff08a2ce 100644 --- a/modules/nf-core/assemblyscan/environment.yml +++ b/modules/nf-core/assemblyscan/environment.yml @@ -1,7 +1,5 @@ -name: assemblyscan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::assembly-scan=0.4.1 diff --git a/modules/nf-core/ataqv/ataqv/environment.yml b/modules/nf-core/ataqv/ataqv/environment.yml index a91f6d9bc6ed..8ad29081b192 100644 --- a/modules/nf-core/ataqv/ataqv/environment.yml +++ b/modules/nf-core/ataqv/ataqv/environment.yml @@ -1,7 +1,5 @@ -name: ataqv_ataqv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ataqv=1.3.1 diff --git a/modules/nf-core/ataqv/mkarv/environment.yml b/modules/nf-core/ataqv/mkarv/environment.yml index 28ff2f69d54c..8ad29081b192 100644 --- a/modules/nf-core/ataqv/mkarv/environment.yml +++ b/modules/nf-core/ataqv/mkarv/environment.yml @@ -1,7 +1,5 @@ -name: ataqv_mkarv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ataqv=1.3.1 diff --git a/modules/nf-core/atlas/call/environment.yml b/modules/nf-core/atlas/call/environment.yml index c872fe054347..51ea2964b5b7 100644 --- a/modules/nf-core/atlas/call/environment.yml +++ b/modules/nf-core/atlas/call/environment.yml @@ -1,7 +1,5 @@ -name: atlas_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::atlas=0.9.9 diff --git a/modules/nf-core/atlas/pmd/environment.yml b/modules/nf-core/atlas/pmd/environment.yml index 24ba39f5835f..51ea2964b5b7 100644 --- a/modules/nf-core/atlas/pmd/environment.yml +++ b/modules/nf-core/atlas/pmd/environment.yml @@ -1,7 +1,5 @@ -name: atlas_pmd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::atlas=0.9.9 diff --git a/modules/nf-core/atlas/recal/environment.yml b/modules/nf-core/atlas/recal/environment.yml index 19265746010b..51ea2964b5b7 100644 --- a/modules/nf-core/atlas/recal/environment.yml +++ b/modules/nf-core/atlas/recal/environment.yml @@ -1,7 +1,5 @@ -name: atlas_recal channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::atlas=0.9.9 diff --git a/modules/nf-core/atlas/splitmerge/environment.yml b/modules/nf-core/atlas/splitmerge/environment.yml index 5c43cec2672d..51ea2964b5b7 100644 --- a/modules/nf-core/atlas/splitmerge/environment.yml +++ b/modules/nf-core/atlas/splitmerge/environment.yml @@ -1,7 +1,5 @@ -name: atlas_splitmerge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::atlas=0.9.9 diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml index 3a613e610082..9c0280fc49eb 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/environment.yml @@ -1,7 +1,5 @@ -name: atlasgeneannotationmanipulation_gtf2featureannotation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::atlas-gene-annotation-manipulation=1.1.1 diff --git a/modules/nf-core/authentict/deam2cont/environment.yml b/modules/nf-core/authentict/deam2cont/environment.yml index 90cf797e6ee6..73d01c656e51 100644 --- a/modules/nf-core/authentict/deam2cont/environment.yml +++ b/modules/nf-core/authentict/deam2cont/environment.yml @@ -1,7 +1,5 @@ -name: authentict_deam2cont channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::authentict=1.0.1 diff --git a/modules/nf-core/bacphlip/environment.yml b/modules/nf-core/bacphlip/environment.yml index 6bc1631b7ec1..bfd7a480b824 100644 --- a/modules/nf-core/bacphlip/environment.yml +++ b/modules/nf-core/bacphlip/environment.yml @@ -1,9 +1,6 @@ -name: bacphlip - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bacphlip=0.9.6 diff --git a/modules/nf-core/bakta/bakta/environment.yml b/modules/nf-core/bakta/bakta/environment.yml index efb92265ae08..b3c302f09be8 100644 --- a/modules/nf-core/bakta/bakta/environment.yml +++ b/modules/nf-core/bakta/bakta/environment.yml @@ -1,7 +1,5 @@ -name: bakta_bakta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bakta=1.9.3 diff --git a/modules/nf-core/bakta/baktadbdownload/environment.yml b/modules/nf-core/bakta/baktadbdownload/environment.yml index f6a53ff7f8ac..b3c302f09be8 100644 --- a/modules/nf-core/bakta/baktadbdownload/environment.yml +++ b/modules/nf-core/bakta/baktadbdownload/environment.yml @@ -1,7 +1,5 @@ -name: bakta_baktadbdownload channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bakta=1.9.3 diff --git a/modules/nf-core/bam2fastx/bam2fastq/environment.yml b/modules/nf-core/bam2fastx/bam2fastq/environment.yml index 2a73c2c9b86d..563a0c17b36f 100644 --- a/modules/nf-core/bam2fastx/bam2fastq/environment.yml +++ b/modules/nf-core/bam2fastx/bam2fastq/environment.yml @@ -1,7 +1,5 @@ -name: bam2fastx_bam2fastq channels: - conda-forge - bioconda - - defaults dependencies: - bam2fastx=1.3.1 diff --git a/modules/nf-core/bamaligncleaner/environment.yml b/modules/nf-core/bamaligncleaner/environment.yml index 963cbf0f2eeb..8b861d9ea881 100644 --- a/modules/nf-core/bamaligncleaner/environment.yml +++ b/modules/nf-core/bamaligncleaner/environment.yml @@ -1,7 +1,5 @@ -name: bamaligncleaner channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamaligncleaner=0.2.2 diff --git a/modules/nf-core/bamclipper/environment.yml b/modules/nf-core/bamclipper/environment.yml index deeb118a14f5..1d24949aa0f3 100644 --- a/modules/nf-core/bamclipper/environment.yml +++ b/modules/nf-core/bamclipper/environment.yml @@ -1,8 +1,6 @@ -name: "bamclipper" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamclipper=1.0.0 - bioconda::samtools=1.12 diff --git a/modules/nf-core/bamcmp/environment.yml b/modules/nf-core/bamcmp/environment.yml index e7b1dbb060fd..351c12ab93be 100644 --- a/modules/nf-core/bamcmp/environment.yml +++ b/modules/nf-core/bamcmp/environment.yml @@ -1,7 +1,5 @@ -name: bamcmp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamcmp=2.2 diff --git a/modules/nf-core/bamstats/generalstats/environment.yml b/modules/nf-core/bamstats/generalstats/environment.yml index 71d07d16ef1f..4591b2cc5c55 100644 --- a/modules/nf-core/bamstats/generalstats/environment.yml +++ b/modules/nf-core/bamstats/generalstats/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "bamstats_generalstats" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bamstats=0.3.5" diff --git a/modules/nf-core/bamtofastq10x/environment.yml b/modules/nf-core/bamtofastq10x/environment.yml index d612f512e6f6..cce34f4b9bd1 100644 --- a/modules/nf-core/bamtofastq10x/environment.yml +++ b/modules/nf-core/bamtofastq10x/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "bamtofastq10x" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::10x_bamtofastq=1.4.1" diff --git a/modules/nf-core/bamtools/convert/environment.yml b/modules/nf-core/bamtools/convert/environment.yml index 1407c34a8c65..5fd41c95be33 100644 --- a/modules/nf-core/bamtools/convert/environment.yml +++ b/modules/nf-core/bamtools/convert/environment.yml @@ -1,7 +1,5 @@ -name: bamtools_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamtools=2.5.2 diff --git a/modules/nf-core/bamtools/split/environment.yml b/modules/nf-core/bamtools/split/environment.yml index 995d25ee86af..5fd41c95be33 100644 --- a/modules/nf-core/bamtools/split/environment.yml +++ b/modules/nf-core/bamtools/split/environment.yml @@ -1,7 +1,5 @@ -name: bamtools_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamtools=2.5.2 diff --git a/modules/nf-core/bamtools/stats/environment.yml b/modules/nf-core/bamtools/stats/environment.yml index a32c319b55a5..5fd41c95be33 100644 --- a/modules/nf-core/bamtools/stats/environment.yml +++ b/modules/nf-core/bamtools/stats/environment.yml @@ -1,7 +1,5 @@ -name: bamtools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamtools=2.5.2 diff --git a/modules/nf-core/bamutil/trimbam/environment.yml b/modules/nf-core/bamutil/trimbam/environment.yml index d9b10c2a4464..d9ac63d520f1 100644 --- a/modules/nf-core/bamutil/trimbam/environment.yml +++ b/modules/nf-core/bamutil/trimbam/environment.yml @@ -1,7 +1,5 @@ -name: bamutil_trimbam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bamutil=1.0.15 diff --git a/modules/nf-core/bandage/image/environment.yml b/modules/nf-core/bandage/image/environment.yml index 61558105e513..018e544b96bd 100644 --- a/modules/nf-core/bandage/image/environment.yml +++ b/modules/nf-core/bandage/image/environment.yml @@ -1,7 +1,5 @@ -name: bandage_image channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bandage=0.8.1 diff --git a/modules/nf-core/barrnap/environment.yml b/modules/nf-core/barrnap/environment.yml index 28436cf13903..3a920f2e3f2b 100644 --- a/modules/nf-core/barrnap/environment.yml +++ b/modules/nf-core/barrnap/environment.yml @@ -1,7 +1,5 @@ -name: barrnap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::barrnap=0.9 diff --git a/modules/nf-core/basicpy/environment.yml b/modules/nf-core/basicpy/environment.yml index 48bb0990a055..3cebeff05bfc 100644 --- a/modules/nf-core/basicpy/environment.yml +++ b/modules/nf-core/basicpy/environment.yml @@ -1,5 +1,3 @@ -name: basicpy channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/bbmap/align/environment.yml b/modules/nf-core/bbmap/align/environment.yml index 96c4c32cbcec..7ff25c7a51be 100644 --- a/modules/nf-core/bbmap/align/environment.yml +++ b/modules/nf-core/bbmap/align/environment.yml @@ -1,8 +1,6 @@ -name: bbmap_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bbmap/bbduk/environment.yml b/modules/nf-core/bbmap/bbduk/environment.yml index 2ae2e0bc88ca..cbe6f2a0c751 100644 --- a/modules/nf-core/bbmap/bbduk/environment.yml +++ b/modules/nf-core/bbmap/bbduk/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_bbduk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.06 diff --git a/modules/nf-core/bbmap/bbmerge/environment.yml b/modules/nf-core/bbmap/bbmerge/environment.yml index be435a82950f..963ad517dbd0 100644 --- a/modules/nf-core/bbmap/bbmerge/environment.yml +++ b/modules/nf-core/bbmap/bbmerge/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "bbmap_bbmerge" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bbmap=39.06" diff --git a/modules/nf-core/bbmap/bbnorm/environment.yml b/modules/nf-core/bbmap/bbnorm/environment.yml index 8b97ffdad599..fa8209c0b54c 100644 --- a/modules/nf-core/bbmap/bbnorm/environment.yml +++ b/modules/nf-core/bbmap/bbnorm/environment.yml @@ -1,8 +1,6 @@ -name: bbmap_bbnorm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 - pigz=2.6 diff --git a/modules/nf-core/bbmap/bbsplit/environment.yml b/modules/nf-core/bbmap/bbsplit/environment.yml index 4c6db627649e..dfd8936e11f6 100644 --- a/modules/nf-core/bbmap/bbsplit/environment.yml +++ b/modules/nf-core/bbmap/bbsplit/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_bbsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/clumpify/environment.yml b/modules/nf-core/bbmap/clumpify/environment.yml index bef6899e7b2b..dfd8936e11f6 100644 --- a/modules/nf-core/bbmap/clumpify/environment.yml +++ b/modules/nf-core/bbmap/clumpify/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_clumpify channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/filterbyname/environment.yml b/modules/nf-core/bbmap/filterbyname/environment.yml index 6f01bc24be15..dfd8936e11f6 100644 --- a/modules/nf-core/bbmap/filterbyname/environment.yml +++ b/modules/nf-core/bbmap/filterbyname/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_filterbyname channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/index/environment.yml b/modules/nf-core/bbmap/index/environment.yml index 515f8d214dfb..dfd8936e11f6 100644 --- a/modules/nf-core/bbmap/index/environment.yml +++ b/modules/nf-core/bbmap/index/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bbmap/pileup/environment.yml b/modules/nf-core/bbmap/pileup/environment.yml index 63767f5f0a87..7ff25c7a51be 100644 --- a/modules/nf-core/bbmap/pileup/environment.yml +++ b/modules/nf-core/bbmap/pileup/environment.yml @@ -1,8 +1,6 @@ -name: bbmap_pileup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bbmap/sendsketch/environment.yml b/modules/nf-core/bbmap/sendsketch/environment.yml index 55f54f5c60ee..dfd8936e11f6 100644 --- a/modules/nf-core/bbmap/sendsketch/environment.yml +++ b/modules/nf-core/bbmap/sendsketch/environment.yml @@ -1,7 +1,5 @@ -name: bbmap_sendsketch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bbmap=39.01 diff --git a/modules/nf-core/bcftools/annotate/environment.yml b/modules/nf-core/bcftools/annotate/environment.yml index 3d4e337992fd..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/annotate/environment.yml +++ b/modules/nf-core/bcftools/annotate/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/call/environment.yml b/modules/nf-core/bcftools/call/environment.yml index 84c4cef4e1c0..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/call/environment.yml +++ b/modules/nf-core/bcftools/call/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/concat/environment.yml b/modules/nf-core/bcftools/concat/environment.yml index 6544e949c858..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/concat/environment.yml +++ b/modules/nf-core/bcftools/concat/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_concat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/consensus/environment.yml b/modules/nf-core/bcftools/consensus/environment.yml index def3fc14ab98..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/consensus/environment.yml +++ b/modules/nf-core/bcftools/consensus/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_consensus channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/convert/environment.yml b/modules/nf-core/bcftools/convert/environment.yml index 3d85cb2c3356..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/convert/environment.yml +++ b/modules/nf-core/bcftools/convert/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/filter/environment.yml b/modules/nf-core/bcftools/filter/environment.yml index 854de139c24b..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/filter/environment.yml +++ b/modules/nf-core/bcftools/filter/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/index/environment.yml b/modules/nf-core/bcftools/index/environment.yml index ea752646fc9f..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/index/environment.yml +++ b/modules/nf-core/bcftools/index/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/isec/environment.yml b/modules/nf-core/bcftools/isec/environment.yml index 01bdcff9703e..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/isec/environment.yml +++ b/modules/nf-core/bcftools/isec/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_isec channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/merge/environment.yml b/modules/nf-core/bcftools/merge/environment.yml index 71e39be309a8..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/merge/environment.yml +++ b/modules/nf-core/bcftools/merge/environment.yml @@ -1,4 +1,3 @@ -name: bcftools_merge channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/mpileup/environment.yml b/modules/nf-core/bcftools/mpileup/environment.yml index 7e479383ba7f..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/mpileup/environment.yml +++ b/modules/nf-core/bcftools/mpileup/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_mpileup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/norm/environment.yml b/modules/nf-core/bcftools/norm/environment.yml index 0c7dfa8f6c2b..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/norm/environment.yml +++ b/modules/nf-core/bcftools/norm/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_norm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginscatter/environment.yml b/modules/nf-core/bcftools/pluginscatter/environment.yml index 51bce4d31def..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/pluginscatter/environment.yml +++ b/modules/nf-core/bcftools/pluginscatter/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_pluginscatter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/pluginsplit/environment.yml b/modules/nf-core/bcftools/pluginsplit/environment.yml index 1f7bb1ff370f..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/pluginsplit/environment.yml +++ b/modules/nf-core/bcftools/pluginsplit/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_pluginsplit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/plugintag2tag/environment.yml b/modules/nf-core/bcftools/plugintag2tag/environment.yml index 776613d9ebdb..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/plugintag2tag/environment.yml +++ b/modules/nf-core/bcftools/plugintag2tag/environment.yml @@ -1,4 +1,3 @@ -name: "bcftools_plugintag2tag" channels: - conda-forge - bioconda diff --git a/modules/nf-core/bcftools/query/environment.yml b/modules/nf-core/bcftools/query/environment.yml index d8c4f4e48606..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/query/environment.yml +++ b/modules/nf-core/bcftools/query/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_query channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/reheader/environment.yml b/modules/nf-core/bcftools/reheader/environment.yml index 48fd72c91c46..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/reheader/environment.yml +++ b/modules/nf-core/bcftools/reheader/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_reheader channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/roh/environment.yml b/modules/nf-core/bcftools/roh/environment.yml index 76187d1217e4..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/roh/environment.yml +++ b/modules/nf-core/bcftools/roh/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_roh channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/sort/environment.yml b/modules/nf-core/bcftools/sort/environment.yml index 2295ecfd1783..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/sort/environment.yml +++ b/modules/nf-core/bcftools/sort/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/split/environment.yml b/modules/nf-core/bcftools/split/environment.yml index 8aefb505c0ad..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/split/environment.yml +++ b/modules/nf-core/bcftools/split/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/bcftools/stats/environment.yml b/modules/nf-core/bcftools/stats/environment.yml index 128fe2042278..93357b41eade 100644 --- a/modules/nf-core/bcftools/stats/environment.yml +++ b/modules/nf-core/bcftools/stats/environment.yml @@ -1,8 +1,6 @@ -name: bcftools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/bcftools/view/environment.yml b/modules/nf-core/bcftools/view/environment.yml index 4b2a21dfaaa1..5c00b116ad90 100644 --- a/modules/nf-core/bcftools/view/environment.yml +++ b/modules/nf-core/bcftools/view/environment.yml @@ -1,7 +1,5 @@ -name: bcftools_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bcftools=1.20 diff --git a/modules/nf-core/beagle5/beagle/environment.yml b/modules/nf-core/beagle5/beagle/environment.yml index 872f78c404b3..55ed1d1bda36 100644 --- a/modules/nf-core/beagle5/beagle/environment.yml +++ b/modules/nf-core/beagle5/beagle/environment.yml @@ -1,7 +1,5 @@ -name: beagle5_beagle channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::beagle=5.2_21Apr21.304 diff --git a/modules/nf-core/bedgovcf/environment.yml b/modules/nf-core/bedgovcf/environment.yml index f19a947e0d44..4b32f5201e1b 100644 --- a/modules/nf-core/bedgovcf/environment.yml +++ b/modules/nf-core/bedgovcf/environment.yml @@ -1,7 +1,5 @@ -name: bedgovcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedgovcf=0.1.1 diff --git a/modules/nf-core/bedops/convert2bed/environment.yml b/modules/nf-core/bedops/convert2bed/environment.yml index 049b29e9b3eb..3c13066f7927 100644 --- a/modules/nf-core/bedops/convert2bed/environment.yml +++ b/modules/nf-core/bedops/convert2bed/environment.yml @@ -1,7 +1,5 @@ -name: "bedops_convert2bed" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bedops=2.4.41" diff --git a/modules/nf-core/bedops/gtf2bed/environment.yml b/modules/nf-core/bedops/gtf2bed/environment.yml index 8aede2428388..3c13066f7927 100644 --- a/modules/nf-core/bedops/gtf2bed/environment.yml +++ b/modules/nf-core/bedops/gtf2bed/environment.yml @@ -1,7 +1,5 @@ -name: "bedops_gtf2bed" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bedops=2.4.41" diff --git a/modules/nf-core/bedtools/bamtobed/environment.yml b/modules/nf-core/bedtools/bamtobed/environment.yml index 4b50139ec596..5683bc05f230 100644 --- a/modules/nf-core/bedtools/bamtobed/environment.yml +++ b/modules/nf-core/bedtools/bamtobed/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_bamtobed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/closest/environment.yml b/modules/nf-core/bedtools/closest/environment.yml index 77483654b943..5683bc05f230 100644 --- a/modules/nf-core/bedtools/closest/environment.yml +++ b/modules/nf-core/bedtools/closest/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_closest channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/complement/environment.yml b/modules/nf-core/bedtools/complement/environment.yml index 396f32433246..5683bc05f230 100644 --- a/modules/nf-core/bedtools/complement/environment.yml +++ b/modules/nf-core/bedtools/complement/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_complement channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/coverage/environment.yml b/modules/nf-core/bedtools/coverage/environment.yml index 016caf0151f7..5683bc05f230 100644 --- a/modules/nf-core/bedtools/coverage/environment.yml +++ b/modules/nf-core/bedtools/coverage/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_coverage channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/genomecov/environment.yml b/modules/nf-core/bedtools/genomecov/environment.yml index 8fbe20c3122a..5683bc05f230 100644 --- a/modules/nf-core/bedtools/genomecov/environment.yml +++ b/modules/nf-core/bedtools/genomecov/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_genomecov channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/getfasta/environment.yml b/modules/nf-core/bedtools/getfasta/environment.yml index a89401f2a3f5..5683bc05f230 100644 --- a/modules/nf-core/bedtools/getfasta/environment.yml +++ b/modules/nf-core/bedtools/getfasta/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_getfasta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/groupby/environment.yml b/modules/nf-core/bedtools/groupby/environment.yml index dab99ea1f24c..5683bc05f230 100644 --- a/modules/nf-core/bedtools/groupby/environment.yml +++ b/modules/nf-core/bedtools/groupby/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_groupby channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/intersect/environment.yml b/modules/nf-core/bedtools/intersect/environment.yml index 2a343050893b..5683bc05f230 100644 --- a/modules/nf-core/bedtools/intersect/environment.yml +++ b/modules/nf-core/bedtools/intersect/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_intersect channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/jaccard/environment.yml b/modules/nf-core/bedtools/jaccard/environment.yml index f0f2a38fcfd4..5683bc05f230 100644 --- a/modules/nf-core/bedtools/jaccard/environment.yml +++ b/modules/nf-core/bedtools/jaccard/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_jaccard channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/makewindows/environment.yml b/modules/nf-core/bedtools/makewindows/environment.yml index 0de3c15d07fa..5683bc05f230 100644 --- a/modules/nf-core/bedtools/makewindows/environment.yml +++ b/modules/nf-core/bedtools/makewindows/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_makewindows channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/map/environment.yml b/modules/nf-core/bedtools/map/environment.yml index f61ee02833e4..5683bc05f230 100644 --- a/modules/nf-core/bedtools/map/environment.yml +++ b/modules/nf-core/bedtools/map/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_map channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/maskfasta/environment.yml b/modules/nf-core/bedtools/maskfasta/environment.yml index 71d18917defc..5683bc05f230 100644 --- a/modules/nf-core/bedtools/maskfasta/environment.yml +++ b/modules/nf-core/bedtools/maskfasta/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_maskfasta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/merge/environment.yml b/modules/nf-core/bedtools/merge/environment.yml index 99707878b0f4..5683bc05f230 100644 --- a/modules/nf-core/bedtools/merge/environment.yml +++ b/modules/nf-core/bedtools/merge/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/multiinter/environment.yml b/modules/nf-core/bedtools/multiinter/environment.yml index 27d9fddc77ac..5683bc05f230 100644 --- a/modules/nf-core/bedtools/multiinter/environment.yml +++ b/modules/nf-core/bedtools/multiinter/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_multiinter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/shift/environment.yml b/modules/nf-core/bedtools/shift/environment.yml index a83d89eb06e3..5683bc05f230 100644 --- a/modules/nf-core/bedtools/shift/environment.yml +++ b/modules/nf-core/bedtools/shift/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_shift channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/slop/environment.yml b/modules/nf-core/bedtools/slop/environment.yml index e03ee9631373..5683bc05f230 100644 --- a/modules/nf-core/bedtools/slop/environment.yml +++ b/modules/nf-core/bedtools/slop/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_slop channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/sort/environment.yml b/modules/nf-core/bedtools/sort/environment.yml index 87b2e4252579..5683bc05f230 100644 --- a/modules/nf-core/bedtools/sort/environment.yml +++ b/modules/nf-core/bedtools/sort/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/split/environment.yml b/modules/nf-core/bedtools/split/environment.yml index 71912c7d5e4f..5683bc05f230 100644 --- a/modules/nf-core/bedtools/split/environment.yml +++ b/modules/nf-core/bedtools/split/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/subtract/environment.yml b/modules/nf-core/bedtools/subtract/environment.yml index 083ba617d2bc..5683bc05f230 100644 --- a/modules/nf-core/bedtools/subtract/environment.yml +++ b/modules/nf-core/bedtools/subtract/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_subtract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/unionbedg/environment.yml b/modules/nf-core/bedtools/unionbedg/environment.yml index 11f4c5424bc7..5683bc05f230 100644 --- a/modules/nf-core/bedtools/unionbedg/environment.yml +++ b/modules/nf-core/bedtools/unionbedg/environment.yml @@ -1,7 +1,5 @@ -name: bedtools_unionbedg channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bioawk/environment.yml b/modules/nf-core/bioawk/environment.yml index 5fdfd4176e9f..527f6cd4b1ce 100644 --- a/modules/nf-core/bioawk/environment.yml +++ b/modules/nf-core/bioawk/environment.yml @@ -1,7 +1,5 @@ -name: bioawk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioawk=1.0 diff --git a/modules/nf-core/biobambam/bammarkduplicates2/environment.yml b/modules/nf-core/biobambam/bammarkduplicates2/environment.yml index 76e81cb0af63..eb19895afd07 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/environment.yml +++ b/modules/nf-core/biobambam/bammarkduplicates2/environment.yml @@ -1,7 +1,5 @@ -name: biobambam_bammarkduplicates2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biobambam=2.0.183 diff --git a/modules/nf-core/biobambam/bammerge/environment.yml b/modules/nf-core/biobambam/bammerge/environment.yml index 6eb5eee8cfb3..eb19895afd07 100644 --- a/modules/nf-core/biobambam/bammerge/environment.yml +++ b/modules/nf-core/biobambam/bammerge/environment.yml @@ -1,7 +1,5 @@ -name: biobambam_bammerge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biobambam=2.0.183 diff --git a/modules/nf-core/biobambam/bamsormadup/environment.yml b/modules/nf-core/biobambam/bamsormadup/environment.yml index 4adac68be0b4..eb19895afd07 100644 --- a/modules/nf-core/biobambam/bamsormadup/environment.yml +++ b/modules/nf-core/biobambam/bamsormadup/environment.yml @@ -1,7 +1,5 @@ -name: biobambam_bamsormadup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biobambam=2.0.183 diff --git a/modules/nf-core/biohansel/environment.yml b/modules/nf-core/biohansel/environment.yml index 7ef2a3dc7999..b20be7488bf6 100644 --- a/modules/nf-core/biohansel/environment.yml +++ b/modules/nf-core/biohansel/environment.yml @@ -1,7 +1,5 @@ -name: biohansel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bio_hansel=2.6.1 diff --git a/modules/nf-core/biscuit/align/environment.yml b/modules/nf-core/biscuit/align/environment.yml index 90e26ee680ea..b4bab59944c3 100644 --- a/modules/nf-core/biscuit/align/environment.yml +++ b/modules/nf-core/biscuit/align/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/biscuit/biscuitblaster/environment.yml b/modules/nf-core/biscuit/biscuitblaster/environment.yml index 1cf1fbc0f2ed..ba50e31d11c0 100644 --- a/modules/nf-core/biscuit/biscuitblaster/environment.yml +++ b/modules/nf-core/biscuit/biscuitblaster/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_blaster channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samblaster=0.1.26 diff --git a/modules/nf-core/biscuit/bsconv/environment.yml b/modules/nf-core/biscuit/bsconv/environment.yml index 937dbadfba06..56b7e967693e 100644 --- a/modules/nf-core/biscuit/bsconv/environment.yml +++ b/modules/nf-core/biscuit/bsconv/environment.yml @@ -1,7 +1,5 @@ -name: biscuit_bsconv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 diff --git a/modules/nf-core/biscuit/epiread/environment.yml b/modules/nf-core/biscuit/epiread/environment.yml index 2d7915474bd2..b4bab59944c3 100644 --- a/modules/nf-core/biscuit/epiread/environment.yml +++ b/modules/nf-core/biscuit/epiread/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_epiread channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/biscuit/index/environment.yml b/modules/nf-core/biscuit/index/environment.yml index 66b9fde82f6b..56b7e967693e 100644 --- a/modules/nf-core/biscuit/index/environment.yml +++ b/modules/nf-core/biscuit/index/environment.yml @@ -1,7 +1,5 @@ -name: biscuit_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 diff --git a/modules/nf-core/biscuit/mergecg/environment.yml b/modules/nf-core/biscuit/mergecg/environment.yml index eb9d77b4a1f5..b4bab59944c3 100644 --- a/modules/nf-core/biscuit/mergecg/environment.yml +++ b/modules/nf-core/biscuit/mergecg/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_mergecg channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/biscuit/pileup/environment.yml b/modules/nf-core/biscuit/pileup/environment.yml index 60132b4def8d..b4bab59944c3 100644 --- a/modules/nf-core/biscuit/pileup/environment.yml +++ b/modules/nf-core/biscuit/pileup/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_pileup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/biscuit/qc/environment.yml b/modules/nf-core/biscuit/qc/environment.yml index 9e9f3a26b5f3..56b7e967693e 100644 --- a/modules/nf-core/biscuit/qc/environment.yml +++ b/modules/nf-core/biscuit/qc/environment.yml @@ -1,7 +1,5 @@ -name: biscuit_qc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 diff --git a/modules/nf-core/biscuit/vcf2bed/environment.yml b/modules/nf-core/biscuit/vcf2bed/environment.yml index ed6dca0cde94..b4bab59944c3 100644 --- a/modules/nf-core/biscuit/vcf2bed/environment.yml +++ b/modules/nf-core/biscuit/vcf2bed/environment.yml @@ -1,8 +1,6 @@ -name: biscuit_vcf2bed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::biscuit=1.1.0.20220707 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bismark/align/environment.yml b/modules/nf-core/bismark/align/environment.yml index d7cb8a298bf7..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/align/environment.yml +++ b/modules/nf-core/bismark/align/environment.yml @@ -1,7 +1,5 @@ -name: bismark_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/coverage2cytosine/environment.yml b/modules/nf-core/bismark/coverage2cytosine/environment.yml index abda284757e8..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/coverage2cytosine/environment.yml +++ b/modules/nf-core/bismark/coverage2cytosine/environment.yml @@ -1,7 +1,5 @@ -name: bismark_coverage2cytosine channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/deduplicate/environment.yml b/modules/nf-core/bismark/deduplicate/environment.yml index 6160c2e6d360..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/deduplicate/environment.yml +++ b/modules/nf-core/bismark/deduplicate/environment.yml @@ -1,7 +1,5 @@ -name: bismark_deduplicate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml index e27febfcbfd4..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/genomepreparation/environment.yml +++ b/modules/nf-core/bismark/genomepreparation/environment.yml @@ -1,7 +1,5 @@ -name: bismark_genomepreparation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/methylationextractor/environment.yml b/modules/nf-core/bismark/methylationextractor/environment.yml index 33ca119004aa..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/methylationextractor/environment.yml +++ b/modules/nf-core/bismark/methylationextractor/environment.yml @@ -1,7 +1,5 @@ -name: bismark_methylationextractor channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/report/environment.yml b/modules/nf-core/bismark/report/environment.yml index 2725a6054fed..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/report/environment.yml +++ b/modules/nf-core/bismark/report/environment.yml @@ -1,7 +1,5 @@ -name: bismark_report channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/bismark/summary/environment.yml b/modules/nf-core/bismark/summary/environment.yml index 8c0fe3d2c643..fbc3fdf202c8 100644 --- a/modules/nf-core/bismark/summary/environment.yml +++ b/modules/nf-core/bismark/summary/environment.yml @@ -1,7 +1,5 @@ -name: bismark_summary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bismark=0.24.0 diff --git a/modules/nf-core/blast/blastdbcmd/environment.yml b/modules/nf-core/blast/blastdbcmd/environment.yml index b90a0b74587e..78ed204d7f97 100644 --- a/modules/nf-core/blast/blastdbcmd/environment.yml +++ b/modules/nf-core/blast/blastdbcmd/environment.yml @@ -1,7 +1,5 @@ -name: "blast_blastdbcmd" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::blast=2.15.0" diff --git a/modules/nf-core/blast/blastn/environment.yml b/modules/nf-core/blast/blastn/environment.yml index e4a72800e9e7..777e097ed751 100644 --- a/modules/nf-core/blast/blastn/environment.yml +++ b/modules/nf-core/blast/blastn/environment.yml @@ -1,7 +1,5 @@ -name: blast_blastn channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/blastp/environment.yml b/modules/nf-core/blast/blastp/environment.yml index 7cb7c0e4805b..777e097ed751 100644 --- a/modules/nf-core/blast/blastp/environment.yml +++ b/modules/nf-core/blast/blastp/environment.yml @@ -1,7 +1,5 @@ -name: blast_blastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/makeblastdb/environment.yml b/modules/nf-core/blast/makeblastdb/environment.yml index a20783b0f80e..777e097ed751 100644 --- a/modules/nf-core/blast/makeblastdb/environment.yml +++ b/modules/nf-core/blast/makeblastdb/environment.yml @@ -1,7 +1,5 @@ -name: blast_makeblastdb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/tblastn/environment.yml b/modules/nf-core/blast/tblastn/environment.yml index 98d2454090f4..777e097ed751 100644 --- a/modules/nf-core/blast/tblastn/environment.yml +++ b/modules/nf-core/blast/tblastn/environment.yml @@ -1,7 +1,5 @@ -name: blast_tblastn channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/blast/updateblastdb/environment.yml b/modules/nf-core/blast/updateblastdb/environment.yml index 564c310fd87c..78ed204d7f97 100644 --- a/modules/nf-core/blast/updateblastdb/environment.yml +++ b/modules/nf-core/blast/updateblastdb/environment.yml @@ -1,7 +1,5 @@ -name: "blast_updateblastdb" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::blast=2.15.0" diff --git a/modules/nf-core/blat/environment.yml b/modules/nf-core/blat/environment.yml index ec2b1ff56ddc..2a85c07875d3 100644 --- a/modules/nf-core/blat/environment.yml +++ b/modules/nf-core/blat/environment.yml @@ -1,7 +1,5 @@ -name: blat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blat=36 diff --git a/modules/nf-core/bowtie/align/environment.yml b/modules/nf-core/bowtie/align/environment.yml index fb5d7c1ef12e..4434c7e71437 100644 --- a/modules/nf-core/bowtie/align/environment.yml +++ b/modules/nf-core/bowtie/align/environment.yml @@ -1,8 +1,6 @@ -name: bowtie_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bowtie=1.3.0 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/bowtie/build/environment.yml b/modules/nf-core/bowtie/build/environment.yml index 0907b0f840f5..ab5a842215c3 100644 --- a/modules/nf-core/bowtie/build/environment.yml +++ b/modules/nf-core/bowtie/build/environment.yml @@ -1,7 +1,5 @@ -name: bowtie_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bowtie=1.3.0 diff --git a/modules/nf-core/bowtie2/align/environment.yml b/modules/nf-core/bowtie2/align/environment.yml index d2796359aeb5..9090f218834b 100644 --- a/modules/nf-core/bowtie2/align/environment.yml +++ b/modules/nf-core/bowtie2/align/environment.yml @@ -1,8 +1,6 @@ -name: bowtie2_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bowtie2=2.5.2 - bioconda::samtools=1.18 diff --git a/modules/nf-core/bowtie2/build/environment.yml b/modules/nf-core/bowtie2/build/environment.yml index 22bbfc3749fb..e590f7ce3263 100644 --- a/modules/nf-core/bowtie2/build/environment.yml +++ b/modules/nf-core/bowtie2/build/environment.yml @@ -1,7 +1,5 @@ -name: bowtie2_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bowtie2=2.5.2 diff --git a/modules/nf-core/bracken/bracken/environment.yml b/modules/nf-core/bracken/bracken/environment.yml index 6eb5b1b9a345..b96b00d7a3bb 100644 --- a/modules/nf-core/bracken/bracken/environment.yml +++ b/modules/nf-core/bracken/bracken/environment.yml @@ -1,7 +1,5 @@ -name: bracken_bracken channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/build/environment.yml b/modules/nf-core/bracken/build/environment.yml index 7288a38a1b2e..d9ea9a61e52a 100644 --- a/modules/nf-core/bracken/build/environment.yml +++ b/modules/nf-core/bracken/build/environment.yml @@ -1,8 +1,6 @@ --- -name: "bracken_build" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bracken=2.9" diff --git a/modules/nf-core/bracken/combinebrackenoutputs/environment.yml b/modules/nf-core/bracken/combinebrackenoutputs/environment.yml index 37a5fb2503b0..b96b00d7a3bb 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/environment.yml +++ b/modules/nf-core/bracken/combinebrackenoutputs/environment.yml @@ -1,7 +1,5 @@ -name: bracken_combinebrackenoutputs channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bracken=2.9" diff --git a/modules/nf-core/busco/busco/environment.yml b/modules/nf-core/busco/busco/environment.yml index 06a5d9307bf1..5b918b45b2d3 100644 --- a/modules/nf-core/busco/busco/environment.yml +++ b/modules/nf-core/busco/busco/environment.yml @@ -1,7 +1,5 @@ -name: busco_busco channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::busco=5.7.1 diff --git a/modules/nf-core/busco/generateplot/environment.yml b/modules/nf-core/busco/generateplot/environment.yml index 1ca5babb0a26..766c0f406b07 100644 --- a/modules/nf-core/busco/generateplot/environment.yml +++ b/modules/nf-core/busco/generateplot/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "busco_generateplot" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::busco=5.7.1 diff --git a/modules/nf-core/bwa/aln/environment.yml b/modules/nf-core/bwa/aln/environment.yml index a131461be99e..d8789a209282 100644 --- a/modules/nf-core/bwa/aln/environment.yml +++ b/modules/nf-core/bwa/aln/environment.yml @@ -1,7 +1,5 @@ -name: bwa_aln channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwa=0.7.18 diff --git a/modules/nf-core/bwa/index/environment.yml b/modules/nf-core/bwa/index/environment.yml index 126e0034488c..d8789a209282 100644 --- a/modules/nf-core/bwa/index/environment.yml +++ b/modules/nf-core/bwa/index/environment.yml @@ -1,7 +1,5 @@ -name: bwa_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwa=0.7.18 diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 3aa9f0cca234..24f7f4436a6e 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,8 +1,6 @@ -name: bwa_mem channels: - conda-forge - bioconda - - defaults dependencies: - bwa=0.7.18 # renovate: datasource=conda depName=bioconda/samtools diff --git a/modules/nf-core/bwa/sampe/environment.yml b/modules/nf-core/bwa/sampe/environment.yml index aa8a48001a49..7576715281c0 100644 --- a/modules/nf-core/bwa/sampe/environment.yml +++ b/modules/nf-core/bwa/sampe/environment.yml @@ -1,9 +1,6 @@ -name: bwa_sampe - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwa=0.7.17 diff --git a/modules/nf-core/bwa/samse/environment.yml b/modules/nf-core/bwa/samse/environment.yml index 638842c89f6e..7576715281c0 100644 --- a/modules/nf-core/bwa/samse/environment.yml +++ b/modules/nf-core/bwa/samse/environment.yml @@ -1,9 +1,6 @@ -name: bwa_samse - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwa=0.7.17 diff --git a/modules/nf-core/bwamem2/index/environment.yml b/modules/nf-core/bwamem2/index/environment.yml index 26b439172abc..15cee2387675 100644 --- a/modules/nf-core/bwamem2/index/environment.yml +++ b/modules/nf-core/bwamem2/index/environment.yml @@ -1,7 +1,5 @@ -name: bwamem2_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwa-mem2=2.2.1 diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index cbf06d399352..633712cf1412 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,8 +1,6 @@ -name: bwamem2_mem channels: - conda-forge - bioconda - - defaults dependencies: - bwa-mem2=2.2.1 # renovate: datasource=conda depName=bioconda/samtools diff --git a/modules/nf-core/bwameme/index/environment.yml b/modules/nf-core/bwameme/index/environment.yml index 5d76ea18865a..f209d62e86ea 100644 --- a/modules/nf-core/bwameme/index/environment.yml +++ b/modules/nf-core/bwameme/index/environment.yml @@ -1,7 +1,5 @@ -name: "bwameme_index" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bwa-meme=1.0.6" diff --git a/modules/nf-core/bwameme/mem/environment.yml b/modules/nf-core/bwameme/mem/environment.yml index 388eedd21bdc..cad7944049ab 100644 --- a/modules/nf-core/bwameme/mem/environment.yml +++ b/modules/nf-core/bwameme/mem/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "bwameme_mem" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bwa-meme=1.0.6" - "bioconda::mbuffer=20160228" diff --git a/modules/nf-core/bwameth/align/environment.yml b/modules/nf-core/bwameth/align/environment.yml index 39b4d7cdc439..707376ebf904 100644 --- a/modules/nf-core/bwameth/align/environment.yml +++ b/modules/nf-core/bwameth/align/environment.yml @@ -1,7 +1,5 @@ -name: bwameth_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwameth=0.2.7 diff --git a/modules/nf-core/bwameth/index/environment.yml b/modules/nf-core/bwameth/index/environment.yml index 032f259c9699..707376ebf904 100644 --- a/modules/nf-core/bwameth/index/environment.yml +++ b/modules/nf-core/bwameth/index/environment.yml @@ -1,7 +1,5 @@ -name: bwameth_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bwameth=0.2.7 diff --git a/modules/nf-core/cadd/environment.yml b/modules/nf-core/cadd/environment.yml index 26f170e9ddd5..4477e16e5b29 100644 --- a/modules/nf-core/cadd/environment.yml +++ b/modules/nf-core/cadd/environment.yml @@ -1,8 +1,6 @@ -name: cadd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cadd-scripts=1.6.post1 - conda-forge::conda=4.14.0 diff --git a/modules/nf-core/cafe/environment.yml b/modules/nf-core/cafe/environment.yml index 58ff885989ae..79c9b6f28fcd 100644 --- a/modules/nf-core/cafe/environment.yml +++ b/modules/nf-core/cafe/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "cafe" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::cafe=5.1.0" diff --git a/modules/nf-core/calder2/environment.yml b/modules/nf-core/calder2/environment.yml index b29100dbfc3a..6bbba46df2de 100644 --- a/modules/nf-core/calder2/environment.yml +++ b/modules/nf-core/calder2/environment.yml @@ -1,7 +1,5 @@ -name: calder2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-calder2=0.7 diff --git a/modules/nf-core/canu/environment.yml b/modules/nf-core/canu/environment.yml index 752bbbed7033..9c7f6dd49b18 100644 --- a/modules/nf-core/canu/environment.yml +++ b/modules/nf-core/canu/environment.yml @@ -1,7 +1,5 @@ -name: canu channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::canu=2.2 diff --git a/modules/nf-core/cat/cat/environment.yml b/modules/nf-core/cat/cat/environment.yml index 17a04ef2324f..9b01c865a285 100644 --- a/modules/nf-core/cat/cat/environment.yml +++ b/modules/nf-core/cat/cat/environment.yml @@ -1,7 +1,5 @@ -name: cat_cat channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::pigz=2.3.4 diff --git a/modules/nf-core/cat/fastq/environment.yml b/modules/nf-core/cat/fastq/environment.yml index 8c69b121f73f..c7eb9bd1c3ca 100644 --- a/modules/nf-core/cat/fastq/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,5 @@ -name: cat_fastq channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cdhit/cdhit/environment.yml b/modules/nf-core/cdhit/cdhit/environment.yml index fb5b89fc8620..59e671e484c6 100644 --- a/modules/nf-core/cdhit/cdhit/environment.yml +++ b/modules/nf-core/cdhit/cdhit/environment.yml @@ -1,7 +1,5 @@ -name: cdhit_cdhit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cd-hit=4.8.1 diff --git a/modules/nf-core/cdhit/cdhitest/environment.yml b/modules/nf-core/cdhit/cdhitest/environment.yml index 0ddd42629a20..59e671e484c6 100644 --- a/modules/nf-core/cdhit/cdhitest/environment.yml +++ b/modules/nf-core/cdhit/cdhitest/environment.yml @@ -1,7 +1,5 @@ -name: cdhit_cdhitest channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cd-hit=4.8.1 diff --git a/modules/nf-core/cellbender/merge/environment.yml b/modules/nf-core/cellbender/merge/environment.yml index d1d21c116c14..a157c522b2b4 100644 --- a/modules/nf-core/cellbender/merge/environment.yml +++ b/modules/nf-core/cellbender/merge/environment.yml @@ -1,7 +1,5 @@ -name: cellbender_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cellbender=0.3.0 diff --git a/modules/nf-core/cellbender/removebackground/environment.yml b/modules/nf-core/cellbender/removebackground/environment.yml index ef70cd088c14..a157c522b2b4 100644 --- a/modules/nf-core/cellbender/removebackground/environment.yml +++ b/modules/nf-core/cellbender/removebackground/environment.yml @@ -1,7 +1,5 @@ -name: cellbender_removebackground channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cellbender=0.3.0 diff --git a/modules/nf-core/cellrangeratac/count/environment.yml b/modules/nf-core/cellrangeratac/count/environment.yml index e8225b81a151..3cebeff05bfc 100644 --- a/modules/nf-core/cellrangeratac/count/environment.yml +++ b/modules/nf-core/cellrangeratac/count/environment.yml @@ -1,5 +1,3 @@ -name: cellrangeratac_count channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/cellrangeratac/mkfastq/environment.yml b/modules/nf-core/cellrangeratac/mkfastq/environment.yml index 50b7fc6c2b1e..3cebeff05bfc 100644 --- a/modules/nf-core/cellrangeratac/mkfastq/environment.yml +++ b/modules/nf-core/cellrangeratac/mkfastq/environment.yml @@ -1,5 +1,3 @@ -name: cellrangeratac_mkfastq channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/cellrangeratac/mkref/environment.yml b/modules/nf-core/cellrangeratac/mkref/environment.yml index 53306bce2887..3cebeff05bfc 100644 --- a/modules/nf-core/cellrangeratac/mkref/environment.yml +++ b/modules/nf-core/cellrangeratac/mkref/environment.yml @@ -1,5 +1,3 @@ -name: cellrangeratac_mkref channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/cellsnp/modea/environment.yml b/modules/nf-core/cellsnp/modea/environment.yml index 2a6f6cab9655..c8b70f595e24 100644 --- a/modules/nf-core/cellsnp/modea/environment.yml +++ b/modules/nf-core/cellsnp/modea/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "cellsnp_modea" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::cellsnp-lite=1.2.3" diff --git a/modules/nf-core/centrifuge/build/environment.yml b/modules/nf-core/centrifuge/build/environment.yml index fc62576d9b04..42592891580c 100644 --- a/modules/nf-core/centrifuge/build/environment.yml +++ b/modules/nf-core/centrifuge/build/environment.yml @@ -1,7 +1,5 @@ -name: centrifuge_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::centrifuge=1.0.4.1 diff --git a/modules/nf-core/centrifuge/centrifuge/environment.yml b/modules/nf-core/centrifuge/centrifuge/environment.yml index cf34dc0e9b72..42592891580c 100644 --- a/modules/nf-core/centrifuge/centrifuge/environment.yml +++ b/modules/nf-core/centrifuge/centrifuge/environment.yml @@ -1,7 +1,5 @@ -name: centrifuge_centrifuge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::centrifuge=1.0.4.1 diff --git a/modules/nf-core/centrifuge/kreport/environment.yml b/modules/nf-core/centrifuge/kreport/environment.yml index 5c8fb451b7a0..42592891580c 100644 --- a/modules/nf-core/centrifuge/kreport/environment.yml +++ b/modules/nf-core/centrifuge/kreport/environment.yml @@ -1,7 +1,5 @@ -name: centrifuge_kreport channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::centrifuge=1.0.4.1 diff --git a/modules/nf-core/checkm/lineagewf/environment.yml b/modules/nf-core/checkm/lineagewf/environment.yml index 2947d7e4d36b..1b87050296b6 100644 --- a/modules/nf-core/checkm/lineagewf/environment.yml +++ b/modules/nf-core/checkm/lineagewf/environment.yml @@ -1,7 +1,5 @@ -name: checkm_lineagewf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkm-genome=1.2.3 diff --git a/modules/nf-core/checkm/qa/environment.yml b/modules/nf-core/checkm/qa/environment.yml index 3937f98bfe4b..06c5639e07df 100644 --- a/modules/nf-core/checkm/qa/environment.yml +++ b/modules/nf-core/checkm/qa/environment.yml @@ -1,7 +1,5 @@ -name: checkm_qa channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkm-genome=1.2.2 diff --git a/modules/nf-core/checkm2/databasedownload/environment.yml b/modules/nf-core/checkm2/databasedownload/environment.yml index 549ef9cee688..18fd1f51a80c 100644 --- a/modules/nf-core/checkm2/databasedownload/environment.yml +++ b/modules/nf-core/checkm2/databasedownload/environment.yml @@ -1,7 +1,5 @@ -name: checkm2_databasedownload channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkm2=1.0.2 diff --git a/modules/nf-core/checkm2/predict/environment.yml b/modules/nf-core/checkm2/predict/environment.yml index 1d897ac0728f..18fd1f51a80c 100644 --- a/modules/nf-core/checkm2/predict/environment.yml +++ b/modules/nf-core/checkm2/predict/environment.yml @@ -1,7 +1,5 @@ -name: checkm2_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkm2=1.0.2 diff --git a/modules/nf-core/checkqc/environment.yml b/modules/nf-core/checkqc/environment.yml index e60237d5c5f0..1a0541303d55 100644 --- a/modules/nf-core/checkqc/environment.yml +++ b/modules/nf-core/checkqc/environment.yml @@ -1,8 +1,6 @@ -name: checkqc channels: - conda-forge - bioconda - - defaults dependencies: - python=3.8 - numpy=1.26 diff --git a/modules/nf-core/checkv/downloaddatabase/environment.yml b/modules/nf-core/checkv/downloaddatabase/environment.yml index 9dfdcd12c66c..affce8dddbf4 100644 --- a/modules/nf-core/checkv/downloaddatabase/environment.yml +++ b/modules/nf-core/checkv/downloaddatabase/environment.yml @@ -1,7 +1,5 @@ -name: checkv_downloaddatabase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkv=1.0.1 diff --git a/modules/nf-core/checkv/endtoend/environment.yml b/modules/nf-core/checkv/endtoend/environment.yml index 2acd38517695..affce8dddbf4 100644 --- a/modules/nf-core/checkv/endtoend/environment.yml +++ b/modules/nf-core/checkv/endtoend/environment.yml @@ -1,7 +1,5 @@ -name: checkv_endtoend channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkv=1.0.1 diff --git a/modules/nf-core/checkv/updatedatabase/environment.yml b/modules/nf-core/checkv/updatedatabase/environment.yml index 8b1eeaad0b05..affce8dddbf4 100644 --- a/modules/nf-core/checkv/updatedatabase/environment.yml +++ b/modules/nf-core/checkv/updatedatabase/environment.yml @@ -1,7 +1,5 @@ -name: checkv_updatedatabase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::checkv=1.0.1 diff --git a/modules/nf-core/chewbbaca/createschema/environment.yml b/modules/nf-core/chewbbaca/createschema/environment.yml index 9b5924e1aa0f..22fd2e2e8427 100644 --- a/modules/nf-core/chewbbaca/createschema/environment.yml +++ b/modules/nf-core/chewbbaca/createschema/environment.yml @@ -1,9 +1,6 @@ -name: chewbbaca_createschema - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::chewbbaca=3.3.5 diff --git a/modules/nf-core/chopper/environment.yml b/modules/nf-core/chopper/environment.yml index ef9aaa425a25..e80840e15144 100644 --- a/modules/nf-core/chopper/environment.yml +++ b/modules/nf-core/chopper/environment.yml @@ -1,7 +1,5 @@ -name: chopper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::chopper=0.3.0 diff --git a/modules/nf-core/chromap/chromap/environment.yml b/modules/nf-core/chromap/chromap/environment.yml index 616ea6d2e4ec..a59614c03c42 100644 --- a/modules/nf-core/chromap/chromap/environment.yml +++ b/modules/nf-core/chromap/chromap/environment.yml @@ -1,8 +1,6 @@ -name: chromap_chromap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::chromap=0.2.6 - bioconda::samtools=1.20 diff --git a/modules/nf-core/chromap/index/environment.yml b/modules/nf-core/chromap/index/environment.yml index d83b301af318..1eb3f8703d68 100644 --- a/modules/nf-core/chromap/index/environment.yml +++ b/modules/nf-core/chromap/index/environment.yml @@ -1,7 +1,5 @@ -name: chromap_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::chromap=0.2.6 diff --git a/modules/nf-core/chromograph/environment.yml b/modules/nf-core/chromograph/environment.yml index 4fe69462af45..47881b1fb6fe 100644 --- a/modules/nf-core/chromograph/environment.yml +++ b/modules/nf-core/chromograph/environment.yml @@ -1,7 +1,5 @@ -name: chromograph channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::chromograph=1.3.1 diff --git a/modules/nf-core/circexplorer2/annotate/environment.yml b/modules/nf-core/circexplorer2/annotate/environment.yml index def886e93599..c703b088a04f 100644 --- a/modules/nf-core/circexplorer2/annotate/environment.yml +++ b/modules/nf-core/circexplorer2/annotate/environment.yml @@ -1,7 +1,5 @@ -name: circexplorer2_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::circexplorer2=2.3.8 diff --git a/modules/nf-core/circexplorer2/parse/environment.yml b/modules/nf-core/circexplorer2/parse/environment.yml index 17613a2a1914..c703b088a04f 100644 --- a/modules/nf-core/circexplorer2/parse/environment.yml +++ b/modules/nf-core/circexplorer2/parse/environment.yml @@ -1,4 +1,3 @@ -name: circexplorer2_parse channels: - conda-forge - bioconda diff --git a/modules/nf-core/circularmapper/circulargenerator/environment.yml b/modules/nf-core/circularmapper/circulargenerator/environment.yml index f1e1201ef44a..39e62b9baacd 100644 --- a/modules/nf-core/circularmapper/circulargenerator/environment.yml +++ b/modules/nf-core/circularmapper/circulargenerator/environment.yml @@ -1,9 +1,7 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "circularmapper_circulargenerator" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::circularmapper=1.93.5 diff --git a/modules/nf-core/circularmapper/realignsamfile/environment.yml b/modules/nf-core/circularmapper/realignsamfile/environment.yml index d9beb5ae1fb9..ad2c59881267 100644 --- a/modules/nf-core/circularmapper/realignsamfile/environment.yml +++ b/modules/nf-core/circularmapper/realignsamfile/environment.yml @@ -1,7 +1,5 @@ -name: circularmapper_realignsamfile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::circularmapper=1.93.5 diff --git a/modules/nf-core/clame/environment.yml b/modules/nf-core/clame/environment.yml index 365b97c44ab5..4a4f0722745d 100644 --- a/modules/nf-core/clame/environment.yml +++ b/modules/nf-core/clame/environment.yml @@ -1,7 +1,5 @@ -name: clame channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::clame=1.0 diff --git a/modules/nf-core/clippy/environment.yml b/modules/nf-core/clippy/environment.yml index 31f239754b5d..4fe9b8860ce6 100644 --- a/modules/nf-core/clippy/environment.yml +++ b/modules/nf-core/clippy/environment.yml @@ -1,7 +1,5 @@ -name: clippy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::clippy=1.5.0 diff --git a/modules/nf-core/clonalframeml/environment.yml b/modules/nf-core/clonalframeml/environment.yml index 97b5467cd6e8..f6e2a73cdf89 100644 --- a/modules/nf-core/clonalframeml/environment.yml +++ b/modules/nf-core/clonalframeml/environment.yml @@ -1,7 +1,5 @@ -name: clonalframeml channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::clonalframeml=1.12 diff --git a/modules/nf-core/clustalo/align/environment.yml b/modules/nf-core/clustalo/align/environment.yml index be1eef95ebfe..80bc6a5ad2f8 100644 --- a/modules/nf-core/clustalo/align/environment.yml +++ b/modules/nf-core/clustalo/align/environment.yml @@ -1,8 +1,6 @@ -name: clustalo_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::clustalo=1.2.4 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/clustalo/guidetree/environment.yml b/modules/nf-core/clustalo/guidetree/environment.yml index 38b2f5b92fc3..ef4d67285cd3 100644 --- a/modules/nf-core/clustalo/guidetree/environment.yml +++ b/modules/nf-core/clustalo/guidetree/environment.yml @@ -1,7 +1,5 @@ -name: clustalo_guidetree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::clustalo=1.2.4 diff --git a/modules/nf-core/cmseq/polymut/environment.yml b/modules/nf-core/cmseq/polymut/environment.yml index 01309aa4ca9a..d4417bb1904c 100644 --- a/modules/nf-core/cmseq/polymut/environment.yml +++ b/modules/nf-core/cmseq/polymut/environment.yml @@ -1,7 +1,5 @@ -name: cmseq_polymut channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cmseq=1.0.4 diff --git a/modules/nf-core/cnvkit/access/environment.yml b/modules/nf-core/cnvkit/access/environment.yml index 8c435f16992b..152af54d19dc 100644 --- a/modules/nf-core/cnvkit/access/environment.yml +++ b/modules/nf-core/cnvkit/access/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_access channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/antitarget/environment.yml b/modules/nf-core/cnvkit/antitarget/environment.yml index a33a12e23c38..b683406cc539 100644 --- a/modules/nf-core/cnvkit/antitarget/environment.yml +++ b/modules/nf-core/cnvkit/antitarget/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_antitarget channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.11 diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml index 7c3c88339614..5d793601194c 100644 --- a/modules/nf-core/cnvkit/batch/environment.yml +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -1,9 +1,6 @@ -name: cnvkit_batch - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/call/environment.yml b/modules/nf-core/cnvkit/call/environment.yml index 4aaf29c04f0e..152af54d19dc 100644 --- a/modules/nf-core/cnvkit/call/environment.yml +++ b/modules/nf-core/cnvkit/call/environment.yml @@ -1,4 +1,3 @@ -name: cnvkit_call channels: - conda-forge - bioconda diff --git a/modules/nf-core/cnvkit/export/environment.yml b/modules/nf-core/cnvkit/export/environment.yml index a61b2765f62e..152af54d19dc 100644 --- a/modules/nf-core/cnvkit/export/environment.yml +++ b/modules/nf-core/cnvkit/export/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_export channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/genemetrics/environment.yml b/modules/nf-core/cnvkit/genemetrics/environment.yml index 14deb0ef7396..152af54d19dc 100644 --- a/modules/nf-core/cnvkit/genemetrics/environment.yml +++ b/modules/nf-core/cnvkit/genemetrics/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_genemetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvkit/reference/environment.yml b/modules/nf-core/cnvkit/reference/environment.yml index e3070044d079..b683406cc539 100644 --- a/modules/nf-core/cnvkit/reference/environment.yml +++ b/modules/nf-core/cnvkit/reference/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_reference channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.11 diff --git a/modules/nf-core/cnvkit/target/environment.yml b/modules/nf-core/cnvkit/target/environment.yml index ca4159b5ac73..152af54d19dc 100644 --- a/modules/nf-core/cnvkit/target/environment.yml +++ b/modules/nf-core/cnvkit/target/environment.yml @@ -1,7 +1,5 @@ -name: cnvkit_target channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvkit=0.9.10 diff --git a/modules/nf-core/cnvnator/cnvnator/environment.yml b/modules/nf-core/cnvnator/cnvnator/environment.yml index 8b7ecaef9c3c..9cd8ebf353e1 100644 --- a/modules/nf-core/cnvnator/cnvnator/environment.yml +++ b/modules/nf-core/cnvnator/cnvnator/environment.yml @@ -1,7 +1,5 @@ -name: cnvnator_cnvnator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvnator=0.4.1 diff --git a/modules/nf-core/cnvnator/convert2vcf/environment.yml b/modules/nf-core/cnvnator/convert2vcf/environment.yml index d324fb04541f..9cd8ebf353e1 100644 --- a/modules/nf-core/cnvnator/convert2vcf/environment.yml +++ b/modules/nf-core/cnvnator/convert2vcf/environment.yml @@ -1,7 +1,5 @@ -name: cnvnator_convert2vcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvnator=0.4.1 diff --git a/modules/nf-core/cnvpytor/callcnvs/environment.yml b/modules/nf-core/cnvpytor/callcnvs/environment.yml index 24a5455cc55a..e66cc1fc8e33 100644 --- a/modules/nf-core/cnvpytor/callcnvs/environment.yml +++ b/modules/nf-core/cnvpytor/callcnvs/environment.yml @@ -1,7 +1,5 @@ -name: cnvpytor_callcnvs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvpytor=1.2.1 diff --git a/modules/nf-core/cnvpytor/histogram/environment.yml b/modules/nf-core/cnvpytor/histogram/environment.yml index 21032cdfcf94..e66cc1fc8e33 100644 --- a/modules/nf-core/cnvpytor/histogram/environment.yml +++ b/modules/nf-core/cnvpytor/histogram/environment.yml @@ -1,7 +1,5 @@ -name: cnvpytor_histogram channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvpytor=1.2.1 diff --git a/modules/nf-core/cnvpytor/importreaddepth/environment.yml b/modules/nf-core/cnvpytor/importreaddepth/environment.yml index d17fc3cb044d..cff5d1cd6f07 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/environment.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/environment.yml @@ -1,8 +1,6 @@ -name: cnvpytor_importreaddepth channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvpytor=1.3.1 - conda-forge::numpy=1.24.3 # Locked from container diff --git a/modules/nf-core/cnvpytor/partition/environment.yml b/modules/nf-core/cnvpytor/partition/environment.yml index b43496229290..e66cc1fc8e33 100644 --- a/modules/nf-core/cnvpytor/partition/environment.yml +++ b/modules/nf-core/cnvpytor/partition/environment.yml @@ -1,7 +1,5 @@ -name: cnvpytor_partition channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvpytor=1.2.1 diff --git a/modules/nf-core/cnvpytor/view/environment.yml b/modules/nf-core/cnvpytor/view/environment.yml index 4190901fa860..e66cc1fc8e33 100644 --- a/modules/nf-core/cnvpytor/view/environment.yml +++ b/modules/nf-core/cnvpytor/view/environment.yml @@ -1,7 +1,5 @@ -name: cnvpytor_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cnvpytor=1.2.1 diff --git a/modules/nf-core/cobrameta/environment.yml b/modules/nf-core/cobrameta/environment.yml index ecb9058319de..6e473af8d40d 100644 --- a/modules/nf-core/cobrameta/environment.yml +++ b/modules/nf-core/cobrameta/environment.yml @@ -1,7 +1,5 @@ -name: cobrameta channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::cobra-meta=1.2.3" diff --git a/modules/nf-core/cobs/classicconstruct/environment.yml b/modules/nf-core/cobs/classicconstruct/environment.yml index 187c6b09a18c..d1f296a1c0dc 100644 --- a/modules/nf-core/cobs/classicconstruct/environment.yml +++ b/modules/nf-core/cobs/classicconstruct/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "cobs_classicconstruct" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::cobs=0.3.0" diff --git a/modules/nf-core/cobs/compactconstruct/environment.yml b/modules/nf-core/cobs/compactconstruct/environment.yml index daec31ae5f33..d1f296a1c0dc 100644 --- a/modules/nf-core/cobs/compactconstruct/environment.yml +++ b/modules/nf-core/cobs/compactconstruct/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "cobs_compactconstruct" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::cobs=0.3.0" diff --git a/modules/nf-core/concoct/concoct/environment.yml b/modules/nf-core/concoct/concoct/environment.yml index af1c59f06f9d..7db6566e4763 100644 --- a/modules/nf-core/concoct/concoct/environment.yml +++ b/modules/nf-core/concoct/concoct/environment.yml @@ -1,7 +1,5 @@ -name: concoct_concoct channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::concoct=1.1.0 diff --git a/modules/nf-core/concoct/concoctcoveragetable/environment.yml b/modules/nf-core/concoct/concoctcoveragetable/environment.yml index 4152605fdd42..7db6566e4763 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/environment.yml +++ b/modules/nf-core/concoct/concoctcoveragetable/environment.yml @@ -1,7 +1,5 @@ -name: concoct_concoctcoveragetable channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::concoct=1.1.0 diff --git a/modules/nf-core/concoct/cutupfasta/environment.yml b/modules/nf-core/concoct/cutupfasta/environment.yml index c69271975cf0..7db6566e4763 100644 --- a/modules/nf-core/concoct/cutupfasta/environment.yml +++ b/modules/nf-core/concoct/cutupfasta/environment.yml @@ -1,7 +1,5 @@ -name: concoct_cutupfasta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::concoct=1.1.0 diff --git a/modules/nf-core/concoct/extractfastabins/environment.yml b/modules/nf-core/concoct/extractfastabins/environment.yml index e31d2e860396..7db6566e4763 100644 --- a/modules/nf-core/concoct/extractfastabins/environment.yml +++ b/modules/nf-core/concoct/extractfastabins/environment.yml @@ -1,7 +1,5 @@ -name: concoct_extractfastabins channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::concoct=1.1.0 diff --git a/modules/nf-core/concoct/mergecutupclustering/environment.yml b/modules/nf-core/concoct/mergecutupclustering/environment.yml index 459d65c740b9..7db6566e4763 100644 --- a/modules/nf-core/concoct/mergecutupclustering/environment.yml +++ b/modules/nf-core/concoct/mergecutupclustering/environment.yml @@ -1,7 +1,5 @@ -name: concoct_mergecutupclustering channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::concoct=1.1.0 diff --git a/modules/nf-core/conifer/environment.yml b/modules/nf-core/conifer/environment.yml index ab1703d4ab0c..387668d754f6 100644 --- a/modules/nf-core/conifer/environment.yml +++ b/modules/nf-core/conifer/environment.yml @@ -1,7 +1,5 @@ -name: conifer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::conifer=1.0.2 diff --git a/modules/nf-core/controlfreec/assesssignificance/environment.yml b/modules/nf-core/controlfreec/assesssignificance/environment.yml index 94d4d2275a04..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/assesssignificance/environment.yml +++ b/modules/nf-core/controlfreec/assesssignificance/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_assesssignificance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec/environment.yml b/modules/nf-core/controlfreec/freec/environment.yml index cb76c6ba933c..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/freec/environment.yml +++ b/modules/nf-core/controlfreec/freec/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_freec channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec2bed/environment.yml b/modules/nf-core/controlfreec/freec2bed/environment.yml index 12601ffa5561..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/freec2bed/environment.yml +++ b/modules/nf-core/controlfreec/freec2bed/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_freec2bed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/freec2circos/environment.yml b/modules/nf-core/controlfreec/freec2circos/environment.yml index 1915abfd7f47..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/freec2circos/environment.yml +++ b/modules/nf-core/controlfreec/freec2circos/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_freec2circos channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/makegraph/environment.yml b/modules/nf-core/controlfreec/makegraph/environment.yml index 897eadf3bd4e..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/makegraph/environment.yml +++ b/modules/nf-core/controlfreec/makegraph/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_makegraph channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/controlfreec/makegraph2/environment.yml b/modules/nf-core/controlfreec/makegraph2/environment.yml index 720c2e950eb6..f6b64529bced 100644 --- a/modules/nf-core/controlfreec/makegraph2/environment.yml +++ b/modules/nf-core/controlfreec/makegraph2/environment.yml @@ -1,7 +1,5 @@ -name: controlfreec_makegraph2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::control-freec=11.6b diff --git a/modules/nf-core/cooler/balance/environment.yml b/modules/nf-core/cooler/balance/environment.yml index b39304dee232..f8165ca96f07 100644 --- a/modules/nf-core/cooler/balance/environment.yml +++ b/modules/nf-core/cooler/balance/environment.yml @@ -1,7 +1,5 @@ -name: cooler_balance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/cooler/cload/environment.yml b/modules/nf-core/cooler/cload/environment.yml index 03abee73254d..f8165ca96f07 100644 --- a/modules/nf-core/cooler/cload/environment.yml +++ b/modules/nf-core/cooler/cload/environment.yml @@ -1,7 +1,5 @@ -name: cooler_cload channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/cooler/digest/environment.yml b/modules/nf-core/cooler/digest/environment.yml index 2b374d5ee55c..f8165ca96f07 100644 --- a/modules/nf-core/cooler/digest/environment.yml +++ b/modules/nf-core/cooler/digest/environment.yml @@ -1,7 +1,5 @@ -name: cooler_digest channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/cooler/dump/environment.yml b/modules/nf-core/cooler/dump/environment.yml index ab2ca69e9264..45f3b64be0c4 100644 --- a/modules/nf-core/cooler/dump/environment.yml +++ b/modules/nf-core/cooler/dump/environment.yml @@ -1,7 +1,5 @@ -name: cooler_dump channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.10.2 diff --git a/modules/nf-core/cooler/makebins/environment.yml b/modules/nf-core/cooler/makebins/environment.yml index e48b3a17519e..f8165ca96f07 100644 --- a/modules/nf-core/cooler/makebins/environment.yml +++ b/modules/nf-core/cooler/makebins/environment.yml @@ -1,7 +1,5 @@ -name: cooler_makebins channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/cooler/merge/environment.yml b/modules/nf-core/cooler/merge/environment.yml index 1b3ea8da82a6..f8165ca96f07 100644 --- a/modules/nf-core/cooler/merge/environment.yml +++ b/modules/nf-core/cooler/merge/environment.yml @@ -1,7 +1,5 @@ -name: cooler_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/cooler/zoomify/environment.yml b/modules/nf-core/cooler/zoomify/environment.yml index 2288f3762626..f8165ca96f07 100644 --- a/modules/nf-core/cooler/zoomify/environment.yml +++ b/modules/nf-core/cooler/zoomify/environment.yml @@ -1,7 +1,5 @@ -name: cooler_zoomify channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cooler=0.9.2 diff --git a/modules/nf-core/coreograph/environment.yml b/modules/nf-core/coreograph/environment.yml index 0ee4a964b040..3cebeff05bfc 100644 --- a/modules/nf-core/coreograph/environment.yml +++ b/modules/nf-core/coreograph/environment.yml @@ -1,5 +1,3 @@ -name: coreograph channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/crabz/compress/environment.yml b/modules/nf-core/crabz/compress/environment.yml index 65ce81e02da5..bce375204f01 100644 --- a/modules/nf-core/crabz/compress/environment.yml +++ b/modules/nf-core/crabz/compress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "crabz_compress" channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::crabz=0.9.0 diff --git a/modules/nf-core/crabz/decompress/environment.yml b/modules/nf-core/crabz/decompress/environment.yml index 158559c9db55..bce375204f01 100644 --- a/modules/nf-core/crabz/decompress/environment.yml +++ b/modules/nf-core/crabz/decompress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "crabz_decompress" channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::crabz=0.9.0 diff --git a/modules/nf-core/crisprcleanr/normalize/environment.yml b/modules/nf-core/crisprcleanr/normalize/environment.yml index b183c62dcae0..7bd199600335 100644 --- a/modules/nf-core/crisprcleanr/normalize/environment.yml +++ b/modules/nf-core/crisprcleanr/normalize/environment.yml @@ -1,7 +1,5 @@ -name: crisprcleanr_normalize channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-crisprcleanr=3.0.0 diff --git a/modules/nf-core/crumble/environment.yml b/modules/nf-core/crumble/environment.yml index de739022aecf..80d35678bfa8 100644 --- a/modules/nf-core/crumble/environment.yml +++ b/modules/nf-core/crumble/environment.yml @@ -1,7 +1,5 @@ -name: crumble channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::crumble=0.9.1 diff --git a/modules/nf-core/csvtk/concat/environment.yml b/modules/nf-core/csvtk/concat/environment.yml index ac58390c39b0..5b97e54e7b37 100644 --- a/modules/nf-core/csvtk/concat/environment.yml +++ b/modules/nf-core/csvtk/concat/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "csvtk_concat" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::csvtk=0.30.0" diff --git a/modules/nf-core/csvtk/join/environment.yml b/modules/nf-core/csvtk/join/environment.yml index 5b6c6468f4a4..ea951bdb74c4 100644 --- a/modules/nf-core/csvtk/join/environment.yml +++ b/modules/nf-core/csvtk/join/environment.yml @@ -1,7 +1,5 @@ -name: csvtk_join channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::csvtk=0.30.0 diff --git a/modules/nf-core/csvtk/split/environment.yml b/modules/nf-core/csvtk/split/environment.yml index ec08bb439082..ea951bdb74c4 100644 --- a/modules/nf-core/csvtk/split/environment.yml +++ b/modules/nf-core/csvtk/split/environment.yml @@ -1,7 +1,5 @@ -name: csvtk_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::csvtk=0.30.0 diff --git a/modules/nf-core/custom/catadditionalfasta/environment.yml b/modules/nf-core/custom/catadditionalfasta/environment.yml index e587338b5ecf..1d80d11a940e 100644 --- a/modules/nf-core/custom/catadditionalfasta/environment.yml +++ b/modules/nf-core/custom/catadditionalfasta/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "custom_catadditionalfasta" channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::python=3.9.5 diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml index b48ced2690f7..9d79af939281 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,7 +1,5 @@ -name: custom_dumpsoftwareversions channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.20 diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index 2ecd0128fc61..da2df5e43a40 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,8 +1,6 @@ -name: custom_getchromsizes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/custom/gtffilter/environment.yml b/modules/nf-core/custom/gtffilter/environment.yml index 115f41235962..800eff9bce16 100644 --- a/modules/nf-core/custom/gtffilter/environment.yml +++ b/modules/nf-core/custom/gtffilter/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "custom_gtffilter" channels: - conda-forge - bioconda - - defaults dependencies: - "conda-forge::python=3.9.5" diff --git a/modules/nf-core/custom/matrixfilter/environment.yml b/modules/nf-core/custom/matrixfilter/environment.yml index 322c673ea2a4..fb4ebfaa36e6 100644 --- a/modules/nf-core/custom/matrixfilter/environment.yml +++ b/modules/nf-core/custom/matrixfilter/environment.yml @@ -1,7 +1,5 @@ -name: custom_matrixfilter channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-base=4.2.1 diff --git a/modules/nf-core/custom/sratoolsncbisettings/environment.yml b/modules/nf-core/custom/sratoolsncbisettings/environment.yml index 44a1b008e2ec..cd4c3fbe0111 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/environment.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/environment.yml @@ -1,7 +1,5 @@ -name: custom_sratoolsncbisettings channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sra-tools=3.0.8 diff --git a/modules/nf-core/custom/tabulartogseacls/environment.yml b/modules/nf-core/custom/tabulartogseacls/environment.yml index 89ed4246ef02..c7eb9bd1c3ca 100644 --- a/modules/nf-core/custom/tabulartogseacls/environment.yml +++ b/modules/nf-core/custom/tabulartogseacls/environment.yml @@ -1,7 +1,5 @@ -name: custom_tabulartogseacls channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/tabulartogseagct/environment.yml b/modules/nf-core/custom/tabulartogseagct/environment.yml index bb55b68a08e5..c7eb9bd1c3ca 100644 --- a/modules/nf-core/custom/tabulartogseagct/environment.yml +++ b/modules/nf-core/custom/tabulartogseagct/environment.yml @@ -1,7 +1,5 @@ -name: custom_tabulartogseagct channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index a859dc881fef..9f5f9fb9b470 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "custom_tx2gene" channels: - conda-forge - bioconda - - defaults dependencies: - python=3.9.5 diff --git a/modules/nf-core/cutadapt/environment.yml b/modules/nf-core/cutadapt/environment.yml index 288ea6f06189..dfdbd1c2a8e0 100644 --- a/modules/nf-core/cutadapt/environment.yml +++ b/modules/nf-core/cutadapt/environment.yml @@ -1,7 +1,5 @@ -name: cutadapt channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cutadapt=4.6 diff --git a/modules/nf-core/cutesv/environment.yml b/modules/nf-core/cutesv/environment.yml index e757dfc275f0..4d17f4eda5f3 100644 --- a/modules/nf-core/cutesv/environment.yml +++ b/modules/nf-core/cutesv/environment.yml @@ -1,7 +1,5 @@ -name: cutesv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cutesv=2.0.2 diff --git a/modules/nf-core/damageprofiler/environment.yml b/modules/nf-core/damageprofiler/environment.yml index e91d4077c29f..83cbf0934140 100644 --- a/modules/nf-core/damageprofiler/environment.yml +++ b/modules/nf-core/damageprofiler/environment.yml @@ -1,7 +1,5 @@ -name: damageprofiler channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::damageprofiler=1.1 diff --git a/modules/nf-core/dastool/dastool/environment.yml b/modules/nf-core/dastool/dastool/environment.yml index 8c40a88b6f9a..0ede57bfb27e 100644 --- a/modules/nf-core/dastool/dastool/environment.yml +++ b/modules/nf-core/dastool/dastool/environment.yml @@ -1,7 +1,5 @@ -name: dastool_dastool channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::das_tool=1.1.6 diff --git a/modules/nf-core/dastool/fastatocontig2bin/environment.yml b/modules/nf-core/dastool/fastatocontig2bin/environment.yml index 1085cd27cffe..0ede57bfb27e 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/environment.yml +++ b/modules/nf-core/dastool/fastatocontig2bin/environment.yml @@ -1,7 +1,5 @@ -name: dastool_fastatocontig2bin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::das_tool=1.1.6 diff --git a/modules/nf-core/dastool/scaffolds2bin/environment.yml b/modules/nf-core/dastool/scaffolds2bin/environment.yml index 27ca5da19fbd..507ee795b47c 100644 --- a/modules/nf-core/dastool/scaffolds2bin/environment.yml +++ b/modules/nf-core/dastool/scaffolds2bin/environment.yml @@ -1,7 +1,5 @@ -name: dastool_scaffolds2bin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::das_tool=1.1.3 diff --git a/modules/nf-core/datavzrd/environment.yml b/modules/nf-core/datavzrd/environment.yml index 879e964efaf4..06593466ffab 100644 --- a/modules/nf-core/datavzrd/environment.yml +++ b/modules/nf-core/datavzrd/environment.yml @@ -1,7 +1,5 @@ -name: datavzrd channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::datavzrd==2.36.12 diff --git a/modules/nf-core/dedup/environment.yml b/modules/nf-core/dedup/environment.yml index e3e3866143d1..66c1b235d3fc 100644 --- a/modules/nf-core/dedup/environment.yml +++ b/modules/nf-core/dedup/environment.yml @@ -1,7 +1,5 @@ -name: dedup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dedup=0.12.8 diff --git a/modules/nf-core/deeparg/downloaddata/environment.yml b/modules/nf-core/deeparg/downloaddata/environment.yml index 87435be5b098..074c6501fcb0 100644 --- a/modules/nf-core/deeparg/downloaddata/environment.yml +++ b/modules/nf-core/deeparg/downloaddata/environment.yml @@ -1,7 +1,5 @@ -name: deeparg_downloaddata channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::deeparg=1.0.4 diff --git a/modules/nf-core/deeparg/predict/environment.yml b/modules/nf-core/deeparg/predict/environment.yml index aa6867011c92..074c6501fcb0 100644 --- a/modules/nf-core/deeparg/predict/environment.yml +++ b/modules/nf-core/deeparg/predict/environment.yml @@ -1,7 +1,5 @@ -name: deeparg_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::deeparg=1.0.4 diff --git a/modules/nf-core/deepbgc/download/environment.yml b/modules/nf-core/deepbgc/download/environment.yml index 84d467f07c18..36cb903fa63f 100644 --- a/modules/nf-core/deepbgc/download/environment.yml +++ b/modules/nf-core/deepbgc/download/environment.yml @@ -1,7 +1,5 @@ -name: deepbgc_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::deepbgc=0.1.31 diff --git a/modules/nf-core/deepbgc/pipeline/environment.yml b/modules/nf-core/deepbgc/pipeline/environment.yml index fe0087a24863..36cb903fa63f 100644 --- a/modules/nf-core/deepbgc/pipeline/environment.yml +++ b/modules/nf-core/deepbgc/pipeline/environment.yml @@ -1,7 +1,5 @@ -name: deepbgc_pipeline channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::deepbgc=0.1.31 diff --git a/modules/nf-core/deeptmhmm/environment.yml b/modules/nf-core/deeptmhmm/environment.yml index 84311c8e2818..b4bc7415a682 100644 --- a/modules/nf-core/deeptmhmm/environment.yml +++ b/modules/nf-core/deeptmhmm/environment.yml @@ -1,7 +1,5 @@ -name: deeptmhmm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pybiolib=1.1.1393 diff --git a/modules/nf-core/deeptools/bamcoverage/environment.yml b/modules/nf-core/deeptools/bamcoverage/environment.yml index 95c58dd442e3..d8e208ca8302 100644 --- a/modules/nf-core/deeptools/bamcoverage/environment.yml +++ b/modules/nf-core/deeptools/bamcoverage/environment.yml @@ -1,8 +1,6 @@ -name: deeptools_bamcoverage channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::deeptools=3.5.5 - bioconda::samtools=1.20 diff --git a/modules/nf-core/deeptools/computematrix/environment.yml b/modules/nf-core/deeptools/computematrix/environment.yml index 279d1eac62c3..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/computematrix/environment.yml +++ b/modules/nf-core/deeptools/computematrix/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_computematrix channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/multibamsummary/environment.yml b/modules/nf-core/deeptools/multibamsummary/environment.yml index efc674230997..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/multibamsummary/environment.yml +++ b/modules/nf-core/deeptools/multibamsummary/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_multibamsummary channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/plotcorrelation/environment.yml b/modules/nf-core/deeptools/plotcorrelation/environment.yml index 2feb3ff47416..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/plotcorrelation/environment.yml +++ b/modules/nf-core/deeptools/plotcorrelation/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_plotcorrelation channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/plotfingerprint/environment.yml b/modules/nf-core/deeptools/plotfingerprint/environment.yml index b867b9a542e1..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/plotfingerprint/environment.yml +++ b/modules/nf-core/deeptools/plotfingerprint/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_plotfingerprint channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/plotheatmap/environment.yml b/modules/nf-core/deeptools/plotheatmap/environment.yml index 3e0f55990481..72135bc4c75a 100644 --- a/modules/nf-core/deeptools/plotheatmap/environment.yml +++ b/modules/nf-core/deeptools/plotheatmap/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "deeptools_plotheatmap" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/plotpca/environment.yml b/modules/nf-core/deeptools/plotpca/environment.yml index 076a7ce8d282..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/plotpca/environment.yml +++ b/modules/nf-core/deeptools/plotpca/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_plotpca channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/deeptools/plotprofile/environment.yml b/modules/nf-core/deeptools/plotprofile/environment.yml index 44784d3a1183..8880b9b6d2ef 100644 --- a/modules/nf-core/deeptools/plotprofile/environment.yml +++ b/modules/nf-core/deeptools/plotprofile/environment.yml @@ -1,7 +1,5 @@ -name: deeptools_plotprofile channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::deeptools=3.5.5" diff --git a/modules/nf-core/delly/call/environment.yml b/modules/nf-core/delly/call/environment.yml index 39da899525f5..5598247e1aee 100644 --- a/modules/nf-core/delly/call/environment.yml +++ b/modules/nf-core/delly/call/environment.yml @@ -1,7 +1,5 @@ -name: delly_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::delly=1.2.6 diff --git a/modules/nf-core/demuxem/environment.yml b/modules/nf-core/demuxem/environment.yml index 1b56f172a7bd..c74f84be28b5 100644 --- a/modules/nf-core/demuxem/environment.yml +++ b/modules/nf-core/demuxem/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "demuxem" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::demuxem=0.1.7.post1" diff --git a/modules/nf-core/deseq2/differential/environment.yml b/modules/nf-core/deseq2/differential/environment.yml index 0ab1d0b6d95a..4f0b1d103a30 100644 --- a/modules/nf-core/deseq2/differential/environment.yml +++ b/modules/nf-core/deseq2/differential/environment.yml @@ -1,7 +1,5 @@ -name: deseq2_differential channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-deseq2=1.34.0 diff --git a/modules/nf-core/diamond/blastp/environment.yml b/modules/nf-core/diamond/blastp/environment.yml index 922ea7ed1783..950c3c5c55ea 100644 --- a/modules/nf-core/diamond/blastp/environment.yml +++ b/modules/nf-core/diamond/blastp/environment.yml @@ -1,7 +1,5 @@ -name: diamond_blastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::diamond=2.1.8 diff --git a/modules/nf-core/diamond/blastx/environment.yml b/modules/nf-core/diamond/blastx/environment.yml index 70d6857d1dd5..950c3c5c55ea 100644 --- a/modules/nf-core/diamond/blastx/environment.yml +++ b/modules/nf-core/diamond/blastx/environment.yml @@ -1,7 +1,5 @@ -name: diamond_blastx channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::diamond=2.1.8 diff --git a/modules/nf-core/diamond/cluster/environment.yml b/modules/nf-core/diamond/cluster/environment.yml index 88e9a2bbbadb..216da62694cc 100644 --- a/modules/nf-core/diamond/cluster/environment.yml +++ b/modules/nf-core/diamond/cluster/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "diamond_cluster" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::diamond=2.1.9" diff --git a/modules/nf-core/diamond/makedb/environment.yml b/modules/nf-core/diamond/makedb/environment.yml index 0196bd65bced..950c3c5c55ea 100644 --- a/modules/nf-core/diamond/makedb/environment.yml +++ b/modules/nf-core/diamond/makedb/environment.yml @@ -1,7 +1,5 @@ -name: diamond_makedb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::diamond=2.1.8 diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml index ccccf9c95f06..2f1191b2ec6c 100644 --- a/modules/nf-core/dragmap/align/environment.yml +++ b/modules/nf-core/dragmap/align/environment.yml @@ -1,8 +1,6 @@ -name: dragmap_align channels: - conda-forge - bioconda - - defaults dependencies: - dragmap=1.3.0 # renovate: datasource=conda depName=bioconda/samtools diff --git a/modules/nf-core/dragmap/hashtable/environment.yml b/modules/nf-core/dragmap/hashtable/environment.yml index 254a74260737..06e608fde72c 100644 --- a/modules/nf-core/dragmap/hashtable/environment.yml +++ b/modules/nf-core/dragmap/hashtable/environment.yml @@ -1,7 +1,5 @@ -name: dragmap_hashtable channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dragmap=1.3.0 diff --git a/modules/nf-core/dragonflye/environment.yml b/modules/nf-core/dragonflye/environment.yml index 21a905178174..6111fba13b72 100644 --- a/modules/nf-core/dragonflye/environment.yml +++ b/modules/nf-core/dragonflye/environment.yml @@ -1,7 +1,5 @@ -name: dragonflye channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dragonflye=1.1.2 diff --git a/modules/nf-core/dshbio/exportsegments/environment.yml b/modules/nf-core/dshbio/exportsegments/environment.yml index 3a2680e664d4..cd022f8776b5 100644 --- a/modules/nf-core/dshbio/exportsegments/environment.yml +++ b/modules/nf-core/dshbio/exportsegments/environment.yml @@ -1,7 +1,5 @@ -name: dshbio_exportsegments channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dsh-bio=2.4 diff --git a/modules/nf-core/dshbio/filterbed/environment.yml b/modules/nf-core/dshbio/filterbed/environment.yml index d4e4014ae2b7..cd022f8776b5 100644 --- a/modules/nf-core/dshbio/filterbed/environment.yml +++ b/modules/nf-core/dshbio/filterbed/environment.yml @@ -1,7 +1,5 @@ -name: dshbio_filterbed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dsh-bio=2.4 diff --git a/modules/nf-core/dshbio/filtergff3/environment.yml b/modules/nf-core/dshbio/filtergff3/environment.yml index 7076b7fd0837..cd022f8776b5 100644 --- a/modules/nf-core/dshbio/filtergff3/environment.yml +++ b/modules/nf-core/dshbio/filtergff3/environment.yml @@ -1,7 +1,5 @@ -name: dshbio_filtergff3 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dsh-bio=2.4 diff --git a/modules/nf-core/dshbio/splitbed/environment.yml b/modules/nf-core/dshbio/splitbed/environment.yml index 8ee99e21f904..cd022f8776b5 100644 --- a/modules/nf-core/dshbio/splitbed/environment.yml +++ b/modules/nf-core/dshbio/splitbed/environment.yml @@ -1,7 +1,5 @@ -name: dshbio_splitbed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dsh-bio=2.4 diff --git a/modules/nf-core/dshbio/splitgff3/environment.yml b/modules/nf-core/dshbio/splitgff3/environment.yml index 4781c4998fde..cd022f8776b5 100644 --- a/modules/nf-core/dshbio/splitgff3/environment.yml +++ b/modules/nf-core/dshbio/splitgff3/environment.yml @@ -1,7 +1,5 @@ -name: dshbio_splitgff3 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::dsh-bio=2.4 diff --git a/modules/nf-core/duphold/environment.yml b/modules/nf-core/duphold/environment.yml index cf3fe32ba5f7..d607f1f48ef6 100644 --- a/modules/nf-core/duphold/environment.yml +++ b/modules/nf-core/duphold/environment.yml @@ -1,7 +1,5 @@ -name: duphold channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::duphold=0.2.1 diff --git a/modules/nf-core/dupradar/environment.yml b/modules/nf-core/dupradar/environment.yml index 58b2bf11dccb..fb16938d2029 100644 --- a/modules/nf-core/dupradar/environment.yml +++ b/modules/nf-core/dupradar/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "dupradar" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-dupradar=1.32.0" diff --git a/modules/nf-core/dysgu/environment.yml b/modules/nf-core/dysgu/environment.yml index 5efb6db61ade..f3b35f5ac4f8 100644 --- a/modules/nf-core/dysgu/environment.yml +++ b/modules/nf-core/dysgu/environment.yml @@ -1,7 +1,5 @@ -name: dysgu channels: - conda-forge - bioconda - - defaults dependencies: - dysgu diff --git a/modules/nf-core/ectyper/environment.yml b/modules/nf-core/ectyper/environment.yml index 1fb6b720756b..7e7f57a874d1 100644 --- a/modules/nf-core/ectyper/environment.yml +++ b/modules/nf-core/ectyper/environment.yml @@ -1,7 +1,5 @@ -name: ectyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ectyper=1.0.0 diff --git a/modules/nf-core/eggnogmapper/environment.yml b/modules/nf-core/eggnogmapper/environment.yml index f4fb6fdc0fbe..2092ea512bae 100644 --- a/modules/nf-core/eggnogmapper/environment.yml +++ b/modules/nf-core/eggnogmapper/environment.yml @@ -1,7 +1,5 @@ -name: eggnogmapper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::eggnog-mapper=2.1.12 diff --git a/modules/nf-core/eido/convert/environment.yml b/modules/nf-core/eido/convert/environment.yml index 2ffb6f2fd325..de4dc4859119 100644 --- a/modules/nf-core/eido/convert/environment.yml +++ b/modules/nf-core/eido/convert/environment.yml @@ -1,4 +1,3 @@ -name: eido_convert channels: - conda-forge - bioconda diff --git a/modules/nf-core/eido/validate/environment.yml b/modules/nf-core/eido/validate/environment.yml index b529a66f4cb6..1bbd80bb62f9 100644 --- a/modules/nf-core/eido/validate/environment.yml +++ b/modules/nf-core/eido/validate/environment.yml @@ -1,7 +1,5 @@ -name: eido_validate channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::eido=0.1.9 diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml index 9ac9ee9fe55c..405868379483 100644 --- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml +++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/environment.yml @@ -1,7 +1,5 @@ -name: eigenstratdatabasetools_eigenstratsnpcoverage channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::eigenstratdatabasetools=1.1.0 diff --git a/modules/nf-core/eklipse/environment.yml b/modules/nf-core/eklipse/environment.yml index e33007095e3e..b638fba1d1d6 100644 --- a/modules/nf-core/eklipse/environment.yml +++ b/modules/nf-core/eklipse/environment.yml @@ -1,7 +1,5 @@ -name: eklipse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::eklipse=1.8 diff --git a/modules/nf-core/elprep/filter/environment.yml b/modules/nf-core/elprep/filter/environment.yml index 88fc47856573..841e7cdb7bb0 100644 --- a/modules/nf-core/elprep/filter/environment.yml +++ b/modules/nf-core/elprep/filter/environment.yml @@ -1,7 +1,5 @@ -name: elprep_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::elprep=5.1.2 diff --git a/modules/nf-core/elprep/merge/environment.yml b/modules/nf-core/elprep/merge/environment.yml index 4bfbdb6bc8b0..841e7cdb7bb0 100644 --- a/modules/nf-core/elprep/merge/environment.yml +++ b/modules/nf-core/elprep/merge/environment.yml @@ -1,7 +1,5 @@ -name: elprep_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::elprep=5.1.2 diff --git a/modules/nf-core/elprep/split/environment.yml b/modules/nf-core/elprep/split/environment.yml index 0cf29bcde1f2..38dd4f4724b4 100644 --- a/modules/nf-core/elprep/split/environment.yml +++ b/modules/nf-core/elprep/split/environment.yml @@ -1,7 +1,5 @@ -name: elprep_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::elprep=5.1.3 diff --git a/modules/nf-core/emboss/cons/environment.yml b/modules/nf-core/emboss/cons/environment.yml index 84758784eac8..6c075a72d925 100644 --- a/modules/nf-core/emboss/cons/environment.yml +++ b/modules/nf-core/emboss/cons/environment.yml @@ -1,7 +1,5 @@ -name: emboss_cons channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::emboss=6.6.0 diff --git a/modules/nf-core/emboss/revseq/environment.yml b/modules/nf-core/emboss/revseq/environment.yml index 5e2d20e5b7cf..6c075a72d925 100644 --- a/modules/nf-core/emboss/revseq/environment.yml +++ b/modules/nf-core/emboss/revseq/environment.yml @@ -1,4 +1,3 @@ -name: emboss_revseq channels: - conda-forge - bioconda diff --git a/modules/nf-core/emboss/seqret/environment.yml b/modules/nf-core/emboss/seqret/environment.yml index 5390009c4a10..6c075a72d925 100644 --- a/modules/nf-core/emboss/seqret/environment.yml +++ b/modules/nf-core/emboss/seqret/environment.yml @@ -1,7 +1,5 @@ -name: emboss_seqret channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::emboss=6.6.0 diff --git a/modules/nf-core/emmtyper/environment.yml b/modules/nf-core/emmtyper/environment.yml index e82e5086907c..93aed9cf50ff 100644 --- a/modules/nf-core/emmtyper/environment.yml +++ b/modules/nf-core/emmtyper/environment.yml @@ -1,7 +1,5 @@ -name: emmtyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::emmtyper=0.2.0 diff --git a/modules/nf-core/endorspy/environment.yml b/modules/nf-core/endorspy/environment.yml index ce790813a4ee..fea7004305fb 100644 --- a/modules/nf-core/endorspy/environment.yml +++ b/modules/nf-core/endorspy/environment.yml @@ -1,7 +1,5 @@ -name: endorspy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::endorspy=1.3 diff --git a/modules/nf-core/ensemblvep/download/environment.yml b/modules/nf-core/ensemblvep/download/environment.yml index 91564ccec7e9..283a45bbdf1f 100644 --- a/modules/nf-core/ensemblvep/download/environment.yml +++ b/modules/nf-core/ensemblvep/download/environment.yml @@ -1,7 +1,5 @@ -name: ensemblvep_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/environment.yml b/modules/nf-core/ensemblvep/environment.yml index fd8a592a6133..e94bfeb2cb08 100644 --- a/modules/nf-core/ensemblvep/environment.yml +++ b/modules/nf-core/ensemblvep/environment.yml @@ -1,9 +1,7 @@ # You can use this file to create a conda environment for this module: # conda env create -f environment.yml -name: nf-core-vep-111.0 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=111.0 diff --git a/modules/nf-core/ensemblvep/filtervep/environment.yml b/modules/nf-core/ensemblvep/filtervep/environment.yml index 68e0e3fe3f62..283a45bbdf1f 100644 --- a/modules/nf-core/ensemblvep/filtervep/environment.yml +++ b/modules/nf-core/ensemblvep/filtervep/environment.yml @@ -1,7 +1,5 @@ -name: ensemblvep_filtervep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 3eae4fb1573b..283a45bbdf1f 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,7 +1,5 @@ -name: ensemblvep_vep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ensembl-vep=112.0 diff --git a/modules/nf-core/entrezdirect/esearch/environment.yml b/modules/nf-core/entrezdirect/esearch/environment.yml index 3b0472c3d202..4aee27d35c8f 100644 --- a/modules/nf-core/entrezdirect/esearch/environment.yml +++ b/modules/nf-core/entrezdirect/esearch/environment.yml @@ -1,7 +1,5 @@ -name: entrezdirect_esearch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::entrez-direct=16.2 diff --git a/modules/nf-core/entrezdirect/esummary/environment.yml b/modules/nf-core/entrezdirect/esummary/environment.yml index 022046e3e438..4aee27d35c8f 100644 --- a/modules/nf-core/entrezdirect/esummary/environment.yml +++ b/modules/nf-core/entrezdirect/esummary/environment.yml @@ -1,7 +1,5 @@ -name: entrezdirect_esummary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::entrez-direct=16.2 diff --git a/modules/nf-core/entrezdirect/xtract/environment.yml b/modules/nf-core/entrezdirect/xtract/environment.yml index ec0abcbde259..4aee27d35c8f 100644 --- a/modules/nf-core/entrezdirect/xtract/environment.yml +++ b/modules/nf-core/entrezdirect/xtract/environment.yml @@ -1,7 +1,5 @@ -name: entrezdirect_xtract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::entrez-direct=16.2 diff --git a/modules/nf-core/epang/place/environment.yml b/modules/nf-core/epang/place/environment.yml index a8536b1d486e..6faa55f390e2 100644 --- a/modules/nf-core/epang/place/environment.yml +++ b/modules/nf-core/epang/place/environment.yml @@ -1,7 +1,5 @@ -name: epang_place channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::epa-ng=0.3.8 diff --git a/modules/nf-core/epang/split/environment.yml b/modules/nf-core/epang/split/environment.yml index 5dd7ff7711ae..6faa55f390e2 100644 --- a/modules/nf-core/epang/split/environment.yml +++ b/modules/nf-core/epang/split/environment.yml @@ -1,7 +1,5 @@ -name: epang_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::epa-ng=0.3.8 diff --git a/modules/nf-core/estsfs/environment.yml b/modules/nf-core/estsfs/environment.yml index 7273114ef597..73ad79cc3af2 100644 --- a/modules/nf-core/estsfs/environment.yml +++ b/modules/nf-core/estsfs/environment.yml @@ -1,6 +1,5 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "estsfs" channels: - conda-forge - bioconda diff --git a/modules/nf-core/evigene/tr2aacds/environment.yml b/modules/nf-core/evigene/tr2aacds/environment.yml index e49c50b03d25..ee044641397a 100644 --- a/modules/nf-core/evigene/tr2aacds/environment.yml +++ b/modules/nf-core/evigene/tr2aacds/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "evigene_tr2aacds" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::evigene=23.7.15" diff --git a/modules/nf-core/expansionhunter/environment.yml b/modules/nf-core/expansionhunter/environment.yml index 90a3bfff220b..07db4374d40e 100644 --- a/modules/nf-core/expansionhunter/environment.yml +++ b/modules/nf-core/expansionhunter/environment.yml @@ -1,9 +1,6 @@ -name: expansionhunter - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::expansionhunter=5.0.0 diff --git a/modules/nf-core/expansionhunterdenovo/merge/environment.yml b/modules/nf-core/expansionhunterdenovo/merge/environment.yml index 3409da298435..da1383d53490 100644 --- a/modules/nf-core/expansionhunterdenovo/merge/environment.yml +++ b/modules/nf-core/expansionhunterdenovo/merge/environment.yml @@ -1,7 +1,5 @@ -name: expansionhunterdenovo_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::expansionhunterdenovo=0.9.0 diff --git a/modules/nf-core/expansionhunterdenovo/profile/environment.yml b/modules/nf-core/expansionhunterdenovo/profile/environment.yml index fe58596b8a76..da1383d53490 100644 --- a/modules/nf-core/expansionhunterdenovo/profile/environment.yml +++ b/modules/nf-core/expansionhunterdenovo/profile/environment.yml @@ -1,7 +1,5 @@ -name: expansionhunterdenovo_profile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::expansionhunterdenovo=0.9.0 diff --git a/modules/nf-core/falco/environment.yml b/modules/nf-core/falco/environment.yml index eeedb5b734d3..c48809ccc672 100644 --- a/modules/nf-core/falco/environment.yml +++ b/modules/nf-core/falco/environment.yml @@ -1,7 +1,5 @@ -name: falco channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::falco=1.2.1 diff --git a/modules/nf-core/famsa/align/environment.yml b/modules/nf-core/famsa/align/environment.yml index c41cda2af074..08b6f88908ab 100644 --- a/modules/nf-core/famsa/align/environment.yml +++ b/modules/nf-core/famsa/align/environment.yml @@ -1,7 +1,5 @@ -name: famsa_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::famsa=2.2.2 diff --git a/modules/nf-core/famsa/guidetree/environment.yml b/modules/nf-core/famsa/guidetree/environment.yml index 28be1c7f7fc6..08b6f88908ab 100644 --- a/modules/nf-core/famsa/guidetree/environment.yml +++ b/modules/nf-core/famsa/guidetree/environment.yml @@ -1,7 +1,5 @@ -name: famsa_guidetree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::famsa=2.2.2 diff --git a/modules/nf-core/faqcs/environment.yml b/modules/nf-core/faqcs/environment.yml index fa58ef19c6f3..d019c4f8bfb2 100644 --- a/modules/nf-core/faqcs/environment.yml +++ b/modules/nf-core/faqcs/environment.yml @@ -1,7 +1,5 @@ -name: faqcs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::faqcs=2.10 diff --git a/modules/nf-core/fargene/environment.yml b/modules/nf-core/fargene/environment.yml index 56629ff4051b..ade4d77097e9 100644 --- a/modules/nf-core/fargene/environment.yml +++ b/modules/nf-core/fargene/environment.yml @@ -1,7 +1,5 @@ -name: fargene channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fargene=0.1 diff --git a/modules/nf-core/fastani/environment.yml b/modules/nf-core/fastani/environment.yml index 2d8c92e88596..bcfc7b4a1be2 100644 --- a/modules/nf-core/fastani/environment.yml +++ b/modules/nf-core/fastani/environment.yml @@ -1,7 +1,5 @@ -name: fastani channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastani=1.32 diff --git a/modules/nf-core/fastavalidator/environment.yml b/modules/nf-core/fastavalidator/environment.yml index 70f346efe3d7..44d55c1faf98 100644 --- a/modules/nf-core/fastavalidator/environment.yml +++ b/modules/nf-core/fastavalidator/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fastavalidator" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::py_fasta_validator=0.6" diff --git a/modules/nf-core/fastawindows/environment.yml b/modules/nf-core/fastawindows/environment.yml index ce557158c7a2..6775fb2e6ffb 100644 --- a/modules/nf-core/fastawindows/environment.yml +++ b/modules/nf-core/fastawindows/environment.yml @@ -1,7 +1,5 @@ -name: fastawindows channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fasta_windows=0.2.4 diff --git a/modules/nf-core/fastk/fastk/environment.yml b/modules/nf-core/fastk/fastk/environment.yml index efb503e14547..14207ff69aef 100644 --- a/modules/nf-core/fastk/fastk/environment.yml +++ b/modules/nf-core/fastk/fastk/environment.yml @@ -1,7 +1,5 @@ -name: fastk_fastk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::false_flag # False flag to pass nf-core/lint diff --git a/modules/nf-core/fastk/histex/environment.yml b/modules/nf-core/fastk/histex/environment.yml index aefa45f4bdda..3cebeff05bfc 100644 --- a/modules/nf-core/fastk/histex/environment.yml +++ b/modules/nf-core/fastk/histex/environment.yml @@ -1,5 +1,3 @@ -name: fastk_histex channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/fastk/merge/environment.yml b/modules/nf-core/fastk/merge/environment.yml index 7c09dc1a588b..3cebeff05bfc 100644 --- a/modules/nf-core/fastk/merge/environment.yml +++ b/modules/nf-core/fastk/merge/environment.yml @@ -1,5 +1,3 @@ -name: fastk_merge channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/fastme/environment.yml b/modules/nf-core/fastme/environment.yml index 5dd00e12d07e..4a69cb341f9e 100644 --- a/modules/nf-core/fastme/environment.yml +++ b/modules/nf-core/fastme/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fastme" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::fastme=2.1.6.1" diff --git a/modules/nf-core/fastp/environment.yml b/modules/nf-core/fastp/environment.yml index 70389e664c2a..26d4aca5ddd2 100644 --- a/modules/nf-core/fastp/environment.yml +++ b/modules/nf-core/fastp/environment.yml @@ -1,7 +1,5 @@ -name: fastp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastp=0.23.4 diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/fastqc/environment.yml index 1787b38a9aa1..691d4c7638f2 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/fastqc/environment.yml @@ -1,7 +1,5 @@ -name: fastqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastqc=0.12.1 diff --git a/modules/nf-core/fastqscan/environment.yml b/modules/nf-core/fastqscan/environment.yml index 482a73bef8ba..a041ef99ec8c 100644 --- a/modules/nf-core/fastqscan/environment.yml +++ b/modules/nf-core/fastqscan/environment.yml @@ -1,7 +1,5 @@ -name: fastqscan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fastq-scan=0.4.4 diff --git a/modules/nf-core/fastqscreen/buildfromindex/environment.yml b/modules/nf-core/fastqscreen/buildfromindex/environment.yml index 5ffa9787c725..85764e0d22b9 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/environment.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fastqscreen_buildfromindex" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::fastq-screen=0.15.3" diff --git a/modules/nf-core/fastqscreen/fastqscreen/environment.yml b/modules/nf-core/fastqscreen/fastqscreen/environment.yml index 7f8f19cf36ca..c63c61e206a3 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/environment.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fastqscreen_fastqscreen" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::fastq-screen=0.15.3" - bioconda::perl-gdgraph=1.54 diff --git a/modules/nf-core/fasttree/environment.yml b/modules/nf-core/fasttree/environment.yml index 26509484c923..abe21b5a032c 100644 --- a/modules/nf-core/fasttree/environment.yml +++ b/modules/nf-core/fasttree/environment.yml @@ -1,7 +1,5 @@ -name: fasttree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fasttree=2.1.10 diff --git a/modules/nf-core/fastx/collapser/environment.yml b/modules/nf-core/fastx/collapser/environment.yml index b685bd71c96c..bc0c3eb35a25 100644 --- a/modules/nf-core/fastx/collapser/environment.yml +++ b/modules/nf-core/fastx/collapser/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fastx_collapser" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::fastx_toolkit=0.0.14" diff --git a/modules/nf-core/fcs/fcsadaptor/environment.yml b/modules/nf-core/fcs/fcsadaptor/environment.yml index b11cd41563f4..14207ff69aef 100644 --- a/modules/nf-core/fcs/fcsadaptor/environment.yml +++ b/modules/nf-core/fcs/fcsadaptor/environment.yml @@ -1,7 +1,5 @@ -name: fcs_fcsadaptor channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::false_flag # False flag to pass nf-core/lint diff --git a/modules/nf-core/fcs/fcsgx/environment.yml b/modules/nf-core/fcs/fcsgx/environment.yml index 75e5b79fa8de..3cebeff05bfc 100644 --- a/modules/nf-core/fcs/fcsgx/environment.yml +++ b/modules/nf-core/fcs/fcsgx/environment.yml @@ -1,5 +1,3 @@ -name: fcs_fcsgx channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/ffq/environment.yml b/modules/nf-core/ffq/environment.yml index e2a3029eb9a3..14c2f80f07ad 100644 --- a/modules/nf-core/ffq/environment.yml +++ b/modules/nf-core/ffq/environment.yml @@ -1,7 +1,5 @@ -name: ffq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ffq=0.2.1 diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml index 2a480a98f12d..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callduplexconsensusreads/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_callduplexconsensusreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml index d19c0be6aa6f..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_callmolecularconsensusreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml index a21a0a390e6c..48539f033bc1 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "fgbio_collectduplexseqmetrics" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::fgbio=2.0.2" - "conda-forge::r-ggplot2=3.4.4" diff --git a/modules/nf-core/fgbio/fastqtobam/environment.yml b/modules/nf-core/fgbio/fastqtobam/environment.yml index 5a4c8eba8174..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/fastqtobam/environment.yml +++ b/modules/nf-core/fgbio/fastqtobam/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_fastqtobam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/filterconsensusreads/environment.yml b/modules/nf-core/fgbio/filterconsensusreads/environment.yml index e80b3f18863e..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/environment.yml +++ b/modules/nf-core/fgbio/filterconsensusreads/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_filterconsensusreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml index 941a26ecb299..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/environment.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_groupreadsbyumi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/sortbam/environment.yml b/modules/nf-core/fgbio/sortbam/environment.yml index 452613a4b9d2..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/sortbam/environment.yml +++ b/modules/nf-core/fgbio/sortbam/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_sortbam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/fgbio/zipperbams/environment.yml b/modules/nf-core/fgbio/zipperbams/environment.yml index 6cf97f0ddc2b..6f3c75600d87 100644 --- a/modules/nf-core/fgbio/zipperbams/environment.yml +++ b/modules/nf-core/fgbio/zipperbams/environment.yml @@ -1,7 +1,5 @@ -name: fgbio_zipperbams channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fgbio=2.2.1 diff --git a/modules/nf-core/filtlong/environment.yml b/modules/nf-core/filtlong/environment.yml index 0fb7e8b4313b..746c83a45ccf 100644 --- a/modules/nf-core/filtlong/environment.yml +++ b/modules/nf-core/filtlong/environment.yml @@ -1,7 +1,5 @@ -name: filtlong channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::filtlong=0.2.1 diff --git a/modules/nf-core/flash/environment.yml b/modules/nf-core/flash/environment.yml index c958b2d8b69b..eb575fc52ab5 100644 --- a/modules/nf-core/flash/environment.yml +++ b/modules/nf-core/flash/environment.yml @@ -1,7 +1,5 @@ -name: flash channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::flash=1.2.11 diff --git a/modules/nf-core/flye/environment.yml b/modules/nf-core/flye/environment.yml index 958544992b6f..c08deb459a5e 100644 --- a/modules/nf-core/flye/environment.yml +++ b/modules/nf-core/flye/environment.yml @@ -1,7 +1,5 @@ -name: flye channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::flye=2.9 diff --git a/modules/nf-core/foldcomp/compress/environment.yml b/modules/nf-core/foldcomp/compress/environment.yml index 07c749bfc69d..b061ede4c8b7 100644 --- a/modules/nf-core/foldcomp/compress/environment.yml +++ b/modules/nf-core/foldcomp/compress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "foldcomp_compress" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::foldcomp=0.0.7" diff --git a/modules/nf-core/foldcomp/decompress/environment.yml b/modules/nf-core/foldcomp/decompress/environment.yml index 5e22e779e725..b061ede4c8b7 100644 --- a/modules/nf-core/foldcomp/decompress/environment.yml +++ b/modules/nf-core/foldcomp/decompress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "foldcomp_decompress" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::foldcomp=0.0.7" diff --git a/modules/nf-core/foldmason/easymsa/environment.yml b/modules/nf-core/foldmason/easymsa/environment.yml index a40639a7c886..64a5b3671d43 100644 --- a/modules/nf-core/foldmason/easymsa/environment.yml +++ b/modules/nf-core/foldmason/easymsa/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "foldmason_easymsa" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::foldmason=1.763a428 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/foldseek/createdb/environment.yml b/modules/nf-core/foldseek/createdb/environment.yml index 88bf98956549..5467561cf935 100644 --- a/modules/nf-core/foldseek/createdb/environment.yml +++ b/modules/nf-core/foldseek/createdb/environment.yml @@ -1,7 +1,5 @@ -name: foldseek_createdb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::foldseek=9.427df8a diff --git a/modules/nf-core/foldseek/easysearch/environment.yml b/modules/nf-core/foldseek/easysearch/environment.yml index b10b3962a7d5..5467561cf935 100644 --- a/modules/nf-core/foldseek/easysearch/environment.yml +++ b/modules/nf-core/foldseek/easysearch/environment.yml @@ -1,7 +1,5 @@ -name: foldseek_easysearch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::foldseek=9.427df8a diff --git a/modules/nf-core/fq/generate/environment.yml b/modules/nf-core/fq/generate/environment.yml index 7ed58f5ac295..eaba9339b678 100644 --- a/modules/nf-core/fq/generate/environment.yml +++ b/modules/nf-core/fq/generate/environment.yml @@ -1,7 +1,5 @@ -name: fq_generate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fq=0.9.1 diff --git a/modules/nf-core/fq/lint/environment.yml b/modules/nf-core/fq/lint/environment.yml index 66145f4c9ec8..eaba9339b678 100644 --- a/modules/nf-core/fq/lint/environment.yml +++ b/modules/nf-core/fq/lint/environment.yml @@ -1,7 +1,5 @@ -name: fq_lint channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fq=0.9.1 diff --git a/modules/nf-core/fq/subsample/environment.yml b/modules/nf-core/fq/subsample/environment.yml index c588de38ab16..eaba9339b678 100644 --- a/modules/nf-core/fq/subsample/environment.yml +++ b/modules/nf-core/fq/subsample/environment.yml @@ -1,7 +1,5 @@ -name: fq_subsample channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fq=0.9.1 diff --git a/modules/nf-core/fqtk/environment.yml b/modules/nf-core/fqtk/environment.yml index 1ea157443981..90897712ab3a 100644 --- a/modules/nf-core/fqtk/environment.yml +++ b/modules/nf-core/fqtk/environment.yml @@ -1,7 +1,5 @@ -name: fqtk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::fqtk=0.2.1 diff --git a/modules/nf-core/freebayes/environment.yml b/modules/nf-core/freebayes/environment.yml index 6846080a2fc2..3f5936968085 100644 --- a/modules/nf-core/freebayes/environment.yml +++ b/modules/nf-core/freebayes/environment.yml @@ -1,7 +1,5 @@ -name: freebayes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::freebayes=1.3.6 diff --git a/modules/nf-core/freyja/boot/environment.yml b/modules/nf-core/freyja/boot/environment.yml index dfab14ec0b53..69da13f76f3c 100644 --- a/modules/nf-core/freyja/boot/environment.yml +++ b/modules/nf-core/freyja/boot/environment.yml @@ -1,7 +1,5 @@ -name: freyja_boot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::freyja=1.5.0 diff --git a/modules/nf-core/freyja/demix/environment.yml b/modules/nf-core/freyja/demix/environment.yml index 0f29b8cef84d..69da13f76f3c 100644 --- a/modules/nf-core/freyja/demix/environment.yml +++ b/modules/nf-core/freyja/demix/environment.yml @@ -1,7 +1,5 @@ -name: freyja_demix channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::freyja=1.5.0 diff --git a/modules/nf-core/freyja/update/environment.yml b/modules/nf-core/freyja/update/environment.yml index 9dbffbb6554a..69da13f76f3c 100644 --- a/modules/nf-core/freyja/update/environment.yml +++ b/modules/nf-core/freyja/update/environment.yml @@ -1,7 +1,5 @@ -name: freyja_update channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::freyja=1.5.0 diff --git a/modules/nf-core/freyja/variants/environment.yml b/modules/nf-core/freyja/variants/environment.yml index 871a07450bef..69da13f76f3c 100644 --- a/modules/nf-core/freyja/variants/environment.yml +++ b/modules/nf-core/freyja/variants/environment.yml @@ -1,7 +1,5 @@ -name: freyja_variants channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::freyja=1.5.0 diff --git a/modules/nf-core/galah/environment.yml b/modules/nf-core/galah/environment.yml index a7c3169a6347..4300473f60e2 100644 --- a/modules/nf-core/galah/environment.yml +++ b/modules/nf-core/galah/environment.yml @@ -1,7 +1,5 @@ -name: galah channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::galah=0.3.1 diff --git a/modules/nf-core/gamma/gamma/environment.yml b/modules/nf-core/gamma/gamma/environment.yml index bd2ab25e6909..a6672129c76d 100644 --- a/modules/nf-core/gamma/gamma/environment.yml +++ b/modules/nf-core/gamma/gamma/environment.yml @@ -1,7 +1,5 @@ -name: gamma_gamma channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gamma=2.1 diff --git a/modules/nf-core/gangstr/environment.yml b/modules/nf-core/gangstr/environment.yml index 2ae330e9bcde..9d6bce21a1a0 100644 --- a/modules/nf-core/gangstr/environment.yml +++ b/modules/nf-core/gangstr/environment.yml @@ -1,7 +1,5 @@ -name: gangstr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gangstr=2.5.0 diff --git a/modules/nf-core/ganon/buildcustom/environment.yml b/modules/nf-core/ganon/buildcustom/environment.yml index 7bace0c271ea..98f34de89e17 100644 --- a/modules/nf-core/ganon/buildcustom/environment.yml +++ b/modules/nf-core/ganon/buildcustom/environment.yml @@ -1,7 +1,5 @@ -name: ganon_buildcustom channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ganon=2.0.0 diff --git a/modules/nf-core/ganon/classify/environment.yml b/modules/nf-core/ganon/classify/environment.yml index 0abe536f92dc..98f34de89e17 100644 --- a/modules/nf-core/ganon/classify/environment.yml +++ b/modules/nf-core/ganon/classify/environment.yml @@ -1,7 +1,5 @@ -name: ganon_classify channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ganon=2.0.0 diff --git a/modules/nf-core/ganon/report/environment.yml b/modules/nf-core/ganon/report/environment.yml index 187daa294b99..98f34de89e17 100644 --- a/modules/nf-core/ganon/report/environment.yml +++ b/modules/nf-core/ganon/report/environment.yml @@ -1,7 +1,5 @@ -name: ganon_report channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ganon=2.0.0 diff --git a/modules/nf-core/ganon/table/environment.yml b/modules/nf-core/ganon/table/environment.yml index 7ca1bacec75f..98f34de89e17 100644 --- a/modules/nf-core/ganon/table/environment.yml +++ b/modules/nf-core/ganon/table/environment.yml @@ -1,7 +1,5 @@ -name: ganon_table channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ganon=2.0.0 diff --git a/modules/nf-core/gappa/examineassign/environment.yml b/modules/nf-core/gappa/examineassign/environment.yml index 4930e72458ab..0059e1a49975 100644 --- a/modules/nf-core/gappa/examineassign/environment.yml +++ b/modules/nf-core/gappa/examineassign/environment.yml @@ -1,7 +1,5 @@ -name: gappa_examineassign channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gappa=0.8.0 diff --git a/modules/nf-core/gappa/examinegraft/environment.yml b/modules/nf-core/gappa/examinegraft/environment.yml index c22460d204b1..0059e1a49975 100644 --- a/modules/nf-core/gappa/examinegraft/environment.yml +++ b/modules/nf-core/gappa/examinegraft/environment.yml @@ -1,7 +1,5 @@ -name: gappa_examinegraft channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gappa=0.8.0 diff --git a/modules/nf-core/gappa/examineheattree/environment.yml b/modules/nf-core/gappa/examineheattree/environment.yml index a5ee8d48f0d1..0059e1a49975 100644 --- a/modules/nf-core/gappa/examineheattree/environment.yml +++ b/modules/nf-core/gappa/examineheattree/environment.yml @@ -1,7 +1,5 @@ -name: gappa_examineheattree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gappa=0.8.0 diff --git a/modules/nf-core/gatk/indelrealigner/environment.yml b/modules/nf-core/gatk/indelrealigner/environment.yml index 5a30ceb74fef..6a147cb08665 100644 --- a/modules/nf-core/gatk/indelrealigner/environment.yml +++ b/modules/nf-core/gatk/indelrealigner/environment.yml @@ -1,7 +1,5 @@ -name: gatk_indelrealigner channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk=3.5 diff --git a/modules/nf-core/gatk/realignertargetcreator/environment.yml b/modules/nf-core/gatk/realignertargetcreator/environment.yml index 68ca7b5433f8..6a147cb08665 100644 --- a/modules/nf-core/gatk/realignertargetcreator/environment.yml +++ b/modules/nf-core/gatk/realignertargetcreator/environment.yml @@ -1,7 +1,5 @@ -name: gatk_realignertargetcreator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk=3.5 diff --git a/modules/nf-core/gatk/unifiedgenotyper/environment.yml b/modules/nf-core/gatk/unifiedgenotyper/environment.yml index 4137c34897fd..182579ab24ea 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/environment.yml +++ b/modules/nf-core/gatk/unifiedgenotyper/environment.yml @@ -1,8 +1,6 @@ -name: gatk_unifiedgenotyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk=3.5 - bioconda::tabix=1.11 ## Needed for bgzip diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml index 82f9173806ee..55993f440cd4 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_addorreplacereadgroups channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml index 523753c32358..55993f440cd4 100644 --- a/modules/nf-core/gatk4/annotateintervals/environment.yml +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_annotateintervals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/applybqsr/environment.yml b/modules/nf-core/gatk4/applybqsr/environment.yml index 80c811e6c149..55993f440cd4 100644 --- a/modules/nf-core/gatk4/applybqsr/environment.yml +++ b/modules/nf-core/gatk4/applybqsr/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_applybqsr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/applyvqsr/environment.yml b/modules/nf-core/gatk4/applyvqsr/environment.yml index c043cd632a38..55993f440cd4 100644 --- a/modules/nf-core/gatk4/applyvqsr/environment.yml +++ b/modules/nf-core/gatk4/applyvqsr/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_applyvqsr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/asereadcounter/environment.yml b/modules/nf-core/gatk4/asereadcounter/environment.yml index d0c8c2e80517..55993f440cd4 100644 --- a/modules/nf-core/gatk4/asereadcounter/environment.yml +++ b/modules/nf-core/gatk4/asereadcounter/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_asereadcounter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/baserecalibrator/environment.yml b/modules/nf-core/gatk4/baserecalibrator/environment.yml index 365e5c63198e..55993f440cd4 100644 --- a/modules/nf-core/gatk4/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4/baserecalibrator/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_baserecalibrator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/bedtointervallist/environment.yml b/modules/nf-core/gatk4/bedtointervallist/environment.yml index d6fbe2e7779d..55993f440cd4 100644 --- a/modules/nf-core/gatk4/bedtointervallist/environment.yml +++ b/modules/nf-core/gatk4/bedtointervallist/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_bedtointervallist channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/calculatecontamination/environment.yml b/modules/nf-core/gatk4/calculatecontamination/environment.yml index 5ec9c482935d..55993f440cd4 100644 --- a/modules/nf-core/gatk4/calculatecontamination/environment.yml +++ b/modules/nf-core/gatk4/calculatecontamination/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_calculatecontamination channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml index 810eade13caf..55993f440cd4 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_calibratedragstrmodel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml index d09cd890376b..55993f440cd4 100644 --- a/modules/nf-core/gatk4/collectreadcounts/environment.yml +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_collectreadcounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/collectsvevidence/environment.yml b/modules/nf-core/gatk4/collectsvevidence/environment.yml index 78f98f170dd4..55993f440cd4 100644 --- a/modules/nf-core/gatk4/collectsvevidence/environment.yml +++ b/modules/nf-core/gatk4/collectsvevidence/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_collectsvevidence channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/combinegvcfs/environment.yml b/modules/nf-core/gatk4/combinegvcfs/environment.yml index e4510f97b4ab..55993f440cd4 100644 --- a/modules/nf-core/gatk4/combinegvcfs/environment.yml +++ b/modules/nf-core/gatk4/combinegvcfs/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_combinegvcfs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/composestrtablefile/environment.yml b/modules/nf-core/gatk4/composestrtablefile/environment.yml index ffbda0fb5f88..55993f440cd4 100644 --- a/modules/nf-core/gatk4/composestrtablefile/environment.yml +++ b/modules/nf-core/gatk4/composestrtablefile/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_composestrtablefile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/condensedepthevidence/environment.yml b/modules/nf-core/gatk4/condensedepthevidence/environment.yml index 7a237c88f94a..55993f440cd4 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/environment.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_condensedepthevidence channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml index b4f4e774f56b..55993f440cd4 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_createreadcountpanelofnormals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createsequencedictionary/environment.yml b/modules/nf-core/gatk4/createsequencedictionary/environment.yml index 78822ad03f90..55993f440cd4 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/environment.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_createsequencedictionary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml index ae543c699933..55993f440cd4 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_createsomaticpanelofnormals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/denoisereadcounts/environment.yml b/modules/nf-core/gatk4/denoisereadcounts/environment.yml index a03cf4a97b9d..55993f440cd4 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/environment.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_denoisereadcounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml index 5fdd85af802b..55993f440cd4 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_estimatelibrarycomplexity channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/fastqtosam/environment.yml b/modules/nf-core/gatk4/fastqtosam/environment.yml index b4e759d311ef..55993f440cd4 100644 --- a/modules/nf-core/gatk4/fastqtosam/environment.yml +++ b/modules/nf-core/gatk4/fastqtosam/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_fastqtosam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml index 853995e2f5dc..55993f440cd4 100644 --- a/modules/nf-core/gatk4/filterintervals/environment.yml +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_filterintervals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/filtermutectcalls/environment.yml b/modules/nf-core/gatk4/filtermutectcalls/environment.yml index 7494d84dbc70..55993f440cd4 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/environment.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_filtermutectcalls channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/filtervarianttranches/environment.yml b/modules/nf-core/gatk4/filtervarianttranches/environment.yml index 9763cf1effa9..55993f440cd4 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/environment.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_filtervarianttranches channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml index 4248a298125a..55993f440cd4 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/environment.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_gatherbqsrreports channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml index 217387f9c066..55993f440cd4 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_gatherpileupsummaries channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/genomicsdbimport/environment.yml b/modules/nf-core/gatk4/genomicsdbimport/environment.yml index a3a13636c673..55993f440cd4 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/environment.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_genomicsdbimport channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/genotypegvcfs/environment.yml b/modules/nf-core/gatk4/genotypegvcfs/environment.yml index 6e1b7c04a025..55993f440cd4 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/environment.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_genotypegvcfs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/getpileupsummaries/environment.yml b/modules/nf-core/gatk4/getpileupsummaries/environment.yml index b99a28c177cb..55993f440cd4 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/environment.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_getpileupsummaries channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/haplotypecaller/environment.yml b/modules/nf-core/gatk4/haplotypecaller/environment.yml index d4e8d36026c0..55993f440cd4 100644 --- a/modules/nf-core/gatk4/haplotypecaller/environment.yml +++ b/modules/nf-core/gatk4/haplotypecaller/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_haplotypecaller channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/indexfeaturefile/environment.yml b/modules/nf-core/gatk4/indexfeaturefile/environment.yml index dccdb15e8b71..55993f440cd4 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/environment.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_indexfeaturefile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/intervallisttobed/environment.yml b/modules/nf-core/gatk4/intervallisttobed/environment.yml index d4d2eba24cc6..55993f440cd4 100644 --- a/modules/nf-core/gatk4/intervallisttobed/environment.yml +++ b/modules/nf-core/gatk4/intervallisttobed/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_intervallisttobed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml index a4026f98ffd2..55993f440cd4 100644 --- a/modules/nf-core/gatk4/intervallisttools/environment.yml +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_intervallisttools channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml index a4c2a764dd41..55993f440cd4 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_learnreadorientationmodel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml index 5495c7a7c3d6..55993f440cd4 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_leftalignandtrimvariants channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 7362eea6f2e9..9fe34eb36c88 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,8 +1,6 @@ -name: gatk4_markduplicates channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/mergebamalignment/environment.yml b/modules/nf-core/gatk4/mergebamalignment/environment.yml index 0ea7b0d78c98..55993f440cd4 100644 --- a/modules/nf-core/gatk4/mergebamalignment/environment.yml +++ b/modules/nf-core/gatk4/mergebamalignment/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_mergebamalignment channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/mergemutectstats/environment.yml b/modules/nf-core/gatk4/mergemutectstats/environment.yml index 756d4083017e..55993f440cd4 100644 --- a/modules/nf-core/gatk4/mergemutectstats/environment.yml +++ b/modules/nf-core/gatk4/mergemutectstats/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_mergemutectstats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/mergevcfs/environment.yml b/modules/nf-core/gatk4/mergevcfs/environment.yml index efd9faa22234..55993f440cd4 100644 --- a/modules/nf-core/gatk4/mergevcfs/environment.yml +++ b/modules/nf-core/gatk4/mergevcfs/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_mergevcfs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/mutect2/environment.yml b/modules/nf-core/gatk4/mutect2/environment.yml index 86f4bfae9893..55993f440cd4 100644 --- a/modules/nf-core/gatk4/mutect2/environment.yml +++ b/modules/nf-core/gatk4/mutect2/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_mutect2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml index ec0b09e9d1a2..55993f440cd4 100644 --- a/modules/nf-core/gatk4/preprocessintervals/environment.yml +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_preprocessintervals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/printreads/environment.yml b/modules/nf-core/gatk4/printreads/environment.yml index d1dd0b3e90ca..55993f440cd4 100644 --- a/modules/nf-core/gatk4/printreads/environment.yml +++ b/modules/nf-core/gatk4/printreads/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_printreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/printsvevidence/environment.yml b/modules/nf-core/gatk4/printsvevidence/environment.yml index d9b753d9c25c..55993f440cd4 100644 --- a/modules/nf-core/gatk4/printsvevidence/environment.yml +++ b/modules/nf-core/gatk4/printsvevidence/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_printsvevidence channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/reblockgvcf/environment.yml b/modules/nf-core/gatk4/reblockgvcf/environment.yml index 67e453054453..55993f440cd4 100644 --- a/modules/nf-core/gatk4/reblockgvcf/environment.yml +++ b/modules/nf-core/gatk4/reblockgvcf/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_reblockgvcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/revertsam/environment.yml b/modules/nf-core/gatk4/revertsam/environment.yml index f169a89a067d..55993f440cd4 100644 --- a/modules/nf-core/gatk4/revertsam/environment.yml +++ b/modules/nf-core/gatk4/revertsam/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_revertsam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/samtofastq/environment.yml b/modules/nf-core/gatk4/samtofastq/environment.yml index 1f881bb7c997..55993f440cd4 100644 --- a/modules/nf-core/gatk4/samtofastq/environment.yml +++ b/modules/nf-core/gatk4/samtofastq/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_samtofastq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/selectvariants/environment.yml b/modules/nf-core/gatk4/selectvariants/environment.yml index f2711e44bcea..55993f440cd4 100644 --- a/modules/nf-core/gatk4/selectvariants/environment.yml +++ b/modules/nf-core/gatk4/selectvariants/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_selectvariants channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/shiftfasta/environment.yml b/modules/nf-core/gatk4/shiftfasta/environment.yml index 58ebf089b885..55993f440cd4 100644 --- a/modules/nf-core/gatk4/shiftfasta/environment.yml +++ b/modules/nf-core/gatk4/shiftfasta/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_shiftfasta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml index 28ad3fb0c947..55993f440cd4 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/environment.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_sitedepthtobaf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/splitcram/environment.yml b/modules/nf-core/gatk4/splitcram/environment.yml index 7bc7f5426e45..55993f440cd4 100644 --- a/modules/nf-core/gatk4/splitcram/environment.yml +++ b/modules/nf-core/gatk4/splitcram/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_splitcram channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/splitintervals/environment.yml b/modules/nf-core/gatk4/splitintervals/environment.yml index b2e8c1b05d13..55993f440cd4 100644 --- a/modules/nf-core/gatk4/splitintervals/environment.yml +++ b/modules/nf-core/gatk4/splitintervals/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_splitintervals channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/splitncigarreads/environment.yml b/modules/nf-core/gatk4/splitncigarreads/environment.yml index 834d24866abe..55993f440cd4 100644 --- a/modules/nf-core/gatk4/splitncigarreads/environment.yml +++ b/modules/nf-core/gatk4/splitncigarreads/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_splitncigarreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/svannotate/environment.yml b/modules/nf-core/gatk4/svannotate/environment.yml index aa67e7da4222..55993f440cd4 100644 --- a/modules/nf-core/gatk4/svannotate/environment.yml +++ b/modules/nf-core/gatk4/svannotate/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_svannotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/svcluster/environment.yml b/modules/nf-core/gatk4/svcluster/environment.yml index d88cfebdc952..55993f440cd4 100644 --- a/modules/nf-core/gatk4/svcluster/environment.yml +++ b/modules/nf-core/gatk4/svcluster/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_svcluster channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/variantfiltration/environment.yml b/modules/nf-core/gatk4/variantfiltration/environment.yml index 0812b6f2c1bf..55993f440cd4 100644 --- a/modules/nf-core/gatk4/variantfiltration/environment.yml +++ b/modules/nf-core/gatk4/variantfiltration/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_variantfiltration channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/variantrecalibrator/environment.yml b/modules/nf-core/gatk4/variantrecalibrator/environment.yml index 95b744c46b46..55993f440cd4 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/environment.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/environment.yml @@ -1,7 +1,5 @@ -name: gatk4_variantrecalibrator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4spark/applybqsr/environment.yml b/modules/nf-core/gatk4spark/applybqsr/environment.yml index de07029794ac..14075a574acf 100644 --- a/modules/nf-core/gatk4spark/applybqsr/environment.yml +++ b/modules/nf-core/gatk4spark/applybqsr/environment.yml @@ -1,7 +1,5 @@ -name: gatk4spark_applybqsr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4-spark=4.5.0.0 diff --git a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml index 84615886c165..14075a574acf 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/environment.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/environment.yml @@ -1,7 +1,5 @@ -name: gatk4spark_baserecalibrator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4-spark=4.5.0.0 diff --git a/modules/nf-core/gatk4spark/markduplicates/environment.yml b/modules/nf-core/gatk4spark/markduplicates/environment.yml index 94dd4a3c68b2..14075a574acf 100644 --- a/modules/nf-core/gatk4spark/markduplicates/environment.yml +++ b/modules/nf-core/gatk4spark/markduplicates/environment.yml @@ -1,7 +1,5 @@ -name: gatk4spark_markduplicates channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gatk4-spark=4.5.0.0 diff --git a/modules/nf-core/gawk/environment.yml b/modules/nf-core/gawk/environment.yml index 3d98a08b0c8c..315f6dc67e26 100644 --- a/modules/nf-core/gawk/environment.yml +++ b/modules/nf-core/gawk/environment.yml @@ -1,7 +1,5 @@ -name: gawk channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::gawk=5.3.0 diff --git a/modules/nf-core/gecco/run/environment.yml b/modules/nf-core/gecco/run/environment.yml index 9d7cde8d9b24..7db7dc87b41a 100644 --- a/modules/nf-core/gecco/run/environment.yml +++ b/modules/nf-core/gecco/run/environment.yml @@ -1,7 +1,5 @@ -name: gecco_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gecco=0.9.10 diff --git a/modules/nf-core/gem2/gem2bedmappability/environment.yml b/modules/nf-core/gem2/gem2bedmappability/environment.yml index 4977e7e52bcd..bf74e3f0e304 100644 --- a/modules/nf-core/gem2/gem2bedmappability/environment.yml +++ b/modules/nf-core/gem2/gem2bedmappability/environment.yml @@ -1,7 +1,5 @@ -name: gem2_gem2bedmappability channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gem2=20200110 diff --git a/modules/nf-core/gem2/gemindexer/environment.yml b/modules/nf-core/gem2/gemindexer/environment.yml index 58aca5dc8ee8..bf74e3f0e304 100644 --- a/modules/nf-core/gem2/gemindexer/environment.yml +++ b/modules/nf-core/gem2/gemindexer/environment.yml @@ -1,7 +1,5 @@ -name: gem2_gemindexer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gem2=20200110 diff --git a/modules/nf-core/gem2/gemmappability/environment.yml b/modules/nf-core/gem2/gemmappability/environment.yml index d9846ad5e7da..bf74e3f0e304 100644 --- a/modules/nf-core/gem2/gemmappability/environment.yml +++ b/modules/nf-core/gem2/gemmappability/environment.yml @@ -1,7 +1,5 @@ -name: gem2_gemmappability channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gem2=20200110 diff --git a/modules/nf-core/gem3/gem3indexer/environment.yml b/modules/nf-core/gem3/gem3indexer/environment.yml index 980027d01ba0..f9e5bd2c1883 100644 --- a/modules/nf-core/gem3/gem3indexer/environment.yml +++ b/modules/nf-core/gem3/gem3indexer/environment.yml @@ -1,7 +1,5 @@ -name: gem3_gem3indexer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gem3-mapper=3.6.1 diff --git a/modules/nf-core/gem3/gem3mapper/environment.yml b/modules/nf-core/gem3/gem3mapper/environment.yml index f5ce5c7f639f..3915ff106118 100644 --- a/modules/nf-core/gem3/gem3mapper/environment.yml +++ b/modules/nf-core/gem3/gem3mapper/environment.yml @@ -1,8 +1,6 @@ -name: gem3_gem3mapper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gem3-mapper=3.6.1 - bioconda::samtools=1.17 diff --git a/modules/nf-core/genescopefk/environment.yml b/modules/nf-core/genescopefk/environment.yml index 79cdc3177b38..3cebeff05bfc 100644 --- a/modules/nf-core/genescopefk/environment.yml +++ b/modules/nf-core/genescopefk/environment.yml @@ -1,5 +1,3 @@ -name: genescopefk channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/genmap/index/environment.yml b/modules/nf-core/genmap/index/environment.yml index a5c2a87aecdd..f54626e43ba9 100644 --- a/modules/nf-core/genmap/index/environment.yml +++ b/modules/nf-core/genmap/index/environment.yml @@ -1,7 +1,5 @@ -name: genmap_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmap=1.3.0 diff --git a/modules/nf-core/genmap/map/environment.yml b/modules/nf-core/genmap/map/environment.yml index a36a737e49ba..f54626e43ba9 100644 --- a/modules/nf-core/genmap/map/environment.yml +++ b/modules/nf-core/genmap/map/environment.yml @@ -1,7 +1,5 @@ -name: genmap_map channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmap=1.3.0 diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml index ac8140fd636f..1eca76fad2ca 100644 --- a/modules/nf-core/genmod/annotate/environment.yml +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -1,7 +1,5 @@ -name: genmod_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml index 1e2561fdb50f..1eca76fad2ca 100644 --- a/modules/nf-core/genmod/compound/environment.yml +++ b/modules/nf-core/genmod/compound/environment.yml @@ -1,7 +1,5 @@ -name: genmod_compound channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml index 62a746c7c494..1eca76fad2ca 100644 --- a/modules/nf-core/genmod/models/environment.yml +++ b/modules/nf-core/genmod/models/environment.yml @@ -1,7 +1,5 @@ -name: genmod_models channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml index bacc4cec4070..1eca76fad2ca 100644 --- a/modules/nf-core/genmod/score/environment.yml +++ b/modules/nf-core/genmod/score/environment.yml @@ -1,7 +1,5 @@ -name: genmod_score channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genmod=3.8.2 diff --git a/modules/nf-core/genomad/download/environment.yml b/modules/nf-core/genomad/download/environment.yml index 5c9b27a84055..443789ef2263 100644 --- a/modules/nf-core/genomad/download/environment.yml +++ b/modules/nf-core/genomad/download/environment.yml @@ -1,7 +1,5 @@ -name: genomad_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genomad=1.7.4 diff --git a/modules/nf-core/genomad/endtoend/environment.yml b/modules/nf-core/genomad/endtoend/environment.yml index 6ec4ebe9714d..443789ef2263 100644 --- a/modules/nf-core/genomad/endtoend/environment.yml +++ b/modules/nf-core/genomad/endtoend/environment.yml @@ -1,7 +1,5 @@ -name: genomad_endtoend channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genomad=1.7.4 diff --git a/modules/nf-core/genomescope2/environment.yml b/modules/nf-core/genomescope2/environment.yml index e085ab404554..2b48c6d9ca01 100644 --- a/modules/nf-core/genomescope2/environment.yml +++ b/modules/nf-core/genomescope2/environment.yml @@ -1,7 +1,5 @@ -name: genomescope2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genomescope2=2.0 diff --git a/modules/nf-core/genotyphi/parse/environment.yml b/modules/nf-core/genotyphi/parse/environment.yml index 9c1c38d5fe01..a8ca10817aae 100644 --- a/modules/nf-core/genotyphi/parse/environment.yml +++ b/modules/nf-core/genotyphi/parse/environment.yml @@ -1,7 +1,5 @@ -name: genotyphi_parse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genotyphi=1.9.1 diff --git a/modules/nf-core/genrich/environment.yml b/modules/nf-core/genrich/environment.yml index 9e76305cbe6c..cef503551e98 100644 --- a/modules/nf-core/genrich/environment.yml +++ b/modules/nf-core/genrich/environment.yml @@ -1,7 +1,5 @@ -name: genrich channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::genrich=0.6.1 diff --git a/modules/nf-core/geofetch/environment.yml b/modules/nf-core/geofetch/environment.yml index 56b8d450197d..e22890b0929a 100644 --- a/modules/nf-core/geofetch/environment.yml +++ b/modules/nf-core/geofetch/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "geofetch" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::geofetch=0.12.6" diff --git a/modules/nf-core/geoquery/getgeo/environment.yml b/modules/nf-core/geoquery/getgeo/environment.yml index 3385fdc5e478..3d4f8cd98497 100644 --- a/modules/nf-core/geoquery/getgeo/environment.yml +++ b/modules/nf-core/geoquery/getgeo/environment.yml @@ -1,4 +1,3 @@ -name: geoquery_getgeo channels: - conda-forge - bioconda diff --git a/modules/nf-core/getorganelle/config/environment.yml b/modules/nf-core/getorganelle/config/environment.yml index 01e427819aca..6b5a3b01cfbc 100644 --- a/modules/nf-core/getorganelle/config/environment.yml +++ b/modules/nf-core/getorganelle/config/environment.yml @@ -1,6 +1,5 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "getorganelle_config" channels: - conda-forge - bioconda diff --git a/modules/nf-core/gfaffix/environment.yml b/modules/nf-core/gfaffix/environment.yml index 77262a47394c..3da9f04984a1 100644 --- a/modules/nf-core/gfaffix/environment.yml +++ b/modules/nf-core/gfaffix/environment.yml @@ -1,4 +1,3 @@ -name: gfaffix channels: - conda-forge - bioconda diff --git a/modules/nf-core/gfastats/environment.yml b/modules/nf-core/gfastats/environment.yml index 1c875ce0f894..b47bbdbbaf94 100644 --- a/modules/nf-core/gfastats/environment.yml +++ b/modules/nf-core/gfastats/environment.yml @@ -1,7 +1,5 @@ -name: gfastats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gfastats=1.3.6 diff --git a/modules/nf-core/gfatools/gfa2fa/environment.yml b/modules/nf-core/gfatools/gfa2fa/environment.yml index 24da810536fa..476a4fcf2ac0 100644 --- a/modules/nf-core/gfatools/gfa2fa/environment.yml +++ b/modules/nf-core/gfatools/gfa2fa/environment.yml @@ -1,7 +1,5 @@ -name: gfatools_gfa2fa channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gfatools=0.5 diff --git a/modules/nf-core/gfatools/stat/environment.yml b/modules/nf-core/gfatools/stat/environment.yml index 63dcb4d0e7f2..476a4fcf2ac0 100644 --- a/modules/nf-core/gfatools/stat/environment.yml +++ b/modules/nf-core/gfatools/stat/environment.yml @@ -1,7 +1,5 @@ -name: gfatools_stat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gfatools=0.5 diff --git a/modules/nf-core/gffcompare/environment.yml b/modules/nf-core/gffcompare/environment.yml index bcd633ea250b..2b52417df44d 100644 --- a/modules/nf-core/gffcompare/environment.yml +++ b/modules/nf-core/gffcompare/environment.yml @@ -1,7 +1,5 @@ -name: gffcompare channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gffcompare=0.12.6 diff --git a/modules/nf-core/gffread/environment.yml b/modules/nf-core/gffread/environment.yml index c6df58ad0654..ee2398416cfb 100644 --- a/modules/nf-core/gffread/environment.yml +++ b/modules/nf-core/gffread/environment.yml @@ -1,7 +1,5 @@ -name: gffread channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gffread=0.12.7 diff --git a/modules/nf-core/gget/gget/environment.yml b/modules/nf-core/gget/gget/environment.yml index 3205a5319000..f8dae7c70b25 100644 --- a/modules/nf-core/gget/gget/environment.yml +++ b/modules/nf-core/gget/gget/environment.yml @@ -1,7 +1,5 @@ -name: gget_gget channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gget=0.27.2 diff --git a/modules/nf-core/glimpse/chunk/environment.yml b/modules/nf-core/glimpse/chunk/environment.yml index 8d71aa915f49..6247794bdd50 100644 --- a/modules/nf-core/glimpse/chunk/environment.yml +++ b/modules/nf-core/glimpse/chunk/environment.yml @@ -1,7 +1,5 @@ -name: glimpse_chunk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=1.1.1 diff --git a/modules/nf-core/glimpse/concordance/environment.yml b/modules/nf-core/glimpse/concordance/environment.yml index 739ab78d7bde..6247794bdd50 100644 --- a/modules/nf-core/glimpse/concordance/environment.yml +++ b/modules/nf-core/glimpse/concordance/environment.yml @@ -1,7 +1,5 @@ -name: glimpse_concordance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=1.1.1 diff --git a/modules/nf-core/glimpse/ligate/environment.yml b/modules/nf-core/glimpse/ligate/environment.yml index 0f9e9a3327e0..6247794bdd50 100644 --- a/modules/nf-core/glimpse/ligate/environment.yml +++ b/modules/nf-core/glimpse/ligate/environment.yml @@ -1,7 +1,5 @@ -name: glimpse_ligate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=1.1.1 diff --git a/modules/nf-core/glimpse/phase/environment.yml b/modules/nf-core/glimpse/phase/environment.yml index fc79765abbd1..6247794bdd50 100644 --- a/modules/nf-core/glimpse/phase/environment.yml +++ b/modules/nf-core/glimpse/phase/environment.yml @@ -1,7 +1,5 @@ -name: glimpse_phase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=1.1.1 diff --git a/modules/nf-core/glimpse/sample/environment.yml b/modules/nf-core/glimpse/sample/environment.yml index d1fe7cad0188..6247794bdd50 100644 --- a/modules/nf-core/glimpse/sample/environment.yml +++ b/modules/nf-core/glimpse/sample/environment.yml @@ -1,7 +1,5 @@ -name: glimpse_sample channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=1.1.1 diff --git a/modules/nf-core/glimpse2/chunk/environment.yml b/modules/nf-core/glimpse2/chunk/environment.yml index 54e5a11143d1..75b862396eff 100644 --- a/modules/nf-core/glimpse2/chunk/environment.yml +++ b/modules/nf-core/glimpse2/chunk/environment.yml @@ -1,7 +1,5 @@ -name: glimpse2_chunk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=2.0.1 diff --git a/modules/nf-core/glimpse2/concordance/environment.yml b/modules/nf-core/glimpse2/concordance/environment.yml index f40e83177c60..75b862396eff 100644 --- a/modules/nf-core/glimpse2/concordance/environment.yml +++ b/modules/nf-core/glimpse2/concordance/environment.yml @@ -1,7 +1,5 @@ -name: glimpse2_concordance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=2.0.1 diff --git a/modules/nf-core/glimpse2/ligate/environment.yml b/modules/nf-core/glimpse2/ligate/environment.yml index 1e5316005ad1..75b862396eff 100644 --- a/modules/nf-core/glimpse2/ligate/environment.yml +++ b/modules/nf-core/glimpse2/ligate/environment.yml @@ -1,7 +1,5 @@ -name: glimpse2_ligate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=2.0.1 diff --git a/modules/nf-core/glimpse2/phase/environment.yml b/modules/nf-core/glimpse2/phase/environment.yml index 0e3938c787c1..75b862396eff 100644 --- a/modules/nf-core/glimpse2/phase/environment.yml +++ b/modules/nf-core/glimpse2/phase/environment.yml @@ -1,7 +1,5 @@ -name: glimpse2_phase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=2.0.1 diff --git a/modules/nf-core/glimpse2/splitreference/environment.yml b/modules/nf-core/glimpse2/splitreference/environment.yml index b283e8356ded..75b862396eff 100644 --- a/modules/nf-core/glimpse2/splitreference/environment.yml +++ b/modules/nf-core/glimpse2/splitreference/environment.yml @@ -1,7 +1,5 @@ -name: glimpse2_splitreference channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glimpse-bio=2.0.1 diff --git a/modules/nf-core/glnexus/environment.yml b/modules/nf-core/glnexus/environment.yml index 922214e8c4a8..9190508a96f4 100644 --- a/modules/nf-core/glnexus/environment.yml +++ b/modules/nf-core/glnexus/environment.yml @@ -1,7 +1,5 @@ -name: glnexus channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::glnexus=1.4.1 diff --git a/modules/nf-core/gmmdemux/environment.yml b/modules/nf-core/gmmdemux/environment.yml index c2b6b8a9d87a..d8580796f2ff 100644 --- a/modules/nf-core/gmmdemux/environment.yml +++ b/modules/nf-core/gmmdemux/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gmmdemux" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::gmm-demux=0.2.2.3" diff --git a/modules/nf-core/gnu/sort/environment.yml b/modules/nf-core/gnu/sort/environment.yml index eb9b77edda30..babcfb551679 100644 --- a/modules/nf-core/gnu/sort/environment.yml +++ b/modules/nf-core/gnu/sort/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: gnu_sort channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=9.3 diff --git a/modules/nf-core/gnu/split/environment.yml b/modules/nf-core/gnu/split/environment.yml index 5d5d86446477..babcfb551679 100644 --- a/modules/nf-core/gnu/split/environment.yml +++ b/modules/nf-core/gnu/split/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: gnu_split channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=9.3 diff --git a/modules/nf-core/goat/taxonsearch/environment.yml b/modules/nf-core/goat/taxonsearch/environment.yml index e56e71f1e444..e09c2a19b213 100644 --- a/modules/nf-core/goat/taxonsearch/environment.yml +++ b/modules/nf-core/goat/taxonsearch/environment.yml @@ -1,7 +1,5 @@ -name: goat_taxonsearch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::goat=0.2.5 diff --git a/modules/nf-core/goleft/indexcov/environment.yml b/modules/nf-core/goleft/indexcov/environment.yml index 691377901c88..813146929cbe 100644 --- a/modules/nf-core/goleft/indexcov/environment.yml +++ b/modules/nf-core/goleft/indexcov/environment.yml @@ -1,8 +1,6 @@ -name: goleft_indexcov channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::goleft=0.2.4 - bioconda::htslib=1.12 diff --git a/modules/nf-core/goleft/indexsplit/environment.yml b/modules/nf-core/goleft/indexsplit/environment.yml index 192482ae4576..127c0c7a52b3 100644 --- a/modules/nf-core/goleft/indexsplit/environment.yml +++ b/modules/nf-core/goleft/indexsplit/environment.yml @@ -1,4 +1,3 @@ -name: goleft_indexsplit channels: - conda-forge - bioconda diff --git a/modules/nf-core/gprofiler2/gost/environment.yml b/modules/nf-core/gprofiler2/gost/environment.yml index 65e5d8f20da0..14376015da8d 100644 --- a/modules/nf-core/gprofiler2/gost/environment.yml +++ b/modules/nf-core/gprofiler2/gost/environment.yml @@ -1,8 +1,6 @@ -name: gprofiler2_gost channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-ggplot2=3.4.3 - conda-forge::r-gprofiler2=0.2.2 diff --git a/modules/nf-core/grabix/check/environment.yml b/modules/nf-core/grabix/check/environment.yml index d8c21804e1c3..58787b9b4d2a 100644 --- a/modules/nf-core/grabix/check/environment.yml +++ b/modules/nf-core/grabix/check/environment.yml @@ -1,7 +1,5 @@ -name: grabix_check channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::grabix=0.1.8 diff --git a/modules/nf-core/graphmap2/align/environment.yml b/modules/nf-core/graphmap2/align/environment.yml index f6cd9ca5c890..2138c7f46a43 100644 --- a/modules/nf-core/graphmap2/align/environment.yml +++ b/modules/nf-core/graphmap2/align/environment.yml @@ -1,7 +1,5 @@ -name: graphmap2_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::graphmap=0.6.3 diff --git a/modules/nf-core/graphmap2/index/environment.yml b/modules/nf-core/graphmap2/index/environment.yml index f2472bd92c14..2138c7f46a43 100644 --- a/modules/nf-core/graphmap2/index/environment.yml +++ b/modules/nf-core/graphmap2/index/environment.yml @@ -1,7 +1,5 @@ -name: graphmap2_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::graphmap=0.6.3 diff --git a/modules/nf-core/graphtyper/genotype/environment.yml b/modules/nf-core/graphtyper/genotype/environment.yml index b4d95c026183..57b5ac801cfc 100644 --- a/modules/nf-core/graphtyper/genotype/environment.yml +++ b/modules/nf-core/graphtyper/genotype/environment.yml @@ -1,7 +1,5 @@ -name: graphtyper_genotype channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::graphtyper=2.7.2 diff --git a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml index 0f22a4f9d518..57b5ac801cfc 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/environment.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/environment.yml @@ -1,4 +1,3 @@ -name: graphtyper_vcfconcatenate channels: - conda-forge - bioconda diff --git a/modules/nf-core/gridss/gridss/environment.yml b/modules/nf-core/gridss/gridss/environment.yml index 88b385610954..db37d675e605 100644 --- a/modules/nf-core/gridss/gridss/environment.yml +++ b/modules/nf-core/gridss/gridss/environment.yml @@ -1,7 +1,5 @@ -name: gridss_gridss channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gridss=2.13.2 diff --git a/modules/nf-core/gsea/gsea/environment.yml b/modules/nf-core/gsea/gsea/environment.yml index cb3c41e7ae7d..c5780466ab45 100644 --- a/modules/nf-core/gsea/gsea/environment.yml +++ b/modules/nf-core/gsea/gsea/environment.yml @@ -1,7 +1,5 @@ -name: gsea_gsea channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gsea=4.3.2 diff --git a/modules/nf-core/gstama/collapse/environment.yml b/modules/nf-core/gstama/collapse/environment.yml index c58245ecd6bd..cef33450cda3 100644 --- a/modules/nf-core/gstama/collapse/environment.yml +++ b/modules/nf-core/gstama/collapse/environment.yml @@ -1,7 +1,5 @@ -name: gstama_collapse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gstama/merge/environment.yml b/modules/nf-core/gstama/merge/environment.yml index 44d574131a09..cef33450cda3 100644 --- a/modules/nf-core/gstama/merge/environment.yml +++ b/modules/nf-core/gstama/merge/environment.yml @@ -1,7 +1,5 @@ -name: gstama_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gstama/polyacleanup/environment.yml b/modules/nf-core/gstama/polyacleanup/environment.yml index 7c143ffa4c25..cef33450cda3 100644 --- a/modules/nf-core/gstama/polyacleanup/environment.yml +++ b/modules/nf-core/gstama/polyacleanup/environment.yml @@ -1,7 +1,5 @@ -name: gstama_polyacleanup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gs-tama=1.0.3 diff --git a/modules/nf-core/gt/gff3/environment.yml b/modules/nf-core/gt/gff3/environment.yml index 8289fb311eb1..666eb47f1168 100644 --- a/modules/nf-core/gt/gff3/environment.yml +++ b/modules/nf-core/gt/gff3/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gt_gff3" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::genometools-genometools=1.6.5" diff --git a/modules/nf-core/gt/gff3validator/environment.yml b/modules/nf-core/gt/gff3validator/environment.yml index ea57ebe06a8f..666eb47f1168 100644 --- a/modules/nf-core/gt/gff3validator/environment.yml +++ b/modules/nf-core/gt/gff3validator/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gt_gff3validator" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::genometools-genometools=1.6.5" diff --git a/modules/nf-core/gt/ltrharvest/environment.yml b/modules/nf-core/gt/ltrharvest/environment.yml index b4ca03d06b49..666eb47f1168 100644 --- a/modules/nf-core/gt/ltrharvest/environment.yml +++ b/modules/nf-core/gt/ltrharvest/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gt_ltrharvest" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::genometools-genometools=1.6.5" diff --git a/modules/nf-core/gt/stat/environment.yml b/modules/nf-core/gt/stat/environment.yml index dca959b3b2cb..666eb47f1168 100644 --- a/modules/nf-core/gt/stat/environment.yml +++ b/modules/nf-core/gt/stat/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gt_stat" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::genometools-genometools=1.6.5" diff --git a/modules/nf-core/gt/suffixerator/environment.yml b/modules/nf-core/gt/suffixerator/environment.yml index 5e602d5a3c6d..666eb47f1168 100644 --- a/modules/nf-core/gt/suffixerator/environment.yml +++ b/modules/nf-core/gt/suffixerator/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gt_suffixerator" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::genometools-genometools=1.6.5" diff --git a/modules/nf-core/gtdbtk/classifywf/environment.yml b/modules/nf-core/gtdbtk/classifywf/environment.yml index 16b8dbb6dc7a..500531eadc7a 100644 --- a/modules/nf-core/gtdbtk/classifywf/environment.yml +++ b/modules/nf-core/gtdbtk/classifywf/environment.yml @@ -1,7 +1,5 @@ -name: gtdbtk_classifywf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gtdbtk=2.4.0 diff --git a/modules/nf-core/gtfsort/environment.yml b/modules/nf-core/gtfsort/environment.yml index 88233be343cb..34753e4dd2c9 100644 --- a/modules/nf-core/gtfsort/environment.yml +++ b/modules/nf-core/gtfsort/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "gtfsort" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::gtfsort=0.2.2" diff --git a/modules/nf-core/gubbins/environment.yml b/modules/nf-core/gubbins/environment.yml index 0e8285b41c2d..25ae21c00580 100644 --- a/modules/nf-core/gubbins/environment.yml +++ b/modules/nf-core/gubbins/environment.yml @@ -1,4 +1,3 @@ -name: gubbins channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunc/downloaddb/environment.yml b/modules/nf-core/gunc/downloaddb/environment.yml index 25540dddd2fe..d7301428db4d 100644 --- a/modules/nf-core/gunc/downloaddb/environment.yml +++ b/modules/nf-core/gunc/downloaddb/environment.yml @@ -1,4 +1,3 @@ -name: gunc_downloaddb channels: - conda-forge - bioconda diff --git a/modules/nf-core/gunc/mergecheckm/environment.yml b/modules/nf-core/gunc/mergecheckm/environment.yml index 12513be8caeb..d7301428db4d 100644 --- a/modules/nf-core/gunc/mergecheckm/environment.yml +++ b/modules/nf-core/gunc/mergecheckm/environment.yml @@ -1,7 +1,5 @@ -name: gunc_mergecheckm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gunc=1.0.5 diff --git a/modules/nf-core/gunc/run/environment.yml b/modules/nf-core/gunc/run/environment.yml index 80bbec3001ab..d7301428db4d 100644 --- a/modules/nf-core/gunc/run/environment.yml +++ b/modules/nf-core/gunc/run/environment.yml @@ -1,7 +1,5 @@ -name: gunc_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gunc=1.0.5 diff --git a/modules/nf-core/gunzip/environment.yml b/modules/nf-core/gunzip/environment.yml index dfc02a7b54e9..c7794856d84c 100644 --- a/modules/nf-core/gunzip/environment.yml +++ b/modules/nf-core/gunzip/environment.yml @@ -1,8 +1,6 @@ -name: gunzip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/gvcftools/extractvariants/environment.yml b/modules/nf-core/gvcftools/extractvariants/environment.yml index b5c8b28d8800..ebe01104141e 100644 --- a/modules/nf-core/gvcftools/extractvariants/environment.yml +++ b/modules/nf-core/gvcftools/extractvariants/environment.yml @@ -1,7 +1,5 @@ -name: gvcftools_extractvariants channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::gvcftools=0.17.0 diff --git a/modules/nf-core/hamronization/abricate/environment.yml b/modules/nf-core/hamronization/abricate/environment.yml index 75f349f162f0..791b9c96108c 100644 --- a/modules/nf-core/hamronization/abricate/environment.yml +++ b/modules/nf-core/hamronization/abricate/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_abricate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hamronization/amrfinderplus/environment.yml b/modules/nf-core/hamronization/amrfinderplus/environment.yml index 2f9cb27fb357..791b9c96108c 100644 --- a/modules/nf-core/hamronization/amrfinderplus/environment.yml +++ b/modules/nf-core/hamronization/amrfinderplus/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_amrfinderplus channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hamronization/deeparg/environment.yml b/modules/nf-core/hamronization/deeparg/environment.yml index c9db54c6a5ec..791b9c96108c 100644 --- a/modules/nf-core/hamronization/deeparg/environment.yml +++ b/modules/nf-core/hamronization/deeparg/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_deeparg channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hamronization/fargene/environment.yml b/modules/nf-core/hamronization/fargene/environment.yml index 6507e7d42c63..791b9c96108c 100644 --- a/modules/nf-core/hamronization/fargene/environment.yml +++ b/modules/nf-core/hamronization/fargene/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_fargene channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hamronization/rgi/environment.yml b/modules/nf-core/hamronization/rgi/environment.yml index 91d03e499b4e..791b9c96108c 100644 --- a/modules/nf-core/hamronization/rgi/environment.yml +++ b/modules/nf-core/hamronization/rgi/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_rgi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hamronization/summarize/environment.yml b/modules/nf-core/hamronization/summarize/environment.yml index 1872a689cb51..791b9c96108c 100644 --- a/modules/nf-core/hamronization/summarize/environment.yml +++ b/modules/nf-core/hamronization/summarize/environment.yml @@ -1,7 +1,5 @@ -name: hamronization_summarize channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hamronization=1.1.4 diff --git a/modules/nf-core/hapibd/environment.yml b/modules/nf-core/hapibd/environment.yml index 4c2f52d3d384..0e4cf39fb4b5 100644 --- a/modules/nf-core/hapibd/environment.yml +++ b/modules/nf-core/hapibd/environment.yml @@ -1,4 +1,3 @@ -name: hapibd channels: - conda-forge - bioconda diff --git a/modules/nf-core/haplocheck/environment.yml b/modules/nf-core/haplocheck/environment.yml index 8d06a67e5ceb..4fb40238b7da 100644 --- a/modules/nf-core/haplocheck/environment.yml +++ b/modules/nf-core/haplocheck/environment.yml @@ -1,7 +1,5 @@ -name: haplocheck channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::haplocheck=1.3.3 diff --git a/modules/nf-core/haplogrep2/classify/environment.yml b/modules/nf-core/haplogrep2/classify/environment.yml index 12949452f810..b84579e6747b 100644 --- a/modules/nf-core/haplogrep2/classify/environment.yml +++ b/modules/nf-core/haplogrep2/classify/environment.yml @@ -1,7 +1,5 @@ -name: haplogrep2_classify channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::haplogrep=2.4.0 diff --git a/modules/nf-core/happy/ftxpy/environment.yml b/modules/nf-core/happy/ftxpy/environment.yml index 7324e7b2c584..cc251479f644 100644 --- a/modules/nf-core/happy/ftxpy/environment.yml +++ b/modules/nf-core/happy/ftxpy/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "happy_ftxpy" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::hap.py=0.3.15" diff --git a/modules/nf-core/happy/happy/environment.yml b/modules/nf-core/happy/happy/environment.yml index 3d29dcb276d6..d65fa5db90a6 100644 --- a/modules/nf-core/happy/happy/environment.yml +++ b/modules/nf-core/happy/happy/environment.yml @@ -1,7 +1,5 @@ -name: happy_happy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hap.py=0.3.14 diff --git a/modules/nf-core/happy/prepy/environment.yml b/modules/nf-core/happy/prepy/environment.yml index d1598343f2f7..d65fa5db90a6 100644 --- a/modules/nf-core/happy/prepy/environment.yml +++ b/modules/nf-core/happy/prepy/environment.yml @@ -1,7 +1,5 @@ -name: happy_prepy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hap.py=0.3.14 diff --git a/modules/nf-core/happy/sompy/environment.yml b/modules/nf-core/happy/sompy/environment.yml index 64ed7f55643a..d65fa5db90a6 100644 --- a/modules/nf-core/happy/sompy/environment.yml +++ b/modules/nf-core/happy/sompy/environment.yml @@ -1,7 +1,5 @@ -name: happy_sompy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hap.py=0.3.14 diff --git a/modules/nf-core/hicap/environment.yml b/modules/nf-core/hicap/environment.yml index a8c3e9de5ba5..6eb0186fd8de 100644 --- a/modules/nf-core/hicap/environment.yml +++ b/modules/nf-core/hicap/environment.yml @@ -1,7 +1,5 @@ -name: hicap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hicap=1.0.3 diff --git a/modules/nf-core/hicexplorer/hicpca/environment.yml b/modules/nf-core/hicexplorer/hicpca/environment.yml index 0838ab5da610..4b8b663fb7a2 100644 --- a/modules/nf-core/hicexplorer/hicpca/environment.yml +++ b/modules/nf-core/hicexplorer/hicpca/environment.yml @@ -1,8 +1,6 @@ -name: hicexplorer_hicpca channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hicexplorer=3.7.2 - numpy=1.23.5 diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml index ede93247d8a6..d3bd7d0cea29 100644 --- a/modules/nf-core/hifiasm/environment.yml +++ b/modules/nf-core/hifiasm/environment.yml @@ -1,7 +1,5 @@ -name: hifiasm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hifiasm=0.19.8 diff --git a/modules/nf-core/hisat2/align/environment.yml b/modules/nf-core/hisat2/align/environment.yml index 0c1415f94e6b..26c62a3bfda4 100644 --- a/modules/nf-core/hisat2/align/environment.yml +++ b/modules/nf-core/hisat2/align/environment.yml @@ -1,8 +1,6 @@ -name: hisat2_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/hisat2/build/environment.yml b/modules/nf-core/hisat2/build/environment.yml index 2e67cd3eaaf5..afced73382db 100644 --- a/modules/nf-core/hisat2/build/environment.yml +++ b/modules/nf-core/hisat2/build/environment.yml @@ -1,7 +1,5 @@ -name: hisat2_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hisat2/extractsplicesites/environment.yml b/modules/nf-core/hisat2/extractsplicesites/environment.yml index 4b03e5e46665..afced73382db 100644 --- a/modules/nf-core/hisat2/extractsplicesites/environment.yml +++ b/modules/nf-core/hisat2/extractsplicesites/environment.yml @@ -1,7 +1,5 @@ -name: hisat2_extractsplicesites channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hisat2=2.2.1 diff --git a/modules/nf-core/hlala/preparegraph/environment.yml b/modules/nf-core/hlala/preparegraph/environment.yml index eddce47af2f5..3cebeff05bfc 100644 --- a/modules/nf-core/hlala/preparegraph/environment.yml +++ b/modules/nf-core/hlala/preparegraph/environment.yml @@ -1,5 +1,3 @@ -name: hlala_preparegraph channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/hlala/typing/environment.yml b/modules/nf-core/hlala/typing/environment.yml index 330ab0a26c92..00695d608270 100644 --- a/modules/nf-core/hlala/typing/environment.yml +++ b/modules/nf-core/hlala/typing/environment.yml @@ -1,7 +1,5 @@ -name: hlala_typing channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hla-la=1.0.3 diff --git a/modules/nf-core/hmmcopy/gccounter/environment.yml b/modules/nf-core/hmmcopy/gccounter/environment.yml index ee209530e1af..8284f1c20950 100644 --- a/modules/nf-core/hmmcopy/gccounter/environment.yml +++ b/modules/nf-core/hmmcopy/gccounter/environment.yml @@ -1,7 +1,5 @@ -name: hmmcopy_gccounter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmcopy=0.1.1 diff --git a/modules/nf-core/hmmcopy/generatemap/environment.yml b/modules/nf-core/hmmcopy/generatemap/environment.yml index 0c647804495b..8284f1c20950 100644 --- a/modules/nf-core/hmmcopy/generatemap/environment.yml +++ b/modules/nf-core/hmmcopy/generatemap/environment.yml @@ -1,7 +1,5 @@ -name: hmmcopy_generatemap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmcopy=0.1.1 diff --git a/modules/nf-core/hmmcopy/mapcounter/environment.yml b/modules/nf-core/hmmcopy/mapcounter/environment.yml index 4bdfe0fbad62..8284f1c20950 100644 --- a/modules/nf-core/hmmcopy/mapcounter/environment.yml +++ b/modules/nf-core/hmmcopy/mapcounter/environment.yml @@ -1,7 +1,5 @@ -name: hmmcopy_mapcounter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmcopy=0.1.1 diff --git a/modules/nf-core/hmmcopy/readcounter/environment.yml b/modules/nf-core/hmmcopy/readcounter/environment.yml index cfbdf8ac8532..8284f1c20950 100644 --- a/modules/nf-core/hmmcopy/readcounter/environment.yml +++ b/modules/nf-core/hmmcopy/readcounter/environment.yml @@ -1,7 +1,5 @@ -name: hmmcopy_readcounter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmcopy=0.1.1 diff --git a/modules/nf-core/hmmer/eslalimask/environment.yml b/modules/nf-core/hmmer/eslalimask/environment.yml index ed14ff8637c2..7c62eac7e3a5 100644 --- a/modules/nf-core/hmmer/eslalimask/environment.yml +++ b/modules/nf-core/hmmer/eslalimask/environment.yml @@ -1,7 +1,5 @@ -name: hmmer_eslalimask channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/eslreformat/environment.yml b/modules/nf-core/hmmer/eslreformat/environment.yml index a847b7d31947..7c62eac7e3a5 100644 --- a/modules/nf-core/hmmer/eslreformat/environment.yml +++ b/modules/nf-core/hmmer/eslreformat/environment.yml @@ -1,7 +1,5 @@ -name: hmmer_eslreformat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmalign/environment.yml b/modules/nf-core/hmmer/hmmalign/environment.yml index 9fa6bdafc0d3..7c62eac7e3a5 100644 --- a/modules/nf-core/hmmer/hmmalign/environment.yml +++ b/modules/nf-core/hmmer/hmmalign/environment.yml @@ -1,7 +1,5 @@ -name: hmmer_hmmalign channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmbuild/environment.yml b/modules/nf-core/hmmer/hmmbuild/environment.yml index 5eb083ed9ed9..7c62eac7e3a5 100644 --- a/modules/nf-core/hmmer/hmmbuild/environment.yml +++ b/modules/nf-core/hmmer/hmmbuild/environment.yml @@ -1,4 +1,3 @@ -name: hmmer_hmmbuild channels: - conda-forge - bioconda diff --git a/modules/nf-core/hmmer/hmmfetch/environment.yml b/modules/nf-core/hmmer/hmmfetch/environment.yml index 05544c29d991..7c62eac7e3a5 100644 --- a/modules/nf-core/hmmer/hmmfetch/environment.yml +++ b/modules/nf-core/hmmer/hmmfetch/environment.yml @@ -1,7 +1,5 @@ -name: hmmer_hmmfetch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.3.2 diff --git a/modules/nf-core/hmmer/hmmrank/environment.yml b/modules/nf-core/hmmer/hmmrank/environment.yml index 789fc97c98b5..653e9ea1d517 100644 --- a/modules/nf-core/hmmer/hmmrank/environment.yml +++ b/modules/nf-core/hmmer/hmmrank/environment.yml @@ -1,9 +1,6 @@ -name: hmmer_hmmrank - channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-base=4.2.3 diff --git a/modules/nf-core/hmmer/hmmsearch/environment.yml b/modules/nf-core/hmmer/hmmsearch/environment.yml index d672c2b31c7c..c5ddec5d9128 100644 --- a/modules/nf-core/hmmer/hmmsearch/environment.yml +++ b/modules/nf-core/hmmer/hmmsearch/environment.yml @@ -1,7 +1,5 @@ -name: hmmer_hmmsearch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmmer=3.4 diff --git a/modules/nf-core/hmtnote/annotate/environment.yml b/modules/nf-core/hmtnote/annotate/environment.yml index 46bd87aa052b..1d9d20e3fe9c 100644 --- a/modules/nf-core/hmtnote/annotate/environment.yml +++ b/modules/nf-core/hmtnote/annotate/environment.yml @@ -1,7 +1,5 @@ -name: hmtnote_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hmtnote=0.7.2 diff --git a/modules/nf-core/homer/annotatepeaks/environment.yml b/modules/nf-core/homer/annotatepeaks/environment.yml index f6522d695038..631357d04a2d 100644 --- a/modules/nf-core/homer/annotatepeaks/environment.yml +++ b/modules/nf-core/homer/annotatepeaks/environment.yml @@ -1,4 +1,3 @@ -name: homer_annotatepeaks channels: - conda-forge - bioconda diff --git a/modules/nf-core/homer/findpeaks/environment.yml b/modules/nf-core/homer/findpeaks/environment.yml index a5766cfb740b..73aba35d3d9f 100644 --- a/modules/nf-core/homer/findpeaks/environment.yml +++ b/modules/nf-core/homer/findpeaks/environment.yml @@ -1,7 +1,5 @@ -name: homer_findpeaks channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11=pl526hc9558a2_3 diff --git a/modules/nf-core/homer/maketagdirectory/environment.yml b/modules/nf-core/homer/maketagdirectory/environment.yml index c3ad2cc9db4a..e1a60845799a 100644 --- a/modules/nf-core/homer/maketagdirectory/environment.yml +++ b/modules/nf-core/homer/maketagdirectory/environment.yml @@ -1,8 +1,6 @@ -name: homer_maketagdirectory channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11 - bioconda::samtools=1.11 diff --git a/modules/nf-core/homer/makeucscfile/environment.yml b/modules/nf-core/homer/makeucscfile/environment.yml index 79963b3491c4..73aba35d3d9f 100644 --- a/modules/nf-core/homer/makeucscfile/environment.yml +++ b/modules/nf-core/homer/makeucscfile/environment.yml @@ -1,7 +1,5 @@ -name: homer_makeucscfile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11=pl526hc9558a2_3 diff --git a/modules/nf-core/homer/pos2bed/environment.yml b/modules/nf-core/homer/pos2bed/environment.yml index 94ed99048832..631357d04a2d 100644 --- a/modules/nf-core/homer/pos2bed/environment.yml +++ b/modules/nf-core/homer/pos2bed/environment.yml @@ -1,7 +1,5 @@ -name: homer_pos2bed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::homer=4.11 diff --git a/modules/nf-core/hpsuissero/environment.yml b/modules/nf-core/hpsuissero/environment.yml index 3abdae453d38..000ffe9112b3 100644 --- a/modules/nf-core/hpsuissero/environment.yml +++ b/modules/nf-core/hpsuissero/environment.yml @@ -1,7 +1,5 @@ -name: hpsuissero channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hpsuissero=1.0.1 diff --git a/modules/nf-core/htseq/count/environment.yml b/modules/nf-core/htseq/count/environment.yml index 4c11f606f2ae..f1f6a7f0cc87 100644 --- a/modules/nf-core/htseq/count/environment.yml +++ b/modules/nf-core/htseq/count/environment.yml @@ -1,7 +1,5 @@ -name: htseq_count channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htseq=2.0.3 diff --git a/modules/nf-core/htsnimtools/vcfcheck/environment.yml b/modules/nf-core/htsnimtools/vcfcheck/environment.yml index d4c9841e0c22..1129a644718d 100644 --- a/modules/nf-core/htsnimtools/vcfcheck/environment.yml +++ b/modules/nf-core/htsnimtools/vcfcheck/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "htsnimtools_vcfcheck" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::hts-nim-tools=0.3.11" diff --git a/modules/nf-core/humid/environment.yml b/modules/nf-core/humid/environment.yml index d8004476697a..b5e4a814c429 100644 --- a/modules/nf-core/humid/environment.yml +++ b/modules/nf-core/humid/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "humid" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::humid=1.0.4" diff --git a/modules/nf-core/hypo/environment.yml b/modules/nf-core/hypo/environment.yml index 70e432fada78..9182668f41fa 100644 --- a/modules/nf-core/hypo/environment.yml +++ b/modules/nf-core/hypo/environment.yml @@ -1,4 +1,3 @@ -name: hypo channels: - conda-forge - bioconda diff --git a/modules/nf-core/ichorcna/createpon/environment.yml b/modules/nf-core/ichorcna/createpon/environment.yml index a26548740d23..a676ae360e35 100644 --- a/modules/nf-core/ichorcna/createpon/environment.yml +++ b/modules/nf-core/ichorcna/createpon/environment.yml @@ -1,7 +1,5 @@ -name: ichorcna_createpon channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-ichorcna=0.5.1 diff --git a/modules/nf-core/ichorcna/run/environment.yml b/modules/nf-core/ichorcna/run/environment.yml index ae6a1571fa01..a676ae360e35 100644 --- a/modules/nf-core/ichorcna/run/environment.yml +++ b/modules/nf-core/ichorcna/run/environment.yml @@ -1,7 +1,5 @@ -name: ichorcna_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-ichorcna=0.5.1 diff --git a/modules/nf-core/icountmini/metagene/environment.yml b/modules/nf-core/icountmini/metagene/environment.yml index f2edecc4f0f4..d1ebc705ec03 100644 --- a/modules/nf-core/icountmini/metagene/environment.yml +++ b/modules/nf-core/icountmini/metagene/environment.yml @@ -1,7 +1,5 @@ -name: icountmini_metagene channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::icount-mini=3.0.1 diff --git a/modules/nf-core/icountmini/peaks/environment.yml b/modules/nf-core/icountmini/peaks/environment.yml index 11a5125dcc96..02e0549f55c6 100644 --- a/modules/nf-core/icountmini/peaks/environment.yml +++ b/modules/nf-core/icountmini/peaks/environment.yml @@ -1,7 +1,5 @@ -name: icountmini_peaks channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::icount-mini=2.0.3 diff --git a/modules/nf-core/icountmini/segment/environment.yml b/modules/nf-core/icountmini/segment/environment.yml index ec8622049885..02e0549f55c6 100644 --- a/modules/nf-core/icountmini/segment/environment.yml +++ b/modules/nf-core/icountmini/segment/environment.yml @@ -1,7 +1,5 @@ -name: icountmini_segment channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::icount-mini=2.0.3 diff --git a/modules/nf-core/icountmini/sigxls/environment.yml b/modules/nf-core/icountmini/sigxls/environment.yml index 083f6cd3bcc0..02e0549f55c6 100644 --- a/modules/nf-core/icountmini/sigxls/environment.yml +++ b/modules/nf-core/icountmini/sigxls/environment.yml @@ -1,7 +1,5 @@ -name: icountmini_sigxls channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::icount-mini=2.0.3 diff --git a/modules/nf-core/icountmini/summary/environment.yml b/modules/nf-core/icountmini/summary/environment.yml index 253eaf5179ca..02e0549f55c6 100644 --- a/modules/nf-core/icountmini/summary/environment.yml +++ b/modules/nf-core/icountmini/summary/environment.yml @@ -1,7 +1,5 @@ -name: icountmini_summary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::icount-mini=2.0.3 diff --git a/modules/nf-core/idemux/environment.yml b/modules/nf-core/idemux/environment.yml index fa878d7a8d12..0ab6c3fa1b2d 100644 --- a/modules/nf-core/idemux/environment.yml +++ b/modules/nf-core/idemux/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "idemux" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::idemux=0.1.6" diff --git a/modules/nf-core/idr/environment.yml b/modules/nf-core/idr/environment.yml index 2790cc3fa4af..60af1d2e0b08 100644 --- a/modules/nf-core/idr/environment.yml +++ b/modules/nf-core/idr/environment.yml @@ -1,4 +1,3 @@ -name: idr channels: - conda-forge - bioconda diff --git a/modules/nf-core/igv/js/environment.yml b/modules/nf-core/igv/js/environment.yml index e6046ef8437d..c7794856d84c 100644 --- a/modules/nf-core/igv/js/environment.yml +++ b/modules/nf-core/igv/js/environment.yml @@ -1,8 +1,6 @@ -name: igv_js channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/igvreports/environment.yml b/modules/nf-core/igvreports/environment.yml index 5ed725f46e92..fc4c39fd65f0 100644 --- a/modules/nf-core/igvreports/environment.yml +++ b/modules/nf-core/igvreports/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "igvreports" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::igv-reports=1.12.0" diff --git a/modules/nf-core/ilastik/multicut/environment.yml b/modules/nf-core/ilastik/multicut/environment.yml index ecd6fa335bbe..3cebeff05bfc 100644 --- a/modules/nf-core/ilastik/multicut/environment.yml +++ b/modules/nf-core/ilastik/multicut/environment.yml @@ -1,5 +1,3 @@ -name: ilastik_multicut channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/ilastik/pixelclassification/environment.yml b/modules/nf-core/ilastik/pixelclassification/environment.yml index a8dafc2c0b2e..3cebeff05bfc 100644 --- a/modules/nf-core/ilastik/pixelclassification/environment.yml +++ b/modules/nf-core/ilastik/pixelclassification/environment.yml @@ -1,5 +1,3 @@ -name: ilastik_pixelclassification channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/instrain/compare/environment.yml b/modules/nf-core/instrain/compare/environment.yml index c132becfd363..38edb5dc5ff0 100644 --- a/modules/nf-core/instrain/compare/environment.yml +++ b/modules/nf-core/instrain/compare/environment.yml @@ -1,8 +1,6 @@ -name: instrain_compare channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::instrain=1.7.1 - bioconda::samtools=1.16.1 # Version from container diff --git a/modules/nf-core/instrain/profile/environment.yml b/modules/nf-core/instrain/profile/environment.yml index 064c12cad5c1..38edb5dc5ff0 100644 --- a/modules/nf-core/instrain/profile/environment.yml +++ b/modules/nf-core/instrain/profile/environment.yml @@ -1,8 +1,6 @@ -name: instrain_profile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::instrain=1.7.1 - bioconda::samtools=1.16.1 # Version from container diff --git a/modules/nf-core/interproscan/environment.yml b/modules/nf-core/interproscan/environment.yml index 36ec6fafd8c8..d1ce2af7927f 100644 --- a/modules/nf-core/interproscan/environment.yml +++ b/modules/nf-core/interproscan/environment.yml @@ -1,7 +1,5 @@ -name: interproscan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::interproscan=5.59_91.0 diff --git a/modules/nf-core/iphop/download/environment.yml b/modules/nf-core/iphop/download/environment.yml index 7b90c7ba16d6..871100c66a5b 100644 --- a/modules/nf-core/iphop/download/environment.yml +++ b/modules/nf-core/iphop/download/environment.yml @@ -1,7 +1,5 @@ -name: iphop_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::iphop=1.3.2 diff --git a/modules/nf-core/iphop/predict/environment.yml b/modules/nf-core/iphop/predict/environment.yml index 5dda3a70a99b..871100c66a5b 100644 --- a/modules/nf-core/iphop/predict/environment.yml +++ b/modules/nf-core/iphop/predict/environment.yml @@ -1,7 +1,5 @@ -name: iphop_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::iphop=1.3.2 diff --git a/modules/nf-core/iqtree/environment.yml b/modules/nf-core/iqtree/environment.yml index 106878180ba9..702c05086bee 100644 --- a/modules/nf-core/iqtree/environment.yml +++ b/modules/nf-core/iqtree/environment.yml @@ -1,7 +1,5 @@ -name: iqtree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::iqtree=2.3.4 diff --git a/modules/nf-core/islandpath/environment.yml b/modules/nf-core/islandpath/environment.yml index 13982a73fec9..71cb9ec6b947 100644 --- a/modules/nf-core/islandpath/environment.yml +++ b/modules/nf-core/islandpath/environment.yml @@ -1,7 +1,5 @@ -name: islandpath channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::islandpath=1.0.6 diff --git a/modules/nf-core/ismapper/environment.yml b/modules/nf-core/ismapper/environment.yml index 0a178373f8fd..5249a0a86b70 100644 --- a/modules/nf-core/ismapper/environment.yml +++ b/modules/nf-core/ismapper/environment.yml @@ -1,7 +1,5 @@ -name: ismapper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ismapper=2.0.2 diff --git a/modules/nf-core/isoseq/cluster/environment.yml b/modules/nf-core/isoseq/cluster/environment.yml index bb5355772c6d..f048d21c2e1f 100644 --- a/modules/nf-core/isoseq/cluster/environment.yml +++ b/modules/nf-core/isoseq/cluster/environment.yml @@ -1,7 +1,5 @@ -name: isoseq_cluster channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::isoseq=4.0.0 diff --git a/modules/nf-core/isoseq/refine/environment.yml b/modules/nf-core/isoseq/refine/environment.yml index 05fb46ff5e48..f048d21c2e1f 100644 --- a/modules/nf-core/isoseq/refine/environment.yml +++ b/modules/nf-core/isoseq/refine/environment.yml @@ -1,7 +1,5 @@ -name: isoseq_refine channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::isoseq=4.0.0 diff --git a/modules/nf-core/isoseq3/tag/environment.yml b/modules/nf-core/isoseq3/tag/environment.yml index d773d60297e2..ec4d15e58a82 100644 --- a/modules/nf-core/isoseq3/tag/environment.yml +++ b/modules/nf-core/isoseq3/tag/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "isoseq3_tag" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::isoseq3=4.0.0" diff --git a/modules/nf-core/ivar/consensus/environment.yml b/modules/nf-core/ivar/consensus/environment.yml index 75e6ef41745f..6d04535789f7 100644 --- a/modules/nf-core/ivar/consensus/environment.yml +++ b/modules/nf-core/ivar/consensus/environment.yml @@ -1,4 +1,3 @@ -name: ivar_consensus channels: - conda-forge - bioconda diff --git a/modules/nf-core/ivar/trim/environment.yml b/modules/nf-core/ivar/trim/environment.yml index c1119609e145..6d04535789f7 100644 --- a/modules/nf-core/ivar/trim/environment.yml +++ b/modules/nf-core/ivar/trim/environment.yml @@ -1,7 +1,5 @@ -name: ivar_trim channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ivar=1.4.3 diff --git a/modules/nf-core/ivar/variants/environment.yml b/modules/nf-core/ivar/variants/environment.yml index 6b1443eb15ff..6d04535789f7 100644 --- a/modules/nf-core/ivar/variants/environment.yml +++ b/modules/nf-core/ivar/variants/environment.yml @@ -1,4 +1,3 @@ -name: ivar_variants channels: - conda-forge - bioconda diff --git a/modules/nf-core/jasminesv/environment.yml b/modules/nf-core/jasminesv/environment.yml index 7b26adfe3504..a0ef927ea416 100644 --- a/modules/nf-core/jasminesv/environment.yml +++ b/modules/nf-core/jasminesv/environment.yml @@ -1,8 +1,6 @@ -name: jasminesv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::jasminesv=1.1.5 - bioconda::htslib=1.15.1 diff --git a/modules/nf-core/jupyternotebook/environment.yml b/modules/nf-core/jupyternotebook/environment.yml index 98fc481a700b..d9ef11a3a9f2 100644 --- a/modules/nf-core/jupyternotebook/environment.yml +++ b/modules/nf-core/jupyternotebook/environment.yml @@ -1,8 +1,6 @@ -name: jupyternotebook channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::ipykernel=6.0.3 - conda-forge::jupytext=1.11.4 diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml index cf7e84012ee9..e71f3d436687 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -1,6 +1,5 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "jvarkit_vcfpolyx" channels: - bioconda - conda-forge diff --git a/modules/nf-core/kaiju/kaiju/environment.yml b/modules/nf-core/kaiju/kaiju/environment.yml index baac450b265f..3bb316c1caf6 100644 --- a/modules/nf-core/kaiju/kaiju/environment.yml +++ b/modules/nf-core/kaiju/kaiju/environment.yml @@ -1,7 +1,5 @@ -name: kaiju_kaiju channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kaiju=1.10.0 diff --git a/modules/nf-core/kaiju/kaiju2krona/environment.yml b/modules/nf-core/kaiju/kaiju2krona/environment.yml index 2905be97f692..3bb316c1caf6 100644 --- a/modules/nf-core/kaiju/kaiju2krona/environment.yml +++ b/modules/nf-core/kaiju/kaiju2krona/environment.yml @@ -1,7 +1,5 @@ -name: kaiju_kaiju2krona channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kaiju=1.10.0 diff --git a/modules/nf-core/kaiju/kaiju2table/environment.yml b/modules/nf-core/kaiju/kaiju2table/environment.yml index 18685f415760..3bb316c1caf6 100644 --- a/modules/nf-core/kaiju/kaiju2table/environment.yml +++ b/modules/nf-core/kaiju/kaiju2table/environment.yml @@ -1,7 +1,5 @@ -name: kaiju_kaiju2table channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kaiju=1.10.0 diff --git a/modules/nf-core/kaiju/mergeoutputs/environment.yml b/modules/nf-core/kaiju/mergeoutputs/environment.yml index c42f573c1319..3ecb973eeec8 100644 --- a/modules/nf-core/kaiju/mergeoutputs/environment.yml +++ b/modules/nf-core/kaiju/mergeoutputs/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "kaiju_mergeoutputs" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kaiju=1.10.0" diff --git a/modules/nf-core/kaiju/mkfmi/environment.yml b/modules/nf-core/kaiju/mkfmi/environment.yml index 9b66ea1eaa1f..3bb316c1caf6 100644 --- a/modules/nf-core/kaiju/mkfmi/environment.yml +++ b/modules/nf-core/kaiju/mkfmi/environment.yml @@ -1,7 +1,5 @@ -name: kaiju_mkfmi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kaiju=1.10.0 diff --git a/modules/nf-core/kalign/align/environment.yml b/modules/nf-core/kalign/align/environment.yml index 93563eaeb56c..1e47a646888e 100644 --- a/modules/nf-core/kalign/align/environment.yml +++ b/modules/nf-core/kalign/align/environment.yml @@ -1,8 +1,6 @@ -name: kalign_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kalign3=3.4.0 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/kallisto/index/environment.yml b/modules/nf-core/kallisto/index/environment.yml index 471b006a898b..27be649180f1 100644 --- a/modules/nf-core/kallisto/index/environment.yml +++ b/modules/nf-core/kallisto/index/environment.yml @@ -1,7 +1,5 @@ -name: kallisto_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallisto/quant/environment.yml b/modules/nf-core/kallisto/quant/environment.yml index c2d6306bb2ce..27be649180f1 100644 --- a/modules/nf-core/kallisto/quant/environment.yml +++ b/modules/nf-core/kallisto/quant/environment.yml @@ -1,7 +1,5 @@ -name: kallisto_quant channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kallisto=0.48.0 diff --git a/modules/nf-core/kallistobustools/count/environment.yml b/modules/nf-core/kallistobustools/count/environment.yml index 024f0afcad8a..5aa2fdb9548f 100644 --- a/modules/nf-core/kallistobustools/count/environment.yml +++ b/modules/nf-core/kallistobustools/count/environment.yml @@ -1,7 +1,5 @@ -name: kallistobustools_count channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kb-python=0.28.2 diff --git a/modules/nf-core/kallistobustools/ref/environment.yml b/modules/nf-core/kallistobustools/ref/environment.yml index 6ae07a8c395f..698eff03032d 100644 --- a/modules/nf-core/kallistobustools/ref/environment.yml +++ b/modules/nf-core/kallistobustools/ref/environment.yml @@ -1,8 +1,6 @@ -name: kallistobustools_ref channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kb-python=0.28.2 - conda-forge::requests>=2.23.0 diff --git a/modules/nf-core/kat/hist/environment.yml b/modules/nf-core/kat/hist/environment.yml index 430a40fbee95..bde5501d43b2 100644 --- a/modules/nf-core/kat/hist/environment.yml +++ b/modules/nf-core/kat/hist/environment.yml @@ -1,7 +1,5 @@ -name: kat_hist channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kat=2.4.2 diff --git a/modules/nf-core/khmer/normalizebymedian/environment.yml b/modules/nf-core/khmer/normalizebymedian/environment.yml index 1ffa182980fb..66a065a0a017 100644 --- a/modules/nf-core/khmer/normalizebymedian/environment.yml +++ b/modules/nf-core/khmer/normalizebymedian/environment.yml @@ -1,7 +1,5 @@ -name: khmer_normalizebymedian channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::khmer=3.0.0a3 diff --git a/modules/nf-core/khmer/uniquekmers/environment.yml b/modules/nf-core/khmer/uniquekmers/environment.yml index 9b7b75460b13..66a065a0a017 100644 --- a/modules/nf-core/khmer/uniquekmers/environment.yml +++ b/modules/nf-core/khmer/uniquekmers/environment.yml @@ -1,7 +1,5 @@ -name: khmer_uniquekmers channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::khmer=3.0.0a3 diff --git a/modules/nf-core/kleborate/environment.yml b/modules/nf-core/kleborate/environment.yml index 63ee9f40b47b..2c6f7bc1dfb8 100644 --- a/modules/nf-core/kleborate/environment.yml +++ b/modules/nf-core/kleborate/environment.yml @@ -1,7 +1,5 @@ -name: kleborate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kleborate=2.1.0 diff --git a/modules/nf-core/kmcp/compute/environment.yml b/modules/nf-core/kmcp/compute/environment.yml index e8da5a5ca563..ae5b92028ac4 100644 --- a/modules/nf-core/kmcp/compute/environment.yml +++ b/modules/nf-core/kmcp/compute/environment.yml @@ -1,7 +1,5 @@ -name: kmcp_compute channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kmcp=0.9.4 diff --git a/modules/nf-core/kmcp/index/environment.yml b/modules/nf-core/kmcp/index/environment.yml index 0490aaa025c1..ae5b92028ac4 100644 --- a/modules/nf-core/kmcp/index/environment.yml +++ b/modules/nf-core/kmcp/index/environment.yml @@ -1,7 +1,5 @@ -name: kmcp_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kmcp=0.9.4 diff --git a/modules/nf-core/kmcp/merge/environment.yml b/modules/nf-core/kmcp/merge/environment.yml index 5436b8bbb7fe..99b1b7bbfbf4 100644 --- a/modules/nf-core/kmcp/merge/environment.yml +++ b/modules/nf-core/kmcp/merge/environment.yml @@ -1,7 +1,5 @@ -name: kmcp_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kmcp=0.9.1 diff --git a/modules/nf-core/kmcp/profile/environment.yml b/modules/nf-core/kmcp/profile/environment.yml index 43de2a643b8a..ae5b92028ac4 100644 --- a/modules/nf-core/kmcp/profile/environment.yml +++ b/modules/nf-core/kmcp/profile/environment.yml @@ -1,7 +1,5 @@ -name: kmcp_profile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kmcp=0.9.4 diff --git a/modules/nf-core/kmcp/search/environment.yml b/modules/nf-core/kmcp/search/environment.yml index 397fcb8af0f3..ae5b92028ac4 100644 --- a/modules/nf-core/kmcp/search/environment.yml +++ b/modules/nf-core/kmcp/search/environment.yml @@ -1,7 +1,5 @@ -name: kmcp_search channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kmcp=0.9.4 diff --git a/modules/nf-core/kofamscan/environment.yml b/modules/nf-core/kofamscan/environment.yml index 12a6b4bfb790..a9d8ce4a54b5 100644 --- a/modules/nf-core/kofamscan/environment.yml +++ b/modules/nf-core/kofamscan/environment.yml @@ -1,7 +1,5 @@ -name: kofamscan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::kofamscan=1.3.0 diff --git a/modules/nf-core/kraken2/add/environment.yml b/modules/nf-core/kraken2/add/environment.yml index 24b1c0e10116..9e63d98cc045 100644 --- a/modules/nf-core/kraken2/add/environment.yml +++ b/modules/nf-core/kraken2/add/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "kraken2_add" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/kraken2/build/environment.yml b/modules/nf-core/kraken2/build/environment.yml index 5624c5eaa393..9e63d98cc045 100644 --- a/modules/nf-core/kraken2/build/environment.yml +++ b/modules/nf-core/kraken2/build/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "kraken2_build" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/kraken2/buildstandard/environment.yml b/modules/nf-core/kraken2/buildstandard/environment.yml index 19d9cc692bc0..9e63d98cc045 100644 --- a/modules/nf-core/kraken2/buildstandard/environment.yml +++ b/modules/nf-core/kraken2/buildstandard/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "kraken2_buildstandard" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/kraken2/kraken2/environment.yml b/modules/nf-core/kraken2/kraken2/environment.yml index 0c067feebb48..ba776d315ebf 100644 --- a/modules/nf-core/kraken2/kraken2/environment.yml +++ b/modules/nf-core/kraken2/kraken2/environment.yml @@ -1,8 +1,6 @@ -name: kraken2_kraken2 channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::kraken2=2.1.3" - "coreutils=9.4" diff --git a/modules/nf-core/krakentools/combinekreports/environment.yml b/modules/nf-core/krakentools/combinekreports/environment.yml index 770cdde08ee6..13814bc27e18 100644 --- a/modules/nf-core/krakentools/combinekreports/environment.yml +++ b/modules/nf-core/krakentools/combinekreports/environment.yml @@ -1,7 +1,5 @@ -name: krakentools_combinekreports channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krakentools=1.2 diff --git a/modules/nf-core/krakentools/extractkrakenreads/environment.yml b/modules/nf-core/krakentools/extractkrakenreads/environment.yml index 96eb7fd1544e..c35d4f25bec0 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/environment.yml +++ b/modules/nf-core/krakentools/extractkrakenreads/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "krakentools_extractkrakenreads" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::krakentools=1.2" diff --git a/modules/nf-core/krakentools/kreport2krona/environment.yml b/modules/nf-core/krakentools/kreport2krona/environment.yml index ea49a77ccbcb..13814bc27e18 100644 --- a/modules/nf-core/krakentools/kreport2krona/environment.yml +++ b/modules/nf-core/krakentools/kreport2krona/environment.yml @@ -1,7 +1,5 @@ -name: krakentools_kreport2krona channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krakentools=1.2 diff --git a/modules/nf-core/krakenuniq/build/environment.yml b/modules/nf-core/krakenuniq/build/environment.yml index d99b5ef94227..bbf85c33574b 100644 --- a/modules/nf-core/krakenuniq/build/environment.yml +++ b/modules/nf-core/krakenuniq/build/environment.yml @@ -1,7 +1,5 @@ -name: krakenuniq_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krakenuniq=1.0.4 diff --git a/modules/nf-core/krakenuniq/download/environment.yml b/modules/nf-core/krakenuniq/download/environment.yml index 4160fbec0fd4..bbf85c33574b 100644 --- a/modules/nf-core/krakenuniq/download/environment.yml +++ b/modules/nf-core/krakenuniq/download/environment.yml @@ -1,7 +1,5 @@ -name: krakenuniq_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krakenuniq=1.0.4 diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml index 11bbb879fc27..bbf85c33574b 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/environment.yml @@ -1,7 +1,5 @@ -name: krakenuniq_preloadedkrakenuniq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krakenuniq=1.0.4 diff --git a/modules/nf-core/krona/kronadb/environment.yml b/modules/nf-core/krona/kronadb/environment.yml index 1646628f01c1..cb06934b14e1 100644 --- a/modules/nf-core/krona/kronadb/environment.yml +++ b/modules/nf-core/krona/kronadb/environment.yml @@ -1,7 +1,5 @@ -name: krona_kronadb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krona=2.7.1 diff --git a/modules/nf-core/krona/ktimporttaxonomy/environment.yml b/modules/nf-core/krona/ktimporttaxonomy/environment.yml index e74f72de2a2a..342c589237f2 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/environment.yml +++ b/modules/nf-core/krona/ktimporttaxonomy/environment.yml @@ -1,7 +1,5 @@ -name: krona_ktimporttaxonomy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krona=2.8.1 diff --git a/modules/nf-core/krona/ktimporttext/environment.yml b/modules/nf-core/krona/ktimporttext/environment.yml index d36bd65a35a5..342c589237f2 100644 --- a/modules/nf-core/krona/ktimporttext/environment.yml +++ b/modules/nf-core/krona/ktimporttext/environment.yml @@ -1,7 +1,5 @@ -name: krona_ktimporttext channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::krona=2.8.1 diff --git a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml index ba3c11062b68..cb06934b14e1 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/environment.yml +++ b/modules/nf-core/krona/ktupdatetaxonomy/environment.yml @@ -1,4 +1,3 @@ -name: krona_ktupdatetaxonomy channels: - conda-forge - bioconda diff --git a/modules/nf-core/last/dotplot/environment.yml b/modules/nf-core/last/dotplot/environment.yml index 064a3a459da4..3ea815cd7b8c 100644 --- a/modules/nf-core/last/dotplot/environment.yml +++ b/modules/nf-core/last/dotplot/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_dotplot" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/lastal/environment.yml b/modules/nf-core/last/lastal/environment.yml index 49f3e794c0ce..3ea815cd7b8c 100644 --- a/modules/nf-core/last/lastal/environment.yml +++ b/modules/nf-core/last/lastal/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_lastal" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/lastdb/environment.yml b/modules/nf-core/last/lastdb/environment.yml index e8249083e74b..3ea815cd7b8c 100644 --- a/modules/nf-core/last/lastdb/environment.yml +++ b/modules/nf-core/last/lastdb/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_lastdb" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/mafconvert/environment.yml b/modules/nf-core/last/mafconvert/environment.yml index 9aea0cbe6ee3..3ea815cd7b8c 100644 --- a/modules/nf-core/last/mafconvert/environment.yml +++ b/modules/nf-core/last/mafconvert/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_mafconvert" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/mafswap/environment.yml b/modules/nf-core/last/mafswap/environment.yml index 15e3c6b8ba55..3ea815cd7b8c 100644 --- a/modules/nf-core/last/mafswap/environment.yml +++ b/modules/nf-core/last/mafswap/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_mafswap" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/postmask/environment.yml b/modules/nf-core/last/postmask/environment.yml index 899e8fee491d..3ea815cd7b8c 100644 --- a/modules/nf-core/last/postmask/environment.yml +++ b/modules/nf-core/last/postmask/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_postmask" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/split/environment.yml b/modules/nf-core/last/split/environment.yml index c4608dd218ce..3ea815cd7b8c 100644 --- a/modules/nf-core/last/split/environment.yml +++ b/modules/nf-core/last/split/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_split" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/last/train/environment.yml b/modules/nf-core/last/train/environment.yml index 1a59871b7a57..3ea815cd7b8c 100644 --- a/modules/nf-core/last/train/environment.yml +++ b/modules/nf-core/last/train/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "last_train" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::last=1571" diff --git a/modules/nf-core/learnmsa/align/environment.yml b/modules/nf-core/learnmsa/align/environment.yml index 124b8d8412a9..1c1d69fd765b 100644 --- a/modules/nf-core/learnmsa/align/environment.yml +++ b/modules/nf-core/learnmsa/align/environment.yml @@ -1,8 +1,6 @@ -name: learnmsa_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::learnmsa=2.0.1 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/leehom/environment.yml b/modules/nf-core/leehom/environment.yml index 85e856fac6f1..eaae12b1a54f 100644 --- a/modules/nf-core/leehom/environment.yml +++ b/modules/nf-core/leehom/environment.yml @@ -1,7 +1,5 @@ -name: leehom channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::leehom=1.2.15 diff --git a/modules/nf-core/legsta/environment.yml b/modules/nf-core/legsta/environment.yml index ae157ec4a905..ca9f7ef3e7bd 100644 --- a/modules/nf-core/legsta/environment.yml +++ b/modules/nf-core/legsta/environment.yml @@ -1,4 +1,3 @@ -name: legsta channels: - conda-forge - bioconda diff --git a/modules/nf-core/leviosam2/index/environment.yml b/modules/nf-core/leviosam2/index/environment.yml index f59fd991b8f0..2998a4af4e42 100644 --- a/modules/nf-core/leviosam2/index/environment.yml +++ b/modules/nf-core/leviosam2/index/environment.yml @@ -1,8 +1,6 @@ --- -name: "leviosam2_index" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::leviosam2=0.4.2" diff --git a/modules/nf-core/leviosam2/lift/environment.yml b/modules/nf-core/leviosam2/lift/environment.yml index 35d02420f33b..2998a4af4e42 100644 --- a/modules/nf-core/leviosam2/lift/environment.yml +++ b/modules/nf-core/leviosam2/lift/environment.yml @@ -1,8 +1,6 @@ --- -name: "leviosam2_lift" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::leviosam2=0.4.2" diff --git a/modules/nf-core/liftoff/environment.yml b/modules/nf-core/liftoff/environment.yml index 7f3eadf4c53c..94c10a3dfce2 100644 --- a/modules/nf-core/liftoff/environment.yml +++ b/modules/nf-core/liftoff/environment.yml @@ -1,9 +1,6 @@ -name: liftoff - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::liftoff=1.6.3 diff --git a/modules/nf-core/lima/environment.yml b/modules/nf-core/lima/environment.yml index a9718bc190db..16a072aebb97 100644 --- a/modules/nf-core/lima/environment.yml +++ b/modules/nf-core/lima/environment.yml @@ -1,7 +1,5 @@ -name: lima channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lima=2.9.0 diff --git a/modules/nf-core/limma/differential/environment.yml b/modules/nf-core/limma/differential/environment.yml index 20188f1254f0..f70a20eff5b6 100644 --- a/modules/nf-core/limma/differential/environment.yml +++ b/modules/nf-core/limma/differential/environment.yml @@ -1,7 +1,5 @@ -name: limma_differential channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-limma=3.54.0 diff --git a/modules/nf-core/lissero/environment.yml b/modules/nf-core/lissero/environment.yml index 468585536075..81e172e4051b 100644 --- a/modules/nf-core/lissero/environment.yml +++ b/modules/nf-core/lissero/environment.yml @@ -1,7 +1,5 @@ -name: lissero channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lissero=0.4.9 diff --git a/modules/nf-core/lofreq/alnqual/environment.yml b/modules/nf-core/lofreq/alnqual/environment.yml index 601f477fcc82..15312b90a64a 100644 --- a/modules/nf-core/lofreq/alnqual/environment.yml +++ b/modules/nf-core/lofreq/alnqual/environment.yml @@ -1,8 +1,6 @@ -name: "lofreq_alnqual" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 - bioconda::samtools=1.17 diff --git a/modules/nf-core/lofreq/call/environment.yml b/modules/nf-core/lofreq/call/environment.yml index fbba018d7ba1..011ce6cbda39 100644 --- a/modules/nf-core/lofreq/call/environment.yml +++ b/modules/nf-core/lofreq/call/environment.yml @@ -1,7 +1,5 @@ -name: lofreq_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 diff --git a/modules/nf-core/lofreq/callparallel/environment.yml b/modules/nf-core/lofreq/callparallel/environment.yml index 222d145021fc..011ce6cbda39 100644 --- a/modules/nf-core/lofreq/callparallel/environment.yml +++ b/modules/nf-core/lofreq/callparallel/environment.yml @@ -1,7 +1,5 @@ -name: lofreq_callparallel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 diff --git a/modules/nf-core/lofreq/filter/environment.yml b/modules/nf-core/lofreq/filter/environment.yml index a5a2389c4581..011ce6cbda39 100644 --- a/modules/nf-core/lofreq/filter/environment.yml +++ b/modules/nf-core/lofreq/filter/environment.yml @@ -1,7 +1,5 @@ -name: lofreq_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 diff --git a/modules/nf-core/lofreq/indelqual/environment.yml b/modules/nf-core/lofreq/indelqual/environment.yml index 43d9f2afdcb9..011ce6cbda39 100644 --- a/modules/nf-core/lofreq/indelqual/environment.yml +++ b/modules/nf-core/lofreq/indelqual/environment.yml @@ -1,7 +1,5 @@ -name: lofreq_indelqual channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 diff --git a/modules/nf-core/lofreq/somatic/environment.yml b/modules/nf-core/lofreq/somatic/environment.yml index af6a98fb8678..011ce6cbda39 100644 --- a/modules/nf-core/lofreq/somatic/environment.yml +++ b/modules/nf-core/lofreq/somatic/environment.yml @@ -1,7 +1,5 @@ -name: lofreq_somatic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 diff --git a/modules/nf-core/lofreq/viterbi/environment.yml b/modules/nf-core/lofreq/viterbi/environment.yml index d81bc2292705..15312b90a64a 100644 --- a/modules/nf-core/lofreq/viterbi/environment.yml +++ b/modules/nf-core/lofreq/viterbi/environment.yml @@ -1,8 +1,6 @@ -name: "lofreq_viterbi" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::lofreq=2.1.5 - bioconda::samtools=1.17 diff --git a/modules/nf-core/longphase/haplotag/environment.yml b/modules/nf-core/longphase/haplotag/environment.yml index d0aea06c3199..06445a930d7c 100644 --- a/modules/nf-core/longphase/haplotag/environment.yml +++ b/modules/nf-core/longphase/haplotag/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "longphase_haplotag" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::longphase=1.7.3" diff --git a/modules/nf-core/longphase/phase/environment.yml b/modules/nf-core/longphase/phase/environment.yml index eabc1f7c9cec..96e04eb61b97 100644 --- a/modules/nf-core/longphase/phase/environment.yml +++ b/modules/nf-core/longphase/phase/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "longphase_phase" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::longphase=1.7.3" - "bioconda::htslib=1.20" diff --git a/modules/nf-core/ltrfinder/environment.yml b/modules/nf-core/ltrfinder/environment.yml index 7f3545975a88..2932d5cfc9d2 100644 --- a/modules/nf-core/ltrfinder/environment.yml +++ b/modules/nf-core/ltrfinder/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ltrfinder" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ltr_finder_parallel=1.1" diff --git a/modules/nf-core/ltrharvest/environment.yml b/modules/nf-core/ltrharvest/environment.yml index 9337fe23f156..c6cac36f5997 100644 --- a/modules/nf-core/ltrharvest/environment.yml +++ b/modules/nf-core/ltrharvest/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ltrharvest" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ltr_harvest_parallel=1.1" diff --git a/modules/nf-core/ltrretriever/lai/environment.yml b/modules/nf-core/ltrretriever/lai/environment.yml index e0e4968237ba..f1c392a2c00b 100644 --- a/modules/nf-core/ltrretriever/lai/environment.yml +++ b/modules/nf-core/ltrretriever/lai/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ltrretriever_lai" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::LTR_retriever=2.9.9" diff --git a/modules/nf-core/ltrretriever/ltrretriever/environment.yml b/modules/nf-core/ltrretriever/ltrretriever/environment.yml index f49f07e702a1..f1c392a2c00b 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/environment.yml +++ b/modules/nf-core/ltrretriever/ltrretriever/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ltrretriever_ltrretriever" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::LTR_retriever=2.9.9" diff --git a/modules/nf-core/macrel/contigs/environment.yml b/modules/nf-core/macrel/contigs/environment.yml index 681d60797275..bb5ce1a6e680 100644 --- a/modules/nf-core/macrel/contigs/environment.yml +++ b/modules/nf-core/macrel/contigs/environment.yml @@ -1,7 +1,5 @@ -name: macrel_contigs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::macrel=1.4.0 diff --git a/modules/nf-core/macs2/callpeak/environment.yml b/modules/nf-core/macs2/callpeak/environment.yml index ce76403e04fa..caa3ed9f0960 100644 --- a/modules/nf-core/macs2/callpeak/environment.yml +++ b/modules/nf-core/macs2/callpeak/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "macs2_callpeak" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::macs2=2.2.9.1" diff --git a/modules/nf-core/macs3/callpeak/environment.yml b/modules/nf-core/macs3/callpeak/environment.yml index d9caa561d23c..4aa6a32ddd5c 100644 --- a/modules/nf-core/macs3/callpeak/environment.yml +++ b/modules/nf-core/macs3/callpeak/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "macs3_callpeak" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::macs3=3.0.1" diff --git a/modules/nf-core/mafft/environment.yml b/modules/nf-core/mafft/environment.yml index 595252e08c0b..97a13e685ee7 100644 --- a/modules/nf-core/mafft/environment.yml +++ b/modules/nf-core/mafft/environment.yml @@ -1,8 +1,6 @@ -name: mafft channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mafft=7.520 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/mageck/count/environment.yml b/modules/nf-core/mageck/count/environment.yml index c7221d6f77c8..7cc6f8880225 100644 --- a/modules/nf-core/mageck/count/environment.yml +++ b/modules/nf-core/mageck/count/environment.yml @@ -1,7 +1,5 @@ -name: mageck_count channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mageck=0.5.9.5 diff --git a/modules/nf-core/mageck/mle/environment.yml b/modules/nf-core/mageck/mle/environment.yml index ed2cf00173a8..7cc6f8880225 100644 --- a/modules/nf-core/mageck/mle/environment.yml +++ b/modules/nf-core/mageck/mle/environment.yml @@ -1,7 +1,5 @@ -name: mageck_mle channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mageck=0.5.9.5 diff --git a/modules/nf-core/mageck/test/environment.yml b/modules/nf-core/mageck/test/environment.yml index 1d056e5a392e..7cc6f8880225 100644 --- a/modules/nf-core/mageck/test/environment.yml +++ b/modules/nf-core/mageck/test/environment.yml @@ -1,7 +1,5 @@ -name: mageck_test channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mageck=0.5.9.5 diff --git a/modules/nf-core/magus/align/environment.yml b/modules/nf-core/magus/align/environment.yml index 685f5a878401..2934cc977ccc 100644 --- a/modules/nf-core/magus/align/environment.yml +++ b/modules/nf-core/magus/align/environment.yml @@ -1,8 +1,6 @@ -name: magus_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::magus-msa=0.2.0 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/magus/guidetree/environment.yml b/modules/nf-core/magus/guidetree/environment.yml index 8e7503342dcd..423a598583bb 100644 --- a/modules/nf-core/magus/guidetree/environment.yml +++ b/modules/nf-core/magus/guidetree/environment.yml @@ -1,7 +1,5 @@ -name: magus_guidetree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::magus-msa=0.2.0 diff --git a/modules/nf-core/malt/build/environment.yml b/modules/nf-core/malt/build/environment.yml index a3b37a673bb9..15a775008fcb 100644 --- a/modules/nf-core/malt/build/environment.yml +++ b/modules/nf-core/malt/build/environment.yml @@ -1,7 +1,5 @@ -name: malt_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::malt=0.61 diff --git a/modules/nf-core/malt/run/environment.yml b/modules/nf-core/malt/run/environment.yml index c53d72056827..15a775008fcb 100644 --- a/modules/nf-core/malt/run/environment.yml +++ b/modules/nf-core/malt/run/environment.yml @@ -1,7 +1,5 @@ -name: malt_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::malt=0.61 diff --git a/modules/nf-core/maltextract/environment.yml b/modules/nf-core/maltextract/environment.yml index f87a299c238f..d78219cbe01e 100644 --- a/modules/nf-core/maltextract/environment.yml +++ b/modules/nf-core/maltextract/environment.yml @@ -1,7 +1,5 @@ -name: maltextract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::hops=0.35 diff --git a/modules/nf-core/manta/convertinversion/environment.yml b/modules/nf-core/manta/convertinversion/environment.yml index 433a423fa910..802a9f4ddc05 100644 --- a/modules/nf-core/manta/convertinversion/environment.yml +++ b/modules/nf-core/manta/convertinversion/environment.yml @@ -1,8 +1,6 @@ -name: manta_convertinversion channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.16 - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/germline/environment.yml b/modules/nf-core/manta/germline/environment.yml index 4a63d3084b20..fe5ade5068fe 100644 --- a/modules/nf-core/manta/germline/environment.yml +++ b/modules/nf-core/manta/germline/environment.yml @@ -1,7 +1,5 @@ -name: manta_germline channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/somatic/environment.yml b/modules/nf-core/manta/somatic/environment.yml index aac8827dfcb2..fe5ade5068fe 100644 --- a/modules/nf-core/manta/somatic/environment.yml +++ b/modules/nf-core/manta/somatic/environment.yml @@ -1,7 +1,5 @@ -name: manta_somatic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::manta=1.6.0 diff --git a/modules/nf-core/manta/tumoronly/environment.yml b/modules/nf-core/manta/tumoronly/environment.yml index cf5db361e008..fe5ade5068fe 100644 --- a/modules/nf-core/manta/tumoronly/environment.yml +++ b/modules/nf-core/manta/tumoronly/environment.yml @@ -1,7 +1,5 @@ -name: manta_tumoronly channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::manta=1.6.0 diff --git a/modules/nf-core/mapad/index/environment.yml b/modules/nf-core/mapad/index/environment.yml index 20e36f6bba60..540878543d15 100644 --- a/modules/nf-core/mapad/index/environment.yml +++ b/modules/nf-core/mapad/index/environment.yml @@ -1,7 +1,5 @@ -name: mapad_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mapad=0.43.0 diff --git a/modules/nf-core/mapad/map/environment.yml b/modules/nf-core/mapad/map/environment.yml index a6122ef55825..540878543d15 100644 --- a/modules/nf-core/mapad/map/environment.yml +++ b/modules/nf-core/mapad/map/environment.yml @@ -1,7 +1,5 @@ -name: mapad_map channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mapad=0.43.0 diff --git a/modules/nf-core/mapdamage2/environment.yml b/modules/nf-core/mapdamage2/environment.yml index 92be8ef3ebef..2476b31af9a2 100644 --- a/modules/nf-core/mapdamage2/environment.yml +++ b/modules/nf-core/mapdamage2/environment.yml @@ -1,7 +1,5 @@ -name: mapdamage2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mapdamage2=2.2.1 diff --git a/modules/nf-core/mash/dist/environment.yml b/modules/nf-core/mash/dist/environment.yml index 34a5237d0992..5911571d7fec 100644 --- a/modules/nf-core/mash/dist/environment.yml +++ b/modules/nf-core/mash/dist/environment.yml @@ -1,7 +1,5 @@ -name: mash_dist channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mash=2.3 diff --git a/modules/nf-core/mash/screen/environment.yml b/modules/nf-core/mash/screen/environment.yml index d892dee5525f..5911571d7fec 100644 --- a/modules/nf-core/mash/screen/environment.yml +++ b/modules/nf-core/mash/screen/environment.yml @@ -1,7 +1,5 @@ -name: mash_screen channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mash=2.3 diff --git a/modules/nf-core/mash/sketch/environment.yml b/modules/nf-core/mash/sketch/environment.yml index 968725ed3bdb..5911571d7fec 100644 --- a/modules/nf-core/mash/sketch/environment.yml +++ b/modules/nf-core/mash/sketch/environment.yml @@ -1,7 +1,5 @@ -name: mash_sketch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mash=2.3 diff --git a/modules/nf-core/mashmap/environment.yml b/modules/nf-core/mashmap/environment.yml index 9ee3e8f73eb9..af0aef9d1a13 100644 --- a/modules/nf-core/mashmap/environment.yml +++ b/modules/nf-core/mashmap/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "mashmap" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::mashmap=3.1.3" diff --git a/modules/nf-core/mashtree/environment.yml b/modules/nf-core/mashtree/environment.yml index 5bb235c79758..0de7d6108b18 100644 --- a/modules/nf-core/mashtree/environment.yml +++ b/modules/nf-core/mashtree/environment.yml @@ -1,7 +1,5 @@ -name: mashtree channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mashtree=1.2.0 diff --git a/modules/nf-core/maxbin2/environment.yml b/modules/nf-core/maxbin2/environment.yml index 84066ce65162..8a881999670a 100644 --- a/modules/nf-core/maxbin2/environment.yml +++ b/modules/nf-core/maxbin2/environment.yml @@ -1,7 +1,5 @@ -name: maxbin2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::maxbin2=2.2.7 diff --git a/modules/nf-core/maxquant/lfq/environment.yml b/modules/nf-core/maxquant/lfq/environment.yml index 22c40f04c056..3344ce5a4e2b 100644 --- a/modules/nf-core/maxquant/lfq/environment.yml +++ b/modules/nf-core/maxquant/lfq/environment.yml @@ -1,7 +1,5 @@ -name: maxquant_lfq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::maxquant=2.0.3.0=py310hdfd78af_1 diff --git a/modules/nf-core/mcroni/environment.yml b/modules/nf-core/mcroni/environment.yml index 572bc527c7bf..c20f9a9bd09d 100644 --- a/modules/nf-core/mcroni/environment.yml +++ b/modules/nf-core/mcroni/environment.yml @@ -1,7 +1,5 @@ -name: mcroni channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mcroni=1.0.4 diff --git a/modules/nf-core/mcstaging/imc2mc/environment.yml b/modules/nf-core/mcstaging/imc2mc/environment.yml index b18f2f50b6ff..238492beb735 100644 --- a/modules/nf-core/mcstaging/imc2mc/environment.yml +++ b/modules/nf-core/mcstaging/imc2mc/environment.yml @@ -1,5 +1,3 @@ -name: mcstaging_imc2mc - channels: - conda-forge - bioconda diff --git a/modules/nf-core/md5sum/environment.yml b/modules/nf-core/md5sum/environment.yml index c196b0138a9b..c7eb9bd1c3ca 100644 --- a/modules/nf-core/md5sum/environment.yml +++ b/modules/nf-core/md5sum/environment.yml @@ -1,7 +1,5 @@ -name: md5sum channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/medaka/environment.yml b/modules/nf-core/medaka/environment.yml index 20e2cbbed3e9..1165f7c8f7db 100644 --- a/modules/nf-core/medaka/environment.yml +++ b/modules/nf-core/medaka/environment.yml @@ -1,7 +1,5 @@ -name: medaka channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::medaka=1.4.4 diff --git a/modules/nf-core/megahit/environment.yml b/modules/nf-core/megahit/environment.yml index 101c24dc0bf4..eed8b7257744 100644 --- a/modules/nf-core/megahit/environment.yml +++ b/modules/nf-core/megahit/environment.yml @@ -1,8 +1,6 @@ -name: megahit channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::megahit=1.2.9 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/megan/daa2info/environment.yml b/modules/nf-core/megan/daa2info/environment.yml index 6b12a615430d..e31aa147bebe 100644 --- a/modules/nf-core/megan/daa2info/environment.yml +++ b/modules/nf-core/megan/daa2info/environment.yml @@ -1,7 +1,5 @@ -name: megan_daa2info channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::megan=6.21.7 diff --git a/modules/nf-core/megan/rma2info/environment.yml b/modules/nf-core/megan/rma2info/environment.yml index bc744a9adc72..520b771daabe 100644 --- a/modules/nf-core/megan/rma2info/environment.yml +++ b/modules/nf-core/megan/rma2info/environment.yml @@ -1,7 +1,5 @@ -name: megan_rma2info channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::megan=6.25.9 diff --git a/modules/nf-core/meningotype/environment.yml b/modules/nf-core/meningotype/environment.yml index 6e3dd5136e53..e2f6f59bc79b 100644 --- a/modules/nf-core/meningotype/environment.yml +++ b/modules/nf-core/meningotype/environment.yml @@ -1,7 +1,5 @@ -name: meningotype channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::meningotype=0.8.5 diff --git a/modules/nf-core/merfin/hist/environment.yml b/modules/nf-core/merfin/hist/environment.yml index 6e420c7c83a6..8a01363ee799 100644 --- a/modules/nf-core/merfin/hist/environment.yml +++ b/modules/nf-core/merfin/hist/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "merfin_hist" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::merfin=1.0" diff --git a/modules/nf-core/merqury/hapmers/environment.yml b/modules/nf-core/merqury/hapmers/environment.yml index 5f7977cd6185..93a0c984346d 100644 --- a/modules/nf-core/merqury/hapmers/environment.yml +++ b/modules/nf-core/merqury/hapmers/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "merqury_hapmers" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::merqury=1.3" diff --git a/modules/nf-core/merqury/merqury/environment.yml b/modules/nf-core/merqury/merqury/environment.yml index 722c47c1f20b..a62b4b9200cf 100644 --- a/modules/nf-core/merqury/merqury/environment.yml +++ b/modules/nf-core/merqury/merqury/environment.yml @@ -1,7 +1,5 @@ -name: merqury_merqury channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::merqury=1.3 diff --git a/modules/nf-core/merquryfk/katcomp/environment.yml b/modules/nf-core/merquryfk/katcomp/environment.yml index 80174c194530..3cebeff05bfc 100644 --- a/modules/nf-core/merquryfk/katcomp/environment.yml +++ b/modules/nf-core/merquryfk/katcomp/environment.yml @@ -1,5 +1,3 @@ -name: merquryfk_katcomp channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/merquryfk/katgc/environment.yml b/modules/nf-core/merquryfk/katgc/environment.yml index 4213934f4183..3cebeff05bfc 100644 --- a/modules/nf-core/merquryfk/katgc/environment.yml +++ b/modules/nf-core/merquryfk/katgc/environment.yml @@ -1,5 +1,3 @@ -name: merquryfk_katgc channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/meryl/count/environment.yml b/modules/nf-core/meryl/count/environment.yml index 808565ee796a..e37d79019af2 100644 --- a/modules/nf-core/meryl/count/environment.yml +++ b/modules/nf-core/meryl/count/environment.yml @@ -1,7 +1,5 @@ -name: meryl_count channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/meryl/histogram/environment.yml b/modules/nf-core/meryl/histogram/environment.yml index 09a324884da5..e37d79019af2 100644 --- a/modules/nf-core/meryl/histogram/environment.yml +++ b/modules/nf-core/meryl/histogram/environment.yml @@ -1,7 +1,5 @@ -name: meryl_histogram channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/meryl/unionsum/environment.yml b/modules/nf-core/meryl/unionsum/environment.yml index b8bdcbe87671..e37d79019af2 100644 --- a/modules/nf-core/meryl/unionsum/environment.yml +++ b/modules/nf-core/meryl/unionsum/environment.yml @@ -1,7 +1,5 @@ -name: meryl_unionsum channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::meryl=1.4.1 diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml index 887fc413fd69..eaa9cbe93257 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/environment.yml @@ -1,4 +1,3 @@ -name: metabat2_jgisummarizebamcontigdepths channels: - conda-forge - bioconda diff --git a/modules/nf-core/metabat2/metabat2/environment.yml b/modules/nf-core/metabat2/metabat2/environment.yml index 7ff056c096d2..eaa9cbe93257 100644 --- a/modules/nf-core/metabat2/metabat2/environment.yml +++ b/modules/nf-core/metabat2/metabat2/environment.yml @@ -1,7 +1,5 @@ -name: metabat2_metabat2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metabat2=2.15 diff --git a/modules/nf-core/metaeuk/easypredict/environment.yml b/modules/nf-core/metaeuk/easypredict/environment.yml index f56445fe0eed..f05430210132 100644 --- a/modules/nf-core/metaeuk/easypredict/environment.yml +++ b/modules/nf-core/metaeuk/easypredict/environment.yml @@ -1,7 +1,5 @@ -name: metaeuk_easypredict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaeuk=6.a5d39d9 diff --git a/modules/nf-core/metamaps/classify/environment.yml b/modules/nf-core/metamaps/classify/environment.yml index 3e66c559514d..18ab06802db2 100644 --- a/modules/nf-core/metamaps/classify/environment.yml +++ b/modules/nf-core/metamaps/classify/environment.yml @@ -1,7 +1,5 @@ -name: "metamaps_classify" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::metamaps=0.1.633d2e0" diff --git a/modules/nf-core/metamaps/mapdirectly/environment.yml b/modules/nf-core/metamaps/mapdirectly/environment.yml index 19287be0aa3e..18ab06802db2 100644 --- a/modules/nf-core/metamaps/mapdirectly/environment.yml +++ b/modules/nf-core/metamaps/mapdirectly/environment.yml @@ -1,7 +1,5 @@ -name: "metamaps_mapdirectly" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::metamaps=0.1.633d2e0" diff --git a/modules/nf-core/metaphlan/makedb/environment.yml b/modules/nf-core/metaphlan/makedb/environment.yml index 022c2fe25f73..709ddf70a545 100644 --- a/modules/nf-core/metaphlan/makedb/environment.yml +++ b/modules/nf-core/metaphlan/makedb/environment.yml @@ -1,7 +1,5 @@ -name: metaphlan_makedb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaphlan=4.1.1 diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml b/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml index f41f321e19c3..709ddf70a545 100644 --- a/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml +++ b/modules/nf-core/metaphlan/mergemetaphlantables/environment.yml @@ -1,7 +1,5 @@ -name: metaphlan_mergemetaphlantables channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaphlan=4.1.1 diff --git a/modules/nf-core/metaphlan/metaphlan/environment.yml b/modules/nf-core/metaphlan/metaphlan/environment.yml index 4e4d8a72115c..709ddf70a545 100644 --- a/modules/nf-core/metaphlan/metaphlan/environment.yml +++ b/modules/nf-core/metaphlan/metaphlan/environment.yml @@ -1,7 +1,5 @@ -name: metaphlan_metaphlan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaphlan=4.1.1 diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml b/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml index 2ba8b925ad2f..4e44149666cf 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/environment.yml @@ -1,7 +1,5 @@ -name: metaphlan3_mergemetaphlantables channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaphlan=3.0.12 diff --git a/modules/nf-core/metaphlan3/metaphlan3/environment.yml b/modules/nf-core/metaphlan3/metaphlan3/environment.yml index 9c0b5674a731..4e44149666cf 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/environment.yml +++ b/modules/nf-core/metaphlan3/metaphlan3/environment.yml @@ -1,7 +1,5 @@ -name: metaphlan3_metaphlan3 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::metaphlan=3.0.12 diff --git a/modules/nf-core/methyldackel/extract/environment.yml b/modules/nf-core/methyldackel/extract/environment.yml index 02a77db13550..34beddbee520 100644 --- a/modules/nf-core/methyldackel/extract/environment.yml +++ b/modules/nf-core/methyldackel/extract/environment.yml @@ -1,7 +1,5 @@ -name: methyldackel_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::methyldackel=0.6.1 diff --git a/modules/nf-core/methyldackel/mbias/environment.yml b/modules/nf-core/methyldackel/mbias/environment.yml index 4fe69016b33d..34beddbee520 100644 --- a/modules/nf-core/methyldackel/mbias/environment.yml +++ b/modules/nf-core/methyldackel/mbias/environment.yml @@ -1,7 +1,5 @@ -name: methyldackel_mbias channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::methyldackel=0.6.1 diff --git a/modules/nf-core/midas/run/environment.yml b/modules/nf-core/midas/run/environment.yml index 368cb74ff44e..c6b3b735046c 100644 --- a/modules/nf-core/midas/run/environment.yml +++ b/modules/nf-core/midas/run/environment.yml @@ -1,7 +1,5 @@ -name: midas_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::midas=1.3.2 diff --git a/modules/nf-core/mindagap/duplicatefinder/environment.yml b/modules/nf-core/mindagap/duplicatefinder/environment.yml index ad9815283914..ac5d66877831 100644 --- a/modules/nf-core/mindagap/duplicatefinder/environment.yml +++ b/modules/nf-core/mindagap/duplicatefinder/environment.yml @@ -1,7 +1,5 @@ -name: "MINDAGAP_DUPLICATEFINDER" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::mindagap=0.0.2" diff --git a/modules/nf-core/mindagap/mindagap/environment.yml b/modules/nf-core/mindagap/mindagap/environment.yml index f380feeccba2..56fd98bf8df5 100644 --- a/modules/nf-core/mindagap/mindagap/environment.yml +++ b/modules/nf-core/mindagap/mindagap/environment.yml @@ -1,7 +1,5 @@ -name: mindagap_mindagap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mindagap=0.0.2 diff --git a/modules/nf-core/minia/environment.yml b/modules/nf-core/minia/environment.yml index 10e455291fa7..ff73cbb95e02 100644 --- a/modules/nf-core/minia/environment.yml +++ b/modules/nf-core/minia/environment.yml @@ -1,7 +1,5 @@ -name: minia channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minia=3.2.6 diff --git a/modules/nf-core/miniasm/environment.yml b/modules/nf-core/miniasm/environment.yml index 34a35e5da7c4..eeba4d737874 100644 --- a/modules/nf-core/miniasm/environment.yml +++ b/modules/nf-core/miniasm/environment.yml @@ -1,7 +1,5 @@ -name: miniasm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::miniasm=0.3_r179 diff --git a/modules/nf-core/minimap2/align/environment.yml b/modules/nf-core/minimap2/align/environment.yml index 41e8fe9fc5ae..dc6476b721e1 100644 --- a/modules/nf-core/minimap2/align/environment.yml +++ b/modules/nf-core/minimap2/align/environment.yml @@ -1,9 +1,6 @@ -name: minimap2_align - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/minimap2/index/environment.yml b/modules/nf-core/minimap2/index/environment.yml index 8a912a12136b..d1c1b471bec9 100644 --- a/modules/nf-core/minimap2/index/environment.yml +++ b/modules/nf-core/minimap2/index/environment.yml @@ -1,7 +1,5 @@ -name: minimap2_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.28 diff --git a/modules/nf-core/miniprot/align/environment.yml b/modules/nf-core/miniprot/align/environment.yml index d437e07a24ce..7e258a047a59 100644 --- a/modules/nf-core/miniprot/align/environment.yml +++ b/modules/nf-core/miniprot/align/environment.yml @@ -1,7 +1,5 @@ -name: miniprot_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::miniprot=0.11=he4a0461_2 diff --git a/modules/nf-core/miniprot/index/environment.yml b/modules/nf-core/miniprot/index/environment.yml index 1de55fae09e2..7e258a047a59 100644 --- a/modules/nf-core/miniprot/index/environment.yml +++ b/modules/nf-core/miniprot/index/environment.yml @@ -1,7 +1,5 @@ -name: miniprot_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::miniprot=0.11=he4a0461_2 diff --git a/modules/nf-core/miranda/environment.yml b/modules/nf-core/miranda/environment.yml index a04ca7f84b14..c0053666cc4d 100644 --- a/modules/nf-core/miranda/environment.yml +++ b/modules/nf-core/miranda/environment.yml @@ -1,7 +1,5 @@ -name: miranda channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::miranda=3.3a diff --git a/modules/nf-core/mirtrace/qc/environment.yml b/modules/nf-core/mirtrace/qc/environment.yml index 253b36b8d4e3..c83822c4dee2 100644 --- a/modules/nf-core/mirtrace/qc/environment.yml +++ b/modules/nf-core/mirtrace/qc/environment.yml @@ -1,6 +1,5 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "mirtrace_qc" channels: - conda-forge - bioconda diff --git a/modules/nf-core/mlst/environment.yml b/modules/nf-core/mlst/environment.yml index 898008d37825..c0eeb7c80f75 100644 --- a/modules/nf-core/mlst/environment.yml +++ b/modules/nf-core/mlst/environment.yml @@ -1,7 +1,5 @@ -name: mlst channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mlst=2.23.0 diff --git a/modules/nf-core/mmseqs/cluster/environment.yml b/modules/nf-core/mmseqs/cluster/environment.yml index 2fbf680f826a..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/cluster/environment.yml +++ b/modules/nf-core/mmseqs/cluster/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_cluster channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/createdb/environment.yml b/modules/nf-core/mmseqs/createdb/environment.yml index 77b28f590783..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/createdb/environment.yml +++ b/modules/nf-core/mmseqs/createdb/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_createdb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/createindex/environment.yml b/modules/nf-core/mmseqs/createindex/environment.yml index 71ebe34c51b2..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/createindex/environment.yml +++ b/modules/nf-core/mmseqs/createindex/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_createindex channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/createtsv/environment.yml b/modules/nf-core/mmseqs/createtsv/environment.yml index 6f1bd86b3120..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/createtsv/environment.yml +++ b/modules/nf-core/mmseqs/createtsv/environment.yml @@ -1,4 +1,3 @@ -name: mmseqs_createtsv channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/databases/environment.yml b/modules/nf-core/mmseqs/databases/environment.yml index cad92fadd85f..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/databases/environment.yml +++ b/modules/nf-core/mmseqs/databases/environment.yml @@ -1,4 +1,3 @@ -name: mmseqs_databases channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/easysearch/environment.yml b/modules/nf-core/mmseqs/easysearch/environment.yml index e11670c54832..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/easysearch/environment.yml +++ b/modules/nf-core/mmseqs/easysearch/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_easysearch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/linclust/environment.yml b/modules/nf-core/mmseqs/linclust/environment.yml index 5797982659ea..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/linclust/environment.yml +++ b/modules/nf-core/mmseqs/linclust/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_linclust channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/search/environment.yml b/modules/nf-core/mmseqs/search/environment.yml index ba6d42098c51..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/search/environment.yml +++ b/modules/nf-core/mmseqs/search/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_search channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mmseqs/taxonomy/environment.yml b/modules/nf-core/mmseqs/taxonomy/environment.yml index 89bc7c503d60..65f1e5cde043 100644 --- a/modules/nf-core/mmseqs/taxonomy/environment.yml +++ b/modules/nf-core/mmseqs/taxonomy/environment.yml @@ -1,6 +1,5 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "mmseqs_taxonomy" channels: - conda-forge - bioconda diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml index 56a8a7121191..18547591a2e4 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/environment.yml @@ -1,7 +1,5 @@ -name: mmseqs_tsv2exprofiledb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mmseqs2=15.6f452 diff --git a/modules/nf-core/mobsuite/recon/environment.yml b/modules/nf-core/mobsuite/recon/environment.yml index 27727f5664ee..91e0be51014c 100644 --- a/modules/nf-core/mobsuite/recon/environment.yml +++ b/modules/nf-core/mobsuite/recon/environment.yml @@ -1,5 +1,3 @@ -name: mobsuite_recon - channels: - conda-forge - bioconda diff --git a/modules/nf-core/modkit/pileup/environment.yml b/modules/nf-core/modkit/pileup/environment.yml index 95074539ed63..1343a05bbf42 100644 --- a/modules/nf-core/modkit/pileup/environment.yml +++ b/modules/nf-core/modkit/pileup/environment.yml @@ -1,7 +1,5 @@ -name: modkit_pileup channels: - conda-forge - bioconda - - defaults dependencies: - ont-modkit=0.3.0 diff --git a/modules/nf-core/mosdepth/environment.yml b/modules/nf-core/mosdepth/environment.yml index bcb9d64a7a04..e9379873800a 100644 --- a/modules/nf-core/mosdepth/environment.yml +++ b/modules/nf-core/mosdepth/environment.yml @@ -1,8 +1,6 @@ -name: mosdepth channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/mosdepth - mosdepth=0.3.8 diff --git a/modules/nf-core/motus/downloaddb/environment.yml b/modules/nf-core/motus/downloaddb/environment.yml index 896e2bbc68b2..736a527eb446 100644 --- a/modules/nf-core/motus/downloaddb/environment.yml +++ b/modules/nf-core/motus/downloaddb/environment.yml @@ -1,7 +1,5 @@ -name: motus_downloaddb channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::motus=3.0.3 diff --git a/modules/nf-core/motus/merge/environment.yml b/modules/nf-core/motus/merge/environment.yml index d8a79e84e7f0..736a527eb446 100644 --- a/modules/nf-core/motus/merge/environment.yml +++ b/modules/nf-core/motus/merge/environment.yml @@ -1,7 +1,5 @@ -name: motus_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::motus=3.0.3 diff --git a/modules/nf-core/motus/profile/environment.yml b/modules/nf-core/motus/profile/environment.yml index 6d9c542cf382..b8ef520eaa2a 100644 --- a/modules/nf-core/motus/profile/environment.yml +++ b/modules/nf-core/motus/profile/environment.yml @@ -1,7 +1,5 @@ -name: motus_profile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::motus=3.1.0 diff --git a/modules/nf-core/msisensor/msi/environment.yml b/modules/nf-core/msisensor/msi/environment.yml index d600fa9aa60a..ca813399634c 100644 --- a/modules/nf-core/msisensor/msi/environment.yml +++ b/modules/nf-core/msisensor/msi/environment.yml @@ -1,7 +1,5 @@ -name: msisensor_msi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor=0.5 diff --git a/modules/nf-core/msisensor/scan/environment.yml b/modules/nf-core/msisensor/scan/environment.yml index e6e524d5a824..ca813399634c 100644 --- a/modules/nf-core/msisensor/scan/environment.yml +++ b/modules/nf-core/msisensor/scan/environment.yml @@ -1,7 +1,5 @@ -name: msisensor_scan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor=0.5 diff --git a/modules/nf-core/msisensor2/msi/environment.yml b/modules/nf-core/msisensor2/msi/environment.yml index ea5622b36d58..7f17071a91f1 100644 --- a/modules/nf-core/msisensor2/msi/environment.yml +++ b/modules/nf-core/msisensor2/msi/environment.yml @@ -1,7 +1,5 @@ -name: msisensor2_msi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor2=0.1 diff --git a/modules/nf-core/msisensor2/scan/environment.yml b/modules/nf-core/msisensor2/scan/environment.yml index 3c74c52059f3..7f17071a91f1 100644 --- a/modules/nf-core/msisensor2/scan/environment.yml +++ b/modules/nf-core/msisensor2/scan/environment.yml @@ -1,7 +1,5 @@ -name: msisensor2_scan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor2=0.1 diff --git a/modules/nf-core/msisensorpro/msisomatic/environment.yml b/modules/nf-core/msisensorpro/msisomatic/environment.yml index 147a9d6b855a..f67b9b733e9a 100644 --- a/modules/nf-core/msisensorpro/msisomatic/environment.yml +++ b/modules/nf-core/msisensorpro/msisomatic/environment.yml @@ -1,7 +1,5 @@ -name: msisensorpro_msisomatic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor-pro=1.2.0 diff --git a/modules/nf-core/msisensorpro/scan/environment.yml b/modules/nf-core/msisensorpro/scan/environment.yml index 377c28a61b14..f67b9b733e9a 100644 --- a/modules/nf-core/msisensorpro/scan/environment.yml +++ b/modules/nf-core/msisensorpro/scan/environment.yml @@ -1,7 +1,5 @@ -name: msisensorpro_scan channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::msisensor-pro=1.2.0 diff --git a/modules/nf-core/mtmalign/align/environment.yml b/modules/nf-core/mtmalign/align/environment.yml index 59d426bb597b..131c0648d8fe 100644 --- a/modules/nf-core/mtmalign/align/environment.yml +++ b/modules/nf-core/mtmalign/align/environment.yml @@ -1,8 +1,6 @@ -name: mtmalign_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mtm-align=20220104 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/mtnucratio/environment.yml b/modules/nf-core/mtnucratio/environment.yml index 98919877b33a..3c7cd4b87b5e 100644 --- a/modules/nf-core/mtnucratio/environment.yml +++ b/modules/nf-core/mtnucratio/environment.yml @@ -1,7 +1,5 @@ -name: mtnucratio channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mtnucratio=0.7 diff --git a/modules/nf-core/mudskipper/bulk/environment.yml b/modules/nf-core/mudskipper/bulk/environment.yml index 6de96a965fca..162b00681c93 100644 --- a/modules/nf-core/mudskipper/bulk/environment.yml +++ b/modules/nf-core/mudskipper/bulk/environment.yml @@ -1,7 +1,5 @@ -name: mudskipper_bulk channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mudskipper=0.1.0 diff --git a/modules/nf-core/mudskipper/index/environment.yml b/modules/nf-core/mudskipper/index/environment.yml index 8318f01a3513..162b00681c93 100644 --- a/modules/nf-core/mudskipper/index/environment.yml +++ b/modules/nf-core/mudskipper/index/environment.yml @@ -1,7 +1,5 @@ -name: mudskipper_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mudskipper=0.1.0 diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index a31464c9710a..f1cd99b07923 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -1,7 +1,5 @@ -name: multiqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multivcfanalyzer/environment.yml b/modules/nf-core/multivcfanalyzer/environment.yml index 37f96f5e31db..3361a5a42989 100644 --- a/modules/nf-core/multivcfanalyzer/environment.yml +++ b/modules/nf-core/multivcfanalyzer/environment.yml @@ -1,7 +1,5 @@ -name: multivcfanalyzer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::multivcfanalyzer=0.85.2 diff --git a/modules/nf-core/mummer/environment.yml b/modules/nf-core/mummer/environment.yml index 5028135e1f36..643eff0f7409 100644 --- a/modules/nf-core/mummer/environment.yml +++ b/modules/nf-core/mummer/environment.yml @@ -1,7 +1,5 @@ -name: mummer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mummer=3.23 diff --git a/modules/nf-core/muscle/environment.yml b/modules/nf-core/muscle/environment.yml index e183f55ce43d..eb0feb4cb559 100644 --- a/modules/nf-core/muscle/environment.yml +++ b/modules/nf-core/muscle/environment.yml @@ -1,7 +1,5 @@ -name: muscle channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::muscle=3.8.1551 diff --git a/modules/nf-core/muscle5/super5/environment.yml b/modules/nf-core/muscle5/super5/environment.yml index fbaf4a2ef9f3..3167b8453232 100644 --- a/modules/nf-core/muscle5/super5/environment.yml +++ b/modules/nf-core/muscle5/super5/environment.yml @@ -1,8 +1,6 @@ -name: muscle5_super5 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::muscle=5.1 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/mygene/environment.yml b/modules/nf-core/mygene/environment.yml index 45442c49eda4..69dc92378a5a 100644 --- a/modules/nf-core/mygene/environment.yml +++ b/modules/nf-core/mygene/environment.yml @@ -1,7 +1,5 @@ -name: mygene channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mygene=3.2.2 diff --git a/modules/nf-core/mykrobe/predict/environment.yml b/modules/nf-core/mykrobe/predict/environment.yml index 13cb49d4d024..3d9a6d9c729a 100644 --- a/modules/nf-core/mykrobe/predict/environment.yml +++ b/modules/nf-core/mykrobe/predict/environment.yml @@ -1,7 +1,5 @@ -name: mykrobe_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mykrobe=0.11.0 diff --git a/modules/nf-core/nanocomp/environment.yml b/modules/nf-core/nanocomp/environment.yml index dc92191398c7..dad3490ff8b0 100644 --- a/modules/nf-core/nanocomp/environment.yml +++ b/modules/nf-core/nanocomp/environment.yml @@ -1,7 +1,5 @@ -name: nanocomp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda:nanocomp=1.21.0 diff --git a/modules/nf-core/nanofilt/environment.yml b/modules/nf-core/nanofilt/environment.yml index 7260c9be9980..497adfdfee6a 100644 --- a/modules/nf-core/nanofilt/environment.yml +++ b/modules/nf-core/nanofilt/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "nanofilt" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::nanofilt=2.8.0" diff --git a/modules/nf-core/nanolyse/environment.yml b/modules/nf-core/nanolyse/environment.yml index 7d738ba92c72..70e4421c5b50 100644 --- a/modules/nf-core/nanolyse/environment.yml +++ b/modules/nf-core/nanolyse/environment.yml @@ -1,7 +1,5 @@ -name: nanolyse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nanolyse=1.2.0 diff --git a/modules/nf-core/nanomonsv/parse/environment.yml b/modules/nf-core/nanomonsv/parse/environment.yml index 3288de7a3918..0311de25eb88 100644 --- a/modules/nf-core/nanomonsv/parse/environment.yml +++ b/modules/nf-core/nanomonsv/parse/environment.yml @@ -1,7 +1,5 @@ -name: nanomonsv_parse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nanomonsv=0.5.0 diff --git a/modules/nf-core/nanoplot/environment.yml b/modules/nf-core/nanoplot/environment.yml index 219cd2e3e0e9..821318c167b6 100644 --- a/modules/nf-core/nanoplot/environment.yml +++ b/modules/nf-core/nanoplot/environment.yml @@ -1,7 +1,5 @@ -name: nanoplot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nanoplot=1.41.6 diff --git a/modules/nf-core/nanoq/environment.yml b/modules/nf-core/nanoq/environment.yml index 41448d5b31dd..1a95d24e4b36 100644 --- a/modules/nf-core/nanoq/environment.yml +++ b/modules/nf-core/nanoq/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "nanoq" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::nanoq=0.10.0" diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml index 62629829d362..57ce13586f1f 100644 --- a/modules/nf-core/narfmap/align/environment.yml +++ b/modules/nf-core/narfmap/align/environment.yml @@ -1,8 +1,6 @@ -name: narfmap_align channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/narfmap - narfmap=1.4.2 diff --git a/modules/nf-core/narfmap/hashtable/environment.yml b/modules/nf-core/narfmap/hashtable/environment.yml index d4492db958e9..7f169f10b6a6 100644 --- a/modules/nf-core/narfmap/hashtable/environment.yml +++ b/modules/nf-core/narfmap/hashtable/environment.yml @@ -1,8 +1,6 @@ -name: narfmap_hashtable channels: - conda-forge - bioconda - - defaults dependencies: # renovate: datasource=conda depName=bioconda/narfmap - bioconda::narfmap=1.4.2 diff --git a/modules/nf-core/ncbigenomedownload/environment.yml b/modules/nf-core/ncbigenomedownload/environment.yml index 746c6086daab..7068048d404b 100644 --- a/modules/nf-core/ncbigenomedownload/environment.yml +++ b/modules/nf-core/ncbigenomedownload/environment.yml @@ -1,7 +1,5 @@ -name: ncbigenomedownload channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ncbi-genome-download=0.3.3 diff --git a/modules/nf-core/nextclade/datasetget/environment.yml b/modules/nf-core/nextclade/datasetget/environment.yml index cdd9f646f4a3..58a06b619f0f 100644 --- a/modules/nf-core/nextclade/datasetget/environment.yml +++ b/modules/nf-core/nextclade/datasetget/environment.yml @@ -1,7 +1,5 @@ -name: nextclade_datasetget channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nextclade=2.12.0 diff --git a/modules/nf-core/nextclade/run/environment.yml b/modules/nf-core/nextclade/run/environment.yml index 1e50e8d47b13..58a06b619f0f 100644 --- a/modules/nf-core/nextclade/run/environment.yml +++ b/modules/nf-core/nextclade/run/environment.yml @@ -1,7 +1,5 @@ -name: nextclade_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nextclade=2.12.0 diff --git a/modules/nf-core/nextgenmap/environment.yml b/modules/nf-core/nextgenmap/environment.yml index f5808831232c..7e7355a83a55 100644 --- a/modules/nf-core/nextgenmap/environment.yml +++ b/modules/nf-core/nextgenmap/environment.yml @@ -1,7 +1,5 @@ -name: nextgenmap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nextgenmap=0.5.5 diff --git a/modules/nf-core/ngmaster/environment.yml b/modules/nf-core/ngmaster/environment.yml index f6dc6ffa37bd..f9405cb4f4ed 100644 --- a/modules/nf-core/ngmaster/environment.yml +++ b/modules/nf-core/ngmaster/environment.yml @@ -1,8 +1,6 @@ -name: ngmaster channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngmaster=0.5.8 - conda-forge::python=3.9.7 # Lock from container diff --git a/modules/nf-core/ngmerge/environment.yml b/modules/nf-core/ngmerge/environment.yml index 55edab567982..2c5ed5437fb4 100644 --- a/modules/nf-core/ngmerge/environment.yml +++ b/modules/nf-core/ngmerge/environment.yml @@ -1,7 +1,5 @@ -name: ngmerge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngmerge=0.3 diff --git a/modules/nf-core/ngsbits/samplegender/environment.yml b/modules/nf-core/ngsbits/samplegender/environment.yml index 486c233c2f76..932d1556a7a8 100644 --- a/modules/nf-core/ngsbits/samplegender/environment.yml +++ b/modules/nf-core/ngsbits/samplegender/environment.yml @@ -1,7 +1,5 @@ -name: ngsbits_samplegender channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngs-bits=2023_02 diff --git a/modules/nf-core/ngscheckmate/fastq/environment.yml b/modules/nf-core/ngscheckmate/fastq/environment.yml index 8360b8c4000d..117b4e5783b2 100644 --- a/modules/nf-core/ngscheckmate/fastq/environment.yml +++ b/modules/nf-core/ngscheckmate/fastq/environment.yml @@ -1,7 +1,5 @@ -name: ngscheckmate_fastq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngscheckmate=1.0.1 diff --git a/modules/nf-core/ngscheckmate/ncm/environment.yml b/modules/nf-core/ngscheckmate/ncm/environment.yml index bf185fc23e35..117b4e5783b2 100644 --- a/modules/nf-core/ngscheckmate/ncm/environment.yml +++ b/modules/nf-core/ngscheckmate/ncm/environment.yml @@ -1,7 +1,5 @@ -name: ngscheckmate_ncm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngscheckmate=1.0.1 diff --git a/modules/nf-core/ngscheckmate/patterngenerator/environment.yml b/modules/nf-core/ngscheckmate/patterngenerator/environment.yml index b58ea344a76e..117b4e5783b2 100644 --- a/modules/nf-core/ngscheckmate/patterngenerator/environment.yml +++ b/modules/nf-core/ngscheckmate/patterngenerator/environment.yml @@ -1,7 +1,5 @@ -name: ngscheckmate_patterngenerator channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngscheckmate=1.0.1 diff --git a/modules/nf-core/ngscheckmate/vafncm/environment.yml b/modules/nf-core/ngscheckmate/vafncm/environment.yml index 63fed805afc1..117b4e5783b2 100644 --- a/modules/nf-core/ngscheckmate/vafncm/environment.yml +++ b/modules/nf-core/ngscheckmate/vafncm/environment.yml @@ -1,7 +1,5 @@ -name: ngscheckmate_vafncm channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ngscheckmate=1.0.1 diff --git a/modules/nf-core/nonpareil/curve/environment.yml b/modules/nf-core/nonpareil/curve/environment.yml index 0852362a6085..89d5aa6e9159 100644 --- a/modules/nf-core/nonpareil/curve/environment.yml +++ b/modules/nf-core/nonpareil/curve/environment.yml @@ -1,7 +1,5 @@ -name: nonpareil_curve channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nonpareil=3.5.5 diff --git a/modules/nf-core/nonpareil/nonpareil/environment.yml b/modules/nf-core/nonpareil/nonpareil/environment.yml index b1ebb2a2ab5f..89d5aa6e9159 100644 --- a/modules/nf-core/nonpareil/nonpareil/environment.yml +++ b/modules/nf-core/nonpareil/nonpareil/environment.yml @@ -1,7 +1,5 @@ -name: nonpareil_nonpareil channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nonpareil=3.5.5 diff --git a/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml b/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml index a5461c1cf41d..78bc8437c158 100644 --- a/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml +++ b/modules/nf-core/nonpareil/nonpareilcurvesr/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "nonpareil_nonpareilcurvesr" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::nonpareil=3.5.5" diff --git a/modules/nf-core/nonpareil/set/environment.yml b/modules/nf-core/nonpareil/set/environment.yml index 1e79bbbaac59..89d5aa6e9159 100644 --- a/modules/nf-core/nonpareil/set/environment.yml +++ b/modules/nf-core/nonpareil/set/environment.yml @@ -1,7 +1,5 @@ -name: nonpareil_set channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::nonpareil=3.5.5 diff --git a/modules/nf-core/nucmer/environment.yml b/modules/nf-core/nucmer/environment.yml index c46a65938bb7..643eff0f7409 100644 --- a/modules/nf-core/nucmer/environment.yml +++ b/modules/nf-core/nucmer/environment.yml @@ -1,7 +1,5 @@ -name: nucmer channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mummer=3.23 diff --git a/modules/nf-core/oatk/environment.yml b/modules/nf-core/oatk/environment.yml index d1c70c08ce71..5e5438aac0d6 100644 --- a/modules/nf-core/oatk/environment.yml +++ b/modules/nf-core/oatk/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "oatk" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::oatk=1.0" diff --git a/modules/nf-core/odgi/build/environment.yml b/modules/nf-core/odgi/build/environment.yml index 4ae56d26dcc1..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/build/environment.yml +++ b/modules/nf-core/odgi/build/environment.yml @@ -1,7 +1,5 @@ -name: odgi_build channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/draw/environment.yml b/modules/nf-core/odgi/draw/environment.yml index 2424dff67a82..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/draw/environment.yml +++ b/modules/nf-core/odgi/draw/environment.yml @@ -1,7 +1,5 @@ -name: odgi_draw channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/layout/environment.yml b/modules/nf-core/odgi/layout/environment.yml index 82212fc85b34..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/layout/environment.yml +++ b/modules/nf-core/odgi/layout/environment.yml @@ -1,7 +1,5 @@ -name: odgi_layout channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/sort/environment.yml b/modules/nf-core/odgi/sort/environment.yml index 1c1abb89a127..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/sort/environment.yml +++ b/modules/nf-core/odgi/sort/environment.yml @@ -1,7 +1,5 @@ -name: odgi_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/squeeze/environment.yml b/modules/nf-core/odgi/squeeze/environment.yml index 298458f0b021..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/squeeze/environment.yml +++ b/modules/nf-core/odgi/squeeze/environment.yml @@ -1,7 +1,5 @@ -name: odgi_squeeze channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/stats/environment.yml b/modules/nf-core/odgi/stats/environment.yml index e404f09f9ed4..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/stats/environment.yml +++ b/modules/nf-core/odgi/stats/environment.yml @@ -1,7 +1,5 @@ -name: odgi_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/unchop/environment.yml b/modules/nf-core/odgi/unchop/environment.yml index 1dadcdc9722b..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/unchop/environment.yml +++ b/modules/nf-core/odgi/unchop/environment.yml @@ -1,7 +1,5 @@ -name: odgi_unchop channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/view/environment.yml b/modules/nf-core/odgi/view/environment.yml index 94bf48f5ddac..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/view/environment.yml +++ b/modules/nf-core/odgi/view/environment.yml @@ -1,7 +1,5 @@ -name: odgi_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/odgi/viz/environment.yml b/modules/nf-core/odgi/viz/environment.yml index 8931e0ec3977..79e67e2e69cc 100644 --- a/modules/nf-core/odgi/viz/environment.yml +++ b/modules/nf-core/odgi/viz/environment.yml @@ -1,7 +1,5 @@ -name: odgi_viz channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::odgi=0.8.4 diff --git a/modules/nf-core/oncocnv/environment.yml b/modules/nf-core/oncocnv/environment.yml index 4ff4416f7cf1..97fc9a5446ca 100644 --- a/modules/nf-core/oncocnv/environment.yml +++ b/modules/nf-core/oncocnv/environment.yml @@ -1,7 +1,5 @@ -name: oncocnv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::oncocnv=7.0 diff --git a/modules/nf-core/openms/decoydatabase/environment.yml b/modules/nf-core/openms/decoydatabase/environment.yml index b98b2d49eb48..3391b183243c 100644 --- a/modules/nf-core/openms/decoydatabase/environment.yml +++ b/modules/nf-core/openms/decoydatabase/environment.yml @@ -1,7 +1,5 @@ -name: openms_decoydatabase channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::openms=3.1.0 diff --git a/modules/nf-core/openms/idfilter/environment.yml b/modules/nf-core/openms/idfilter/environment.yml index 57ca316347eb..5793e993cc53 100644 --- a/modules/nf-core/openms/idfilter/environment.yml +++ b/modules/nf-core/openms/idfilter/environment.yml @@ -1,7 +1,5 @@ -name: "openms_idfilter" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/openms/idmerger/environment.yml b/modules/nf-core/openms/idmerger/environment.yml index f2c8ade1ea45..3391b183243c 100644 --- a/modules/nf-core/openms/idmerger/environment.yml +++ b/modules/nf-core/openms/idmerger/environment.yml @@ -1,7 +1,5 @@ -name: openms_idmerger channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::openms=3.1.0 diff --git a/modules/nf-core/openms/idripper/environment.yml b/modules/nf-core/openms/idripper/environment.yml index 565bdaf7d913..5793e993cc53 100644 --- a/modules/nf-core/openms/idripper/environment.yml +++ b/modules/nf-core/openms/idripper/environment.yml @@ -1,7 +1,5 @@ -name: "openms_idripper" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/openms/idscoreswitcher/environment.yml b/modules/nf-core/openms/idscoreswitcher/environment.yml index f31b2bcaaad3..5793e993cc53 100644 --- a/modules/nf-core/openms/idscoreswitcher/environment.yml +++ b/modules/nf-core/openms/idscoreswitcher/environment.yml @@ -1,7 +1,5 @@ -name: "openms_idscoreswitcher" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/openms/peakpickerhires/environment.yml b/modules/nf-core/openms/peakpickerhires/environment.yml index 362acf0cfd96..456a019bf148 100644 --- a/modules/nf-core/openms/peakpickerhires/environment.yml +++ b/modules/nf-core/openms/peakpickerhires/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "openms_peakpickerhires" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/openms/peptideindexer/environment.yml b/modules/nf-core/openms/peptideindexer/environment.yml index 62ff1bbe7f89..e4ec4037ee8a 100644 --- a/modules/nf-core/openms/peptideindexer/environment.yml +++ b/modules/nf-core/openms/peptideindexer/environment.yml @@ -1,8 +1,6 @@ --- -name: "openms_peptideindexer" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/optitype/environment.yml b/modules/nf-core/optitype/environment.yml index d03e5e6d8551..add1d36c65f2 100644 --- a/modules/nf-core/optitype/environment.yml +++ b/modules/nf-core/optitype/environment.yml @@ -1,8 +1,6 @@ -name: optitype channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::optitype=1.3.5 - conda-forge::coincbc=2.10.10 diff --git a/modules/nf-core/orthofinder/environment.yml b/modules/nf-core/orthofinder/environment.yml index 4239c4c18154..68c475f8ddb1 100644 --- a/modules/nf-core/orthofinder/environment.yml +++ b/modules/nf-core/orthofinder/environment.yml @@ -1,4 +1,3 @@ -name: orthofinder channels: - conda-forge - bioconda diff --git a/modules/nf-core/paftools/sam2paf/environment.yml b/modules/nf-core/paftools/sam2paf/environment.yml index a2f0c8e94c4a..988733dd5c56 100644 --- a/modules/nf-core/paftools/sam2paf/environment.yml +++ b/modules/nf-core/paftools/sam2paf/environment.yml @@ -1,8 +1,6 @@ -name: paftools_sam2paf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::minimap2=2.24 - bioconda::samtools=1.14 diff --git a/modules/nf-core/pairix/environment.yml b/modules/nf-core/pairix/environment.yml index 51ab40072d1f..d544ae499c2f 100644 --- a/modules/nf-core/pairix/environment.yml +++ b/modules/nf-core/pairix/environment.yml @@ -1,7 +1,5 @@ -name: pairix channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairix=0.3.7 diff --git a/modules/nf-core/pairtools/dedup/environment.yml b/modules/nf-core/pairtools/dedup/environment.yml index 2f7ccc10cccd..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/dedup/environment.yml +++ b/modules/nf-core/pairtools/dedup/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_dedup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/flip/environment.yml b/modules/nf-core/pairtools/flip/environment.yml index f6fbc216e062..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/flip/environment.yml +++ b/modules/nf-core/pairtools/flip/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_flip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/merge/environment.yml b/modules/nf-core/pairtools/merge/environment.yml index f85858a7014c..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/merge/environment.yml +++ b/modules/nf-core/pairtools/merge/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/parse/environment.yml b/modules/nf-core/pairtools/parse/environment.yml index 0bd69ca2b2f9..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/parse/environment.yml +++ b/modules/nf-core/pairtools/parse/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_parse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/restrict/environment.yml b/modules/nf-core/pairtools/restrict/environment.yml index 4ba65c72272c..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/restrict/environment.yml +++ b/modules/nf-core/pairtools/restrict/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_restrict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/select/environment.yml b/modules/nf-core/pairtools/select/environment.yml index ef1b0d40f5f8..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/select/environment.yml +++ b/modules/nf-core/pairtools/select/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_select channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/sort/environment.yml b/modules/nf-core/pairtools/sort/environment.yml index 21bd011a167c..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/sort/environment.yml +++ b/modules/nf-core/pairtools/sort/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/split/environment.yml b/modules/nf-core/pairtools/split/environment.yml index 69a0fd910241..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/split/environment.yml +++ b/modules/nf-core/pairtools/split/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/pairtools/stats/environment.yml b/modules/nf-core/pairtools/stats/environment.yml index c1f95fbc880a..e88acbcd0c50 100644 --- a/modules/nf-core/pairtools/stats/environment.yml +++ b/modules/nf-core/pairtools/stats/environment.yml @@ -1,8 +1,6 @@ -name: pairtools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pairtools=1.0.2 - conda-forge::numpy=1.23 diff --git a/modules/nf-core/panacus/histgrowth/environment.yml b/modules/nf-core/panacus/histgrowth/environment.yml index d1f5fc5e2513..f08d28e1caca 100644 --- a/modules/nf-core/panacus/histgrowth/environment.yml +++ b/modules/nf-core/panacus/histgrowth/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "panacus_histgrowth" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::panacus=0.2.3" diff --git a/modules/nf-core/panacus/visualize/environment.yml b/modules/nf-core/panacus/visualize/environment.yml index d040fdb2a393..f08d28e1caca 100644 --- a/modules/nf-core/panacus/visualize/environment.yml +++ b/modules/nf-core/panacus/visualize/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "panacus_visualize" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::panacus=0.2.3" diff --git a/modules/nf-core/panaroo/run/environment.yml b/modules/nf-core/panaroo/run/environment.yml index b9022649ad56..a2de1fe403b0 100644 --- a/modules/nf-core/panaroo/run/environment.yml +++ b/modules/nf-core/panaroo/run/environment.yml @@ -1,7 +1,5 @@ -name: panaroo_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::panaroo=1.3.2 diff --git a/modules/nf-core/pangolin/environment.yml b/modules/nf-core/pangolin/environment.yml index 3c4d98c8075b..4fcf2f1f85a2 100644 --- a/modules/nf-core/pangolin/environment.yml +++ b/modules/nf-core/pangolin/environment.yml @@ -1,7 +1,5 @@ -name: pangolin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pangolin=4.2 diff --git a/modules/nf-core/parabricks/applybqsr/environment.yml b/modules/nf-core/parabricks/applybqsr/environment.yml index 034391085a73..3cebeff05bfc 100644 --- a/modules/nf-core/parabricks/applybqsr/environment.yml +++ b/modules/nf-core/parabricks/applybqsr/environment.yml @@ -1,5 +1,3 @@ -name: parabricks_applybqsr channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/paraclu/environment.yml b/modules/nf-core/paraclu/environment.yml index da9b2686a34e..505ec1b49b9a 100644 --- a/modules/nf-core/paraclu/environment.yml +++ b/modules/nf-core/paraclu/environment.yml @@ -1,7 +1,5 @@ -name: paraclu channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::paraclu=10 diff --git a/modules/nf-core/paragraph/idxdepth/environment.yml b/modules/nf-core/paragraph/idxdepth/environment.yml index 6b2e8e782495..e0718a758675 100644 --- a/modules/nf-core/paragraph/idxdepth/environment.yml +++ b/modules/nf-core/paragraph/idxdepth/environment.yml @@ -1,7 +1,5 @@ -name: paragraph_idxdepth channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::paragraph=2.3 diff --git a/modules/nf-core/paragraph/multigrmpy/environment.yml b/modules/nf-core/paragraph/multigrmpy/environment.yml index 78f50758d794..e0718a758675 100644 --- a/modules/nf-core/paragraph/multigrmpy/environment.yml +++ b/modules/nf-core/paragraph/multigrmpy/environment.yml @@ -1,7 +1,5 @@ -name: paragraph_multigrmpy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::paragraph=2.3 diff --git a/modules/nf-core/paragraph/vcf2paragraph/environment.yml b/modules/nf-core/paragraph/vcf2paragraph/environment.yml index 4071e82f9b38..ced1599f3d0d 100644 --- a/modules/nf-core/paragraph/vcf2paragraph/environment.yml +++ b/modules/nf-core/paragraph/vcf2paragraph/environment.yml @@ -1,9 +1,6 @@ -name: paragraph_vcf2paragraph - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.10.2 diff --git a/modules/nf-core/paraphase/environment.yml b/modules/nf-core/paraphase/environment.yml index 64b4a9172dcc..3722ded70466 100644 --- a/modules/nf-core/paraphase/environment.yml +++ b/modules/nf-core/paraphase/environment.yml @@ -1,5 +1,3 @@ -name: paraphase - channels: - conda-forge - bioconda diff --git a/modules/nf-core/pasty/environment.yml b/modules/nf-core/pasty/environment.yml index 6e4a7593aa48..2992999068aa 100644 --- a/modules/nf-core/pasty/environment.yml +++ b/modules/nf-core/pasty/environment.yml @@ -1,7 +1,5 @@ -name: pasty channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pasty=1.0.0 diff --git a/modules/nf-core/pbbam/pbmerge/environment.yml b/modules/nf-core/pbbam/pbmerge/environment.yml index 2ce6ea94953c..7d11d83d6988 100644 --- a/modules/nf-core/pbbam/pbmerge/environment.yml +++ b/modules/nf-core/pbbam/pbmerge/environment.yml @@ -1,7 +1,5 @@ -name: pbbam_pbmerge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pbbam=2.4.0 diff --git a/modules/nf-core/pbccs/environment.yml b/modules/nf-core/pbccs/environment.yml index bdc662b00274..7801a4fd8480 100644 --- a/modules/nf-core/pbccs/environment.yml +++ b/modules/nf-core/pbccs/environment.yml @@ -1,7 +1,5 @@ -name: pbccs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pbccs=6.4.0 diff --git a/modules/nf-core/pbptyper/environment.yml b/modules/nf-core/pbptyper/environment.yml index 204091673939..bc43f54a8d79 100644 --- a/modules/nf-core/pbptyper/environment.yml +++ b/modules/nf-core/pbptyper/environment.yml @@ -1,7 +1,5 @@ -name: pbptyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pbptyper=1.0.2 diff --git a/modules/nf-core/pbtk/bam2fastq/environment.yml b/modules/nf-core/pbtk/bam2fastq/environment.yml index 3c81f7fd039b..38649e1fd0db 100644 --- a/modules/nf-core/pbtk/bam2fastq/environment.yml +++ b/modules/nf-core/pbtk/bam2fastq/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pbtk_bam2fastq" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pbtk=3.1.1 diff --git a/modules/nf-core/pbtk/pbindex/environment.yml b/modules/nf-core/pbtk/pbindex/environment.yml index 9ce87decbc1f..e208868ba9ee 100644 --- a/modules/nf-core/pbtk/pbindex/environment.yml +++ b/modules/nf-core/pbtk/pbindex/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pbtk_pbindex" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::pbtk=3.1.1" diff --git a/modules/nf-core/pear/environment.yml b/modules/nf-core/pear/environment.yml index 127af628306d..c0908a54eb28 100644 --- a/modules/nf-core/pear/environment.yml +++ b/modules/nf-core/pear/environment.yml @@ -1,7 +1,5 @@ -name: pear channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pear=0.9.6 diff --git a/modules/nf-core/peddy/environment.yml b/modules/nf-core/peddy/environment.yml index 00e7cebe6869..8d7fa2b6ac21 100644 --- a/modules/nf-core/peddy/environment.yml +++ b/modules/nf-core/peddy/environment.yml @@ -1,7 +1,5 @@ -name: peddy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::peddy=0.4.8 diff --git a/modules/nf-core/peka/environment.yml b/modules/nf-core/peka/environment.yml index 21b6b106bef3..2aaf62b2f683 100644 --- a/modules/nf-core/peka/environment.yml +++ b/modules/nf-core/peka/environment.yml @@ -1,7 +1,5 @@ -name: peka channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::peka=1.0.0 diff --git a/modules/nf-core/phantompeakqualtools/environment.yml b/modules/nf-core/phantompeakqualtools/environment.yml index 095b7b4b5331..8967e158aadd 100644 --- a/modules/nf-core/phantompeakqualtools/environment.yml +++ b/modules/nf-core/phantompeakqualtools/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "phantompeakqualtools" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::phantompeakqualtools=1.2.2" diff --git a/modules/nf-core/pharokka/installdatabases/environment.yml b/modules/nf-core/pharokka/installdatabases/environment.yml index 933bacfc13a6..2c0e6a0f03cc 100644 --- a/modules/nf-core/pharokka/installdatabases/environment.yml +++ b/modules/nf-core/pharokka/installdatabases/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pharokka_installdatabases" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::pharokka=1.7.3" diff --git a/modules/nf-core/pharokka/pharokka/environment.yml b/modules/nf-core/pharokka/pharokka/environment.yml index f91be0507248..2c0e6a0f03cc 100644 --- a/modules/nf-core/pharokka/pharokka/environment.yml +++ b/modules/nf-core/pharokka/pharokka/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pharokka_pharokka" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::pharokka=1.7.3" diff --git a/modules/nf-core/phispy/environment.yml b/modules/nf-core/phispy/environment.yml index a5f60d0e719d..6b1821934dd0 100644 --- a/modules/nf-core/phispy/environment.yml +++ b/modules/nf-core/phispy/environment.yml @@ -1,8 +1,6 @@ -name: phispy channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::phispy=4.2.21 - conda-forge::biopython=1.81 diff --git a/modules/nf-core/phyloflash/environment.yml b/modules/nf-core/phyloflash/environment.yml index bf4ede4d29d3..2ebb5e261a16 100644 --- a/modules/nf-core/phyloflash/environment.yml +++ b/modules/nf-core/phyloflash/environment.yml @@ -1,7 +1,5 @@ -name: phyloflash channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::phyloflash=3.4 diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index 5c6ba5530749..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -1,7 +1,5 @@ -name: picard_addorreplacereadgroups channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml index 1d12dbf858bf..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/bedtointervallist/environment.yml +++ b/modules/nf-core/picard/bedtointervallist/environment.yml @@ -1,7 +1,5 @@ -name: picard_bedtointervallist channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml index 0f00fd740ed8..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/cleansam/environment.yml +++ b/modules/nf-core/picard/cleansam/environment.yml @@ -1,7 +1,5 @@ -name: picard_cleansam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index b00842b1b734..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -1,7 +1,5 @@ -name: picard_collecthsmetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml index 87a8c7d80553..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -1,7 +1,5 @@ -name: picard_collectinsertsizemetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index 6a16f00dcc68..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -1,7 +1,5 @@ -name: picard_collectmultiplemetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml index 1dfb96548891..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml @@ -1,7 +1,5 @@ -name: picard_collectrnaseqmetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 9f87553465b2..58d525818627 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -1,8 +1,6 @@ -name: picard_collectwgsmetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 - r::r-base diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml index 48a31a26dccc..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/createsequencedictionary/environment.yml +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -1,7 +1,5 @@ -name: picard_createsequencedictionary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml index 5df18044c3c1..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml @@ -1,7 +1,5 @@ -name: picard_crosscheckfingerprints channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml index b6d7eef616ca..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/extractfingerprint/environment.yml +++ b/modules/nf-core/picard/extractfingerprint/environment.yml @@ -1,7 +1,5 @@ -name: picard_extractfingerprint channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml index 4c97b78f3292..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/fastqtosam/environment.yml +++ b/modules/nf-core/picard/fastqtosam/environment.yml @@ -1,7 +1,5 @@ -name: picard_fastqtosam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml index 88248ad425ef..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/filtersamreads/environment.yml +++ b/modules/nf-core/picard/filtersamreads/environment.yml @@ -1,7 +1,5 @@ -name: picard_filtersamreads channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml index cf197ce646ff..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/fixmateinformation/environment.yml +++ b/modules/nf-core/picard/fixmateinformation/environment.yml @@ -1,7 +1,5 @@ -name: picard_fixmateinformation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index 16dd9f61307c..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -1,7 +1,5 @@ -name: picard_liftovervcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index a27db11865c7..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -1,7 +1,5 @@ -name: picard_markduplicates channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml index af6a04a1613d..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/mergesamfiles/environment.yml +++ b/modules/nf-core/picard/mergesamfiles/environment.yml @@ -1,7 +1,5 @@ -name: picard_mergesamfiles channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml b/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml index 1eaa76b3dcac..5f919a9a9b50 100644 --- a/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml +++ b/modules/nf-core/picard/positionbaseddownsamplesam/environment.yml @@ -1,7 +1,5 @@ -name: picard_positionbaseddownsamplesam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.1.1 diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index b7ccb0089f36..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -1,7 +1,5 @@ -name: picard_renamesampleinvcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml index b36f96bf1cee..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml @@ -1,7 +1,5 @@ -name: picard_scatterintervalsbyns channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml index 967b9f9f5673..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/sortsam/environment.yml +++ b/modules/nf-core/picard/sortsam/environment.yml @@ -1,7 +1,5 @@ -name: picard_sortsam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index a2f96e80fd3a..ff4a85edb5f1 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -1,7 +1,5 @@ -name: picard_sortvcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::picard=3.2.0 diff --git a/modules/nf-core/pigz/compress/environment.yml b/modules/nf-core/pigz/compress/environment.yml index 7551d1870f7a..5016d22697de 100644 --- a/modules/nf-core/pigz/compress/environment.yml +++ b/modules/nf-core/pigz/compress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pigz_compress" channels: - conda-forge - bioconda - - defaults dependencies: - "pigz=2.8" diff --git a/modules/nf-core/pilon/environment.yml b/modules/nf-core/pilon/environment.yml index f38ef8c30a24..a67d286906e0 100644 --- a/modules/nf-core/pilon/environment.yml +++ b/modules/nf-core/pilon/environment.yml @@ -1,7 +1,5 @@ -name: pilon channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pilon=1.24 diff --git a/modules/nf-core/pindel/pindel/environment.yml b/modules/nf-core/pindel/pindel/environment.yml index 262d5bf85f90..0941ad7feb21 100644 --- a/modules/nf-core/pindel/pindel/environment.yml +++ b/modules/nf-core/pindel/pindel/environment.yml @@ -1,7 +1,5 @@ -name: pindel_pindel channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pindel=0.2.5b9 diff --git a/modules/nf-core/pints/caller/environment.yml b/modules/nf-core/pints/caller/environment.yml index 96760dfae37e..afcdc7eb7f3f 100644 --- a/modules/nf-core/pints/caller/environment.yml +++ b/modules/nf-core/pints/caller/environment.yml @@ -1,7 +1,5 @@ -name: pints_caller channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pypints=1.1.10 diff --git a/modules/nf-core/pirate/environment.yml b/modules/nf-core/pirate/environment.yml index 9fa738905489..4a770adcbefd 100644 --- a/modules/nf-core/pirate/environment.yml +++ b/modules/nf-core/pirate/environment.yml @@ -1,9 +1,6 @@ -name: pirate - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::perl-bioperl=1.7.2 diff --git a/modules/nf-core/plasmidfinder/environment.yml b/modules/nf-core/plasmidfinder/environment.yml index c95be21364b1..f38092872c18 100644 --- a/modules/nf-core/plasmidfinder/environment.yml +++ b/modules/nf-core/plasmidfinder/environment.yml @@ -1,7 +1,5 @@ -name: plasmidfinder channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plasmidfinder=2.1.6=py310hdfd78af_1 diff --git a/modules/nf-core/plasmidid/environment.yml b/modules/nf-core/plasmidid/environment.yml index 1eda21d59f9e..173c247532ce 100644 --- a/modules/nf-core/plasmidid/environment.yml +++ b/modules/nf-core/plasmidid/environment.yml @@ -1,7 +1,5 @@ -name: plasmidid channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plasmidid=1.6.5 diff --git a/modules/nf-core/platypus/environment.yml b/modules/nf-core/platypus/environment.yml index 9eb0ff89d5a0..39bd8ad6325f 100644 --- a/modules/nf-core/platypus/environment.yml +++ b/modules/nf-core/platypus/environment.yml @@ -1,7 +1,5 @@ -name: platypus channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::platypus-variant=0.8.1 diff --git a/modules/nf-core/plink/bcf/environment.yml b/modules/nf-core/plink/bcf/environment.yml index a929846afd75..d860c8337c73 100644 --- a/modules/nf-core/plink/bcf/environment.yml +++ b/modules/nf-core/plink/bcf/environment.yml @@ -1,7 +1,5 @@ -name: plink_bcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/epistasis/environment.yml b/modules/nf-core/plink/epistasis/environment.yml index 1e0f3792deec..dbc6dbb3349b 100644 --- a/modules/nf-core/plink/epistasis/environment.yml +++ b/modules/nf-core/plink/epistasis/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "plink_epistasis" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/exclude/environment.yml b/modules/nf-core/plink/exclude/environment.yml index 0a545956ec3d..d860c8337c73 100644 --- a/modules/nf-core/plink/exclude/environment.yml +++ b/modules/nf-core/plink/exclude/environment.yml @@ -1,7 +1,5 @@ -name: plink_exclude channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/extract/environment.yml b/modules/nf-core/plink/extract/environment.yml index a43207f0ec8a..d860c8337c73 100644 --- a/modules/nf-core/plink/extract/environment.yml +++ b/modules/nf-core/plink/extract/environment.yml @@ -1,7 +1,5 @@ -name: plink_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/fastepistasis/environment.yml b/modules/nf-core/plink/fastepistasis/environment.yml index 6bd1701d725f..dbc6dbb3349b 100644 --- a/modules/nf-core/plink/fastepistasis/environment.yml +++ b/modules/nf-core/plink/fastepistasis/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "plink_fastepistasis" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/gwas/environment.yml b/modules/nf-core/plink/gwas/environment.yml index 289e15ada0d6..dbc6dbb3349b 100644 --- a/modules/nf-core/plink/gwas/environment.yml +++ b/modules/nf-core/plink/gwas/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "plink_gwas" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/hwe/environment.yml b/modules/nf-core/plink/hwe/environment.yml index f0a66233814d..dbc6dbb3349b 100644 --- a/modules/nf-core/plink/hwe/environment.yml +++ b/modules/nf-core/plink/hwe/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "plink_hwe" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/indep/environment.yml b/modules/nf-core/plink/indep/environment.yml index 7514d8478d55..d860c8337c73 100644 --- a/modules/nf-core/plink/indep/environment.yml +++ b/modules/nf-core/plink/indep/environment.yml @@ -1,7 +1,5 @@ -name: plink_indep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/indeppairwise/environment.yml b/modules/nf-core/plink/indeppairwise/environment.yml index d91bff441354..d860c8337c73 100644 --- a/modules/nf-core/plink/indeppairwise/environment.yml +++ b/modules/nf-core/plink/indeppairwise/environment.yml @@ -1,7 +1,5 @@ -name: plink_indeppairwise channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/ld/environment.yml b/modules/nf-core/plink/ld/environment.yml index d19c721f9005..dbc6dbb3349b 100644 --- a/modules/nf-core/plink/ld/environment.yml +++ b/modules/nf-core/plink/ld/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "plink_ld" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::plink=1.90b6.21" diff --git a/modules/nf-core/plink/recode/environment.yml b/modules/nf-core/plink/recode/environment.yml index e1ea7acb6fef..d860c8337c73 100644 --- a/modules/nf-core/plink/recode/environment.yml +++ b/modules/nf-core/plink/recode/environment.yml @@ -1,7 +1,5 @@ -name: plink_recode channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink/vcf/environment.yml b/modules/nf-core/plink/vcf/environment.yml index 08b151adec4c..d860c8337c73 100644 --- a/modules/nf-core/plink/vcf/environment.yml +++ b/modules/nf-core/plink/vcf/environment.yml @@ -1,7 +1,5 @@ -name: plink_vcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink=1.90b6.21 diff --git a/modules/nf-core/plink2/extract/environment.yml b/modules/nf-core/plink2/extract/environment.yml index 3664377ccee2..b0a71e149e05 100644 --- a/modules/nf-core/plink2/extract/environment.yml +++ b/modules/nf-core/plink2/extract/environment.yml @@ -1,7 +1,5 @@ -name: plink2_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink2=2.00a2.3 diff --git a/modules/nf-core/plink2/score/environment.yml b/modules/nf-core/plink2/score/environment.yml index 56fca34bfac8..b0a71e149e05 100644 --- a/modules/nf-core/plink2/score/environment.yml +++ b/modules/nf-core/plink2/score/environment.yml @@ -1,7 +1,5 @@ -name: plink2_score channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink2=2.00a2.3 diff --git a/modules/nf-core/plink2/vcf/environment.yml b/modules/nf-core/plink2/vcf/environment.yml index 2d062228f797..b0a71e149e05 100644 --- a/modules/nf-core/plink2/vcf/environment.yml +++ b/modules/nf-core/plink2/vcf/environment.yml @@ -1,7 +1,5 @@ -name: plink2_vcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::plink2=2.00a2.3 diff --git a/modules/nf-core/pmdtools/filter/environment.yml b/modules/nf-core/pmdtools/filter/environment.yml index d4d8c11781cc..efbb77ebd119 100644 --- a/modules/nf-core/pmdtools/filter/environment.yml +++ b/modules/nf-core/pmdtools/filter/environment.yml @@ -1,8 +1,6 @@ -name: pmdtools_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pmdtools=0.60 - bioconda::samtools=1.14 # Version lock with container diff --git a/modules/nf-core/pneumocat/environment.yml b/modules/nf-core/pneumocat/environment.yml index 30d01766ad6e..55fec0f5d480 100644 --- a/modules/nf-core/pneumocat/environment.yml +++ b/modules/nf-core/pneumocat/environment.yml @@ -1,7 +1,5 @@ -name: pneumocat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pneumocat=1.2.1 diff --git a/modules/nf-core/poolsnp/environment.yml b/modules/nf-core/poolsnp/environment.yml index 87b56af84e38..489d578f266c 100644 --- a/modules/nf-core/poolsnp/environment.yml +++ b/modules/nf-core/poolsnp/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "poolsnp" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::poolsnp=1.0.1" diff --git a/modules/nf-core/popscle/demuxlet/environment.yml b/modules/nf-core/popscle/demuxlet/environment.yml index ed2cce7712b8..555c9debb1b8 100644 --- a/modules/nf-core/popscle/demuxlet/environment.yml +++ b/modules/nf-core/popscle/demuxlet/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "popscle_demuxlet" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::popscle=0.1" diff --git a/modules/nf-core/popscle/dscpileup/environment.yml b/modules/nf-core/popscle/dscpileup/environment.yml index 469927670a3a..555c9debb1b8 100644 --- a/modules/nf-core/popscle/dscpileup/environment.yml +++ b/modules/nf-core/popscle/dscpileup/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "popscle_dscpileup" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::popscle=0.1" diff --git a/modules/nf-core/popscle/freemuxlet/environment.yml b/modules/nf-core/popscle/freemuxlet/environment.yml index c6747a0ae1e9..555c9debb1b8 100644 --- a/modules/nf-core/popscle/freemuxlet/environment.yml +++ b/modules/nf-core/popscle/freemuxlet/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "popscle_freemuxlet" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::popscle=0.1" diff --git a/modules/nf-core/porechop/abi/environment.yml b/modules/nf-core/porechop/abi/environment.yml index 4dd2eab15c49..dabb4921eae8 100644 --- a/modules/nf-core/porechop/abi/environment.yml +++ b/modules/nf-core/porechop/abi/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: porechop_abi channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::porechop_abi=0.5.0 diff --git a/modules/nf-core/porechop/porechop/environment.yml b/modules/nf-core/porechop/porechop/environment.yml index 28b67c16d0b5..4defeb335139 100644 --- a/modules/nf-core/porechop/porechop/environment.yml +++ b/modules/nf-core/porechop/porechop/environment.yml @@ -1,7 +1,5 @@ -name: porechop_porechop channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::porechop=0.2.4 diff --git a/modules/nf-core/preseq/ccurve/environment.yml b/modules/nf-core/preseq/ccurve/environment.yml index d05e5ff31841..926d7aece8db 100644 --- a/modules/nf-core/preseq/ccurve/environment.yml +++ b/modules/nf-core/preseq/ccurve/environment.yml @@ -1,7 +1,5 @@ -name: preseq_ccurve channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/preseq/lcextrap/environment.yml b/modules/nf-core/preseq/lcextrap/environment.yml index 57b8b9c671a6..926d7aece8db 100644 --- a/modules/nf-core/preseq/lcextrap/environment.yml +++ b/modules/nf-core/preseq/lcextrap/environment.yml @@ -1,7 +1,5 @@ -name: preseq_lcextrap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::preseq=3.1.2 diff --git a/modules/nf-core/president/environment.yml b/modules/nf-core/president/environment.yml index b2f02eeb16fd..2aa904b76907 100644 --- a/modules/nf-core/president/environment.yml +++ b/modules/nf-core/president/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "president" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::president=0.6.8 diff --git a/modules/nf-core/presto/filterseq/environment.yml b/modules/nf-core/presto/filterseq/environment.yml index 4a61937021f8..8896f444ba69 100644 --- a/modules/nf-core/presto/filterseq/environment.yml +++ b/modules/nf-core/presto/filterseq/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "presto_filterseq" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::presto=0.7.1" diff --git a/modules/nf-core/pretextmap/environment.yml b/modules/nf-core/pretextmap/environment.yml index 1b1b90b7fe8d..bfbbee2b72fb 100644 --- a/modules/nf-core/pretextmap/environment.yml +++ b/modules/nf-core/pretextmap/environment.yml @@ -1,8 +1,6 @@ -name: pretextmap channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pretextmap=0.1.9 - bioconda::samtools=1.17 diff --git a/modules/nf-core/pretextsnapshot/environment.yml b/modules/nf-core/pretextsnapshot/environment.yml index 812c59753fd6..ed7215226412 100644 --- a/modules/nf-core/pretextsnapshot/environment.yml +++ b/modules/nf-core/pretextsnapshot/environment.yml @@ -1,7 +1,5 @@ -name: pretextsnapshot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pretextsnapshot=0.0.4 diff --git a/modules/nf-core/prinseqplusplus/environment.yml b/modules/nf-core/prinseqplusplus/environment.yml index 5ab5a12663c9..fe598ef114e3 100644 --- a/modules/nf-core/prinseqplusplus/environment.yml +++ b/modules/nf-core/prinseqplusplus/environment.yml @@ -1,7 +1,5 @@ -name: prinseqplusplus channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::prinseq-plus-plus=1.2.3 diff --git a/modules/nf-core/prodigal/environment.yml b/modules/nf-core/prodigal/environment.yml index 857465345806..7609bf3bd161 100644 --- a/modules/nf-core/prodigal/environment.yml +++ b/modules/nf-core/prodigal/environment.yml @@ -1,8 +1,6 @@ -name: prodigal channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::prodigal=2.6.3 - conda-forge::pigz=2.6 diff --git a/modules/nf-core/prokka/environment.yml b/modules/nf-core/prokka/environment.yml index d7c44d5a39ea..7c9753fc104b 100644 --- a/modules/nf-core/prokka/environment.yml +++ b/modules/nf-core/prokka/environment.yml @@ -1,7 +1,5 @@ -name: prokka channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::prokka=1.14.6 diff --git a/modules/nf-core/propr/grea/environment.yml b/modules/nf-core/propr/grea/environment.yml index c6897c730598..2bb015a10479 100644 --- a/modules/nf-core/propr/grea/environment.yml +++ b/modules/nf-core/propr/grea/environment.yml @@ -1,7 +1,5 @@ -name: propr_grea channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-propr=5.0.4 diff --git a/modules/nf-core/propr/logratio/environment.yml b/modules/nf-core/propr/logratio/environment.yml index 61e573211250..7064f1712b44 100644 --- a/modules/nf-core/propr/logratio/environment.yml +++ b/modules/nf-core/propr/logratio/environment.yml @@ -1,7 +1,5 @@ -name: propr_logratio channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-propr=4.2.6 diff --git a/modules/nf-core/propr/propd/environment.yml b/modules/nf-core/propr/propd/environment.yml index 058f30a04103..f7da56ebc393 100644 --- a/modules/nf-core/propr/propd/environment.yml +++ b/modules/nf-core/propr/propd/environment.yml @@ -1,7 +1,5 @@ -name: propr_propd channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-propr=5.0.3 diff --git a/modules/nf-core/propr/propr/environment.yml b/modules/nf-core/propr/propr/environment.yml index cb163068ff11..f7da56ebc393 100644 --- a/modules/nf-core/propr/propr/environment.yml +++ b/modules/nf-core/propr/propr/environment.yml @@ -1,7 +1,5 @@ -name: propr_propr channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-propr=5.0.3 diff --git a/modules/nf-core/proteinortho/environment.yml b/modules/nf-core/proteinortho/environment.yml index 9db21f278e08..d4ca9e72fc18 100644 --- a/modules/nf-core/proteinortho/environment.yml +++ b/modules/nf-core/proteinortho/environment.yml @@ -1,7 +1,5 @@ -name: proteinortho channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::proteinortho=6.3.0 diff --git a/modules/nf-core/proteus/readproteingroups/environment.yml b/modules/nf-core/proteus/readproteingroups/environment.yml index 3ac338bc0896..47fc6415956e 100644 --- a/modules/nf-core/proteus/readproteingroups/environment.yml +++ b/modules/nf-core/proteus/readproteingroups/environment.yml @@ -1,8 +1,6 @@ -name: proteus_readproteingroups channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-base=4.2.1 - bioconda::r-proteus-bartongroup=0.2.16 diff --git a/modules/nf-core/pureclip/environment.yml b/modules/nf-core/pureclip/environment.yml index ff4f455fcc5a..2bea248a17ae 100644 --- a/modules/nf-core/pureclip/environment.yml +++ b/modules/nf-core/pureclip/environment.yml @@ -1,7 +1,5 @@ -name: pureclip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pureclip=1.3.1 diff --git a/modules/nf-core/purecn/coverage/environment.yml b/modules/nf-core/purecn/coverage/environment.yml index 12a6aff2af3a..cbd210aa4960 100644 --- a/modules/nf-core/purecn/coverage/environment.yml +++ b/modules/nf-core/purecn/coverage/environment.yml @@ -1,8 +1,6 @@ -name: purecn_coverage channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 diff --git a/modules/nf-core/purecn/intervalfile/environment.yml b/modules/nf-core/purecn/intervalfile/environment.yml index 1597c765c500..9717427ab5d6 100644 --- a/modules/nf-core/purecn/intervalfile/environment.yml +++ b/modules/nf-core/purecn/intervalfile/environment.yml @@ -1,9 +1,6 @@ -name: purecn_intervalfile - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-org.hs.eg.db=3.18.0 diff --git a/modules/nf-core/purecn/normaldb/environment.yml b/modules/nf-core/purecn/normaldb/environment.yml index f89d4b2c0c1f..9717427ab5d6 100644 --- a/modules/nf-core/purecn/normaldb/environment.yml +++ b/modules/nf-core/purecn/normaldb/environment.yml @@ -1,9 +1,6 @@ -name: purecn_normaldb - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-org.hs.eg.db=3.18.0 diff --git a/modules/nf-core/purecn/run/environment.yml b/modules/nf-core/purecn/run/environment.yml index 04c48aecf807..cbd210aa4960 100644 --- a/modules/nf-core/purecn/run/environment.yml +++ b/modules/nf-core/purecn/run/environment.yml @@ -1,8 +1,6 @@ -name: purecn_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 diff --git a/modules/nf-core/purgedups/calcuts/environment.yml b/modules/nf-core/purgedups/calcuts/environment.yml index acfed4ba3b57..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/calcuts/environment.yml +++ b/modules/nf-core/purgedups/calcuts/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_calcuts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/purgedups/getseqs/environment.yml b/modules/nf-core/purgedups/getseqs/environment.yml index 60075d540c44..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/getseqs/environment.yml +++ b/modules/nf-core/purgedups/getseqs/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_getseqs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/purgedups/histplot/environment.yml b/modules/nf-core/purgedups/histplot/environment.yml index 29749d6b5484..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/histplot/environment.yml +++ b/modules/nf-core/purgedups/histplot/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_histplot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/purgedups/pbcstat/environment.yml b/modules/nf-core/purgedups/pbcstat/environment.yml index e8b5a325b0c1..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/pbcstat/environment.yml +++ b/modules/nf-core/purgedups/pbcstat/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_pbcstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/purgedups/purgedups/environment.yml b/modules/nf-core/purgedups/purgedups/environment.yml index 2a58463958a1..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/purgedups/environment.yml +++ b/modules/nf-core/purgedups/purgedups/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_purgedups channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/purgedups/splitfa/environment.yml b/modules/nf-core/purgedups/splitfa/environment.yml index b70d75a1e8a3..8c4861fa61af 100644 --- a/modules/nf-core/purgedups/splitfa/environment.yml +++ b/modules/nf-core/purgedups/splitfa/environment.yml @@ -1,7 +1,5 @@ -name: purgedups_splitfa channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::purge_dups=1.2.6 diff --git a/modules/nf-core/pycoqc/environment.yml b/modules/nf-core/pycoqc/environment.yml index c2a3a4d100b9..6c0c93e98c0f 100644 --- a/modules/nf-core/pycoqc/environment.yml +++ b/modules/nf-core/pycoqc/environment.yml @@ -1,7 +1,5 @@ -name: pycoqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pycoqc=2.5.2 diff --git a/modules/nf-core/pydamage/analyze/environment.yml b/modules/nf-core/pydamage/analyze/environment.yml index ed8a58ad4ec8..f1193aab4ea1 100644 --- a/modules/nf-core/pydamage/analyze/environment.yml +++ b/modules/nf-core/pydamage/analyze/environment.yml @@ -1,7 +1,5 @@ -name: pydamage_analyze channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pydamage=0.70 diff --git a/modules/nf-core/pydamage/filter/environment.yml b/modules/nf-core/pydamage/filter/environment.yml index 83bafd69001d..f1193aab4ea1 100644 --- a/modules/nf-core/pydamage/filter/environment.yml +++ b/modules/nf-core/pydamage/filter/environment.yml @@ -1,7 +1,5 @@ -name: pydamage_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pydamage=0.70 diff --git a/modules/nf-core/pyrodigal/environment.yml b/modules/nf-core/pyrodigal/environment.yml index 3e538e8c9b5a..b0bbc5158862 100644 --- a/modules/nf-core/pyrodigal/environment.yml +++ b/modules/nf-core/pyrodigal/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "pyrodigal" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::pyrodigal=3.3.0 - conda-forge::pigz=2.8 diff --git a/modules/nf-core/qcat/environment.yml b/modules/nf-core/qcat/environment.yml index b1f79884ae9d..0ab0d71b8f8b 100644 --- a/modules/nf-core/qcat/environment.yml +++ b/modules/nf-core/qcat/environment.yml @@ -1,7 +1,5 @@ -name: qcat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::qcat=1.1.0 diff --git a/modules/nf-core/qualimap/bamqc/environment.yml b/modules/nf-core/qualimap/bamqc/environment.yml index 3f30d0cd3b1c..4fa5f4e8e9d9 100644 --- a/modules/nf-core/qualimap/bamqc/environment.yml +++ b/modules/nf-core/qualimap/bamqc/environment.yml @@ -1,7 +1,5 @@ -name: qualimap_bamqc channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::qualimap=2.3 diff --git a/modules/nf-core/qualimap/bamqccram/environment.yml b/modules/nf-core/qualimap/bamqccram/environment.yml index b3d0dfd72758..609b5f74a807 100644 --- a/modules/nf-core/qualimap/bamqccram/environment.yml +++ b/modules/nf-core/qualimap/bamqccram/environment.yml @@ -1,8 +1,6 @@ -name: qualimap_bamqccram channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::qualimap=2.2.2d - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/qualimap/rnaseq/environment.yml b/modules/nf-core/qualimap/rnaseq/environment.yml index 590ae85f744b..4fa5f4e8e9d9 100644 --- a/modules/nf-core/qualimap/rnaseq/environment.yml +++ b/modules/nf-core/qualimap/rnaseq/environment.yml @@ -1,7 +1,5 @@ -name: qualimap_rnaseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::qualimap=2.3 diff --git a/modules/nf-core/quartonotebook/environment.yml b/modules/nf-core/quartonotebook/environment.yml index 1084ec03ee07..3a48c788a764 100644 --- a/modules/nf-core/quartonotebook/environment.yml +++ b/modules/nf-core/quartonotebook/environment.yml @@ -1,9 +1,6 @@ -name: quartonotebook - channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::jupyter=1.0.0 diff --git a/modules/nf-core/quast/environment.yml b/modules/nf-core/quast/environment.yml index 0f9e3079f1c4..2c14403de7ad 100644 --- a/modules/nf-core/quast/environment.yml +++ b/modules/nf-core/quast/environment.yml @@ -1,7 +1,5 @@ -name: quast channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::quast=5.2.0 diff --git a/modules/nf-core/quilt/quilt/environment.yml b/modules/nf-core/quilt/quilt/environment.yml index a2161a6515df..967b84ba3147 100644 --- a/modules/nf-core/quilt/quilt/environment.yml +++ b/modules/nf-core/quilt/quilt/environment.yml @@ -1,8 +1,6 @@ -name: quilt_quilt channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-quilt=1.0.5=r43h06b5641_0 - r-base=4.3.1 diff --git a/modules/nf-core/racon/environment.yml b/modules/nf-core/racon/environment.yml index abc5d78431a8..b210a3db8fac 100644 --- a/modules/nf-core/racon/environment.yml +++ b/modules/nf-core/racon/environment.yml @@ -1,7 +1,5 @@ -name: racon channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::racon=1.4.20 diff --git a/modules/nf-core/rapidnj/environment.yml b/modules/nf-core/rapidnj/environment.yml index 060c087e0568..d18144a400ae 100644 --- a/modules/nf-core/rapidnj/environment.yml +++ b/modules/nf-core/rapidnj/environment.yml @@ -1,8 +1,6 @@ -name: rapidnj channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rapidnj=2.3.2 - conda-forge::biopython=1.78 diff --git a/modules/nf-core/rasusa/environment.yml b/modules/nf-core/rasusa/environment.yml index c0d67ecc3028..e2e81834b6d1 100644 --- a/modules/nf-core/rasusa/environment.yml +++ b/modules/nf-core/rasusa/environment.yml @@ -1,7 +1,5 @@ -name: rasusa channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rasusa=0.3.0 diff --git a/modules/nf-core/raven/environment.yml b/modules/nf-core/raven/environment.yml index 395d95cb4c08..c520dacbfb27 100644 --- a/modules/nf-core/raven/environment.yml +++ b/modules/nf-core/raven/environment.yml @@ -1,7 +1,5 @@ -name: raven channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::raven-assembler=1.6.1 diff --git a/modules/nf-core/raxmlng/environment.yml b/modules/nf-core/raxmlng/environment.yml index e597d7f4bead..28e81c36a38d 100644 --- a/modules/nf-core/raxmlng/environment.yml +++ b/modules/nf-core/raxmlng/environment.yml @@ -1,7 +1,5 @@ -name: raxmlng channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::raxml-ng=1.0.3 diff --git a/modules/nf-core/repeatmodeler/builddatabase/environment.yml b/modules/nf-core/repeatmodeler/builddatabase/environment.yml index ecc282e68546..531430738c6a 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/environment.yml +++ b/modules/nf-core/repeatmodeler/builddatabase/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "repeatmodeler_builddatabase" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::repeatmodeler=2.0.5" diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml index 24220717e0ae..531430738c6a 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml +++ b/modules/nf-core/repeatmodeler/repeatmodeler/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "repeatmodeler_repeatmodeler" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::repeatmodeler=2.0.5" diff --git a/modules/nf-core/resfinder/run/environment.yml b/modules/nf-core/resfinder/run/environment.yml index c6fa6780344e..823ba2117773 100644 --- a/modules/nf-core/resfinder/run/environment.yml +++ b/modules/nf-core/resfinder/run/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "resfinder_run" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::resfinder=4.1.11" diff --git a/modules/nf-core/rgi/cardannotation/environment.yml b/modules/nf-core/rgi/cardannotation/environment.yml index f1c5872aa72c..609693fe947d 100644 --- a/modules/nf-core/rgi/cardannotation/environment.yml +++ b/modules/nf-core/rgi/cardannotation/environment.yml @@ -1,7 +1,5 @@ -name: rgi_cardannotation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rgi=6.0.3 diff --git a/modules/nf-core/rgi/main/environment.yml b/modules/nf-core/rgi/main/environment.yml index f229cc213fde..609693fe947d 100644 --- a/modules/nf-core/rgi/main/environment.yml +++ b/modules/nf-core/rgi/main/environment.yml @@ -1,7 +1,5 @@ -name: rgi_main channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rgi=6.0.3 diff --git a/modules/nf-core/rhocall/annotate/environment.yml b/modules/nf-core/rhocall/annotate/environment.yml index 5a00600fdc6e..ba95c3cbeb1d 100644 --- a/modules/nf-core/rhocall/annotate/environment.yml +++ b/modules/nf-core/rhocall/annotate/environment.yml @@ -1,7 +1,5 @@ -name: rhocall_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rhocall=0.5.1 diff --git a/modules/nf-core/rhocall/viz/environment.yml b/modules/nf-core/rhocall/viz/environment.yml index 6e5b352f5fdc..538db5092da8 100644 --- a/modules/nf-core/rhocall/viz/environment.yml +++ b/modules/nf-core/rhocall/viz/environment.yml @@ -1,7 +1,5 @@ -name: "rhocall_viz" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::rhocall=0.5.1" diff --git a/modules/nf-core/ribotish/predict/environment.yml b/modules/nf-core/ribotish/predict/environment.yml index 77b054ec0efd..c96eb9589db2 100644 --- a/modules/nf-core/ribotish/predict/environment.yml +++ b/modules/nf-core/ribotish/predict/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ribotish_predict" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ribotish=0.2.7" diff --git a/modules/nf-core/ribotish/quality/environment.yml b/modules/nf-core/ribotish/quality/environment.yml index a21049b3b463..c96eb9589db2 100644 --- a/modules/nf-core/ribotish/quality/environment.yml +++ b/modules/nf-core/ribotish/quality/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ribotish_quality" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ribotish=0.2.7" diff --git a/modules/nf-core/ribotricer/detectorfs/environment.yml b/modules/nf-core/ribotricer/detectorfs/environment.yml index 74d510404f78..3284c86d00bb 100644 --- a/modules/nf-core/ribotricer/detectorfs/environment.yml +++ b/modules/nf-core/ribotricer/detectorfs/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ribotricer_detectorfs" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ribotricer=1.3.3" diff --git a/modules/nf-core/ribotricer/prepareorfs/environment.yml b/modules/nf-core/ribotricer/prepareorfs/environment.yml index 95bb38aaa029..3284c86d00bb 100644 --- a/modules/nf-core/ribotricer/prepareorfs/environment.yml +++ b/modules/nf-core/ribotricer/prepareorfs/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ribotricer_prepareorfs" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ribotricer=1.3.3" diff --git a/modules/nf-core/ribowaltz/environment.yml b/modules/nf-core/ribowaltz/environment.yml index 04faff75747d..8cc74d39146f 100644 --- a/modules/nf-core/ribowaltz/environment.yml +++ b/modules/nf-core/ribowaltz/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "ribowaltz" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::ribowaltz=2.0" diff --git a/modules/nf-core/rmarkdownnotebook/environment.yml b/modules/nf-core/rmarkdownnotebook/environment.yml index c7fe8cf2aa5e..26cd9e2e1387 100644 --- a/modules/nf-core/rmarkdownnotebook/environment.yml +++ b/modules/nf-core/rmarkdownnotebook/environment.yml @@ -1,8 +1,6 @@ -name: rmarkdownnotebook channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::r-base=4.1.0 - conda-forge::r-rmarkdown=2.9 diff --git a/modules/nf-core/roary/environment.yml b/modules/nf-core/roary/environment.yml index 5ec37900641c..87b7f3906dc6 100644 --- a/modules/nf-core/roary/environment.yml +++ b/modules/nf-core/roary/environment.yml @@ -1,7 +1,5 @@ -name: roary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::roary=3.13.0 diff --git a/modules/nf-core/rrnatranscripts/environment.yml b/modules/nf-core/rrnatranscripts/environment.yml index e812273bf8eb..6f09494b4bdf 100644 --- a/modules/nf-core/rrnatranscripts/environment.yml +++ b/modules/nf-core/rrnatranscripts/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "rrnatranscripts" channels: - conda-forge - bioconda - - defaults dependencies: - python=3.12.2 diff --git a/modules/nf-core/rsem/calculateexpression/environment.yml b/modules/nf-core/rsem/calculateexpression/environment.yml index b811fa6fe84c..bcf70fa9adfa 100644 --- a/modules/nf-core/rsem/calculateexpression/environment.yml +++ b/modules/nf-core/rsem/calculateexpression/environment.yml @@ -1,8 +1,6 @@ -name: rsem_calculateexpression channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rsem=1.3.3 - bioconda::star=2.7.10a diff --git a/modules/nf-core/rsem/preparereference/environment.yml b/modules/nf-core/rsem/preparereference/environment.yml index c80e69106f90..bcf70fa9adfa 100644 --- a/modules/nf-core/rsem/preparereference/environment.yml +++ b/modules/nf-core/rsem/preparereference/environment.yml @@ -1,8 +1,6 @@ -name: rsem_preparereference channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rsem=1.3.3 - bioconda::star=2.7.10a diff --git a/modules/nf-core/rseqc/bamstat/environment.yml b/modules/nf-core/rseqc/bamstat/environment.yml index e960c99434f8..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/bamstat/environment.yml +++ b/modules/nf-core/rseqc/bamstat/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_bamstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/inferexperiment/environment.yml b/modules/nf-core/rseqc/inferexperiment/environment.yml index 78215985af25..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/inferexperiment/environment.yml +++ b/modules/nf-core/rseqc/inferexperiment/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_inferexperiment channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/innerdistance/environment.yml b/modules/nf-core/rseqc/innerdistance/environment.yml index fb6e9e9253d9..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/innerdistance/environment.yml +++ b/modules/nf-core/rseqc/innerdistance/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_innerdistance channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionannotation/environment.yml b/modules/nf-core/rseqc/junctionannotation/environment.yml index 35276b715290..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/junctionannotation/environment.yml +++ b/modules/nf-core/rseqc/junctionannotation/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_junctionannotation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/junctionsaturation/environment.yml b/modules/nf-core/rseqc/junctionsaturation/environment.yml index 7b9cc4fa7c3f..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/junctionsaturation/environment.yml +++ b/modules/nf-core/rseqc/junctionsaturation/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_junctionsaturation channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readdistribution/environment.yml b/modules/nf-core/rseqc/readdistribution/environment.yml index 59be9fa88f13..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/readdistribution/environment.yml +++ b/modules/nf-core/rseqc/readdistribution/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_readdistribution channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/readduplication/environment.yml b/modules/nf-core/rseqc/readduplication/environment.yml index c99f107a1bea..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/readduplication/environment.yml +++ b/modules/nf-core/rseqc/readduplication/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_readduplication channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rseqc/tin/environment.yml b/modules/nf-core/rseqc/tin/environment.yml index 288da4300e17..304e38fcfd00 100644 --- a/modules/nf-core/rseqc/tin/environment.yml +++ b/modules/nf-core/rseqc/tin/environment.yml @@ -1,8 +1,6 @@ -name: rseqc_tin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rseqc=5.0.3 - conda-forge::r-base>=3.5 diff --git a/modules/nf-core/rtgtools/format/environment.yml b/modules/nf-core/rtgtools/format/environment.yml index 15b3df5be040..8aa83cdc41d6 100644 --- a/modules/nf-core/rtgtools/format/environment.yml +++ b/modules/nf-core/rtgtools/format/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_format channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/pedfilter/environment.yml b/modules/nf-core/rtgtools/pedfilter/environment.yml index 62fcaa1cccfd..8aa83cdc41d6 100644 --- a/modules/nf-core/rtgtools/pedfilter/environment.yml +++ b/modules/nf-core/rtgtools/pedfilter/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_pedfilter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/rocplot/environment.yml b/modules/nf-core/rtgtools/rocplot/environment.yml index 093462a56fea..8aa83cdc41d6 100644 --- a/modules/nf-core/rtgtools/rocplot/environment.yml +++ b/modules/nf-core/rtgtools/rocplot/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_rocplot channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtgtools/vcfeval/environment.yml b/modules/nf-core/rtgtools/vcfeval/environment.yml index e3c64996737a..8aa83cdc41d6 100644 --- a/modules/nf-core/rtgtools/vcfeval/environment.yml +++ b/modules/nf-core/rtgtools/vcfeval/environment.yml @@ -1,7 +1,5 @@ -name: rtgtools_vcfeval channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::rtg-tools=3.12.1 diff --git a/modules/nf-core/rtn/tni/environment.yml b/modules/nf-core/rtn/tni/environment.yml index cbf8c866bcb3..f72fef209e3b 100644 --- a/modules/nf-core/rtn/tni/environment.yml +++ b/modules/nf-core/rtn/tni/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "rtn_tni" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bioconductor-rtn=2.26.0 diff --git a/modules/nf-core/sageproteomics/sage/environment.yml b/modules/nf-core/sageproteomics/sage/environment.yml index d2346060ea13..8fdc7c73fbcf 100644 --- a/modules/nf-core/sageproteomics/sage/environment.yml +++ b/modules/nf-core/sageproteomics/sage/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "sageproteomics_sage" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::sage-proteomics=0.14.7" diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index a6607d964f3c..471164faadc5 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -1,7 +1,5 @@ -name: salmon_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 86266724196d..471164faadc5 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -1,7 +1,5 @@ -name: salmon_quant channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::salmon=1.10.1 diff --git a/modules/nf-core/salsa2/environment.yml b/modules/nf-core/salsa2/environment.yml index bfbaa64ff099..8684652eee3d 100644 --- a/modules/nf-core/salsa2/environment.yml +++ b/modules/nf-core/salsa2/environment.yml @@ -1,7 +1,5 @@ -name: salsa2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::salsa2=2.3 diff --git a/modules/nf-core/sam2lca/analyze/environment.yml b/modules/nf-core/sam2lca/analyze/environment.yml index d1b8eefd455e..7d8bbaa297e3 100644 --- a/modules/nf-core/sam2lca/analyze/environment.yml +++ b/modules/nf-core/sam2lca/analyze/environment.yml @@ -1,7 +1,5 @@ -name: sam2lca_analyze channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sam2lca=1.1.2 diff --git a/modules/nf-core/sambamba/flagstat/environment.yml b/modules/nf-core/sambamba/flagstat/environment.yml index f12ca214f8ea..cebae1edf708 100644 --- a/modules/nf-core/sambamba/flagstat/environment.yml +++ b/modules/nf-core/sambamba/flagstat/environment.yml @@ -1,7 +1,5 @@ -name: sambamba_flagstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sambamba=1.0.1 diff --git a/modules/nf-core/sambamba/markdup/environment.yml b/modules/nf-core/sambamba/markdup/environment.yml index 2fc90daf3af9..cebae1edf708 100644 --- a/modules/nf-core/sambamba/markdup/environment.yml +++ b/modules/nf-core/sambamba/markdup/environment.yml @@ -1,7 +1,5 @@ -name: sambamba_markdup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sambamba=1.0.1 diff --git a/modules/nf-core/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml index ac83824150fa..fc8cd9e51589 100644 --- a/modules/nf-core/samblaster/environment.yml +++ b/modules/nf-core/samblaster/environment.yml @@ -1,9 +1,6 @@ -name: samblaster - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.19.1 diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index 2827df00c80e..da2df5e43a40 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -1,8 +1,6 @@ -name: samtools_ampliconclip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index 9c98946adcff..da2df5e43a40 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -1,8 +1,6 @@ -name: samtools_bam2fq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index a704df31bc9c..da2df5e43a40 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -1,8 +1,6 @@ -name: samtools_calmd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index a368198719ab..da2df5e43a40 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -1,8 +1,6 @@ -name: samtools_cat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index 2fc97e044836..da2df5e43a40 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -1,8 +1,6 @@ -name: samtools_collate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index 047b27426429..b98cbb99092d 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -1,9 +1,6 @@ -name: samtools_collatefastq - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index de15288cf51d..5a85438e08a8 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "samtools_consensus" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::samtools=1.20" diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 7a95ca614a76..da2df5e43a40 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,8 +1,6 @@ -name: samtools_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index 74461be7c454..da2df5e43a40 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -1,8 +1,6 @@ -name: samtools_coverage channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/cramsize/environment.yml b/modules/nf-core/samtools/cramsize/environment.yml index 26948ded9ee5..b98cbb99092d 100644 --- a/modules/nf-core/samtools/cramsize/environment.yml +++ b/modules/nf-core/samtools/cramsize/environment.yml @@ -1,9 +1,6 @@ -name: samtools_cramsize - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index 7e9c05a4251f..b98cbb99092d 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -1,9 +1,6 @@ -name: samtools_depth - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index 14a893cdc2ff..da2df5e43a40 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -1,8 +1,6 @@ -name: samtools_dict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index f8450fa5662e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,9 +1,6 @@ -name: samtools_faidx - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index ff79c5f9364e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -1,9 +1,6 @@ -name: samtools_fasta - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index 4455904e0a86..da2df5e43a40 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -1,8 +1,6 @@ -name: samtools_fastq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index d0316622b52c..da2df5e43a40 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -1,8 +1,6 @@ -name: samtools_fixmate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 68b81558e3ec..da2df5e43a40 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,8 +1,6 @@ -name: samtools_flagstat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index 98e74daca39e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -1,9 +1,6 @@ -name: samtools_getrg - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index eb6c8809912b..da2df5e43a40 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_idxstats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index 33eca13b880c..b98cbb99092d 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -1,9 +1,6 @@ -name: samtools_import - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 260d516be9ff..da2df5e43a40 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,8 +1,6 @@ -name: samtools_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index 99f30db073e9..da2df5e43a40 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -1,8 +1,6 @@ -name: samtools_markdup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index cd366d6de3c3..da2df5e43a40 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,8 +1,6 @@ -name: samtools_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index add717dafc49..da2df5e43a40 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -1,8 +1,6 @@ -name: samtools_mpileup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index aa9c798d75d8..da2df5e43a40 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -1,8 +1,6 @@ -name: samtools_reheader channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index be9a1efc6973..da2df5e43a40 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -1,8 +1,6 @@ -name: "samtools_sormadup" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 36a12eab0f20..da2df5e43a40 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,8 +1,6 @@ -name: samtools_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 1cc83bd954fd..da2df5e43a40 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,8 +1,6 @@ -name: samtools_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 150c377771b9..da2df5e43a40 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,8 +1,6 @@ -name: samtools_view channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.20 - bioconda::htslib=1.20 diff --git a/modules/nf-core/scoary/environment.yml b/modules/nf-core/scoary/environment.yml index 06d40e4975c5..6ee2f49249e8 100644 --- a/modules/nf-core/scoary/environment.yml +++ b/modules/nf-core/scoary/environment.yml @@ -1,7 +1,5 @@ -name: scoary channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::scoary=1.6.16 diff --git a/modules/nf-core/scramble/clusteranalysis/environment.yml b/modules/nf-core/scramble/clusteranalysis/environment.yml index d36b0bff41c0..f0eecd4590f6 100644 --- a/modules/nf-core/scramble/clusteranalysis/environment.yml +++ b/modules/nf-core/scramble/clusteranalysis/environment.yml @@ -1,7 +1,5 @@ -name: scramble_clusteranalysis channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::scramble=1.0.1 diff --git a/modules/nf-core/scramble/clusteridentifier/environment.yml b/modules/nf-core/scramble/clusteridentifier/environment.yml index 752de28349b2..f0eecd4590f6 100644 --- a/modules/nf-core/scramble/clusteridentifier/environment.yml +++ b/modules/nf-core/scramble/clusteridentifier/environment.yml @@ -1,7 +1,5 @@ -name: scramble_clusteridentifier channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::scramble=1.0.1 diff --git a/modules/nf-core/seacr/callpeak/environment.yml b/modules/nf-core/seacr/callpeak/environment.yml index af670e8e835a..4fac3de656e3 100644 --- a/modules/nf-core/seacr/callpeak/environment.yml +++ b/modules/nf-core/seacr/callpeak/environment.yml @@ -1,9 +1,6 @@ -name: seacr_callpeak - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::bedtools=2.30.0 diff --git a/modules/nf-core/segemehl/align/environment.yml b/modules/nf-core/segemehl/align/environment.yml index e7dbc66288e4..e37058da852f 100644 --- a/modules/nf-core/segemehl/align/environment.yml +++ b/modules/nf-core/segemehl/align/environment.yml @@ -1,7 +1,5 @@ -name: segemehl_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::segemehl=0.3.4 diff --git a/modules/nf-core/segemehl/index/environment.yml b/modules/nf-core/segemehl/index/environment.yml index c06413305ab2..e37058da852f 100644 --- a/modules/nf-core/segemehl/index/environment.yml +++ b/modules/nf-core/segemehl/index/environment.yml @@ -1,7 +1,5 @@ -name: segemehl_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::segemehl=0.3.4 diff --git a/modules/nf-core/semibin/singleeasybin/environment.yml b/modules/nf-core/semibin/singleeasybin/environment.yml index 261623bc5d17..5830810b1f40 100644 --- a/modules/nf-core/semibin/singleeasybin/environment.yml +++ b/modules/nf-core/semibin/singleeasybin/environment.yml @@ -1,7 +1,5 @@ -name: semibin_singleeasybin channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::semibin=1.4.0 diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml index 0af79bedcd81..185d95bde824 100644 --- a/modules/nf-core/sentieon/applyvarcal/environment.yml +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_applyvarcal channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/bwaindex/environment.yml b/modules/nf-core/sentieon/bwaindex/environment.yml index c806ed0eb53e..185d95bde824 100644 --- a/modules/nf-core/sentieon/bwaindex/environment.yml +++ b/modules/nf-core/sentieon/bwaindex/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_bwaindex channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index f03db6f8a383..185d95bde824 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_bwamem channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/collectvcmetrics/environment.yml b/modules/nf-core/sentieon/collectvcmetrics/environment.yml index 30e9a8460366..f065ece32f49 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/environment.yml +++ b/modules/nf-core/sentieon/collectvcmetrics/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "sentieon_collectvcmetrics" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::sentieon=202308.02" diff --git a/modules/nf-core/sentieon/coveragemetrics/environment.yml b/modules/nf-core/sentieon/coveragemetrics/environment.yml index fa0013df8971..f065ece32f49 100644 --- a/modules/nf-core/sentieon/coveragemetrics/environment.yml +++ b/modules/nf-core/sentieon/coveragemetrics/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "sentieon_coveragemetrics" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::sentieon=202308.02" diff --git a/modules/nf-core/sentieon/datametrics/environment.yml b/modules/nf-core/sentieon/datametrics/environment.yml index b5ea91f6f49a..185d95bde824 100644 --- a/modules/nf-core/sentieon/datametrics/environment.yml +++ b/modules/nf-core/sentieon/datametrics/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_datametrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index e29cfff3e482..185d95bde824 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_dedup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index a2f881931388..185d95bde824 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_dnamodelapply channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index e6da2dde3ef2..185d95bde824 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_dnascope channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml index 732e2ca8463e..185d95bde824 100644 --- a/modules/nf-core/sentieon/gvcftyper/environment.yml +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_gvcftyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml index 89108f8e8bca..185d95bde824 100644 --- a/modules/nf-core/sentieon/haplotyper/environment.yml +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_haplotyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/qualcal/environment.yml b/modules/nf-core/sentieon/qualcal/environment.yml index fb07c4ac455a..d1a652d95867 100644 --- a/modules/nf-core/sentieon/qualcal/environment.yml +++ b/modules/nf-core/sentieon/qualcal/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "sentieon_qualcal" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::sentieon=202308.03" diff --git a/modules/nf-core/sentieon/readwriter/environment.yml b/modules/nf-core/sentieon/readwriter/environment.yml index 423de42da2f4..185d95bde824 100644 --- a/modules/nf-core/sentieon/readwriter/environment.yml +++ b/modules/nf-core/sentieon/readwriter/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_readwriter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/tnfilter/environment.yml b/modules/nf-core/sentieon/tnfilter/environment.yml index 842e515a2c03..185d95bde824 100644 --- a/modules/nf-core/sentieon/tnfilter/environment.yml +++ b/modules/nf-core/sentieon/tnfilter/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_tnfilter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml index a90abca26722..185d95bde824 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml +++ b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_tnhaplotyper2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/tnscope/environment.yml b/modules/nf-core/sentieon/tnscope/environment.yml index 94ab594aaf4b..185d95bde824 100644 --- a/modules/nf-core/sentieon/tnscope/environment.yml +++ b/modules/nf-core/sentieon/tnscope/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_tnscope channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml index 481da2ce84c5..185d95bde824 100644 --- a/modules/nf-core/sentieon/varcal/environment.yml +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_varcal channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/sentieon/wgsmetrics/environment.yml b/modules/nf-core/sentieon/wgsmetrics/environment.yml index a33a3fcc62b6..185d95bde824 100644 --- a/modules/nf-core/sentieon/wgsmetrics/environment.yml +++ b/modules/nf-core/sentieon/wgsmetrics/environment.yml @@ -1,7 +1,5 @@ -name: sentieon_wgsmetrics channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sentieon=202308.02 diff --git a/modules/nf-core/seqfu/derep/environment.yml b/modules/nf-core/seqfu/derep/environment.yml index 16419e9d721d..8fa07dfce059 100644 --- a/modules/nf-core/seqfu/derep/environment.yml +++ b/modules/nf-core/seqfu/derep/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqfu_derep" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqfu=1.20.3" diff --git a/modules/nf-core/seqfu/stats/environment.yml b/modules/nf-core/seqfu/stats/environment.yml index abd60be65b47..8fa07dfce059 100644 --- a/modules/nf-core/seqfu/stats/environment.yml +++ b/modules/nf-core/seqfu/stats/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqfu_stats" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqfu=1.20.3" diff --git a/modules/nf-core/seqkit/concat/environment.yml b/modules/nf-core/seqkit/concat/environment.yml index 9d2470eff2f4..4f8058a9a573 100644 --- a/modules/nf-core/seqkit/concat/environment.yml +++ b/modules/nf-core/seqkit/concat/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqkit_concat" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqkit=2.8.1" diff --git a/modules/nf-core/seqkit/fq2fa/environment.yml b/modules/nf-core/seqkit/fq2fa/environment.yml index aede6767d151..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/fq2fa/environment.yml +++ b/modules/nf-core/seqkit/fq2fa/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_fq2fa channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/fx2tab/environment.yml b/modules/nf-core/seqkit/fx2tab/environment.yml index 4900a5dfc267..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/fx2tab/environment.yml +++ b/modules/nf-core/seqkit/fx2tab/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_fx2tab channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/grep/environment.yml b/modules/nf-core/seqkit/grep/environment.yml index 6f59f2970596..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/grep/environment.yml +++ b/modules/nf-core/seqkit/grep/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_grep channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/pair/environment.yml b/modules/nf-core/seqkit/pair/environment.yml index 9af6653e7f12..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/pair/environment.yml +++ b/modules/nf-core/seqkit/pair/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_pair channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/replace/environment.yml b/modules/nf-core/seqkit/replace/environment.yml index 30fcb2827303..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/replace/environment.yml +++ b/modules/nf-core/seqkit/replace/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_replace channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/rmdup/environment.yml b/modules/nf-core/seqkit/rmdup/environment.yml index 6cb8fe9d75c0..4f8058a9a573 100644 --- a/modules/nf-core/seqkit/rmdup/environment.yml +++ b/modules/nf-core/seqkit/rmdup/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqkit_rmdup" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqkit=2.8.1" diff --git a/modules/nf-core/seqkit/seq/environment.yml b/modules/nf-core/seqkit/seq/environment.yml index 74e0dd765af9..4f8058a9a573 100644 --- a/modules/nf-core/seqkit/seq/environment.yml +++ b/modules/nf-core/seqkit/seq/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqkit_seq" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqkit=2.8.1" diff --git a/modules/nf-core/seqkit/sliding/environment.yml b/modules/nf-core/seqkit/sliding/environment.yml index a4839c42346d..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/sliding/environment.yml +++ b/modules/nf-core/seqkit/sliding/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_sliding channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/sort/environment.yml b/modules/nf-core/seqkit/sort/environment.yml index 3a02d156c78b..4f8058a9a573 100644 --- a/modules/nf-core/seqkit/sort/environment.yml +++ b/modules/nf-core/seqkit/sort/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "seqkit_sort" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::seqkit=2.8.1" diff --git a/modules/nf-core/seqkit/split2/environment.yml b/modules/nf-core/seqkit/split2/environment.yml index 85716aae35b3..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/split2/environment.yml +++ b/modules/nf-core/seqkit/split2/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_split2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/stats/environment.yml b/modules/nf-core/seqkit/stats/environment.yml index 157edd300565..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/stats/environment.yml +++ b/modules/nf-core/seqkit/stats/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqkit/tab2fx/environment.yml b/modules/nf-core/seqkit/tab2fx/environment.yml index f0bfdcda0c41..41f3e7de43d8 100644 --- a/modules/nf-core/seqkit/tab2fx/environment.yml +++ b/modules/nf-core/seqkit/tab2fx/environment.yml @@ -1,7 +1,5 @@ -name: seqkit_tab2fx channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqkit=2.8.1 diff --git a/modules/nf-core/seqsero2/environment.yml b/modules/nf-core/seqsero2/environment.yml index e26f2b2c6d67..b312bdd67b63 100644 --- a/modules/nf-core/seqsero2/environment.yml +++ b/modules/nf-core/seqsero2/environment.yml @@ -1,7 +1,5 @@ -name: seqsero2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqsero2=1.2.1 diff --git a/modules/nf-core/seqtk/cutn/environment.yml b/modules/nf-core/seqtk/cutn/environment.yml index a57afbb6fc83..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/cutn/environment.yml +++ b/modules/nf-core/seqtk/cutn/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_cutn channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/mergepe/environment.yml b/modules/nf-core/seqtk/mergepe/environment.yml index 6eeccc54bf67..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/mergepe/environment.yml +++ b/modules/nf-core/seqtk/mergepe/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_mergepe channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/rename/environment.yml b/modules/nf-core/seqtk/rename/environment.yml index e10317b6dd25..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/rename/environment.yml +++ b/modules/nf-core/seqtk/rename/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_rename channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/sample/environment.yml b/modules/nf-core/seqtk/sample/environment.yml index 3f856d31b65a..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/sample/environment.yml +++ b/modules/nf-core/seqtk/sample/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_sample channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/seq/environment.yml b/modules/nf-core/seqtk/seq/environment.yml index 78dc2c842466..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/seq/environment.yml +++ b/modules/nf-core/seqtk/seq/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_seq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/subseq/environment.yml b/modules/nf-core/seqtk/subseq/environment.yml index 7abe3644b33e..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/subseq/environment.yml +++ b/modules/nf-core/seqtk/subseq/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_subseq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/seqtk/trim/environment.yml b/modules/nf-core/seqtk/trim/environment.yml index 389a3a92fdad..693aa5c1770f 100644 --- a/modules/nf-core/seqtk/trim/environment.yml +++ b/modules/nf-core/seqtk/trim/environment.yml @@ -1,7 +1,5 @@ -name: seqtk_trim channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqtk=1.4 diff --git a/modules/nf-core/sequencetools/pileupcaller/environment.yml b/modules/nf-core/sequencetools/pileupcaller/environment.yml index 98ac1fa58860..487e2fcd7282 100644 --- a/modules/nf-core/sequencetools/pileupcaller/environment.yml +++ b/modules/nf-core/sequencetools/pileupcaller/environment.yml @@ -1,7 +1,5 @@ -name: sequencetools_pileupcaller channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sequencetools=1.5.2 diff --git a/modules/nf-core/sequenzautils/bam2seqz/environment.yml b/modules/nf-core/sequenzautils/bam2seqz/environment.yml index b06a793b6fa4..b98667bf0634 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/environment.yml +++ b/modules/nf-core/sequenzautils/bam2seqz/environment.yml @@ -1,8 +1,6 @@ -name: sequenzautils_bam2seqz channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.15.1 - bioconda::sequenza-utils=3.0.0 diff --git a/modules/nf-core/sequenzautils/gcwiggle/environment.yml b/modules/nf-core/sequenzautils/gcwiggle/environment.yml index 801d539968eb..6713252e2d9c 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/environment.yml +++ b/modules/nf-core/sequenzautils/gcwiggle/environment.yml @@ -1,8 +1,6 @@ -name: sequenzautils_gcwiggle channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sequenza-utils=3.0.0 - conda-forge::python=3.8.5 diff --git a/modules/nf-core/seqwish/induce/environment.yml b/modules/nf-core/seqwish/induce/environment.yml index 63711c0b216f..eca0130c9732 100644 --- a/modules/nf-core/seqwish/induce/environment.yml +++ b/modules/nf-core/seqwish/induce/environment.yml @@ -1,7 +1,5 @@ -name: seqwish_induce channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seqwish=0.7.9 diff --git a/modules/nf-core/seroba/run/environment.yml b/modules/nf-core/seroba/run/environment.yml index 724c39c91af2..470f75381758 100644 --- a/modules/nf-core/seroba/run/environment.yml +++ b/modules/nf-core/seroba/run/environment.yml @@ -1,7 +1,5 @@ -name: seroba_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::seroba=1.0.2 diff --git a/modules/nf-core/severus/environment.yml b/modules/nf-core/severus/environment.yml index c8e532b7e457..49e4fbc2060f 100644 --- a/modules/nf-core/severus/environment.yml +++ b/modules/nf-core/severus/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "severus" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::severus=1.1" diff --git a/modules/nf-core/sexdeterrmine/environment.yml b/modules/nf-core/sexdeterrmine/environment.yml index 285ea9777d49..62fc8995223f 100644 --- a/modules/nf-core/sexdeterrmine/environment.yml +++ b/modules/nf-core/sexdeterrmine/environment.yml @@ -1,7 +1,5 @@ -name: sexdeterrmine channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sexdeterrmine=1.1.2 diff --git a/modules/nf-core/sgdemux/environment.yml b/modules/nf-core/sgdemux/environment.yml index 57eccdd22770..ce09711afd0b 100644 --- a/modules/nf-core/sgdemux/environment.yml +++ b/modules/nf-core/sgdemux/environment.yml @@ -1,7 +1,5 @@ -name: sgdemux channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sgdemux=1.1.1 diff --git a/modules/nf-core/shapeit5/ligate/environment.yml b/modules/nf-core/shapeit5/ligate/environment.yml index d4c71302f22d..7b8e63bba476 100644 --- a/modules/nf-core/shapeit5/ligate/environment.yml +++ b/modules/nf-core/shapeit5/ligate/environment.yml @@ -1,7 +1,5 @@ -name: shapeit5_ligate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shapeit5=1.0.0 diff --git a/modules/nf-core/shapeit5/phasecommon/environment.yml b/modules/nf-core/shapeit5/phasecommon/environment.yml index 8bc91822d31e..7b8e63bba476 100644 --- a/modules/nf-core/shapeit5/phasecommon/environment.yml +++ b/modules/nf-core/shapeit5/phasecommon/environment.yml @@ -1,7 +1,5 @@ -name: shapeit5_phasecommon channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shapeit5=1.0.0 diff --git a/modules/nf-core/shapeit5/phaserare/environment.yml b/modules/nf-core/shapeit5/phaserare/environment.yml index 2ce985bb44af..7b8e63bba476 100644 --- a/modules/nf-core/shapeit5/phaserare/environment.yml +++ b/modules/nf-core/shapeit5/phaserare/environment.yml @@ -1,7 +1,5 @@ -name: shapeit5_phaserare channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shapeit5=1.0.0 diff --git a/modules/nf-core/shapeit5/switch/environment.yml b/modules/nf-core/shapeit5/switch/environment.yml index 8a55b59d6860..7b8e63bba476 100644 --- a/modules/nf-core/shapeit5/switch/environment.yml +++ b/modules/nf-core/shapeit5/switch/environment.yml @@ -1,7 +1,5 @@ -name: shapeit5_switch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shapeit5=1.0.0 diff --git a/modules/nf-core/shasta/environment.yml b/modules/nf-core/shasta/environment.yml index 1a822a92f22a..6b8d44850ece 100644 --- a/modules/nf-core/shasta/environment.yml +++ b/modules/nf-core/shasta/environment.yml @@ -1,7 +1,5 @@ -name: shasta channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shasta=0.8.0 diff --git a/modules/nf-core/shasum/environment.yml b/modules/nf-core/shasum/environment.yml index 8af2d3783743..c7eb9bd1c3ca 100644 --- a/modules/nf-core/shasum/environment.yml +++ b/modules/nf-core/shasum/environment.yml @@ -1,7 +1,5 @@ -name: shasum channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/shigatyper/environment.yml b/modules/nf-core/shigatyper/environment.yml index b94852819163..e48e73b7ae74 100644 --- a/modules/nf-core/shigatyper/environment.yml +++ b/modules/nf-core/shigatyper/environment.yml @@ -1,7 +1,5 @@ -name: shigatyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shigatyper=2.0.5 diff --git a/modules/nf-core/shigeifinder/environment.yml b/modules/nf-core/shigeifinder/environment.yml index 44bccb481e05..8ea18f13b52e 100644 --- a/modules/nf-core/shigeifinder/environment.yml +++ b/modules/nf-core/shigeifinder/environment.yml @@ -1,7 +1,5 @@ -name: shigeifinder channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shigeifinder=1.3.2 diff --git a/modules/nf-core/shinyngs/app/environment.yml b/modules/nf-core/shinyngs/app/environment.yml index 43a09fffc9d1..89b523b2df8a 100644 --- a/modules/nf-core/shinyngs/app/environment.yml +++ b/modules/nf-core/shinyngs/app/environment.yml @@ -1,7 +1,5 @@ -name: shinyngs_app channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-shinyngs=2.0.0 diff --git a/modules/nf-core/shinyngs/staticdifferential/environment.yml b/modules/nf-core/shinyngs/staticdifferential/environment.yml index f352c61eec29..89b523b2df8a 100644 --- a/modules/nf-core/shinyngs/staticdifferential/environment.yml +++ b/modules/nf-core/shinyngs/staticdifferential/environment.yml @@ -1,7 +1,5 @@ -name: shinyngs_staticdifferential channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-shinyngs=2.0.0 diff --git a/modules/nf-core/shinyngs/staticexploratory/environment.yml b/modules/nf-core/shinyngs/staticexploratory/environment.yml index 74f9d52fd3f3..89b523b2df8a 100644 --- a/modules/nf-core/shinyngs/staticexploratory/environment.yml +++ b/modules/nf-core/shinyngs/staticexploratory/environment.yml @@ -1,7 +1,5 @@ -name: shinyngs_staticexploratory channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-shinyngs=2.0.0 diff --git a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml index 07485298d20e..89b523b2df8a 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/environment.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/environment.yml @@ -1,7 +1,5 @@ -name: shinyngs_validatefomcomponents channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-shinyngs=2.0.0 diff --git a/modules/nf-core/shovill/environment.yml b/modules/nf-core/shovill/environment.yml index 8bb573de9004..4f351ad0052a 100644 --- a/modules/nf-core/shovill/environment.yml +++ b/modules/nf-core/shovill/environment.yml @@ -1,7 +1,5 @@ -name: shovill channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::shovill=1.1.0 diff --git a/modules/nf-core/sickle/environment.yml b/modules/nf-core/sickle/environment.yml index caf398019224..d03c86e18e35 100644 --- a/modules/nf-core/sickle/environment.yml +++ b/modules/nf-core/sickle/environment.yml @@ -1,7 +1,5 @@ -name: sickle channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sickle-trim=1.33 diff --git a/modules/nf-core/simpleaf/index/environment.yml b/modules/nf-core/simpleaf/index/environment.yml index c8bc5d87e366..2a6838c2bbd9 100644 --- a/modules/nf-core/simpleaf/index/environment.yml +++ b/modules/nf-core/simpleaf/index/environment.yml @@ -1,9 +1,6 @@ -name: simpleaf_index - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::alevin-fry=0.8.2 diff --git a/modules/nf-core/simpleaf/quant/environment.yml b/modules/nf-core/simpleaf/quant/environment.yml index 560c01f45582..2a6838c2bbd9 100644 --- a/modules/nf-core/simpleaf/quant/environment.yml +++ b/modules/nf-core/simpleaf/quant/environment.yml @@ -1,9 +1,6 @@ -name: simpleaf_quant - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::alevin-fry=0.8.2 diff --git a/modules/nf-core/sistr/environment.yml b/modules/nf-core/sistr/environment.yml index 8aa248b839c0..4ddd5b607762 100644 --- a/modules/nf-core/sistr/environment.yml +++ b/modules/nf-core/sistr/environment.yml @@ -1,7 +1,5 @@ -name: sistr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sistr_cmd=1.1.1 diff --git a/modules/nf-core/slimfastq/environment.yml b/modules/nf-core/slimfastq/environment.yml index be359c71a3db..cafcb690d54c 100644 --- a/modules/nf-core/slimfastq/environment.yml +++ b/modules/nf-core/slimfastq/environment.yml @@ -1,7 +1,5 @@ -name: slimfastq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::slimfastq=2.04 diff --git a/modules/nf-core/smncopynumbercaller/environment.yml b/modules/nf-core/smncopynumbercaller/environment.yml index 3da92eeb2983..afbc40076918 100644 --- a/modules/nf-core/smncopynumbercaller/environment.yml +++ b/modules/nf-core/smncopynumbercaller/environment.yml @@ -1,7 +1,5 @@ -name: smncopynumbercaller channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::smncopynumbercaller=1.1.2 diff --git a/modules/nf-core/smoothxg/environment.yml b/modules/nf-core/smoothxg/environment.yml index 76ca4b86c855..a837203d0004 100644 --- a/modules/nf-core/smoothxg/environment.yml +++ b/modules/nf-core/smoothxg/environment.yml @@ -1,7 +1,5 @@ -name: smoothxg channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::smoothxg=0.7.2 diff --git a/modules/nf-core/smoove/call/environment.yml b/modules/nf-core/smoove/call/environment.yml index 751de65791a5..39632516a583 100644 --- a/modules/nf-core/smoove/call/environment.yml +++ b/modules/nf-core/smoove/call/environment.yml @@ -1,7 +1,5 @@ -name: smoove_call channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::smoove=0.2.8 diff --git a/modules/nf-core/snakemake/environment.yml b/modules/nf-core/snakemake/environment.yml index bb68502e3dc4..e306cbd10738 100644 --- a/modules/nf-core/snakemake/environment.yml +++ b/modules/nf-core/snakemake/environment.yml @@ -1,7 +1,5 @@ -name: snakemake channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snakemake=7.31.0 diff --git a/modules/nf-core/snapaligner/align/environment.yml b/modules/nf-core/snapaligner/align/environment.yml index cc8b82da8745..8324d125823d 100644 --- a/modules/nf-core/snapaligner/align/environment.yml +++ b/modules/nf-core/snapaligner/align/environment.yml @@ -1,7 +1,5 @@ -name: snapaligner_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snap-aligner=2.0.3 diff --git a/modules/nf-core/snapaligner/index/environment.yml b/modules/nf-core/snapaligner/index/environment.yml index b6d07d08421d..8324d125823d 100644 --- a/modules/nf-core/snapaligner/index/environment.yml +++ b/modules/nf-core/snapaligner/index/environment.yml @@ -1,7 +1,5 @@ -name: snapaligner_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snap-aligner=2.0.3 diff --git a/modules/nf-core/sniffles/environment.yml b/modules/nf-core/sniffles/environment.yml index 99c39b9882b2..b3d97d0e8466 100644 --- a/modules/nf-core/sniffles/environment.yml +++ b/modules/nf-core/sniffles/environment.yml @@ -1,7 +1,5 @@ -name: sniffles channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sniffles=2.4 diff --git a/modules/nf-core/snippy/core/environment.yml b/modules/nf-core/snippy/core/environment.yml index dad60324ee1b..e0f44bc81f45 100644 --- a/modules/nf-core/snippy/core/environment.yml +++ b/modules/nf-core/snippy/core/environment.yml @@ -1,7 +1,5 @@ -name: snippy_core channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snippy=4.6.0 diff --git a/modules/nf-core/snippy/run/environment.yml b/modules/nf-core/snippy/run/environment.yml index 2152ec52578a..e0f44bc81f45 100644 --- a/modules/nf-core/snippy/run/environment.yml +++ b/modules/nf-core/snippy/run/environment.yml @@ -1,7 +1,5 @@ -name: snippy_run channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snippy=4.6.0 diff --git a/modules/nf-core/snpdists/environment.yml b/modules/nf-core/snpdists/environment.yml index 2aeaa0a33ce4..71c52aacf185 100644 --- a/modules/nf-core/snpdists/environment.yml +++ b/modules/nf-core/snpdists/environment.yml @@ -1,7 +1,5 @@ -name: snpdists channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snp-dists=0.8.2 diff --git a/modules/nf-core/snpeff/download/environment.yml b/modules/nf-core/snpeff/download/environment.yml index 62f3d5aad630..f2ad925161e4 100644 --- a/modules/nf-core/snpeff/download/environment.yml +++ b/modules/nf-core/snpeff/download/environment.yml @@ -1,7 +1,5 @@ -name: snpeff_download channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/environment.yml b/modules/nf-core/snpeff/environment.yml index e0527690a67a..6ac55ab765af 100644 --- a/modules/nf-core/snpeff/environment.yml +++ b/modules/nf-core/snpeff/environment.yml @@ -1,10 +1,8 @@ # You can use this file to create a conda environment for this module: # conda env create -f environment.yml -name: nf-core-snpeff-5.1 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpeff/snpeff/environment.yml b/modules/nf-core/snpeff/snpeff/environment.yml index b492e6a88e28..f2ad925161e4 100644 --- a/modules/nf-core/snpeff/snpeff/environment.yml +++ b/modules/nf-core/snpeff/snpeff/environment.yml @@ -1,7 +1,5 @@ -name: snpeff_snpeff channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpeff=5.1 diff --git a/modules/nf-core/snpsift/annotate/environment.yml b/modules/nf-core/snpsift/annotate/environment.yml index 05a89b8aae47..f38678bf7ef6 100644 --- a/modules/nf-core/snpsift/annotate/environment.yml +++ b/modules/nf-core/snpsift/annotate/environment.yml @@ -1,7 +1,5 @@ -name: snpsift_annotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpsift=5.1 diff --git a/modules/nf-core/snpsift/dbnsfp/environment.yml b/modules/nf-core/snpsift/dbnsfp/environment.yml index 19f0b7f12460..f38678bf7ef6 100644 --- a/modules/nf-core/snpsift/dbnsfp/environment.yml +++ b/modules/nf-core/snpsift/dbnsfp/environment.yml @@ -1,7 +1,5 @@ -name: snpsift_dbnsfp channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpsift=5.1 diff --git a/modules/nf-core/snpsift/split/environment.yml b/modules/nf-core/snpsift/split/environment.yml index 68a6dc11bb31..931bc9093f57 100644 --- a/modules/nf-core/snpsift/split/environment.yml +++ b/modules/nf-core/snpsift/split/environment.yml @@ -1,7 +1,5 @@ -name: snpsift_split channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snpsift=4.3.1t diff --git a/modules/nf-core/snpsites/environment.yml b/modules/nf-core/snpsites/environment.yml index b5462aa9a1e0..642d9a79c96f 100644 --- a/modules/nf-core/snpsites/environment.yml +++ b/modules/nf-core/snpsites/environment.yml @@ -1,7 +1,5 @@ -name: snpsites channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::snp-sites=2.5.1 diff --git a/modules/nf-core/somalier/ancestry/environment.yml b/modules/nf-core/somalier/ancestry/environment.yml index 8cc3ce21039c..783e5d8d1626 100644 --- a/modules/nf-core/somalier/ancestry/environment.yml +++ b/modules/nf-core/somalier/ancestry/environment.yml @@ -1,7 +1,5 @@ -name: somalier_ancestry channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.15 diff --git a/modules/nf-core/somalier/extract/environment.yml b/modules/nf-core/somalier/extract/environment.yml index 723977747ce4..d6ce68f6ece1 100644 --- a/modules/nf-core/somalier/extract/environment.yml +++ b/modules/nf-core/somalier/extract/environment.yml @@ -1,7 +1,5 @@ -name: somalier_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/somalier/relate/environment.yml b/modules/nf-core/somalier/relate/environment.yml index 5295646bd64a..d6ce68f6ece1 100644 --- a/modules/nf-core/somalier/relate/environment.yml +++ b/modules/nf-core/somalier/relate/environment.yml @@ -1,7 +1,5 @@ -name: somalier_relate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::somalier=0.2.19 diff --git a/modules/nf-core/sortmerna/environment.yml b/modules/nf-core/sortmerna/environment.yml index f40f9958d25a..fab44081fa2f 100644 --- a/modules/nf-core/sortmerna/environment.yml +++ b/modules/nf-core/sortmerna/environment.yml @@ -1,7 +1,5 @@ -name: sortmerna channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sortmerna=4.3.6 diff --git a/modules/nf-core/sourmash/compare/environment.yml b/modules/nf-core/sourmash/compare/environment.yml index 47ede1eccfd9..25e14afa58c8 100644 --- a/modules/nf-core/sourmash/compare/environment.yml +++ b/modules/nf-core/sourmash/compare/environment.yml @@ -1,7 +1,5 @@ -name: sourmash_compare channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sourmash=4.8.4 diff --git a/modules/nf-core/sourmash/gather/environment.yml b/modules/nf-core/sourmash/gather/environment.yml index 261d9405a944..25e14afa58c8 100644 --- a/modules/nf-core/sourmash/gather/environment.yml +++ b/modules/nf-core/sourmash/gather/environment.yml @@ -1,7 +1,5 @@ -name: sourmash_gather channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sourmash=4.8.4 diff --git a/modules/nf-core/sourmash/index/environment.yml b/modules/nf-core/sourmash/index/environment.yml index 4f64cb7a07e5..25e14afa58c8 100644 --- a/modules/nf-core/sourmash/index/environment.yml +++ b/modules/nf-core/sourmash/index/environment.yml @@ -1,7 +1,5 @@ -name: sourmash_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sourmash=4.8.4 diff --git a/modules/nf-core/sourmash/sketch/environment.yml b/modules/nf-core/sourmash/sketch/environment.yml index 1387777af1f3..25e14afa58c8 100644 --- a/modules/nf-core/sourmash/sketch/environment.yml +++ b/modules/nf-core/sourmash/sketch/environment.yml @@ -1,7 +1,5 @@ -name: sourmash_sketch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sourmash=4.8.4 diff --git a/modules/nf-core/sourmash/taxannotate/environment.yml b/modules/nf-core/sourmash/taxannotate/environment.yml index ea3ff96fc38f..25e14afa58c8 100644 --- a/modules/nf-core/sourmash/taxannotate/environment.yml +++ b/modules/nf-core/sourmash/taxannotate/environment.yml @@ -1,7 +1,5 @@ -name: sourmash_taxannotate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sourmash=4.8.4 diff --git a/modules/nf-core/spades/environment.yml b/modules/nf-core/spades/environment.yml index 3191fde44fb4..8cc5321fd3e1 100644 --- a/modules/nf-core/spades/environment.yml +++ b/modules/nf-core/spades/environment.yml @@ -1,7 +1,5 @@ -name: spades channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::spades=4.0.0 diff --git a/modules/nf-core/spatyper/environment.yml b/modules/nf-core/spatyper/environment.yml index c03d9eb67201..cbe256c5a978 100644 --- a/modules/nf-core/spatyper/environment.yml +++ b/modules/nf-core/spatyper/environment.yml @@ -1,7 +1,5 @@ -name: spatyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::spatyper=0.3.3 diff --git a/modules/nf-core/splitubam/environment.yml b/modules/nf-core/splitubam/environment.yml index ef128202df2d..382f9112c4ef 100644 --- a/modules/nf-core/splitubam/environment.yml +++ b/modules/nf-core/splitubam/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "splitubam" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::splitubam=0.1.1" diff --git a/modules/nf-core/spotiflow/environment.yml b/modules/nf-core/spotiflow/environment.yml index a42c2d209979..5a69c468fc96 100644 --- a/modules/nf-core/spotiflow/environment.yml +++ b/modules/nf-core/spotiflow/environment.yml @@ -1,4 +1,3 @@ -name: spotiflow channels: - pytorch - conda-forge diff --git a/modules/nf-core/spring/compress/environment.yml b/modules/nf-core/spring/compress/environment.yml index f857bf30b664..abeb16b095c7 100644 --- a/modules/nf-core/spring/compress/environment.yml +++ b/modules/nf-core/spring/compress/environment.yml @@ -1,7 +1,5 @@ -name: spring_compress channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::spring=1.1.1 diff --git a/modules/nf-core/spring/decompress/environment.yml b/modules/nf-core/spring/decompress/environment.yml index d960ee714ad1..abeb16b095c7 100644 --- a/modules/nf-core/spring/decompress/environment.yml +++ b/modules/nf-core/spring/decompress/environment.yml @@ -1,7 +1,5 @@ -name: spring_decompress channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::spring=1.1.1 diff --git a/modules/nf-core/sratools/fasterqdump/environment.yml b/modules/nf-core/sratools/fasterqdump/environment.yml index 4011b6914a08..970dfbc0de7b 100644 --- a/modules/nf-core/sratools/fasterqdump/environment.yml +++ b/modules/nf-core/sratools/fasterqdump/environment.yml @@ -1,8 +1,6 @@ -name: sratools_fasterqdump channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sra-tools=3.0.8 - conda-forge::pigz=2.6 diff --git a/modules/nf-core/sratools/prefetch/environment.yml b/modules/nf-core/sratools/prefetch/environment.yml index 0abad336cbc8..6596bc7cf74f 100644 --- a/modules/nf-core/sratools/prefetch/environment.yml +++ b/modules/nf-core/sratools/prefetch/environment.yml @@ -1,8 +1,6 @@ -name: sratools_prefetch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::sra-tools=3.1.0 - conda-forge::curl=8.5.0 diff --git a/modules/nf-core/srst2/srst2/environment.yml b/modules/nf-core/srst2/srst2/environment.yml index 4c9d6516a25b..ecce1cf9726e 100644 --- a/modules/nf-core/srst2/srst2/environment.yml +++ b/modules/nf-core/srst2/srst2/environment.yml @@ -1,7 +1,5 @@ -name: srst2_srst2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::srst2=0.2.0 diff --git a/modules/nf-core/ssuissero/environment.yml b/modules/nf-core/ssuissero/environment.yml index 06f426d206ac..042a9c5b03f7 100644 --- a/modules/nf-core/ssuissero/environment.yml +++ b/modules/nf-core/ssuissero/environment.yml @@ -1,7 +1,5 @@ -name: ssuissero channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ssuissero=1.0.1 diff --git a/modules/nf-core/stadeniolib/scramble/environment.yml b/modules/nf-core/stadeniolib/scramble/environment.yml index c1a2d2e02691..da097f418649 100644 --- a/modules/nf-core/stadeniolib/scramble/environment.yml +++ b/modules/nf-core/stadeniolib/scramble/environment.yml @@ -1,7 +1,5 @@ -name: stadeniolib_scramble channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::staden_io_lib=1.14.14 diff --git a/modules/nf-core/staphopiasccmec/environment.yml b/modules/nf-core/staphopiasccmec/environment.yml index ce91347ad472..fc31f4bc2703 100644 --- a/modules/nf-core/staphopiasccmec/environment.yml +++ b/modules/nf-core/staphopiasccmec/environment.yml @@ -1,7 +1,5 @@ -name: staphopiasccmec channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::staphopia-sccmec=1.0.0 diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index 8bd58cff5a08..e3d1c714d30d 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,6 @@ -name: star_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::star=2.7.10a - bioconda::samtools=1.18 diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 791f255e5c25..38611dfa26e6 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,6 @@ -name: star_genomegenerate channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.18 - bioconda::htslib=1.18 diff --git a/modules/nf-core/star/starsolo/environment.yml b/modules/nf-core/star/starsolo/environment.yml index e7c4b1a63b83..8f201da74438 100644 --- a/modules/nf-core/star/starsolo/environment.yml +++ b/modules/nf-core/star/starsolo/environment.yml @@ -1,7 +1,5 @@ -name: starsolo channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::star=2.7.10b diff --git a/modules/nf-core/staramr/search/environment.yml b/modules/nf-core/staramr/search/environment.yml index 78d2dd7be46d..c90c2637db16 100644 --- a/modules/nf-core/staramr/search/environment.yml +++ b/modules/nf-core/staramr/search/environment.yml @@ -1,9 +1,6 @@ -name: staramr_search - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::mlst=2.23.0 diff --git a/modules/nf-core/stardist/environment.yml b/modules/nf-core/stardist/environment.yml index 8980e8c85f8a..33c9530f40f9 100644 --- a/modules/nf-core/stardist/environment.yml +++ b/modules/nf-core/stardist/environment.yml @@ -1,9 +1,6 @@ -name: stardist - channels: - conda-forge - bioconda - - defaults dependencies: - python=3.9 diff --git a/modules/nf-core/stecfinder/environment.yml b/modules/nf-core/stecfinder/environment.yml index 19919d9c6bdc..d533f168fed3 100644 --- a/modules/nf-core/stecfinder/environment.yml +++ b/modules/nf-core/stecfinder/environment.yml @@ -1,7 +1,5 @@ -name: stecfinder channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::stecfinder=1.1.0 diff --git a/modules/nf-core/stitch/environment.yml b/modules/nf-core/stitch/environment.yml index 3facc1bcaea6..039968d65c9a 100644 --- a/modules/nf-core/stitch/environment.yml +++ b/modules/nf-core/stitch/environment.yml @@ -1,7 +1,5 @@ -name: stitch channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::r-stitch=1.6.10 diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml index 530ce37554c3..910bcae7d2dd 100644 --- a/modules/nf-core/stranger/environment.yml +++ b/modules/nf-core/stranger/environment.yml @@ -1,7 +1,5 @@ -name: stranger channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::stranger=0.9.1 diff --git a/modules/nf-core/strelka/germline/environment.yml b/modules/nf-core/strelka/germline/environment.yml index 23bd165b2140..052c6baa5f39 100644 --- a/modules/nf-core/strelka/germline/environment.yml +++ b/modules/nf-core/strelka/germline/environment.yml @@ -1,7 +1,5 @@ -name: strelka_germline channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::strelka=2.9.10 diff --git a/modules/nf-core/strelka/somatic/environment.yml b/modules/nf-core/strelka/somatic/environment.yml index ecbc865ec94a..052c6baa5f39 100644 --- a/modules/nf-core/strelka/somatic/environment.yml +++ b/modules/nf-core/strelka/somatic/environment.yml @@ -1,7 +1,5 @@ -name: strelka_somatic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::strelka=2.9.10 diff --git a/modules/nf-core/stringtie/merge/environment.yml b/modules/nf-core/stringtie/merge/environment.yml index 9914b2025bb5..0556de41a75a 100644 --- a/modules/nf-core/stringtie/merge/environment.yml +++ b/modules/nf-core/stringtie/merge/environment.yml @@ -1,7 +1,5 @@ -name: stringtie_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 7a0eccdb89a8..0556de41a75a 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -1,7 +1,5 @@ -name: stringtie_stringtie channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::stringtie=2.2.1 diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index ca19439d73a4..7e919aa31774 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -1,7 +1,5 @@ -name: subread_featurecounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::subread=2.0.1 diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml index 252ace7910a6..dc4e6c936a7a 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "summarizedexperiment_summarizedexperiment" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-summarizedexperiment=1.32.0" diff --git a/modules/nf-core/survivor/bedpetovcf/environment.yml b/modules/nf-core/survivor/bedpetovcf/environment.yml index 65e9d04ecaa1..ce3babdc92e7 100644 --- a/modules/nf-core/survivor/bedpetovcf/environment.yml +++ b/modules/nf-core/survivor/bedpetovcf/environment.yml @@ -1,8 +1,6 @@ --- -name: "survivor_bedpetovcf" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::survivor=1.0.7" diff --git a/modules/nf-core/survivor/filter/environment.yml b/modules/nf-core/survivor/filter/environment.yml index 56839cee2628..6603bdcc0242 100644 --- a/modules/nf-core/survivor/filter/environment.yml +++ b/modules/nf-core/survivor/filter/environment.yml @@ -1,7 +1,5 @@ -name: survivor_filter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::survivor=1.0.7 diff --git a/modules/nf-core/survivor/merge/environment.yml b/modules/nf-core/survivor/merge/environment.yml index 9f46e0dfd7d1..6603bdcc0242 100644 --- a/modules/nf-core/survivor/merge/environment.yml +++ b/modules/nf-core/survivor/merge/environment.yml @@ -1,7 +1,5 @@ -name: survivor_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::survivor=1.0.7 diff --git a/modules/nf-core/survivor/simsv/environment.yml b/modules/nf-core/survivor/simsv/environment.yml index 285b0222bf41..6603bdcc0242 100644 --- a/modules/nf-core/survivor/simsv/environment.yml +++ b/modules/nf-core/survivor/simsv/environment.yml @@ -1,7 +1,5 @@ -name: survivor_simsv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::survivor=1.0.7 diff --git a/modules/nf-core/survivor/stats/environment.yml b/modules/nf-core/survivor/stats/environment.yml index 4f640071cfd6..6603bdcc0242 100644 --- a/modules/nf-core/survivor/stats/environment.yml +++ b/modules/nf-core/survivor/stats/environment.yml @@ -1,7 +1,5 @@ -name: survivor_stats channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::survivor=1.0.7 diff --git a/modules/nf-core/svaba/environment.yml b/modules/nf-core/svaba/environment.yml index 60b1aa0159ea..2f1177599471 100644 --- a/modules/nf-core/svaba/environment.yml +++ b/modules/nf-core/svaba/environment.yml @@ -1,7 +1,5 @@ -name: svaba channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svaba=1.1.0 diff --git a/modules/nf-core/svanalyzer/svbenchmark/environment.yml b/modules/nf-core/svanalyzer/svbenchmark/environment.yml index 2e20a2cf804c..e1f68b71a301 100644 --- a/modules/nf-core/svanalyzer/svbenchmark/environment.yml +++ b/modules/nf-core/svanalyzer/svbenchmark/environment.yml @@ -1,9 +1,6 @@ -name: svanalyzer_svbenchmark - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svanalyzer=0.36 diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index e6fec0887734..bf44cd967b36 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -1,8 +1,6 @@ -name: svdb_merge channels: - conda-forge - bioconda - - defaults dependencies: - svdb=2.8.1 # renovate: datasource=conda depName=bioconda/samtools diff --git a/modules/nf-core/svdb/query/environment.yml b/modules/nf-core/svdb/query/environment.yml index bf048232f54e..cd35cf488a5b 100644 --- a/modules/nf-core/svdb/query/environment.yml +++ b/modules/nf-core/svdb/query/environment.yml @@ -1,7 +1,5 @@ -name: svdb_query channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svdb=2.8.1 diff --git a/modules/nf-core/svtk/baftest/environment.yml b/modules/nf-core/svtk/baftest/environment.yml index 30a921f7035f..42aa12a2126a 100644 --- a/modules/nf-core/svtk/baftest/environment.yml +++ b/modules/nf-core/svtk/baftest/environment.yml @@ -1,7 +1,5 @@ -name: svtk_baftest channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtk=0.0.20190615 diff --git a/modules/nf-core/svtk/countsvtypes/environment.yml b/modules/nf-core/svtk/countsvtypes/environment.yml index 342ade7680ed..42aa12a2126a 100644 --- a/modules/nf-core/svtk/countsvtypes/environment.yml +++ b/modules/nf-core/svtk/countsvtypes/environment.yml @@ -1,7 +1,5 @@ -name: svtk_countsvtypes channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtk=0.0.20190615 diff --git a/modules/nf-core/svtk/rdtest2vcf/environment.yml b/modules/nf-core/svtk/rdtest2vcf/environment.yml index 80da8ec2db3f..42aa12a2126a 100644 --- a/modules/nf-core/svtk/rdtest2vcf/environment.yml +++ b/modules/nf-core/svtk/rdtest2vcf/environment.yml @@ -1,7 +1,5 @@ -name: svtk_rdtest2vcf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtk=0.0.20190615 diff --git a/modules/nf-core/svtk/standardize/environment.yml b/modules/nf-core/svtk/standardize/environment.yml index f9ab247dda37..42aa12a2126a 100644 --- a/modules/nf-core/svtk/standardize/environment.yml +++ b/modules/nf-core/svtk/standardize/environment.yml @@ -1,7 +1,5 @@ -name: svtk_standardize channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtk=0.0.20190615 diff --git a/modules/nf-core/svtk/vcf2bed/environment.yml b/modules/nf-core/svtk/vcf2bed/environment.yml index e05599070ebf..42aa12a2126a 100644 --- a/modules/nf-core/svtk/vcf2bed/environment.yml +++ b/modules/nf-core/svtk/vcf2bed/environment.yml @@ -1,7 +1,5 @@ -name: svtk_vcf2bed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtk=0.0.20190615 diff --git a/modules/nf-core/svtyper/svtyper/environment.yml b/modules/nf-core/svtyper/svtyper/environment.yml index 5b3c6c9152a8..c173b4339106 100644 --- a/modules/nf-core/svtyper/svtyper/environment.yml +++ b/modules/nf-core/svtyper/svtyper/environment.yml @@ -1,7 +1,5 @@ -name: svtyper_svtyper channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::svtyper=0.7.0 diff --git a/modules/nf-core/svtyper/svtypersso/environment.yml b/modules/nf-core/svtyper/svtypersso/environment.yml index b00cc4338ba1..c9b7d5450d1f 100644 --- a/modules/nf-core/svtyper/svtypersso/environment.yml +++ b/modules/nf-core/svtyper/svtypersso/environment.yml @@ -1,7 +1,5 @@ -name: "svtyper_svtypersso" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::svtyper=0.7.1" diff --git a/modules/nf-core/svync/environment.yml b/modules/nf-core/svync/environment.yml index fb7a1db84b03..dbdfe4bbd820 100644 --- a/modules/nf-core/svync/environment.yml +++ b/modules/nf-core/svync/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "svync" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::svync=0.1.2" diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index 56cc0fb1e5a6..c863e9207c07 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,8 +1,6 @@ -name: tabix_bgzip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tabix=1.11 - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index b9644de9d708..c863e9207c07 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,8 +1,6 @@ -name: tabix_bgziptabix channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tabix=1.11 - bioconda::htslib=1.20 diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 4d1f9dd43ff7..017c259da1cb 100644 --- a/modules/nf-core/tabix/tabix/environment.yml +++ b/modules/nf-core/tabix/tabix/environment.yml @@ -1,9 +1,6 @@ -name: tabix_tabix - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 diff --git a/modules/nf-core/tailfindr/environment.yml b/modules/nf-core/tailfindr/environment.yml index f8ff002c69fa..833397eac74b 100644 --- a/modules/nf-core/tailfindr/environment.yml +++ b/modules/nf-core/tailfindr/environment.yml @@ -1,8 +1,6 @@ -name: tailfindr channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ont-fast5-api=0.4.1 - bioconda::r-tailfindr=1.3 diff --git a/modules/nf-core/taxonkit/name2taxid/environment.yml b/modules/nf-core/taxonkit/name2taxid/environment.yml index ecf63d7ee8c8..37c42979ba4a 100644 --- a/modules/nf-core/taxonkit/name2taxid/environment.yml +++ b/modules/nf-core/taxonkit/name2taxid/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "taxonkit_name2taxid" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::taxonkit=0.15.1" diff --git a/modules/nf-core/taxpasta/merge/environment.yml b/modules/nf-core/taxpasta/merge/environment.yml index ca1a10b793c8..eb48f4365822 100644 --- a/modules/nf-core/taxpasta/merge/environment.yml +++ b/modules/nf-core/taxpasta/merge/environment.yml @@ -1,7 +1,5 @@ -name: taxpasta_merge channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::taxpasta=0.7.0 diff --git a/modules/nf-core/taxpasta/standardise/environment.yml b/modules/nf-core/taxpasta/standardise/environment.yml index a48f08e0b729..eb48f4365822 100644 --- a/modules/nf-core/taxpasta/standardise/environment.yml +++ b/modules/nf-core/taxpasta/standardise/environment.yml @@ -1,7 +1,5 @@ -name: taxpasta_standardise channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::taxpasta=0.7.0 diff --git a/modules/nf-core/tbprofiler/profile/environment.yml b/modules/nf-core/tbprofiler/profile/environment.yml index ae2d3b9bdcfb..3185d0c187fd 100644 --- a/modules/nf-core/tbprofiler/profile/environment.yml +++ b/modules/nf-core/tbprofiler/profile/environment.yml @@ -1,7 +1,5 @@ -name: tbprofiler_profile channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tb-profiler=3.0.8 diff --git a/modules/nf-core/tcoffee/align/environment.yml b/modules/nf-core/tcoffee/align/environment.yml index 28f159fd459e..26a17e709832 100644 --- a/modules/nf-core/tcoffee/align/environment.yml +++ b/modules/nf-core/tcoffee/align/environment.yml @@ -1,8 +1,6 @@ -name: tcoffee_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/alncompare/environment.yml b/modules/nf-core/tcoffee/alncompare/environment.yml index dfa14141528f..26a17e709832 100644 --- a/modules/nf-core/tcoffee/alncompare/environment.yml +++ b/modules/nf-core/tcoffee/alncompare/environment.yml @@ -1,8 +1,6 @@ -name: "tcoffee_alncompare" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/consensus/environment.yml b/modules/nf-core/tcoffee/consensus/environment.yml index f5c828409f72..26a17e709832 100644 --- a/modules/nf-core/tcoffee/consensus/environment.yml +++ b/modules/nf-core/tcoffee/consensus/environment.yml @@ -1,8 +1,6 @@ -name: "tcoffee_consensus" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/irmsd/environment.yml b/modules/nf-core/tcoffee/irmsd/environment.yml index 4065fe70bd68..26a17e709832 100644 --- a/modules/nf-core/tcoffee/irmsd/environment.yml +++ b/modules/nf-core/tcoffee/irmsd/environment.yml @@ -1,8 +1,6 @@ -name: "tcoffee_irmsd" channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/seqreformat/environment.yml b/modules/nf-core/tcoffee/seqreformat/environment.yml index 84afe8aa255e..7cc504fcaa03 100644 --- a/modules/nf-core/tcoffee/seqreformat/environment.yml +++ b/modules/nf-core/tcoffee/seqreformat/environment.yml @@ -1,7 +1,5 @@ -name: tcoffee_seqreformat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::t-coffee=13.46.0.919e8c6b diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml index 50480cd89b9e..615d140e6bb7 100644 --- a/modules/nf-core/tcoffee/tcs/environment.yml +++ b/modules/nf-core/tcoffee/tcs/environment.yml @@ -1,10 +1,8 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tcoffee_tcs" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::t-coffee=13.46.0.919e8c6b" - conda-forge::pigz=2.8 diff --git a/modules/nf-core/thermorawfileparser/environment.yml b/modules/nf-core/thermorawfileparser/environment.yml index 77323cbb69b9..e7bfd0b107f7 100644 --- a/modules/nf-core/thermorawfileparser/environment.yml +++ b/modules/nf-core/thermorawfileparser/environment.yml @@ -1,7 +1,5 @@ -name: "thermorawfileparser" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::thermorawfileparser=1.4.3" diff --git a/modules/nf-core/tiara/tiara/environment.yml b/modules/nf-core/tiara/tiara/environment.yml index 18d44734100c..2fc0d3657490 100644 --- a/modules/nf-core/tiara/tiara/environment.yml +++ b/modules/nf-core/tiara/tiara/environment.yml @@ -1,7 +1,5 @@ -name: tiara_tiara channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::tiara=1.0.3 diff --git a/modules/nf-core/tiddit/cov/environment.yml b/modules/nf-core/tiddit/cov/environment.yml index 6b024492e46b..2fd01cfd4b9f 100644 --- a/modules/nf-core/tiddit/cov/environment.yml +++ b/modules/nf-core/tiddit/cov/environment.yml @@ -1,7 +1,5 @@ -name: tiddit_cov channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tiddit=3.6.1 diff --git a/modules/nf-core/tiddit/sv/environment.yml b/modules/nf-core/tiddit/sv/environment.yml index d0367f17175d..2fd01cfd4b9f 100644 --- a/modules/nf-core/tiddit/sv/environment.yml +++ b/modules/nf-core/tiddit/sv/environment.yml @@ -1,7 +1,5 @@ -name: tiddit_sv channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tiddit=3.6.1 diff --git a/modules/nf-core/tidk/explore/environment.yml b/modules/nf-core/tidk/explore/environment.yml index 4fe55407ce10..22eb538bcfb3 100644 --- a/modules/nf-core/tidk/explore/environment.yml +++ b/modules/nf-core/tidk/explore/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tidk_explore" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::tidk=0.2.41" diff --git a/modules/nf-core/tidk/plot/environment.yml b/modules/nf-core/tidk/plot/environment.yml index ed1706e305b2..22eb538bcfb3 100644 --- a/modules/nf-core/tidk/plot/environment.yml +++ b/modules/nf-core/tidk/plot/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tidk_plot" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::tidk=0.2.41" diff --git a/modules/nf-core/tidk/search/environment.yml b/modules/nf-core/tidk/search/environment.yml index eaf92acc603d..22eb538bcfb3 100644 --- a/modules/nf-core/tidk/search/environment.yml +++ b/modules/nf-core/tidk/search/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tidk_search" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::tidk=0.2.41" diff --git a/modules/nf-core/topas/gencons/environment.yml b/modules/nf-core/topas/gencons/environment.yml index 7fbf438641bc..83e393086b39 100644 --- a/modules/nf-core/topas/gencons/environment.yml +++ b/modules/nf-core/topas/gencons/environment.yml @@ -1,7 +1,5 @@ -name: topas_gencons channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::topas=1.0.1 diff --git a/modules/nf-core/toulligqc/environment.yml b/modules/nf-core/toulligqc/environment.yml index ff82a4aa1b25..2d160afe2dab 100644 --- a/modules/nf-core/toulligqc/environment.yml +++ b/modules/nf-core/toulligqc/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "toulligqc" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::toulligqc=2.5.6" diff --git a/modules/nf-core/transdecoder/longorf/environment.yml b/modules/nf-core/transdecoder/longorf/environment.yml index dc90ac29f54c..19be873fc94a 100644 --- a/modules/nf-core/transdecoder/longorf/environment.yml +++ b/modules/nf-core/transdecoder/longorf/environment.yml @@ -1,7 +1,5 @@ -name: transdecoder_longorf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::transdecoder=5.7.1 diff --git a/modules/nf-core/transdecoder/predict/environment.yml b/modules/nf-core/transdecoder/predict/environment.yml index 07efaa4f0769..2484d15af090 100644 --- a/modules/nf-core/transdecoder/predict/environment.yml +++ b/modules/nf-core/transdecoder/predict/environment.yml @@ -1,7 +1,5 @@ -name: transdecoder_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::transdecoder=5.5.0 diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index 0981320c144d..f172c1b39e9b 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -1,9 +1,6 @@ -name: trimgalore - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::cutadapt=3.4 diff --git a/modules/nf-core/trimmomatic/environment.yml b/modules/nf-core/trimmomatic/environment.yml index 91145bb75e75..ab4b72b77a42 100644 --- a/modules/nf-core/trimmomatic/environment.yml +++ b/modules/nf-core/trimmomatic/environment.yml @@ -1,7 +1,5 @@ -name: trimmomatic channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::trimmomatic=0.39 diff --git a/modules/nf-core/trinity/environment.yml b/modules/nf-core/trinity/environment.yml index dd9f6cdbc542..844b0996ff64 100644 --- a/modules/nf-core/trinity/environment.yml +++ b/modules/nf-core/trinity/environment.yml @@ -1,7 +1,5 @@ -name: trinity channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::trinity=2.15.1 diff --git a/modules/nf-core/trust4/environment.yml b/modules/nf-core/trust4/environment.yml index 9270eee23054..7e07e377e551 100644 --- a/modules/nf-core/trust4/environment.yml +++ b/modules/nf-core/trust4/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "trust4" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::trust4=1.0.13" diff --git a/modules/nf-core/truvari/bench/environment.yml b/modules/nf-core/truvari/bench/environment.yml index 033354b4a662..7c5429e003bd 100644 --- a/modules/nf-core/truvari/bench/environment.yml +++ b/modules/nf-core/truvari/bench/environment.yml @@ -1,7 +1,5 @@ -name: truvari_bench channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::truvari=4.1.0 diff --git a/modules/nf-core/truvari/consistency/environment.yml b/modules/nf-core/truvari/consistency/environment.yml index d35fac085215..0844cd49096e 100644 --- a/modules/nf-core/truvari/consistency/environment.yml +++ b/modules/nf-core/truvari/consistency/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "truvari_consistency" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::truvari=4.1.0" diff --git a/modules/nf-core/truvari/segment/environment.yml b/modules/nf-core/truvari/segment/environment.yml index f01601c31931..0844cd49096e 100644 --- a/modules/nf-core/truvari/segment/environment.yml +++ b/modules/nf-core/truvari/segment/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "truvari_segment" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::truvari=4.1.0" diff --git a/modules/nf-core/trycycler/cluster/environment.yml b/modules/nf-core/trycycler/cluster/environment.yml index 52adae7015b8..15112089c7ed 100644 --- a/modules/nf-core/trycycler/cluster/environment.yml +++ b/modules/nf-core/trycycler/cluster/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "trycycler_cluster" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::trycycler=0.5.3" diff --git a/modules/nf-core/trycycler/subsample/environment.yml b/modules/nf-core/trycycler/subsample/environment.yml index 0713e720debc..15112089c7ed 100644 --- a/modules/nf-core/trycycler/subsample/environment.yml +++ b/modules/nf-core/trycycler/subsample/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "trycycler_subsample" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::trycycler=0.5.3" diff --git a/modules/nf-core/tsebra/environment.yml b/modules/nf-core/tsebra/environment.yml index 657cd82f910e..f189f6bda7a0 100644 --- a/modules/nf-core/tsebra/environment.yml +++ b/modules/nf-core/tsebra/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tsebra" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::tsebra=1.1.2.5" diff --git a/modules/nf-core/tximeta/tximport/environment.yml b/modules/nf-core/tximeta/tximport/environment.yml index 24b202222e35..4b6df0cfe5cd 100644 --- a/modules/nf-core/tximeta/tximport/environment.yml +++ b/modules/nf-core/tximeta/tximport/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "tximeta_tximport" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::bioconductor-tximeta=1.20.1" diff --git a/modules/nf-core/ucsc/bedclip/environment.yml b/modules/nf-core/ucsc/bedclip/environment.yml index 571dc2749bfe..94e825f03ea4 100644 --- a/modules/nf-core/ucsc/bedclip/environment.yml +++ b/modules/nf-core/ucsc/bedclip/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bedclip channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bedclip=377 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index f91e216f5875..a54fb8f1654b 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bedgraphtobigwig channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bedgraphtobigwig=445 diff --git a/modules/nf-core/ucsc/bedtobigbed/environment.yml b/modules/nf-core/ucsc/bedtobigbed/environment.yml index fc04b7cda1ba..62670c4eba4a 100644 --- a/modules/nf-core/ucsc/bedtobigbed/environment.yml +++ b/modules/nf-core/ucsc/bedtobigbed/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bedtobigbed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bedtobigbed=447 diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml b/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml index 62deb297e269..94d3fc6053ef 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_bigwigaverageoverbed channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-bigwigaverageoverbed=377 diff --git a/modules/nf-core/ucsc/gtftogenepred/environment.yml b/modules/nf-core/ucsc/gtftogenepred/environment.yml index 5216fc8ffbf4..5c4f6c2fa638 100644 --- a/modules/nf-core/ucsc/gtftogenepred/environment.yml +++ b/modules/nf-core/ucsc/gtftogenepred/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_gtftogenepred channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-gtftogenepred=447 diff --git a/modules/nf-core/ucsc/liftover/environment.yml b/modules/nf-core/ucsc/liftover/environment.yml index 687955dc0286..db54ca2b5c95 100644 --- a/modules/nf-core/ucsc/liftover/environment.yml +++ b/modules/nf-core/ucsc/liftover/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_liftover channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-liftover=377 diff --git a/modules/nf-core/ucsc/wigtobigwig/environment.yml b/modules/nf-core/ucsc/wigtobigwig/environment.yml index 3e88a5dd421a..331ad3b27c4d 100644 --- a/modules/nf-core/ucsc/wigtobigwig/environment.yml +++ b/modules/nf-core/ucsc/wigtobigwig/environment.yml @@ -1,7 +1,5 @@ -name: ucsc_wigtobigwig channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ucsc-wigtobigwig=447 diff --git a/modules/nf-core/ultra/align/environment.yml b/modules/nf-core/ultra/align/environment.yml index 74ccba490fc0..39d65509991f 100644 --- a/modules/nf-core/ultra/align/environment.yml +++ b/modules/nf-core/ultra/align/environment.yml @@ -1,8 +1,6 @@ -name: ultra_align channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ultra_bioinformatics=0.1 - bioconda::samtools=1.17 diff --git a/modules/nf-core/ultra/index/environment.yml b/modules/nf-core/ultra/index/environment.yml index 81f92d0e0450..30271567b3cb 100644 --- a/modules/nf-core/ultra/index/environment.yml +++ b/modules/nf-core/ultra/index/environment.yml @@ -1,7 +1,5 @@ -name: ultra_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ultra_bioinformatics=0.1 diff --git a/modules/nf-core/ultra/pipeline/environment.yml b/modules/nf-core/ultra/pipeline/environment.yml index f37e3ba74be2..30271567b3cb 100644 --- a/modules/nf-core/ultra/pipeline/environment.yml +++ b/modules/nf-core/ultra/pipeline/environment.yml @@ -1,7 +1,5 @@ -name: ultra_pipeline channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ultra_bioinformatics=0.1 diff --git a/modules/nf-core/ultraplex/environment.yml b/modules/nf-core/ultraplex/environment.yml index ccbeb1060f60..df623d5cabdb 100644 --- a/modules/nf-core/ultraplex/environment.yml +++ b/modules/nf-core/ultraplex/environment.yml @@ -1,7 +1,5 @@ -name: ultraplex channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::ultraplex=1.2.5 diff --git a/modules/nf-core/umicollapse/environment.yml b/modules/nf-core/umicollapse/environment.yml index 8dbc65dc4481..3847980dde40 100644 --- a/modules/nf-core/umicollapse/environment.yml +++ b/modules/nf-core/umicollapse/environment.yml @@ -1,7 +1,5 @@ -name: umicollapse channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umicollapse=1.0.0 diff --git a/modules/nf-core/umitools/dedup/environment.yml b/modules/nf-core/umitools/dedup/environment.yml index bc497824f752..9f9e03c4972e 100644 --- a/modules/nf-core/umitools/dedup/environment.yml +++ b/modules/nf-core/umitools/dedup/environment.yml @@ -1,7 +1,5 @@ -name: umitools_dedup channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/extract/environment.yml b/modules/nf-core/umitools/extract/environment.yml index aab452d1e186..9f9e03c4972e 100644 --- a/modules/nf-core/umitools/extract/environment.yml +++ b/modules/nf-core/umitools/extract/environment.yml @@ -1,7 +1,5 @@ -name: umitools_extract channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/group/environment.yml b/modules/nf-core/umitools/group/environment.yml index 12e2b8d0c160..9f9e03c4972e 100644 --- a/modules/nf-core/umitools/group/environment.yml +++ b/modules/nf-core/umitools/group/environment.yml @@ -1,7 +1,5 @@ -name: umitools_group channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/umitools/prepareforrsem/environment.yml b/modules/nf-core/umitools/prepareforrsem/environment.yml index dbb1bde77b76..9f9e03c4972e 100644 --- a/modules/nf-core/umitools/prepareforrsem/environment.yml +++ b/modules/nf-core/umitools/prepareforrsem/environment.yml @@ -1,7 +1,5 @@ -name: umitools_prepareforrsem channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::umi_tools=1.1.5 diff --git a/modules/nf-core/unicycler/environment.yml b/modules/nf-core/unicycler/environment.yml index ffe491b81abc..bcafec00cb62 100644 --- a/modules/nf-core/unicycler/environment.yml +++ b/modules/nf-core/unicycler/environment.yml @@ -1,7 +1,5 @@ -name: unicycler channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::unicycler=0.5.0 diff --git a/modules/nf-core/universc/environment.yml b/modules/nf-core/universc/environment.yml index e9cdf650779e..3cebeff05bfc 100644 --- a/modules/nf-core/universc/environment.yml +++ b/modules/nf-core/universc/environment.yml @@ -1,5 +1,3 @@ -name: universc channels: - conda-forge - bioconda - - defaults diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244afb2..c7794856d84c 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,8 +1,6 @@ -name: untar channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::grep=3.11 - conda-forge::sed=4.8 diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml index be5a6da9d886..30ff7d8f5882 100644 --- a/modules/nf-core/untarfiles/environment.yml +++ b/modules/nf-core/untarfiles/environment.yml @@ -1,9 +1,6 @@ -name: untarfiles - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::grep=3.4 diff --git a/modules/nf-core/unzip/environment.yml b/modules/nf-core/unzip/environment.yml index d3a535f17063..e93c649f4434 100644 --- a/modules/nf-core/unzip/environment.yml +++ b/modules/nf-core/unzip/environment.yml @@ -1,7 +1,5 @@ -name: unzip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::p7zip=16.02 diff --git a/modules/nf-core/unzipfiles/environment.yml b/modules/nf-core/unzipfiles/environment.yml index 2f2ef1eb986e..e93c649f4434 100644 --- a/modules/nf-core/unzipfiles/environment.yml +++ b/modules/nf-core/unzipfiles/environment.yml @@ -1,7 +1,5 @@ -name: unzipfiles channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::p7zip=16.02 diff --git a/modules/nf-core/upd/environment.yml b/modules/nf-core/upd/environment.yml index 77b652272f92..307f13b3796a 100644 --- a/modules/nf-core/upd/environment.yml +++ b/modules/nf-core/upd/environment.yml @@ -1,7 +1,5 @@ -name: upd channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::upd=0.1.1 diff --git a/modules/nf-core/vardictjava/environment.yml b/modules/nf-core/vardictjava/environment.yml index 4e8905e52c06..a835c6db4b55 100644 --- a/modules/nf-core/vardictjava/environment.yml +++ b/modules/nf-core/vardictjava/environment.yml @@ -1,8 +1,6 @@ -name: vardictjava channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::htslib=1.20 - bioconda::vardict-java=1.8.3 diff --git a/modules/nf-core/variantbam/environment.yml b/modules/nf-core/variantbam/environment.yml index 8aa2fb39963c..3f39419da170 100644 --- a/modules/nf-core/variantbam/environment.yml +++ b/modules/nf-core/variantbam/environment.yml @@ -1,7 +1,5 @@ -name: variantbam channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::variantbam=1.4.4a diff --git a/modules/nf-core/varlociraptor/callvariants/environment.yml b/modules/nf-core/varlociraptor/callvariants/environment.yml index 84cd28fe86ec..0d1519bec7c7 100644 --- a/modules/nf-core/varlociraptor/callvariants/environment.yml +++ b/modules/nf-core/varlociraptor/callvariants/environment.yml @@ -1,7 +1,5 @@ -name: varlociraptor_callvariants channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::varlociraptor=8.1.1 diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml b/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml index 9ff535e8fb2e..0d1519bec7c7 100644 --- a/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml +++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/environment.yml @@ -1,7 +1,5 @@ -name: varlociraptor_estimatealignmentproperties channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::varlociraptor=8.1.1 diff --git a/modules/nf-core/varlociraptor/preprocess/environment.yml b/modules/nf-core/varlociraptor/preprocess/environment.yml index 3c433c57c5fc..0d1519bec7c7 100644 --- a/modules/nf-core/varlociraptor/preprocess/environment.yml +++ b/modules/nf-core/varlociraptor/preprocess/environment.yml @@ -1,7 +1,5 @@ -name: varlociraptor_preprocess channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::varlociraptor=8.1.1 diff --git a/modules/nf-core/vcf2cytosure/environment.yml b/modules/nf-core/vcf2cytosure/environment.yml index d4bf99590c12..d078bfaed58e 100644 --- a/modules/nf-core/vcf2cytosure/environment.yml +++ b/modules/nf-core/vcf2cytosure/environment.yml @@ -1,7 +1,5 @@ -name: vcf2cytosure channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcf2cytosure=0.9.1 diff --git a/modules/nf-core/vcf2db/environment.yml b/modules/nf-core/vcf2db/environment.yml index 51a8ab8a9b9b..58c477f95911 100644 --- a/modules/nf-core/vcf2db/environment.yml +++ b/modules/nf-core/vcf2db/environment.yml @@ -1,7 +1,5 @@ -name: vcf2db channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcf2db=2020.02.24 diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml index ee3f531ff47a..2d273cd05f57 100644 --- a/modules/nf-core/vcf2maf/environment.yml +++ b/modules/nf-core/vcf2maf/environment.yml @@ -1,8 +1,6 @@ -name: vcf2maf channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcf2maf=1.6.21 - bioconda::ensembl-vep=106.1 diff --git a/modules/nf-core/vcfanno/environment.yml b/modules/nf-core/vcfanno/environment.yml index f336cc6b0b02..32c48b15bf30 100644 --- a/modules/nf-core/vcfanno/environment.yml +++ b/modules/nf-core/vcfanno/environment.yml @@ -1,7 +1,5 @@ -name: vcfanno channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcfanno=0.3.5 diff --git a/modules/nf-core/vcflib/vcfbreakmulti/environment.yml b/modules/nf-core/vcflib/vcfbreakmulti/environment.yml index dc722a43f34f..e918887f9d0f 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/environment.yml +++ b/modules/nf-core/vcflib/vcfbreakmulti/environment.yml @@ -1,7 +1,5 @@ -name: vcflib_vcfbreakmulti channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcflib=1.0.3 diff --git a/modules/nf-core/vcflib/vcffilter/environment.yml b/modules/nf-core/vcflib/vcffilter/environment.yml index 263943bcd5a7..e918887f9d0f 100644 --- a/modules/nf-core/vcflib/vcffilter/environment.yml +++ b/modules/nf-core/vcflib/vcffilter/environment.yml @@ -1,7 +1,5 @@ -name: vcflib_vcffilter channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcflib=1.0.3 diff --git a/modules/nf-core/vcflib/vcffixup/environment.yml b/modules/nf-core/vcflib/vcffixup/environment.yml index d06c4c7bdfc4..d0a99ffd7614 100644 --- a/modules/nf-core/vcflib/vcffixup/environment.yml +++ b/modules/nf-core/vcflib/vcffixup/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "vcflib_vcffixup" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::vcflib=1.0.3" diff --git a/modules/nf-core/vcflib/vcfuniq/environment.yml b/modules/nf-core/vcflib/vcfuniq/environment.yml index dff6ed89716e..e918887f9d0f 100644 --- a/modules/nf-core/vcflib/vcfuniq/environment.yml +++ b/modules/nf-core/vcflib/vcfuniq/environment.yml @@ -1,7 +1,5 @@ -name: vcflib_vcfuniq channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcflib=1.0.3 diff --git a/modules/nf-core/vcftools/environment.yml b/modules/nf-core/vcftools/environment.yml index 503449e833eb..7dcc752b86e6 100644 --- a/modules/nf-core/vcftools/environment.yml +++ b/modules/nf-core/vcftools/environment.yml @@ -1,7 +1,5 @@ -name: vcftools channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vcftools=0.1.16 diff --git a/modules/nf-core/velocyto/environment.yml b/modules/nf-core/velocyto/environment.yml index b9c137385289..6c59ad55e699 100644 --- a/modules/nf-core/velocyto/environment.yml +++ b/modules/nf-core/velocyto/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "velocyto" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::velocyto.py=0.17.17" diff --git a/modules/nf-core/verifybamid/verifybamid/environment.yml b/modules/nf-core/verifybamid/verifybamid/environment.yml index 9a887c5ac0b3..6f40151d0aaa 100644 --- a/modules/nf-core/verifybamid/verifybamid/environment.yml +++ b/modules/nf-core/verifybamid/verifybamid/environment.yml @@ -1,7 +1,5 @@ -name: verifybamid_verifybamid channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::verifybamid=1.1.3 diff --git a/modules/nf-core/verifybamid/verifybamid2/environment.yml b/modules/nf-core/verifybamid/verifybamid2/environment.yml index b01882696d5c..0375f1107d8b 100644 --- a/modules/nf-core/verifybamid/verifybamid2/environment.yml +++ b/modules/nf-core/verifybamid/verifybamid2/environment.yml @@ -1,7 +1,5 @@ -name: VERIFYBAMID_VERIFYBAMID2 channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::verifybamid2=2.0.1 diff --git a/modules/nf-core/vg/construct/environment.yml b/modules/nf-core/vg/construct/environment.yml index f18cc21c4026..502b6f7effd6 100644 --- a/modules/nf-core/vg/construct/environment.yml +++ b/modules/nf-core/vg/construct/environment.yml @@ -1,7 +1,5 @@ -name: vg_construct channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vg=1.45.0 diff --git a/modules/nf-core/vg/deconstruct/environment.yml b/modules/nf-core/vg/deconstruct/environment.yml index 36f0853b2959..58a7728b0cdd 100644 --- a/modules/nf-core/vg/deconstruct/environment.yml +++ b/modules/nf-core/vg/deconstruct/environment.yml @@ -1,7 +1,5 @@ -name: vg_deconstruct channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vg=1.43.0 diff --git a/modules/nf-core/vg/index/environment.yml b/modules/nf-core/vg/index/environment.yml index 6417fd696e23..502b6f7effd6 100644 --- a/modules/nf-core/vg/index/environment.yml +++ b/modules/nf-core/vg/index/environment.yml @@ -1,7 +1,5 @@ -name: vg_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vg=1.45.0 diff --git a/modules/nf-core/viennarna/rnacofold/environment.yml b/modules/nf-core/viennarna/rnacofold/environment.yml index 25e241a857e3..757186a7076b 100644 --- a/modules/nf-core/viennarna/rnacofold/environment.yml +++ b/modules/nf-core/viennarna/rnacofold/environment.yml @@ -1,7 +1,5 @@ -name: "viennarna_rnacofold" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::viennarna=2.6.4" diff --git a/modules/nf-core/viennarna/rnafold/environment.yml b/modules/nf-core/viennarna/rnafold/environment.yml index 73b4fe2a2e4b..eb62ef69af87 100644 --- a/modules/nf-core/viennarna/rnafold/environment.yml +++ b/modules/nf-core/viennarna/rnafold/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "viennarna_rnafold" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::viennarna=2.6.4" diff --git a/modules/nf-core/viennarna/rnalfold/environment.yml b/modules/nf-core/viennarna/rnalfold/environment.yml index 688cf1527bf8..757186a7076b 100644 --- a/modules/nf-core/viennarna/rnalfold/environment.yml +++ b/modules/nf-core/viennarna/rnalfold/environment.yml @@ -1,7 +1,5 @@ -name: "viennarna_rnalfold" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::viennarna=2.6.4" diff --git a/modules/nf-core/vireo/environment.yml b/modules/nf-core/vireo/environment.yml index e21041126747..cc87fb829999 100644 --- a/modules/nf-core/vireo/environment.yml +++ b/modules/nf-core/vireo/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "vireo" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::vireosnp=0.5.8" diff --git a/modules/nf-core/vrhyme/extractunbinned/environment.yml b/modules/nf-core/vrhyme/extractunbinned/environment.yml index cac99a06b5fd..4908e2bce3d1 100644 --- a/modules/nf-core/vrhyme/extractunbinned/environment.yml +++ b/modules/nf-core/vrhyme/extractunbinned/environment.yml @@ -1,7 +1,5 @@ -name: vrhyme_extractunbinned channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vrhyme=1.1.0 diff --git a/modules/nf-core/vrhyme/linkbins/environment.yml b/modules/nf-core/vrhyme/linkbins/environment.yml index 45f42bb0d290..4908e2bce3d1 100644 --- a/modules/nf-core/vrhyme/linkbins/environment.yml +++ b/modules/nf-core/vrhyme/linkbins/environment.yml @@ -1,7 +1,5 @@ -name: vrhyme_linkbins channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vrhyme=1.1.0 diff --git a/modules/nf-core/vrhyme/vrhyme/environment.yml b/modules/nf-core/vrhyme/vrhyme/environment.yml index f9b791358853..c343a66a1655 100644 --- a/modules/nf-core/vrhyme/vrhyme/environment.yml +++ b/modules/nf-core/vrhyme/vrhyme/environment.yml @@ -1,4 +1,3 @@ -name: vrhyme_vrhyme channels: - conda-forge - bioconda diff --git a/modules/nf-core/vsearch/cluster/environment.yml b/modules/nf-core/vsearch/cluster/environment.yml index 5532375ca82f..e9b4c9dc6a1f 100644 --- a/modules/nf-core/vsearch/cluster/environment.yml +++ b/modules/nf-core/vsearch/cluster/environment.yml @@ -1,9 +1,6 @@ -name: vsearch_cluster - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/vsearch/dereplicate/environment.yml b/modules/nf-core/vsearch/dereplicate/environment.yml index 22ff40e57994..534299a8eaee 100644 --- a/modules/nf-core/vsearch/dereplicate/environment.yml +++ b/modules/nf-core/vsearch/dereplicate/environment.yml @@ -1,7 +1,5 @@ -name: "vsearch_dereplicate" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::vsearch=2.28.1" diff --git a/modules/nf-core/vsearch/fastqfilter/environment.yml b/modules/nf-core/vsearch/fastqfilter/environment.yml index a7ff8133b140..534299a8eaee 100644 --- a/modules/nf-core/vsearch/fastqfilter/environment.yml +++ b/modules/nf-core/vsearch/fastqfilter/environment.yml @@ -1,7 +1,5 @@ -name: "vsearch_fastqfilter" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::vsearch=2.28.1" diff --git a/modules/nf-core/vsearch/sintax/environment.yml b/modules/nf-core/vsearch/sintax/environment.yml index 16e8d3004f38..acba2f679e8b 100644 --- a/modules/nf-core/vsearch/sintax/environment.yml +++ b/modules/nf-core/vsearch/sintax/environment.yml @@ -1,7 +1,5 @@ -name: vsearch_sintax channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vsearch=2.21.1 diff --git a/modules/nf-core/vsearch/sort/environment.yml b/modules/nf-core/vsearch/sort/environment.yml index dd39854ec04d..acba2f679e8b 100644 --- a/modules/nf-core/vsearch/sort/environment.yml +++ b/modules/nf-core/vsearch/sort/environment.yml @@ -1,7 +1,5 @@ -name: vsearch_sort channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vsearch=2.21.1 diff --git a/modules/nf-core/vsearch/usearchglobal/environment.yml b/modules/nf-core/vsearch/usearchglobal/environment.yml index a4f4e86251d5..acba2f679e8b 100644 --- a/modules/nf-core/vsearch/usearchglobal/environment.yml +++ b/modules/nf-core/vsearch/usearchglobal/environment.yml @@ -1,7 +1,5 @@ -name: vsearch_usearchglobal channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vsearch=2.21.1 diff --git a/modules/nf-core/vt/decompose/environment.yml b/modules/nf-core/vt/decompose/environment.yml index 6dd7d9355fc4..36139fa76a95 100644 --- a/modules/nf-core/vt/decompose/environment.yml +++ b/modules/nf-core/vt/decompose/environment.yml @@ -1,7 +1,5 @@ -name: vt_decompose channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vt=2015.11.10 diff --git a/modules/nf-core/vt/normalize/environment.yml b/modules/nf-core/vt/normalize/environment.yml index 8990f1b46f93..36139fa76a95 100644 --- a/modules/nf-core/vt/normalize/environment.yml +++ b/modules/nf-core/vt/normalize/environment.yml @@ -1,7 +1,5 @@ -name: vt_normalize channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::vt=2015.11.10 diff --git a/modules/nf-core/wfmash/environment.yml b/modules/nf-core/wfmash/environment.yml index ba16050d0c87..7981870f2048 100644 --- a/modules/nf-core/wfmash/environment.yml +++ b/modules/nf-core/wfmash/environment.yml @@ -1,7 +1,5 @@ -name: wfmash channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wfmash=0.13.0 diff --git a/modules/nf-core/wgsim/environment.yml b/modules/nf-core/wgsim/environment.yml index 0f4567400b12..5ca5c63a6dc5 100644 --- a/modules/nf-core/wgsim/environment.yml +++ b/modules/nf-core/wgsim/environment.yml @@ -1,7 +1,5 @@ -name: wgsim channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wgsim=1.0 diff --git a/modules/nf-core/whamg/environment.yml b/modules/nf-core/whamg/environment.yml index 363d8a908234..cedbc531078c 100644 --- a/modules/nf-core/whamg/environment.yml +++ b/modules/nf-core/whamg/environment.yml @@ -1,9 +1,6 @@ -name: whamg - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::tabix=1.11 diff --git a/modules/nf-core/windowmasker/convert/environment.yml b/modules/nf-core/windowmasker/convert/environment.yml index 91e56e5cee1f..777e097ed751 100644 --- a/modules/nf-core/windowmasker/convert/environment.yml +++ b/modules/nf-core/windowmasker/convert/environment.yml @@ -1,7 +1,5 @@ -name: windowmasker_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/windowmasker/mkcounts/environment.yml b/modules/nf-core/windowmasker/mkcounts/environment.yml index e4d721081a91..777e097ed751 100644 --- a/modules/nf-core/windowmasker/mkcounts/environment.yml +++ b/modules/nf-core/windowmasker/mkcounts/environment.yml @@ -1,7 +1,5 @@ -name: windowmasker_mkcounts channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/windowmasker/ustat/environment.yml b/modules/nf-core/windowmasker/ustat/environment.yml index b83d82e52eb6..777e097ed751 100644 --- a/modules/nf-core/windowmasker/ustat/environment.yml +++ b/modules/nf-core/windowmasker/ustat/environment.yml @@ -1,7 +1,5 @@ -name: windowmasker_ustat channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::blast=2.15.0 diff --git a/modules/nf-core/wisecondorx/convert/environment.yml b/modules/nf-core/wisecondorx/convert/environment.yml index 504aa86e6c67..90e62a7c4949 100644 --- a/modules/nf-core/wisecondorx/convert/environment.yml +++ b/modules/nf-core/wisecondorx/convert/environment.yml @@ -1,7 +1,5 @@ -name: wisecondorx_convert channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wisecondorx=1.2.9 diff --git a/modules/nf-core/wisecondorx/gender/environment.yml b/modules/nf-core/wisecondorx/gender/environment.yml index 18f5fd279e53..90e62a7c4949 100644 --- a/modules/nf-core/wisecondorx/gender/environment.yml +++ b/modules/nf-core/wisecondorx/gender/environment.yml @@ -1,7 +1,5 @@ -name: wisecondorx_gender channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wisecondorx=1.2.9 diff --git a/modules/nf-core/wisecondorx/newref/environment.yml b/modules/nf-core/wisecondorx/newref/environment.yml index 8bf45d6751b5..90e62a7c4949 100644 --- a/modules/nf-core/wisecondorx/newref/environment.yml +++ b/modules/nf-core/wisecondorx/newref/environment.yml @@ -1,7 +1,5 @@ -name: wisecondorx_newref channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wisecondorx=1.2.9 diff --git a/modules/nf-core/wisecondorx/predict/environment.yml b/modules/nf-core/wisecondorx/predict/environment.yml index 119ed59308bf..90e62a7c4949 100644 --- a/modules/nf-core/wisecondorx/predict/environment.yml +++ b/modules/nf-core/wisecondorx/predict/environment.yml @@ -1,7 +1,5 @@ -name: wisecondorx_predict channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::wisecondorx=1.2.9 diff --git a/modules/nf-core/wittyer/environment.yml b/modules/nf-core/wittyer/environment.yml index f8378df24793..c90cb8dccbf3 100644 --- a/modules/nf-core/wittyer/environment.yml +++ b/modules/nf-core/wittyer/environment.yml @@ -1,7 +1,5 @@ -name: wittyer channels: - conda-forge - bioconda - - defaults dependencies: - tabix diff --git a/modules/nf-core/xengsort/index/environment.yml b/modules/nf-core/xengsort/index/environment.yml index e92893855e31..43a6ecdce0b8 100644 --- a/modules/nf-core/xengsort/index/environment.yml +++ b/modules/nf-core/xengsort/index/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "xengsort_index" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::xengsort=2.0.5" diff --git a/modules/nf-core/xz/compress/environment.yml b/modules/nf-core/xz/compress/environment.yml index 6275039992d1..240428da6af7 100644 --- a/modules/nf-core/xz/compress/environment.yml +++ b/modules/nf-core/xz/compress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "xz_compress" channels: - conda-forge - bioconda - - defaults dependencies: - "xz=5.2.6" diff --git a/modules/nf-core/xz/decompress/environment.yml b/modules/nf-core/xz/decompress/environment.yml index 90b8de1e5d89..240428da6af7 100644 --- a/modules/nf-core/xz/decompress/environment.yml +++ b/modules/nf-core/xz/decompress/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "xz_decompress" channels: - conda-forge - bioconda - - defaults dependencies: - "xz=5.2.6" diff --git a/modules/nf-core/yahs/environment.yml b/modules/nf-core/yahs/environment.yml index 8dcf601942f7..cb2acec87edb 100644 --- a/modules/nf-core/yahs/environment.yml +++ b/modules/nf-core/yahs/environment.yml @@ -1,7 +1,5 @@ -name: yahs channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::yahs=1.2a.2 diff --git a/modules/nf-core/yak/count/environment.yml b/modules/nf-core/yak/count/environment.yml index 5961f3346f4b..907edbb62f6c 100644 --- a/modules/nf-core/yak/count/environment.yml +++ b/modules/nf-core/yak/count/environment.yml @@ -1,9 +1,7 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json -name: "yak_count" channels: - conda-forge - bioconda - - defaults dependencies: - "bioconda::yak=0.1" diff --git a/modules/nf-core/yara/index/environment.yml b/modules/nf-core/yara/index/environment.yml index 127f0e293fb6..90714436ab0a 100644 --- a/modules/nf-core/yara/index/environment.yml +++ b/modules/nf-core/yara/index/environment.yml @@ -1,7 +1,5 @@ -name: yara_index channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::yara=1.0.2 diff --git a/modules/nf-core/yara/mapper/environment.yml b/modules/nf-core/yara/mapper/environment.yml index 970b832a5327..5daa89921449 100644 --- a/modules/nf-core/yara/mapper/environment.yml +++ b/modules/nf-core/yara/mapper/environment.yml @@ -1,9 +1,6 @@ -name: yara_mapper - channels: - conda-forge - bioconda - - defaults dependencies: - bioconda::samtools=1.16.1 diff --git a/modules/nf-core/zip/environment.yml b/modules/nf-core/zip/environment.yml index 8104a7210b1e..e93c649f4434 100644 --- a/modules/nf-core/zip/environment.yml +++ b/modules/nf-core/zip/environment.yml @@ -1,7 +1,5 @@ -name: zip channels: - conda-forge - bioconda - - defaults dependencies: - conda-forge::p7zip=16.02 From 15086c852c860f785a3654cba03f0ee00533cd08 Mon Sep 17 00:00:00 2001 From: Daniel Lundin Date: Fri, 6 Sep 2024 11:31:51 +0200 Subject: [PATCH 027/486] hmmsearch, rank and output fasta (#6601) * New subworkflow fasta_hmmsearch_rank_fastas * Add euk and mito SSU rRNA to tests * More tests * Fix trailing whitespace --- .../fasta_hmmsearch_rank_fastas/main.nf | 55 +++++++++ .../fasta_hmmsearch_rank_fastas/meta.yml | 46 ++++++++ .../tests/main.nf.test | 90 +++++++++++++++ .../tests/main.nf.test.snap | 108 ++++++++++++++++++ .../tests/tags.yml | 2 + 5 files changed, 301 insertions(+) create mode 100644 subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf create mode 100644 subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml create mode 100644 subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test create mode 100644 subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/tags.yml diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf new file mode 100644 index 000000000000..8f7a5cae7e53 --- /dev/null +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/main.nf @@ -0,0 +1,55 @@ +include { HMMER_HMMSEARCH } from '../../../modules/nf-core/hmmer/hmmsearch/main' +include { HMMER_HMMRANK } from '../../../modules/nf-core/hmmer/hmmrank/main' +include { SEQTK_SUBSEQ } from '../../../modules/nf-core/seqtk/subseq/main' + +workflow FASTA_HMMSEARCH_RANK_FASTAS { + + take: + ch_hmms // channel: [ val(meta), file(hmm) ], i.e. a list of hmm profiles, each with its meta object + ch_fasta // channel: file(fasta), a single fasta file + + main: + + ch_versions = Channel.empty() + + ch_hmms + .combine(ch_fasta) + .map { [ it[0], it[1], it[2], false, true, false ] } + .set { ch_hmmsearch } + + HMMER_HMMSEARCH ( ch_hmmsearch ) + ch_versions = ch_versions.mix(HMMER_HMMSEARCH.out.versions.first()) + + HMMER_HMMSEARCH.out.target_summary + .collect { it[1] } + .map { [ [ id: 'rank' ], it ] } + .set { ch_hmmrank } + + HMMER_HMMRANK ( ch_hmmrank ) + ch_versions = ch_versions.mix(HMMER_HMMRANK.out.versions.first()) + + HMMER_HMMRANK.out.hmmrank + .map { it[1] } + .splitCsv(header: true, sep: '\t') + .filter { it.rank == '1' } + .collectFile { [ "${it.profile}.txt", "${it.accno}\n" ] } + .map { [ [ id: it.baseName ], it ] } + .groupTuple(sort: true) + .set { ch_subseq_filter } + + ch_subseq_filter + .combine(ch_fasta) + .map { [ it[0], it[2] ] } + .groupTuple(sort: true) + .set { ch_subseq_fasta } + + SEQTK_SUBSEQ ( ch_subseq_fasta, ch_subseq_filter.map { it[1] } ) + ch_versions = ch_versions.mix(SEQTK_SUBSEQ.out.versions.first()) + + emit: + hmmrank = HMMER_HMMRANK.out.hmmrank // channel: [ [ id: 'rank' ], hmmrank_tsv ] + seqfastas = SEQTK_SUBSEQ.out.sequences // channel: [ meta, fasta ] + + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml new file mode 100644 index 000000000000..6584ff527215 --- /dev/null +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/meta.yml @@ -0,0 +1,46 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "fasta_hmmsearch_rank_fastas" +description: Run hmmsearch and output separate fasta files for top scoring hits to each profile +keywords: + - hmmer + - search + - rank + - fasta +components: + - hmmer/hmmsearch + - hmmer/hmmrank + - seqtk/subseq +input: + - ch_hmms: + type: file + description: | + The input channel containing hmm profiles + Structure: [ val(meta), path(hmm) ] + pattern: "*.{hmm}" + - ch_fasta: + type: file + description: | + The input channel containing sequences to be searched and ranked +output: + - hmmrank: + type: file + description: | + Channel containing the TSV file from ranking hmmsearch hits + Structure: [ val(meta), path(hmmrank) ] + pattern: "*.hmmrank.tsv.gz" + - bai: + type: file + description: | + Channel containing subsets of sequences + Structure: [ val(meta), path(fasta) ] + pattern: "*.fa.gz" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@erikrikarddaniel" +maintainers: + - "@erikrikarddaniel" diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test new file mode 100644 index 000000000000..f52301012a12 --- /dev/null +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test @@ -0,0 +1,90 @@ +// nf-core subworkflows test fasta_hmmsearch_rank_fastas +nextflow_workflow { + + name "Test Subworkflow FASTA_HMMSEARCH_RANK_FASTAS" + script "../main.nf" + workflow "FASTA_HMMSEARCH_RANK_FASTAS" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fasta_hmmsearch_rank_fastas" + tag "hmmer" + tag "hmmer/hmmfetch" + tag "hmmer/hmmsearch" + tag "hmmer/hmmrank" + tag "seqtk/subseq" + + test("SSU rRNA - hmm/fasta") { + + setup { + run("HMMER_HMMFETCH") { + script "../../../../modules/nf-core/hmmer/hmmfetch/main.nf" + process { + """ + input[0] = Channel.fromList([ + tuple([ id: 'arc16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/arc.hmm")), + tuple([ id: 'bac16s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/bac.hmm")), + tuple([ id: 'euk18s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/euk.hmm")), + tuple([ id: 'mito12s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/mito.hmm")) + ]) + input[1] = Channel.of('16S_rRNA', '16S_rRNA', '18S_rRNA', '12S_rRNA') + input[2] = [] + input[3] = [] + """ + } + } + } + + when { + workflow { + """ + input[0] = HMMER_HMMFETCH.out.hmm + input[1] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/domain_16s.fna") + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match('16s_out') } + ) + } + } + + // The profile used here doesn't give any significant results, and no output fastas are expected + test("LSU rRNA - hmm/fasta") { + + setup { + run("HMMER_HMMFETCH") { + script "../../../../modules/nf-core/hmmer/hmmfetch/main.nf" + process { + """ + input[0] = Channel.fromList([ + tuple([ id: 'euk28s' ], file("https://raw.githubusercontent.com/tseemann/barrnap/master/db/euk.hmm")) + ]) + input[1] = Channel.of('28S_rRNA') + input[2] = [] + input[3] = [] + """ + } + } + } + + when { + workflow { + """ + input[0] = HMMER_HMMFETCH.out.hmm + input[1] = Channel.fromPath("https://raw.githubusercontent.com/nf-core/test-datasets/phyloplace/testdata/domain_16s.fna") + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out).match('28s_out') } + ) + } + } +} diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap new file mode 100644 index 000000000000..7d59abb358a5 --- /dev/null +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/main.nf.test.snap @@ -0,0 +1,108 @@ +{ + "28s_out": { + "content": [ + { + "0": [ + [ + { + "id": "rank" + }, + "rank.hmmrank.tsv.gz:md5,d07a8a166c4795c2c375435bc30336cd" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", + "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" + ], + "hmmrank": [ + [ + { + "id": "rank" + }, + "rank.hmmrank.tsv.gz:md5,d07a8a166c4795c2c375435bc30336cd" + ] + ], + "seqfastas": [ + + ], + "versions": [ + "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", + "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-12T20:13:12.239271103" + }, + "16s_out": { + "content": [ + { + "0": [ + [ + { + "id": "rank" + }, + "rank.hmmrank.tsv.gz:md5,bc2b70023376221de9efd160d29a4418" + ] + ], + "1": [ + [ + { + "id": "arc16s" + }, + "domain_16s.fnaarc16s.fa.gz:md5,1b0a4343017e4183de898567b34ed079" + ], + [ + { + "id": "bac16s" + }, + "domain_16s.fnabac16s.fa.gz:md5,6a8ed428cfd947c2d6e3a58e9bdf5560" + ] + ], + "2": [ + "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", + "versions.yml:md5,a4108b7257b01a1ccdb51311656cdaca", + "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" + ], + "hmmrank": [ + [ + { + "id": "rank" + }, + "rank.hmmrank.tsv.gz:md5,bc2b70023376221de9efd160d29a4418" + ] + ], + "seqfastas": [ + [ + { + "id": "arc16s" + }, + "domain_16s.fnaarc16s.fa.gz:md5,1b0a4343017e4183de898567b34ed079" + ], + [ + { + "id": "bac16s" + }, + "domain_16s.fnabac16s.fa.gz:md5,6a8ed428cfd947c2d6e3a58e9bdf5560" + ] + ], + "versions": [ + "versions.yml:md5,73a97cda6003d8459e51bf335131fc8f", + "versions.yml:md5,a4108b7257b01a1ccdb51311656cdaca", + "versions.yml:md5,afe27ad9b11150e9c2ff77ff1d63e587" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-12T20:05:14.789661218" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/tags.yml b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/tags.yml new file mode 100644 index 000000000000..b59d6638bfd0 --- /dev/null +++ b/subworkflows/nf-core/fasta_hmmsearch_rank_fastas/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/fasta_hmmsearch_rank_fastas: + - subworkflows/nf-core/fasta_hmmsearch_rank_fastas/** From e743b2dea725bcfc4b76a209981808987332013a Mon Sep 17 00:00:00 2001 From: Phil Ewels Date: Fri, 6 Sep 2024 17:22:24 +0200 Subject: [PATCH 028/486] Pre commit all files (#6604) * GitHub Actions: Always run pre-commit with all files. * First attempt at pre-commit on all files, automatic fixes * Ruff lint: DecryptionTimeout -> DecryptionTimeoutError * Ruff: disable block in template that uses Nextflow variables * Module meta.yml licenses - arrays in strings should not be in strings * License arrays: formatting * Add keywords to module meta files that were too short * Misc module meta.yml fixes * Wrap string licenses as arrays * Type: string instead of value * Fix more meta types * More types, keywords * Apply suggestions from code review Co-authored-by: Mahesh Binzer-Panchal * Boolean flag types --------- Co-authored-by: Mahesh Binzer-Panchal --- .github/scripts/license_message.py | 10 ++++---- .github/workflows/test.yml | 2 +- modules/nf-core/artic/minion/meta.yml | 6 ++--- modules/nf-core/ataqv/mkarv/meta.yml | 2 +- modules/nf-core/authentict/deam2cont/meta.yml | 2 +- modules/nf-core/basicpy/meta.yml | 2 +- modules/nf-core/biohansel/meta.yml | 2 +- modules/nf-core/blat/meta.yml | 2 +- modules/nf-core/canu/meta.yml | 6 ++--- .../cellbender/merge/templates/merge.py | 9 +++---- .../count/templates/cellranger_count.py | 6 ++--- .../multi/templates/cellranger_multi.py | 18 +++++++------- modules/nf-core/cellrangeratac/count/meta.yml | 2 +- .../nf-core/cellrangeratac/mkfastq/meta.yml | 2 +- modules/nf-core/cellrangeratac/mkref/meta.yml | 2 +- modules/nf-core/clippy/meta.yml | 2 +- modules/nf-core/cnvnator/cnvnator/meta.yml | 2 +- modules/nf-core/cnvnator/convert2vcf/meta.yml | 2 +- modules/nf-core/cnvpytor/histogram/meta.yml | 1 + modules/nf-core/cnvpytor/partition/meta.yml | 1 + modules/nf-core/coreograph/meta.yml | 2 +- .../nf-core/crisprcleanr/normalize/meta.yml | 2 +- .../catadditionalfasta/templates/fasta2gtf.py | 4 ++-- .../templates/dumpsoftwareversions.py | 3 ++- .../custom/gtffilter/templates/gtffilter.py | 24 +++++++------------ .../custom/tx2gene/templates/tx2gene.py | 7 +++--- modules/nf-core/cutesv/meta.yml | 1 + modules/nf-core/damageprofiler/meta.yml | 2 +- .../dastool/fastatocontig2bin/meta.yml | 2 +- .../nf-core/dastool/scaffolds2bin/meta.yml | 2 +- modules/nf-core/duphold/meta.yml | 5 +++- .../eigenstratsnpcoverage/meta.yml | 2 +- modules/nf-core/elprep/filter/meta.yml | 2 +- modules/nf-core/elprep/merge/meta.yml | 2 +- modules/nf-core/endorspy/meta.yml | 2 +- modules/nf-core/entrezdirect/esearch/meta.yml | 4 ++-- modules/nf-core/entrezdirect/xtract/meta.yml | 6 ++--- modules/nf-core/epang/split/meta.yml | 2 +- .../expansionhunterdenovo/merge/meta.yml | 2 +- modules/nf-core/fastk/histex/meta.yml | 3 ++- modules/nf-core/fastk/merge/meta.yml | 2 +- modules/nf-core/fcs/fcsgx/meta.yml | 2 +- modules/nf-core/flye/meta.yml | 2 +- modules/nf-core/fq/generate/meta.yml | 4 +++- modules/nf-core/galah/meta.yml | 2 +- modules/nf-core/gangstr/meta.yml | 2 +- modules/nf-core/gatk/indelrealigner/meta.yml | 7 +++++- .../nf-core/gem2/gem2bedmappability/meta.yml | 2 +- modules/nf-core/gem2/gemindexer/meta.yml | 2 +- modules/nf-core/gem2/gemmappability/meta.yml | 2 +- modules/nf-core/genescopefk/meta.yml | 2 +- modules/nf-core/genotyphi/parse/meta.yml | 3 ++- modules/nf-core/gfastats/meta.yml | 2 +- modules/nf-core/gget/gget/meta.yml | 4 ++-- modules/nf-core/glimpse2/concordance/meta.yml | 2 +- modules/nf-core/glnexus/meta.yml | 1 + modules/nf-core/graphtyper/genotype/meta.yml | 2 +- .../gridss/gridssgenerateponbedpe/meta.yml | 2 +- .../gridss/gridsssomaticfilter/meta.yml | 2 +- modules/nf-core/hicexplorer/hicpca/meta.yml | 2 +- modules/nf-core/hlala/preparegraph/meta.yml | 2 +- modules/nf-core/hlala/typing/meta.yml | 2 +- modules/nf-core/hmmer/eslalimask/meta.yml | 12 +++++----- modules/nf-core/hmmer/eslreformat/meta.yml | 2 ++ modules/nf-core/hmmer/hmmalign/meta.yml | 4 ++++ modules/nf-core/ilastik/multicut/meta.yml | 2 +- .../ilastik/pixelclassification/meta.yml | 2 +- modules/nf-core/iphop/download/meta.yml | 2 +- modules/nf-core/iphop/predict/meta.yml | 2 +- modules/nf-core/jupyternotebook/meta.yml | 6 ++--- modules/nf-core/kat/hist/meta.yml | 2 +- .../nf-core/khmer/normalizebymedian/meta.yml | 5 ++-- modules/nf-core/khmer/uniquekmers/meta.yml | 3 +-- modules/nf-core/kmcp/merge/meta.yml | 2 +- modules/nf-core/kofamscan/meta.yml | 2 +- modules/nf-core/maxquant/lfq/meta.yml | 2 ++ modules/nf-core/megan/daa2info/meta.yml | 2 +- modules/nf-core/merquryfk/katcomp/meta.yml | 2 +- modules/nf-core/merquryfk/katgc/meta.yml | 2 +- modules/nf-core/metaeuk/easypredict/meta.yml | 2 +- modules/nf-core/midas/run/meta.yml | 2 +- modules/nf-core/motus/downloaddb/meta.yml | 2 +- modules/nf-core/motus/merge/meta.yml | 2 +- modules/nf-core/msisensor/msi/meta.yml | 5 +++- modules/nf-core/msisensor/scan/meta.yml | 4 +++- modules/nf-core/msisensor2/msi/meta.yml | 6 ++++- modules/nf-core/muscle/meta.yml | 1 + modules/nf-core/mygene/templates/mygene.py | 4 ++-- modules/nf-core/nanomonsv/parse/meta.yml | 2 +- modules/nf-core/nextclade/run/meta.yml | 2 +- modules/nf-core/nucmer/meta.yml | 1 + modules/nf-core/oncocnv/meta.yml | 2 +- modules/nf-core/parabricks/applybqsr/meta.yml | 2 +- modules/nf-core/paraclu/meta.yml | 2 ++ modules/nf-core/paragraph/idxdepth/meta.yml | 2 +- modules/nf-core/paragraph/multigrmpy/meta.yml | 2 +- modules/nf-core/plink/exclude/meta.yml | 1 + modules/nf-core/plink/extract/meta.yml | 2 ++ modules/nf-core/plink/indep/meta.yml | 9 +++---- modules/nf-core/plink/indeppairwise/meta.yml | 9 +++---- modules/nf-core/plink/recode/meta.yml | 5 +++- modules/nf-core/pneumocat/meta.yml | 2 +- modules/nf-core/purecn/coverage/meta.yml | 2 +- modules/nf-core/purecn/run/meta.yml | 2 +- modules/nf-core/purgedups/getseqs/meta.yml | 2 +- modules/nf-core/purgedups/histplot/meta.yml | 2 +- modules/nf-core/rhocall/annotate/meta.yml | 2 +- modules/nf-core/rmarkdownnotebook/meta.yml | 2 +- modules/nf-core/rtgtools/format/meta.yml | 2 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 2 +- .../nf-core/scramble/clusteranalysis/meta.yml | 4 +++- .../nf-core/semibin/singleeasybin/meta.yml | 2 +- .../sequencetools/pileupcaller/meta.yml | 6 ++--- modules/nf-core/sexdeterrmine/meta.yml | 2 +- modules/nf-core/shapeit5/phasecommon/meta.yml | 2 +- modules/nf-core/shapeit5/phaserare/meta.yml | 2 +- modules/nf-core/shapeit5/switch/meta.yml | 2 +- modules/nf-core/shigeifinder/meta.yml | 2 +- modules/nf-core/snakemake/meta.yml | 2 +- modules/nf-core/snapaligner/align/meta.yml | 2 +- modules/nf-core/snippy/core/meta.yml | 2 +- modules/nf-core/somalier/ancestry/meta.yml | 2 +- modules/nf-core/spatyper/meta.yml | 1 + modules/nf-core/srst2/srst2/meta.yml | 2 +- modules/nf-core/stecfinder/meta.yml | 2 +- modules/nf-core/stitch/meta.yml | 2 +- modules/nf-core/survivor/filter/meta.yml | 2 +- modules/nf-core/survivor/simsv/meta.yml | 2 +- modules/nf-core/svaba/meta.yml | 2 +- modules/nf-core/svtk/baftest/meta.yml | 2 +- modules/nf-core/svtk/rdtest2vcf/meta.yml | 2 +- modules/nf-core/svtk/standardize/meta.yml | 2 +- modules/nf-core/svtk/vcf2bed/meta.yml | 2 +- modules/nf-core/topas/gencons/meta.yml | 2 +- modules/nf-core/transdecoder/predict/meta.yml | 10 ++++---- modules/nf-core/truvari/bench/meta.yml | 2 +- modules/nf-core/ultra/align/meta.yml | 2 +- modules/nf-core/ultra/index/meta.yml | 2 +- .../varlociraptor/callvariants/meta.yml | 2 +- .../nf-core/varlociraptor/preprocess/meta.yml | 2 +- modules/nf-core/vcf2maf/meta.yml | 2 +- .../nf-core/verifybamid/verifybamid2/meta.yml | 4 +++- .../nf-core/vrhyme/extractunbinned/meta.yml | 2 +- modules/nf-core/vrhyme/linkbins/meta.yml | 2 +- .../bam_variant_demix_boot_freyja/meta.yml | 4 ++-- .../nf-core/fastq_trim_fastp_fastqc/meta.yml | 2 +- subworkflows/nf-core/initialise/meta.yml | 2 +- .../nf-core/sentieon/license_message.py | 6 ++--- tests/test_versions_yml.py | 5 ++-- 149 files changed, 247 insertions(+), 209 deletions(-) diff --git a/.github/scripts/license_message.py b/.github/scripts/license_message.py index 5447490e11d5..f30af9b4e16a 100644 --- a/.github/scripts/license_message.py +++ b/.github/scripts/license_message.py @@ -12,15 +12,15 @@ import re import secrets import sys +from datetime import datetime as dt from cryptography.hazmat.primitives.ciphers.aead import AESGCM -from datetime import datetime as dt MESSAGE_TIMEOUT = 60 * 60 * 24 # Messages are valid for 1 day NONCE_BYTES = 12 -class DecryptionTimeout(Exception): +class DecryptionTimeoutError(Exception): # Decrypting a message that is too old pass @@ -60,7 +60,7 @@ def decrypt_message(key, ciphertext, timeout=MESSAGE_TIMEOUT): msg_timestamp = int.from_bytes(msg_timestamp, byteorder="big") timestamp = calendar.timegm(dt.now().utctimetuple()) if (timestamp - msg_timestamp) > timeout: - raise DecryptionTimeout("The message has an expired timeout") + raise DecryptionTimeoutError("The message has an expired timeout") return message.decode("utf-8") @@ -82,9 +82,7 @@ def parse_args(argv=None): subparsers = parser.add_subparsers(help="Available sub-commands") - gen_parser = subparsers.add_parser( - "generate_key", help="Generate a random key string" - ) + gen_parser = subparsers.add_parser("generate_key", help="Generate a random key string") gen_parser.set_defaults(func=handle_generate_key) encrypt_parser = subparsers.add_parser("encrypt", help="Encrypt a message") diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 72d7594e7c38..53cdc88e172d 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -36,7 +36,7 @@ jobs: # this so it will only run against changed files. It'll make it much # easier to fix these as they come up rather than everything at once. with: - extra_args: "" + extra_args: "--all-files" prettier: runs-on: ubuntu-latest diff --git a/modules/nf-core/artic/minion/meta.yml b/modules/nf-core/artic/minion/meta.yml index 9092edd3b163..26ff4ad8576f 100644 --- a/modules/nf-core/artic/minion/meta.yml +++ b/modules/nf-core/artic/minion/meta.yml @@ -47,15 +47,15 @@ input: Medaka model file to use (if option --medaka is set) pattern: "*.hdf5" - medaka_model_string: - type: value + type: string description: | Medaka model string to use (if option --medaka is set) pattern: "*" - scheme: - type: value + type: string description: Name of the primer scheme - scheme_version: - type: value + type: string description: Version of the primer scheme output: - meta: diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml index aecbb13d1628..be4ff3ed519e 100644 --- a/modules/nf-core/ataqv/mkarv/meta.yml +++ b/modules/nf-core/ataqv/mkarv/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" tool_dev_url: "https://github.com/ParkerLab/ataqv" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - json: type: file diff --git a/modules/nf-core/authentict/deam2cont/meta.yml b/modules/nf-core/authentict/deam2cont/meta.yml index 097f6079aa40..0c05fbc46337 100644 --- a/modules/nf-core/authentict/deam2cont/meta.yml +++ b/modules/nf-core/authentict/deam2cont/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/StephanePeyregne/AuthentiCT" tool_dev_url: "https://github.com/StephanePeyregne/AuthentiCT" doi: "10.1186/s13059-020-02123-y" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml index 446762008d3c..61e03566697c 100644 --- a/modules/nf-core/basicpy/meta.yml +++ b/modules/nf-core/basicpy/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://basicpy.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/peng-lab/BaSiCPy" doi: 10.1038/ncomms14836 - licence: "MIT License" + license: ["MIT License"] input: - meta: type: map diff --git a/modules/nf-core/biohansel/meta.yml b/modules/nf-core/biohansel/meta.yml index e3ffc82e6799..41aa8b6ee8e2 100644 --- a/modules/nf-core/biohansel/meta.yml +++ b/modules/nf-core/biohansel/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/phac-nml/biohansel" tool_dev_url: "https://github.com/phac-nml/biohansel" doi: "10.1101/2020.01.10.902056" - licence: "['Apache-2.0 license']" + licence: ["Apache-2.0 license"] input: - meta: type: map diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml index f03142d9b366..25deca1aea3a 100644 --- a/modules/nf-core/blat/meta.yml +++ b/modules/nf-core/blat/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://kentinformatics.com/" documentation: "https://kentinformatics.com/documentation" doi: "10.1101/gr.229202" - licence: "['Free for academic, nonprofit and personal use']" + licence: ["Free for academic, nonprofit and personal use"] input: - meta: type: map diff --git a/modules/nf-core/canu/meta.yml b/modules/nf-core/canu/meta.yml index 2feed43fa7a3..afcaa55b9e9c 100644 --- a/modules/nf-core/canu/meta.yml +++ b/modules/nf-core/canu/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://canu.readthedocs.io/en/latest/tutorial.html" tool_dev_url: "https://github.com/marbl/canu" doi: "10.1101/gr.215087.116" - licence: "['GPL v2 and others']" + licence: ["GPL v2 and others"] input: - meta: type: map @@ -24,11 +24,11 @@ input: description: fasta/fastq file pattern: "*.{fasta,fastq}" - mode: - type: value + type: string description: Canu mode depending on the input data (source and error rate) pattern: "-pacbio|-nanopore|-pacbio-hifi" - genomesize: - type: value + type: string description: An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g pattern: "[g|m|k]" output: diff --git a/modules/nf-core/cellbender/merge/templates/merge.py b/modules/nf-core/cellbender/merge/templates/merge.py index 62e4c4f21db5..d8c011d64b92 100644 --- a/modules/nf-core/cellbender/merge/templates/merge.py +++ b/modules/nf-core/cellbender/merge/templates/merge.py @@ -1,10 +1,12 @@ #!/usr/bin/env python3 import platform -import cellbender + import anndata as ad +import cellbender from cellbender.remove_background.downstream import load_anndata_from_input_and_output + def format_yaml_like(data: dict, indent: int = 0) -> str: """Formats a dictionary to a YAML-like string. @@ -27,8 +29,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: adata = ad.read_h5ad("${filtered}") -adata_cellbender = load_anndata_from_input_and_output("${unfiltered}", "${cellbender_h5}", - analyzed_barcodes_only=False) +adata_cellbender = load_anndata_from_input_and_output("${unfiltered}", "${cellbender_h5}", analyzed_barcodes_only=False) adata_cellbender = adata_cellbender[adata.obs_names] @@ -45,7 +46,7 @@ def format_yaml_like(data: dict, indent: int = 0) -> str: "${task.process}": { "python": platform.python_version(), "cellbender": cellbender.__version__, - "anndata": ad.__version__ + "anndata": ad.__version__, } } diff --git a/modules/nf-core/cellranger/count/templates/cellranger_count.py b/modules/nf-core/cellranger/count/templates/cellranger_count.py index 7cd68e279949..55f93b61790d 100644 --- a/modules/nf-core/cellranger/count/templates/cellranger_count.py +++ b/modules/nf-core/cellranger/count/templates/cellranger_count.py @@ -5,11 +5,11 @@ Copyright (c) Gregor Sturm 2023 - MIT License """ -from subprocess import run +import re +import shlex from pathlib import Path +from subprocess import run from textwrap import dedent -import shlex -import re def chunk_iter(seq, size): diff --git a/modules/nf-core/cellranger/multi/templates/cellranger_multi.py b/modules/nf-core/cellranger/multi/templates/cellranger_multi.py index bff70be8f6e5..6f1bf85d6a45 100644 --- a/modules/nf-core/cellranger/multi/templates/cellranger_multi.py +++ b/modules/nf-core/cellranger/multi/templates/cellranger_multi.py @@ -5,11 +5,11 @@ Copyright (c) Felipe Almeida 2024 - MIT License """ -from subprocess import run +import re +import shlex from pathlib import Path +from subprocess import run from textwrap import dedent -import shlex -import re def chunk_iter(seq, size): @@ -96,7 +96,8 @@ def chunk_iter(seq, size): # # generate config file for cellranger multi # -config_txt = f"""${include_gex} +config_txt = ( # noqa + f"""${include_gex} {gex_reference_path} {frna_probeset} ${gex_options_filter_probes} @@ -134,22 +135,23 @@ def chunk_iter(seq, size): {fastq_beam} {fastq_crispr} {fastq_cmo} -""" +""" # noqa +) # # check the extra data that is included # if len("${include_cmo}") > 0: - with open("${cmo_csv_text}", "r") as input_conf: + with open("${cmo_csv_text}") as input_conf: config_txt = config_txt + "\\n${include_cmo}\\n" + input_conf.read() + "\\n" if len("${include_beam}") > 0: - with open("${beam_csv_text}", "r") as input_conf, open("${beam_antigen_csv}", "r") as input_csv: + with open("${beam_csv_text}") as input_conf, open("${beam_antigen_csv}") as input_csv: config_txt = config_txt + "\\n${include_beam}\\n" + input_conf.read() + "\\n" config_txt = config_txt + "[feature]\\n" + input_csv.read() + "\\n" if len("${include_frna}") > 0: - with open("${frna_csv_text}", "r") as input_conf: + with open("${frna_csv_text}") as input_conf: config_txt = config_txt + "\\n${include_frna}\\n" + input_conf.read() + "\\n" # Remove blank lines from config text diff --git a/modules/nf-core/cellrangeratac/count/meta.yml b/modules/nf-core/cellrangeratac/count/meta.yml index dc422ad0eda8..2bdef7f60d98 100644 --- a/modules/nf-core/cellrangeratac/count/meta.yml +++ b/modules/nf-core/cellrangeratac/count/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac - licence: 10x Genomics EULA + licence: ["10x Genomics EULA"] input: - meta: type: map diff --git a/modules/nf-core/cellrangeratac/mkfastq/meta.yml b/modules/nf-core/cellrangeratac/mkfastq/meta.yml index 46b01ba70823..fcee368d1ac4 100644 --- a/modules/nf-core/cellrangeratac/mkfastq/meta.yml +++ b/modules/nf-core/cellrangeratac/mkfastq/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac - licence: 10x Genomics EULA + licence: ["10x Genomics EULA"] input: - bcl: type: file diff --git a/modules/nf-core/cellrangeratac/mkref/meta.yml b/modules/nf-core/cellrangeratac/mkref/meta.yml index e1d755c402ad..4baed308375e 100644 --- a/modules/nf-core/cellrangeratac/mkref/meta.yml +++ b/modules/nf-core/cellrangeratac/mkref/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac - licence: 10x Genomics EULA + licence: ["10x Genomics EULA"] input: - fasta: type: file diff --git a/modules/nf-core/clippy/meta.yml b/modules/nf-core/clippy/meta.yml index 547bf39bc0e6..cdb9f00b8432 100644 --- a/modules/nf-core/clippy/meta.yml +++ b/modules/nf-core/clippy/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/ulelab/clippy" tool_dev_url: "https://github.com/ulelab/clippy" doi: "10.7554/eLife.84034" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 2afbacdea1db..627b76b993de 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/abyzovlab/CNVnator" documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/cnvnator/convert2vcf/meta.yml b/modules/nf-core/cnvnator/convert2vcf/meta.yml index 8e8c80064c8e..b7d269e04801 100644 --- a/modules/nf-core/cnvnator/convert2vcf/meta.yml +++ b/modules/nf-core/cnvnator/convert2vcf/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/abyzovlab/CNVnator" documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/cnvpytor/histogram/meta.yml b/modules/nf-core/cnvpytor/histogram/meta.yml index 69f0c49396d0..e8fcedd47f6b 100644 --- a/modules/nf-core/cnvpytor/histogram/meta.yml +++ b/modules/nf-core/cnvpytor/histogram/meta.yml @@ -3,6 +3,7 @@ description: calculates read depth histograms keywords: - cnv calling - histogram + - read depth tools: - cnvpytor: description: calling CNVs using read depth diff --git a/modules/nf-core/cnvpytor/partition/meta.yml b/modules/nf-core/cnvpytor/partition/meta.yml index 5775fa76de29..c9a04d305166 100644 --- a/modules/nf-core/cnvpytor/partition/meta.yml +++ b/modules/nf-core/cnvpytor/partition/meta.yml @@ -3,6 +3,7 @@ description: partitioning read depth histograms keywords: - cnv calling - partition histograms + - read depth tools: - cnvpytor: description: calling CNVs using read depth diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml index cbff776e19ec..fa61fec708e0 100644 --- a/modules/nf-core/coreograph/meta.yml +++ b/modules/nf-core/coreograph/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html" tool_dev_url: "https://github.com/HMS-IDAC/UNetCoreograph" doi: 10.1038/s41592-021-01308-y - licence: "MIT License" + license: ["MIT License"] input: - image: type: file diff --git a/modules/nf-core/crisprcleanr/normalize/meta.yml b/modules/nf-core/crisprcleanr/normalize/meta.yml index e76a414fa336..f20492fd7449 100644 --- a/modules/nf-core/crisprcleanr/normalize/meta.yml +++ b/modules/nf-core/crisprcleanr/normalize/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf" tool_dev_url: "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0" doi: "10.1186/s12864-018-4989-y" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py index 194a04160202..c7351e568a89 100755 --- a/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py +++ b/modules/nf-core/custom/catadditionalfasta/templates/fasta2gtf.py @@ -2,11 +2,11 @@ # Written by Pranathi Vemuri, later modified by Jonathan Manning and released under the MIT license. -import os import logging +import os import platform -from typing import Iterator, Tuple from itertools import groupby +from typing import Iterator, Tuple def setup_logging() -> logging.Logger: diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py index 9a493ace1d6c..b83b32c4d424 100755 --- a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -3,10 +3,11 @@ """Provide functions to merge multiple versions.yml files.""" -import yaml import platform from textwrap import dedent +import yaml + def _make_versions_html(versions): """Generate a tabular HTML output of all versions for MultiQC.""" diff --git a/modules/nf-core/custom/gtffilter/templates/gtffilter.py b/modules/nf-core/custom/gtffilter/templates/gtffilter.py index 764ec2eff7b0..0ac964e57a92 100644 --- a/modules/nf-core/custom/gtffilter/templates/gtffilter.py +++ b/modules/nf-core/custom/gtffilter/templates/gtffilter.py @@ -22,11 +22,11 @@ # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE # SOFTWARE. +import gzip import logging +import platform import re -import gzip import statistics -import platform from typing import Set # Create a logger @@ -73,23 +73,19 @@ def extract_fasta_seq_names(fasta_name: str) -> Set[str]: def tab_delimited(file: str) -> float: """Check if file is tab-delimited and return median number of tabs.""" - with open(file, "r") as f: + with open(file) as f: data = f.read(102400) return statistics.median(line.count("\\t") for line in data.split("\\n")) -def filter_gtf( - fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool -) -> None: +def filter_gtf(fasta: str, gtf_in: str, filtered_gtf_out: str, skip_transcript_id_check: bool) -> None: """Filter GTF file based on FASTA sequence names.""" if tab_delimited(gtf_in) != 8: raise ValueError("Invalid GTF file: Expected 9 tab-separated columns.") seq_names_in_genome = extract_fasta_seq_names(fasta) logger.info(f"Extracted chromosome sequence names from {fasta}") - logger.debug( - "All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome)) - ) + logger.debug("All sequence IDs from FASTA: " + ", ".join(sorted(seq_names_in_genome))) seq_names_in_gtf = set() try: @@ -103,23 +99,19 @@ def filter_gtf( seq_names_in_gtf.add(seq_name) # Add sequence name to the set if seq_name in seq_names_in_genome: - if skip_transcript_id_check or re.search( - r'transcript_id "([^"]+)"', line - ): + if skip_transcript_id_check or re.search(r'transcript_id "([^"]+)"', line): out.write(line.encode() if is_gz else line) line_count += 1 if line_count == 0: raise ValueError("All GTF lines removed by filters") - except IOError as e: + except OSError as e: logger.error(f"File operation failed: {e}") return logger.debug("All sequence IDs from GTF: " + ", ".join(sorted(seq_names_in_gtf))) - logger.info( - f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}" - ) + logger.info(f"Extracted {line_count} matching sequences from {gtf_in} into {filtered_gtf_out}") filter_gtf("${fasta}", "${gtf}", "${prefix}.${suffix}", False) diff --git a/modules/nf-core/custom/tx2gene/templates/tx2gene.py b/modules/nf-core/custom/tx2gene/templates/tx2gene.py index 8c2e3b1f4328..4d769513ded8 100755 --- a/modules/nf-core/custom/tx2gene/templates/tx2gene.py +++ b/modules/nf-core/custom/tx2gene/templates/tx2gene.py @@ -2,13 +2,12 @@ # Written by Lorena Pantano with subsequent reworking by Jonathan Manning. Released under the MIT license. -import logging -import argparse import glob +import logging import os import platform import re -from collections import Counter, defaultdict, OrderedDict +from collections import Counter, OrderedDict from collections.abc import Set from typing import Dict @@ -52,7 +51,7 @@ def read_top_transcripts(quant_dir: str, file_pattern: str) -> Set[str]: try: # Find the quantification file within the directory quant_file_path = glob.glob(os.path.join(quant_dir, "*", file_pattern))[0] - with open(quant_file_path, "r") as file_handle: + with open(quant_file_path) as file_handle: # Read the file and extract the top 100 transcripts return {line.split()[0] for i, line in enumerate(file_handle) if i > 0 and i <= 100} except IndexError: diff --git a/modules/nf-core/cutesv/meta.yml b/modules/nf-core/cutesv/meta.yml index 9054101f1256..480efafd0996 100644 --- a/modules/nf-core/cutesv/meta.yml +++ b/modules/nf-core/cutesv/meta.yml @@ -3,6 +3,7 @@ description: structural-variant calling with cutesv keywords: - cutesv - structural-variant calling + - sv tools: - cutesv: description: a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. diff --git a/modules/nf-core/damageprofiler/meta.yml b/modules/nf-core/damageprofiler/meta.yml index 8a9307f1a251..7cf1a4a51461 100644 --- a/modules/nf-core/damageprofiler/meta.yml +++ b/modules/nf-core/damageprofiler/meta.yml @@ -47,7 +47,7 @@ output: description: File containing software versions pattern: "versions.yml" - results: - type: dir + type: directory description: DamageProfiler results directory pattern: "*/*" authors: diff --git a/modules/nf-core/dastool/fastatocontig2bin/meta.yml b/modules/nf-core/dastool/fastatocontig2bin/meta.yml index 8ab64d65ee55..bbecfd27ef76 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/meta.yml +++ b/modules/nf-core/dastool/fastatocontig2bin/meta.yml @@ -31,7 +31,7 @@ input: description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - extension: - type: val + type: string description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input. output: - meta: diff --git a/modules/nf-core/dastool/scaffolds2bin/meta.yml b/modules/nf-core/dastool/scaffolds2bin/meta.yml index f439f41f47df..f57c50ab0176 100644 --- a/modules/nf-core/dastool/scaffolds2bin/meta.yml +++ b/modules/nf-core/dastool/scaffolds2bin/meta.yml @@ -31,7 +31,7 @@ input: description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - extension: - type: val + type: string description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input. output: - meta: diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml index c82cf7545ede..934fe8ed69c3 100644 --- a/modules/nf-core/duphold/meta.yml +++ b/modules/nf-core/duphold/meta.yml @@ -2,6 +2,9 @@ name: "duphold" description: SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content. keywords: - sort + - duphold + - structural variation + - depth information tools: - "duphold": description: "SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls." @@ -9,7 +12,7 @@ tools: documentation: "https://github.com/brentp/duphold" tool_dev_url: "https://github.com/brentp/duphold" doi: "10.1093/gigascience/giz040" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml index cf48d5ce2e48..bb4c7f84b7fa 100644 --- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml +++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml @@ -11,7 +11,7 @@ tools: description: "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases." documentation: "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md" tool_dev_url: "https://github.com/TCLamnidis/EigenStratDatabaseTools" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml index 4876c3bce3e5..7f7ebb2a382c 100644 --- a/modules/nf-core/elprep/filter/meta.yml +++ b/modules/nf-core/elprep/filter/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" - licence: "['AGPL v3']" + licence: ["AGPL v3"] input: - meta: type: map diff --git a/modules/nf-core/elprep/merge/meta.yml b/modules/nf-core/elprep/merge/meta.yml index 6dd8ebacfbad..ec7ec6de292e 100644 --- a/modules/nf-core/elprep/merge/meta.yml +++ b/modules/nf-core/elprep/merge/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" - licence: "['AGPL v3']" + licence: ["AGPL v3"] input: - meta: type: map diff --git a/modules/nf-core/endorspy/meta.yml b/modules/nf-core/endorspy/meta.yml index d1a363e01f4b..4578998425b9 100644 --- a/modules/nf-core/endorspy/meta.yml +++ b/modules/nf-core/endorspy/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/aidaanva/endorS.py" tool_dev_url: "https://github.com/aidaanva/endorS.py" doi: "10.7717/peerj.10947" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/entrezdirect/esearch/meta.yml b/modules/nf-core/entrezdirect/esearch/meta.yml index cc00358aa537..e3e2ffedc908 100644 --- a/modules/nf-core/entrezdirect/esearch/meta.yml +++ b/modules/nf-core/entrezdirect/esearch/meta.yml @@ -27,10 +27,10 @@ input: Groovy Map containing sample information e.g. [ id:'test' ] - database: - type: value + type: string description: Value must be a valid Entrez database name. - term: - type: value + type: string description: | Entrez text query. All special characters must be URL encoded. Spaces may be replaced by '+' signs. diff --git a/modules/nf-core/entrezdirect/xtract/meta.yml b/modules/nf-core/entrezdirect/xtract/meta.yml index 3f69f822a2d0..0b3cdd0321c6 100644 --- a/modules/nf-core/entrezdirect/xtract/meta.yml +++ b/modules/nf-core/entrezdirect/xtract/meta.yml @@ -30,13 +30,13 @@ input: type: file description: XML text file containing query results from database. - pattern: - type: value + type: string description: String in xml_input that encloses element to search. - element: - type: value + type: string description: Space-delimited strings that will be converted to columns. - sep: - type: value + type: string description: Separator/delimiter between columns (for instance "," or "\t"). output: - meta: diff --git a/modules/nf-core/epang/split/meta.yml b/modules/nf-core/epang/split/meta.yml index 5af4234f0ae1..21cb81ae217c 100644 --- a/modules/nf-core/epang/split/meta.yml +++ b/modules/nf-core/epang/split/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/Pbdas/epa-ng/wiki/Full-Stack-Example" tool_dev_url: "https://github.com/Pbdas/epa-ng" doi: "10.1093/sysbio/syy054" - licence: "['GNU Affero General Public License v3.0']" + licence: ["GNU Affero General Public License v3.0"] input: # Only when we have meta - meta: diff --git a/modules/nf-core/expansionhunterdenovo/merge/meta.yml b/modules/nf-core/expansionhunterdenovo/merge/meta.yml index a0eb8e2d6dfb..a7aa59fb4059 100644 --- a/modules/nf-core/expansionhunterdenovo/merge/meta.yml +++ b/modules/nf-core/expansionhunterdenovo/merge/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/Illumina/ExpansionHunterDenovo" documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md" tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo" - licence: "['Apache License 2.0']" + licence: ["Apache License 2.0"] input: - meta: type: map diff --git a/modules/nf-core/fastk/histex/meta.yml b/modules/nf-core/fastk/histex/meta.yml index e7497ffa81bc..6fcd6bd25729 100644 --- a/modules/nf-core/fastk/histex/meta.yml +++ b/modules/nf-core/fastk/histex/meta.yml @@ -3,12 +3,13 @@ description: A fast K-mer counter for high-fidelity shotgun datasets keywords: - k-mer - histogram + - fastk tools: - "fastk": description: "A fast K-mer counter for high-fidelity shotgun datasets" homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" - licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" + license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] input: - meta: type: map diff --git a/modules/nf-core/fastk/merge/meta.yml b/modules/nf-core/fastk/merge/meta.yml index 60bfa39718ca..2a3c72429838 100644 --- a/modules/nf-core/fastk/merge/meta.yml +++ b/modules/nf-core/fastk/merge/meta.yml @@ -10,7 +10,7 @@ tools: description: "A fast K-mer counter for high-fidelity shotgun datasets" homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" - licence: "https://github.com/thegenemyers/FASTK/blob/master/LICENSE" + license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] input: - meta: type: map diff --git a/modules/nf-core/fcs/fcsgx/meta.yml b/modules/nf-core/fcs/fcsgx/meta.yml index 2de17874024b..0537d97c90d4 100644 --- a/modules/nf-core/fcs/fcsgx/meta.yml +++ b/modules/nf-core/fcs/fcsgx/meta.yml @@ -17,7 +17,7 @@ tools: homepage: "https://www.ncbi.nlm.nih.gov/data-hub/cgr/data-quality-tools/" documentation: "https://github.com/ncbi/fcs/wiki/FCS-GX" tool_dev_url: "https://github.com/ncbi/fcs" - licence: "United States Government Work" + license: ["United States Government Work"] input: - meta: type: map diff --git a/modules/nf-core/flye/meta.yml b/modules/nf-core/flye/meta.yml index 5c3c816d7b9b..4b030d9ec528 100644 --- a/modules/nf-core/flye/meta.yml +++ b/modules/nf-core/flye/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md" tool_dev_url: "https://github.com/fenderglass/Flye" doi: "10.1038/s41592-020-00971-x" - licence: "['BSD-3-clause']" + licence: ["BSD-3-clause"] input: - meta: type: map diff --git a/modules/nf-core/fq/generate/meta.yml b/modules/nf-core/fq/generate/meta.yml index 644d51a74e3c..e8fcfce7294a 100644 --- a/modules/nf-core/fq/generate/meta.yml +++ b/modules/nf-core/fq/generate/meta.yml @@ -4,13 +4,15 @@ description: | keywords: - generate - fastq + - random + - sequence tools: - "fq": description: "fq is a library to generate and validate FASTQ file pairs." homepage: "https://github.com/stjude-rust-labs/fq" documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/galah/meta.yml b/modules/nf-core/galah/meta.yml index 95b1cd8d31e1..1a14d8a9f2b9 100644 --- a/modules/nf-core/galah/meta.yml +++ b/modules/nf-core/galah/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/wwood/galah" tool_dev_url: "https://github.com/wwood/galah" doi: "10.1111/NODOI" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/gangstr/meta.yml b/modules/nf-core/gangstr/meta.yml index efb5012ec4fa..963395337291 100644 --- a/modules/nf-core/gangstr/meta.yml +++ b/modules/nf-core/gangstr/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/gymreklab/GangSTR" tool_dev_url: "https://github.com/gymreklab/GangSTR" doi: "10.1093/nar/gkz501" - licence: "['GPL v3-or-later']" + licence: ["GPL v3-or-later"] input: - meta: type: map diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml index 15d9aec41c76..31806e175f00 100644 --- a/modules/nf-core/gatk/indelrealigner/meta.yml +++ b/modules/nf-core/gatk/indelrealigner/meta.yml @@ -11,7 +11,12 @@ tools: description: "The full Genome Analysis Toolkit (GATK) framework, license restricted." homepage: "https://gatk.broadinstitute.org/hc/en-us" documentation: "https://github.com/broadinstitute/gatk-docs" - licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']" + licence: + [ + "https://software.broadinstitute.org/gatk/download/licensing", + "BSD", + "https://www.broadinstitute.org/gatk/about/#licensing", + ] input: - meta: type: map diff --git a/modules/nf-core/gem2/gem2bedmappability/meta.yml b/modules/nf-core/gem2/gem2bedmappability/meta.yml index 8785ff0fd21e..a625c9e87ad9 100644 --- a/modules/nf-core/gem2/gem2bedmappability/meta.yml +++ b/modules/nf-core/gem2/gem2bedmappability/meta.yml @@ -12,7 +12,7 @@ tools: description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise) - licence: "['Custom']" + licence: ["Custom"] input: - meta: type: map diff --git a/modules/nf-core/gem2/gemindexer/meta.yml b/modules/nf-core/gem2/gemindexer/meta.yml index 2e43c6e8d54d..00152b05649d 100644 --- a/modules/nf-core/gem2/gemindexer/meta.yml +++ b/modules/nf-core/gem2/gemindexer/meta.yml @@ -11,7 +11,7 @@ tools: - "gem2": description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" - licence: "['Custom']" + licence: ["Custom"] input: - meta: type: map diff --git a/modules/nf-core/gem2/gemmappability/meta.yml b/modules/nf-core/gem2/gemmappability/meta.yml index 07d9f14d56a1..8157a85a6093 100644 --- a/modules/nf-core/gem2/gemmappability/meta.yml +++ b/modules/nf-core/gem2/gemmappability/meta.yml @@ -11,7 +11,7 @@ tools: - "gem2": description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" - licence: "['Custom']" + licence: ["Custom"] input: - meta: type: map diff --git a/modules/nf-core/genescopefk/meta.yml b/modules/nf-core/genescopefk/meta.yml index bc9b2cb83be2..b54cfbcd9765 100644 --- a/modules/nf-core/genescopefk/meta.yml +++ b/modules/nf-core/genescopefk/meta.yml @@ -9,7 +9,7 @@ tools: description: "A derivative of GenomeScope2.0 modified to work with FastK" homepage: "https://github.com/thegenemyers/GENESCOPE.FK" tool_dev_url: "https://github.com/thegenemyers/GENESCOPE.FK" - licence: "https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE" + licence: ["https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE"] input: - meta: type: map diff --git a/modules/nf-core/genotyphi/parse/meta.yml b/modules/nf-core/genotyphi/parse/meta.yml index d237904ecf48..8648761e0fd3 100644 --- a/modules/nf-core/genotyphi/parse/meta.yml +++ b/modules/nf-core/genotyphi/parse/meta.yml @@ -3,13 +3,14 @@ description: Genotype Salmonella Typhi from Mykrobe results keywords: - genotype - Salmonella Typhi + - Mykrobe tools: - "genotyphi": description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)" homepage: "https://github.com/katholt/genotyphi" documentation: "https://github.com/katholt/genotyphi" tool_dev_url: "https://github.com/katholt/genotyphi" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml index d0e97a8f3191..aaaf47caeb86 100644 --- a/modules/nf-core/gfastats/meta.yml +++ b/modules/nf-core/gfastats/meta.yml @@ -16,7 +16,7 @@ tools: documentation: "https://github.com/vgl-hub/gfastats/tree/main/instructions" tool_dev_url: "https://github.com/vgl-hub/gfastats" doi: "10.1093/bioinformatics/btac460" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/gget/gget/meta.yml b/modules/nf-core/gget/gget/meta.yml index 08aa182939b6..103fd70653f2 100644 --- a/modules/nf-core/gget/gget/meta.yml +++ b/modules/nf-core/gget/gget/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://pachterlab.github.io/gget/" tool_dev_url: "https://github.com/pachterlab/gget" doi: "10.1093/bioinformatics/btac836" - licence: "['BSD-2-clause']" + licence: ["BSD-2-clause"] input: - meta: type: map @@ -21,7 +21,7 @@ input: Groovy Map containing sample information e.g. [ id:'test' ] - files: - type: files + type: file description: | Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle. output: diff --git a/modules/nf-core/glimpse2/concordance/meta.yml b/modules/nf-core/glimpse2/concordance/meta.yml index 7c82c3504809..7d145d2b4b13 100644 --- a/modules/nf-core/glimpse2/concordance/meta.yml +++ b/modules/nf-core/glimpse2/concordance/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index 4944ebde5eee..416829cbf630 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -3,6 +3,7 @@ description: merge gVCF files and perform joint variant calling keywords: - merge - gvcf + - joint-variant-calling tools: - glnexus: description: scalable gVCF merging and joint variant calling for population sequencing projects. diff --git a/modules/nf-core/graphtyper/genotype/meta.yml b/modules/nf-core/graphtyper/genotype/meta.yml index 927b0c2869f4..b440dce4928b 100644 --- a/modules/nf-core/graphtyper/genotype/meta.yml +++ b/modules/nf-core/graphtyper/genotype/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml index c6b3e1b59399..852e5ea402b5 100644 --- a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml +++ b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation" tool_dev_url: "https://github.com/PapenfussLab/gridss" doi: "10.1186/s13059-021-02423-x" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: diff --git a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml index 2b7fc37b0c07..3aea9b8cdd1d 100644 --- a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml +++ b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/PapenfussLab/gridss/wiki/GRIDSS-Documentation" tool_dev_url: "https://github.com/PapenfussLab/gridss" doi: "10.1186/s13059-021-02423-x" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: diff --git a/modules/nf-core/hicexplorer/hicpca/meta.yml b/modules/nf-core/hicexplorer/hicpca/meta.yml index 380f882729a8..742b65148513 100644 --- a/modules/nf-core/hicexplorer/hicpca/meta.yml +++ b/modules/nf-core/hicexplorer/hicpca/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://hicexplorer.readthedocs.io" tool_dev_url: "https://github.com/deeptools/HiCExplorer" doi: "10.1038/s41467-017-02525-w" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml index c08e81778271..a2a2fbf9dad9 100644 --- a/modules/nf-core/hlala/preparegraph/meta.yml +++ b/modules/nf-core/hlala/preparegraph/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" - licence: "['GPL']" + licence: ["GPL"] input: - graph: type: directory diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml index ede373be5048..20c0844aa1d2 100644 --- a/modules/nf-core/hlala/typing/meta.yml +++ b/modules/nf-core/hlala/typing/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/DiltheyLab/HLA-LA#running-hlala" tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" - licence: "['GPL']" + licence: ["GPL"] input: - meta: type: map diff --git a/modules/nf-core/hmmer/eslalimask/meta.yml b/modules/nf-core/hmmer/eslalimask/meta.yml index c4a9a4ccf33d..4a3d84e1bd73 100644 --- a/modules/nf-core/hmmer/eslalimask/meta.yml +++ b/modules/nf-core/hmmer/eslalimask/meta.yml @@ -22,22 +22,22 @@ input: description: multiple sequence alignment, Stockholm or other formats pattern: "*" - fmask_rf: - type: val + type: boolean description: Flag to output optional file with final mask of non-gap RF len - fmask_all: - type: val + type: boolean description: Flag to output optional file with final mask of full aln len - gmask_rf: - type: val + type: boolean description: Flag to output optional file gap-based 0/1 mask of non-gap RF len - gmask_all: - type: val + type: boolean description: Flag to output optional file gap-based 0/1 mask of full aln len - pmask_rf: - type: val + type: boolean description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len - pmask_all: - type: val + type: boolean description: Flag to output optional file with PP-based 0/1 mask of full aln len - maskfile: type: file diff --git a/modules/nf-core/hmmer/eslreformat/meta.yml b/modules/nf-core/hmmer/eslreformat/meta.yml index 7e530d59af43..009e35873a79 100644 --- a/modules/nf-core/hmmer/eslreformat/meta.yml +++ b/modules/nf-core/hmmer/eslreformat/meta.yml @@ -2,6 +2,8 @@ name: "hmmer_eslreformat" description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values. keywords: - sort + - hmmer + - reformat tools: - "hmmer": description: "Biosequence analysis using profile hidden Markov models" diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml index c1ac8f408211..df6a7b3c4fea 100644 --- a/modules/nf-core/hmmer/hmmalign/meta.yml +++ b/modules/nf-core/hmmer/hmmalign/meta.yml @@ -2,6 +2,10 @@ name: hmmer_hmmalign description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile keywords: - alignment + - HMMER + - profile + - amino acid + - nucleotide tools: - hmmer: description: Biosequence analysis using profile hidden Markov models diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml index cb2af37b358b..36ac9e90b0ec 100644 --- a/modules/nf-core/ilastik/multicut/meta.yml +++ b/modules/nf-core/ilastik/multicut/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" - licence: "GPL3" + license: ["GPL3"] input: - meta: type: map diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml index 6a9e8babcc74..ad100d9b827d 100644 --- a/modules/nf-core/ilastik/pixelclassification/meta.yml +++ b/modules/nf-core/ilastik/pixelclassification/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" - licence: "GPL3" + licence: ["GPL3"] input: - meta: type: map diff --git a/modules/nf-core/iphop/download/meta.yml b/modules/nf-core/iphop/download/meta.yml index d5184930dbc1..b3a31992e7b2 100644 --- a/modules/nf-core/iphop/download/meta.yml +++ b/modules/nf-core/iphop/download/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://bitbucket.org/srouxjgi/iphop/src/main/ tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" - licence: "['Modified GPL v3']" + licence: ["Modified GPL v3"] output: - iphop_db: type: directory diff --git a/modules/nf-core/iphop/predict/meta.yml b/modules/nf-core/iphop/predict/meta.yml index 003343555b3e..ce267dd13be6 100644 --- a/modules/nf-core/iphop/predict/meta.yml +++ b/modules/nf-core/iphop/predict/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://bitbucket.org/srouxjgi/iphop/src/main/ tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" - licence: "['Modified GPL v3']" + licence: ["Modified GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/jupyternotebook/meta.yml b/modules/nf-core/jupyternotebook/meta.yml index 216645d3db4d..162171b62d4d 100644 --- a/modules/nf-core/jupyternotebook/meta.yml +++ b/modules/nf-core/jupyternotebook/meta.yml @@ -15,19 +15,19 @@ tools: homepage: https://github.com/mwouts/jupytext/ documentation: https://jupyter.org/documentation tool_dev_url: https://github.com/mwouts/jupytext/ - licence: "MIT" + license: ["MIT"] - papermill: description: Parameterize, execute, and analyze notebooks homepage: https://github.com/nteract/papermill documentation: http://papermill.readthedocs.io/en/latest/ tool_dev_url: https://github.com/nteract/papermill - licence: "BSD 3-clause" + license: ["BSD 3-clause"] - nbconvert: description: Parameterize, execute, and analyze notebooks homepage: https://nbconvert.readthedocs.io/en/latest/ documentation: https://nbconvert.readthedocs.io/en/latest/ tool_dev_url: https://github.com/jupyter/nbconvert - licence: "BSD 3-clause" + license: ["BSD 3-clause"] input: - meta: type: map diff --git a/modules/nf-core/kat/hist/meta.yml b/modules/nf-core/kat/hist/meta.yml index 2d6d783d6c90..c933c9582c3d 100644 --- a/modules/nf-core/kat/hist/meta.yml +++ b/modules/nf-core/kat/hist/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://kat.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/TGAC/KAT doi: 10.1093/bioinformatics/btw663 - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/khmer/normalizebymedian/meta.yml b/modules/nf-core/khmer/normalizebymedian/meta.yml index 568503a3c785..847d2b84d4d3 100644 --- a/modules/nf-core/khmer/normalizebymedian/meta.yml +++ b/modules/nf-core/khmer/normalizebymedian/meta.yml @@ -3,6 +3,7 @@ description: Module that calls normalize-by-median.py from khmer. The module can keywords: - digital normalization - khmer + - k-mer counting tools: - khmer: description: khmer k-mer counting library @@ -13,11 +14,11 @@ tools: licence: ["BSD License"] input: - pe_reads: - type: files + type: file description: Paired-end interleaved fastq files pattern: "*.{fq,fastq}.gz" - se_reads: - type: files + type: file description: Single-end fastq files pattern: "*.{fq,fastq}.gz" - name: diff --git a/modules/nf-core/khmer/uniquekmers/meta.yml b/modules/nf-core/khmer/uniquekmers/meta.yml index bae4e6440513..f875bb7177d0 100644 --- a/modules/nf-core/khmer/uniquekmers/meta.yml +++ b/modules/nf-core/khmer/uniquekmers/meta.yml @@ -18,9 +18,8 @@ input: description: fasta file pattern: "*.{fa,fasta}" - kmer_size: - type: value + type: integer description: k-mer size to use - pattern: "[0-9]+" output: - report: type: file diff --git a/modules/nf-core/kmcp/merge/meta.yml b/modules/nf-core/kmcp/merge/meta.yml index a586a21cb740..3a367fa42e99 100644 --- a/modules/nf-core/kmcp/merge/meta.yml +++ b/modules/nf-core/kmcp/merge/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" - licence: "['MIT']" + license: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/kofamscan/meta.yml b/modules/nf-core/kofamscan/meta.yml index 7876e3ace0ec..06f2872a4e8d 100644 --- a/modules/nf-core/kofamscan/meta.yml +++ b/modules/nf-core/kofamscan/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/takaram/kofam_scan" tool_dev_url: "https://github.com/takaram/kofam_scan" doi: "10.1093/bioinformatics/btz859" - licence: "['MIT License']" + licence: ["MIT License"] input: - meta: type: map diff --git a/modules/nf-core/maxquant/lfq/meta.yml b/modules/nf-core/maxquant/lfq/meta.yml index 200e103693b4..634f70eafd65 100644 --- a/modules/nf-core/maxquant/lfq/meta.yml +++ b/modules/nf-core/maxquant/lfq/meta.yml @@ -2,6 +2,8 @@ name: maxquant_lfq description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" keywords: - sort + - proteomics + - mass-spectroscopy tools: - maxquant: description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted. diff --git a/modules/nf-core/megan/daa2info/meta.yml b/modules/nf-core/megan/daa2info/meta.yml index 7530f7da4d10..5b1c7e366389 100644 --- a/modules/nf-core/megan/daa2info/meta.yml +++ b/modules/nf-core/megan/daa2info/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html" tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" - licence: "['GPL >=3']" + licence: ["GPL >=3"] input: - meta: type: map diff --git a/modules/nf-core/merquryfk/katcomp/meta.yml b/modules/nf-core/merquryfk/katcomp/meta.yml index ee6650cb48dc..15de42949747 100644 --- a/modules/nf-core/merquryfk/katcomp/meta.yml +++ b/modules/nf-core/merquryfk/katcomp/meta.yml @@ -9,7 +9,7 @@ tools: description: "FastK based version of Merqury" homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" - licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE" + license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] input: - meta: type: map diff --git a/modules/nf-core/merquryfk/katgc/meta.yml b/modules/nf-core/merquryfk/katgc/meta.yml index f39322b1b31e..f3689b0370c9 100644 --- a/modules/nf-core/merquryfk/katgc/meta.yml +++ b/modules/nf-core/merquryfk/katgc/meta.yml @@ -10,7 +10,7 @@ tools: description: "FastK based version of Merqury" homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" - licence: "https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE" + license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] input: - meta: type: map diff --git a/modules/nf-core/metaeuk/easypredict/meta.yml b/modules/nf-core/metaeuk/easypredict/meta.yml index 0bea1ccb5de9..3943926ca3de 100644 --- a/modules/nf-core/metaeuk/easypredict/meta.yml +++ b/modules/nf-core/metaeuk/easypredict/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/soedinglab/metaeuk tool_dev_url: https://github.com/soedinglab/metaeuk doi: "10.1186/s40168-020-00808-x" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/midas/run/meta.yml b/modules/nf-core/midas/run/meta.yml index fae9fd155b68..e41505ebd1c0 100644 --- a/modules/nf-core/midas/run/meta.yml +++ b/modules/nf-core/midas/run/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/snayfach/MIDAS" tool_dev_url: "https://github.com/snayfach/MIDAS" doi: "10.1101/gr.201863.115" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/motus/downloaddb/meta.yml b/modules/nf-core/motus/downloaddb/meta.yml index 63df66fe0593..6cf509e97eec 100644 --- a/modules/nf-core/motus/downloaddb/meta.yml +++ b/modules/nf-core/motus/downloaddb/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/motu-tool/mOTUs/wiki" tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - motus_downloaddb: type: directory diff --git a/modules/nf-core/motus/merge/meta.yml b/modules/nf-core/motus/merge/meta.yml index e8dca6f812aa..0d7af231a9b3 100644 --- a/modules/nf-core/motus/merge/meta.yml +++ b/modules/nf-core/motus/merge/meta.yml @@ -15,7 +15,7 @@ tools: documentation: "https://github.com/motu-tool/mOTUs/wiki" tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - input: type: file diff --git a/modules/nf-core/msisensor/msi/meta.yml b/modules/nf-core/msisensor/msi/meta.yml index bec1ee56e6f0..3d4620b4c2f6 100644 --- a/modules/nf-core/msisensor/msi/meta.yml +++ b/modules/nf-core/msisensor/msi/meta.yml @@ -1,7 +1,10 @@ name: msisensor_msi description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data keywords: - - homoploymer,microsatellite + - homoploymer + - microsatellite + - MSI + - instability tools: - msisensor: description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. diff --git a/modules/nf-core/msisensor/scan/meta.yml b/modules/nf-core/msisensor/scan/meta.yml index 26836b9dc853..2b786cecd850 100644 --- a/modules/nf-core/msisensor/scan/meta.yml +++ b/modules/nf-core/msisensor/scan/meta.yml @@ -1,7 +1,9 @@ name: msisensor_scan description: Scan a reference genome to get microsatellite & homopolymer information keywords: - - homoploymer,microsatellite + - homoploymer + - microsatellite + - MSI tools: - msisensor: description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. diff --git a/modules/nf-core/msisensor2/msi/meta.yml b/modules/nf-core/msisensor2/msi/meta.yml index b930de3f47bc..497225168892 100644 --- a/modules/nf-core/msisensor2/msi/meta.yml +++ b/modules/nf-core/msisensor2/msi/meta.yml @@ -2,13 +2,17 @@ name: "msisensor2_msi" description: msisensor2 detection of MSI regions. keywords: - msi + - microsatellite + - microsatellite instability + - tumor + - cfDNA tools: - "msisensor2": description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data." homepage: "https://github.com/niu-lab/msisensor2" documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md" tool_dev_url: "https://github.com/niu-lab/msisensor2" - licence: "GPL-3.0" + license: ["GPL-3.0"] input: - meta: type: map diff --git a/modules/nf-core/muscle/meta.yml b/modules/nf-core/muscle/meta.yml index 37c898f3f552..c03941bd0504 100644 --- a/modules/nf-core/muscle/meta.yml +++ b/modules/nf-core/muscle/meta.yml @@ -3,6 +3,7 @@ description: MUSCLE is a program for creating multiple alignments of amino acid keywords: - msa - multiple sequence alignment + - phylogeny tools: - muscle: description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput diff --git a/modules/nf-core/mygene/templates/mygene.py b/modules/nf-core/mygene/templates/mygene.py index 2717c467e8c7..83bf21756426 100644 --- a/modules/nf-core/mygene/templates/mygene.py +++ b/modules/nf-core/mygene/templates/mygene.py @@ -1,8 +1,8 @@ #!/usr/bin/env python3 import argparse -import mygene import shlex +import mygene """ This python script uses the mygene module to query the MyGene.info API and @@ -311,7 +311,7 @@ def load_list(filename: str, columname: str) -> list: sep = "," else: raise ValueError("The input file extension should be either tsv or csv.") - with open(filename, "r") as f: + with open(filename) as f: idx = f.readline().strip().split(sep).index(columname) return [line.strip().split(sep)[idx] for line in f] diff --git a/modules/nf-core/nanomonsv/parse/meta.yml b/modules/nf-core/nanomonsv/parse/meta.yml index 3c8d10987313..db42b42adbd3 100644 --- a/modules/nf-core/nanomonsv/parse/meta.yml +++ b/modules/nf-core/nanomonsv/parse/meta.yml @@ -20,7 +20,7 @@ tools: documentation: https://github.com/friend1ws/nanomonsv#commands tool_dev_url: https://github.com/friend1ws/nanomonsv doi: "10.1101/2020.07.22.214262 " - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/nextclade/run/meta.yml b/modules/nf-core/nextclade/run/meta.yml index ceebfe20e577..22fb2450f281 100644 --- a/modules/nf-core/nextclade/run/meta.yml +++ b/modules/nf-core/nextclade/run/meta.yml @@ -18,7 +18,7 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - dataset: - type: path + type: file description: Path containing the dataset files obtained by running nextclade dataset get pattern: "*" - fasta: diff --git a/modules/nf-core/nucmer/meta.yml b/modules/nf-core/nucmer/meta.yml index 52d876ae6ba7..8cc8f1639f05 100644 --- a/modules/nf-core/nucmer/meta.yml +++ b/modules/nf-core/nucmer/meta.yml @@ -3,6 +3,7 @@ description: NUCmer is a pipeline for the alignment of multiple closely related keywords: - align - nucleotide + - sequence tools: - nucmer: description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. diff --git a/modules/nf-core/oncocnv/meta.yml b/modules/nf-core/oncocnv/meta.yml index 48d3e11b5009..4f1bde83f6f3 100644 --- a/modules/nf-core/oncocnv/meta.yml +++ b/modules/nf-core/oncocnv/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/BoevaLab/ONCOCNV/blob/master/README.md" tool_dev_url: "https://github.com/BoevaLab/ONCOCNV/" doi: "10.1093/bioinformatics/btu436" - licence: "GPL-3.0-or-later" + license: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml index 5fd02c0b3b7a..d76ee61a066d 100644 --- a/modules/nf-core/parabricks/applybqsr/meta.yml +++ b/modules/nf-core/parabricks/applybqsr/meta.yml @@ -10,7 +10,7 @@ tools: description: "NVIDIA Clara Parabricks GPU-accelerated genomics tools" homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/" - licence: "custom" + licence: ["https://docs.nvidia.com/clara/parabricks/3.8.0/gettingstarted.html#licensing"] input: - meta: type: map diff --git a/modules/nf-core/paraclu/meta.yml b/modules/nf-core/paraclu/meta.yml index 01ea897d47e6..fc61d788dbb8 100644 --- a/modules/nf-core/paraclu/meta.yml +++ b/modules/nf-core/paraclu/meta.yml @@ -2,6 +2,8 @@ name: paraclu description: Paraclu finds clusters in data attached to sequences. keywords: - sort + - cluster + - bed tools: - paraclu: description: Paraclu finds clusters in data attached to sequences. diff --git a/modules/nf-core/paragraph/idxdepth/meta.yml b/modules/nf-core/paragraph/idxdepth/meta.yml index 042e5f8a944e..19e90df24b8e 100644 --- a/modules/nf-core/paragraph/idxdepth/meta.yml +++ b/modules/nf-core/paragraph/idxdepth/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/Illumina/paragraph" tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" - licence: "['Apache License 2.0']" + licence: ["Apache License 2.0"] input: - meta: type: map diff --git a/modules/nf-core/paragraph/multigrmpy/meta.yml b/modules/nf-core/paragraph/multigrmpy/meta.yml index 84b435b75d49..56075bbf1da7 100644 --- a/modules/nf-core/paragraph/multigrmpy/meta.yml +++ b/modules/nf-core/paragraph/multigrmpy/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/Illumina/paragraph" tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" - licence: "['Apache License 2.0']" + licence: ["Apache License 2.0"] input: - meta: type: map diff --git a/modules/nf-core/plink/exclude/meta.yml b/modules/nf-core/plink/exclude/meta.yml index a04c12d6b76d..5f861ce3b0b3 100644 --- a/modules/nf-core/plink/exclude/meta.yml +++ b/modules/nf-core/plink/exclude/meta.yml @@ -3,6 +3,7 @@ description: Exclude variant identifiers from plink bfiles keywords: - exclude - plink + - variant identifiers tools: - plink: description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. diff --git a/modules/nf-core/plink/extract/meta.yml b/modules/nf-core/plink/extract/meta.yml index b4cd092640dd..859ea49e52c1 100644 --- a/modules/nf-core/plink/extract/meta.yml +++ b/modules/nf-core/plink/extract/meta.yml @@ -3,6 +3,8 @@ description: Subset plink bfiles with a text file of variant identifiers keywords: - extract - plink + - subset + - bfiles tools: - plink: description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. diff --git a/modules/nf-core/plink/indep/meta.yml b/modules/nf-core/plink/indep/meta.yml index 258b31198210..9d6b7500ec93 100644 --- a/modules/nf-core/plink/indep/meta.yml +++ b/modules/nf-core/plink/indep/meta.yml @@ -32,17 +32,14 @@ input: description: PLINK sample information file pattern: "*.{fam}" - window_size: - type: value + type: string description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - pattern: "*.{}" - variant_count: - type: value + type: string description: Variant count to shift the window at the end of each step. - pattern: "*.{}" - variance_inflation_factor: - type: value + type: string description: Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed. - pattern: "*.{}" output: - meta: type: map diff --git a/modules/nf-core/plink/indeppairwise/meta.yml b/modules/nf-core/plink/indeppairwise/meta.yml index c77a79bc2485..470ce24880ee 100644 --- a/modules/nf-core/plink/indeppairwise/meta.yml +++ b/modules/nf-core/plink/indeppairwise/meta.yml @@ -32,17 +32,14 @@ input: description: PLINK sample information file pattern: "*.{fam}" - window_size: - type: number + type: string description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - pattern: "*.{}" - variant_count: - type: number + type: string description: Variant count to shift the window at the end of each step. - pattern: "*.{}" - r2_threshold: - type: number + type: string description: Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain - pattern: "*.{}" output: - meta: type: map diff --git a/modules/nf-core/plink/recode/meta.yml b/modules/nf-core/plink/recode/meta.yml index 057878b4c47f..7f2bd053f52b 100644 --- a/modules/nf-core/plink/recode/meta.yml +++ b/modules/nf-core/plink/recode/meta.yml @@ -2,13 +2,16 @@ name: "plink_recode" description: Recodes plink bfiles into a new text fileset applying different modifiers keywords: - recode + - bfiles + - plink + - whole genome association tools: - "plink": description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" - licence: "['GPL']" + licence: ["GPL"] input: - meta: type: map diff --git a/modules/nf-core/pneumocat/meta.yml b/modules/nf-core/pneumocat/meta.yml index 0a7124639cde..8015826add92 100644 --- a/modules/nf-core/pneumocat/meta.yml +++ b/modules/nf-core/pneumocat/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/ukhsa-collaboration/PneumoCaT" tool_dev_url: "https://github.com/ukhsa-collaboration/PneumoCaT" doi: "10.7717/peerj.2477" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/purecn/coverage/meta.yml b/modules/nf-core/purecn/coverage/meta.yml index c18f08f9fbad..e88bb21a1480 100644 --- a/modules/nf-core/purecn/coverage/meta.yml +++ b/modules/nf-core/purecn/coverage/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" - licence: "Artistic-2.0" + license: ["Artistic-2.0"] args_id: "$args" input: - meta: diff --git a/modules/nf-core/purecn/run/meta.yml b/modules/nf-core/purecn/run/meta.yml index afbe95325234..f70f780e8694 100644 --- a/modules/nf-core/purecn/run/meta.yml +++ b/modules/nf-core/purecn/run/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" - licence: "Artistic-2.0" + license: ["Artistic-2.0"] args_id: "$args" input: - meta: diff --git a/modules/nf-core/purgedups/getseqs/meta.yml b/modules/nf-core/purgedups/getseqs/meta.yml index e581b8a470c3..2b759ce4f022 100644 --- a/modules/nf-core/purgedups/getseqs/meta.yml +++ b/modules/nf-core/purgedups/getseqs/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/purgedups/histplot/meta.yml b/modules/nf-core/purgedups/histplot/meta.yml index bfd5a0d4a732..47596104f217 100644 --- a/modules/nf-core/purgedups/histplot/meta.yml +++ b/modules/nf-core/purgedups/histplot/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml index ecc8e1e43a92..09a64d2591ff 100644 --- a/modules/nf-core/rhocall/annotate/meta.yml +++ b/modules/nf-core/rhocall/annotate/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://github.com/dnil/rhocall" documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml index f84f068216a8..379690f7528a 100644 --- a/modules/nf-core/rmarkdownnotebook/meta.yml +++ b/modules/nf-core/rmarkdownnotebook/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://rmarkdown.rstudio.com/ documentation: https://rmarkdown.rstudio.com/lesson-1.html tool_dev_url: https://github.com/rstudio/rmarkdown - licence: GPL-3 + licence: ["GPL-3"] params: - parametrize: type: boolean diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index 8ed18f5407d8..1991b807d01a 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index f67a35c0dbfd..5023ac91822e 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -10,7 +10,7 @@ tools: homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" - licence: "['BSD']" + licence: ["BSD"] input: - meta: type: map diff --git a/modules/nf-core/scramble/clusteranalysis/meta.yml b/modules/nf-core/scramble/clusteranalysis/meta.yml index d60e9dc96cf5..4e5200fcc71c 100644 --- a/modules/nf-core/scramble/clusteranalysis/meta.yml +++ b/modules/nf-core/scramble/clusteranalysis/meta.yml @@ -3,13 +3,15 @@ description: The Cluster Analysis tool of Scramble analyses and interprets the s keywords: - soft-clipped clusters - scramble + - cluster analysis + - clusteridentifier tools: - "scramble": description: "Soft Clipped Read Alignment Mapper" homepage: "https://github.com/GeneDx/scramble" documentation: "https://github.com/GeneDx/scramble" tool_dev_url: "https://github.com/GeneDx/scramble" - licence: "['CC']" + licence: ["CC"] input: - meta: type: map diff --git a/modules/nf-core/semibin/singleeasybin/meta.yml b/modules/nf-core/semibin/singleeasybin/meta.yml index f752fe6ff153..9e7c491a4614 100644 --- a/modules/nf-core/semibin/singleeasybin/meta.yml +++ b/modules/nf-core/semibin/singleeasybin/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://semibin.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/BigDataBiology/SemiBin" doi: "10.1038/s41467-022-29843-y" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/sequencetools/pileupcaller/meta.yml b/modules/nf-core/sequencetools/pileupcaller/meta.yml index 54ed15b0f2e8..c33142844c0b 100644 --- a/modules/nf-core/sequencetools/pileupcaller/meta.yml +++ b/modules/nf-core/sequencetools/pileupcaller/meta.yml @@ -16,7 +16,7 @@ tools: homepage: "https://github.com/stschiff/sequenceTools" documentation: "https://github.com/stschiff/sequenceTools#readme" tool_dev_url: "https://github.com/stschiff/sequenceTools" - licence: "['MIT']" + licence: ["MIT"] input: # Only when we have meta - meta: @@ -33,10 +33,10 @@ input: Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. Only alleles matching the Ref and Alt alleles of the provided snp file will be called. - calling_method: - type: value + type: string description: The desired calling method for pileupcaller. One of 'randomHaploid', 'randomDiploid', or 'majorityCall'. - output_format: - type: value + type: string description: The desired output format. One of 'PLINK', 'EIGENSTRAT', or 'FREQSUM'. output: #Only when we have meta diff --git a/modules/nf-core/sexdeterrmine/meta.yml b/modules/nf-core/sexdeterrmine/meta.yml index 1c4b33b1fd22..f1b57a8f3ec9 100644 --- a/modules/nf-core/sexdeterrmine/meta.yml +++ b/modules/nf-core/sexdeterrmine/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md" tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine" doi: "10.1038/s41467-018-07483-5" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/shapeit5/phasecommon/meta.yml b/modules/nf-core/shapeit5/phasecommon/meta.yml index 5d1381fba5b9..47197291ea9b 100644 --- a/modules/nf-core/shapeit5/phasecommon/meta.yml +++ b/modules/nf-core/shapeit5/phasecommon/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://odelaneau.github.io/shapeit5/docs/documentation" tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/shapeit5/phaserare/meta.yml b/modules/nf-core/shapeit5/phaserare/meta.yml index b607053d732d..dbc0aa13d03b 100644 --- a/modules/nf-core/shapeit5/phaserare/meta.yml +++ b/modules/nf-core/shapeit5/phaserare/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://odelaneau.github.io/shapeit5/docs/documentation" tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " - licence: "['MIT']" + licence: ["MIT"] requirement: AVX2 input: - meta: diff --git a/modules/nf-core/shapeit5/switch/meta.yml b/modules/nf-core/shapeit5/switch/meta.yml index 9832e8166bbc..73dd86e49d40 100644 --- a/modules/nf-core/shapeit5/switch/meta.yml +++ b/modules/nf-core/shapeit5/switch/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://odelaneau.github.io/shapeit5/docs/documentation" tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/shigeifinder/meta.yml b/modules/nf-core/shigeifinder/meta.yml index 9096affa2ed6..8951b5299b6d 100644 --- a/modules/nf-core/shigeifinder/meta.yml +++ b/modules/nf-core/shigeifinder/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/LanLab/ShigEiFinder" tool_dev_url: "https://github.com/LanLab/ShigEiFinder" doi: "10.1099/mgen.0.000704" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/snakemake/meta.yml b/modules/nf-core/snakemake/meta.yml index efbe01d2adf1..3da2765988e5 100644 --- a/modules/nf-core/snakemake/meta.yml +++ b/modules/nf-core/snakemake/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://snakemake.readthedocs.io/en/stable/" tool_dev_url: "https://github.com/snakemake/snakemake" doi: "10.1093/bioinformatics/bty350" - licence: "['MIT']" + licence: ["MIT"] input: # Only when we have meta - meta: diff --git a/modules/nf-core/snapaligner/align/meta.yml b/modules/nf-core/snapaligner/align/meta.yml index 16e2a5e6f100..137b67e18aba 100644 --- a/modules/nf-core/snapaligner/align/meta.yml +++ b/modules/nf-core/snapaligner/align/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug" tool_dev_url: "https://github.com/amplab/snap" doi: "10.1101/2021.11.23.469039" - licence: "['Apache v2']" + licence: ["Apache v2"] input: - meta: type: map diff --git a/modules/nf-core/snippy/core/meta.yml b/modules/nf-core/snippy/core/meta.yml index afb245c7432a..cd548b67ed42 100644 --- a/modules/nf-core/snippy/core/meta.yml +++ b/modules/nf-core/snippy/core/meta.yml @@ -11,7 +11,7 @@ tools: homepage: "https://github.com/tseemann/snippy" documentation: "https://github.com/tseemann/snippy" tool_dev_url: "https://github.com/tseemann/snippy" - licence: "['GPL v2']" + licence: ["GPL v2"] input: - meta: type: map diff --git a/modules/nf-core/somalier/ancestry/meta.yml b/modules/nf-core/somalier/ancestry/meta.yml index 0aadac517b40..6cc67ba6d6ec 100644 --- a/modules/nf-core/somalier/ancestry/meta.yml +++ b/modules/nf-core/somalier/ancestry/meta.yml @@ -19,7 +19,7 @@ tools: documentation: "https://github.com/brentp/somalier" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/spatyper/meta.yml b/modules/nf-core/spatyper/meta.yml index 73ffce6fb000..2af1abca8a51 100644 --- a/modules/nf-core/spatyper/meta.yml +++ b/modules/nf-core/spatyper/meta.yml @@ -3,6 +3,7 @@ description: Computational method for finding spa types. keywords: - fasta - spatype + - spa tools: - spatyper: description: Computational method for finding spa types. diff --git a/modules/nf-core/srst2/srst2/meta.yml b/modules/nf-core/srst2/srst2/meta.yml index ff6f3413ee17..5d5a6876a6e0 100644 --- a/modules/nf-core/srst2/srst2/meta.yml +++ b/modules/nf-core/srst2/srst2/meta.yml @@ -17,7 +17,7 @@ tools: licence: ["BSD"] input: - meta: - type: map0.2.0-4 + type: map description: | Groovy Map containing sample information id: should be the identification number or sample name diff --git a/modules/nf-core/stecfinder/meta.yml b/modules/nf-core/stecfinder/meta.yml index 93e30b86bdd3..a4efed3190dc 100644 --- a/modules/nf-core/stecfinder/meta.yml +++ b/modules/nf-core/stecfinder/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/LanLab/STECFinder" tool_dev_url: "https://github.com/LanLab/STECFinder" doi: "10.3389/fcimb.2021.772574" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/stitch/meta.yml b/modules/nf-core/stitch/meta.yml index a36d61cd8960..2596fa379282 100644 --- a/modules/nf-core/stitch/meta.yml +++ b/modules/nf-core/stitch/meta.yml @@ -17,7 +17,7 @@ tools: documentation: "https://github.com/rwdavies/stitch" tool_dev_url: "https://github.com/rwdavies/stitch" doi: "10.1038/ng.3594" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/survivor/filter/meta.yml b/modules/nf-core/survivor/filter/meta.yml index 4cb29051c3ae..64565408d306 100644 --- a/modules/nf-core/survivor/filter/meta.yml +++ b/modules/nf-core/survivor/filter/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/fritzsedlazeck/SURVIVOR/wiki" tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/survivor/simsv/meta.yml b/modules/nf-core/survivor/simsv/meta.yml index 88caacadee89..80b6d1c918ab 100644 --- a/modules/nf-core/survivor/simsv/meta.yml +++ b/modules/nf-core/survivor/simsv/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/fritzsedlazeck/SURVIVOR/wiki" tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/svaba/meta.yml b/modules/nf-core/svaba/meta.yml index af04fe1a2f25..d78ea0e8c991 100644 --- a/modules/nf-core/svaba/meta.yml +++ b/modules/nf-core/svaba/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5880247/" tool_dev_url: "https://github.com/walaj/svaba" doi: "10.1101/gr.221028.117" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/svtk/baftest/meta.yml b/modules/nf-core/svtk/baftest/meta.yml index 920c0af36ce8..fcae45bd8dd2 100644 --- a/modules/nf-core/svtk/baftest/meta.yml +++ b/modules/nf-core/svtk/baftest/meta.yml @@ -13,7 +13,7 @@ tools: homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/svtk/rdtest2vcf/meta.yml b/modules/nf-core/svtk/rdtest2vcf/meta.yml index c89ac97a1c67..c1851f5738d2 100644 --- a/modules/nf-core/svtk/rdtest2vcf/meta.yml +++ b/modules/nf-core/svtk/rdtest2vcf/meta.yml @@ -13,7 +13,7 @@ tools: documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" doi: "10.1038/s41586-020-2287-8" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/svtk/standardize/meta.yml b/modules/nf-core/svtk/standardize/meta.yml index f0581cd29a87..e0d35cf4dde7 100644 --- a/modules/nf-core/svtk/standardize/meta.yml +++ b/modules/nf-core/svtk/standardize/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" - licence: "['MIT']" + licence: ["MIT"] input: - args: type: map diff --git a/modules/nf-core/svtk/vcf2bed/meta.yml b/modules/nf-core/svtk/vcf2bed/meta.yml index 768b9b7c7555..4b1d2e63e13c 100644 --- a/modules/nf-core/svtk/vcf2bed/meta.yml +++ b/modules/nf-core/svtk/vcf2bed/meta.yml @@ -12,7 +12,7 @@ tools: homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/topas/gencons/meta.yml b/modules/nf-core/topas/gencons/meta.yml index 5e7c8770c1ab..4bef8632826c 100644 --- a/modules/nf-core/topas/gencons/meta.yml +++ b/modules/nf-core/topas/gencons/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/subwaystation/TOPAS/wiki/Overview-Modules" tool_dev_url: "https://github.com/subwaystation/TOPAS" doi: "10.1038/s41598-017-17723-1" - licence: "['CC-BY']" + licence: ["CC-BY"] input: - meta: type: map diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml index ea2c9b8eca0d..b3bd9da1e99c 100644 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ b/modules/nf-core/transdecoder/predict/meta.yml @@ -3,6 +3,8 @@ description: TransDecoder identifies candidate coding regions within transcript keywords: - eukaryotes - gff + - cds + - transcroder tools: - transdecoder: description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. @@ -35,19 +37,19 @@ output: description: File containing software versions pattern: "versions.yml" - pep: - type: amino acids fasta file + type: file description: All ORFs meeting the minimum length criteria, regardless of coding potential pattern: "*.{pep}" - gff3: - type: gff3 file + type: file description: Positions of all ORFs as found in the target transcripts pattern: "*.{gff3}" - cds: - type: nucleotide fasta file + type: file description: the nucleotide coding sequence for all detected ORFs pattern: "*{cds}" - bed: - type: bed file + type: file description: bed file pattern: "*{bed}" authors: diff --git a/modules/nf-core/truvari/bench/meta.yml b/modules/nf-core/truvari/bench/meta.yml index 78f9abff8f85..1d8cf5bb2373 100644 --- a/modules/nf-core/truvari/bench/meta.yml +++ b/modules/nf-core/truvari/bench/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/acenglish/truvari/wiki" tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/ultra/align/meta.yml b/modules/nf-core/ultra/align/meta.yml index 264e9ab89881..79b9e30aadb6 100644 --- a/modules/nf-core/ultra/align/meta.yml +++ b/modules/nf-core/ultra/align/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/ksahlin/uLTRA" tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" - licence: "['GNU GPLV3']" + licence: ["GNU GPLV3"] input: - meta: type: map diff --git a/modules/nf-core/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml index 3c0eda987713..1bf59abab07b 100644 --- a/modules/nf-core/ultra/index/meta.yml +++ b/modules/nf-core/ultra/index/meta.yml @@ -14,7 +14,7 @@ tools: documentation: "https://github.com/ksahlin/uLTRA" tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" - licence: "['GNU GPLV3']" + licence: ["GNU GPLV3"] input: - fasta: type: file diff --git a/modules/nf-core/varlociraptor/callvariants/meta.yml b/modules/nf-core/varlociraptor/callvariants/meta.yml index 5845db58ff99..85ef816d34f3 100644 --- a/modules/nf-core/varlociraptor/callvariants/meta.yml +++ b/modules/nf-core/varlociraptor/callvariants/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/varlociraptor/preprocess/meta.yml b/modules/nf-core/varlociraptor/preprocess/meta.yml index 00a6227d2710..7fd3de5bb8f2 100644 --- a/modules/nf-core/varlociraptor/preprocess/meta.yml +++ b/modules/nf-core/varlociraptor/preprocess/meta.yml @@ -11,7 +11,7 @@ tools: documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" - licence: "['GPL v3']" + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml index 17f9c38db74f..b091f2b10153 100644 --- a/modules/nf-core/vcf2maf/meta.yml +++ b/modules/nf-core/vcf2maf/meta.yml @@ -12,7 +12,7 @@ tools: documentation: "https://github.com/mskcc/vcf2maf" tool_dev_url: "https://github.com/mskcc/vcf2maf" doi: "10.5281/zenodo.593251" - licence: "['Apache-2.0']" + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index 91f41f0d2005..313047deb64e 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -3,6 +3,8 @@ description: Detecting and estimating inter-sample DNA contamination became a cr keywords: - contamination - bam + - verifybamid + - DNA contamination estimation tools: - "verifybamid2": description: "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method." @@ -10,7 +12,7 @@ tools: documentation: "http://griffan.github.io/VerifyBamID" tool_dev_url: "https://github.com/Griffan/VerifyBamID" doi: "10.1101/gr.246934.118" - licence: "['MIT']" + licence: ["MIT"] input: - meta: type: map diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml index f9cdcd951a52..ef52cf111c54 100644 --- a/modules/nf-core/vrhyme/extractunbinned/meta.yml +++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 - licence: "['GPL v3 license', 'GPL v3']" + licence: ["GPL v3 license", "GPL v3"] input: - meta: type: map diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml index a2076618c00a..df8aea7c9bb0 100644 --- a/modules/nf-core/vrhyme/linkbins/meta.yml +++ b/modules/nf-core/vrhyme/linkbins/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 - licence: "['GPL v3 license', 'GPL v3']" + licence: ["GPL v3 license", "GPL v3"] input: - meta: type: map diff --git a/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml b/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml index 3afe864a42e7..f7275e8eb8b6 100644 --- a/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml +++ b/subworkflows/nf-core/bam_variant_demix_boot_freyja/meta.yml @@ -22,10 +22,10 @@ input: Structure: [ val(meta), path(fasta) ] Groovy Map containing sample information e.g. [ id:'test', single_end:false ] and the fasta reference used for the sorted BAM file - val_repeats: - type: value (int) + type: integer description: Number of bootstrap repeats to perform - val_db_name: - type: value (string) + type: string description: Name of the dir where UShER's files will be stored - ch_barcodes: type: file diff --git a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml index 9f4e12e009bc..fb2d12fd27cd 100644 --- a/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml +++ b/subworkflows/nf-core/fastq_trim_fastp_fastqc/meta.yml @@ -46,7 +46,7 @@ input: skip the fastp process if true output: - meta: - type: value + type: string description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: type: file diff --git a/subworkflows/nf-core/initialise/meta.yml b/subworkflows/nf-core/initialise/meta.yml index 7dedcb6b14a2..322ae9e9de3b 100644 --- a/subworkflows/nf-core/initialise/meta.yml +++ b/subworkflows/nf-core/initialise/meta.yml @@ -30,7 +30,7 @@ input: Boolean to show the pipeline logo and exit. output: - summary_params: - type: value + type: string description: | Structure: val(summary_params) A map of the parameters used in the pipeline. diff --git a/tests/modules/nf-core/sentieon/license_message.py b/tests/modules/nf-core/sentieon/license_message.py index 5b36e365409b..c4a34f92407a 100644 --- a/tests/modules/nf-core/sentieon/license_message.py +++ b/tests/modules/nf-core/sentieon/license_message.py @@ -21,15 +21,15 @@ import re import secrets import sys +from datetime import datetime as dt from cryptography.hazmat.primitives.ciphers.aead import AESGCM -from datetime import datetime as dt MESSAGE_TIMEOUT = 60 * 60 * 24 # Messages are valid for 1 day NONCE_BYTES = 12 -class DecryptionTimeout(Exception): +class DecryptionTimeoutError(Exception): # Decrypting a message that is too old pass @@ -69,7 +69,7 @@ def decrypt_message(key, ciphertext, timeout=MESSAGE_TIMEOUT): msg_timestamp = int.from_bytes(msg_timestamp, byteorder="big") timestamp = calendar.timegm(dt.now().utctimetuple()) if (timestamp - msg_timestamp) > timeout: - raise DecryptionTimeout("The message has an expired timeout") + raise DecryptionTimeoutError("The message has an expired timeout") return message.decode("utf-8") diff --git a/tests/test_versions_yml.py b/tests/test_versions_yml.py index ca17e2026959..26e7712bb3fa 100644 --- a/tests/test_versions_yml.py +++ b/tests/test_versions_yml.py @@ -1,8 +1,9 @@ +import re from pathlib import Path +from textwrap import dedent + import pytest import yaml -import re -from textwrap import dedent def _get_workflow_names(): From 3545b52c76849d66a6312ea570363b9b8f958a4b Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Sat, 7 Sep 2024 04:00:59 +1200 Subject: [PATCH 029/486] Added nf-test for elprep/filter (#6517) * Added nf-test for elprep/filter * Updated power assertion * Now emitting logs --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/elprep/filter/environment.yml | 2 +- modules/nf-core/elprep/filter/main.nf | 24 +++- modules/nf-core/elprep/filter/meta.yml | 6 +- .../nf-core/elprep/filter/tests/main.nf.test | 103 ++++++++++++++++++ .../elprep/filter/tests/main.nf.test.snap | 90 +++++++++++++++ .../elprep/filter/tests/nextflow.config | 5 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/elprep/filter/main.nf | 18 --- .../nf-core/elprep/filter/nextflow.config | 7 -- tests/modules/nf-core/elprep/filter/test.yml | 13 --- 10 files changed, 226 insertions(+), 45 deletions(-) create mode 100644 modules/nf-core/elprep/filter/tests/main.nf.test create mode 100644 modules/nf-core/elprep/filter/tests/main.nf.test.snap create mode 100644 modules/nf-core/elprep/filter/tests/nextflow.config delete mode 100644 tests/modules/nf-core/elprep/filter/main.nf delete mode 100644 tests/modules/nf-core/elprep/filter/nextflow.config delete mode 100644 tests/modules/nf-core/elprep/filter/test.yml diff --git a/modules/nf-core/elprep/filter/environment.yml b/modules/nf-core/elprep/filter/environment.yml index 841e7cdb7bb0..38dd4f4724b4 100644 --- a/modules/nf-core/elprep/filter/environment.yml +++ b/modules/nf-core/elprep/filter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::elprep=5.1.2 + - bioconda::elprep=5.1.3 diff --git a/modules/nf-core/elprep/filter/main.nf b/modules/nf-core/elprep/filter/main.nf index abe59bb087cd..07fcf2121462 100644 --- a/modules/nf-core/elprep/filter/main.nf +++ b/modules/nf-core/elprep/filter/main.nf @@ -4,8 +4,8 @@ process ELPREP_FILTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0': - 'biocontainers/elprep:5.1.2--he881be0_0' }" + 'https://depot.galaxyproject.org/singularity/elprep:5.1.3--he881be0_1': + 'biocontainers/elprep:5.1.3--he881be0_1' }" input: tuple val(meta), path(bam) @@ -24,6 +24,7 @@ process ELPREP_FILTER { output: tuple val(meta), path("output/**.{bam,sam}") ,emit: bam + tuple val(meta), path("logs/elprep/elprep*") ,emit: logs tuple val(meta), path("*.metrics.txt") ,optional: true, emit: metrics tuple val(meta), path("*.recall") ,optional: true, emit: recall tuple val(meta), path("*.vcf.gz") ,optional: true, emit: gvcf @@ -79,6 +80,7 @@ process ELPREP_FILTER { ${activity_profile_cmd} \\ ${assembly_regions_cmd} \\ --nr-of-threads ${task.cpus} \\ + --log-path ./ \\ $args cat <<-END_VERSIONS > versions.yml @@ -86,4 +88,22 @@ process ELPREP_FILTER { elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = args.contains("--output-type sam") ? "sam" : "bam" + def timestamp = "${java.time.OffsetDateTime.now().format(java.time.format.DateTimeFormatter.ISO_DATE_TIME)}" + """ + mkdir output + mkdir -p logs/elprep + + touch output/${prefix}.${suffix} + touch logs/elprep/elprep-${timestamp}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml index 7f7ebb2a382c..01d76648e919 100644 --- a/modules/nf-core/elprep/filter/meta.yml +++ b/modules/nf-core/elprep/filter/meta.yml @@ -42,7 +42,7 @@ input: type: file description: Elfasta file, required for BQSR and variant calling. pattern: "*.elfasta" - - known_sites: + - known_sites_elsites: type: file description: Optional elsites file containing known SNPs for BQSR. pattern: "*.elsites" @@ -77,6 +77,10 @@ output: type: file description: Sorted, markdup, optionally BQSR BAM/SAM file pattern: "*.{bam,sam}" + - logs: + type: list + description: Runtime log files + pattern: "elprep-*.log" - metrics: type: file description: Optional duplicate metrics file generated by elprep diff --git a/modules/nf-core/elprep/filter/tests/main.nf.test b/modules/nf-core/elprep/filter/tests/main.nf.test new file mode 100644 index 000000000000..413bff1a5a8c --- /dev/null +++ b/modules/nf-core/elprep/filter/tests/main.nf.test @@ -0,0 +1,103 @@ + +nextflow_process { + + name "Test Process ELPREP_FILTER" + script "../main.nf" + process "ELPREP_FILTER" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "elprep" + tag "elprep/filter" + + test("test-elprep-filter") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = true + input[2] = true + input[3] = [] + input[4] = [] + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.elfasta', checkIfExists: true) + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + input[8] = [] + input[9] = [] + input[10] = true + input[11] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.logs }, // name is unstable + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + file(process.out.metrics[0][1]).readLines()[5..7], + process.out.recall, + file(process.out.gvcf[0][1]).name, // unstable + process.out.table, + process.out.activity_profile, + process.out.assembly_regions, + process.out.versions + ).match() + } + ) + } + } + + test("test-elprep-filter-stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = true + input[2] = true + input[3] = [] + input[4] = [] + input[5] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.elfasta', checkIfExists: true) + input[6] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.elsites', checkIfExists: true) + input[7] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + input[8] = [] + input[9] = [] + input[10] = true + input[11] = true + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.logs }, // name is unstable + { assert snapshot( + process.out.bam, + process.out.metrics, + process.out.recall, + process.out.gvcf, + process.out.table, + process.out.activity_profile, + process.out.assembly_regions, + process.out.versions + ).match() + } + ) + } + } + +} diff --git a/modules/nf-core/elprep/filter/tests/main.nf.test.snap b/modules/nf-core/elprep/filter/tests/main.nf.test.snap new file mode 100644 index 000000000000..49b13c2408fd --- /dev/null +++ b/modules/nf-core/elprep/filter/tests/main.nf.test.snap @@ -0,0 +1,90 @@ +{ + "test-elprep-filter": { + "content": [ + "463ac3b905fbf4ddf113a94dbfa8d69f", + [ + "## METRICS CLASS\tpicard.sam.DuplicationMetrics", + "LIBRARY\tUNPAIRED_READS_EXAMINED\tREAD_PAIRS_EXAMINED\tSECONDARY_OR_SUPPLEMENTARY_RDS\tUNMAPPED_READS\tUNPAIRED_READ_DUPLICATES\tREAD_PAIR_DUPLICATES\tREAD_PAIR_OPTICAL_DUPLICATES\tPERCENT_DUPLICATION\tESTIMATED_LIBRARY_SIZE", + "Unknown Library\t0\t0\t0\t0\t0\t0\t0\tNaN" + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.recall:md5,291d996c0bb26193df85a0c9d7390073" + ] + ], + "test.g.vcf.gz", + [ + + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.activity_profile.igv:md5,52f765837ac969cb82c3c75be5608d4f" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.assembly_regions.igv:md5,861fd57e241bd89cebe8f21267fb4c78" + ] + ], + [ + "versions.yml:md5,8193703d0cedd662b76ea48940dac55d" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T19:53:43.782054" + }, + "test-elprep-filter-stub": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml:md5,8193703d0cedd662b76ea48940dac55d" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T19:56:09.856424" + } +} \ No newline at end of file diff --git a/modules/nf-core/elprep/filter/tests/nextflow.config b/modules/nf-core/elprep/filter/tests/nextflow.config new file mode 100644 index 000000000000..3304bd3555fe --- /dev/null +++ b/modules/nf-core/elprep/filter/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: ELPREP_FILTER { + ext.args = "--mark-duplicates " + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 63f10b608ab0..fda0a092c3f8 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -157,9 +157,6 @@ duphold: eigenstratdatabasetools/eigenstratsnpcoverage: - modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** - tests/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** -elprep/filter: - - modules/nf-core/elprep/filter/** - - tests/modules/nf-core/elprep/filter/** elprep/merge: - modules/nf-core/elprep/merge/** - tests/modules/nf-core/elprep/merge/** diff --git a/tests/modules/nf-core/elprep/filter/main.nf b/tests/modules/nf-core/elprep/filter/main.nf deleted file mode 100644 index 834198a46fa4..000000000000 --- a/tests/modules/nf-core/elprep/filter/main.nf +++ /dev/null @@ -1,18 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ELPREP_FILTER } from '../../../../../modules/nf-core/elprep/filter/main.nf' - -workflow test_elprep_filter { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - reference_elfasta = file(params.test_data['homo_sapiens']['genome']['genome_elfasta'], checkIfExists: true) - known_sites_elsites = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_elsites'], checkIfExists: true) - target_regions_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - - ELPREP_FILTER ( input, true, true, [], [], reference_elfasta, known_sites_elsites, target_regions_bed, [], [], true, true) -} diff --git a/tests/modules/nf-core/elprep/filter/nextflow.config b/tests/modules/nf-core/elprep/filter/nextflow.config deleted file mode 100644 index d53a3d2d4122..000000000000 --- a/tests/modules/nf-core/elprep/filter/nextflow.config +++ /dev/null @@ -1,7 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: ELPREP_FILTER { - ext.args = "--mark-duplicates " - } -} diff --git a/tests/modules/nf-core/elprep/filter/test.yml b/tests/modules/nf-core/elprep/filter/test.yml deleted file mode 100644 index 8425e30406c3..000000000000 --- a/tests/modules/nf-core/elprep/filter/test.yml +++ /dev/null @@ -1,13 +0,0 @@ -- name: elprep filter test_elprep_filter - command: nextflow run ./tests/modules/nf-core/elprep/filter -entry test_elprep_filter -c ./tests/config/nextflow.config - tags: - - elprep - - elprep/filter - files: - - path: output/elprep/test.activity_profile.igv - - path: output/elprep/test.assembly_regions.igv - - path: output/elprep/output/test.bam - - path: output/elprep/test.g.vcf.gz - - path: output/elprep/test.metrics.txt - - path: output/elprep/test.recall - - path: output/elprep/versions.yml From 49852039cccef84bbf5a3c0e069fac81fa3f0202 Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Sat, 7 Sep 2024 05:05:41 +1200 Subject: [PATCH 030/486] Added nf-test for blat (#6603) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/blat/tests/main.nf.test | 75 ++++++++++++++++++++ modules/nf-core/blat/tests/main.nf.test.snap | 72 +++++++++++++++++++ modules/nf-core/blat/tests/nextflow.config | 5 ++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/blat/main.nf | 21 ------ tests/modules/nf-core/blat/nextflow.config | 9 --- tests/modules/nf-core/blat/test.yml | 8 --- 7 files changed, 152 insertions(+), 41 deletions(-) create mode 100644 modules/nf-core/blat/tests/main.nf.test create mode 100644 modules/nf-core/blat/tests/main.nf.test.snap create mode 100644 modules/nf-core/blat/tests/nextflow.config delete mode 100644 tests/modules/nf-core/blat/main.nf delete mode 100644 tests/modules/nf-core/blat/nextflow.config delete mode 100644 tests/modules/nf-core/blat/test.yml diff --git a/modules/nf-core/blat/tests/main.nf.test b/modules/nf-core/blat/tests/main.nf.test new file mode 100644 index 000000000000..8b07e5cf72f7 --- /dev/null +++ b/modules/nf-core/blat/tests/main.nf.test @@ -0,0 +1,75 @@ + +nextflow_process { + + name "Test Process BLAT" + script "../main.nf" + process "BLAT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "blat" + tag "seqtk/seq" + + setup { + run("SEQTK_SEQ") { + script "../../seqtk/seq/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + + """ + } + } + } + + test("test-blat") { + + when { + process { + """ + input[0] = SEQTK_SEQ.out.fastx + input[1] = [ + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-blat-stub") { + options '-stub' + when { + process { + """ + input[0] = SEQTK_SEQ.out.fastx + input[1] = [ + [ id:'sarscov2' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/blat/tests/main.nf.test.snap b/modules/nf-core/blat/tests/main.nf.test.snap new file mode 100644 index 000000000000..d46a3320a6e8 --- /dev/null +++ b/modules/nf-core/blat/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test-blat": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33" + ] + ], + "1": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ], + "psl": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,6e2e5b3be48c84877f3c54b32bb9ec33" + ] + ], + "versions": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T20:38:03.56409" + }, + "test-blat-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ], + "psl": [ + [ + { + "id": "test", + "single_end": false + }, + "test.psl:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d9cde833b3f9cf6d359ef0f8a119380a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T20:38:09.736595" + } +} \ No newline at end of file diff --git a/modules/nf-core/blat/tests/nextflow.config b/modules/nf-core/blat/tests/nextflow.config new file mode 100644 index 000000000000..58bc3f25502a --- /dev/null +++ b/modules/nf-core/blat/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: SEQTK_SEQ { + ext.args = '-A' + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index fda0a092c3f8..e8273e4aa4c7 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -52,9 +52,6 @@ bedtools/unionbedg: biohansel: - modules/nf-core/biohansel/** - tests/modules/nf-core/biohansel/** -blat: - - modules/nf-core/blat/** - - tests/modules/nf-core/blat/** cadd: - modules/nf-core/cadd/** - tests/modules/nf-core/cadd/** diff --git a/tests/modules/nf-core/blat/main.nf b/tests/modules/nf-core/blat/main.nf deleted file mode 100644 index ad4184d084c2..000000000000 --- a/tests/modules/nf-core/blat/main.nf +++ /dev/null @@ -1,21 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SEQTK_SEQ } from '../../../../modules/nf-core/seqtk/seq/main.nf' -include { BLAT } from '../../../../modules/nf-core/blat/main.nf' - -workflow test_blat { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - sequences = [ - [ id:'sarscov2' ], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - SEQTK_SEQ ( input ) - BLAT ( SEQTK_SEQ.out.fastx, sequences ) -} diff --git a/tests/modules/nf-core/blat/nextflow.config b/tests/modules/nf-core/blat/nextflow.config deleted file mode 100644 index f688ab59e76a..000000000000 --- a/tests/modules/nf-core/blat/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: SEQTK_SEQ { - ext.args = '-A' - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/blat/test.yml b/tests/modules/nf-core/blat/test.yml deleted file mode 100644 index 0d8377d889e1..000000000000 --- a/tests/modules/nf-core/blat/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: blat test_blat - command: nextflow run ./tests/modules/nf-core/blat -entry test_blat -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/blat/nextflow.config - tags: - - blat - files: - - path: output/blat/test.psl - md5sum: 6e2e5b3be48c84877f3c54b32bb9ec33 - - path: output/blat/versions.yml From 8afa912ec913c5f6dda3dcfee650da1fd4cab558 Mon Sep 17 00:00:00 2001 From: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Date: Fri, 6 Sep 2024 18:06:42 +0100 Subject: [PATCH 031/486] Added nf-test for quast (#6554) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Added nf-test for quast * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Tests for each optional input and removed pytest * Removed "ref, nogff" test --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --- modules/nf-core/quast/tests/main.nf.test | 105 ++++++ modules/nf-core/quast/tests/main.nf.test.snap | 331 ++++++++++++++++++ modules/nf-core/quast/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/quast/main.nf | 40 --- tests/modules/nf-core/quast/nextflow.config | 5 - tests/modules/nf-core/quast/test.yml | 233 ------------ 7 files changed, 438 insertions(+), 281 deletions(-) create mode 100644 modules/nf-core/quast/tests/main.nf.test create mode 100644 modules/nf-core/quast/tests/main.nf.test.snap create mode 100644 modules/nf-core/quast/tests/tags.yml delete mode 100644 tests/modules/nf-core/quast/main.nf delete mode 100644 tests/modules/nf-core/quast/nextflow.config delete mode 100644 tests/modules/nf-core/quast/test.yml diff --git a/modules/nf-core/quast/tests/main.nf.test b/modules/nf-core/quast/tests/main.nf.test new file mode 100644 index 000000000000..44655a526ac2 --- /dev/null +++ b/modules/nf-core/quast/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_process { + + name "Test Process QUAST" + script "../main.nf" + process "QUAST" + + tag "modules" + tag "modules_nfcore" + tag "quast" + + test("sarscov2 - ref") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.results[0][1]).list().size() == 15 }, + { assert snapshot( + process.out.tsv, + process.out.misassemblies, + process.out.unaligned, + process.out.versions, + ).match() } + ) + } + } + + test("sarscov2 - noref") { + + when { + process { + """ + input[0] = [ + [ id: 'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.results[0][1]).list().size() == 12 }, + { assert snapshot( + process.out.tsv, + process.out.versions, + ).match() } + ) + } + } + + + test("sarscov2 - all - stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true) + ] + input[1] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id: 'test1' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/quast/tests/main.nf.test.snap b/modules/nf-core/quast/tests/main.nf.test.snap new file mode 100644 index 000000000000..f408a299c935 --- /dev/null +++ b/modules/nf-core/quast/tests/main.nf.test.snap @@ -0,0 +1,331 @@ +{ + "sarscov2 - ref, gff": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,1fc09ef5115692ed558cb31482bf3db0" + ] + ], + [ + [ + { + "id": "test" + }, + "test_misassemblies.tsv:md5,b2c977af2f6e07603e0a0f4d1e32d058" + ] + ], + [ + [ + { + "id": "test" + }, + "test_unaligned.tsv:md5,a3a36c1d206f89d12af74cef0c412f94" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:45.436004" + }, + "sarscov2 - noref, nogff": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,6c4891c111a46ed20d5e3062b71aa390" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:50.435479" + }, + "sarscov2 - all - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test1" + }, + [ + [ + "NAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "Nx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "gc.icarus.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "all_alignments_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.mis_contigs.info:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stderr:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stdout:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.unaligned.info:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "transcriptome.coords:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords.filtered:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords_tmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.sf:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.unaligned:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.used_snps:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "misassemblies_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.mis_contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "features_cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "features_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome_gaps.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "icarus.html:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "alignment_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "contig_size_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "quast.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + [ + { + "id": "test1" + }, + "test1.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test1" + }, + "test1_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test1" + }, + "test1_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test1" + }, + "test1_unaligned.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ], + "misassemblies": [ + [ + { + "id": "test1" + }, + "test1_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "results": [ + [ + { + "id": "test1" + }, + [ + [ + "NAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGAx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "NGx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "Nx_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "gc.icarus.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_GC_content_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "all_alignments_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.mis_contigs.info:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stderr:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.stdout:md5,d41d8cd98f00b204e9800998ecf8427e", + "contigs_report_transcriptome.unaligned.info:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "transcriptome.coords:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords.filtered:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.coords_tmp:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.sf:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.unaligned:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.used_snps:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "misassemblies_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "misassemblies_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome.mis_contigs.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report_misassemblies.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "unaligned_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + [ + "features_cumulative_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "features_frcurve_plot.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "genome_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transcriptome_gaps.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "icarus.html:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "alignment_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "contig_size_viewer.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "quast.log:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.html:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.pdf:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + "report.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.tex:md5,d41d8cd98f00b204e9800998ecf8427e", + "transposed_report.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "transcriptome": [ + [ + { + "id": "test1" + }, + "test1_transcriptome.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + [ + { + "id": "test1" + }, + "test1.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "unaligned": [ + [ + { + "id": "test1" + }, + "test1_unaligned.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T13:13:54.219263" + }, + "sarscov2 - ref": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,1fc09ef5115692ed558cb31482bf3db0" + ] + ], + [ + [ + { + "id": "test" + }, + "test_misassemblies.tsv:md5,b2c977af2f6e07603e0a0f4d1e32d058" + ] + ], + [ + [ + { + "id": "test" + }, + "test_unaligned.tsv:md5,a3a36c1d206f89d12af74cef0c412f94" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:58:43.030275" + }, + "sarscov2 - noref": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.tsv:md5,6c4891c111a46ed20d5e3062b71aa390" + ] + ], + [ + "versions.yml:md5,51393275b26f4f0f3c7c107a0b9756f9" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T15:58:58.400864" + } +} \ No newline at end of file diff --git a/modules/nf-core/quast/tests/tags.yml b/modules/nf-core/quast/tests/tags.yml new file mode 100644 index 000000000000..2bd72f4c0aba --- /dev/null +++ b/modules/nf-core/quast/tests/tags.yml @@ -0,0 +1,2 @@ +quast: + - modules/nf-core/quast/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e8273e4aa4c7..f286ae2c2a49 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -575,9 +575,6 @@ purgedups/purgedups: pydamage/filter: - modules/nf-core/pydamage/filter/** - tests/modules/nf-core/pydamage/filter/** -quast: - - modules/nf-core/quast/** - - tests/modules/nf-core/quast/** raxmlng: - modules/nf-core/raxmlng/** - tests/modules/nf-core/raxmlng/** diff --git a/tests/modules/nf-core/quast/main.nf b/tests/modules/nf-core/quast/main.nf deleted file mode 100644 index 08c03106ee8e..000000000000 --- a/tests/modules/nf-core/quast/main.nf +++ /dev/null @@ -1,40 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { QUAST as QUAST_REF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOREF_NOGFF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOGFF } from '../../../../modules/nf-core/quast/main.nf' -include { QUAST as QUAST_NOREF } from '../../../../modules/nf-core/quast/main.nf' - -workflow test_quast_ref { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] - gff = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)] - - QUAST_REF ( consensus, fasta, gff ) -} - -workflow test_quast_noref_nogff { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[:],[]] - gff = [[:],[]] - - QUAST_NOREF_NOGFF ( consensus, fasta, gff ) -} - -workflow test_quast_nogff { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)] - gff = [[:],[]] - - QUAST_NOGFF ( consensus, fasta, gff ) -} - -workflow test_quast_noref { - consensus = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['transcriptome_fasta'], checkIfExists: true)] - fasta = [[:],[]] - gff = [[ id:'test', single_end:false ], file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true)] - - QUAST_NOREF ( consensus, fasta, gff ) -} diff --git a/tests/modules/nf-core/quast/nextflow.config b/tests/modules/nf-core/quast/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/quast/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/quast/test.yml b/tests/modules/nf-core/quast/test.yml deleted file mode 100644 index 54fddcd38b86..000000000000 --- a/tests/modules/nf-core/quast/test.yml +++ /dev/null @@ -1,233 +0,0 @@ -- name: quast test_quast_ref - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_ref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: f9b9f817bde917c1672a17ad1d072d6c - - path: output/quast/test/aligned_stats/NAx_plot.pdf - - path: output/quast/test/aligned_stats/NGAx_plot.pdf - - path: output/quast/test/aligned_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/NGx_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/gc.icarus.txt - md5sum: bdf3e7481880ee7dafbd53add5291da1 - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/contigs_reports/all_alignments_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.mis_contigs.info - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stderr - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stdout - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.unaligned.info - md5sum: a8505cf206bf53ca369f7e3073fee587 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords - md5sum: dda3fc0addc41ecc0d5183dee6f95886 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords.filtered - md5sum: ec9191d0acb5d5bce56b4842551a8598 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords_tmp - md5sum: e5e26685b36489cbcff906fb07320cde - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.sf - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.unaligned - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.used_snps - md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 - - path: output/quast/test/contigs_reports/misassemblies_frcurve_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_report.tex - md5sum: ec1f7a1d1fb4a1b465057cf897b90b51 - - path: output/quast/test/contigs_reports/misassemblies_report.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test/contigs_reports/misassemblies_report.txt - md5sum: 8b9a6d675a41bab6bf344dde2a20a939 - - path: output/quast/test/contigs_reports/transcriptome.mis_contigs.fa - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tex - md5sum: d778f337899736cc62ed837b739b375c - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tsv - md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3 - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.txt - md5sum: fdb440c653e2f0306286798cacceaadb - - path: output/quast/test/contigs_reports/unaligned_report.tex - md5sum: e8e3bcb86da2cbd8eded980de80fa45c - - path: output/quast/test/contigs_reports/unaligned_report.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/test/contigs_reports/unaligned_report.txt - md5sum: 7e6ba6918574fd4b4cf090ead9a55d78 - - path: output/quast/test/genome_stats/features_cumulative_plot.pdf - - path: output/quast/test/genome_stats/features_frcurve_plot.pdf - - path: output/quast/test/genome_stats/genome_info.txt - md5sum: d0193b322079565dc78608291e9c44d1 - - path: output/quast/test/genome_stats/transcriptome_gaps.txt - md5sum: c52381f09ea40b6141be5232494727b6 - - path: output/quast/test/genome_stats/transcriptome_genomic_features_any.txt - md5sum: 307b3bb1f42fc2f11a60a2e9846021d7 - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/alignment_viewer.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: 881df38fdcd5ce2a7b78ac3cbfebbde1 - - path: output/quast/test/report.tsv - md5sum: f9b9f817bde917c1672a17ad1d072d6c - - path: output/quast/test/report.txt - md5sum: dd24fa9b6f95676006dc0928130d7d0b - - path: output/quast/test/transposed_report.tex - md5sum: 8d74e5b3d7967820b0e61acdeeee6dcb - - path: output/quast/test/transposed_report.tsv - md5sum: c0a0d2f998087b307f1a372ed31f5cde - - path: output/quast/test/transposed_report.txt - md5sum: 1dacbc04dfea073cbd74488d8b3cf821 - - path: output/quast/test_misassemblies.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test_unaligned.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/versions.yml - -- name: quast test_quast_noref_nogff - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_noref_nogff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: e76bb5838fcf3fb5a4841f83a8c33a32 - - path: output/quast/test/report.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/report.txt - md5sum: 2c39a11678f941cc927305019a13f478 - - path: output/quast/test/transposed_report.tex - md5sum: 12b4d146d5f48cf4817eafbfa5b8820f - - path: output/quast/test/transposed_report.tsv - md5sum: 0d6da89a9b434069b7c7b8f09884cc70 - - path: output/quast/test/transposed_report.txt - md5sum: f3c8820d6a3a13c5b891f772b8b4a887 - - path: output/quast/versions.yml - -- name: quast test_quast_nogff - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_nogff -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: 665d29c4767bb42355b8a9302bace646 - - path: output/quast/test/aligned_stats/NAx_plot.pdf - - path: output/quast/test/aligned_stats/NGAx_plot.pdf - - path: output/quast/test/aligned_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/NGx_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/gc.icarus.txt - md5sum: bdf3e7481880ee7dafbd53add5291da1 - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/contigs_reports/all_alignments_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.mis_contigs.info - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stderr - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.stdout - - path: output/quast/test/contigs_reports/contigs_report_transcriptome.unaligned.info - md5sum: a8505cf206bf53ca369f7e3073fee587 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords - md5sum: dda3fc0addc41ecc0d5183dee6f95886 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords.filtered - md5sum: ec9191d0acb5d5bce56b4842551a8598 - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.coords_tmp - md5sum: e5e26685b36489cbcff906fb07320cde - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.sf - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.unaligned - - path: output/quast/test/contigs_reports/minimap_output/transcriptome.used_snps - md5sum: 7b1db1b433cd95243a949bcb72e7e3a6 - - path: output/quast/test/contigs_reports/misassemblies_frcurve_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_plot.pdf - - path: output/quast/test/contigs_reports/misassemblies_report.tex - md5sum: ec1f7a1d1fb4a1b465057cf897b90b51 - - path: output/quast/test/contigs_reports/misassemblies_report.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test/contigs_reports/misassemblies_report.txt - md5sum: 8b9a6d675a41bab6bf344dde2a20a939 - - path: output/quast/test/contigs_reports/transcriptome.mis_contigs.fa - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tex - md5sum: d778f337899736cc62ed837b739b375c - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.tsv - md5sum: 3e8f449dd4481d1cfd4ce3ddab97b8e3 - - path: output/quast/test/contigs_reports/transposed_report_misassemblies.txt - md5sum: fdb440c653e2f0306286798cacceaadb - - path: output/quast/test/contigs_reports/unaligned_report.tex - md5sum: e8e3bcb86da2cbd8eded980de80fa45c - - path: output/quast/test/contigs_reports/unaligned_report.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/test/contigs_reports/unaligned_report.txt - md5sum: 7e6ba6918574fd4b4cf090ead9a55d78 - - path: output/quast/test/genome_stats/genome_info.txt - md5sum: 8186ae63e910796afff33cf000885b74 - - path: output/quast/test/genome_stats/transcriptome_gaps.txt - md5sum: c52381f09ea40b6141be5232494727b6 - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/alignment_viewer.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: 35243bf9fb51f6a11fac0cfe4556a9a9 - - path: output/quast/test/report.tsv - md5sum: 665d29c4767bb42355b8a9302bace646 - - path: output/quast/test/report.txt - md5sum: d7d2a1a477c74e70f6a906d02c88b36b - - path: output/quast/test/transposed_report.tex - md5sum: 77190dcdd1acb8cb8692c9da523e26f8 - - path: output/quast/test/transposed_report.tsv - md5sum: bc2bddf6a787e835ff9c77dfc1a49458 - - path: output/quast/test/transposed_report.txt - md5sum: 395352dadaf01d490b250d2bffef4dea - - path: output/quast/test_misassemblies.tsv - md5sum: a32a09a0df811d1a75fbfe124081d1ca - - path: output/quast/test_transcriptome.tsv - md5sum: c247152eb82b361106492642fd796e2c - - path: output/quast/test_unaligned.tsv - md5sum: 81d9597314356363a6b4e0d67027345a - - path: output/quast/versions.yml - -- name: quast test_quast_noref - command: nextflow run ./tests/modules/nf-core/quast -entry test_quast_noref -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/quast/nextflow.config - tags: - - quast - files: - - path: output/quast/test.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/basic_stats/GC_content_plot.pdf - - path: output/quast/test/basic_stats/Nx_plot.pdf - - path: output/quast/test/basic_stats/cumulative_plot.pdf - - path: output/quast/test/basic_stats/transcriptome_GC_content_plot.pdf - - path: output/quast/test/icarus.html - - path: output/quast/test/icarus_viewers/contig_size_viewer.html - - path: output/quast/test/quast.log - - path: output/quast/test/report.html - - path: output/quast/test/report.pdf - - path: output/quast/test/report.tex - md5sum: e76bb5838fcf3fb5a4841f83a8c33a32 - - path: output/quast/test/report.tsv - md5sum: e77011c67e59ae54d42dc0be264dd0c5 - - path: output/quast/test/report.txt - md5sum: 2c39a11678f941cc927305019a13f478 - - path: output/quast/test/transposed_report.tex - md5sum: 12b4d146d5f48cf4817eafbfa5b8820f - - path: output/quast/test/transposed_report.tsv - md5sum: 0d6da89a9b434069b7c7b8f09884cc70 - - path: output/quast/test/transposed_report.txt - md5sum: f3c8820d6a3a13c5b891f772b8b4a887 - - path: output/quast/versions.yml From c3e4418fd55a6634a640e5d082983c2bf95d1a90 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Fri, 6 Sep 2024 22:31:17 +0200 Subject: [PATCH 032/486] bcftools csq (#6605) * bcftools csq * fix lint / format * env.yml * move fun at bottom * Update modules/nf-core/bcftools/csq/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- modules/nf-core/bcftools/csq/environment.yml | 5 ++ modules/nf-core/bcftools/csq/main.nf | 81 +++++++++++++++++++ modules/nf-core/bcftools/csq/meta.yml | 81 +++++++++++++++++++ .../nf-core/bcftools/csq/tests/main.nf.test | 51 ++++++++++++ .../bcftools/csq/tests/main.nf.test.snap | 15 ++++ modules/nf-core/bcftools/csq/tests/tags.yml | 2 + modules/nf-core/bcftools/csq/tests/vcf.config | 4 + 7 files changed, 239 insertions(+) create mode 100644 modules/nf-core/bcftools/csq/environment.yml create mode 100644 modules/nf-core/bcftools/csq/main.nf create mode 100644 modules/nf-core/bcftools/csq/meta.yml create mode 100644 modules/nf-core/bcftools/csq/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/csq/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/csq/tests/tags.yml create mode 100644 modules/nf-core/bcftools/csq/tests/vcf.config diff --git a/modules/nf-core/bcftools/csq/environment.yml b/modules/nf-core/bcftools/csq/environment.yml new file mode 100644 index 000000000000..20fc663a5e33 --- /dev/null +++ b/modules/nf-core/bcftools/csq/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::bcftools=1.20" diff --git a/modules/nf-core/bcftools/csq/main.nf b/modules/nf-core/bcftools/csq/main.nf new file mode 100644 index 000000000000..38a348cda8a8 --- /dev/null +++ b/modules/nf-core/bcftools/csq/main.nf @@ -0,0 +1,81 @@ + +process BCFTOOLS_CSQ { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_1': + 'biocontainers/bcftools:1.20--h8b25389_1' }" + + + input: + tuple val(meta), path(vcf) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gff3) + + output: + tuple val(meta), path("*.${extension}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + extension = getVcfExtension(args); + + if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + + """ + bcftools csq \\ + --output ${prefix}.${extension} \\ + --threads ${task.cpus} \\ + --fasta-ref ${fasta} \\ + --gff-annot ${gff3} \\ + $args \\ + $vcf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + extension = getVcfExtension(args); + + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} +// Custom Functions +String getVcfExtension(String args) { + return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf"; +} diff --git a/modules/nf-core/bcftools/csq/meta.yml b/modules/nf-core/bcftools/csq/meta.yml new file mode 100644 index 000000000000..a45d007c300a --- /dev/null +++ b/modules/nf-core/bcftools/csq/meta.yml @@ -0,0 +1,81 @@ +name: bcftools_csq +description: bcftools Haplotype-aware consequence caller +keywords: + - annotation + - gff + - gff3 + - protein + - functional + - vcf + - bcf + - bcftools +tools: + - reheader: + description: | + Haplotype-aware consequence caller + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://samtools.github.io/bcftools/bcftools.html#csq + doi: 10.1093/gigascience/giab008 + licence: ["MIT"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: Fasta reference + pattern: "*.{fasta,fa}" + - meta3: + type: map + description: | + Groovy Map containing fai information + - fai: + type: file + description: Fasta index + pattern: "*.{fai}" + - meta4: + type: map + description: | + Groovy Map containing gff3 information + - gff3: + type: file + description: GFF3 file + pattern: "*.{gff,gff.gz,gff3,gff3.gz}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF with annotation, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@lindenb" + +maintainers: + - "@lindenb" diff --git a/modules/nf-core/bcftools/csq/tests/main.nf.test b/modules/nf-core/bcftools/csq/tests/main.nf.test new file mode 100644 index 000000000000..7eafc6caa691 --- /dev/null +++ b/modules/nf-core/bcftools/csq/tests/main.nf.test @@ -0,0 +1,51 @@ +nextflow_process { + + name "Test Process BCFTOOLS_CSQ" + script "../main.nf" + process "BCFTOOLS_CSQ" + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/csq" + + test("homo_sapiens") { + + config "./vcf.config" + when { + + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz', checkIfExists: true) + ] + input[1] = [ + [ : ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ : ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ : ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gff3', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } + ) + } + + } + +} diff --git a/modules/nf-core/bcftools/csq/tests/main.nf.test.snap b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap new file mode 100644 index 000000000000..8997e0dec824 --- /dev/null +++ b/modules/nf-core/bcftools/csq/tests/main.nf.test.snap @@ -0,0 +1,15 @@ +{ + "homo_sapiens": { + "content": [ + "807319f441f639c33708781757da53ee", + [ + "versions.yml:md5,13a1a38a47f60c47fd15a32552492bbf" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T16:02:00.380988135" + } +} diff --git a/modules/nf-core/bcftools/csq/tests/tags.yml b/modules/nf-core/bcftools/csq/tests/tags.yml new file mode 100644 index 000000000000..5584914b9a03 --- /dev/null +++ b/modules/nf-core/bcftools/csq/tests/tags.yml @@ -0,0 +1,2 @@ +bcftools/csq: + - "modules/nf-core/bcftools/csq/**" diff --git a/modules/nf-core/bcftools/csq/tests/vcf.config b/modules/nf-core/bcftools/csq/tests/vcf.config new file mode 100644 index 000000000000..08f772b15aee --- /dev/null +++ b/modules/nf-core/bcftools/csq/tests/vcf.config @@ -0,0 +1,4 @@ +process { + ext.args = { "--local-csq --ncsq 20 --unify-chr-names 1 -Ov " } + ext.prefix = "tested" +} From 9897e69c5b47e68b2adb051a2eedf7632efcbe4d Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 6 Sep 2024 19:53:32 -0300 Subject: [PATCH 033/486] Add module and subworkflow mirtop (#6587) * add mirtop gff module * add mirtop/counts module * add mirtop/export module * add mirtop/stats module * update yml * add bam_stats_mirna_mirtop subworkflow * add required dependencies * update test * update subworkflow test * update yml and output files * fix tag linting issue? * fix linting * run prettier * try to solve conda issue * add a compatible pandas * fix linting * update failing ci mirtop/gff test --- modules/nf-core/mirtop/counts/environment.yml | 9 ++ modules/nf-core/mirtop/counts/main.nf | 53 +++++++++ modules/nf-core/mirtop/counts/meta.yml | 57 ++++++++++ .../nf-core/mirtop/counts/tests/main.nf.test | 97 +++++++++++++++++ .../mirtop/counts/tests/main.nf.test.snap | 47 ++++++++ .../mirtop/counts/tests/nextflow.config | 5 + modules/nf-core/mirtop/export/environment.yml | 10 ++ modules/nf-core/mirtop/export/main.nf | 57 ++++++++++ modules/nf-core/mirtop/export/meta.yml | 65 +++++++++++ .../nf-core/mirtop/export/tests/main.nf.test | 92 ++++++++++++++++ .../mirtop/export/tests/main.nf.test.snap | 102 ++++++++++++++++++ modules/nf-core/mirtop/gff/environment.yml | 8 ++ modules/nf-core/mirtop/gff/main.nf | 55 ++++++++++ modules/nf-core/mirtop/gff/meta.yml | 61 +++++++++++ modules/nf-core/mirtop/gff/tests/main.nf.test | 81 ++++++++++++++ .../mirtop/gff/tests/main.nf.test.snap | 67 ++++++++++++ modules/nf-core/mirtop/stats/environment.yml | 8 ++ modules/nf-core/mirtop/stats/main.nf | 51 +++++++++ modules/nf-core/mirtop/stats/meta.yml | 46 ++++++++ .../nf-core/mirtop/stats/tests/main.nf.test | 81 ++++++++++++++ .../mirtop/stats/tests/main.nf.test.snap | 100 +++++++++++++++++ .../nf-core/bam_stats_mirna_mirtop/main.nf | 36 +++++++ .../nf-core/bam_stats_mirna_mirtop/meta.yml | 61 +++++++++++ .../bam_stats_mirna_mirtop/tests/main.nf.test | 49 +++++++++ .../tests/main.nf.test.snap | 41 +++++++ .../tests/nextflow.config | 5 + 26 files changed, 1344 insertions(+) create mode 100644 modules/nf-core/mirtop/counts/environment.yml create mode 100644 modules/nf-core/mirtop/counts/main.nf create mode 100644 modules/nf-core/mirtop/counts/meta.yml create mode 100644 modules/nf-core/mirtop/counts/tests/main.nf.test create mode 100644 modules/nf-core/mirtop/counts/tests/main.nf.test.snap create mode 100644 modules/nf-core/mirtop/counts/tests/nextflow.config create mode 100644 modules/nf-core/mirtop/export/environment.yml create mode 100644 modules/nf-core/mirtop/export/main.nf create mode 100644 modules/nf-core/mirtop/export/meta.yml create mode 100644 modules/nf-core/mirtop/export/tests/main.nf.test create mode 100644 modules/nf-core/mirtop/export/tests/main.nf.test.snap create mode 100644 modules/nf-core/mirtop/gff/environment.yml create mode 100644 modules/nf-core/mirtop/gff/main.nf create mode 100644 modules/nf-core/mirtop/gff/meta.yml create mode 100644 modules/nf-core/mirtop/gff/tests/main.nf.test create mode 100644 modules/nf-core/mirtop/gff/tests/main.nf.test.snap create mode 100644 modules/nf-core/mirtop/stats/environment.yml create mode 100644 modules/nf-core/mirtop/stats/main.nf create mode 100644 modules/nf-core/mirtop/stats/meta.yml create mode 100644 modules/nf-core/mirtop/stats/tests/main.nf.test create mode 100644 modules/nf-core/mirtop/stats/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf create mode 100644 subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml create mode 100644 subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test create mode 100644 subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/bam_stats_mirna_mirtop/tests/nextflow.config diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml new file mode 100644 index 000000000000..ed1198d82609 --- /dev/null +++ b/modules/nf-core/mirtop/counts/environment.yml @@ -0,0 +1,9 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirtop=0.4.25" + - "conda-forge::r-base=4.1.1" + - "conda-forge::r-data.table=1.14.2" diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf new file mode 100644 index 000000000000..9b623bff8f3b --- /dev/null +++ b/modules/nf-core/mirtop/counts/main.nf @@ -0,0 +1,53 @@ +process MIRTOP_COUNTS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : + 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + + input: + tuple val(meta), path(mirtop_gff) + tuple val(meta2), path(hairpin) + tuple val(meta3), path(gtf), val(species) + + output: + tuple val(meta), path("counts/*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mirtop \\ + counts \\ + $args \\ + --hairpin $hairpin \\ + --gtf $gtf \\ + --sps $species \\ + --gff $mirtop_gff \\ + -o counts + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir counts + touch counts/mirtop.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirtop/counts/meta.yml b/modules/nf-core/mirtop/counts/meta.yml new file mode 100644 index 000000000000..904dbd3102f7 --- /dev/null +++ b/modules/nf-core/mirtop/counts/meta.yml @@ -0,0 +1,57 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "mirtop_counts" +description: mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples. +keywords: + - mirna + - isomir + - gff +tools: + - "mirtop": + description: "Small RNA-seq annotation" + homepage: "https://github.com/miRTop/mirtop" + documentation: "https://mirtop.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/miRTop/mirtop" + licence: ["MIT License"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - tsv: + type: file + description: TSV file + pattern: "*.{tsv}" + +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test new file mode 100644 index 000000000000..8283d5b489be --- /dev/null +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -0,0 +1,97 @@ +nextflow_process { + + name "Test Process MIRTOP_COUNTS" + script "../main.nf" + config "./nextflow.config" + process "MIRTOP_COUNTS" + + tag "modules" + tag "modules_nfcore" + tag "mirtop" + tag "mirtop/gff" + tag "mirtop/counts" + + setup { + run("MIRTOP_GFF") { + script "../../gff/main.nf" + process { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + } + + test("isomir - bam") { + + when { + process { + """ + input[0] = MIRTOP_GFF.out.mirtop_gff + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions + ).match() + }, + // md5sum is not stable, order of elements in column "variant" change + { assert file(process.out.tsv[0][1]).readLines().findAll { it.contains("iso-22-I0S21NSLN") }} + ) + } + + } + + test("isomir - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = MIRTOP_GFF.out.mirtop_gff + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap new file mode 100644 index 000000000000..d05798b0bb6c --- /dev/null +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap @@ -0,0 +1,47 @@ +{ + "isomir - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + ], + "tsv": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T13:24:41.148536938" + }, + "isomir - bam": { + "content": [ + [ + "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T18:39:50.607483472" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirtop/counts/tests/nextflow.config b/modules/nf-core/mirtop/counts/tests/nextflow.config new file mode 100644 index 000000000000..83d77e209c25 --- /dev/null +++ b/modules/nf-core/mirtop/counts/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MIRTOP_COUNTS' { + ext.args = '--add-extra' + } +} diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml new file mode 100644 index 000000000000..4b5ae03a45a3 --- /dev/null +++ b/modules/nf-core/mirtop/export/environment.yml @@ -0,0 +1,10 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirtop=0.4.25" + - "bioconda::samtools=1.15.1" + - "conda-forge::r-base=4.1.1" + - "conda-forge::r-data.table=1.14.2" diff --git a/modules/nf-core/mirtop/export/main.nf b/modules/nf-core/mirtop/export/main.nf new file mode 100644 index 000000000000..33f6c3032623 --- /dev/null +++ b/modules/nf-core/mirtop/export/main.nf @@ -0,0 +1,57 @@ +process MIRTOP_EXPORT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : + 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + + input: + tuple val(meta), path(mirtop_gff) + tuple val(meta2), path(hairpin) + tuple val(meta3), path(gtf), val(species) + + output: + tuple val(meta), path("export/*_rawData.tsv") , emit: tsv, optional: true + tuple val(meta), path("export/*.fasta") , emit: fasta, optional: true + tuple val(meta), path("export/*.vcf*") , emit: vcf , optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '--format isomir' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mirtop \\ + export \\ + $args \\ + --hairpin $hairpin\\ + --gtf $gtf \\ + --sps $species \\ + -o export \\ + $mirtop_gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir export + touch export/${prefix}.fasta + touch export/${prefix}.vcf + touch export/${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirtop/export/meta.yml b/modules/nf-core/mirtop/export/meta.yml new file mode 100644 index 000000000000..d797f78373d5 --- /dev/null +++ b/modules/nf-core/mirtop/export/meta.yml @@ -0,0 +1,65 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "mirtop_export" +description: mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package +keywords: + - mirna + - isomir + - gff +tools: + - "mirtop": + description: "Small RNA-seq annotation" + homepage: "https://github.com/miRTop/mirtop" + documentation: "https://mirtop.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/miRTop/mirtop" + licence: ["MIT License"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - tsv: + type: file + description: TSV file + pattern: "*.{tsv}" + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa}" + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test b/modules/nf-core/mirtop/export/tests/main.nf.test new file mode 100644 index 000000000000..0a7f80710b74 --- /dev/null +++ b/modules/nf-core/mirtop/export/tests/main.nf.test @@ -0,0 +1,92 @@ +nextflow_process { + + name "Test Process MIRTOP_EXPORT" + script "../main.nf" + process "MIRTOP_EXPORT" + + tag "modules" + tag "modules_nfcore" + tag "mirtop" + tag "mirtop/gff" + tag "mirtop/export" + + setup { + run("MIRTOP_GFF") { + script "../../gff/main.nf" + process { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + } + + test("isomir - bam") { + + when { + process { + """ + input[0] = MIRTOP_GFF.out.mirtop_gff + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("isomir - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = MIRTOP_GFF.out.mirtop_gff + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + +} diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap new file mode 100644 index 000000000000..1a7784b08d16 --- /dev/null +++ b/modules/nf-core/mirtop/export/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "isomir - bam - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + ], + "fasta": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + + ], + "vcf": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam.vcf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T15:25:40.531010949" + }, + "isomir - bam": { + "content": [ + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + ], + "fasta": [ + + ], + "tsv": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" + ] + ], + "vcf": [ + + ], + "versions": [ + "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T15:25:24.528528611" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml new file mode 100644 index 000000000000..6e57308ae1cd --- /dev/null +++ b/modules/nf-core/mirtop/gff/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirtop=0.4.25" + - "bioconda::samtools=1.15.1" diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf new file mode 100644 index 000000000000..1f951e2fada3 --- /dev/null +++ b/modules/nf-core/mirtop/gff/main.nf @@ -0,0 +1,55 @@ +process MIRTOP_GFF { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : + 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + + input: + tuple val(meta), path(bam) + tuple val(meta2), path(hairpin) + tuple val(meta3), path(gtf), val(species) + + output: + tuple val(meta), path("mirtop/${bam.baseName}.gff") , emit: sample_gff + tuple val(meta), path("mirtop/mirtop.gff") , emit: mirtop_gff + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mirtop \\ + gff \\ + $args \\ + --sps $species \\ + --hairpin $hairpin \\ + --gtf $gtf \\ + -o mirtop \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir mirtop + touch mirtop/mirtop.gff + touch mirtop/sim_isomir_sort.gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml new file mode 100644 index 000000000000..9d593210d2ee --- /dev/null +++ b/modules/nf-core/mirtop/gff/meta.yml @@ -0,0 +1,61 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "mirtop_gff" +description: mirtop gff generates the GFF3 adapter format to capture miRNA variations +keywords: + - mirna + - isomir + - gff +tools: + - "mirtop": + description: "Small RNA-seq annotation" + homepage: "https://github.com/miRTop/mirtop" + documentation: "https://mirtop.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/miRTop/mirtop" + licence: ["MIT License"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - sample_gff: + type: file + description: GFF file + pattern: "*.{gff}" + +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test new file mode 100644 index 000000000000..67b7ef3cf86a --- /dev/null +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process MIRTOP_GFF" + script "../main.nf" + process "MIRTOP_GFF" + + tag "modules" + tag "modules_nfcore" + tag "mirtop" + tag "mirtop/gff" + + test("isomir - bam") { + + when { + process { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.bam, + file(process.out.sample_gff[0][1]).readLines().findAll { it.contains("hsa-let-7a-2 miRBasev21 isomiR 3 25 0 + . Read TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;") }, + process.out.versions, + ).match() + }, + // md5sum is not stable, order of elements in section "variant" may change + { assert file(process.out.mirtop_gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} + ) + } + + } + + test("isomir - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap new file mode 100644 index 000000000000..8283d5ad2abd --- /dev/null +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap @@ -0,0 +1,67 @@ +{ + "isomir - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + ], + "mirtop_gff": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "sample_gff": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T12:47:11.610449763" + }, + "isomir - bam": { + "content": [ + null, + [ + "hsa-let-7a-2\tmiRBasev21\tisomiR\t3\t25\t0\t+\t.\tRead TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;" + ], + [ + "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T21:42:47.26306174" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml new file mode 100644 index 000000000000..3c24c43e8052 --- /dev/null +++ b/modules/nf-core/mirtop/stats/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirtop=0.4.25" + - "conda-forge::pandas=1.3.5" diff --git a/modules/nf-core/mirtop/stats/main.nf b/modules/nf-core/mirtop/stats/main.nf new file mode 100644 index 000000000000..51d33019a99b --- /dev/null +++ b/modules/nf-core/mirtop/stats/main.nf @@ -0,0 +1,51 @@ + +process MIRTOP_STATS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : + 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + + input: + tuple val(meta), path(mirtop_gff) + + output: + tuple val(meta), path("stats/*.txt") , emit: txt + tuple val(meta), path("stats/*_stats.log") , emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mirtop \\ + stats \\ + $args \\ + --out stats \\ + $mirtop_gff + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir stats + touch stats/${prefix}.txt + touch stats/${prefix}_stats.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml new file mode 100644 index 000000000000..7df0f7bca043 --- /dev/null +++ b/modules/nf-core/mirtop/stats/meta.yml @@ -0,0 +1,46 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "mirtop_stats" +description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category. +keywords: + - mirna + - isomir + - gff +tools: + - "mirtop": + description: "Small RNA-seq annotation" + homepage: "https://github.com/miRTop/mirtop" + documentation: "https://mirtop.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/miRTop/mirtop" + licence: ["MIT License"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: Mirtop GFF file obtained with mirtop_gff + pattern: "*.{gff}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - txt: + type: file + description: TXT file with stats + pattern: "*.{txt}" + +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test b/modules/nf-core/mirtop/stats/tests/main.nf.test new file mode 100644 index 000000000000..0309885fa121 --- /dev/null +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test @@ -0,0 +1,81 @@ + +nextflow_process { + + name "Test Process MIRTOP_STATS" + script "../main.nf" + process "MIRTOP_STATS" + + tag "modules" + tag "modules_nfcore" + tag "mirtop" + tag "mirtop/gff" + tag "mirtop/stats" + + setup { + run("MIRTOP_GFF") { + script "../../gff/main.nf" + process { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + } + + test("isomir - bam") { + + when { + process { + """ + input[0] = [ + [ id:'mirtop_gff_sample1'], // meta map + file("https://github.com/miRTop/mirtop/raw/master/data/examples/gff/correct_file.gff", checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("isomir - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'mirtop_gff_sample1'], // meta map + file("https://github.com/miRTop/mirtop/raw/master/data/examples/gff/correct_file.gff", checkIfExists: true), + ] """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap new file mode 100644 index 000000000000..ba9633d12a2c --- /dev/null +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap @@ -0,0 +1,100 @@ +{ + "isomir - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_gff_sample1.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_gff_sample1_stats.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + ], + "log": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_gff_sample1_stats.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "txt": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_gff_sample1.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T17:49:32.73944037" + }, + "isomir - bam": { + "content": [ + { + "0": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + ] + ], + "1": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + ] + ], + "2": [ + "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + ], + "log": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + ] + ], + "txt": [ + [ + { + "id": "mirtop_gff_sample1" + }, + "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + ] + ], + "versions": [ + "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T17:47:39.121648755" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf b/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf new file mode 100644 index 000000000000..17c2695fa9b6 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf @@ -0,0 +1,36 @@ +include { MIRTOP_GFF } from '../../../modules/nf-core/mirtop/gff' +include { MIRTOP_COUNTS } from '../../../modules/nf-core/mirtop/counts' +include { MIRTOP_EXPORT } from '../../../modules/nf-core/mirtop/export' +include { MIRTOP_STATS } from '../../../modules/nf-core/mirtop/stats' + + +workflow BAM_STATS_MIRNA_MIRTOP { + + take: + ch_bam // channel: [ val(meta), [ bam ] ] + ch_hairpin // channel: [ val(meta), [ hairpin ] ] + ch_gtf_species // channel: [ val(meta), [ gtf ], val(species) ] + + main: + + ch_versions = Channel.empty() + + MIRTOP_GFF ( ch_bam, ch_hairpin, ch_gtf_species ) + ch_versions = ch_versions.mix(MIRTOP_GFF.out.versions.first()) + + MIRTOP_COUNTS ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species ) + ch_versions = ch_versions.mix(MIRTOP_COUNTS.out.versions.first()) + + MIRTOP_EXPORT ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species ) + ch_versions = ch_versions.mix(MIRTOP_EXPORT.out.versions.first()) + + MIRTOP_STATS ( MIRTOP_GFF.out.mirtop_gff ) + ch_versions = ch_versions.mix(MIRTOP_STATS.out.versions.first()) + + emit: + rawdata_tsv = MIRTOP_EXPORT.out.tsv // channel: [ val(meta), [ tsv ] ] + stats_txt = MIRTOP_STATS.out.txt // channel: [ val(meta), [ txt ] ] + stats_log = MIRTOP_STATS.out.log // channel: [ val(meta), [ log ] ] + versions = ch_versions // channel: [ versions.yml ] +} + diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml b/subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml new file mode 100644 index 000000000000..e7cf4e733c1c --- /dev/null +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/meta.yml @@ -0,0 +1,61 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: "bam_stats_mirna_mirtop" +description: mirtop is a command line tool to annotate miRNAs and isomiRs and compute general statistics using the mirGFF3 format. +keywords: + - miRNA + - isomirs + - bam + - stats +components: + - mirtop/gff + - mirtop/counts + - mirtop/export + - mirtop/stats +input: + - ch_bam: + type: file + description: | + The input channel containing the BAM/CRAM/SAM files + Structure: [ val(meta), path(bam) ] + pattern: "*.{bam/cram/sam}" + - ch_hairpin: + type: file + description: | + Input channel containing the hairpin fasta file + Structure: [ val(meta), path(fasta) ] + pattern: "*.{fasta,fa}" + - ch_gtf_species: + type: file + description: | + Input channel containing the species gtf and the name of species in miRbase format + Structure: [ val(meta), path(gtf), val(species)] + pattern: "*.{gtf}" +output: + - rawdata_tsv: + type: file + description: | + Channel containing isomiRs compatible files + Structure: [ val(meta), path(tsv) ] + pattern: "*.tsv" + - stats_txt: + type: file + description: | + Channel containing TXT file with a table with different statistics for each type of isomiRs: total counts, average counts, total sequences. + Structure: [ val(meta), path(txt) ] + pattern: "*.txt" + - stats_log: + type: file + description: | + Channel containing log files in JSON format with the same information as stats_txt + Structure: [ val(meta), path(log) ] + pattern: "*.log" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test new file mode 100644 index 000000000000..064fd6547563 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test @@ -0,0 +1,49 @@ + +nextflow_workflow { + + name "Test Subworkflow BAM_STATS_MIRNA_MIRTOP" + script "../main.nf" + workflow "BAM_STATS_MIRNA_MIRTOP" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/bam_stats_mirna_mirtop" + tag "mirtop" + tag "mirtop/gff" + tag "mirtop/export" + tag "mirtop/stats" + tag "mirtop/counts" + + test("isomir - bam") { + + when { + workflow { + """ + input[0] = [ + [ id:'sample_sim_isomir_bam'], // meta map + file("https://github.com/nf-core/test-datasets/raw/smrnaseq/nf-test_data/mirtop/SRX8195117_SRR11631013_seqcluster.bam", checkIfExists: true), + ] + input[1] = [ + [ id:'hairpin'], // meta map + file("https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hairpin.fa", checkIfExists: true), + ] + input[2] = [ + [ id:'hsa' ], // meta map + file("https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/hsa.gff3", checkIfExists: true), + "hsa"] + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.rawdata_tsv, + workflow.out.stats_txt, + workflow.out.stats_log, + workflow.out.versions).match() } + ) + } + } +} diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap new file mode 100644 index 000000000000..02a07ab1b18b --- /dev/null +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap @@ -0,0 +1,41 @@ +{ + "isomir - bam": { + "content": [ + [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop_rawData.tsv:md5,4a065e444c54b0e816352bf1640594dd" + ] + ], + [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop_stats.txt:md5,e89c014047ffffed65f1ec4fb328e3bc" + ] + ], + [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "mirtop_stats.log:md5,49b85517828253858cc60a0390567585" + ] + ], + [ + "versions.yml:md5,04fed9539a0164a116d37bf090613d42", + "versions.yml:md5,13a50e3cef16f8bb981197bbc9a46d8e", + "versions.yml:md5,5f6bea8a46cdfec82b3d8f1b6c906ac7", + "versions.yml:md5,976382d50b05cded89483e2415fde415" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T21:31:21.204039357" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/nextflow.config b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/nextflow.config new file mode 100644 index 000000000000..83d77e209c25 --- /dev/null +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MIRTOP_COUNTS' { + ext.args = '--add-extra' + } +} From 97504fc033dd832a9589e44f4c1621bc4fc5c17f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Mon, 9 Sep 2024 18:06:41 +1200 Subject: [PATCH 034/486] Added nf-test for angsd/contamination (#6602) * Added nf-test for angsd/contamination * Swap container version * Update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Phil Ewels --- modules/nf-core/angsd/contamination/main.nf | 16 +++- modules/nf-core/angsd/contamination/meta.yml | 5 ++ .../angsd/contamination/tests/main.nf.test | 78 +++++++++++++++++++ .../contamination/tests/main.nf.test.snap | 60 ++++++++++++++ .../angsd/contamination/tests/nextflow.config | 5 ++ tests/config/pytest_modules.yml | 3 - .../nf-core/angsd/contamination/main.nf | 23 ------ .../angsd/contamination/nextflow.config | 9 --- .../nf-core/angsd/contamination/test.yml | 11 --- 9 files changed, 162 insertions(+), 48 deletions(-) create mode 100644 modules/nf-core/angsd/contamination/tests/main.nf.test create mode 100644 modules/nf-core/angsd/contamination/tests/main.nf.test.snap create mode 100644 modules/nf-core/angsd/contamination/tests/nextflow.config delete mode 100644 tests/modules/nf-core/angsd/contamination/main.nf delete mode 100644 tests/modules/nf-core/angsd/contamination/nextflow.config delete mode 100644 tests/modules/nf-core/angsd/contamination/test.yml diff --git a/modules/nf-core/angsd/contamination/main.nf b/modules/nf-core/angsd/contamination/main.nf index b33171b31df1..823db07f27c9 100644 --- a/modules/nf-core/angsd/contamination/main.nf +++ b/modules/nf-core/angsd/contamination/main.nf @@ -4,8 +4,8 @@ process ANGSD_CONTAMINATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/angsd:0.939--h468462d_0': - 'biocontainers/angsd:0.939--h468462d_0' }" + 'https://depot.galaxyproject.org/singularity/angsd:0.940--hf5e1c6e_3': + 'biocontainers/angsd:0.940--hf5e1c6e_3' }" input: tuple val(meta), path(icounts) @@ -30,6 +30,18 @@ process ANGSD_CONTAMINATION { 2> >(tee ${prefix}.txt >&2) + cat <<-END_VERSIONS > versions.yml + "${task.process}": + angsd: \$(echo \$(angsd 2>&1) | grep version | head -n 1 | sed 's/.*version: //g;s/ .*//g') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.txt + + cat <<-END_VERSIONS > versions.yml "${task.process}": angsd: \$(echo \$(angsd 2>&1) | grep version | head -n 1 | sed 's/.*version: //g;s/ .*//g') diff --git a/modules/nf-core/angsd/contamination/meta.yml b/modules/nf-core/angsd/contamination/meta.yml index dc01c90c03e8..ffe6428d6443 100644 --- a/modules/nf-core/angsd/contamination/meta.yml +++ b/modules/nf-core/angsd/contamination/meta.yml @@ -22,6 +22,11 @@ input: type: file description: Internal format for dumping binary single chrs. Useful for ANGSD contamination pattern: "*.icnts.gz" + - meta2: + type: map + description: | + Groovy Map containing information related to the hapmap_file. + e.g. [ id:'test' ] - hapmap_file: type: file description: A list of variable sites to look for heterozygosity. diff --git a/modules/nf-core/angsd/contamination/tests/main.nf.test b/modules/nf-core/angsd/contamination/tests/main.nf.test new file mode 100644 index 000000000000..1b5737d012cc --- /dev/null +++ b/modules/nf-core/angsd/contamination/tests/main.nf.test @@ -0,0 +1,78 @@ + +nextflow_process { + + name "Test Process ANGSD_CONTAMINATION" + script "../main.nf" + process "ANGSD_CONTAMINATION" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "angsd" + tag "angsd/contamination" + tag "angsd/docounts" + + setup { + run("ANGSD_DOCOUNTS") { + script "../../../angsd/docounts/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.markduplicates.sorted.bam.bai', checkIfExists: true), + [] + ] + + """ + } + } + } + + test("test-angsd-contamination") { + + when { + process { + """ + input[0] = ANGSD_DOCOUNTS.out.icounts + input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.txt[0][1]).readLines()[3..7], + file(process.out.versions[0]).readLines(), + process.out.versions + ).match() + } + ) + } + } + + test("test-angsd-contamination-stub") { + options '-stub' + + when { + process { + """ + input[0] = ANGSD_DOCOUNTS.out.icounts + input[1] = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/angsd/contamination/tests/main.nf.test.snap b/modules/nf-core/angsd/contamination/tests/main.nf.test.snap new file mode 100644 index 000000000000..585dedcb5c0a --- /dev/null +++ b/modules/nf-core/angsd/contamination/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "test-angsd-contamination": { + "content": [ + [ + "Seed value of 0 (zero) will use time as seed", + "-----------------", + "[readhap] We now have: 58190 snpSites after filtering based on hapMapfile", + "[readicnts] fname:test.icnts.gz minDepth:2 maxDepth:200", + "[readicnts] Has read:1557012 sites, 1517472 sites (after depfilter) from ANGSD icnts file" + ], + [ + "\"ANGSD_CONTAMINATION\":", + " angsd: 0.940-dirty" + ], + [ + "versions.yml:md5,e496b7eb11be581adf1781883ba2abff" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-09T05:53:42.620175303" + }, + "test-angsd-contamination-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,e496b7eb11be581adf1781883ba2abff" + ], + "txt": [ + [ + { + "id": "test", + "single_end": false + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e496b7eb11be581adf1781883ba2abff" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-09T05:53:56.844309422" + } +} \ No newline at end of file diff --git a/modules/nf-core/angsd/contamination/tests/nextflow.config b/modules/nf-core/angsd/contamination/tests/nextflow.config new file mode 100644 index 000000000000..6209ade19eb3 --- /dev/null +++ b/modules/nf-core/angsd/contamination/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: ANGSD_DOCOUNTS { + ext.args = "-iCounts 1 -doDepth -dumpCounts 2" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index f286ae2c2a49..87dbeaad348d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,9 +1,6 @@ amps: - modules/nf-core/amps/** - tests/modules/nf-core/amps/** -angsd/contamination: - - modules/nf-core/angsd/contamination/** - - tests/modules/nf-core/angsd/contamination/** arriba/arriba: - modules/nf-core/arriba/arriba/** - tests/modules/nf-core/arriba/arriba/** diff --git a/tests/modules/nf-core/angsd/contamination/main.nf b/tests/modules/nf-core/angsd/contamination/main.nf deleted file mode 100644 index 2c2b528090c9..000000000000 --- a/tests/modules/nf-core/angsd/contamination/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ANGSD_CONTAMINATION } from '../../../../../modules/nf-core/angsd/contamination/main.nf' -include { ANGSD_DOCOUNTS } from '../../../../../modules/nf-core/angsd/docounts/main.nf' - -workflow test_angsd_contamination { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_markduplicates_sorted_bam_bai'], checkIfExists: true), - [] - ] - - hapmap_file = [ [id:'test2'], file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/angsd/HapMapChrX.gz")] - - ANGSD_DOCOUNTS ( input ) - ANGSD_CONTAMINATION ( ANGSD_DOCOUNTS.out.icounts, hapmap_file ) - - ANGSD_CONTAMINATION.out.txt.view() -} diff --git a/tests/modules/nf-core/angsd/contamination/nextflow.config b/tests/modules/nf-core/angsd/contamination/nextflow.config deleted file mode 100644 index 3aadf73c538a..000000000000 --- a/tests/modules/nf-core/angsd/contamination/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: ANGSD_DOCOUNTS { - ext.args = "-iCounts 1 -doDepth -dumpCounts 2" - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/angsd/contamination/test.yml b/tests/modules/nf-core/angsd/contamination/test.yml deleted file mode 100644 index 63f63b0cdc2d..000000000000 --- a/tests/modules/nf-core/angsd/contamination/test.yml +++ /dev/null @@ -1,11 +0,0 @@ -- name: angsd contamination test_angsd_contamination - command: nextflow run ./tests/modules/nf-core/angsd/contamination -entry test_angsd_contamination -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/angsd/contamination/nextflow.config - tags: - - angsd - - angsd/contamination - files: - - path: output/angsd/test.txt - contains: - - "Method1: old_llh" - - "Method2: old_llh" - - path: output/angsd/versions.yml From c3c0c5fe7336c4e60b875e6604605ba3b6bbf2a4 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 9 Sep 2024 09:24:23 +0200 Subject: [PATCH 035/486] Add support for pip dependencies and force version pinning in conda (#6588) * Add support for pip dependencies and force version pinning in conda * [automated] Fix linting with Prettier --------- Co-authored-by: nf-core-bot --- modules/environment-schema.json | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/modules/environment-schema.json b/modules/environment-schema.json index 48382b080872..cf0d09815acd 100644 --- a/modules/environment-schema.json +++ b/modules/environment-schema.json @@ -14,7 +14,26 @@ "dependencies": { "type": "array", "items": { - "type": "string" + "oneOf": [ + { + "type": "string", + "pattern": "^.*[^><]=[^><].*$", + "$comment": "The above pattern ensures that all packages are pinned to a specific version. This ensures the reproducibility of the environment" + }, + { + "type": "object", + "properties": { + "pip": { + "type": "array", + "items": { + "type": "string", + "pattern": "^.*==.*$", + "$comment": "The above pattern ensures that all packages are pinned to a specific version. This ensures the reproducibility of the environment" + } + } + } + } + ] } } }, From ebfbd5ea430aa35eca1fbe029043dd2c94457a41 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 9 Sep 2024 11:13:28 -0300 Subject: [PATCH 036/486] Add `seqcluster` module (#6614) * add seqcluster module * run prettier * Update modules/nf-core/seqcluster/collapse/environment.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/meta.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .../seqcluster/collapse/environment.yml | 5 ++ modules/nf-core/seqcluster/collapse/main.nf | 48 +++++++++++++ modules/nf-core/seqcluster/collapse/meta.yml | 46 ++++++++++++ .../seqcluster/collapse/tests/main.nf.test | 58 +++++++++++++++ .../collapse/tests/main.nf.test.snap | 72 +++++++++++++++++++ .../seqcluster/collapse/tests/nextflow.config | 6 ++ 6 files changed, 235 insertions(+) create mode 100644 modules/nf-core/seqcluster/collapse/environment.yml create mode 100644 modules/nf-core/seqcluster/collapse/main.nf create mode 100644 modules/nf-core/seqcluster/collapse/meta.yml create mode 100644 modules/nf-core/seqcluster/collapse/tests/main.nf.test create mode 100644 modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap create mode 100644 modules/nf-core/seqcluster/collapse/tests/nextflow.config diff --git a/modules/nf-core/seqcluster/collapse/environment.yml b/modules/nf-core/seqcluster/collapse/environment.yml new file mode 100644 index 000000000000..1263856a43e0 --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::seqcluster=1.2.9" diff --git a/modules/nf-core/seqcluster/collapse/main.nf b/modules/nf-core/seqcluster/collapse/main.nf new file mode 100644 index 000000000000..3bbb3aa092c8 --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/main.nf @@ -0,0 +1,48 @@ +process SEQCLUSTER_COLLAPSE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqcluster:1.2.9--pyh5e36f6f_0': + 'biocontainers/seqcluster:1.2.9--pyh5e36f6f_0' }" + + input: + tuple val(meta), path(fastq) + + output: + tuple val(meta), path("*.fastq.gz") , emit: fastq + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("$fastq" == "${prefix}.fastq.gz") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + seqcluster \\ + collapse \\ + $args \\ + -f $fastq \\ + -o - | gzip > ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqcluster: \$(echo \$(seqcluster --version 2>&1) | sed 's/^.*seqcluster //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqcluster: \$(echo \$(seqcluster --version 2>&1) | sed 's/^.*seqcluster //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/seqcluster/collapse/meta.yml b/modules/nf-core/seqcluster/collapse/meta.yml new file mode 100644 index 000000000000..03e9dc6330bb --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/meta.yml @@ -0,0 +1,46 @@ +name: "seqcluster_collapse" +description: Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file. +keywords: + - smrnaseq + - cluster + - mirna +tools: + - "seqcluster": + description: "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project." + homepage: "https://github.com/lpantano/seqcluster" + documentation: "https://github.com/lpantano/seqcluster" + tool_dev_url: "https://github.com/lpantano/seqcluster" + doi: "10.1093/bioinformatics/btr527" + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - fastq: + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" + +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/seqcluster/collapse/tests/main.nf.test b/modules/nf-core/seqcluster/collapse/tests/main.nf.test new file mode 100644 index 000000000000..21d54b9967fa --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/tests/main.nf.test @@ -0,0 +1,58 @@ +nextflow_process { + + name "Test Process SEQCLUSTER_COLLAPSE" + script "../main.nf" + process "SEQCLUSTER_COLLAPSE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "seqcluster" + tag "seqcluster/collapse" + + test("human - fastq") { + when { + process { + """ + input[0] = [ + [ id:'test_1', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("human - fastq - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test_1', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap b/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap new file mode 100644 index 000000000000..bd59894bff32 --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "human - fastq": { + "content": [ + { + "0": [ + [ + { + "id": "test_1", + "single_end": false + }, + "test_1_seqcluster.fastq.gz:md5,16bd8345663060489286738f384e8e0f" + ] + ], + "1": [ + "versions.yml:md5,3eac6df59cc79fecd4d39b164e25a61b" + ], + "fastq": [ + [ + { + "id": "test_1", + "single_end": false + }, + "test_1_seqcluster.fastq.gz:md5,16bd8345663060489286738f384e8e0f" + ] + ], + "versions": [ + "versions.yml:md5,3eac6df59cc79fecd4d39b164e25a61b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T16:36:22.010506414" + }, + "human - fastq - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_1", + "single_end": false + }, + "test_1_seqcluster.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,3eac6df59cc79fecd4d39b164e25a61b" + ], + "fastq": [ + [ + { + "id": "test_1", + "single_end": false + }, + "test_1_seqcluster.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,3eac6df59cc79fecd4d39b164e25a61b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T16:36:36.069537603" + } +} \ No newline at end of file diff --git a/modules/nf-core/seqcluster/collapse/tests/nextflow.config b/modules/nf-core/seqcluster/collapse/tests/nextflow.config new file mode 100644 index 000000000000..eb86c1b2e255 --- /dev/null +++ b/modules/nf-core/seqcluster/collapse/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: SEQCLUSTER_COLLAPSE { + ext.args = "-m 1 --min_size 15" + ext.prefix = {"${meta.id}_seqcluster"} + } +} From cfebb244d8c83ae533bf2db399f9af361927d504 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 9 Sep 2024 18:27:07 +0200 Subject: [PATCH 037/486] Add PREFIX to SPADES warnings log (#6615) * Update main.nf * Update main.nf.test.snap --- modules/nf-core/spades/main.nf | 8 ++++++-- modules/nf-core/spades/tests/main.nf.test.snap | 6 +++--- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/modules/nf-core/spades/main.nf b/modules/nf-core/spades/main.nf index 81b36809ebdf..36cdfe444cc0 100644 --- a/modules/nf-core/spades/main.nf +++ b/modules/nf-core/spades/main.nf @@ -18,7 +18,7 @@ process SPADES { tuple val(meta), path('*.transcripts.fa.gz') , optional:true, emit: transcripts tuple val(meta), path('*.gene_clusters.fa.gz'), optional:true, emit: gene_clusters tuple val(meta), path('*.assembly.gfa.gz') , optional:true, emit: gfa - tuple val(meta), path('warnings.log') , optional:true, emit: warnings + tuple val(meta), path('*.warnings.log') , optional:true, emit: warnings tuple val(meta), path('*.spades.log') , emit: log path "versions.yml" , emit: versions @@ -66,6 +66,10 @@ process SPADES { gzip -n ${prefix}.gene_clusters.fa fi + if [ -f warnings.log ]; then + mv warnings.log ${prefix}.warnings.log + fi + cat <<-END_VERSIONS > versions.yml "${task.process}": spades: \$(spades.py --version 2>&1 | sed -n 's/^.*SPAdes genome assembler v//p') @@ -88,7 +92,7 @@ process SPADES { echo "" | gzip > ${prefix}.gene_clusters.fa.gz echo "" | gzip > ${prefix}.assembly.gfa.gz touch ${prefix}.spades.log - touch warnings.log + touch ${prefix}.warnings.log cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/spades/tests/main.nf.test.snap b/modules/nf-core/spades/tests/main.nf.test.snap index 3f8c7718cdd0..e1b3b652fd20 100644 --- a/modules/nf-core/spades/tests/main.nf.test.snap +++ b/modules/nf-core/spades/tests/main.nf.test.snap @@ -311,7 +311,7 @@ "id": "test", "single_end": false }, - "warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -389,7 +389,7 @@ "id": "test", "single_end": false }, - "warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.warnings.log:md5,d41d8cd98f00b204e9800998ecf8427e" ] ] } @@ -400,4 +400,4 @@ }, "timestamp": "2024-06-07T07:20:07.195881734" } -} \ No newline at end of file +} From 3a267da7aa47ef59bb9d62aba580221a3371ccbf Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 10 Sep 2024 06:24:24 +0100 Subject: [PATCH 038/486] Update actions/setup-java digest to 2dfa201 (#6617) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/test.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 53cdc88e172d..413f31a8b1bf 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -166,7 +166,7 @@ jobs: - name: Install pip run: python -m pip install --upgrade pip - - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4 + - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 with: distribution: "temurin" java-version: "17" @@ -204,7 +204,7 @@ jobs: - name: Install pip run: python -m pip install --upgrade pip - - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4 + - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 with: distribution: "temurin" java-version: "17" @@ -416,7 +416,7 @@ jobs: - name: Install Python dependencies run: python -m pip install --upgrade pip pytest-workflow cryptography - - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4 + - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 with: distribution: "temurin" java-version: "17" @@ -643,7 +643,7 @@ jobs: steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4 + - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 with: distribution: "temurin" java-version: "17" From c44b5e99aea273adf455d8c40babeb3885083ff9 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 10 Sep 2024 11:59:37 +0200 Subject: [PATCH 039/486] Update GTDBTK/CLASSIFYWF: Fix bash failing if nothing to move in output directory (#6618) * Fix bash failing if nothing to move in output directory (which is a valid behaviour) * HarshilAlignmentTM --- modules/nf-core/gtdbtk/classifywf/main.nf | 55 +++++++++++------------ 1 file changed, 26 insertions(+), 29 deletions(-) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 9fc7a32df7f9..9aa13ee477fc 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -1,29 +1,25 @@ process GTDBTK_CLASSIFYWF { tag "${prefix}" label 'process_medium' - - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' : - 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gtdbtk:2.4.0--pyhdfd78af_1' : 'biocontainers/gtdbtk:2.4.0--pyhdfd78af_1'}" input: - tuple val(meta), path("bins/*") + tuple val(meta) , path("bins/*") tuple val(db_name), path("database/*") - path(mash_db) + path mash_db output: - tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv") , emit: summary - tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz") , emit: tree, optional: true - tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv") , emit: markers, optional: true - tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz") , emit: msa, optional: true - tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz") , emit: user_msa, optional: true - tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv") , emit: filtered, optional: true - tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv") , emit: failed, optional: true - tuple val(meta), path("gtdbtk.${prefix}.log") , emit: log - tuple val(meta), path("gtdbtk.${prefix}.warnings.log") , emit: warnings - path("versions.yml") , emit: versions + tuple val(meta), path("gtdbtk.${prefix}.*.summary.tsv") , emit: summary + tuple val(meta), path("gtdbtk.${prefix}.*.classify.tree.gz") , emit: tree , optional: true + tuple val(meta), path("gtdbtk.${prefix}.*.markers_summary.tsv"), emit: markers , optional: true + tuple val(meta), path("gtdbtk.${prefix}.*.msa.fasta.gz") , emit: msa , optional: true + tuple val(meta), path("gtdbtk.${prefix}.*.user_msa.fasta.gz") , emit: user_msa, optional: true + tuple val(meta), path("gtdbtk.${prefix}.*.filtered.tsv") , emit: filtered, optional: true + tuple val(meta), path("gtdbtk.${prefix}.failed_genomes.tsv") , emit: failed , optional: true + tuple val(meta), path("gtdbtk.${prefix}.log") , emit: log + tuple val(meta), path("gtdbtk.${prefix}.warnings.log") , emit: warnings + path ("versions.yml"), emit: versions when: task.ext.when == null || task.ext.when @@ -31,7 +27,7 @@ process GTDBTK_CLASSIFYWF { script: def args = task.ext.args ?: '' def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : "" - def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen" + def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen" prefix = task.ext.prefix ?: "${meta.id}" """ @@ -41,27 +37,27 @@ process GTDBTK_CLASSIFYWF { fi gtdbtk classify_wf \\ - $args \\ + ${args} \\ --genome_dir bins \\ --prefix "gtdbtk.${prefix}" \\ --out_dir "\${PWD}" \\ - --cpus $task.cpus \\ - $mash_mode \\ - $pplacer_scratch \\ - --min_perc_aa $params.gtdbtk_min_perc_aa \\ - --min_af $params.gtdbtk_min_af + --cpus ${task.cpus} \\ + ${mash_mode} \\ + ${pplacer_scratch} \\ + --min_perc_aa ${params.gtdbtk_min_perc_aa} \\ + --min_af ${params.gtdbtk_min_af} ## If mash db given, classify/ and identify/ directories won't be created - if [[ -d classify/ ]]; then + if [[ -d classify/ && \$(ls -A classify/) ]]; then mv classify/* . fi - if [[ -d identify/ ]]; then + if [[ -d identify/ && \$(ls -A identify/) ]]; then mv identify/* . fi ## If nothing aligns, no output, so only run - if [[ -d align/ ]]; then + if [[ -d align/ && \$(ls -A align/) ]]; then mv align/* . fi @@ -78,7 +74,8 @@ process GTDBTK_CLASSIFYWF { """ stub: - def VERSION = '2.3.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '2.3.2' + // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. prefix = task.ext.prefix ?: "${meta.id}" """ touch gtdbtk.${prefix}.stub.summary.tsv @@ -93,7 +90,7 @@ process GTDBTK_CLASSIFYWF { cat <<-END_VERSIONS > versions.yml "${task.process}": - gtdbtk: \$(echo "$VERSION") + gtdbtk: \$(echo "${VERSION}") END_VERSIONS """ } From 4bf5e869d8e8ba26a3e9c510e4d822b6c5fa25ab Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 10 Sep 2024 13:08:54 +0100 Subject: [PATCH 040/486] Fix fq/generate (#6610) Update snapshot, add stub --- modules/nf-core/fq/generate/main.nf | 12 ++++ .../nf-core/fq/generate/tests/main.nf.test | 23 +++++++- .../fq/generate/tests/main.nf.test.snap | 57 +++++++++++++++++-- .../nf-core/fq/generate/tests/nextflow.config | 5 +- 4 files changed, 84 insertions(+), 13 deletions(-) diff --git a/modules/nf-core/fq/generate/main.nf b/modules/nf-core/fq/generate/main.nf index bdebcc4739d4..7809f3344841 100644 --- a/modules/nf-core/fq/generate/main.nf +++ b/modules/nf-core/fq/generate/main.nf @@ -30,4 +30,16 @@ process FQ_GENERATE { fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g')) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo | gzip > ${prefix}_R1.fastq.gz + echo | gzip > ${prefix}_R2.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + fq: \$(echo \$(fq generate --version | sed 's/fq-generate //g')) + END_VERSIONS + """ } diff --git a/modules/nf-core/fq/generate/tests/main.nf.test b/modules/nf-core/fq/generate/tests/main.nf.test index ebdce4a62619..9029120333a1 100644 --- a/modules/nf-core/fq/generate/tests/main.nf.test +++ b/modules/nf-core/fq/generate/tests/main.nf.test @@ -9,12 +9,28 @@ nextflow_process { tag "fq" tag "fq/generate" - test("test_fq_lint_fail") { + test("test fq") { config "./nextflow.config" when { - params { - outdir = "$outputDir" + process { + """ + input[0] = Channel.of( [ id:'test', single_end:false ] ) + """ } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("test fq -stub") { + options "-stub" + when { process { """ input[0] = Channel.of( [ id:'test', single_end:false ] ) @@ -30,4 +46,5 @@ nextflow_process { } } + } diff --git a/modules/nf-core/fq/generate/tests/main.nf.test.snap b/modules/nf-core/fq/generate/tests/main.nf.test.snap index d7700686431a..9af0b8bfaa4d 100644 --- a/modules/nf-core/fq/generate/tests/main.nf.test.snap +++ b/modules/nf-core/fq/generate/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test_fq_lint_fail": { + "test fq -stub": { "content": [ { "0": [ @@ -9,8 +9,8 @@ "single_end": false }, [ - "test_R1.fastq.gz:md5,1d262f7028e65d291c4a46f890f539e1", - "test_R2.fastq.gz:md5,d7bd728bb013edced318e2a797ad60b3" + "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -24,8 +24,8 @@ "single_end": false }, [ - "test_R1.fastq.gz:md5,1d262f7028e65d291c4a46f890f539e1", - "test_R2.fastq.gz:md5,d7bd728bb013edced318e2a797ad60b3" + "test_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -34,6 +34,51 @@ ] } ], - "timestamp": "2023-10-17T11:27:57.943374" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T16:03:12.733228308" + }, + "test fq": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_R1.fastq.gz:md5,3acdc5cb66c65a6fb1e8a87c37dec288", + "test_R2.fastq.gz:md5,026a0d0711dc3cd581ab26c5b1757eee" + ] + ] + ], + "1": [ + "versions.yml:md5,def2d5900b648a4fc802b237e985efb7" + ], + "fastq": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_R1.fastq.gz:md5,3acdc5cb66c65a6fb1e8a87c37dec288", + "test_R2.fastq.gz:md5,026a0d0711dc3cd581ab26c5b1757eee" + ] + ] + ], + "versions": [ + "versions.yml:md5,def2d5900b648a4fc802b237e985efb7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-06T16:03:01.858857277" } } \ No newline at end of file diff --git a/modules/nf-core/fq/generate/tests/nextflow.config b/modules/nf-core/fq/generate/tests/nextflow.config index 4582e854e18f..9890b87916b5 100644 --- a/modules/nf-core/fq/generate/tests/nextflow.config +++ b/modules/nf-core/fq/generate/tests/nextflow.config @@ -1,8 +1,5 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: FQ_GENERATE { ext.args = '-s 123' } -} \ No newline at end of file +} From 407ff4b579f5ae5a3b842b675cd75005d112b8ba Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Tue, 10 Sep 2024 09:13:50 -0300 Subject: [PATCH 041/486] Fix `seqcluster` (#6616) * change test data with smrnaseq data and fix fastq capturing * point to nf-core repo --- modules/nf-core/seqcluster/collapse/main.nf | 5 ++++- modules/nf-core/seqcluster/collapse/tests/main.nf.test | 4 ++-- .../nf-core/seqcluster/collapse/tests/main.nf.test.snap | 8 ++++---- 3 files changed, 10 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/seqcluster/collapse/main.nf b/modules/nf-core/seqcluster/collapse/main.nf index 3bbb3aa092c8..8c3f2256b616 100644 --- a/modules/nf-core/seqcluster/collapse/main.nf +++ b/modules/nf-core/seqcluster/collapse/main.nf @@ -26,7 +26,10 @@ process SEQCLUSTER_COLLAPSE { collapse \\ $args \\ -f $fastq \\ - -o - | gzip > ${prefix}.fastq.gz + -o collapsed + + gzip collapsed/*_trimmed.fastq + mv collapsed/*_trimmed.fastq.gz ${prefix}.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/seqcluster/collapse/tests/main.nf.test b/modules/nf-core/seqcluster/collapse/tests/main.nf.test index 21d54b9967fa..ffca4e92579c 100644 --- a/modules/nf-core/seqcluster/collapse/tests/main.nf.test +++ b/modules/nf-core/seqcluster/collapse/tests/main.nf.test @@ -16,7 +16,7 @@ nextflow_process { """ input[0] = [ [ id:'test_1', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz", checkIfExists: true), ] """ } @@ -40,7 +40,7 @@ nextflow_process { """ input[0] = [ [ id:'test_1', single_end:false ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file("https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz", checkIfExists: true), ] """ } diff --git a/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap b/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap index bd59894bff32..6f29d70ea7eb 100644 --- a/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap +++ b/modules/nf-core/seqcluster/collapse/tests/main.nf.test.snap @@ -8,7 +8,7 @@ "id": "test_1", "single_end": false }, - "test_1_seqcluster.fastq.gz:md5,16bd8345663060489286738f384e8e0f" + "test_1_seqcluster.fastq.gz:md5,21c736de10e306f14ec296eaeb38ef45" ] ], "1": [ @@ -20,7 +20,7 @@ "id": "test_1", "single_end": false }, - "test_1_seqcluster.fastq.gz:md5,16bd8345663060489286738f384e8e0f" + "test_1_seqcluster.fastq.gz:md5,21c736de10e306f14ec296eaeb38ef45" ] ], "versions": [ @@ -32,7 +32,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-06T16:36:22.010506414" + "timestamp": "2024-09-09T19:48:39.444011681" }, "human - fastq - stub": { "content": [ @@ -67,6 +67,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-06T16:36:36.069537603" + "timestamp": "2024-09-09T19:41:17.429861126" } } \ No newline at end of file From f195be83629b25d271a11612afd61062bf85ec7b Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 10 Sep 2024 14:36:35 +0200 Subject: [PATCH 042/486] add pairhmm threads to haplotypecaller (#6620) --- modules/nf-core/gatk4/haplotypecaller/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/gatk4/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 3043ee07aba9..b2aff48969ee 100644 --- a/modules/nf-core/gatk4/haplotypecaller/main.nf +++ b/modules/nf-core/gatk4/haplotypecaller/main.nf @@ -44,6 +44,7 @@ process GATK4_HAPLOTYPECALLER { --input $input \\ --output ${prefix}.vcf.gz \\ --reference $fasta \\ + --native-pair-hmm-threads ${task.cpus} \\ $dbsnp_command \\ $interval_command \\ $dragstr_command \\ From 1d73b33d2e4885be77cce31fdd9405de135d7e0f Mon Sep 17 00:00:00 2001 From: Nur M Shahir Date: Tue, 10 Sep 2024 10:40:43 -0400 Subject: [PATCH 043/486] Nextclade vers bump (#6356) * Update environment.yml * Update main.nf Updated containers to 3.8.2 * Update meta.yml * Update main.nf * Create nf-test.config * Create main.nf.test nf-test module * Create main.nf.test.snap * Create nextflow.config * Update main.nf fixing biocontainer issue * Update meta.yml * nextclade version bump from 2.12 to 3.8.2 * Update meta.yml * Update test.yml regenerated test.yml * Update modules/nf-core/nextclade/datasetget/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nextclade/run/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Delete tests/modules/nf-core/nextclade/run/test.yml deleted * Delete modules/nf-core/nextclade/run/tests/nextflow.config Deleting * Delete modules/nf-core/nextclade/run/nf-test.config * Delete modules/nf-core/nextclade/datasetget/tests/nextflow.config * Delete modules/nf-core/nextclade/datasetget/nf-test.config * Update main.nf.test * Update main.nf.test making tag adhere to guidelines * Update main.nf.test add params block [this mainly because I couldn't run the test locally without it) * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test add stub * Update main.nf.test * Update tests/config/pytest_modules.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update pytest_modules.yml * Delete tests/modules/nf-core/nextclade/datasetget/main.nf * Delete tests/modules/nf-core/nextclade/datasetget/test.yml * Delete tests/modules/nf-core/nextclade/run/main.nf * Update main.nf.test add stub to nextclade/datasetget test * Delete tests/modules/nf-core/nextclade/datasetget/nextflow.config * Update snapshot * Update meta.yml * Update main.nf.test updated main.nf.test * Update main.nf.test.snap * Add stubs and swap to only snapshoting part of the json * Update modules/nf-core/nextclade/datasetget/main.nf --------- Co-authored-by: shahirnm Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../nextclade/datasetget/environment.yml | 2 +- modules/nf-core/nextclade/datasetget/main.nf | 26 +- modules/nf-core/nextclade/datasetget/meta.yml | 6 +- .../nextclade/datasetget/tests/main.nf.test | 31 ++- .../datasetget/tests/main.nf.test.snap | 36 ++- modules/nf-core/nextclade/run/environment.yml | 2 +- modules/nf-core/nextclade/run/main.nf | 24 +- modules/nf-core/nextclade/run/meta.yml | 32 ++- .../nf-core/nextclade/run/tests/main.nf.test | 82 ++++++ .../nextclade/run/tests/main.nf.test.snap | 245 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/nextclade/run/main.nf | 23 -- tests/modules/nf-core/nextclade/run/test.yml | 62 ----- 13 files changed, 445 insertions(+), 129 deletions(-) create mode 100644 modules/nf-core/nextclade/run/tests/main.nf.test create mode 100644 modules/nf-core/nextclade/run/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/nextclade/run/main.nf delete mode 100644 tests/modules/nf-core/nextclade/run/test.yml diff --git a/modules/nf-core/nextclade/datasetget/environment.yml b/modules/nf-core/nextclade/datasetget/environment.yml index 58a06b619f0f..09c0ba1a8460 100644 --- a/modules/nf-core/nextclade/datasetget/environment.yml +++ b/modules/nf-core/nextclade/datasetget/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::nextclade=2.12.0 + - bioconda::nextclade=3.8.2 diff --git a/modules/nf-core/nextclade/datasetget/main.nf b/modules/nf-core/nextclade/datasetget/main.nf index 70c900a5f70a..4f8783812310 100644 --- a/modules/nf-core/nextclade/datasetget/main.nf +++ b/modules/nf-core/nextclade/datasetget/main.nf @@ -4,12 +4,11 @@ process NEXTCLADE_DATASETGET { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/nextclade:2.12.0--h9ee0642_0' : - 'biocontainers/nextclade:2.12.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/nextclade:3.8.2--h9ee0642_0' : + 'biocontainers/nextclade:3.8.2--h9ee0642_0' }" input: val dataset - val reference val tag output: @@ -22,7 +21,6 @@ process NEXTCLADE_DATASETGET { script: def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${dataset}" - def fasta = reference ? "--reference ${reference}" : '' def version = tag ? "--tag ${tag}" : '' """ nextclade \\ @@ -30,7 +28,6 @@ process NEXTCLADE_DATASETGET { get \\ $args \\ --name $dataset \\ - $fasta \\ $version \\ --output-dir $prefix @@ -39,4 +36,23 @@ process NEXTCLADE_DATASETGET { nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${dataset}" + """ + mkdir -p ${prefix} + touch ${prefix}/CHANGELOG.md + touch ${prefix}/README.md + touch ${prefix}/genome_annotation.gff3 + touch ${prefix}/pathogen.json + touch ${prefix}/reference.fasta + touch ${prefix}/sequences.fasta + touch ${prefix}/tree.json + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') + END_VERSIONS + """ + } diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml index 7494b0ed7737..290ed0cd9263 100644 --- a/modules/nf-core/nextclade/datasetget/meta.yml +++ b/modules/nf-core/nextclade/datasetget/meta.yml @@ -16,10 +16,6 @@ input: type: string description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command. pattern: ".+" - - reference: - type: string - description: Accession id to download dataset based on a particular reference sequence. A list of available datasets can be obtained using the nextclade dataset list command. - pattern: ".+" - tag: type: string description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command. @@ -39,3 +35,5 @@ authors: maintainers: - "@antunderwood" - "@drpatelh" +updated on 2024.08.27: + - "@nmshahir" diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test b/modules/nf-core/nextclade/datasetget/tests/main.nf.test index b0d801359992..d7eb12b7dba8 100644 --- a/modules/nf-core/nextclade/datasetget/tests/main.nf.test +++ b/modules/nf-core/nextclade/datasetget/tests/main.nf.test @@ -10,21 +10,40 @@ nextflow_process { tag "nextclade" tag "nextclade/datasetget" - test("species-id-time") { - + test("species-tag") { + + when { + process { + """ + input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' + input[1] = '2024-01-16--20-31-02Z' + + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + + test("species-tag-stub") { + options '-stub' + when { process { """ - input[0] = 'sars-cov-2' - input[1] = 'MN908947' - input[2] = '2022-01-18T12:00:00Z' + input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' + input[1] = '2024-01-16--20-31-02Z' """ } } then { - assertAll( + assertAll ( { assert process.success }, { assert snapshot(process.out).match() } ) diff --git a/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap b/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap index 02ab3e9ece2a..8de6fd568919 100644 --- a/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap +++ b/modules/nf-core/nextclade/datasetget/tests/main.nf.test.snap @@ -1,43 +1,41 @@ { - "test-nextclade-datasetget": { + "species-tag": { "content": [ { "0": [ [ - "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8", - "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e", - "qc.json:md5,c512f51fda0212b21ffff05779180963", + "CHANGELOG.md:md5,ebbe8be5a3c378ed903c1afb4d8c441d", + "README.md:md5,c69387d632361334f0d7c9b66065f947", + "genome_annotation.gff3:md5,4dff84d2d6ada820e0e3a8bc6798d402", + "pathogen.json:md5,db5bbec52359c1e168ffc5e6dc0ea32a", "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c", - "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b", - "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3", - "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1", - "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81" + "sequences.fasta:md5,c2a4d6cbb837dce22d81f9c36dd0629e", + "tree.json:md5,e180607cd34a6cb6bab101d295f6cedf" ] ], "1": [ - "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7" + "versions.yml:md5,8c64a653330d1c5cb58ee1b8363b22d3" ], "dataset": [ [ - "genemap.gff:md5,21ebebfd0f416eeb959e55ebffd808e8", - "primers.csv:md5,5990c3483bf66ce607aeb90a44e7ef2e", - "qc.json:md5,c512f51fda0212b21ffff05779180963", + "CHANGELOG.md:md5,ebbe8be5a3c378ed903c1afb4d8c441d", + "README.md:md5,c69387d632361334f0d7c9b66065f947", + "genome_annotation.gff3:md5,4dff84d2d6ada820e0e3a8bc6798d402", + "pathogen.json:md5,db5bbec52359c1e168ffc5e6dc0ea32a", "reference.fasta:md5,c7ce05f28e4ec0322c96f24e064ef55c", - "sequences.fasta:md5,41129d255b99e0e92bdf20e866b99a1b", - "tag.json:md5,402ac2b87e2a6a64a3fbf5ad16497af3", - "tree.json:md5,b8f32f547ff9e2131d6fc66b68fc54b1", - "virus_properties.json:md5,5f2de3949e07cb633f3d9e4a7654dc81" + "sequences.fasta:md5,c2a4d6cbb837dce22d81f9c36dd0629e", + "tree.json:md5,e180607cd34a6cb6bab101d295f6cedf" ] ], "versions": [ - "versions.yml:md5,12e8751f1d841b9aee87d31206c102a7" + "versions.yml:md5,8c64a653330d1c5cb58ee1b8363b22d3" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:33:31.41372" + "timestamp": "2024-08-27T19:55:42.211731791" } } \ No newline at end of file diff --git a/modules/nf-core/nextclade/run/environment.yml b/modules/nf-core/nextclade/run/environment.yml index 58a06b619f0f..09c0ba1a8460 100644 --- a/modules/nf-core/nextclade/run/environment.yml +++ b/modules/nf-core/nextclade/run/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::nextclade=2.12.0 + - bioconda::nextclade=3.8.2 diff --git a/modules/nf-core/nextclade/run/main.nf b/modules/nf-core/nextclade/run/main.nf index 33fb34c6b315..cdb44437ab49 100644 --- a/modules/nf-core/nextclade/run/main.nf +++ b/modules/nf-core/nextclade/run/main.nf @@ -4,8 +4,8 @@ process NEXTCLADE_RUN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/nextclade:2.12.0--h9ee0642_0' : - 'biocontainers/nextclade:2.12.0--h9ee0642_0' }" + 'https://depot.galaxyproject.org/singularity/nextclade:3.8.2--h9ee0642_0' : + 'biocontainers/nextclade:3.8.2--h9ee0642_0' }" input: tuple val(meta), path(fasta) @@ -20,7 +20,8 @@ process NEXTCLADE_RUN { tuple val(meta), path("${prefix}.auspice.json") , optional:true, emit: json_auspice tuple val(meta), path("${prefix}.ndjson") , optional:true, emit: ndjson tuple val(meta), path("${prefix}.aligned.fasta") , optional:true, emit: fasta_aligned - tuple val(meta), path("*.translation.fasta") , optional:true, emit: fasta_translation + tuple val(meta), path("*_translation.*.fasta") , optional:true, emit: fasta_translation + tuple val(meta), path("${prefix}.nwk") , optional:true, emit: nwk path "versions.yml" , emit: versions when: @@ -44,4 +45,21 @@ process NEXTCLADE_RUN { nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') END_VERSIONS """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.csv + touch ${prefix}.tsv + touch ${prefix}.json + touch ${prefix}.auspice.json + touch ${prefix}.aligned.fasta + touch ${prefix}.cds_translation.test.fasta + touch ${prefix}.nwk + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + nextclade: \$(echo \$(nextclade --version 2>&1) | sed 's/^.*nextclade //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/nextclade/run/meta.yml b/modules/nf-core/nextclade/run/meta.yml index 22fb2450f281..bb7bf6c2d0ef 100644 --- a/modules/nf-core/nextclade/run/meta.yml +++ b/modules/nf-core/nextclade/run/meta.yml @@ -18,13 +18,14 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - dataset: - type: file + type: directory description: Path containing the dataset files obtained by running nextclade dataset get pattern: "*" - fasta: type: file description: FASTA file containing one or more consensus sequences pattern: "*.{fasta,fa}" + output: - meta: type: map @@ -39,11 +40,31 @@ output: type: file description: CSV file containing nextclade results pattern: "*.{csv}" + - csv_errors: + type: file + description: CSV file containing errors from nextclade results + pattern: "*.{errors.csv}" + - csv_insertions: + type: file + description: CSV file containing insertions from nextclade results + pattern: "*.{insertions.csv}" + - fasta_aligned: + type: file + description: FASTA file containing aligned sequences from nextclade results + pattern: "*.{aligned.fasta}" + - fasta_translation: + type: file + description: FASTA file containing aligned peptides from nextclade results + pattern: "*.{_translation.}*.{fasta}" + - ndjson: + type: file + description: newline-delimited JSON file containing nextclade results + pattern: "*.{ndjson}" - json: type: file description: JSON file containing nextclade results pattern: "*.{json}" - - json_tree: + - json_auspice: type: file description: Auspice JSON V2 containing nextclade results pattern: "*.{tree.json}" @@ -51,9 +72,16 @@ output: type: file description: TSV file containing nextclade results pattern: "*.{tsv}" + - nwk: + type: file + description: NWK file containing nextclade results + pattern: "*.{nwk}" authors: - "@antunderwood" - "@drpatelh" maintainers: - "@antunderwood" - "@drpatelh" + - "@drpatelh" +updated on 2024.08.23: + - "@nmshahir" diff --git a/modules/nf-core/nextclade/run/tests/main.nf.test b/modules/nf-core/nextclade/run/tests/main.nf.test new file mode 100644 index 000000000000..b486a3fe6b83 --- /dev/null +++ b/modules/nf-core/nextclade/run/tests/main.nf.test @@ -0,0 +1,82 @@ + +nextflow_process { + + name "Test Process NEXTCLADE_RUN" + script "../main.nf" + process "NEXTCLADE_RUN" + + tag "modules" + tag "modules_nfcore" + tag "nextclade" + tag "nextclade/datasetget" + tag "nextclade/run" + + setup { + run("NEXTCLADE_DATASETGET") { + script "../../datasetget/main.nf" + process { + """ + input[0] = 'nextstrain/sars-cov-2/wuhan-hu-1/orfs' + input[1] = '2024-01-16--20-31-02Z' + + """ + } + } + } + + test("sarscov2 default") { + + when { + process { + """ + input[0] = [[id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = NEXTCLADE_DATASETGET.out.dataset + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.csv, + process.out.csv_errors, + process.out.csv_insertions, + process.out.fasta_aligned, + process.out.fasta_translation, + file(process.out.json[0][1]).readLines()[4..10], + process.out.json_auspice, + process.out.ndjson, + process.out.nwk, + process.out.tsv, + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 default-stub") { + options '-stub' + + when { + process { + """ + input[0] = [[id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = NEXTCLADE_DATASETGET.out.dataset + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/nextclade/run/tests/main.nf.test.snap b/modules/nf-core/nextclade/run/tests/main.nf.test.snap new file mode 100644 index 000000000000..9294ed3a203b --- /dev/null +++ b/modules/nf-core/nextclade/run/tests/main.nf.test.snap @@ -0,0 +1,245 @@ +{ + "sarscov2 default-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "10": [ + "versions.yml:md5,f279e9049492abc589365716afc17d78" + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.auspice.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + + ], + "7": [ + [ + { + "id": "test" + }, + "test.aligned.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.cds_translation.test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.nwk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csv": [ + [ + { + "id": "test" + }, + "test.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "csv_errors": [ + + ], + "csv_insertions": [ + + ], + "fasta_aligned": [ + [ + { + "id": "test" + }, + "test.aligned.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fasta_translation": [ + [ + { + "id": "test" + }, + "test.cds_translation.test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "json": [ + [ + { + "id": "test" + }, + "test.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "json_auspice": [ + [ + { + "id": "test" + }, + "test.auspice.json:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "ndjson": [ + + ], + "nwk": [ + [ + { + "id": "test" + }, + "test.nwk:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tsv": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f279e9049492abc589365716afc17d78" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-07T07:21:00.853787859" + }, + "sarscov2 default": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.csv:md5,59667a74af31daf6151b809cb4645942" + ] + ], + [ + + ], + [ + + ], + [ + [ + { + "id": "test" + }, + "test.aligned.fasta:md5,1bf54662837b0df37f1857c7fa631225" + ] + ], + [ + [ + { + "id": "test" + }, + [ + "test.cds_translation.E.fasta:md5,1a6d93bd7abfeb193476a86950f07202", + "test.cds_translation.M.fasta:md5,6f79ab0742c078fcd9d2a474518c7022", + "test.cds_translation.N.fasta:md5,bef9912f101777bfff36225d7e5c3c1f", + "test.cds_translation.ORF1a.fasta:md5,4dc0e2eb1f2a61939ba49500ee3fa41a", + "test.cds_translation.ORF1b.fasta:md5,9c2e83d26161b5c887ff51cd64bd15bb", + "test.cds_translation.ORF3a.fasta:md5,adcbede4ebc2cac7af755a9d29d28ea3", + "test.cds_translation.ORF6.fasta:md5,3785b34cce978c95256f83db6ee82af0", + "test.cds_translation.ORF7a.fasta:md5,6ede1acb9e75afc84aa30bbc40551d37", + "test.cds_translation.ORF7b.fasta:md5,460e4cbc5f8c632c2bc9a8aedad5cf43", + "test.cds_translation.ORF8.fasta:md5,c733c88e61b29542664368fbf6dd4c76", + "test.cds_translation.ORF9b.fasta:md5,0aa13afc6cbf445fc92caa2e6c0a7548", + "test.cds_translation.S.fasta:md5,77740927a3f00b7e5bfac392fa6d264c" + ] + ] + ], + [ + " \"cladeNodeAttrKeys\": [", + " {", + " \"name\": \"Nextclade_pango\",", + " \"displayName\": \"Pango lineage (Nextclade)\",", + " \"description\": \"Pango lineage as inferred by Nextclade from the nearest neighbour in the reference tree. 98% accurate for recent sequences, for higher accuracy use dedicated pangolin software in UShER or pangoLEARN mode. Recombinants may get (wrongly) assigned to a designated recombinant lineage if they have similar breakpoints.\",", + " \"hideInWeb\": false,", + " \"skipAsReference\": false" + ], + [ + [ + { + "id": "test" + }, + "test.auspice.json:md5,84f57eb4611ffdf73eefb855819acb1d" + ] + ], + [ + [ + { + "id": "test" + }, + "test.ndjson:md5,946c0a0038ae937dab725d08a67c3c64" + ] + ], + [ + [ + { + "id": "test" + }, + "test.nwk:md5,70e9847b5fd44172e21323fe95ea57f8" + ] + ], + [ + [ + { + "id": "test" + }, + "test.tsv:md5,165384807e9a323da6bd15fc7f92420d" + ] + ], + [ + "versions.yml:md5,f279e9049492abc589365716afc17d78" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-07T07:20:48.066964467" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 87dbeaad348d..f10ddc6b929b 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -470,9 +470,6 @@ nanomonsv/parse: ncbitools/vecscreen: - modules/nf-core/ncbitools/vecscreen/** - tests/modules/nf-core/ncbitools/vecscreen/** -nextclade/run: - - modules/nf-core/nextclade/run/** - - tests/modules/nf-core/nextclade/run/** nucmer: - modules/nf-core/nucmer/** - tests/modules/nf-core/nucmer/** diff --git a/tests/modules/nf-core/nextclade/run/main.nf b/tests/modules/nf-core/nextclade/run/main.nf deleted file mode 100644 index 5c44ea4e7f3b..000000000000 --- a/tests/modules/nf-core/nextclade/run/main.nf +++ /dev/null @@ -1,23 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { NEXTCLADE_DATASETGET } from '../../../../../modules/nf-core/nextclade/datasetget/main.nf' -include { NEXTCLADE_RUN } from '../../../../../modules/nf-core/nextclade/run/main.nf' - -workflow test_nextclade_run { - - dataset = 'sars-cov-2' - reference = 'MN908947' - tag = '2022-01-18T12:00:00Z' - - NEXTCLADE_DATASETGET ( dataset, reference, tag ) - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - NEXTCLADE_RUN ( input, NEXTCLADE_DATASETGET.out.dataset ) -} - diff --git a/tests/modules/nf-core/nextclade/run/test.yml b/tests/modules/nf-core/nextclade/run/test.yml deleted file mode 100644 index ea6b9cf57f94..000000000000 --- a/tests/modules/nf-core/nextclade/run/test.yml +++ /dev/null @@ -1,62 +0,0 @@ -- name: nextclade run test_nextclade_run - command: nextflow run ./tests/modules/nf-core/nextclade/run -entry test_nextclade_run -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/nextclade/run/nextflow.config - tags: - - nextclade/run - - nextclade - files: - - path: output/nextclade/sars-cov-2/genemap.gff - md5sum: 21ebebfd0f416eeb959e55ebffd808e8 - - path: output/nextclade/sars-cov-2/primers.csv - md5sum: 5990c3483bf66ce607aeb90a44e7ef2e - - path: output/nextclade/sars-cov-2/qc.json - md5sum: c512f51fda0212b21ffff05779180963 - - path: output/nextclade/sars-cov-2/reference.fasta - md5sum: c7ce05f28e4ec0322c96f24e064ef55c - - path: output/nextclade/sars-cov-2/sequences.fasta - md5sum: 41129d255b99e0e92bdf20e866b99a1b - - path: output/nextclade/sars-cov-2/tag.json - md5sum: 402ac2b87e2a6a64a3fbf5ad16497af3 - - path: output/nextclade/sars-cov-2/tree.json - md5sum: b8f32f547ff9e2131d6fc66b68fc54b1 - - path: output/nextclade/sars-cov-2/virus_properties.json - md5sum: 5f2de3949e07cb633f3d9e4a7654dc81 - - path: output/nextclade/test.aligned.fasta - md5sum: 1bf54662837b0df37f1857c7fa631225 - - path: output/nextclade/test.auspice.json - md5sum: 04d8c32f141435ca45bf430dcb59bcba - - path: output/nextclade/test.csv - md5sum: 7ff4df651dd4199ec9e6b02134271fb5 - - path: output/nextclade/test.errors.csv - md5sum: 810d1c72e1ed010a9a017afba7ce8063 - - path: output/nextclade/test.insertions.csv - md5sum: c3aa7071d06122ec07ba7c7c4ba6e84a - - path: output/nextclade/test.json - contains: ["nextcladeAlgoVersion"] - - path: output/nextclade/test.ndjson - md5sum: 0aa70ebfa0c9cc262de4cfc6544cd20f - - path: output/nextclade/test.tsv - md5sum: cae39bb97064867ddf748c2f75ca0ae9 - - path: output/nextclade/test_gene_E.translation.fasta - md5sum: 1a6d93bd7abfeb193476a86950f07202 - - path: output/nextclade/test_gene_M.translation.fasta - md5sum: 6f79ab0742c078fcd9d2a474518c7022 - - path: output/nextclade/test_gene_N.translation.fasta - md5sum: bef9912f101777bfff36225d7e5c3c1f - - path: output/nextclade/test_gene_ORF1a.translation.fasta - md5sum: 4dc0e2eb1f2a61939ba49500ee3fa41a - - path: output/nextclade/test_gene_ORF1b.translation.fasta - md5sum: 9c2e83d26161b5c887ff51cd64bd15bb - - path: output/nextclade/test_gene_ORF3a.translation.fasta - md5sum: adcbede4ebc2cac7af755a9d29d28ea3 - - path: output/nextclade/test_gene_ORF6.translation.fasta - md5sum: 3785b34cce978c95256f83db6ee82af0 - - path: output/nextclade/test_gene_ORF7a.translation.fasta - md5sum: 6ede1acb9e75afc84aa30bbc40551d37 - - path: output/nextclade/test_gene_ORF7b.translation.fasta - md5sum: 460e4cbc5f8c632c2bc9a8aedad5cf43 - - path: output/nextclade/test_gene_ORF8.translation.fasta - md5sum: c733c88e61b29542664368fbf6dd4c76 - - path: output/nextclade/test_gene_ORF9b.translation.fasta - md5sum: 0aa13afc6cbf445fc92caa2e6c0a7548 - - path: output/nextclade/test_gene_S.translation.fasta - md5sum: 77740927a3f00b7e5bfac392fa6d264c From 6dd363c9b9b7cf30c4418597d20b6861848f0475 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Wed, 11 Sep 2024 02:52:53 -0300 Subject: [PATCH 044/486] Add optional config mode in `mirtrace/qc` (#6623) * add optional config file * update mirtrace/qc --- modules/nf-core/mirtrace/qc/main.nf | 5 +- modules/nf-core/mirtrace/qc/meta.yml | 3 + .../nf-core/mirtrace/qc/tests/main.nf.test | 53 ++++++++++++++- .../mirtrace/qc/tests/main.nf.test.snap | 65 ++++++++++++++++++- 4 files changed, 119 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/mirtrace/qc/main.nf b/modules/nf-core/mirtrace/qc/main.nf index 9d047a7a1e36..5893c0d72e62 100644 --- a/modules/nf-core/mirtrace/qc/main.nf +++ b/modules/nf-core/mirtrace/qc/main.nf @@ -8,7 +8,7 @@ process MIRTRACE_QC { 'biocontainers/mirtrace:1.0.1--0' }" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads), path(mirtrace_config) val(mirtrace_species) output: @@ -25,6 +25,7 @@ process MIRTRACE_QC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def mirtrace_mode = mirtrace_config ? "--config ${mirtrace_config}": "${reads}" """ mirtrace qc \\ @@ -32,7 +33,7 @@ process MIRTRACE_QC { --write-fasta \\ --output-dir . \\ --force \\ - ${reads} + ${mirtrace_mode} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/mirtrace/qc/meta.yml b/modules/nf-core/mirtrace/qc/meta.yml index 7f58ae2bd02d..9870437d98d6 100644 --- a/modules/nf-core/mirtrace/qc/meta.yml +++ b/modules/nf-core/mirtrace/qc/meta.yml @@ -25,6 +25,9 @@ input: type: file description: microRNA sequencing data pattern: "*.{fastq,fastq.gz}" + - mirtrace_config: + type: file + description: (Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns "FASTQ file path, id, adapter, PHRED-ASCII-offset". - mirtrace_species: type: string description: Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens) diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test b/modules/nf-core/mirtrace/qc/tests/main.nf.test index 9ce14fd468c3..d0ef1c7b3bd0 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test @@ -18,7 +18,8 @@ nextflow_process { [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) - ] + ], + [] ] input[1] = "hsa" """ @@ -61,7 +62,8 @@ nextflow_process { [ id:'test', single_end:false ], // meta map [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), - ] + ], + [] ] input[1] = "hsa" """ @@ -77,4 +79,51 @@ nextflow_process { } + test("human - fastq - optional config") { + + when { + process { + """ + ch_reads = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true) + ] + ]) + + ch_mirtrace_config = Channel.of( + "./test_rnaseq_1.fastq.gz,test_rnaseq_1,TGGAATTCTCGGGTGCCAAGG,33") + .collectFile(name: "mirtrace_config.txt", newLine: true) + + input[0] = ch_reads + .combine(ch_mirtrace_config) + + input[1] = "hsa" + + """ + } + } + + then { + assertAll( + { assert process.success }, + + // Check HTML + { assert path(process.out.html.get(0).get(1)).text.contains("This file is part of miRTrace.")} , + + // Check JSON + { assert path(process.out.json.get(0).get(1)).json.results[0].stats.uniqueQCPassedSeqsCount == 912 }, + + // Check TSV + { assert snapshot(process.out.tsv).match("tsv_config") }, + + // Check FASTA files + { assert snapshot(process.out.rnatype_unknown_fa).match("rnatype_unknown_fa_config") }, + { assert snapshot(process.out.all_fa).match("all_fa_config") }, + + ) + } + + } + } diff --git a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap index 22efdd9e9b9b..3f5593b73a13 100644 --- a/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap +++ b/modules/nf-core/mirtrace/qc/tests/main.nf.test.snap @@ -1,4 +1,21 @@ { + "all_fa_config": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_rnaseq_1.fasta:md5,125963c9ee39a49b3a680903e28e7c9d" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T18:35:10.022991825" + }, "all_fa": { "content": [ [ @@ -15,7 +32,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T18:05:42.043272808" + "timestamp": "2024-09-10T18:33:02.971744888" }, "versions": { "content": [ @@ -29,6 +46,31 @@ }, "timestamp": "2024-09-02T14:00:50.712738593" }, + "tsv_config": { + "content": [ + [ + [ + { + "id": "test" + }, + [ + "mirtrace-stats-contamination_basic.tsv:md5,ac69ca6d2a709854f1048b635d06e927", + "mirtrace-stats-contamination_detailed.tsv:md5,ef80997ac12662c64cbcf5fe9851e786", + "mirtrace-stats-length.tsv:md5,630b3a845953321ae4cf2fc4a4943ab5", + "mirtrace-stats-mirna-complexity.tsv:md5,ab2a7600a2daa5c1797eea13d0abc2f0", + "mirtrace-stats-phred.tsv:md5,44eaeae26ec629e71fb31e56bfb5a548", + "mirtrace-stats-qcstatus.tsv:md5,623cf3a0c5e363488966844feb0dd978", + "mirtrace-stats-rnatype.tsv:md5,ed8d3a76247a1432a365def87c3f4c67" + ] + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T18:35:09.99291948" + }, "tsv": { "content": [ [ @@ -53,7 +95,24 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T18:05:41.888457948" + "timestamp": "2024-09-10T18:33:02.856967195" + }, + "rnatype_unknown_fa_config": { + "content": [ + [ + [ + { + "id": "test" + }, + "test_rnaseq_1.fasta:md5,125963c9ee39a49b3a680903e28e7c9d" + ] + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T18:35:10.010723637" }, "human - fastq - stub": { "content": [ @@ -178,6 +237,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-05T18:05:41.978281344" + "timestamp": "2024-09-10T18:33:02.917439516" } } \ No newline at end of file From 29110ddccbbf5fa50f340af94c66affdc69ceb0a Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Thu, 12 Sep 2024 13:37:00 +0200 Subject: [PATCH 045/486] new module gatk/variants2table (#6619) * gatk/variants2table * Update modules/nf-core/gatk4/variantstotable/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix for https://github.com/nf-core/modules/pull/6619 * add optional file arguments This is a suggestion to add additional optional file arguments per the modules guidelines: https://nf-co.re/docs/guidelines/components/modules#required-and-optional-input-files These suggestions are untested. I did not add the [gatk_config_file](https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable#--gatk-config-file) argument. My current opinion is that the type of settings this would control are best set elsewhere. * update add args, update tests * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix md5 --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Chase Mateusiak --- .../gatk4/variantstotable/environment.yml | 6 ++ modules/nf-core/gatk4/variantstotable/main.nf | 63 +++++++++++++ .../nf-core/gatk4/variantstotable/meta.yml | 83 +++++++++++++++++ .../gatk4/variantstotable/tests/main.nf.test | 91 +++++++++++++++++++ .../variantstotable/tests/main.nf.test.snap | 69 ++++++++++++++ .../variantstotable/tests/nextflow.config | 6 ++ .../gatk4/variantstotable/tests/tags.yml | 2 + 7 files changed, 320 insertions(+) create mode 100644 modules/nf-core/gatk4/variantstotable/environment.yml create mode 100644 modules/nf-core/gatk4/variantstotable/main.nf create mode 100644 modules/nf-core/gatk4/variantstotable/meta.yml create mode 100644 modules/nf-core/gatk4/variantstotable/tests/main.nf.test create mode 100644 modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap create mode 100644 modules/nf-core/gatk4/variantstotable/tests/nextflow.config create mode 100644 modules/nf-core/gatk4/variantstotable/tests/tags.yml diff --git a/modules/nf-core/gatk4/variantstotable/environment.yml b/modules/nf-core/gatk4/variantstotable/environment.yml new file mode 100644 index 000000000000..aa7d804d4ade --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/environment.yml @@ -0,0 +1,6 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::gatk4=4.5.0.0 diff --git a/modules/nf-core/gatk4/variantstotable/main.nf b/modules/nf-core/gatk4/variantstotable/main.nf new file mode 100644 index 000000000000..5a189beed616 --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/main.nf @@ -0,0 +1,63 @@ +process GATK4_VARIANTSTOTABLE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.5.0.0--py36hdfd78af_0': + 'biocontainers/gatk4:4.5.0.0--py36hdfd78af_0' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(arguments_file), path(include_intervals), path(exclude_intervals) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + + output: + tuple val(meta), path("*.tsv"), emit: table + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?:'' + def prefix = task.ext.prefix ?: "${meta.id}" + def arguments_file_arg = arguments_file ? "--arguments_file ${arguments_file}" : "" + def include_intervals_arg = include_intervals ? "-L ${include_intervals}" : "" + def exclude_intervals_arg = exclude_intervals ? "-XL ${exclude_intervals}" : "" + + def avail_mem = 3072 + if (!task.memory) { + log.info '[GATK VariantsToTable] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = (task.memory.mega*0.8).intValue() + } + """ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + VariantsToTable \\ + ${args} \\ + --variant $vcf \\ + --output ${prefix}.tsv \\ + --reference $fasta \\ + --tmp-dir . \\ + $arguments_file_arg \\ + $include_intervals \\ + $exclude_intervals + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/gatk4/variantstotable/meta.yml b/modules/nf-core/gatk4/variantstotable/meta.yml new file mode 100644 index 000000000000..80d31265c4f4 --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/meta.yml @@ -0,0 +1,83 @@ +name: gatk4_variantstotable +description: Extract fields from a VCF file to a tab-delimited table +keywords: + - filter + - gatk4 + - table + - vcf +tools: + - gatk4: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] +input: + - meta: + type: map + description: | + Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. + e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD'] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: Index of VCF file. + pattern: "*.{idx,tbi}" + - arguments_file: + type: file + description: "optional GATK arguments file" + pattern: "*.{txt,list,args,arguments}" + - include_intervals: + type: file + description: "optional GATK region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - exclude_intervals: + type: file + description: "optional GATK exclude region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" +output: + - table: + type: file + description: GATK output + pattern: "*.tsv" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test new file mode 100644 index 000000000000..e6eb8207ac3d --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test @@ -0,0 +1,91 @@ +nextflow_process { + + name "Test Process GATK4_VARIANTSTOTABLE" + script "../main.nf" + process "GATK4_VARIANTSTOTABLE" + config './nextflow.config' + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/variantstotable" + + test("test1_gatk4_variant_to_table") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + + test("test1_gatk4_variant_to_table - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true), + [], + [], + [] + ] + input[1] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + +} diff --git a/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap new file mode 100644 index 000000000000..6560ddd65dac --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/tests/main.nf.test.snap @@ -0,0 +1,69 @@ +{ + "test1_gatk4_variant_to_table": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,fd8256465233e335beb509b0a8b43536" + ] + ], + "1": [ + "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" + ], + "table": [ + [ + { + "id": "test" + }, + "test.tsv:md5,fd8256465233e335beb509b0a8b43536" + ] + ], + "versions": [ + "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:43:27.609784" + }, + + "test1_gatk4_variant_to_table - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" + ], + "table": [ + [ + { + "id": "test" + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,82324614419a32fa266b86ad8d4e6daa" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.2" + }, + "timestamp": "2024-05-22T22:43:27.609784" + } +} diff --git a/modules/nf-core/gatk4/variantstotable/tests/nextflow.config b/modules/nf-core/gatk4/variantstotable/tests/nextflow.config new file mode 100644 index 000000000000..0c5fde343e0b --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + + withName: GATK4_VARIANTSTOTABLE { + ext.args = "-F CHROM -F POS -F TYPE -GF AD" + } +} diff --git a/modules/nf-core/gatk4/variantstotable/tests/tags.yml b/modules/nf-core/gatk4/variantstotable/tests/tags.yml new file mode 100644 index 000000000000..1f2c45b01c5c --- /dev/null +++ b/modules/nf-core/gatk4/variantstotable/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/variantstotable: + - "modules/nf-core/gatk4/variantstotable/**" From a004c86eea62d4eed15768c0edb3adcc3f2c1424 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Marius=20Bj=C3=B8rnstad?= Date: Thu, 12 Sep 2024 14:03:33 +0200 Subject: [PATCH 046/486] Split deepvariant 3 (#6172) * Move DeepVariant into a subcommand module rundeepvariant, preparing for split modules The test snapshot is updated because the process name in the version file changed. * Add a split DeepVariant workflow with individual processes for each step * Remove hash unique ID and fix input structure issue * Fixes for call_variants outputing sharded file * Fix test * Remove --channels insert_size, which is only applicable for short read data The channels should be specified in the pipeline config * Replace the model type value input with ext.args config * Fix tests: should run twice for two samples in input channel * Fix linting issues and input channel description * Fix formatting of md files Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Corrections / imrpovements from @fellen31 review * Check tfrecord file names * Updating conda skipping options, because the paths have changed * Add deprecation warning for top-level process and test for the deprecated process * also skip conda for the new deprecated module --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia --- .github/workflows/test.yml | 10 + modules/nf-core/deepvariant/README.md | 50 +++ .../nf-core/deepvariant/callvariants/main.nf | 58 ++++ .../nf-core/deepvariant/callvariants/meta.yml | 40 +++ .../callvariants/tests/main.nf.test | 85 +++++ .../callvariants/tests/main.nf.test.snap | 59 ++++ .../callvariants/tests/nextflow.config | 11 + .../deepvariant/callvariants/tests/tags.yml | 2 + modules/nf-core/deepvariant/main.nf | 67 +--- .../nf-core/deepvariant/makeexamples/main.nf | 66 ++++ .../nf-core/deepvariant/makeexamples/meta.yml | 88 +++++ .../makeexamples/tests/main.nf.test | 228 +++++++++++++ .../makeexamples/tests/main.nf.test.snap | 134 ++++++++ .../makeexamples/tests/nextflow.config | 6 + .../deepvariant/makeexamples/tests/tags.yml | 2 + modules/nf-core/deepvariant/meta.yml | 2 +- .../deepvariant/postprocessvariants/main.nf | 77 +++++ .../deepvariant/postprocessvariants/meta.yml | 90 ++++++ .../postprocessvariants/tests/main.nf.test | 118 +++++++ .../tests/main.nf.test.snap | 180 +++++++++++ .../postprocessvariants/tests/nextflow.config | 10 + .../postprocessvariants/tests/tags.yml | 2 + .../deepvariant/rundeepvariant/main.nf | 78 +++++ .../deepvariant/rundeepvariant/meta.yml | 92 ++++++ .../rundeepvariant/tests/main.nf.test | 166 ++++++++++ .../tests/main.nf.test.snap | 40 +-- .../tests/nextflow-intervals.config | 2 +- .../nextflow-non-autosomal-calling.config | 2 +- .../tests/nextflow.config | 2 +- .../deepvariant/rundeepvariant/tests/tags.yml | 2 + .../nf-core/deepvariant/tests/main.nf.test | 128 +------- subworkflows/nf-core/deepvariant/README.md | 8 + subworkflows/nf-core/deepvariant/main.nf | 45 +++ subworkflows/nf-core/deepvariant/meta.yml | 76 +++++ .../nf-core/deepvariant/tests/main.nf.test | 105 ++++++ .../deepvariant/tests/main.nf.test.snap | 300 ++++++++++++++++++ .../nf-core/deepvariant/tests/nextflow.config | 8 + .../nf-core/deepvariant/tests/tags.yml | 2 + 38 files changed, 2241 insertions(+), 200 deletions(-) create mode 100644 modules/nf-core/deepvariant/callvariants/main.nf create mode 100644 modules/nf-core/deepvariant/callvariants/meta.yml create mode 100644 modules/nf-core/deepvariant/callvariants/tests/main.nf.test create mode 100644 modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap create mode 100644 modules/nf-core/deepvariant/callvariants/tests/nextflow.config create mode 100644 modules/nf-core/deepvariant/callvariants/tests/tags.yml create mode 100644 modules/nf-core/deepvariant/makeexamples/main.nf create mode 100644 modules/nf-core/deepvariant/makeexamples/meta.yml create mode 100644 modules/nf-core/deepvariant/makeexamples/tests/main.nf.test create mode 100644 modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap create mode 100644 modules/nf-core/deepvariant/makeexamples/tests/nextflow.config create mode 100644 modules/nf-core/deepvariant/makeexamples/tests/tags.yml create mode 100644 modules/nf-core/deepvariant/postprocessvariants/main.nf create mode 100644 modules/nf-core/deepvariant/postprocessvariants/meta.yml create mode 100644 modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test create mode 100644 modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap create mode 100644 modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config create mode 100644 modules/nf-core/deepvariant/postprocessvariants/tests/tags.yml create mode 100644 modules/nf-core/deepvariant/rundeepvariant/main.nf create mode 100644 modules/nf-core/deepvariant/rundeepvariant/meta.yml create mode 100644 modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test rename modules/nf-core/deepvariant/{ => rundeepvariant}/tests/main.nf.test.snap (91%) rename modules/nf-core/deepvariant/{ => rundeepvariant}/tests/nextflow-intervals.config (70%) rename modules/nf-core/deepvariant/{ => rundeepvariant}/tests/nextflow-non-autosomal-calling.config (74%) rename modules/nf-core/deepvariant/{ => rundeepvariant}/tests/nextflow.config (75%) create mode 100644 modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml create mode 100644 subworkflows/nf-core/deepvariant/README.md create mode 100644 subworkflows/nf-core/deepvariant/main.nf create mode 100644 subworkflows/nf-core/deepvariant/meta.yml create mode 100644 subworkflows/nf-core/deepvariant/tests/main.nf.test create mode 100644 subworkflows/nf-core/deepvariant/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/deepvariant/tests/nextflow.config create mode 100644 subworkflows/nf-core/deepvariant/tests/tags.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 413f31a8b1bf..4a44189f3e8a 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -540,6 +540,14 @@ jobs: path: modules/nf-core/deepcell/mesmer - profile: conda path: modules/nf-core/deepvariant + - profile: conda + path: modules/nf-core/deepvariant/callvariants + - profile: conda + path: modules/nf-core/deepvariant/makeexamples + - profile: conda + path: modules/nf-core/deepvariant/postprocessvariants + - profile: conda + path: modules/nf-core/deepvariant/rundeepvariant - profile: conda path: modules/nf-core/ensemblvep/vep - profile: conda @@ -630,6 +638,8 @@ jobs: path: subworkflows/nf-core/vcf_annotate_ensemblvep - profile: conda path: subworkflows/nf-core/bcl_demultiplex + - profile: conda + path: subworkflows/nf-core/deepvariant - profile: conda path: subworkflows/nf-core/fastq_align_bamcmp_bwa - profile: conda diff --git a/modules/nf-core/deepvariant/README.md b/modules/nf-core/deepvariant/README.md index 9d1ceb344ba8..4b3ed086899e 100644 --- a/modules/nf-core/deepvariant/README.md +++ b/modules/nf-core/deepvariant/README.md @@ -1,3 +1,7 @@ +# DeepVariant module / subworkflow options + +The DeepVariant tool can be run using the `deepvariant/rundeepvariant` subcommand, or the subworkflow `deepvariant`, which calls the subcommands `makeexamples`, `callvariants` and `postprocessvariants`. The subcommand `rundeepvariant` is simpler, but the subworkflow may be useful if you want to run `callvariants` on GPU. + # Conda is not supported at the moment The [bioconda](https://bioconda.github.io/recipes/deepvariant/README.html) recipe is not fully working as expected. @@ -9,3 +13,49 @@ Hence, we are using the docker container provided by the authors of the tool: - [google/deepvariant](https://hub.docker.com/r/google/deepvariant) This image is mirrored on the [nf-core quay.io](https://quay.io/repository/nf-core/deepvariant) for convenience. + +# DeepVariant subworkflow + +You can use the subworkflow `nf-core/deepvariant`, which integrates the three +processes to perform variant calling with common file formats. + +These module subcommands incorporate the individual steps of the DeepVariant pipeline: + + * makeexamples: Converts the input alignment file to a tfrecord format suitable for the deep learning model + * callvariants: Call variants based on input tfrecords. The output is also in + tfrecord format, and needs postprocessing to convert it to vcf. + * postprocessvariants: Convert variant calls from callvariants to VCF, and + also create GVCF files based on genomic information from makeexamples. + +# Recommended parameters + +## makeexamples + +This process imports the data used for calling, and thus decides what information is available to the +deep neural network. It's important to import the correct channels for the model you want to use. + +The script `run_deepvariant` (not used in the subworkflow) does this automatically. You can refer to +the implementation in the DeepVariant repo: + +https://github.com/google/deepvariant/blob/bf9ed7e6de97cf6c8381694cb996317a740625ad/scripts/run_deepvariant.py#L367 + +For WGS and WES models you need to enable the `insert_size` channel. Specify the following in the config: + +``` +withName: "DEEPVARIANT_MAKEEXAMPLES" { + ext.args = '--channels "insert_size"' +} +``` + +## callvariants + +It is mandatory to specify a model type. The models are available on the container filesystem in +`/opt/models` - specify the one you want with the `--checkpoint` argument. + +``` +withName: "DEEPVARIANT_CALLVARIANTS" { + ext.args = '--checkpoint "/opt/models/wgs' +} +``` + +The channels specified in the `makeexamples` process must match the model used for calling. diff --git a/modules/nf-core/deepvariant/callvariants/main.nf b/modules/nf-core/deepvariant/callvariants/main.nf new file mode 100644 index 000000000000..668b51ae4cca --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/main.nf @@ -0,0 +1,58 @@ + +process DEEPVARIANT_CALLVARIANTS { + tag "$meta.id" + label 'process_high' + + //Conda is not supported at the moment + container "nf-core/deepvariant:1.6.1" + + input: + tuple val(meta), path(make_examples_tfrecords) + + output: + tuple val(meta), path("${prefix}.call-*-of-*.tfrecord.gz"), emit: call_variants_tfrecords + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + def matcher = make_examples_tfrecords[0].baseName =~ /^(.+)-\d{5}-of-(\d{5})$/ + if (!matcher.matches()) { + throw new IllegalArgumentException("tfrecord baseName '" + make_examples_tfrecords[0].baseName + "' doesn't match the expected pattern") + } + def examples_tfrecord_name = matcher[0][1] + def shardCount = matcher[0][2] + // Reconstruct the logical name - ${tfrecord_name}.examples.tfrecord@${task.cpus}.gz + def examples_tfrecords_logical_name = "${examples_tfrecord_name}@${shardCount}.gz" + + """ + /opt/deepvariant/bin/call_variants \\ + ${args} \\ + --outfile "${prefix}.call.tfrecord.gz" \\ + --examples "${examples_tfrecords_logical_name}" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_callvariants: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.call-00000-of-00001.tfrecord.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_callvariants: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/deepvariant/callvariants/meta.yml b/modules/nf-core/deepvariant/callvariants/meta.yml new file mode 100644 index 000000000000..db779c62ba04 --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/meta.yml @@ -0,0 +1,40 @@ +name: deepvariant_callvariants +description: Call variants from the examples produced by make_examples +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - make_examples_tfrecords: + type: file + description: The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process + pattern: "*.gz" +output: + - call_variants_tfrecords: + type: list + description: | + Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. + - versions: + type: file + description: File containing software version + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@ramprasadn" + - "@fa2k" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/callvariants/tests/main.nf.test b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test new file mode 100644 index 000000000000..72f04b51f3bc --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_process { + + name "Test Process DEEPVARIANT_CALLVARIANTS" + script "../main.nf" + config "./nextflow.config" + process "DEEPVARIANT_CALLVARIANTS" + + tag "deepvariant/makeexamples" + tag "deepvariant/callvariants" + tag "deepvariant" + tag "modules" + tag "modules_nfcore" + + test("homo_sapiens - wgs") { + setup { + run("DEEPVARIANT_MAKEEXAMPLES") { + script "../../makeexamples/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + } + when { + process { + """ + input[0] = DEEPVARIANT_MAKEEXAMPLES.out.examples + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.call_variants_tfrecords.get(0).get(0) == [ id:'test', single_end:false ] }, + // The tfrecord binary representation is not stable, but we check the name of the output. + { assert snapshot(file(process.out.call_variants_tfrecords.get(0).get(1)).name).match("homo_sapiens-wgs-call_variants_tfrecords-filenames")}, + { assert snapshot(process.out.versions).match("versions") }, + ) + } + } + + test("homo_sapiens - wgs - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta + [] // No input paths are needed in stub mode + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap new file mode 100644 index 000000000000..8f04ede70ebd --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/tests/main.nf.test.snap @@ -0,0 +1,59 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,5ff99ffba1e56e4e919d3dfc2d0f3cbb" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:38:47.927241" + }, + "homo_sapiens-wgs-call_variants_tfrecords-filenames": { + "content": [ + "test.call-00000-of-00001.tfrecord.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T17:04:33.276938" + }, + "homo_sapiens - wgs - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.call-00000-of-00001.tfrecord.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,5ff99ffba1e56e4e919d3dfc2d0f3cbb" + ], + "call_variants_tfrecords": [ + [ + { + "id": "test", + "single_end": false + }, + "test.call-00000-of-00001.tfrecord.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,5ff99ffba1e56e4e919d3dfc2d0f3cbb" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-13T21:07:17.335788301" + } +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/callvariants/tests/nextflow.config b/modules/nf-core/deepvariant/callvariants/tests/nextflow.config new file mode 100644 index 000000000000..590aa0602375 --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: "DEEPVARIANT_CALLVARIANTS" { + ext.args = '--checkpoint "/opt/models/wgs"' + cpus = 2 // Keep CPUs fixed so the number of output files is reproducible + } +} +process { + withName: "DEEPVARIANT_MAKEEXAMPLES" { + ext.args = '--channels "insert_size"' + } +} diff --git a/modules/nf-core/deepvariant/callvariants/tests/tags.yml b/modules/nf-core/deepvariant/callvariants/tests/tags.yml new file mode 100644 index 000000000000..02e63f50891f --- /dev/null +++ b/modules/nf-core/deepvariant/callvariants/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/callvariants: + - modules/nf-core/deepvariant/callvariants/** diff --git a/modules/nf-core/deepvariant/main.nf b/modules/nf-core/deepvariant/main.nf index 8d3d091119d2..12c9366bb7bc 100644 --- a/modules/nf-core/deepvariant/main.nf +++ b/modules/nf-core/deepvariant/main.nf @@ -1,10 +1,21 @@ +def deprecation_message = """ +WARNING: The deepvariant process has been moved into deepvariant/rundeepvariant. + +Reason: +A subworkflow "deepvariant" was added, to split DeepVariant into three processes, to help optimise +the usage of GPU resources (https://github.com/nf-core/modules/pull/6172). The subworkflow can be +used instead of this module. Alternatively, it is possible to use the subcommand "rundeepvariant" in +this module. "rundeepvariant" (the process DEEPVARIANT_RUNDEEPVARIANT) is the exact same as this +top-level process (DEEPVARIANT) used to be. + +The processing stages used by the subworkflow are implemented as module subcommands, e.g. makeexamples. +""" + + process DEEPVARIANT { tag "$meta.id" label 'process_high' - // FIXME Conda is not supported at the moment - // BUG https://github.com/nf-core/modules/issues/1754 - // BUG https://github.com/bioconda/bioconda-recipes/issues/30310 container "nf-core/deepvariant:1.6.1" input: @@ -25,54 +36,6 @@ process DEEPVARIANT { task.ext.when == null || task.ext.when script: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." - } - def args = task.ext.args ?: '' - prefix = task.ext.prefix ?: "${meta.id}" - def regions = intervals ? "--regions=${intervals}" : "" - def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : "" - // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 - // FIXME Revert this on next version bump - def VERSION = '1.6.1' - - """ - /opt/deepvariant/bin/run_deepvariant \\ - --ref=${fasta} \\ - --reads=${input} \\ - --output_vcf=${prefix}.vcf.gz \\ - --output_gvcf=${prefix}.g.vcf.gz \\ - ${args} \\ - ${regions} \\ - ${par_regions} \\ - --intermediate_results_dir=tmp \\ - --num_shards=${task.cpus} - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - deepvariant: $VERSION - END_VERSIONS - """ - - stub: - // Exit if running this module with -profile conda / -profile mamba - if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { - error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." - } - prefix = task.ext.prefix ?: "${meta.id}" - // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 - // FIXME Revert this on next version bump - def VERSION = '1.6.1' - """ - touch ${prefix}.vcf.gz - touch ${prefix}.vcf.gz.tbi - touch ${prefix}.g.vcf.gz - touch ${prefix}.g.vcf.gz.tbi + assert false: deprecation_message - cat <<-END_VERSIONS > versions.yml - "${task.process}": - deepvariant: $VERSION - END_VERSIONS - """ } diff --git a/modules/nf-core/deepvariant/makeexamples/main.nf b/modules/nf-core/deepvariant/makeexamples/main.nf new file mode 100644 index 000000000000..022d0bf2808e --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/main.nf @@ -0,0 +1,66 @@ +process DEEPVARIANT_MAKEEXAMPLES { + tag "$meta.id" + label 'process_high' + + //Conda is not supported at the moment + container "nf-core/deepvariant:1.6.1" + + input: + tuple val(meta), path(input), path(index), path(intervals) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) + tuple val(meta5), path(par_bed) + + output: + tuple val(meta), path("${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}"), emit: examples + tuple val(meta), path("${prefix}.gvcf.tfrecord-*-of-*.gz"), emit: gvcf + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def regions = intervals ? "--regions ${intervals}" : "" + def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : "" + + """ + seq 0 ${task.cpus - 1} | parallel -q --halt 2 --line-buffer /opt/deepvariant/bin/make_examples \\ + --mode calling \\ + --ref "${fasta}" \\ + --reads "${input}" \\ + --examples "./${prefix}.examples.tfrecord@${task.cpus}.gz" \\ + --gvcf "./${prefix}.gvcf.tfrecord@${task.cpus}.gz" \\ + ${regions} \\ + ${par_regions} \\ + ${args} \\ + --task {} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_makeexamples: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + """ + printf -v SHARD_COUNT "%04d" ${task.cpus} + for i in \$( seq -f "%04g" 0 ${task.cpus-1} ) + do + touch ${prefix}.examples.tfrecord-\$i-of-\$SHARD_COUNT.tfrecord.gz{,.example_info.json} + touch ${prefix}.gvcf.tfrecord-\$i-of-\$SHARD_COUNT.tfrecord.gz + done + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_makeexamples: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/deepvariant/makeexamples/meta.yml b/modules/nf-core/deepvariant/makeexamples/meta.yml new file mode 100644 index 000000000000..ab1d2e589a13 --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/meta.yml @@ -0,0 +1,88 @@ +name: deepvariant_makeexamples +description: Transforms the input alignments to a format suitable for the deep neural network variant caller +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: Interval file for targeted regions + pattern: "*.bed" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + pattern: "*.gzi" + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" +output: + - examples: + type: list + description: | + Tuple containing sample metadata and examples that can be used for calling + - gvcf: + type: list + description: | + Tuple containing sample metadata and the GVCF data in tfrecord format + - versions: + type: file + description: File containing the DeepVariant software version + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@ramprasadn" + - "@fa2k" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test new file mode 100644 index 000000000000..d46dbe6d57cb --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test @@ -0,0 +1,228 @@ +nextflow_process { + + name "Test Process DEEPVARIANT_MAKEEXAMPLES" + script "../main.nf" + config "./nextflow.config" + process "DEEPVARIANT_MAKEEXAMPLES" + + tag "deepvariant/makeexamples" + tag "deepvariant" + tag "modules" + tag "modules_nfcore" + + test("homo_sapiens - [bam, bai] - fasta - fai") { + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + // Test string values and versions. The tfrecords contents are not stable, but we check the names. + { assert process.out.examples.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.gvcf.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.examples.get(0).get(1).size() == 4 }, + { assert snapshot( // Check examples (tfrecord / json) file name list + file(process.out.examples.get(0).get(1).get(0)).name, + file(process.out.examples.get(0).get(1).get(1)).name, + file(process.out.examples.get(0).get(1).get(2)).name, + file(process.out.examples.get(0).get(1).get(3)).name, + ).match("test1-exaamples-filenames")}, + + { assert process.out.gvcf.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.gvcf.get(0).get(1).size() == 2 }, + { assert snapshot( // Check gvcf file name list + file(process.out.gvcf.get(0).get(1).get(0)).name, + file(process.out.gvcf.get(0).get(1).get(1)).name, + ).match("test1-gvcf-filenames")}, + { assert snapshot(process.out.versions).match("test1-versions") }, + ) + } + } + + test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.examples.get(0).get(0) == [ id:'test', single_end:false ] }, + // The test is always run with 2 cpus + { assert process.out.examples.get(0).get(1).size() == 4 }, + { assert snapshot( // Check examples (tfrecord / json) file names + file(process.out.examples.get(0).get(1).get(0)).name, + file(process.out.examples.get(0).get(1).get(1)).name, + file(process.out.examples.get(0).get(1).get(2)).name, + file(process.out.examples.get(0).get(1).get(3)).name, + ).match("test2-examples-filenames")}, + + { assert process.out.gvcf.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.gvcf.get(0).get(1).size() == 2 }, + { assert snapshot( // Check gvcf tfrecord file names + file(process.out.gvcf.get(0).get(1).get(0)).name, + file(process.out.gvcf.get(0).get(1).get(1)).name, + ).match("test2-gvcf-filenames")}, + { assert snapshot(process.out.versions).match("test2-versions") }, + ) + } + } + + test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai") { + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + + { assert process.out.examples.get(0).get(0) == [ id:'test', single_end:false ] }, + // The test is always run with 2 cpus + { assert process.out.examples.get(0).get(1).size() == 4 }, + { assert snapshot( // Check examples (tfrecord / json) file name list + file(process.out.examples.get(0).get(1).get(0)).name, + file(process.out.examples.get(0).get(1).get(1)).name, + file(process.out.examples.get(0).get(1).get(2)).name, + file(process.out.examples.get(0).get(1).get(3)).name, + ).match("test3-examples-filenames")}, + + { assert process.out.gvcf.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.gvcf.get(0).get(1).size() == 2 }, + { assert snapshot( // Check gvcf file name list + file(process.out.gvcf.get(0).get(1).get(0)).name, + file(process.out.gvcf.get(0).get(1).get(1)).name, + ).match("test3-gvcf-filenames")}, + { assert snapshot(process.out.versions).match("test3-versions") }, + ) + } + } + + test("stub") { + + options "-stub" + + when { + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.examples.get(0).get(1).size() == 4 }, + { assert snapshot( // Check examples (tfrecord / json) file name list + file(process.out.examples.get(0).get(1).get(0)).name, + file(process.out.examples.get(0).get(1).get(1)).name, + file(process.out.examples.get(0).get(1).get(2)).name, + file(process.out.examples.get(0).get(1).get(3)).name, + ).match("test4-examples-filenames")}, + + { assert process.out.gvcf.get(0).get(0) == [ id:'test', single_end:false ] }, + { assert process.out.gvcf.get(0).get(1).size() == 2 }, + { assert snapshot( // Check gvcf file name list + file(process.out.gvcf.get(0).get(1).get(0)).name, + file(process.out.gvcf.get(0).get(1).get(1)).name, + ).match("test4-gvcf-filenames")}, + ) + } + } + +} diff --git a/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap new file mode 100644 index 000000000000..24182c54a0b5 --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "test1-gvcf-filenames": { + "content": [ + "test.gvcf.tfrecord-00000-of-00002.gz", + "test.gvcf.tfrecord-00001-of-00002.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:09:47.885995" + }, + "test2-examples-filenames": { + "content": [ + "test.examples.tfrecord-00000-of-00002.gz", + "test.examples.tfrecord-00000-of-00002.gz.example_info.json", + "test.examples.tfrecord-00001-of-00002.gz", + "test.examples.tfrecord-00001-of-00002.gz.example_info.json" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:02.757227" + }, + "test2-versions": { + "content": [ + [ + "versions.yml:md5,842dca9323f25aa3cfd67789d18e7e33" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:39:28.960959" + }, + "test4-examples-filenames": { + "content": [ + "test.examples.tfrecord-0000-of-0002.tfrecord.gz", + "test.examples.tfrecord-0000-of-0002.tfrecord.gz.example_info.json", + "test.examples.tfrecord-0001-of-0002.tfrecord.gz", + "test.examples.tfrecord-0001-of-0002.tfrecord.gz.example_info.json" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:27.41698" + }, + "test1-versions": { + "content": [ + [ + "versions.yml:md5,842dca9323f25aa3cfd67789d18e7e33" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:39:13.57526" + }, + "test3-examples-filenames": { + "content": [ + "test.examples.tfrecord-00000-of-00002.gz", + "test.examples.tfrecord-00000-of-00002.gz.example_info.json", + "test.examples.tfrecord-00001-of-00002.gz", + "test.examples.tfrecord-00001-of-00002.gz.example_info.json" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:17.705948" + }, + "test2-gvcf-filenames": { + "content": [ + "test.gvcf.tfrecord-00000-of-00002.gz", + "test.gvcf.tfrecord-00001-of-00002.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:02.765863" + }, + "test4-gvcf-filenames": { + "content": [ + "test.gvcf.tfrecord-0000-of-0002.tfrecord.gz", + "test.gvcf.tfrecord-0001-of-0002.tfrecord.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:27.423442" + }, + "test3-versions": { + "content": [ + [ + "versions.yml:md5,842dca9323f25aa3cfd67789d18e7e33" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:39:44.83616" + }, + "test1-exaamples-filenames": { + "content": [ + "test.examples.tfrecord-00000-of-00002.gz", + "test.examples.tfrecord-00000-of-00002.gz.example_info.json", + "test.examples.tfrecord-00001-of-00002.gz", + "test.examples.tfrecord-00001-of-00002.gz.example_info.json" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:09:47.874585" + }, + "test3-gvcf-filenames": { + "content": [ + "test.gvcf.tfrecord-00000-of-00002.gz", + "test.gvcf.tfrecord-00001-of-00002.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-04T16:10:17.714443" + } +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/makeexamples/tests/nextflow.config b/modules/nf-core/deepvariant/makeexamples/tests/nextflow.config new file mode 100644 index 000000000000..5f071fcb34b7 --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/tests/nextflow.config @@ -0,0 +1,6 @@ +process { + withName: "DEEPVARIANT_MAKEEXAMPLES" { + ext.args = '--channels "insert_size"' + cpus = 2 // The number of output files is determined by cpus - keep it the same for tests + } +} diff --git a/modules/nf-core/deepvariant/makeexamples/tests/tags.yml b/modules/nf-core/deepvariant/makeexamples/tests/tags.yml new file mode 100644 index 000000000000..6a13da095902 --- /dev/null +++ b/modules/nf-core/deepvariant/makeexamples/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/makeexamples: + - modules/nf-core/deepvariant/makeexamples/** diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index 2327dd5f4060..30c0285ae3ee 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -1,5 +1,5 @@ name: deepvariant -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: (DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning diff --git a/modules/nf-core/deepvariant/postprocessvariants/main.nf b/modules/nf-core/deepvariant/postprocessvariants/main.nf new file mode 100644 index 000000000000..90e8563deb6a --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/main.nf @@ -0,0 +1,77 @@ +process DEEPVARIANT_POSTPROCESSVARIANTS { + tag "$meta.id" + label 'process_medium' + + //Conda is not supported at the moment + container "nf-core/deepvariant:1.6.1" + + input: + tuple val(meta), path(variant_calls_tfrecord_files), path(gvcf_tfrecords) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) + + output: + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi + tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf + tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi + + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + def variant_calls_tfrecord_name = variant_calls_tfrecord_files[0].name.replaceFirst(/-\d{5}-of-\d{5}/, "") + + def gvcf_matcher = gvcf_tfrecords[0].baseName =~ /^(.+)-\d{5}-of-(\d{5})$/ + if (!gvcf_matcher.matches()) { + throw new IllegalArgumentException("tfrecord baseName '" + gvcf_tfrecords[0].baseName + "' doesn't match the expected pattern") + } + def gvcf_tfrecord_name = gvcf_matcher[0][1] + def gvcf_shardCount = gvcf_matcher[0][2] + // Reconstruct the logical name - ${tfrecord_name}.examples.tfrecord@${task.cpus}.gz + def gvcf_tfrecords_logical_name = "${gvcf_tfrecord_name}@${gvcf_shardCount}.gz" + + """ + /opt/deepvariant/bin/postprocess_variants \\ + ${args} \\ + --ref "${fasta}" \\ + --infile "${variant_calls_tfrecord_name}" \\ + --outfile "${prefix}.vcf.gz" \\ + --nonvariant_site_tfrecord_path "${gvcf_tfrecords_logical_name}" \\ + --gvcf_outfile "${prefix}.g.vcf.gz" \\ + --cpus $task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_postprocessvariants: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + echo "" | gzip > ${prefix}.g.vcf.gz + touch ${prefix}.g.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant_callvariants: \$(echo \$(/opt/deepvariant/bin/run_deepvariant --version) | sed 's/^.*version //; s/ .*\$//' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/deepvariant/postprocessvariants/meta.yml b/modules/nf-core/deepvariant/postprocessvariants/meta.yml new file mode 100644 index 000000000000..03a0a6b8235a --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/meta.yml @@ -0,0 +1,90 @@ +name: deepvariant_postprocessvariants +description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variant_calls_tfrecord_files: + type: file + description: | + One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS + pattern: "*.tfrecord.gz" + - gvcf_tfrecords: + type: file + description: | + Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output + pattern: "*.gz" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: Index for VCF + pattern: "*.vcf.gz.tbi" + - gvcf: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + type: file + description: Index for GVCF + pattern: "*.g.vcf.gz.tbi" + - versions: + type: file + description: File containing software version + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@ramprasadn" + - "@fa2k" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test new file mode 100644 index 000000000000..e4e9b5570c22 --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test @@ -0,0 +1,118 @@ +nextflow_process { + + name "Test Process DEEPVARIANT_POSTPROCESSVARIANTS" + script "../main.nf" + process "DEEPVARIANT_POSTPROCESSVARIANTS" + config "./nextflow.config" + + tag "deepvariant/makeexamples" + tag "deepvariant/callvariants" + tag "deepvariant/postprocessvariants" + tag "deepvariant" + tag "modules" + tag "modules_nfcore" + + test("homo_sapiens - wgs") { + setup { + run("DEEPVARIANT_MAKEEXAMPLES") { + script "../../makeexamples/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + run("DEEPVARIANT_CALLVARIANTS") { + script "../../callvariants/main.nf" + process { + """ + input[0] = DEEPVARIANT_MAKEEXAMPLES.out.examples + """ + } + } + } + when { + process { + """ + input[0] = DEEPVARIANT_CALLVARIANTS.out.call_variants_tfrecords.join( + DEEPVARIANT_MAKEEXAMPLES.out.gvcf, + failOnMismatch: true + ) + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - wgs - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + [], + [], + [], + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("stub") } + ) + } + } + +} diff --git a/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap new file mode 100644 index 000000000000..5a29c624e50a --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/tests/main.nf.test.snap @@ -0,0 +1,180 @@ +{ + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + "versions.yml:md5,37f0e454a6983de82f7a93eb39849985" + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,37f0e454a6983de82f7a93eb39849985" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:40:38.231189" + }, + "homo_sapiens - wgs": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ] + ], + "4": [ + "versions.yml:md5,b1d5ddb90c4a59a1a3fdace9dcc8445c" + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ] + ], + "versions": [ + "versions.yml:md5,b1d5ddb90c4a59a1a3fdace9dcc8445c" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-09T16:46:15.793662" + } +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config b/modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config new file mode 100644 index 000000000000..070b4892f86b --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/tests/nextflow.config @@ -0,0 +1,10 @@ +process { + withName: "DEEPVARIANT_CALLVARIANTS" { + ext.args = '--checkpoint "/opt/models/wgs"' + } +} +process { + withName: "DEEPVARIANT_MAKEEXAMPLES" { + ext.args = '--channels "insert_size"' + } +} diff --git a/modules/nf-core/deepvariant/postprocessvariants/tests/tags.yml b/modules/nf-core/deepvariant/postprocessvariants/tests/tags.yml new file mode 100644 index 000000000000..d26188cd7a29 --- /dev/null +++ b/modules/nf-core/deepvariant/postprocessvariants/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/postprocessvariants: + - modules/nf-core/deepvariant/postprocessvariants/** diff --git a/modules/nf-core/deepvariant/rundeepvariant/main.nf b/modules/nf-core/deepvariant/rundeepvariant/main.nf new file mode 100644 index 000000000000..7f99c53f6d2b --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/main.nf @@ -0,0 +1,78 @@ +process DEEPVARIANT_RUNDEEPVARIANT { + tag "$meta.id" + label 'process_high' + + // FIXME Conda is not supported at the moment + // BUG https://github.com/nf-core/modules/issues/1754 + // BUG https://github.com/bioconda/bioconda-recipes/issues/30310 + container "nf-core/deepvariant:1.6.1" + + input: + tuple val(meta), path(input), path(index), path(intervals) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(gzi) + tuple val(meta5), path(par_bed) + + output: + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi") , emit: vcf_tbi + tuple val(meta), path("${prefix}.g.vcf.gz") , emit: gvcf + tuple val(meta), path("${prefix}.g.vcf.gz.tbi"), emit: gvcf_tbi + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def regions = intervals ? "--regions=${intervals}" : "" + def par_regions = par_bed ? "--par_regions_bed=${par_bed}" : "" + // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 + // FIXME Revert this on next version bump + def VERSION = '1.6.1' + + """ + /opt/deepvariant/bin/run_deepvariant \\ + --ref=${fasta} \\ + --reads=${input} \\ + --output_vcf=${prefix}.vcf.gz \\ + --output_gvcf=${prefix}.g.vcf.gz \\ + ${args} \\ + ${regions} \\ + ${par_regions} \\ + --intermediate_results_dir=tmp \\ + --num_shards=${task.cpus} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant: $VERSION + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + prefix = task.ext.prefix ?: "${meta.id}" + // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 + // FIXME Revert this on next version bump + def VERSION = '1.6.1' + """ + touch ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + touch ${prefix}.g.vcf.gz + touch ${prefix}.g.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant: $VERSION + END_VERSIONS + """ +} diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml new file mode 100644 index 000000000000..a6ee5499285e --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml @@ -0,0 +1,92 @@ +name: deepvariant_rundeepvariant +description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - interval: + type: file + description: Interval file for targeted regions + pattern: "*.bed" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - gvcf: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@abhi18av" + - "@ramprasadn" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test new file mode 100644 index 000000000000..0790fb81362c --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test @@ -0,0 +1,166 @@ +nextflow_process { + + name "Test Process DEEPVARIANT_RUNDEEPVARIANT" + script "../main.nf" + process "DEEPVARIANT_RUNDEEPVARIANT" + + tag "deepvariant/rundeepvariant" + tag "deepvariant" + tag "modules" + tag "modules_nfcore" + + test("homo_sapiens - [bam, bai] - fasta - fai") { + when { + config "./nextflow.config" + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai") { + config "./nextflow-intervals.config" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed") { + config "./nextflow-non-autosomal-calling.config" + tag "test" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai") { + when { + config "./nextflow.config" + + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) + ] + input[3] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/deepvariant/tests/main.nf.test.snap b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap similarity index 91% rename from modules/nf-core/deepvariant/tests/main.nf.test.snap rename to modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap index 04f87774241a..1ec351eecc94 100644 --- a/modules/nf-core/deepvariant/tests/main.nf.test.snap +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/main.nf.test.snap @@ -39,7 +39,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -78,15 +78,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:09:40.987117305" + "timestamp": "2024-08-29T11:36:27.325363" }, "homo_sapiens - [bam, bai] - fasta - fai": { "content": [ @@ -128,7 +128,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -167,15 +167,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:08:47.058887374" + "timestamp": "2024-08-29T11:34:41.779153" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai": { "content": [ @@ -217,7 +217,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -256,15 +256,15 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-01T12:09:13.952808655" + "timestamp": "2024-08-29T11:35:16.993129" }, "homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed": { "content": [ @@ -306,7 +306,7 @@ ] ], "4": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ], "gvcf": [ [ @@ -345,14 +345,14 @@ ] ], "versions": [ - "versions.yml:md5,efbdcb1ad96e0209b31bcafedd0017a8" + "versions.yml:md5,a251d8d9f5e8b737d8298eead96c0890" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-23T14:29:24.939680679" + "timestamp": "2024-08-29T11:35:52.23093" } -} +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/tests/nextflow-intervals.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config similarity index 70% rename from modules/nf-core/deepvariant/tests/nextflow-intervals.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config index 6d135f9f1096..78d8d5982ae7 100644 --- a/modules/nf-core/deepvariant/tests/nextflow-intervals.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-intervals.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = '--model_type=WGS ' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config similarity index 74% rename from modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config index 4be8986bd6e9..6d265292ab6f 100644 --- a/modules/nf-core/deepvariant/tests/nextflow-non-autosomal-calling.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow-non-autosomal-calling.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = '--model_type=WGS --haploid_contigs chr22' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/tests/nextflow.config b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config similarity index 75% rename from modules/nf-core/deepvariant/tests/nextflow.config rename to modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config index d335d30b54f5..77e355cae82b 100644 --- a/modules/nf-core/deepvariant/tests/nextflow.config +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/nextflow.config @@ -1,6 +1,6 @@ process { - withName: DEEPVARIANT { + withName: DEEPVARIANT_RUNDEEPVARIANT { ext.args = ' --regions=\"chr22:0-40001\" --model_type=WGS ' ext.prefix = { "${meta.id}_out" } } diff --git a/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml new file mode 100644 index 000000000000..958b8e4149bd --- /dev/null +++ b/modules/nf-core/deepvariant/rundeepvariant/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/rundeepvariant: + - modules/nf-core/deepvariant/rundeepvariant/** diff --git a/modules/nf-core/deepvariant/tests/main.nf.test b/modules/nf-core/deepvariant/tests/main.nf.test index 1776523326ad..cf62430fa5af 100644 --- a/modules/nf-core/deepvariant/tests/main.nf.test +++ b/modules/nf-core/deepvariant/tests/main.nf.test @@ -1,6 +1,6 @@ nextflow_process { - name "Test Process DEEPVARIANT" + name "Deprecated module DEEPVARIANT Test" script "../main.nf" process "DEEPVARIANT" @@ -8,10 +8,8 @@ nextflow_process { tag "modules" tag "modules_nfcore" - test("homo_sapiens - [bam, bai] - fasta - fai") { + test("DEEPVARIANT top-level process is deprecated and should fail") { when { - config "./nextflow.config" - process { """ input[0] = [ @@ -40,126 +38,8 @@ nextflow_process { then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai") { - config "./nextflow-intervals.config" - - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] - input[1] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [ - [],[] - ] - input[4] = [ - [],[] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert !process.success } ) } } - - test("homo_sapiens - [cram, crai, genome_bed] - fasta - fai - par_bed") { - config "./nextflow-non-autosomal-calling.config" - tag "test" - when { - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) - ] - input[1] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) - ] - input[2] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) - ] - input[3] = [ - [],[] - ] - input[4] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.blacklist_intervals.bed', checkIfExists: true) - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - - test("homo_sapiens - [bam, bai] - fasta_gz - fasta_gz_fai") { - when { - config "./nextflow.config" - - process { - """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), - [] - ] - input[1] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz', checkIfExists: true) - ] - input[2] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.fai', checkIfExists: true) - ] - input[3] = [ - [ id:'genome'], - file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.gz.gzi', checkIfExists: true) - ] - input[4] = [ - [],[] - ] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } - ) - } - } - -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/deepvariant/README.md b/subworkflows/nf-core/deepvariant/README.md new file mode 100644 index 000000000000..6f816c22ed5e --- /dev/null +++ b/subworkflows/nf-core/deepvariant/README.md @@ -0,0 +1,8 @@ +# DeepVariant subworkflow + +Usage: the input channel should contain tuples of three elements: `meta`, an alignment file in bam or +cram format, and a corresponding index. + +It is very important that the input channel's `meta` is unique for all the input elements, because the subworkflow does a join on `meta`. + +Please note the important configuration items listed in the `deepvariant` module's README file. It is required to use the configuration to specify the input "channels" (data types to extract from bam file) for `DEEPVARIANT_MAKEEXAMPLES`, and the model to run for `DEEPVARIANT_CALLVARIANTS`. The correct arguments for a specific model (data type) can be determined by manually using the `run_deepvariant` command from the Docker / Singularity image with the `--dry_run` option. diff --git a/subworkflows/nf-core/deepvariant/main.nf b/subworkflows/nf-core/deepvariant/main.nf new file mode 100644 index 000000000000..02a5114c30b5 --- /dev/null +++ b/subworkflows/nf-core/deepvariant/main.nf @@ -0,0 +1,45 @@ + +include { DEEPVARIANT_MAKEEXAMPLES } from '../../../modules/nf-core/deepvariant/makeexamples/main' +include { DEEPVARIANT_CALLVARIANTS } from '../../../modules/nf-core/deepvariant/callvariants/main' +include { DEEPVARIANT_POSTPROCESSVARIANTS } from '../../../modules/nf-core/deepvariant/postprocessvariants/main' + +workflow DEEPVARIANT { + take: + ch_input // channel: [ val(meta), path(input), path(index), path(intervals)] + ch_fasta // channel: [ val(meta2), path(fasta) ] + ch_fai // channel: [ val(meta3), path(fail) ] + ch_gzi // channel: [ val(meta4), path(gzi) ] + ch_par_bed // channel: [ val(meta5), path(par_bed) ] + + main: + + ch_versions = Channel.empty() + + DEEPVARIANT_MAKEEXAMPLES(ch_input, ch_fasta, ch_fai, ch_gzi, ch_par_bed) + ch_versions = ch_versions.mix(DEEPVARIANT_MAKEEXAMPLES.out.versions.first()) + + DEEPVARIANT_CALLVARIANTS(DEEPVARIANT_MAKEEXAMPLES.out.examples) + ch_versions = ch_versions.mix(DEEPVARIANT_CALLVARIANTS.out.versions.first()) + + // Input to postprocessing step needs both the gvcfs from MAKEEXAMPLES and the variant + // calls from CALLVARIANTS. Joining on meta, which is assumed to be unique. + ch_postproc_input = DEEPVARIANT_CALLVARIANTS.out.call_variants_tfrecords.join( + DEEPVARIANT_MAKEEXAMPLES.out.gvcf, + failOnMismatch: true + ) + DEEPVARIANT_POSTPROCESSVARIANTS( + ch_postproc_input, + ch_fasta, + ch_fai, + ch_gzi + ) + + ch_versions = ch_versions.mix(DEEPVARIANT_POSTPROCESSVARIANTS.out.versions.first()) + + emit: + vcf = DEEPVARIANT_POSTPROCESSVARIANTS.out.vcf + vcf_tbi = DEEPVARIANT_POSTPROCESSVARIANTS.out.vcf_tbi + gvcf = DEEPVARIANT_POSTPROCESSVARIANTS.out.gvcf + gvcf_tbi = DEEPVARIANT_POSTPROCESSVARIANTS.out.gvcf_tbi + versions = ch_versions +} diff --git a/subworkflows/nf-core/deepvariant/meta.yml b/subworkflows/nf-core/deepvariant/meta.yml new file mode 100644 index 000000000000..6321fc24c66c --- /dev/null +++ b/subworkflows/nf-core/deepvariant/meta.yml @@ -0,0 +1,76 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/subworkflows/yaml-schema.json +name: deepvariant +description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +keywords: + - variant calling + - machine learning + - neural network +components: + - deepvariant/makeexamples + - deepvariant/callvariants + - deepvariant/postprocessvariants +input: + - ch_input: + type: list + description: | + Input aligned reads in bam or cram format, with index, and optional intervals BED file + Structure: [ val(meta), path(bam_or_cram), path(bai_or_crai), path(intervals_bed) ] + - ch_fasta: + type: file + description: | + Reference genome + Structure: [ val(meta2), path(fasta) ] + - ch_fai: + type: string + description: | + Reference genome index in fai format + Structure: [ val(meta3), path(fai) ] + - ch_gzi: + type: string + description: | + Reference genome index in gzi format (either gzi or fai should be used) + Structure: [ val(meta4), val(gzi) ] + - ch_par_bed: + type: string + description: | + bed file of pseudoautosomal regions (optional) + Structure: [ val(meta5), val(par_bed) ] + pattern: "*.bed" +output: + - vcf: + type: file + description: | + Variant calls + Structure: [ val(meta), path(vcf) ] + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: | + Index for variant call file + Structure: [ val(meta), path(vcf_tbi) ] + pattern: "*.tbi" + - gvcf: + type: file + description: | + Variant call file with genomic coverage information + Structure: [ val(meta), path(gvcf) ] + pattern: "*.g.vcf.gz" + - gvcf_tbi: + type: file + description: | + Index for the GVCF. + Structure: [ val(meta), path(gvcf_tbi) ] + pattern: "*.tbi" + - versions: + type: file + description: | + File containing software versions + Structure: path(versions.yml) + pattern: "versions.yml" +authors: + - "@abhi18av" + - "@ramprasadn" + - "@fa2k" +maintainers: + - "@abhi18av" + - "@ramprasadn" diff --git a/subworkflows/nf-core/deepvariant/tests/main.nf.test b/subworkflows/nf-core/deepvariant/tests/main.nf.test new file mode 100644 index 000000000000..4195d4730e70 --- /dev/null +++ b/subworkflows/nf-core/deepvariant/tests/main.nf.test @@ -0,0 +1,105 @@ +nextflow_workflow { + + name "Test Subworkflow DEEPVARIANT" + script "../main.nf" + config "./nextflow.config" + workflow "DEEPVARIANT" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/deepvariant" + + tag "deepvariant" + tag "deepvariant/makeexamples" + tag "deepvariant/callvariants" + tag "deepvariant/postprocessvariants" + + test("homo_sapiens - two inputs - bam - fasta - fai") { + when { + workflow { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ]) + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + + test("homo_sapiens - different samples and regions - cram - fasta - fai") { + + when { + workflow { + """ + input[0] = Channel.of( + [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ], + [ + [ id:'test2', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + ) + input[1] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [ id:'genome'], + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + input[3] = [ + [],[] + ] + input[4] = [ + [],[] + ] + """ + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot(workflow.out).match() } + ) + } + } + +} diff --git a/subworkflows/nf-core/deepvariant/tests/main.nf.test.snap b/subworkflows/nf-core/deepvariant/tests/main.nf.test.snap new file mode 100644 index 000000000000..08105c1b0f06 --- /dev/null +++ b/subworkflows/nf-core/deepvariant/tests/main.nf.test.snap @@ -0,0 +1,300 @@ +{ + "homo_sapiens - different samples and regions - cram - fasta - fai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz:md5,5c36d104b2eb6e410788990928667b93" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz.tbi:md5,5451379c05fa59498b2b8aafcb18c9eb" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz:md5,2aefd9545ffefe9af0730dc4ffc5f638" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz.tbi:md5,58d2e7fa7cf98d56fd734db6d59f8489" + ] + ], + "4": [ + "versions.yml:md5,5e6e7451f9819e2e0c33ad0d1b22d3b3", + "versions.yml:md5,c9c9c7000dc16bcb7e3107e7333481de", + "versions.yml:md5,cb2f0f2fe645633ed7d6528999bde458" + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz:md5,2aefd9545ffefe9af0730dc4ffc5f638" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz.tbi:md5,58d2e7fa7cf98d56fd734db6d59f8489" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz:md5,5c36d104b2eb6e410788990928667b93" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz.tbi:md5,5451379c05fa59498b2b8aafcb18c9eb" + ] + ], + "versions": [ + "versions.yml:md5,5e6e7451f9819e2e0c33ad0d1b22d3b3", + "versions.yml:md5,c9c9c7000dc16bcb7e3107e7333481de", + "versions.yml:md5,cb2f0f2fe645633ed7d6528999bde458" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-08-16T16:20:06.112232952" + }, + "homo_sapiens - two inputs - bam - fasta - fai": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ] + ], + "4": [ + "versions.yml:md5,5e6e7451f9819e2e0c33ad0d1b22d3b3", + "versions.yml:md5,c9c9c7000dc16bcb7e3107e7333481de", + "versions.yml:md5,cb2f0f2fe645633ed7d6528999bde458" + ], + "gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz:md5,0a629e1745926cfcedf4b169046a921a" + ] + ], + "gvcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.g.vcf.gz.tbi:md5,49503913c28ec70a6f4aa52f6b357b4d" + ] + ], + "vcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz:md5,8b8ab4a675f01e437aa72e1438a717d0" + ] + ], + "vcf_tbi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ], + [ + { + "id": "test2", + "single_end": false + }, + "test2.vcf.gz.tbi:md5,0000833138104e87b05eaa906821eb21" + ] + ], + "versions": [ + "versions.yml:md5,5e6e7451f9819e2e0c33ad0d1b22d3b3", + "versions.yml:md5,c9c9c7000dc16bcb7e3107e7333481de", + "versions.yml:md5,cb2f0f2fe645633ed7d6528999bde458" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-08-16T16:18:03.021031138" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/deepvariant/tests/nextflow.config b/subworkflows/nf-core/deepvariant/tests/nextflow.config new file mode 100644 index 000000000000..be9854791fb2 --- /dev/null +++ b/subworkflows/nf-core/deepvariant/tests/nextflow.config @@ -0,0 +1,8 @@ +process { + withName: "DEEPVARIANT_MAKEEXAMPLES" { + ext.args = '--channels "insert_size"' + } + withName: "DEEPVARIANT_CALLVARIANTS" { + ext.args = '--checkpoint "/opt/models/wgs"' + } +} diff --git a/subworkflows/nf-core/deepvariant/tests/tags.yml b/subworkflows/nf-core/deepvariant/tests/tags.yml new file mode 100644 index 000000000000..ae5640d2330f --- /dev/null +++ b/subworkflows/nf-core/deepvariant/tests/tags.yml @@ -0,0 +1,2 @@ +subworkflows/deepvariant: + - subworkflows/nf-core/deepvariant/** From aa8c39be1d4c004e94871a32a8c6450a81ea6d7d Mon Sep 17 00:00:00 2001 From: Stephen Kelly Date: Thu, 12 Sep 2024 11:13:15 -0400 Subject: [PATCH 047/486] 4451 add vcf2maf nf test (#4463) * add nf-test case for vcf2maf without VEP * add VEP test case for vcf2maf nf-test * update linting for vcf2maf * fix prettier for vcf2maf * remove pytest files for vcf2maf * remove vcf2maf from pytest modules yml * add modules/nf-core/vcf2maf/tests/tags.yml * add line count to vcf2maf test * add line number and versions contents yaml to vcf2maf test * remove alternate container from vcf2maf testing and use the same container for testing with or without VEP * update modules/nf-core/vcf2maf/tests/main.nf.test * update modules/nf-core/vcf2maf/tests/main.nf.test * Update and fix tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add conda declaration to nf-test * Remove output in snapshot * Add versions to snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> --- modules/nf-core/vcf2maf/environment.yml | 2 +- modules/nf-core/vcf2maf/tests/main.nf.test | 76 ++++++++++ .../nf-core/vcf2maf/tests/main.nf.test.snap | 143 ++++++++++++++++++ modules/nf-core/vcf2maf/tests/nextflow.config | 11 ++ .../vcf2maf/tests/nextflow.withVEP.config | 9 ++ modules/nf-core/vcf2maf/tests/tags.yml | 2 + tests/config/nextflow.config | 2 + tests/config/pytest_modules.yml | 6 +- tests/modules/nf-core/vcf2maf/main.nf | 30 ---- tests/modules/nf-core/vcf2maf/nextflow.config | 14 -- tests/modules/nf-core/vcf2maf/test.yml | 15 -- 11 files changed, 247 insertions(+), 63 deletions(-) create mode 100644 modules/nf-core/vcf2maf/tests/main.nf.test create mode 100644 modules/nf-core/vcf2maf/tests/main.nf.test.snap create mode 100644 modules/nf-core/vcf2maf/tests/nextflow.config create mode 100644 modules/nf-core/vcf2maf/tests/nextflow.withVEP.config create mode 100644 modules/nf-core/vcf2maf/tests/tags.yml delete mode 100644 tests/modules/nf-core/vcf2maf/main.nf delete mode 100644 tests/modules/nf-core/vcf2maf/nextflow.config delete mode 100644 tests/modules/nf-core/vcf2maf/test.yml diff --git a/modules/nf-core/vcf2maf/environment.yml b/modules/nf-core/vcf2maf/environment.yml index 2d273cd05f57..bfe50913b914 100644 --- a/modules/nf-core/vcf2maf/environment.yml +++ b/modules/nf-core/vcf2maf/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::vcf2maf=1.6.21 - bioconda::ensembl-vep=106.1 + - bioconda::vcf2maf=1.6.21 diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test b/modules/nf-core/vcf2maf/tests/main.nf.test new file mode 100644 index 000000000000..f17e7740ee69 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/main.nf.test @@ -0,0 +1,76 @@ +nextflow_process { + name "Test vcf2maf" + process "VCF2MAF" + script "../main.nf" + + tag "modules" + tag "modules_nfcore" + tag "vcf2maf" + tag "untar" + + test("Run without VEP") { + config "./nextflow.config" + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) + ] + input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] + input[2] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.maf[0][1]).readLines()[5..131], + process.out.versions + ).match() }, + { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] } + ) + } + } + + test("Run with VEP"){ + tag "vcf2maf-withVEP" + config "./nextflow.withVEP.config" + + setup { + run("UNTAR") { + script "../../../../modules/nf-core/untar/main.nf" + process { + """ + input[0] = [ + [ id:'test_genome_vep' ], + file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/vep.tar.gz", checkIfExists: true) + ] + """ + } + } + } + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/gvcf/test.genome.vcf", checkIfExists: true) + ] + input[1] = [ file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/genome.fasta", checkIfExists: true) ] + input[2] = UNTAR.out.untar.map { it[1] } + """ + } + } + + then{ + assertAll( + { assert process.success }, + { assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines + { assert path(process.out.versions[0]).readLines() == ['"VCF2MAF":', ' vcf2maf: 1.6.21', ' ensemblvep: 106.1'] } + ) + } + } +} diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test.snap b/modules/nf-core/vcf2maf/tests/main.nf.test.snap new file mode 100644 index 000000000000..c81d6c6221f6 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/main.nf.test.snap @@ -0,0 +1,143 @@ +{ + "Run without VEP": { + "content": [ + [ + "Unknown\t0\t.\tGRCh38\tchr22\t1955\t1955\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t1955", + "Unknown\t0\t.\tGRCh38\tchr22\t1957\t1957\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTA\t.\t.\t\t\t\t\t\t\t\t\t\t1957", + "Unknown\t0\t.\tGRCh38\tchr22\t1958\t1958\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t1958", + "Unknown\t0\t.\tGRCh38\tchr22\t1959\t1959\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t1959", + "Unknown\t0\t.\tGRCh38\tchr22\t1960\t1960\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAT\t.\t.\t\t\t\t\t\t\t\t\t\t1960", + "Unknown\t0\t.\tGRCh38\tchr22\t1962\t1962\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t1962", + "Unknown\t0\t.\tGRCh38\tchr22\t1963\t1963\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAT\t.\t.\t\t\t\t\t\t\t\t\t\t1963", + "Unknown\t0\t.\tGRCh38\tchr22\t1964\t1964\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t1964", + "Unknown\t0\t.\tGRCh38\tchr22\t1965\t1965\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t1965", + "Unknown\t0\t.\tGRCh38\tchr22\t1966\t1966\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t1966", + "Unknown\t0\t.\tGRCh38\tchr22\t1967\t1967\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t1967", + "Unknown\t0\t.\tGRCh38\tchr22\t1982\t1982\t+\tTargeted_Region\tSNP\tA\tA\tG\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\trs7287620\t176.64\t\t\t\t\t\t\t\t\t\t1982", + "Unknown\t0\t.\tGRCh38\tchr22\t1983\t1983\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t1983", + "Unknown\t0\t.\tGRCh38\tchr22\t2103\t2103\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t2103", + "Unknown\t0\t.\tGRCh38\tchr22\t2104\t2104\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCC\t.\t.\t\t\t\t\t\t\t\t\t\t2104", + "Unknown\t0\t.\tGRCh38\tchr22\t2105\t2105\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t2105", + "Unknown\t0\t.\tGRCh38\tchr22\t2107\t2107\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t2107", + "Unknown\t0\t.\tGRCh38\tchr22\t2108\t2108\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTC\t.\t.\t\t\t\t\t\t\t\t\t\t2108", + "Unknown\t0\t.\tGRCh38\tchr22\t2111\t2111\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCT\t.\t.\t\t\t\t\t\t\t\t\t\t2111", + "Unknown\t0\t.\tGRCh38\tchr22\t2114\t2114\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t2114", + "Unknown\t0\t.\tGRCh38\tchr22\t2115\t2115\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2115", + "Unknown\t0\t.\tGRCh38\tchr22\t2118\t2118\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t2118", + "Unknown\t0\t.\tGRCh38\tchr22\t2123\t2123\t+\tTargeted_Region\tSNP\tC\tC\tG\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCG\t.\t33.97\t\t\t\t\t\t\t\t\t\t2123", + "Unknown\t0\t.\tGRCh38\tchr22\t2124\t2124\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCGC\t.\t.\t\t\t\t\t\t\t\t\t\t2124", + "Unknown\t0\t.\tGRCh38\tchr22\t2717\t2717\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t2717", + "Unknown\t0\t.\tGRCh38\tchr22\t2722\t2722\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t2722", + "Unknown\t0\t.\tGRCh38\tchr22\t2723\t2723\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t2723", + "Unknown\t0\t.\tGRCh38\tchr22\t2724\t2724\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t2724", + "Unknown\t0\t.\tGRCh38\tchr22\t2725\t2725\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2725", + "Unknown\t0\t.\tGRCh38\tchr22\t2837\t2837\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATA\t.\t.\t\t\t\t\t\t\t\t\t\t2837", + "Unknown\t0\t.\tGRCh38\tchr22\t2838\t2838\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2838", + "Unknown\t0\t.\tGRCh38\tchr22\t2908\t2908\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAA\t.\t.\t\t\t\t\t\t\t\t\t\t2908", + "Unknown\t0\t.\tGRCh38\tchr22\t2909\t2909\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2909", + "Unknown\t0\t.\tGRCh38\tchr22\t2910\t2910\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t2910", + "Unknown\t0\t.\tGRCh38\tchr22\t2911\t2911\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t2911", + "Unknown\t0\t.\tGRCh38\tchr22\t2912\t2912\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t2912", + "Unknown\t0\t.\tGRCh38\tchr22\t3120\t3120\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAC\t.\t.\t\t\t\t\t\t\t\t\t\t3120", + "Unknown\t0\t.\tGRCh38\tchr22\t3121\t3121\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACC\t.\t.\t\t\t\t\t\t\t\t\t\t3121", + "Unknown\t0\t.\tGRCh38\tchr22\t3122\t3122\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCC\t.\t.\t\t\t\t\t\t\t\t\t\t3122", + "Unknown\t0\t.\tGRCh38\tchr22\t3125\t3125\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGA\t.\t.\t\t\t\t\t\t\t\t\t\t3125", + "Unknown\t0\t.\tGRCh38\tchr22\t3127\t3127\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATC\t.\t.\t\t\t\t\t\t\t\t\t\t3127", + "Unknown\t0\t.\tGRCh38\tchr22\t3140\t3140\t+\tTargeted_Region\tSNP\tA\tA\tG\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAG\t.\t37.31\t\t\t\t\t\t\t\t\t\t3140", + "Unknown\t0\t.\tGRCh38\tchr22\t3141\t3141\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGT\t.\t.\t\t\t\t\t\t\t\t\t\t3141", + "Unknown\t0\t.\tGRCh38\tchr22\t3145\t3145\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t3145", + "Unknown\t0\t.\tGRCh38\tchr22\t3191\t3191\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t3191", + "Unknown\t0\t.\tGRCh38\tchr22\t3192\t3192\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t3192", + "Unknown\t0\t.\tGRCh38\tchr22\t3197\t3197\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3197", + "Unknown\t0\t.\tGRCh38\tchr22\t3201\t3201\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3201", + "Unknown\t0\t.\tGRCh38\tchr22\t3208\t3208\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3208", + "Unknown\t0\t.\tGRCh38\tchr22\t3210\t3210\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTA\t.\t.\t\t\t\t\t\t\t\t\t\t3210", + "Unknown\t0\t.\tGRCh38\tchr22\t3218\t3218\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t3218", + "Unknown\t0\t.\tGRCh38\tchr22\t3219\t3219\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t3219", + "Unknown\t0\t.\tGRCh38\tchr22\t3266\t3266\t+\tTargeted_Region\tSNP\tT\tT\tC\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\trs4008589\t481.06\t\t\t\t\t\t\t\t\t\t3266", + "Unknown\t0\t.\tGRCh38\tchr22\t3267\t3267\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t3267", + "Unknown\t0\t.\tGRCh38\tchr22\t3303\t3303\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAC\t.\t.\t\t\t\t\t\t\t\t\t\t3303", + "Unknown\t0\t.\tGRCh38\tchr22\t3304\t3304\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t3304", + "Unknown\t0\t.\tGRCh38\tchr22\t3305\t3305\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3305", + "Unknown\t0\t.\tGRCh38\tchr22\t3309\t3309\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3309", + "Unknown\t0\t.\tGRCh38\tchr22\t3310\t3310\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3310", + "Unknown\t0\t.\tGRCh38\tchr22\t3318\t3318\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGC\t.\t.\t\t\t\t\t\t\t\t\t\t3318", + "Unknown\t0\t.\tGRCh38\tchr22\t3321\t3321\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTA\t.\t.\t\t\t\t\t\t\t\t\t\t3321", + "Unknown\t0\t.\tGRCh38\tchr22\t3352\t3352\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTC\t.\t.\t\t\t\t\t\t\t\t\t\t3352", + "Unknown\t0\t.\tGRCh38\tchr22\t3355\t3355\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3355", + "Unknown\t0\t.\tGRCh38\tchr22\t3356\t3356\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTC\t.\t.\t\t\t\t\t\t\t\t\t\t3356", + "Unknown\t0\t.\tGRCh38\tchr22\t3366\t3366\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3366", + "Unknown\t0\t.\tGRCh38\tchr22\t3374\t3374\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3374", + "Unknown\t0\t.\tGRCh38\tchr22\t3375\t3375\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGA\t.\t.\t\t\t\t\t\t\t\t\t\t3375", + "Unknown\t0\t.\tGRCh38\tchr22\t3376\t3376\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t3376", + "Unknown\t0\t.\tGRCh38\tchr22\t3378\t3378\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCG\t.\t.\t\t\t\t\t\t\t\t\t\t3378", + "Unknown\t0\t.\tGRCh38\tchr22\t3379\t3379\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCGG\t.\t.\t\t\t\t\t\t\t\t\t\t3379", + "Unknown\t0\t.\tGRCh38\tchr22\t3382\t3382\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCA\t.\t.\t\t\t\t\t\t\t\t\t\t3382", + "Unknown\t0\t.\tGRCh38\tchr22\t3386\t3386\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCA\t.\t.\t\t\t\t\t\t\t\t\t\t3386", + "Unknown\t0\t.\tGRCh38\tchr22\t3387\t3387\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t3387", + "Unknown\t0\t.\tGRCh38\tchr22\t3391\t3391\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t3391", + "Unknown\t0\t.\tGRCh38\tchr22\t3393\t3393\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3393", + "Unknown\t0\t.\tGRCh38\tchr22\t3394\t3394\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3394", + "Unknown\t0\t.\tGRCh38\tchr22\t3395\t3395\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t3395", + "Unknown\t0\t.\tGRCh38\tchr22\t3396\t3396\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAC\t.\t.\t\t\t\t\t\t\t\t\t\t3396", + "Unknown\t0\t.\tGRCh38\tchr22\t3397\t3397\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACC\t.\t.\t\t\t\t\t\t\t\t\t\t3397", + "Unknown\t0\t.\tGRCh38\tchr22\t3398\t3398\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t3398", + "Unknown\t0\t.\tGRCh38\tchr22\t3399\t3399\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3399", + "Unknown\t0\t.\tGRCh38\tchr22\t3400\t3400\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3400", + "Unknown\t0\t.\tGRCh38\tchr22\t3401\t3401\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t3401", + "Unknown\t0\t.\tGRCh38\tchr22\t3402\t3402\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATT\t.\t.\t\t\t\t\t\t\t\t\t\t3402", + "Unknown\t0\t.\tGRCh38\tchr22\t3403\t3403\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3403", + "Unknown\t0\t.\tGRCh38\tchr22\t3404\t3404\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t3404", + "Unknown\t0\t.\tGRCh38\tchr22\t3405\t3405\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t3405", + "Unknown\t0\t.\tGRCh38\tchr22\t3406\t3406\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t3406", + "Unknown\t0\t.\tGRCh38\tchr22\t3407\t3407\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3407", + "Unknown\t0\t.\tGRCh38\tchr22\t3409\t3409\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3409", + "Unknown\t0\t.\tGRCh38\tchr22\t3410\t3410\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3410", + "Unknown\t0\t.\tGRCh38\tchr22\t3411\t3411\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t3411", + "Unknown\t0\t.\tGRCh38\tchr22\t3413\t3413\t+\tTargeted_Region\tSNP\tT\tT\tG\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t78.64\t\t\t\t\t\t\t\t\t\t3413", + "Unknown\t0\t.\tGRCh38\tchr22\t3414\t3414\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t3414", + "Unknown\t0\t.\tGRCh38\tchr22\t3418\t3418\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t3418", + "Unknown\t0\t.\tGRCh38\tchr22\t3421\t3421\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCT\t.\t.\t\t\t\t\t\t\t\t\t\t3421", + "Unknown\t0\t.\tGRCh38\tchr22\t3422\t3422\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTA\t.\t.\t\t\t\t\t\t\t\t\t\t3422", + "Unknown\t0\t.\tGRCh38\tchr22\t3423\t3423\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTAG\t.\t.\t\t\t\t\t\t\t\t\t\t3423", + "Unknown\t0\t.\tGRCh38\tchr22\t3632\t3632\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGCT\t.\t.\t\t\t\t\t\t\t\t\t\t3632", + "Unknown\t0\t.\tGRCh38\tchr22\t3633\t3633\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t3633", + "Unknown\t0\t.\tGRCh38\tchr22\t3635\t3635\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGGA\t.\t.\t\t\t\t\t\t\t\t\t\t3635", + "Unknown\t0\t.\tGRCh38\tchr22\t3636\t3636\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t3636", + "Unknown\t0\t.\tGRCh38\tchr22\t3637\t3637\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAG\t.\t.\t\t\t\t\t\t\t\t\t\t3637", + "Unknown\t0\t.\tGRCh38\tchr22\t3645\t3645\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCC\t.\t.\t\t\t\t\t\t\t\t\t\t3645", + "Unknown\t0\t.\tGRCh38\tchr22\t4466\t4466\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAT\t.\t.\t\t\t\t\t\t\t\t\t\t4466", + "Unknown\t0\t.\tGRCh38\tchr22\t4488\t4488\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tACT\t.\t.\t\t\t\t\t\t\t\t\t\t4488", + "Unknown\t0\t.\tGRCh38\tchr22\t4489\t4489\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTT\t.\t.\t\t\t\t\t\t\t\t\t\t4489", + "Unknown\t0\t.\tGRCh38\tchr22\t4494\t4494\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCCA\t.\t.\t\t\t\t\t\t\t\t\t\t4494", + "Unknown\t0\t.\tGRCh38\tchr22\t4495\t4495\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAG\t.\t.\t\t\t\t\t\t\t\t\t\t4495", + "Unknown\t0\t.\tGRCh38\tchr22\t4499\t4499\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGGT\t.\t.\t\t\t\t\t\t\t\t\t\t4499", + "Unknown\t0\t.\tGRCh38\tchr22\t4500\t4500\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTT\t.\t.\t\t\t\t\t\t\t\t\t\t4500", + "Unknown\t0\t.\tGRCh38\tchr22\t4501\t4501\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTT\t.\t.\t\t\t\t\t\t\t\t\t\t4501", + "Unknown\t0\t.\tGRCh38\tchr22\t4502\t4502\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTTG\t.\t.\t\t\t\t\t\t\t\t\t\t4502", + "Unknown\t0\t.\tGRCh38\tchr22\t4503\t4503\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGG\t.\t.\t\t\t\t\t\t\t\t\t\t4503", + "Unknown\t0\t.\tGRCh38\tchr22\t4508\t4508\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGC\t.\t.\t\t\t\t\t\t\t\t\t\t4508", + "Unknown\t0\t.\tGRCh38\tchr22\t4576\t4576\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tATG\t.\t.\t\t\t\t\t\t\t\t\t\t4576", + "Unknown\t0\t.\tGRCh38\tchr22\t4579\t4579\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGAA\t.\t.\t\t\t\t\t\t\t\t\t\t4579", + "Unknown\t0\t.\tGRCh38\tchr22\t4580\t4580\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAAA\t.\t.\t\t\t\t\t\t\t\t\t\t4580", + "Unknown\t0\t.\tGRCh38\tchr22\t4583\t4583\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tAGC\t.\t.\t\t\t\t\t\t\t\t\t\t4583", + "Unknown\t0\t.\tGRCh38\tchr22\t4585\t4585\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTC\t.\t.\t\t\t\t\t\t\t\t\t\t4585", + "Unknown\t0\t.\tGRCh38\tchr22\t4586\t4586\t+\tTargeted_Region\tINS\tC\tC\t\t\t\tTUMOR\tNORMAL\tC\tC\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTCA\t.\t.\t\t\t\t\t\t\t\t\t\t4586", + "Unknown\t0\t.\tGRCh38\tchr22\t4587\t4587\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAT\t.\t.\t\t\t\t\t\t\t\t\t\t4587", + "Unknown\t0\t.\tGRCh38\tchr22\t4598\t4598\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCTG\t.\t.\t\t\t\t\t\t\t\t\t\t4598", + "Unknown\t0\t.\tGRCh38\tchr22\t4599\t4599\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGA\t.\t.\t\t\t\t\t\t\t\t\t\t4599", + "Unknown\t0\t.\tGRCh38\tchr22\t4605\t4605\t+\tTargeted_Region\tINS\tG\tG\t\t\t\tTUMOR\tNORMAL\tG\tG\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tTGT\t.\t.\t\t\t\t\t\t\t\t\t\t4605", + "Unknown\t0\t.\tGRCh38\tchr22\t4606\t4606\t+\tTargeted_Region\tINS\tT\tT\t\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTC\t.\t.\t\t\t\t\t\t\t\t\t\t4606", + "Unknown\t0\t.\tGRCh38\tchr22\t4608\t4608\t+\tTargeted_Region\tINS\tA\tA\t\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAA\t.\t.\t\t\t\t\t\t\t\t\t\t4608" + ], + [ + "versions.yml:md5,a81fb1aa49b86f6c9c17e3158336d930" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-12T15:59:58.867897" + } +} \ No newline at end of file diff --git a/modules/nf-core/vcf2maf/tests/nextflow.config b/modules/nf-core/vcf2maf/tests/nextflow.config new file mode 100644 index 000000000000..1f0aad364a75 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/nextflow.config @@ -0,0 +1,11 @@ +// config for running without VEP +params.species = "homo_sapiens" +params.build = "GRCh38" + +process { + container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0" + conda = "bioconda::vcf2maf=1.6.21" + withName: 'VCF2MAF' { + ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" + } +} \ No newline at end of file diff --git a/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config b/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config new file mode 100644 index 000000000000..0991b358b002 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/nextflow.withVEP.config @@ -0,0 +1,9 @@ +// config for running with VEP +params.species = "homo_sapiens" +params.build = "GRCh38" + +process { + withName: 'VCF2MAF' { + ext.args = "--ncbi-build ${params.build} --species ${params.species}" + } +} diff --git a/modules/nf-core/vcf2maf/tests/tags.yml b/modules/nf-core/vcf2maf/tests/tags.yml new file mode 100644 index 000000000000..b0c967f42077 --- /dev/null +++ b/modules/nf-core/vcf2maf/tests/tags.yml @@ -0,0 +1,2 @@ +vcf2maf: + - modules/nf-core/vcf2maf/** diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index c24e252ec579..c86fb134d751 100644 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -16,9 +16,11 @@ if ("$PROFILE" == "singularity") { singularity.autoMounts = true } else if ("$PROFILE" == "conda") { conda.enabled = true + conda.useMicromamba = true } else if ("$PROFILE" == "mamba") { conda.enabled = true conda.useMamba = true + conda.useMicromamba = true } else if ("$PROFILE" == "podman") { podman.enabled = true podman.userEmulation = true diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index f10ddc6b929b..83f3c37d11f9 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -813,9 +813,9 @@ varlociraptor/callvariants: varlociraptor/preprocess: - modules/nf-core/varlociraptor/preprocess/** - tests/modules/nf-core/varlociraptor/preprocess/** -vcf2maf: - - modules/nf-core/vcf2maf/** - - tests/modules/nf-core/vcf2maf/** +vcflib/vcfbreakmulti: + - modules/nf-core/vcflib/vcfbreakmulti/** + - tests/modules/nf-core/vcflib/vcfbreakmulti/** verifybamid/verifybamid2: - modules/nf-core/verifybamid/verifybamid2/** - tests/modules/nf-core/verifybamid/verifybamid2/** diff --git a/tests/modules/nf-core/vcf2maf/main.nf b/tests/modules/nf-core/vcf2maf/main.nf deleted file mode 100644 index 8deed5cf74a1..000000000000 --- a/tests/modules/nf-core/vcf2maf/main.nf +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { VCF2MAF } from '../../../../modules/nf-core/vcf2maf/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' - -workflow test_vcf2maf_no_vep { - - input_vcf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - - VCF2MAF ( input_vcf, fasta, [] ) -} - -workflow test_vcf2maf_vep { - - input_vcf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true) - ] - fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - vep_cache = [ [ id:'test' ], file(params.test_data['homo_sapiens']['genome']['vep_cache'], checkIfExists: true) ] - - vep_cache_unpacked = UNTAR(vep_cache).untar.map { it[1] } - VCF2MAF ( input_vcf, fasta, vep_cache_unpacked) -} diff --git a/tests/modules/nf-core/vcf2maf/nextflow.config b/tests/modules/nf-core/vcf2maf/nextflow.config deleted file mode 100644 index 5505d8ec1e44..000000000000 --- a/tests/modules/nf-core/vcf2maf/nextflow.config +++ /dev/null @@ -1,14 +0,0 @@ -params.species = "homo_sapiens" -params.build = "GRCh38" - -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: 'test_vcf2maf_no_vep:VCF2MAF' { - ext.args = "--ncbi-build ${params.build} --species ${params.species} --inhibit-vep" - container = "biocontainers/vcf2maf:1.6.21--hdfd78af_0" - } - withName: 'test_vcf2maf_vep:VCF2MAF' { - ext.args = "--ncbi-build ${params.build} --species ${params.species}" - } -} diff --git a/tests/modules/nf-core/vcf2maf/test.yml b/tests/modules/nf-core/vcf2maf/test.yml deleted file mode 100644 index e62e39f8e431..000000000000 --- a/tests/modules/nf-core/vcf2maf/test.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: vcf2maf test_vcf2maf_no_vep - command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_no_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config - tags: - - vcf2maf - files: - - path: output/vcf2maf/test.maf - md5sum: c7f357efa774fd5c4003d84f05212ed0 - -- name: vcf2maf test_vcf2maf_vep - command: nextflow run ./tests/modules/nf-core/vcf2maf -entry test_vcf2maf_vep -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/vcf2maf/nextflow.config - tags: - - vcf2maf - files: - - path: output/vcf2maf/test.maf - md5sum: bf114692a2f421225926c9b651eff161 From 43b2b702abd8ab2cb1aa1365763f518413ad5721 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 13 Sep 2024 03:30:18 -0300 Subject: [PATCH 048/486] Update mirtop modules and subworkflow (#6635) * add arity to mirtop/gff * add prefix to mirtop output * update tests and snapshots * update yml --- .../nf-core/mirtop/counts/tests/main.nf.test | 4 +-- .../nf-core/mirtop/export/tests/main.nf.test | 4 +-- .../mirtop/export/tests/main.nf.test.snap | 6 ++--- modules/nf-core/mirtop/gff/main.nf | 8 +++--- modules/nf-core/mirtop/gff/meta.yml | 6 +---- modules/nf-core/mirtop/gff/tests/main.nf.test | 3 +-- .../mirtop/gff/tests/main.nf.test.snap | 27 +++---------------- modules/nf-core/mirtop/stats/meta.yml | 4 +++ .../nf-core/mirtop/stats/tests/main.nf.test | 23 ---------------- .../nf-core/bam_stats_mirna_mirtop/main.nf | 17 ++++++------ .../bam_stats_mirna_mirtop/tests/main.nf.test | 5 ++-- .../tests/main.nf.test.snap | 4 +-- 12 files changed, 35 insertions(+), 76 deletions(-) diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test index 8283d5b489be..52b31db1eb29 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -38,7 +38,7 @@ nextflow_process { when { process { """ - input[0] = MIRTOP_GFF.out.mirtop_gff + input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), @@ -72,7 +72,7 @@ nextflow_process { when { process { """ - input[0] = MIRTOP_GFF.out.mirtop_gff + input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test b/modules/nf-core/mirtop/export/tests/main.nf.test index 0a7f80710b74..234caf573033 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test +++ b/modules/nf-core/mirtop/export/tests/main.nf.test @@ -37,7 +37,7 @@ nextflow_process { when { process { """ - input[0] = MIRTOP_GFF.out.mirtop_gff + input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), @@ -66,7 +66,7 @@ nextflow_process { when { process { """ - input[0] = MIRTOP_GFF.out.mirtop_gff + input[0] = MIRTOP_GFF.out.gff input[1] = [ [ id:'hairpin'], // meta map file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap index 1a7784b08d16..f8c668a62fbb 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/export/tests/main.nf.test.snap @@ -62,7 +62,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" + "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" ] ], "1": [ @@ -82,7 +82,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" + "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,efbcbe67716a4a56f89e538af2251dcc" ] ], "vcf": [ @@ -97,6 +97,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T15:25:24.528528611" + "timestamp": "2024-09-12T23:12:49.612315132" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf index 1f951e2fada3..453b624b9f6f 100644 --- a/modules/nf-core/mirtop/gff/main.nf +++ b/modules/nf-core/mirtop/gff/main.nf @@ -8,13 +8,12 @@ process MIRTOP_GFF { 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(bam, arity:'1..*') tuple val(meta2), path(hairpin) tuple val(meta3), path(gtf), val(species) output: - tuple val(meta), path("mirtop/${bam.baseName}.gff") , emit: sample_gff - tuple val(meta), path("mirtop/mirtop.gff") , emit: mirtop_gff + tuple val(meta), path("mirtop/*mirtop.gff") , emit: gff path "versions.yml" , emit: versions when: @@ -33,6 +32,8 @@ process MIRTOP_GFF { -o mirtop \\ $bam + mv mirtop/mirtop.gff mirtop/${prefix}_mirtop.gff + cat <<-END_VERSIONS > versions.yml "${task.process}": mirtop: \$(echo \$(mirtop --version 2>&1) | sed 's/^.*mirtop //') @@ -45,7 +46,6 @@ process MIRTOP_GFF { """ mkdir mirtop touch mirtop/mirtop.gff - touch mirtop/sim_isomir_sort.gff cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml index 9d593210d2ee..454d5edfe1db 100644 --- a/modules/nf-core/mirtop/gff/meta.yml +++ b/modules/nf-core/mirtop/gff/meta.yml @@ -46,11 +46,7 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - sample_gff: + - gff: type: file description: GFF file pattern: "*.{gff}" diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test index 67b7ef3cf86a..3ce7ef855234 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -35,12 +35,11 @@ nextflow_process { { assert process.success }, { assert snapshot( process.out.bam, - file(process.out.sample_gff[0][1]).readLines().findAll { it.contains("hsa-let-7a-2 miRBasev21 isomiR 3 25 0 + . Read TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;") }, process.out.versions, ).match() }, // md5sum is not stable, order of elements in section "variant" may change - { assert file(process.out.mirtop_gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} + { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} ) } diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap index 8283d5ad2abd..a9e6f852e6ff 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap @@ -3,14 +3,6 @@ "content": [ { "0": [ - [ - { - "id": "sample_sim_isomir_bam" - }, - "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], - "1": [ [ { "id": "sample_sim_isomir_bam" @@ -18,10 +10,10 @@ "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "2": [ + "1": [ "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" ], - "mirtop_gff": [ + "gff": [ [ { "id": "sample_sim_isomir_bam" @@ -29,14 +21,6 @@ "mirtop.gff:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], - "sample_gff": [ - [ - { - "id": "sample_sim_isomir_bam" - }, - "sim_isomir_sort.gff:md5,d41d8cd98f00b204e9800998ecf8427e" - ] - ], "versions": [ "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" ] @@ -46,14 +30,11 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T12:47:11.610449763" + "timestamp": "2024-09-12T22:40:30.542921953" }, "isomir - bam": { "content": [ null, - [ - "hsa-let-7a-2\tmiRBasev21\tisomiR\t3\t25\t0\t+\t.\tRead TTGAGGTAGTAGGTTGTATAGTT; UID iso-23-Z0S31NSL0E; Name hsa-let-7a-5p;Parent hsa-let-7a-2; Variant iso_5p:-1; Cigar 23M;Expression 0; Filter Pass; Hits 1;" - ], [ "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" ] @@ -62,6 +43,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-06T21:42:47.26306174" + "timestamp": "2024-09-12T22:38:09.903017316" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml index 7df0f7bca043..1bcd224832d8 100644 --- a/modules/nf-core/mirtop/stats/meta.yml +++ b/modules/nf-core/mirtop/stats/meta.yml @@ -39,6 +39,10 @@ output: type: file description: TXT file with stats pattern: "*.{txt}" + - log: + type: file + description: log file with stats + pattern: "*.{log}" authors: - "@atrigila" diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test b/modules/nf-core/mirtop/stats/tests/main.nf.test index 0309885fa121..e9d16cdcc2b8 100644 --- a/modules/nf-core/mirtop/stats/tests/main.nf.test +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test @@ -8,31 +8,8 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "mirtop" - tag "mirtop/gff" tag "mirtop/stats" - setup { - run("MIRTOP_GFF") { - script "../../gff/main.nf" - process { - """ - input[0] = [ - [ id:'sample_sim_isomir_bam'], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/sim_isomir_sort.bam", checkIfExists: true), - ] - input[1] = [ - [ id:'hairpin'], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hairpin_mirtop.fa", checkIfExists: true), - ] - input[2] = [ - [ id:'hsa' ], // meta map - file("https://github.com/nf-core/test-datasets/raw/modules/data/delete_me/mirtop/hsa.gff3", checkIfExists: true), - "hsa"] - """ - } - } - } - test("isomir - bam") { when { diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf b/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf index 17c2695fa9b6..ac9393f40d12 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/main.nf @@ -16,19 +16,20 @@ workflow BAM_STATS_MIRNA_MIRTOP { ch_versions = Channel.empty() MIRTOP_GFF ( ch_bam, ch_hairpin, ch_gtf_species ) - ch_versions = ch_versions.mix(MIRTOP_GFF.out.versions.first()) + ch_versions = ch_versions.mix(MIRTOP_GFF.out.versions) - MIRTOP_COUNTS ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species ) - ch_versions = ch_versions.mix(MIRTOP_COUNTS.out.versions.first()) + MIRTOP_COUNTS ( MIRTOP_GFF.out.gff, ch_hairpin, ch_gtf_species ) + ch_versions = ch_versions.mix(MIRTOP_COUNTS.out.versions) - MIRTOP_EXPORT ( MIRTOP_GFF.out.mirtop_gff, ch_hairpin, ch_gtf_species ) - ch_versions = ch_versions.mix(MIRTOP_EXPORT.out.versions.first()) + MIRTOP_EXPORT ( MIRTOP_GFF.out.gff, ch_hairpin, ch_gtf_species ) + ch_versions = ch_versions.mix(MIRTOP_EXPORT.out.versions) - MIRTOP_STATS ( MIRTOP_GFF.out.mirtop_gff ) - ch_versions = ch_versions.mix(MIRTOP_STATS.out.versions.first()) + MIRTOP_STATS ( MIRTOP_GFF.out.gff ) + ch_versions = ch_versions.mix(MIRTOP_STATS.out.versions) emit: - rawdata_tsv = MIRTOP_EXPORT.out.tsv // channel: [ val(meta), [ tsv ] ] + isomirs = MIRTOP_EXPORT.out.tsv // channel: [ val(meta), [ tsv ] ] + counts = MIRTOP_COUNTS.out.tsv // channel: [ val(meta), [ tsv ] ] stats_txt = MIRTOP_STATS.out.txt // channel: [ val(meta), [ txt ] ] stats_log = MIRTOP_STATS.out.log // channel: [ val(meta), [ log ] ] versions = ch_versions // channel: [ versions.yml ] diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test index 064fd6547563..604c747b082f 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test @@ -39,10 +39,11 @@ nextflow_workflow { assertAll( { assert workflow.success}, { assert snapshot( - workflow.out.rawdata_tsv, + workflow.out.isomirs, workflow.out.stats_txt, workflow.out.stats_log, - workflow.out.versions).match() } + workflow.out.versions).match() }, + { assert path("${workflow.out.counts[0][1]}").exists() } ) } } diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap index 02a07ab1b18b..2a0e41a3439a 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_rawData.tsv:md5,4a065e444c54b0e816352bf1640594dd" + "sample_sim_isomir_bam_mirtop_rawData.tsv:md5,4a065e444c54b0e816352bf1640594dd" ] ], [ @@ -36,6 +36,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T21:31:21.204039357" + "timestamp": "2024-09-12T23:13:48.308574263" } } \ No newline at end of file From 264d493cc49aa0ebb2206bd2cc4d3072af04d81a Mon Sep 17 00:00:00 2001 From: Eric Wei Date: Fri, 13 Sep 2024 01:09:04 -0700 Subject: [PATCH 049/486] Add bcftools/pluginimputeinfo (#6624) * Add bcftools/pluginimputeinfo * Remove TODO * Change label * Update meta.yml --------- Co-authored-by: James A. Fellows Yates --- .../bcftools/pluginimputeinfo/environment.yml | 7 + .../nf-core/bcftools/pluginimputeinfo/main.nf | 76 ++++ .../bcftools/pluginimputeinfo/meta.yml | 81 ++++ .../pluginimputeinfo/tests/main.nf.test | 406 ++++++++++++++++++ .../pluginimputeinfo/tests/main.nf.test.snap | 333 ++++++++++++++ .../pluginimputeinfo/tests/nextflow.config | 13 + .../tests/vcf_gz_index.config | 13 + .../tests/vcf_gz_index_csi.config | 13 + .../tests/vcf_gz_index_tbi.config | 13 + 9 files changed, 955 insertions(+) create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/environment.yml create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/main.nf create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/meta.yml create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_tbi.config diff --git a/modules/nf-core/bcftools/pluginimputeinfo/environment.yml b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml new file mode 100644 index 000000000000..bfd03513359c --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::bcftools=1.20" diff --git a/modules/nf-core/bcftools/pluginimputeinfo/main.nf b/modules/nf-core/bcftools/pluginimputeinfo/main.nf new file mode 100644 index 000000000000..395c60ada5f6 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/main.nf @@ -0,0 +1,76 @@ +process BCFTOOLS_PLUGINIMPUTEINFO { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.20--h8b25389_1': + 'biocontainers/bcftools:1.20--h8b25389_1' }" + + input: + tuple val(meta), path(vcf), path(index) + path(regions) + path(targets) + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def regions_file = regions ? "--regions-file ${regions}" : "" + def targets_file = targets ? "--targets-file ${targets}" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + """ + bcftools plugin impute-info \\ + --output ${prefix}.${extension} \\ + ${regions_file} \\ + ${targets_file} \\ + $args \\ + --threads $task.cpus \\ + ${vcf} \\ + -- \\ + $args2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml new file mode 100644 index 000000000000..ca2b6c3c7419 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml @@ -0,0 +1,81 @@ +--- +name: "bcftools_pluginimputeinfo" +description: Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. +keywords: + - impute-info + - bcftools + - imputation + - metrics + - tags + - VCF +tools: + - "bcftools": + description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + homepage: "http://samtools.github.io/bcftools/bcftools.html" + documentation: "https://samtools.github.io/bcftools/bcftools.html#plugin" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args" + - "bcftools plugin impute-info": + description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + homepage: "http://samtools.github.io/bcftools/bcftools.html" + documentation: "https://samtools.github.io/bcftools/howtos/plugins.html" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args2" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF output file containing added INFO/INFO field + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@eweizy" +maintainers: + - "@eweizy" diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test new file mode 100644 index 000000000000..b150b12c7cb6 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test @@ -0,0 +1,406 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINIMPUTEINFO" + script "../main.nf" + process "BCFTOOLS_PLUGINIMPUTEINFO" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginimputeinfo" + tag "bcftools/plugintag2tag" + + test("sarscov2 - [vcf, tbi], [], []") { + + config "./nextflow.config" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], vcf, tsv, []") { + + config "./nextflow.config" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + config "./nextflow.config" + options "-stub" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + setup { + run("BCFTOOLS_PLUGINTAG2TAG") { + script "../../plugintag2tag/main.nf" + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + """ + } + } + } + + when { + process { + """ + input[0] = BCFTOOLS_PLUGINTAG2TAG.out.vcf.join(BCFTOOLS_PLUGINTAG2TAG.out.tbi) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap new file mode 100644 index 000000000000..8e3b4e953891 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/main.nf.test.snap @@ -0,0 +1,333 @@ +{ + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:42:24.860002123" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,d5f57785c1e1496196ee62b72fbd3852" + ] + ], + [ + + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:41:28.801236995" + }, + "sarscov2 - [vcf, tbi], [], []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf:md5,d5f57785c1e1496196ee62b72fbd3852" + ] + ], + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:25:19.761202429" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:42:05.180443538" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:42:49.144650301" + }, + "sarscov2 - [vcf, tbi], vcf, tsv, []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf:md5,d5f57785c1e1496196ee62b72fbd3852" + ] + ], + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:41:40.973896543" + }, + "sarscov2 - [vcf, tbi], [], [], [] - stub": { + "content": [ + "out_vcf.vcf", + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:41:53.257327022" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,d5f57785c1e1496196ee62b72fbd3852" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:41:05.386430406" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,d5f57785c1e1496196ee62b72fbd3852" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,6e1da2ba6a2af2d4b74f8d2efb05a3e7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-10T21:41:17.063459898" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/nextflow.config b/modules/nf-core/bcftools/pluginimputeinfo/tests/nextflow.config new file mode 100644 index 000000000000..d34b30c66a0e --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/nextflow.config @@ -0,0 +1,13 @@ +process { + + withName: BCFTOOLS_PLUGINTAG2TAG { + ext.prefix = { "${meta.id}_gp" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "--PL-to-GP" + } + + withName: BCFTOOLS_PLUGINIMPUTEINFO { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--no-version --output-type v" + } +} diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index.config new file mode 100644 index 000000000000..07289b0c9dc2 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index.config @@ -0,0 +1,13 @@ +process { + + withName: BCFTOOLS_PLUGINTAG2TAG { + ext.prefix = { "${meta.id}_gp" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "--PL-to-GP" + } + + withName: BCFTOOLS_PLUGINIMPUTEINFO { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" + } +} diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_csi.config new file mode 100644 index 000000000000..f2e37081d5ab --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_csi.config @@ -0,0 +1,13 @@ +process { + + withName: BCFTOOLS_PLUGINTAG2TAG { + ext.prefix = { "${meta.id}_gp" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "--PL-to-GP" + } + + withName: BCFTOOLS_PLUGINIMPUTEINFO { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" + } +} diff --git a/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_tbi.config new file mode 100644 index 000000000000..39e29ac35cd5 --- /dev/null +++ b/modules/nf-core/bcftools/pluginimputeinfo/tests/vcf_gz_index_tbi.config @@ -0,0 +1,13 @@ +process { + + withName: BCFTOOLS_PLUGINTAG2TAG { + ext.prefix = { "${meta.id}_gp" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "--PL-to-GP" + } + + withName: BCFTOOLS_PLUGINIMPUTEINFO { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" + } +} From ad30f90cfc383dfaa505771d24f9e292c53157ab Mon Sep 17 00:00:00 2001 From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Date: Fri, 13 Sep 2024 03:10:20 -0500 Subject: [PATCH 050/486] Get HISAT2 version from CLI (#6634) fix: Get version from cli --- modules/nf-core/hisat2/align/main.nf | 9 ++---- modules/nf-core/hisat2/build/main.nf | 7 ++--- .../hisat2/build/tests/main.nf.test.snap | 29 ++----------------- .../nf-core/hisat2/extractsplicesites/main.nf | 7 ++--- 4 files changed, 10 insertions(+), 42 deletions(-) diff --git a/modules/nf-core/hisat2/align/main.nf b/modules/nf-core/hisat2/align/main.nf index ea186f62a7cc..f45f9bccb078 100644 --- a/modules/nf-core/hisat2/align/main.nf +++ b/modules/nf-core/hisat2/align/main.nf @@ -2,7 +2,6 @@ process HISAT2_ALIGN { tag "$meta.id" label 'process_high' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/mulled-v2-a97e90b3b802d1da3d6958e0867610c718cb5eb1:2cdf6bf1e92acbeb9b2834b1c58754167173a410-0' : @@ -25,7 +24,6 @@ process HISAT2_ALIGN { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. def strandedness = '' if (meta.strandedness == 'forward') { @@ -53,7 +51,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -85,7 +83,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -94,7 +92,6 @@ process HISAT2_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" def unaligned = params.save_unaligned ? "echo '' | gzip > ${prefix}.unmapped_1.fastq.gz \n echo '' | gzip > ${prefix}.unmapped_2.fastq.gz" : '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ ${unaligned} @@ -103,7 +100,7 @@ process HISAT2_ALIGN { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ diff --git a/modules/nf-core/hisat2/build/main.nf b/modules/nf-core/hisat2/build/main.nf index 17d8fdd5b2c7..37a3e4565813 100644 --- a/modules/nf-core/hisat2/build/main.nf +++ b/modules/nf-core/hisat2/build/main.nf @@ -3,7 +3,6 @@ process HISAT2_BUILD { label 'process_high' label 'process_high_memory' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : @@ -44,7 +43,6 @@ process HISAT2_BUILD { log.info "[HISAT2 index build] Less than ${hisat2_build_memory} GB available, so NOT using splice sites and exons to build HISAT2 index." log.info "[HISAT2 index build] Use --hisat2_build_memory [small number] to skip this check." } - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ mkdir hisat2 $extract_exons @@ -58,18 +56,17 @@ process HISAT2_BUILD { cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ mkdir hisat2 cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ } diff --git a/modules/nf-core/hisat2/build/tests/main.nf.test.snap b/modules/nf-core/hisat2/build/tests/main.nf.test.snap index 0e3b5c57f884..68fc7ffba806 100644 --- a/modules/nf-core/hisat2/build/tests/main.nf.test.snap +++ b/modules/nf-core/hisat2/build/tests/main.nf.test.snap @@ -1,27 +1,4 @@ { - "test - stub": { - "content": [ - { - "0": [ - - ], - "1": [ - - ], - "index": [ - - ], - "versions": [ - - ] - } - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-20T17:29:31.567024" - }, "Should run without failures - stub": { "content": [ { @@ -31,7 +8,7 @@ "id": "genome" }, [ - + ] ] ], @@ -44,7 +21,7 @@ "id": "genome" }, [ - + ] ] ], @@ -110,4 +87,4 @@ }, "timestamp": "2023-10-16T14:42:22.381609786" } -} +} \ No newline at end of file diff --git a/modules/nf-core/hisat2/extractsplicesites/main.nf b/modules/nf-core/hisat2/extractsplicesites/main.nf index 588a9947a2db..82d2cfbac93a 100644 --- a/modules/nf-core/hisat2/extractsplicesites/main.nf +++ b/modules/nf-core/hisat2/extractsplicesites/main.nf @@ -2,7 +2,6 @@ process HISAT2_EXTRACTSPLICESITES { tag "$gtf" label 'process_medium' - // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/hisat2:2.2.1--h1b792b2_3' : @@ -20,23 +19,21 @@ process HISAT2_EXTRACTSPLICESITES { script: def args = task.ext.args ?: '' - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ hisat2_extract_splice_sites.py $gtf > ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ stub: - def VERSION = '2.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${gtf.baseName}.splice_sites.txt cat <<-END_VERSIONS > versions.yml "${task.process}": - hisat2: $VERSION + hisat2: \$(hisat2 --version | grep -o 'version [^ ]*' | cut -d ' ' -f 2) END_VERSIONS """ } From 625fbbc0531fb1717349c7f1b1c677a3b8619767 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Fri, 13 Sep 2024 11:14:20 +0100 Subject: [PATCH 051/486] Fix tximport summarizedexperiment (#6638) * SummarizedExperiment: don't sanitise column names * tximport: explicitly disable name sanitisation --- .../summarizedexperiment/templates/summarizedexperiment.r | 2 +- modules/nf-core/tximeta/tximport/templates/tximport.r | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r index 6c705350ace2..60ea3179fc23 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/templates/summarizedexperiment.r @@ -13,7 +13,7 @@ library(SummarizedExperiment) #' #' @return output Data frame -read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = TRUE, stringsAsFactors = FALSE){ +read_delim_flexible <- function(file, header = TRUE, row.names = NULL, check.names = FALSE, stringsAsFactors = FALSE){ ext <- tolower(tail(strsplit(basename(file), split = "\\\\.")[[1]], 1)) diff --git a/modules/nf-core/tximeta/tximport/templates/tximport.r b/modules/nf-core/tximeta/tximport/templates/tximport.r index e8235c8b0524..5986c05d946d 100755 --- a/modules/nf-core/tximeta/tximport/templates/tximport.r +++ b/modules/nf-core/tximeta/tximport/templates/tximport.r @@ -26,7 +26,7 @@ library(tximport) #' @return A data frame combining the first two columns of the rowData with the assay data from the specified slot. build_table <- function(se.obj, slot) { - cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]) + data.frame(cbind(rowData(se.obj)[,1:2], assays(se.obj)[[slot]]), check.names = FALSE) } #' Write a table to a file from a SummarizedExperiment object with given parameters From 9941df948085f019c71693eb0eabecd0e8f9d249 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Fri, 13 Sep 2024 12:39:40 +0200 Subject: [PATCH 052/486] MEGAHIT: Add support for multi-libraries, export log (#6632) * Add support for coassembly, export log * Fix formatting * teensy bit more --- modules/nf-core/megahit/main.nf | 19 ++++--- modules/nf-core/megahit/meta.yml | 20 ++++++- modules/nf-core/megahit/tests/main.nf.test | 56 ++++++++++++++++--- .../nf-core/megahit/tests/main.nf.test.snap | 51 ++++++++++++++--- 4 files changed, 118 insertions(+), 28 deletions(-) diff --git a/modules/nf-core/megahit/main.nf b/modules/nf-core/megahit/main.nf index 6559e0241f78..df1f72a77878 100644 --- a/modules/nf-core/megahit/main.nf +++ b/modules/nf-core/megahit/main.nf @@ -1,14 +1,13 @@ process MEGAHIT { - tag "$meta.id" + tag "${meta.id}" label 'process_high' - conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'oras://community.wave.seqera.io/library/megahit_pigz:657d77006ae5f222' : 'community.wave.seqera.io/library/megahit_pigz:87a590163e594224' }" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads1), path(reads2) output: tuple val(meta), path("*.contigs.fa.gz") , emit: contigs @@ -16,6 +15,7 @@ process MEGAHIT { tuple val(meta), path("intermediate_contigs/k*.addi.fa.gz") , emit: addi_contigs tuple val(meta), path("intermediate_contigs/k*.local.fa.gz") , emit: local_contigs tuple val(meta), path("intermediate_contigs/k*.final.contigs.fa.gz"), emit: kfinal_contigs + tuple val(meta), path('*.log') , emit: log path "versions.yml" , emit: versions when: @@ -25,18 +25,18 @@ process MEGAHIT { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reads_command = meta.single_end ? "-r ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}" + def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}" """ megahit \\ ${reads_command} \\ - $args \\ - -t $task.cpus \\ + ${args} \\ + -t ${task.cpus} \\ --out-prefix ${prefix} pigz \\ --no-name \\ - -p $task.cpus \\ - $args2 \\ + -p ${task.cpus} \\ + ${args2} \\ megahit_out/*.fa \\ megahit_out/intermediate_contigs/*.fa @@ -52,7 +52,7 @@ process MEGAHIT { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def reads_command = meta.single_end ? "-r ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}" + def reads_command = meta.single_end || !reads2 ? "-r ${reads1}" : "-1 ${reads1.join(',')} -2 ${reads2.join(',')}" """ mkdir -p intermediate_contigs echo "" | gzip > ${prefix}.contigs.fa.gz @@ -60,6 +60,7 @@ process MEGAHIT { echo "" | gzip > intermediate_contigs/k21.addi.fa.gz echo "" | gzip > intermediate_contigs/k21.local.fa.gz echo "" | gzip > intermediate_contigs/k21.final.contigs.fa.gz + touch ${prefix}.log cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/megahit/meta.yml b/modules/nf-core/megahit/meta.yml index 83b718f07662..656f4f8ac172 100644 --- a/modules/nf-core/megahit/meta.yml +++ b/modules/nf-core/megahit/meta.yml @@ -14,16 +14,28 @@ tools: tool_dev_url: https://github.com/voutcn/megahit doi: "10.1093/bioinformatics/btv033" licence: ["GPL v3"] + args_id: "$args" + - pigz: + description: "Parallel implementation of the gzip algorithm." + homepage: "https://zlib.net/pigz/" + documentation: "https://zlib.net/pigz/pigz.pdf" + args_id: "$args2" + input: - meta: type: map description: | Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) e.g. [ id:'test', single_end:false ] - - reads: + - reads1: type: file description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, + A single or list of input FastQ files for single-end or R1 of paired-end library(s), + respectively in gzipped or uncompressed FASTQ or FASTA format. + - reads2: + type: file + description: | + A single or list of input FastQ files for R2 of paired-end library(s), respectively in gzipped or uncompressed FASTQ or FASTA format. output: - meta: @@ -55,6 +67,10 @@ output: type: file description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty pattern: "k*.final.contigs.fa.gz" + - log: + type: file + description: Log file containing statistics of the assembly output + pattern: "*.log" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/megahit/tests/main.nf.test b/modules/nf-core/megahit/tests/main.nf.test index 15b1dd789f20..b52765d433ec 100644 --- a/modules/nf-core/megahit/tests/main.nf.test +++ b/modules/nf-core/megahit/tests/main.nf.test @@ -14,8 +14,8 @@ nextflow_process { process { """ input[0] = [ [id:"test", single_end:true], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ] + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + []] """ } } @@ -28,7 +28,11 @@ nextflow_process { { assert process.out.addi_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, { assert process.out.local_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, { assert process.out.kfinal_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, - { assert snapshot(process.out.versions).match() } + { assert snapshot( + path(process.out.log[0][1]).readLines().last().contains("ALL DONE. Time elapsed"), + process.out.versions + ).match() + } ) } @@ -39,9 +43,40 @@ nextflow_process { when { process { """ - input[0] = [ [id:"test", single_end:true], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + input[0] = [ [id:"test", single_end:false], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.contigs[0][1]).linesGzip.toString().contains(">k") }, + { assert process.out.k_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, + { assert process.out.addi_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, + { assert process.out.local_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, + { assert process.out.kfinal_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, + { assert snapshot( + path(process.out.log[0][1]).readLines().last().contains("ALL DONE. Time elapsed"), + process.out.versions + ).match() + } + ) + } + + } + + test("sarscov2 - fastq - pe - coassembly") { + + when { + process { + """ + input[0] = [ [id:"test", single_end:false], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true)] , + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] ] """ } @@ -55,7 +90,11 @@ nextflow_process { { assert process.out.addi_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, { assert process.out.local_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, { assert process.out.kfinal_contigs[0][1].each{path(it).linesGzip.toString().contains(">k")}}, - { assert snapshot(process.out.versions).match() } + { assert snapshot( + path(process.out.log[0][1]).readLines().last().contains("ALL DONE. Time elapsed"), + process.out.versions + ).match() + } ) } @@ -69,7 +108,8 @@ nextflow_process { process { """ input[0] = [ [id:"test", single_end:true], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] ] """ } diff --git a/modules/nf-core/megahit/tests/main.nf.test.snap b/modules/nf-core/megahit/tests/main.nf.test.snap index 3842f85c75e0..4677cc337c30 100644 --- a/modules/nf-core/megahit/tests/main.nf.test.snap +++ b/modules/nf-core/megahit/tests/main.nf.test.snap @@ -1,27 +1,29 @@ { "sarscov2 - fastq - se": { "content": [ + true, [ "versions.yml:md5,e3c0731297c9abe2f495ab6d541ac0e6" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-25T10:20:02.764235061" + "timestamp": "2024-09-12T16:45:42.387947698" }, "sarscov2 - fastq - pe": { "content": [ + true, [ "versions.yml:md5,e3c0731297c9abe2f495ab6d541ac0e6" ] ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-25T10:20:47.028761896" + "timestamp": "2024-09-12T16:45:48.679485983" }, "sarscov2 - stub": { "content": [ @@ -75,6 +77,15 @@ ] ], "5": [ + [ + { + "id": "test", + "single_end": true + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ "versions.yml:md5,e3c0731297c9abe2f495ab6d541ac0e6" ], "addi_contigs": [ @@ -125,15 +136,37 @@ "k21.local.fa.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], + "log": [ + [ + { + "id": "test", + "single_end": true + }, + "test.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], "versions": [ "versions.yml:md5,e3c0731297c9abe2f495ab6d541ac0e6" ] } ], "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-12T16:44:35.245399991" + }, + "sarscov2 - fastq - pe - coassembly": { + "content": [ + true, + [ + "versions.yml:md5,e3c0731297c9abe2f495ab6d541ac0e6" + ] + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-25T10:03:05.77753221" + "timestamp": "2024-09-12T16:45:56.23363342" } } \ No newline at end of file From b6b54f3929b0ba4a7c02a49191308ce1d8351f0d Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Fri, 13 Sep 2024 16:51:05 +0200 Subject: [PATCH 053/486] New module jvarkit/wgscoverageplotter (#6633) * wgscoverageplotter * Apply suggestions from code review Co-authored-by: Maxime U Garcia * fix meta * change snap * fix tags * fix env.yml * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Maxime U Garcia Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../wgscoverageplotter/environment.yml | 7 ++ .../jvarkit/wgscoverageplotter/main.nf | 51 ++++++++++++ .../jvarkit/wgscoverageplotter/meta.yml | 79 +++++++++++++++++++ .../wgscoverageplotter/tests/main.nf.test | 71 +++++++++++++++++ .../tests/main.nf.test.snap | 28 +++++++ .../wgscoverageplotter/tests/nextflow.config | 7 ++ .../jvarkit/wgscoverageplotter/tests/tags.yml | 2 + 7 files changed, 245 insertions(+) create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/environment.yml create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/main.nf create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/meta.yml create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test.snap create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/tests/nextflow.config create mode 100644 modules/nf-core/jvarkit/wgscoverageplotter/tests/tags.yml diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml b/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml new file mode 100644 index 000000000000..14d0e3387c56 --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::jvarkit=2024.08.25" diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/main.nf b/modules/nf-core/jvarkit/wgscoverageplotter/main.nf new file mode 100644 index 000000000000..43d816885042 --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/main.nf @@ -0,0 +1,51 @@ +process JVARKIT_WGSCOVERAGEPLOTTER { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(bam), path(bai) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + output: + tuple val(meta), path("*.svg"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p TMP + + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP wgscoverageplotter \\ + -R ${fasta} \\ + ${args} \\ + ${bam} > "${prefix}.svg" + + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.svg" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml new file mode 100644 index 000000000000..f087b0d89b33 --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml @@ -0,0 +1,79 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "jvarkit_wgscoverageplotter" +description: Plot whole genome coverage from BAM/CRAM file as SVG +keywords: + - bam + - cram + - depth + - coverage + - xml + - svg + - visualization +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.6084/m9.figshare.1425030" + licence: ["MIT License"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing reference fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing reference dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" +output: + - meta: + type: map + description: | + Groovy Map containing Sample information + e.g. [ id:'test', single_end:false ] + - output: + type: file + description: Output SVG file + pattern: "*.svg" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test new file mode 100644 index 000000000000..f4f0d7cfcc6b --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test @@ -0,0 +1,71 @@ +// nf-core modules test jvarkit/wgscoverageplotter +nextflow_process { + + name "Test Process JVARKIT_WGSCOVERAGEPLOTTER" + script "../main.nf" + process "JVARKIT_WGSCOVERAGEPLOTTER" + config "./nextflow.config" + + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/wgscoverageplotter" + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [:] , file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.output[0][1]).exists() }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"test"], + [], + [] + ] + input[1] = [ [] , [] ] + input[2] = [ [] , [] ] + input[3] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.output[0][1]).exists() }, + { assert snapshot(process.out.versions).match() } + ) + } + } +} diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test.snap b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test.snap new file mode 100644 index 000000000000..aa6149101eeb --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "sarscov2 - bam": { + "content": [ + [ + "versions.yml:md5,b0860cf56f5babf5590a1fed61e8792f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + + "sarscov2 - bam - stub": { + "content": [ + [ + "versions.yml:md5,b0860cf56f5babf5590a1fed61e8792f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + } + +} diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/tests/nextflow.config b/modules/nf-core/jvarkit/wgscoverageplotter/tests/nextflow.config new file mode 100644 index 000000000000..4e7cacb5563d --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: JVARKIT_WGSCOVERAGEPLOTTER { + ext.args1 =" --max-depth 5 " + } + +} diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/tests/tags.yml b/modules/nf-core/jvarkit/wgscoverageplotter/tests/tags.yml new file mode 100644 index 000000000000..67385596e7be --- /dev/null +++ b/modules/nf-core/jvarkit/wgscoverageplotter/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/wgscoverageplotter: + - "modules/nf-core/jvarkit/wgscoverageplotter/**" From af91cff1085bd23a2e5046273e989857dc3e2eb7 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Fri, 13 Sep 2024 21:37:05 +0200 Subject: [PATCH 054/486] Add openmsthirdparty/cometadapter (#6627) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag --- .../cometadapter/environment.yml | 5 ++ .../openmsthirdparty/cometadapter/main.nf | 55 ++++++++++++ .../openmsthirdparty/cometadapter/meta.yml | 55 ++++++++++++ .../cometadapter/tests/main.nf.test | 86 +++++++++++++++++++ .../cometadapter/tests/main.nf.test.snap | 59 +++++++++++++ .../cometadapter/tests/nextflow.config | 20 +++++ .../cometadapter/tests/tags.yml | 2 + tests/config/test_data.config | 1 + 8 files changed, 283 insertions(+) create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/environment.yml create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/main.nf create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/meta.yml create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/tests/nextflow.config create mode 100644 modules/nf-core/openmsthirdparty/cometadapter/tests/tags.yml diff --git a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml new file mode 100644 index 000000000000..3c2729e75f1b --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::openms-thirdparty=3.1.0" diff --git a/modules/nf-core/openmsthirdparty/cometadapter/main.nf b/modules/nf-core/openmsthirdparty/cometadapter/main.nf new file mode 100644 index 000000000000..b193974ae866 --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/main.nf @@ -0,0 +1,55 @@ +process OPENMSTHIRDPARTY_COMETADAPTER { + tag "$meta.id" + label 'process_high' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_4' : + 'biocontainers/openms-thirdparty:3.1.0--h9ee0642_4' }" + + input: + tuple val(meta), path(mzml), path(fasta) + + output: + tuple val(meta), path("*.idXML"), emit: idxml + tuple val(meta), path("*.tsv") , emit: pin, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + CometAdapter \\ + -in $mzml \\ + -database $fasta \\ + -out ${prefix}.idXML \\ + -threads $task.cpus \\ + $args + + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + CometAdapter: \$(CometAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1 | cut -d '-' -f 1) + Comet: \$(comet 2>&1 | grep -E "Comet version.*" | sed 's/Comet version //g' | sed 's/"//g') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}.idXML + touch ${prefix}_pin.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + CometAdapter: \$(CometAdapter 2>&1 | grep -E '^Version(.*)' | sed 's/Version: //g' | cut -d ' ' -f 1 | cut -d '-' -f 1) + Comet: \$(comet 2>&1 | grep -E "Comet version.*" | sed 's/Comet version //g' | sed 's/"//g') + END_VERSIONS + """ +} diff --git a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml new file mode 100644 index 000000000000..e37f6af8264c --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml @@ -0,0 +1,55 @@ +name: "openmsthirdparty_cometadapter" +description: Annotates MS/MS spectra using Comet. +keywords: + - search engine + - fasta + - mzml + - openms + - proteomics +tools: + - openms: + description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + homepage: "https://openms.de" + documentation: "https://openms.readthedocs.io/en/latest/index.html" + tool_dev_url: "https://github.com/OpenMS/OpenMS" + doi: "10.1038/nmeth.3959" + licence: ["BSD"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mzml: + type: file + description: File containing mass spectra in mzML format + pattern: "*.{mzML}" + - fasta: + type: file + description: Protein sequence database containing targets and decoys + pattern: "*.{fasta}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - idxml: + type: file + description: File containing target and decoy hits in idXML format + pattern: "*.{idXML}" + - pin: + type: file + description: TSV file tailored as Percolator input (pin) file + pattern: "*.{tsv}" + +authors: + - "@jonasscheid" +maintainers: + - "@jonasscheid" diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test new file mode 100644 index 000000000000..cf1a0bcddcd9 --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test @@ -0,0 +1,86 @@ +nextflow_process { + + name "Test Process OPENMSTHIRDPARTY_COMETADAPTER" + script "../main.nf" + process "OPENMSTHIRDPARTY_COMETADAPTER" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "openms" + tag "openmsthirdparty" + tag "openmsthirdparty/cometadapter" + tag "thermorawfileparser" + tag "openms/decoydatabase" + + setup { + run("THERMORAWFILEPARSER") { + script "../../../thermorawfileparser/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], + file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true) + ]) + """ + } + } + + run("OPENMS_DECOYDATABASE") { + script "../../../openms/decoydatabase/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], + file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true) + ]) + """ + } + } + } + + test("proteomics - comet") { + + when { + process { + """ + input[0] = + THERMORAWFILEPARSER.out.spectra.join( + OPENMS_DECOYDATABASE.out.decoy_fasta + ) + """ + } + } + // Comet stores timestamp in output file, so we cannot compare checksums + then { + assert process.success + // Assert the search metadata + assert snapshot(file(process.out.idxml[0][1]).readLines()[0..30]).match() + // Make sure the file is not empty + assert file(process.out.idxml[0][1]).readLines().any { it.contains('ProteinHit') } + assert file(process.out.idxml[0][1]).readLines().any { it.contains('PeptideHit') } + assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") + } + } + + test("proteomics - comet - stub") { + + options "-stub" + + when { + process { + """ + input[0] = + THERMORAWFILEPARSER.out.spectra.join( + OPENMS_DECOYDATABASE.out.decoy_fasta + ) + """ + } + } + + then { + assert process.success + } + } + +} diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap new file mode 100644 index 000000000000..9eb65951ab52 --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap @@ -0,0 +1,59 @@ +{ + "proteomics - comet": { + "content": [ + [ + "", + "", + "", + "\t", + "\t\t", + "\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t", + "\t\t\t\t" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-13T13:57:34.932657501" + }, + "versions": { + "content": [ + { + "OPENMSTHIRDPARTY_COMETADAPTER": { + "CometAdapter": "3.1.0", + "Comet": "2023.01 rev. 2" + } + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-13T13:57:35.577894316" + } +} \ No newline at end of file diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/nextflow.config b/modules/nf-core/openmsthirdparty/cometadapter/tests/nextflow.config new file mode 100644 index 000000000000..04e89d929422 --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/nextflow.config @@ -0,0 +1,20 @@ +process { + + withName:OPENMSTHIRDPARTY_COMETADAPTER { + ext.args = [ + "-instrument low_res", + "-fragment_bin_offset 0.4", + "-precursor_mass_tolerance 5", + "-precursor_error_units 'ppm'", + "-fragment_mass_tolerance 0.50025", + "-digest_mass_range '800:5000'", + "-max_variable_mods_in_peptide 1", + "-precursor_charge '2:5'", + "-activation_method 'CID'", + "-variable_modifications 'Oxidation (M)'", + "-enzyme 'unspecific cleavage'", + "-spectrum_batch_size 0" + ].join(' ').trim() + } + +} diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/tags.yml b/modules/nf-core/openmsthirdparty/cometadapter/tests/tags.yml new file mode 100644 index 000000000000..44dd62ab99a8 --- /dev/null +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/tags.yml @@ -0,0 +1,2 @@ +openmsthirdparty/cometadapter: + - "modules/nf-core/openmsthirdparty/cometadapter/**" diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 3614b827fe2b..852544d51f4b 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -769,6 +769,7 @@ params { } 'database' { yeast_ups = "${params.test_data_base}/data/proteomics/database/yeast_UPS.fasta" + swissprot = "${params.test_data_base}/data/proteomics/database/UP000005640_9606.fasta" } 'maxquant' { mq_contrasts = "${params.test_data_base}/data/proteomics/maxquant/MaxQuant_contrasts.csv" From 368e6c90b91adbd171e7c0a1c85a700b86a915af Mon Sep 17 00:00:00 2001 From: Venkat Malladi Date: Sun, 15 Sep 2024 01:33:35 -0500 Subject: [PATCH 055/486] Update output to use type dir for compatibility with tes. (#6645) Update output to use type dir for commpatibility with tes. --- modules/nf-core/sratools/prefetch/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/sratools/prefetch/main.nf b/modules/nf-core/sratools/prefetch/main.nf index 46e7cb3faa1f..74838d53a5ea 100644 --- a/modules/nf-core/sratools/prefetch/main.nf +++ b/modules/nf-core/sratools/prefetch/main.nf @@ -13,7 +13,7 @@ process SRATOOLS_PREFETCH { path certificate output: - tuple val(meta), path(id), emit: sra + tuple val(meta), path(id, type: 'dir'), emit: sra path 'versions.yml' , emit: versions when: From a25abe62ccf3fe3767d2449d8322a35ab62844e0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sun, 15 Sep 2024 11:45:19 +0100 Subject: [PATCH 056/486] Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.5 (#6642) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index efc08e8cf7a5..595734b39a2f 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.4 + rev: v0.6.5 hooks: - id: ruff files: \.py$ From ee3b8b84da02320fff5f3f2dc1d6f9b72d7cd5af Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Mon, 16 Sep 2024 10:21:54 +0100 Subject: [PATCH 057/486] minor changes to fastq preprocessing (#6643) * minor changes to fastq preprocessing * Update main.nf --- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 4c7b25f8e23b..4ed073efcfb7 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -181,7 +181,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_versions = ch_versions.mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.versions) ch_multiqc_files = FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_raw_zip .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.fastqc_trim_zip) - .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json.map{tuple(it[0], [it[1]])}) + .mix(FASTQ_FASTQC_UMITOOLS_FASTP.out.trim_json) .mix(ch_multiqc_files) } @@ -209,6 +209,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { ch_multiqc_files = ch_multiqc_files .mix( ch_fail_trimming_multiqc.collectFile(name: 'fail_trimmed_samples_mqc.tsv') + .map { [[:], it] } ) // From 265f40c88ed592d7c7ef8eac1184a82932750987 Mon Sep 17 00:00:00 2001 From: Eric Wei Date: Mon, 16 Sep 2024 02:29:33 -0700 Subject: [PATCH 058/486] Update bcftools/pluginimputeinfo meta.yml (#6646) Update meta.yml --- modules/nf-core/bcftools/pluginimputeinfo/meta.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml index ca2b6c3c7419..d944dae78170 100644 --- a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml +++ b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml @@ -7,20 +7,20 @@ keywords: - imputation - metrics - tags - - VCF + - vcf tools: - "bcftools": description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." - homepage: "http://samtools.github.io/bcftools/bcftools.html" - documentation: "https://samtools.github.io/bcftools/bcftools.html#plugin" + homepage: "https://samtools.github.io/bcftools/howtos/index.html" + documentation: "https://samtools.github.io/bcftools/bcftools.html" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] args_id: "$args" - "bcftools plugin impute-info": - description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." - homepage: "http://samtools.github.io/bcftools/bcftools.html" - documentation: "https://samtools.github.io/bcftools/howtos/plugins.html" + description: "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available" + homepage: "https://samtools.github.io/bcftools/howtos/plugins.html" + documentation: "https://samtools.github.io/bcftools/bcftools.html#plugin" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] From 3fb6803fd1cf5a63998216f4254d6d4e487fab21 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 16 Sep 2024 12:54:19 +0200 Subject: [PATCH 059/486] Fix GTDBTK version calling in stub test (#6649) Use the proper version calling now implemented --- modules/nf-core/gtdbtk/classifywf/main.nf | 4 +--- modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap | 8 ++++---- 2 files changed, 5 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index 9aa13ee477fc..f0944fdc33a5 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -74,8 +74,6 @@ process GTDBTK_CLASSIFYWF { """ stub: - def VERSION = '2.3.2' - // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. prefix = task.ext.prefix ?: "${meta.id}" """ touch gtdbtk.${prefix}.stub.summary.tsv @@ -90,7 +88,7 @@ process GTDBTK_CLASSIFYWF { cat <<-END_VERSIONS > versions.yml "${task.process}": - gtdbtk: \$(echo "${VERSION}") + gtdbtk: \$(echo \$(gtdbtk --version -v 2>&1) | sed "s/gtdbtk: version //; s/ Copyright.*//") END_VERSIONS """ } diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap index e821084cfaa5..eb0ee89a7926 100644 --- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap +++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test.snap @@ -93,7 +93,7 @@ ] ], "9": [ - "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2" + "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7" ], "failed": [ [ @@ -176,7 +176,7 @@ ] ], "versions": [ - "versions.yml:md5,a8ab755bce9f17684f235d49ab99f6d2" + "versions.yml:md5,2c94de2b8633b99e11881ab0193835d7" ], "warnings": [ [ @@ -192,8 +192,8 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.4" }, - "timestamp": "2024-03-26T09:39:21.632259941" + "timestamp": "2024-09-16T11:46:32.337929018" } } \ No newline at end of file From e2b2fde139007c9de9782252178013dc3c36056a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20B=C3=A4uerle?= <45968370+famosab@users.noreply.github.com> Date: Mon, 16 Sep 2024 16:15:34 +0200 Subject: [PATCH 060/486] flye: fix nf-test, update module (#6613) * fix nf-test, update module * Update nextflow.config * Update nextflow.config * update test * small hifi dataset * remove raw tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/flye/environment.yml | 2 +- modules/nf-core/flye/main.nf | 4 +- modules/nf-core/flye/tests/main.nf.test | 206 ++++++------------- modules/nf-core/flye/tests/main.nf.test.snap | 202 +++++++++++++++--- modules/nf-core/flye/tests/nextflow.config | 4 - 5 files changed, 239 insertions(+), 179 deletions(-) delete mode 100644 modules/nf-core/flye/tests/nextflow.config diff --git a/modules/nf-core/flye/environment.yml b/modules/nf-core/flye/environment.yml index c08deb459a5e..87b97eb89b84 100644 --- a/modules/nf-core/flye/environment.yml +++ b/modules/nf-core/flye/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::flye=2.9 + - bioconda::flye=2.9.5 diff --git a/modules/nf-core/flye/main.nf b/modules/nf-core/flye/main.nf index 3d892180e438..8803655d4a9f 100644 --- a/modules/nf-core/flye/main.nf +++ b/modules/nf-core/flye/main.nf @@ -4,8 +4,8 @@ process FLYE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/flye:2.9--py39h6935b12_1' : - 'biocontainers/flye:2.9--py39h6935b12_1' }" + 'oras://community.wave.seqera.io/library/flye:2.9.5--eb07d7b7094f222c' : + 'community.wave.seqera.io/library/flye:2.9.5--0221998e9c3ec606' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/flye/tests/main.nf.test b/modules/nf-core/flye/tests/main.nf.test index f06aa1bc5268..afbf926ef49a 100644 --- a/modules/nf-core/flye/tests/main.nf.test +++ b/modules/nf-core/flye/tests/main.nf.test @@ -1,61 +1,17 @@ // According to the issue https://github.com/fenderglass/Flye/issues/164 // Some fluctuations are expected because of the heuristics -// Here we check the that test.assembly_info.txt contains at least one contig +// Here we check the that test.assembly_info.txt contains at least contig_1 nextflow_process { name "Test Process FLYE" script "../main.nf" process "FLYE" - config "./nextflow.config" tag "flye" tag "modules" tag "modules_nfcore" - - test("flye_pacbio_raw") { - tag "flye_pacbio_raw" - - when { - params { - outdir = "$outputDir" - } - process { - """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) - ] - input[1] = "--pacbio-raw" - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - { assert process.out.json.get(0).get(1) ==~ '.*/test.params.json' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - - - ) - } - - } - - test("flye_pacbio_corr") { - tag "flye_pacbio_corr" when { params { @@ -63,9 +19,8 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] input[1] = "--pacbio-corr" """ @@ -75,27 +30,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - - - + { assert snapshot( + file(process.out.fasta.get(0).get(1)).name, + file(process.out.gfa.get(0).get(1)).name, + file(process.out.gv.get(0).get(1)).name, + file(process.out.log.get(0).get(1)).name, + file(process.out.txt.get(0).get(1)).name, + path(process.out.txt.get(0).get(1)).readLines()[1].contains("contig_1"), + process.out.json, + process.out.versions + ).match() } ) } } test("flye_pacbio_hifi") { - tag "flye_pacbio_hifi" when { params { @@ -103,9 +53,8 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] input[1] = "--pacbio-hifi" """ @@ -115,27 +64,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - - - + { assert snapshot( + file(process.out.fasta.get(0).get(1)).name, + file(process.out.gfa.get(0).get(1)).name, + file(process.out.gv.get(0).get(1)).name, + file(process.out.log.get(0).get(1)).name, + file(process.out.txt.get(0).get(1)).name, + path(process.out.txt.get(0).get(1)).readLines()[1].contains("contig_1"), + process.out.json, + process.out.versions + ).match() } ) } } - test("flye_nano_raw") { - tag "flye_nano_raw" + test("flye_nano_corr") { when { params { @@ -143,11 +87,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] - input[1] = "--nano-raw" + input[1] = "--nano-corr" """ } } @@ -155,27 +98,22 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - { assert process.out.json.get(0).get(1) ==~ '.*/test.params.json' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - - + { assert snapshot( + file(process.out.fasta.get(0).get(1)).name, + file(process.out.gfa.get(0).get(1)).name, + file(process.out.gv.get(0).get(1)).name, + file(process.out.log.get(0).get(1)).name, + file(process.out.txt.get(0).get(1)).name, + path(process.out.txt.get(0).get(1)).readLines()[1].contains("contig_1"), + process.out.json, + process.out.versions + ).match() } ) } } - test("flye_nano_corr") { - tag "flye_nano_corr" + test("flye_nano_hq") { when { params { @@ -183,11 +121,10 @@ nextflow_process { } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] - input[1] = "--nano-corr" + input[1] = "--nano-hq" """ } } @@ -195,39 +132,32 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - { assert process.out.json.get(0).get(1) ==~ '.*/test.params.json' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - + { assert snapshot( + file(process.out.fasta.get(0).get(1)).name, + file(process.out.gfa.get(0).get(1)).name, + file(process.out.gv.get(0).get(1)).name, + file(process.out.log.get(0).get(1)).name, + file(process.out.txt.get(0).get(1)).name, + path(process.out.txt.get(0).get(1)).readLines()[1].contains("contig_1"), + process.out.json, + process.out.versions + ).match() } ) } } + test("flye_pacbio_raw - stub") { - test("flye_nano_hq") { - tag "flye_nano_hq" + options "-stub" when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) + input[0] = [ [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true) ] - input[1] = "--nano-hq" + input[1] = "--pacbio-raw" """ } } @@ -235,24 +165,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert process.out.fasta.get(0).get(1) ==~ '.*/test.assembly.fasta.gz' }, - { assert process.out.gfa.get(0).get(1) ==~ '.*/test.assembly_graph.gfa.gz' }, - { assert process.out.gv.get(0).get(1) ==~ '.*/test.assembly_graph.gv.gz' }, - { assert process.out.log.get(0).get(1) ==~ '.*/test.flye.log' }, - { assert process.out.txt.get(0).get(1) ==~ '.*/test.assembly_info.txt' }, - { assert process.out.json.get(0).get(1) ==~ '.*/test.params.json' }, - - // check for contig_1 in assembly_info - { assert path(process.out.txt.get(0).get(1)).text =~ /contig_1/ }, - // Check if test.params.json matches - { assert snapshot(process.out.json).match() } - - + { assert snapshot( + process.out, + path(process.out.versions.get(0)).yaml + ).match() + } ) } } - - } diff --git a/modules/nf-core/flye/tests/main.nf.test.snap b/modules/nf-core/flye/tests/main.nf.test.snap index a4aef731487b..7101f9edf672 100644 --- a/modules/nf-core/flye/tests/main.nf.test.snap +++ b/modules/nf-core/flye/tests/main.nf.test.snap @@ -1,19 +1,12 @@ { - "flye_pacbio_raw": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" - ] - ] - ], - "timestamp": "2023-10-18T09:38:04.835173617" - }, "flye_pacbio_hifi": { "content": [ + "test.assembly.fasta.gz", + "test.assembly_graph.gfa.gz", + "test.assembly_graph.gv.gz", + "test.flye.log", + "test.assembly_info.txt", + false, [ [ { @@ -21,25 +14,25 @@ }, "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" ] - ] - ], - "timestamp": "2023-10-18T08:38:39.624137639" - }, - "flye_nano_raw": { - "content": [ + ], [ - [ - { - "id": "test" - }, - "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" - ] + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" ] ], - "timestamp": "2023-10-18T09:51:24.546896915" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T13:41:09.075217" }, "flye_pacbio_corr": { "content": [ + "test.assembly.fasta.gz", + "test.assembly_graph.gfa.gz", + "test.assembly_graph.gv.gz", + "test.flye.log", + "test.assembly_info.txt", + true, [ [ { @@ -47,12 +40,25 @@ }, "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" ] + ], + [ + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" ] ], - "timestamp": "2023-10-18T08:34:15.751344742" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T13:33:16.267658" }, "flye_nano_corr": { "content": [ + "test.assembly.fasta.gz", + "test.assembly_graph.gfa.gz", + "test.assembly_graph.gv.gz", + "test.flye.log", + "test.assembly_info.txt", + true, [ [ { @@ -60,12 +66,25 @@ }, "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" ] + ], + [ + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" ] ], - "timestamp": "2023-10-18T09:17:49.861781685" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T13:44:28.522592" }, "flye_nano_hq": { "content": [ + "test.assembly.fasta.gz", + "test.assembly_graph.gfa.gz", + "test.assembly_graph.gv.gz", + "test.flye.log", + "test.assembly_info.txt", + true, [ [ { @@ -73,8 +92,133 @@ }, "test.params.json:md5,54b576cb6d4d27656878a7fd3657bde9" ] + ], + [ + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" ] ], - "timestamp": "2023-10-18T09:26:29.081427909" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T13:46:35.912198" + }, + "flye_pacbio_raw - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.assembly.fasta.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.assembly_graph.gfa.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "2": [ + [ + { + "id": "test" + }, + "test.assembly_graph.gv.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.assembly_info.txt:md5,e3aec731279050302fc8d6f126b3030e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.flye.log:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.params.json:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "6": [ + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" + ], + "fasta": [ + [ + { + "id": "test" + }, + "test.assembly.fasta.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "gfa": [ + [ + { + "id": "test" + }, + "test.assembly_graph.gfa.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "gv": [ + [ + { + "id": "test" + }, + "test.assembly_graph.gv.gz:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "json": [ + [ + { + "id": "test" + }, + "test.params.json:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "log": [ + [ + { + "id": "test" + }, + "test.flye.log:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "txt": [ + [ + { + "id": "test" + }, + "test.assembly_info.txt:md5,e3aec731279050302fc8d6f126b3030e" + ] + ], + "versions": [ + "versions.yml:md5,80496e451401dbc0269ec404801a90e3" + ] + }, + { + "FLYE": { + "flye": "2.9.5-b1801" + } + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-12T09:07:05.234775" } } \ No newline at end of file diff --git a/modules/nf-core/flye/tests/nextflow.config b/modules/nf-core/flye/tests/nextflow.config deleted file mode 100644 index 40cf878ccca3..000000000000 --- a/modules/nf-core/flye/tests/nextflow.config +++ /dev/null @@ -1,4 +0,0 @@ -// profile=docker with tests flye_pacbio_raw and flye_nano_raw need more memory that the default of 3.GB -process { - memory = 6.GB -} From f768b283dbd8fc79d0d92b0f68665d7bed94cabc Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Mon, 16 Sep 2024 21:41:03 +0200 Subject: [PATCH 061/486] Add module openms/idmassaccuracy (#6647) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * add idmassaccuracy module * shorten version parsing --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../openms/idmassaccuracy/environment.yml | 5 ++ modules/nf-core/openms/idmassaccuracy/main.nf | 52 +++++++++++ .../nf-core/openms/idmassaccuracy/meta.yml | 55 ++++++++++++ .../openms/idmassaccuracy/tests/main.nf.test | 81 +++++++++++++++++ .../idmassaccuracy/tests/main.nf.test.snap | 90 +++++++++++++++++++ .../idmassaccuracy/tests/nextflow.config | 27 ++++++ 6 files changed, 310 insertions(+) create mode 100644 modules/nf-core/openms/idmassaccuracy/environment.yml create mode 100644 modules/nf-core/openms/idmassaccuracy/main.nf create mode 100644 modules/nf-core/openms/idmassaccuracy/meta.yml create mode 100644 modules/nf-core/openms/idmassaccuracy/tests/main.nf.test create mode 100644 modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap create mode 100644 modules/nf-core/openms/idmassaccuracy/tests/nextflow.config diff --git a/modules/nf-core/openms/idmassaccuracy/environment.yml b/modules/nf-core/openms/idmassaccuracy/environment.yml new file mode 100644 index 000000000000..5793e993cc53 --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::openms=3.1.0" diff --git a/modules/nf-core/openms/idmassaccuracy/main.nf b/modules/nf-core/openms/idmassaccuracy/main.nf new file mode 100644 index 000000000000..9759ad40919a --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/main.nf @@ -0,0 +1,52 @@ +process OPENMS_IDMASSACCURACY { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h191ead1_4' : + 'biocontainers/openms:3.1.0--h191ead1_4' }" + + input: + tuple val(meta), path(mzmls), path(idxmls) + + output: + tuple val(meta), path("*frag_mass_err.tsv") , emit: frag_err + tuple val(meta), path("*prec_mass_err.tsv") , emit: prec_err, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + IDMassAccuracy \\ + -in $mzmls \\ + -id_in $idxmls \\ + -out_fragment ${prefix}_frag_mass_err.tsv \\ + -threads $task.cpus \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1) + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + """ + touch ${prefix}_frag_mass_err.tsv + touch ${prefix}_prec_mass_err.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1) + END_VERSIONS + """ +} diff --git a/modules/nf-core/openms/idmassaccuracy/meta.yml b/modules/nf-core/openms/idmassaccuracy/meta.yml new file mode 100644 index 000000000000..e14a2eb09bb3 --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/meta.yml @@ -0,0 +1,55 @@ +name: "openms_idmassaccuracy" +description: Calculates a distribution of the mass error from given mass spectra and IDs. +keywords: + - mass_error + - openms + - proteomics +tools: + - "openms": + description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + homepage: "https://openms.de" + documentation: "https://openms.readthedocs.io/en/latest/index.html" + tool_dev_url: "https://github.com/OpenMS/OpenMS" + doi: "10.1038/s41592-024-02197-7" + licence: ["BSD"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - mzmls: + type: file + description: | + List containing one or more mzML files + e.g. `[ 'file1.mzML', 'file2.mzML' ]` + pattern: "*.{mzML}" + - idxmls: + type: file + description: | + List containing one or more idXML files + e.g. `[ 'file1.idXML', 'file2.idXML' ]` + pattern: "*.{idXML}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - frag_err: + type: file + description: TSV file containing the fragment mass errors + pattern: "*frag_mass_err.{tsv}" + - prec_err: + type: file + description: Optional TSV file containing the precursor mass errors + pattern: "*prec_mass_err.{tsv}" + +authors: + - "@jonasscheid" diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test new file mode 100644 index 000000000000..b267fe15623d --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process OPENMS_IDMASSACCURACY" + script "../main.nf" + process "OPENMS_IDMASSACCURACY" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "openms" + tag "openms/idmassaccuracy" + tag "thermorawfileparser" + tag "openms/decoydatabase" + tag "openmsthirdparty/cometadapter" + + setup { + run("THERMORAWFILEPARSER") { + script "../../../thermorawfileparser/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], + file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true) + ]) + """ + } + } + run("OPENMS_DECOYDATABASE") { + script "../../../openms/decoydatabase/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test'], + file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true) + ]) + """ + } + } + run("OPENMSTHIRDPARTY_COMETADAPTER") { + script "../../../openmsthirdparty/cometadapter/main.nf" + process { + """ + input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMS_DECOYDATABASE.out.decoy_fasta) + """ + } + } + } + + test("proteomics - openms - mass_error") { + when { + process { + """ + input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("proteomics - openms - mass_error - stub") { + options "-stub" + when { + process { + """ + input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap new file mode 100644 index 000000000000..9accf9a2accf --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap @@ -0,0 +1,90 @@ +{ + "proteomics - openms - mass_error - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_frag_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test_prec_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + ], + "frag_err": [ + [ + { + "id": "test" + }, + "test_frag_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "prec_err": [ + [ + { + "id": "test" + }, + "test_prec_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T05:12:06.655389198" + }, + "proteomics - openms - mass_error": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_frag_mass_err.tsv:md5,c659254bc1305edde65eca890a6cf36f" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + ], + "frag_err": [ + [ + { + "id": "test" + }, + "test_frag_mass_err.tsv:md5,c659254bc1305edde65eca890a6cf36f" + ] + ], + "prec_err": [ + + ], + "versions": [ + "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T05:11:55.087464408" + } +} \ No newline at end of file diff --git a/modules/nf-core/openms/idmassaccuracy/tests/nextflow.config b/modules/nf-core/openms/idmassaccuracy/tests/nextflow.config new file mode 100644 index 000000000000..d104b31303e6 --- /dev/null +++ b/modules/nf-core/openms/idmassaccuracy/tests/nextflow.config @@ -0,0 +1,27 @@ +process { + + withName:OPENMSTHIRDPARTY_COMETADAPTER { + ext.args = [ + "-instrument low_res", + "-fragment_bin_offset 0.4", + "-precursor_mass_tolerance 5", + "-precursor_error_units 'ppm'", + "-fragment_mass_tolerance 0.50025", + "-digest_mass_range '800:5000'", + "-max_variable_mods_in_peptide 1", + "-precursor_charge '2:5'", + "-activation_method 'CID'", + "-variable_modifications 'Oxidation (M)'", + "-enzyme 'unspecific cleavage'", + "-spectrum_batch_size 0" + ].join(' ').trim() + } + + withName:OPENMS_IDMASSACCURACY { + ext.args = [ + "-precursor_error_ppm", + "-fragment_mass_tolerance 0.50025" + ].join(' ').trim() + } + +} From 94ae259d776e2b715a2829d3919d1642e40e8155 Mon Sep 17 00:00:00 2001 From: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Date: Tue, 17 Sep 2024 07:08:57 +0100 Subject: [PATCH 062/486] Stop nf-test complaining about missing dependency (#6652) * Finish filepaths * Fix tags --- modules/nf-core/ltrfinder/tests/main.nf.test | 4 ++-- .../ltrretriever/ltrretriever/tests/main.nf.test | 16 ++++++++-------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/modules/nf-core/ltrfinder/tests/main.nf.test b/modules/nf-core/ltrfinder/tests/main.nf.test index f971f7bb1f76..dc8c8033d355 100644 --- a/modules/nf-core/ltrfinder/tests/main.nf.test +++ b/modules/nf-core/ltrfinder/tests/main.nf.test @@ -7,13 +7,13 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "ltrfinder" - tag "gunzip/main" + tag "gunzip" test("actinidia_chinensis-genome_21_fasta_gz-success") { setup { run('GUNZIP') { - script "../../gunzip/main" + script "../../gunzip/main.nf" process { """ diff --git a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test index 5f67ff168d1a..4d512f3693d5 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test +++ b/modules/nf-core/ltrretriever/ltrretriever/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "modules_nfcore" tag "ltrretriever" tag "ltrretriever/ltrretriever" - tag "gunzip/main" + tag "gunzip" tag "ltrharvest" tag "ltrfinder" tag "cat/cat" @@ -19,7 +19,7 @@ nextflow_process { setup { run("LTRHARVEST") { - script "../../../ltrharvest" + script "../../../ltrharvest/main.nf" process { """ @@ -32,7 +32,7 @@ nextflow_process { } run("LTRFINDER") { - script "../../../ltrfinder" + script "../../../ltrfinder/main.nf" process { """ @@ -45,7 +45,7 @@ nextflow_process { } run("CAT_CAT") { - script "../../../cat/cat" + script "../../../cat/cat/main.nf" process { """ @@ -85,7 +85,7 @@ nextflow_process { setup { run('GUNZIP') { - script "../../../gunzip/main" + script "../../../gunzip/main.nf" process { """ @@ -98,7 +98,7 @@ nextflow_process { } run("LTRHARVEST") { - script "../../../ltrharvest" + script "../../../ltrharvest/main.nf" process { """ @@ -108,7 +108,7 @@ nextflow_process { } run("LTRFINDER") { - script "../../../ltrfinder" + script "../../../ltrfinder/main.nf" process { """ @@ -118,7 +118,7 @@ nextflow_process { } run("CAT_CAT") { - script "../../../cat/cat" + script "../../../cat/cat/main.nf" process { """ From 958e4a6031deefa327f339f11d9baf1ab5a32d5f Mon Sep 17 00:00:00 2001 From: Usman Rashid Date: Tue, 17 Sep 2024 18:11:16 +1200 Subject: [PATCH 063/486] Added nf-test for untarfiles (#6412) * Added nf-test for untarfiles * Matched conda versions with docker/singularity using wave containers * Changed test name * Added deprecation message --- modules/nf-core/untarfiles/environment.yml | 2 +- modules/nf-core/untarfiles/main.nf | 12 +- modules/nf-core/untarfiles/tests/main.nf.test | 104 +++++ .../untarfiles/tests/main.nf.test.snap | 356 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/untarfiles/main.nf | 33 -- .../nf-core/untarfiles/nextflow.config | 5 - tests/modules/nf-core/untarfiles/test.yml | 30 -- 8 files changed, 471 insertions(+), 74 deletions(-) create mode 100644 modules/nf-core/untarfiles/tests/main.nf.test create mode 100644 modules/nf-core/untarfiles/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/untarfiles/main.nf delete mode 100644 tests/modules/nf-core/untarfiles/nextflow.config delete mode 100644 tests/modules/nf-core/untarfiles/test.yml diff --git a/modules/nf-core/untarfiles/environment.yml b/modules/nf-core/untarfiles/environment.yml index 30ff7d8f5882..9ed335529192 100644 --- a/modules/nf-core/untarfiles/environment.yml +++ b/modules/nf-core/untarfiles/environment.yml @@ -4,5 +4,5 @@ channels: dependencies: - bioconda::grep=3.4 - - conda-forge::sed=4.7 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untarfiles/main.nf b/modules/nf-core/untarfiles/main.nf index de27e67cdd1c..bae7838c49b8 100644 --- a/modules/nf-core/untarfiles/main.nf +++ b/modules/nf-core/untarfiles/main.nf @@ -1,11 +1,17 @@ +def deprecation_message = """ +WARNING: This module has been deprecated. + +Reason: +This module is no longer recommended for use. It is recommended to use nf-core/modules/untar +""" process UNTARFILES { tag "$archive" label 'process_single' conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'oras://community.wave.seqera.io/library/grep_sed_tar:40b34489f8e82876' : + 'community.wave.seqera.io/library/grep_sed_tar:16f6591cd62505b3' }" input: tuple val(meta), path(archive) @@ -18,6 +24,7 @@ process UNTARFILES { task.ext.when == null || task.ext.when script: + assert true: deprecation_message def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.baseName.toString().replaceFirst(/\.tar$/, "")) @@ -39,6 +46,7 @@ process UNTARFILES { """ stub: + assert true: deprecation_message prefix = task.ext.prefix ?: "${meta.id}" """ mkdir $prefix diff --git a/modules/nf-core/untarfiles/tests/main.nf.test b/modules/nf-core/untarfiles/tests/main.nf.test new file mode 100644 index 000000000000..4e3acf5bd729 --- /dev/null +++ b/modules/nf-core/untarfiles/tests/main.nf.test @@ -0,0 +1,104 @@ + +nextflow_process { + + name "Test Process UNTARFILES" + script "../main.nf" + process "UNTARFILES" + + tag "modules" + tag "modules_nfcore" + tag "untarfiles" + + test("test-untarfiles") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-untarfiles-subdirectories") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bcl/flowcell.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.files[0][1].collect { file(it).name }.toSorted(), + process.out.versions + ).match() + } + ) + } + } + + test("test-untarfiles-onlyfiles") { + + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-untarfiles-onlyfiles-stub") { + options '-stub' + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/untarfiles/tests/main.nf.test.snap b/modules/nf-core/untarfiles/tests/main.nf.test.snap new file mode 100644 index 000000000000..33452a0827b7 --- /dev/null +++ b/modules/nf-core/untarfiles/tests/main.nf.test.snap @@ -0,0 +1,356 @@ +{ + "test-untarfiles-onlyfiles-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ], + "files": [ + [ + { + "id": "test" + }, + "file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T12:22:11.239416" + }, + "test-untarfiles-subdirectories": { + "content": [ + [ + "ControlMetricsOut.bin", + "CorrectedIntMetricsOut.bin", + "ErrorMetricsOut.bin", + "ExtractionMetricsOut.bin", + "IndexMetricsOut.bin", + "QMetricsOut.bin", + "RTAConfiguration.xml", + "RunInfo.xml", + "TileMetricsOut.bin", + "config.xml", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.bcl", + "s_1_1101.control", + "s_1_1101.filter", + "s_1_1101.locs", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats", + "s_1_1101.stats" + ], + [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-05T15:40:04.563426" + }, + "test-untarfiles": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ], + "files": [ + [ + { + "id": "test" + }, + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "versions": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T12:21:44.153411" + }, + "test-untarfiles-onlyfiles": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ], + "1": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ], + "files": [ + [ + { + "id": "test" + }, + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ], + "versions": [ + "versions.yml:md5,4414b00143ed6076881ba7c68ed8b6cf" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-29T12:22:06.329486" + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 83f3c37d11f9..07e2e0108a20 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -804,9 +804,6 @@ umitools/group: universc: - modules/nf-core/universc/** - tests/modules/nf-core/universc/** -untarfiles: - - modules/nf-core/untarfiles/** - - tests/modules/nf-core/untarfiles/** varlociraptor/callvariants: - modules/nf-core/varlociraptor/callvariants/** - tests/modules/nf-core/varlociraptor/callvariants/** diff --git a/tests/modules/nf-core/untarfiles/main.nf b/tests/modules/nf-core/untarfiles/main.nf deleted file mode 100644 index 92d9b0b06e9d..000000000000 --- a/tests/modules/nf-core/untarfiles/main.nf +++ /dev/null @@ -1,33 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UNTARFILES } from '../../../../modules/nf-core/untarfiles/main.nf' - -workflow test_untarfiles { - input = [ - [id: 'test'], - file(params.test_data['sarscov2']['genome']['kraken2_tar_gz'], checkIfExists: true) - ] - - UNTARFILES ( input ) -} - -workflow test_untarfiles_different_output_path { - input = [ - [id: 'test'], - file(params.test_data['homo_sapiens']['illumina']['test_flowcell'], checkIfExists: true) - ] - - UNTARFILES ( input ) -} - - -workflow test_untarfiles_onlyfiles { - input = [ - [id: 'test'], - file(params.test_data['generic']['tar']['tar_gz'], checkIfExists: true) - ] - - UNTARFILES ( input ) -} diff --git a/tests/modules/nf-core/untarfiles/nextflow.config b/tests/modules/nf-core/untarfiles/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/untarfiles/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/untarfiles/test.yml b/tests/modules/nf-core/untarfiles/test.yml deleted file mode 100644 index 59d77f61c6f7..000000000000 --- a/tests/modules/nf-core/untarfiles/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: untarfiles test_untarfiles - command: nextflow run ./tests/modules/nf-core/untarfiles -entry test_untarfiles -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untarfiles/nextflow.config - tags: - - untarfiles - files: - - path: output/untarfiles/test/kraken2/hash.k2d - md5sum: 8b8598468f54a7087c203ad0190555d9 - - path: output/untarfiles/test/kraken2/opts.k2d - md5sum: a033d00cf6759407010b21700938f543 - - path: output/untarfiles/test/kraken2/taxo.k2d - md5sum: 094d5891cdccf2f1468088855c214b2c - - path: output/untarfiles/versions.yml - -- name: untarfiles test_untarfiles_different_output_path - command: nextflow run ./tests/modules/nf-core/untarfiles -entry test_untarfiles_different_output_path -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untarfiles/nextflow.config - tags: - - untarfiles - files: - - path: output/untarfiles/test/220422_M11111_0222_000000000-K9H97/RunInfo.xml - md5sum: 03038959f4dd181c86bc97ae71fe270a - - path: output/untarfiles/versions.yml - -- name: untarfiles test_untarfiles_onlyfiles - command: nextflow run ./tests/modules/nf-core/untarfiles -entry test_untarfiles_onlyfiles -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/untarfiles/nextflow.config - tags: - - untarfiles - files: - - path: output/untarfiles/test/hello.txt - md5sum: e59ff97941044f85df5297e1c302d260 - - path: output/untarfiles/versions.yml From 7b9ce4b817926f17ec82cc0099d2d0ff095a2fac Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 17 Sep 2024 10:19:43 +0200 Subject: [PATCH 064/486] Remove custom params in GTDBTK/CLASSIFYWF (#6651) * Use the proper version calling now implemented * Remove custom params * Fix test --- modules/nf-core/gtdbtk/classifywf/main.nf | 9 ++++----- modules/nf-core/gtdbtk/classifywf/meta.yml | 3 +++ modules/nf-core/gtdbtk/classifywf/tests/main.nf.test | 7 +++---- 3 files changed, 10 insertions(+), 9 deletions(-) diff --git a/modules/nf-core/gtdbtk/classifywf/main.nf b/modules/nf-core/gtdbtk/classifywf/main.nf index f0944fdc33a5..23862fee5739 100644 --- a/modules/nf-core/gtdbtk/classifywf/main.nf +++ b/modules/nf-core/gtdbtk/classifywf/main.nf @@ -7,6 +7,7 @@ process GTDBTK_CLASSIFYWF { input: tuple val(meta) , path("bins/*") tuple val(db_name), path("database/*") + val use_pplacer_scratch_dir path mash_db output: @@ -26,8 +27,8 @@ process GTDBTK_CLASSIFYWF { script: def args = task.ext.args ?: '' - def pplacer_scratch = params.gtdbtk_pplacer_scratch ? "--scratch_dir pplacer_tmp" : "" - def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen" + def pplacer_scratch = use_pplacer_scratch_dir ? "--scratch_dir pplacer_tmp" : "" + def mash_mode = mash_db ? "--mash_db ${mash_db}" : "--skip_ani_screen" prefix = task.ext.prefix ?: "${meta.id}" """ @@ -43,9 +44,7 @@ process GTDBTK_CLASSIFYWF { --out_dir "\${PWD}" \\ --cpus ${task.cpus} \\ ${mash_mode} \\ - ${pplacer_scratch} \\ - --min_perc_aa ${params.gtdbtk_min_perc_aa} \\ - --min_af ${params.gtdbtk_min_af} + ${pplacer_scratch} ## If mash db given, classify/ and identify/ directories won't be created if [[ -d classify/ && \$(ls -A classify/) ]]; then diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml index d85f99660bee..0667dcd6d73f 100644 --- a/modules/nf-core/gtdbtk/classifywf/meta.yml +++ b/modules/nf-core/gtdbtk/classifywf/meta.yml @@ -30,6 +30,9 @@ input: type: file description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy) pattern: "*" + - use_pplacer_scratch_dir: + type: boolean + description: Set to true to reduce pplacer memory usage by writing to disk (slower) - mash_db: type: file description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional) diff --git a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test index 60bedb684b4f..deca962df931 100644 --- a/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test +++ b/modules/nf-core/gtdbtk/classifywf/tests/main.nf.test @@ -26,7 +26,8 @@ nextflow_process { ] ] input[1] = [[], []] - input[2] = [] + input[2] = false + input[3] = [] """ } } @@ -35,9 +36,7 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot(process.out).match() } - ) + ) } - } - } From 3be751e610b332efd94c2e82ddab5b5c65cfe852 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Tue, 17 Sep 2024 10:35:46 +0200 Subject: [PATCH 065/486] Add UPP (#6546) * Add UPP * fix lint * Update UPP * fix prettier * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * fixes * update * update tests * update * update * Update modules/nf-core/upp/align/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- modules/nf-core/upp/align/environment.yml | 6 ++ modules/nf-core/upp/align/main.nf | 71 ++++++++++++ modules/nf-core/upp/align/meta.yml | 57 ++++++++++ modules/nf-core/upp/align/tests/main.nf.test | 96 +++++++++++++++++ .../nf-core/upp/align/tests/main.nf.test.snap | 101 ++++++++++++++++++ .../nf-core/upp/align/tests/nextflow.config | 7 ++ modules/nf-core/upp/align/tests/tags.yml | 2 + 7 files changed, 340 insertions(+) create mode 100644 modules/nf-core/upp/align/environment.yml create mode 100644 modules/nf-core/upp/align/main.nf create mode 100644 modules/nf-core/upp/align/meta.yml create mode 100644 modules/nf-core/upp/align/tests/main.nf.test create mode 100644 modules/nf-core/upp/align/tests/main.nf.test.snap create mode 100644 modules/nf-core/upp/align/tests/nextflow.config create mode 100644 modules/nf-core/upp/align/tests/tags.yml diff --git a/modules/nf-core/upp/align/environment.yml b/modules/nf-core/upp/align/environment.yml new file mode 100644 index 000000000000..da0eaa9a7450 --- /dev/null +++ b/modules/nf-core/upp/align/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::sepp=4.5.5 + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/upp/align/main.nf b/modules/nf-core/upp/align/main.nf new file mode 100644 index 000000000000..1b254ea47276 --- /dev/null +++ b/modules/nf-core/upp/align/main.nf @@ -0,0 +1,71 @@ +process UPP_ALIGN { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'oras://community.wave.seqera.io/library/sepp_pigz:d72591720d0277b1': + 'community.wave.seqera.io/library/sepp_pigz:ea6dbc7704a2e251' }" + + input: + tuple val(meta) , path(fasta) + tuple val(meta2), path(tree) + val(compress) + + output: + tuple val(meta), path("*.aln{.gz,}"), emit: alignment + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def tree_args = tree ? "-t $tree" : "" + """ + + if [ "$workflow.containerEngine" = 'singularity' ]; then + export CONDA_PREFIX="/opt/conda/" + export PASTA_TOOLS_DEVDIR="/opt/conda/bin/" + fi + + run_upp.py \\ + $args \\ + -x $task.cpus \\ + -s ${fasta} \\ + -d . \\ + -o ${prefix} \\ + -p ./upp-temporary + + mv ${prefix}_alignment.fasta ${prefix}.aln + + if ${compress}; then + pigz -p ${task.cpus} ${prefix}.aln + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + upp: \$(run_upp.py -v | grep "run_upp" | cut -f2 -d" ") + pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + + + if [ "$compress" = true ]; then + echo | gzip > "${prefix}.aln.gz" + else + touch "${prefix}.aln" + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + upp: \$(run_upp.py -v | grep "run_upp" | cut -f2 -d" ") + pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) + END_VERSIONS + """ +} diff --git a/modules/nf-core/upp/align/meta.yml b/modules/nf-core/upp/align/meta.yml new file mode 100644 index 000000000000..a5470c2c087e --- /dev/null +++ b/modules/nf-core/upp/align/meta.yml @@ -0,0 +1,57 @@ +name: "upp_align" +description: Aligns protein structures using UPP +keywords: + - alignment + - MSA + - genomics + - structure +tools: + - "upp": + description: "SATe-enabled phylogenetic placement" + homepage: "https://github.com/smirarab/sepp/tree/master" + documentation: "https://github.com/smirarab/sepp/blob/master/README.UPP.md" + tool_dev_url: "https://github.com/smirarab/sepp/tree/master" + doi: "10.1093/bioinformatics/btad007" + licence: ["GPL v3"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - alignment: + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false + pattern: "*.aln{.gz,}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@luisas" +maintainers: + - "@luisas" diff --git a/modules/nf-core/upp/align/tests/main.nf.test b/modules/nf-core/upp/align/tests/main.nf.test new file mode 100644 index 000000000000..7425d984c600 --- /dev/null +++ b/modules/nf-core/upp/align/tests/main.nf.test @@ -0,0 +1,96 @@ +nextflow_process { + + name "Test Process UPP_ALIGN" + script "../main.nf" + process "UPP_ALIGN" + + tag "modules" + tag "modules_nfcore" + tag "upp" + tag "upp/align" + tag "famsa/guidetree" + + test("fasta - align_sequence - uncompressed") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("fasta - with_tree - compressed") { + config "./nextflow.config" + + setup { + + run("FAMSA_GUIDETREE") { + script "../../../famsa/guidetree/main.nf" + process { + """ + input[0] = [ [ id:'tree' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + + """ + } + } + } + when { + process { + """ + input[0] = [ [ id:'test_tree' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test_tree'], tree]} + input[2] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()} + ) + } + } + + test("stub") { + config "./nextflow.config" + + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], + file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()} + ) + } + } +} diff --git a/modules/nf-core/upp/align/tests/main.nf.test.snap b/modules/nf-core/upp/align/tests/main.nf.test.snap new file mode 100644 index 000000000000..d34254a1a50d --- /dev/null +++ b/modules/nf-core/upp/align/tests/main.nf.test.snap @@ -0,0 +1,101 @@ +{ + "fasta - align_sequence - uncompressed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.aln:md5,e6b5291e9cdb40e9b7c72688e4da533b" + ] + ], + "1": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ], + "alignment": [ + [ + { + "id": "test" + }, + "test.aln:md5,e6b5291e9cdb40e9b7c72688e4da533b" + ] + ], + "versions": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T07:51:30.876772941" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ], + "alignment": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T07:36:19.135281969" + }, + "fasta - with_tree - compressed": { + "content": [ + { + "0": [ + [ + { + "id": "test_tree" + }, + "test_tree.aln.gz:md5,e6b5291e9cdb40e9b7c72688e4da533b" + ] + ], + "1": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ], + "alignment": [ + [ + { + "id": "test_tree" + }, + "test_tree.aln.gz:md5,e6b5291e9cdb40e9b7c72688e4da533b" + ] + ], + "versions": [ + "versions.yml:md5,b431bb15ae86dcd4485d921df1752a98" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T07:52:05.47226891" + } +} \ No newline at end of file diff --git a/modules/nf-core/upp/align/tests/nextflow.config b/modules/nf-core/upp/align/tests/nextflow.config new file mode 100644 index 000000000000..30ae1f4682ed --- /dev/null +++ b/modules/nf-core/upp/align/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: "UPP_ALIGN" { + ext.args = { "-m amino" } + } + +} diff --git a/modules/nf-core/upp/align/tests/tags.yml b/modules/nf-core/upp/align/tests/tags.yml new file mode 100644 index 000000000000..adb26a514206 --- /dev/null +++ b/modules/nf-core/upp/align/tests/tags.yml @@ -0,0 +1,2 @@ +upp/align: + - "modules/nf-core/upp/align/**" From 7c316cae26baf55e0add993bed2b0c9f7105c653 Mon Sep 17 00:00:00 2001 From: Alexander Peltzer Date: Tue, 17 Sep 2024 15:55:22 +0200 Subject: [PATCH 066/486] Bump MQC to 1.25 (#6655) * Bump MQC to 1.25 * Bump snaps --- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 ++-- modules/nf-core/multiqc/tests/main.nf.test.snap | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b07923..0fe1264441d4 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index ceaec139e4c5..b9ccebdbbc0f 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.24.1--pyhdfd78af_0' : - 'biocontainers/multiqc:1.24.1--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 83fa080c8cbd..b779e46924bb 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -17,7 +17,7 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { @@ -29,7 +29,7 @@ "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,6eb13f3b11bbcbfc98ad3166420ff760" + "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" ] ], "meta": { From d5a553e89fbec3e2904b08ae1572840f5a0af880 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Tue, 17 Sep 2024 20:22:20 +0200 Subject: [PATCH 067/486] update for vcfpolyx (#6641) * update for vcfpolyx * fix https://github.com/nf-core/modules/pull/6641#discussion_r1759154226 * remove default param * add test with bed * prevent md5sum for empty file --- .../nf-core/jvarkit/vcfpolyx/environment.yml | 1 + modules/nf-core/jvarkit/vcfpolyx/main.nf | 41 +++++++---- modules/nf-core/jvarkit/vcfpolyx/meta.yml | 25 ++++--- .../jvarkit/vcfpolyx/tests/main.nf.test | 71 +++++++++++++++++-- .../jvarkit/vcfpolyx/tests/main.nf.test.snap | 31 +++++++- .../jvarkit/vcfpolyx/tests/nextflow.config | 5 ++ 6 files changed, 143 insertions(+), 31 deletions(-) create mode 100644 modules/nf-core/jvarkit/vcfpolyx/tests/nextflow.config diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml index e71f3d436687..c70f23523cb6 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -5,3 +5,4 @@ channels: - conda-forge dependencies: - "bioconda::jvarkit=2024.08.25" + - "bioconda:bcftools=1.20" diff --git a/modules/nf-core/jvarkit/vcfpolyx/main.nf b/modules/nf-core/jvarkit/vcfpolyx/main.nf index 77005f6fc469..02060c26be6b 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/main.nf +++ b/modules/nf-core/jvarkit/vcfpolyx/main.nf @@ -8,7 +8,7 @@ process JVARKIT_VCFPOLYX { 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" input: - tuple val(meta), path(vcf) + tuple val(meta), path(vcf), path(tbi), path(regions_file) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) tuple val(meta4), path(dict) @@ -23,24 +23,28 @@ process JVARKIT_VCFPOLYX { task.ext.when == null || task.ext.when script: - def args1 = task.ext.args1 ?: '' - def args2 = meta.vcfpolyx_args ?: (task.ext.args2 ?: ' --tag POLYX --max-repeats 10 ') - def args3 = task.ext.args3 ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args1 = task.ext.args1 ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def regions_cmd = regions_file ? (tbi ? " --regions-file" : " --targets-file") + " '${regions_file}' " : "" - extension = args3.contains("--output-type b") || args3.contains("-Ob") ? "bcf.gz" : - args3.contains("--output-type u") || args3.contains("-Ou") ? "bcf" : - args3.contains("--output-type z") || args3.contains("-Oz") ? "vcf.gz" : - args3.contains("--output-type v") || args3.contains("-Ov") ? "vcf" : - "vcf" + extension = getVcfExtension(args3); /* custom function, see below */ if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" """ mkdir -p TMP - bcftools view -O v ${args1} "${vcf}" |\\ - jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx --reference "${fasta}" ${args2} |\\ - bcftools view --output "${prefix}.${extension}" ${args3} + bcftools view -O v \\ + ${regions_cmd} \\ + ${args1} \\ + "${vcf}" |\\ + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcfpolyx \\ + --reference "${fasta}" \\ + ${args2} |\\ + bcftools view \\ + --output "${prefix}.${extension}" \\ + ${args3} rm -rf TMP @@ -53,6 +57,8 @@ process JVARKIT_VCFPOLYX { stub: def prefix = task.ext.prefix ?: "${meta.id}" + def args3 = task.ext.args3 ?: '' + extension = getVcfExtension(args3); /* custom function, see below */ """ touch "${prefix}.${extension}" @@ -63,3 +69,12 @@ process JVARKIT_VCFPOLYX { END_VERSIONS """ } + +// Custom Function to get VCF extension +String getVcfExtension(String args) { + return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf"; +} diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml index 221f7e9ca516..0e9017047062 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml @@ -5,8 +5,10 @@ description: annotate VCF files for poly repeats keywords: - vcf - bcf + - variant - annotation - repeats + - polyx tools: - "jvarkit": description: "Java utilities for Bioinformatics." @@ -15,6 +17,7 @@ tools: tool_dev_url: "https://github.com/lindenb/jvarkit" doi: "10.6084/m9.figshare.1425030" licence: ["MIT License"] + args_id: "$args2" - "bcftools": description: | @@ -23,48 +26,52 @@ tools: documentation: "http://www.htslib.org/doc/bcftools.html" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] - + args_id: ["$args1", "$args3"] input: - meta: type: map description: | Groovy Map containing VCF information - + e.g. [ id:'test_reference' ] - meta2: type: map description: | Groovy Map containing fasta information - + e.g. [ id:'test_reference' ] - meta3: type: map description: | Groovy Map containing fasta.fai information - + e.g. [ id:'test_reference' ] - meta4: type: map description: | Groovy Map containing fasta.dict information - + e.g. [ id:'test_reference' ] - vcf: type: file description: Groovy Map containing reference genome information for vcf pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - + - tbi: + type: file + description: Optional VCF/BCF index file + pattern: "*.{tbi,csi}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{bed,bed.gz,txt,tsv}" - fasta: type: file description: Groovy Map containing reference genome information for fai reference fasta file pattern: "*.fasta" - - fai: type: file description: Groovy Map containing reference genome information for fai pattern: "*.fasta.fai" - - dict: type: file description: Groovy Map containing reference genome information for GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test index 72ec3a71473d..186ad0a9f95e 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test @@ -4,7 +4,8 @@ nextflow_process { name "Test Process JVARKIT_VCFPOLYX" script "../main.nf" process "JVARKIT_VCFPOLYX" - + config "./nextflow.config" + tag "modules" tag "modules_nfcore" tag "jvarkit" @@ -17,7 +18,9 @@ nextflow_process { """ input[0] =[ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] ] input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] @@ -30,14 +33,70 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - path(process.out.vcf[0][1]).vcf.variantsMD5, - process.out.versions - ).match() - } + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } ) } } + test("sarscov2 - vcf+bed") { + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.vcf[0][1]).exists() }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("sarscov2 - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(path(process.out.vcf[0][1]), process.out.versions).match() } + ) + } + + } } diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap index e5ccf1914720..8b61424c8547 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/main.nf.test.snap @@ -2,14 +2,39 @@ "sarscov2 - vcf": { "content": [ "65a03a6057dc74467c2b7b17230e7f14", - [ - "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c" - ] + [ + "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c" + ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, "timestamp": "2024-09-03T14:00:13.118369362" + }, + "sarscov2 - vcf+bed": { + "content": [ + [ + "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + "sarscov2 - vcf - stub": { + "content": [ + "vcf_test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "versions.yml:md5,b3c351a56da9062295ef90011a9cd48c" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-13T17:17:41.14805166" } } diff --git a/modules/nf-core/jvarkit/vcfpolyx/tests/nextflow.config b/modules/nf-core/jvarkit/vcfpolyx/tests/nextflow.config new file mode 100644 index 000000000000..174e58bfdd6f --- /dev/null +++ b/modules/nf-core/jvarkit/vcfpolyx/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: JVARKIT_VCFPOLYX { + ext.args2=" --tag POLYX --max-repeats 10 " + } +} From 763d4b5c05ffda3ac1ac969dc67f7458cfb2eb1d Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Wed, 18 Sep 2024 13:46:21 +0200 Subject: [PATCH 068/486] bump samtools (#6648) * bump samtools * samtools cat no longer supports * update snapshots * more snapshots * fix consensus test * another attempt at fixing 'consensus' * reheader > nf-test * markdup > nf-test * fix linting for markdup * consensus fix? * fix consensus --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .../samtools/ampliconclip/environment.yml | 4 +- modules/nf-core/samtools/ampliconclip/main.nf | 4 +- .../ampliconclip/tests/main.nf.test.snap | 104 ++++++++--------- .../nf-core/samtools/bam2fq/environment.yml | 4 +- modules/nf-core/samtools/bam2fq/main.nf | 4 +- .../samtools/bam2fq/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/calmd/environment.yml | 4 +- modules/nf-core/samtools/calmd/main.nf | 4 +- .../samtools/calmd/tests/main.nf.test.snap | 16 +-- modules/nf-core/samtools/cat/environment.yml | 4 +- modules/nf-core/samtools/cat/main.nf | 5 +- .../samtools/cat/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/collate/environment.yml | 4 +- modules/nf-core/samtools/collate/main.nf | 4 +- .../samtools/collate/tests/main.nf.test.snap | 16 +-- .../samtools/collatefastq/environment.yml | 4 +- modules/nf-core/samtools/collatefastq/main.nf | 4 +- .../collatefastq/tests/main.nf.test.snap | 60 +++++----- .../samtools/consensus/environment.yml | 3 +- modules/nf-core/samtools/consensus/main.nf | 8 +- .../samtools/consensus/tests/main.nf.test | 15 +-- .../consensus/tests/main.nf.test.snap | 40 +++---- .../nf-core/samtools/convert/environment.yml | 4 +- modules/nf-core/samtools/convert/main.nf | 4 +- .../samtools/convert/tests/main.nf.test.snap | 26 ++--- .../nf-core/samtools/coverage/environment.yml | 4 +- modules/nf-core/samtools/coverage/main.nf | 4 +- .../samtools/coverage/tests/main.nf.test.snap | 30 ++--- .../nf-core/samtools/cramsize/environment.yml | 4 +- modules/nf-core/samtools/cramsize/main.nf | 4 +- .../samtools/cramsize/tests/main.nf.test.snap | 20 ++-- .../nf-core/samtools/depth/environment.yml | 4 +- modules/nf-core/samtools/depth/main.nf | 4 +- .../samtools/depth/tests/main.nf.test.snap | 16 +-- modules/nf-core/samtools/dict/environment.yml | 4 +- modules/nf-core/samtools/dict/main.nf | 4 +- .../samtools/dict/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/faidx/environment.yml | 4 +- modules/nf-core/samtools/faidx/main.nf | 4 +- .../samtools/faidx/tests/main.nf.test.snap | 50 ++++---- .../nf-core/samtools/fasta/environment.yml | 4 +- modules/nf-core/samtools/fasta/main.nf | 4 +- .../samtools/fasta/tests/main.nf.test.snap | 12 +- .../nf-core/samtools/fastq/environment.yml | 4 +- modules/nf-core/samtools/fastq/main.nf | 4 +- .../samtools/fastq/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/fixmate/environment.yml | 4 +- modules/nf-core/samtools/fixmate/main.nf | 4 +- .../samtools/fixmate/tests/main.nf.test.snap | 8 +- .../nf-core/samtools/flagstat/environment.yml | 4 +- modules/nf-core/samtools/flagstat/main.nf | 4 +- .../samtools/flagstat/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/getrg/environment.yml | 4 +- modules/nf-core/samtools/getrg/main.nf | 4 +- .../samtools/getrg/tests/main.nf.test.snap | 6 +- .../nf-core/samtools/idxstats/environment.yml | 4 +- modules/nf-core/samtools/idxstats/main.nf | 4 +- .../samtools/idxstats/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/import/environment.yml | 4 +- modules/nf-core/samtools/import/main.nf | 4 +- .../nf-core/samtools/index/environment.yml | 4 +- modules/nf-core/samtools/index/main.nf | 4 +- .../samtools/index/tests/main.nf.test.snap | 46 ++++---- .../nf-core/samtools/markdup/environment.yml | 4 +- modules/nf-core/samtools/markdup/main.nf | 4 +- .../samtools/markdup/tests/main.nf.test | 90 +++++++++++++++ .../samtools/markdup/tests/main.nf.test.snap | 96 ++++++++++++++++ .../samtools/markdup/tests}/nextflow.config | 10 -- .../nf-core/samtools/merge/environment.yml | 4 +- modules/nf-core/samtools/merge/main.nf | 4 +- .../samtools/merge/tests/main.nf.test.snap | 32 +++--- .../nf-core/samtools/mpileup/environment.yml | 4 +- modules/nf-core/samtools/mpileup/main.nf | 4 +- .../samtools/mpileup/tests/main.nf.test.snap | 16 +-- .../nf-core/samtools/reheader/environment.yml | 4 +- modules/nf-core/samtools/reheader/main.nf | 6 +- .../samtools/reheader/tests/chrdel.config | 6 + .../samtools/reheader/tests/main.nf.test | 80 +++++++++++++ .../samtools/reheader/tests/main.nf.test.snap | 107 ++++++++++++++++++ .../samtools/reheader/tests/rgdel.config | 6 + .../nf-core/samtools/sormadup/environment.yml | 4 +- modules/nf-core/samtools/sormadup/main.nf | 5 +- .../samtools/sormadup/tests/main.nf.test.snap | 24 ++-- modules/nf-core/samtools/sort/environment.yml | 4 +- modules/nf-core/samtools/sort/main.nf | 5 +- .../samtools/sort/tests/main.nf.test.snap | 30 ++--- .../nf-core/samtools/stats/environment.yml | 4 +- modules/nf-core/samtools/stats/main.nf | 4 +- .../samtools/stats/tests/main.nf.test.snap | 40 +++---- modules/nf-core/samtools/view/environment.yml | 4 +- modules/nf-core/samtools/view/main.nf | 4 +- .../samtools/view/tests/main.nf.test.snap | 86 +++++++------- .../tests/main.nf.test.snap | 22 ++-- .../tests/main.nf.test.snap | 42 +++---- .../tests/main.nf.test.snap | 72 ++++++------ .../tests/main.nf.test.snap | 80 ++++++------- .../tests/main.nf.test.snap | 96 ++++++++-------- .../tests/main.nf.test.snap | 34 +++--- .../tests/main.nf.test.snap | 84 +++++++------- tests/config/pytest_modules.yml | 6 - .../modules/nf-core/samtools/markdup/main.nf | 27 ----- .../modules/nf-core/samtools/markdup/test.yml | 8 -- .../modules/nf-core/samtools/reheader/main.nf | 26 ----- .../nf-core/samtools/reheader/nextflow.config | 13 --- .../nf-core/samtools/reheader/test.yml | 17 --- 105 files changed, 1110 insertions(+), 841 deletions(-) create mode 100644 modules/nf-core/samtools/markdup/tests/main.nf.test create mode 100644 modules/nf-core/samtools/markdup/tests/main.nf.test.snap rename {tests/modules/nf-core/samtools/markdup => modules/nf-core/samtools/markdup/tests}/nextflow.config (60%) create mode 100644 modules/nf-core/samtools/reheader/tests/chrdel.config create mode 100644 modules/nf-core/samtools/reheader/tests/main.nf.test create mode 100644 modules/nf-core/samtools/reheader/tests/main.nf.test.snap create mode 100644 modules/nf-core/samtools/reheader/tests/rgdel.config delete mode 100644 tests/modules/nf-core/samtools/markdup/main.nf delete mode 100644 tests/modules/nf-core/samtools/markdup/test.yml delete mode 100644 tests/modules/nf-core/samtools/reheader/main.nf delete mode 100644 tests/modules/nf-core/samtools/reheader/nextflow.config delete mode 100644 tests/modules/nf-core/samtools/reheader/test.yml diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/ampliconclip/main.nf b/modules/nf-core/samtools/ampliconclip/main.nf index 0b7d16b2fa2c..de4acc421af1 100644 --- a/modules/nf-core/samtools/ampliconclip/main.nf +++ b/modules/nf-core/samtools/ampliconclip/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_AMPLICONCLIP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap index 6706f947bf74..036c875d0401 100644 --- a/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/ampliconclip/tests/main.nf.test.snap @@ -1,29 +1,17 @@ { - "bam_bed_versions": { - "content": [ - [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-28T15:43:25.843761003" - }, - "bam_bed_stats": { + "bam_bed_save_all_versions": { "content": [ [ - + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-02T13:43:02.239309" + "timestamp": "2024-09-16T07:45:31.382344883" }, - "bam_bed_save_all_stats": { + "bam_bed_save_all_rejects_bam": { "content": [ [ [ @@ -31,45 +19,27 @@ "id": "test", "single_end": false }, - "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a" + "test.cliprejects.bam:md5,8aa0f82e1c2dbfd9fcfab0fe3efa0ada" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-02T13:43:14.110481" + "timestamp": "2024-09-16T07:45:31.334527155" }, - "bam_bed_save_all_versions": { + "bam_bed_versions": { "content": [ [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:36.405710677" - }, - "bam_bed_save_all_rejects_bam": { - "content": [ - [ - [ - { - "id": "test", - "single_end": false - }, - "test.cliprejects.bam:md5,e3c76daf46d83b2327a1168170b08fca" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-05-28T15:43:36.39935122" + "timestamp": "2024-09-16T07:45:11.300085385" }, "bam_bed_save_clipsats_name": { "content": [ @@ -99,15 +69,27 @@ "id": "test", "single_end": false }, - "test.cliprejects.bam:md5,f29869fea697a5041f588970d9cf2392" + "test.cliprejects.bam:md5,9d0caf53bd9a8ccb4a5ce60393635ee0" ] ] ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T07:45:21.573836864" + }, + "bam_bed_stats": { + "content": [ + [ + + ] + ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" }, - "timestamp": "2024-05-28T15:43:31.133760457" + "timestamp": "2024-02-02T13:43:02.239309" }, "bam_bed_save_clipsats_stats": { "content": [ @@ -121,17 +103,35 @@ }, "timestamp": "2024-02-13T16:13:25.207756781" }, - "bam_bed_save_clipsats_versions": { + "bam_bed_save_all_stats": { "content": [ [ - "versions.yml:md5,377f547954102b9f96e37c8add7b2e4d" + [ + { + "id": "test", + "single_end": false + }, + "test.clipstats.txt:md5,2143cb7e8b5b7fcd3b12403fce17f10a" + ] ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-02T13:43:14.110481" + }, + "bam_bed_save_clipsats_versions": { + "content": [ + [ + "versions.yml:md5,27f110bf9d23f853e9bece1b7f7bfa8e" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:31.138774495" + "timestamp": "2024-09-16T07:45:21.620404522" }, "bam_bed_save_all_name": { "content": [ diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf index a34a13a9848e..1d3049e565dc 100644 --- a/modules/nf-core/samtools/bam2fq/main.nf +++ b/modules/nf-core/samtools/bam2fq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_BAM2FQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(inputbam) diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap index aa0f8c34d108..17ea1d4f9048 100644 --- a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap @@ -51,25 +51,25 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,90c1cf8971540ef05e330db5a560195c" + "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:52.415053401" + "timestamp": "2024-09-16T07:46:07.695175929" }, "bam_split_versions": { "content": [ [ - "versions.yml:md5,90c1cf8971540ef05e330db5a560195c" + "versions.yml:md5,afea8d3a8a729d71eac7d7e034012aee" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:57.740193087" + "timestamp": "2024-09-16T07:46:17.91793415" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/calmd/main.nf b/modules/nf-core/samtools/calmd/main.nf index 4672af6f0022..fba8aa70e649 100644 --- a/modules/nf-core/samtools/calmd/main.nf +++ b/modules/nf-core/samtools/calmd/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CALMD { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/calmd/tests/main.nf.test.snap b/modules/nf-core/samtools/calmd/tests/main.nf.test.snap index fd40d084fa2d..4438609f97d7 100644 --- a/modules/nf-core/samtools/calmd/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/calmd/tests/main.nf.test.snap @@ -22,25 +22,25 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd" + "versions.yml:md5,6082f9d3311ea0138839acc5341c115f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:47.344537089" + "timestamp": "2024-09-16T07:47:04.212973938" }, "bam_versions": { "content": [ [ - "versions.yml:md5,51ce5935fb227e0d66d293442d3a2efd" + "versions.yml:md5,6082f9d3311ea0138839acc5341c115f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:41.963108136" + "timestamp": "2024-09-16T07:46:53.00613089" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/cat/main.nf b/modules/nf-core/samtools/cat/main.nf index 9447b657220b..0490b81d3f50 100644 --- a/modules/nf-core/samtools/cat/main.nf +++ b/modules/nf-core/samtools/cat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") @@ -26,7 +26,6 @@ process SAMTOOLS_CAT { """ samtools \\ cat \\ - --threads ${task.cpus-1} \\ $args \\ -o ${prefix}.${file_type} \\ $input_files diff --git a/modules/nf-core/samtools/cat/tests/main.nf.test.snap b/modules/nf-core/samtools/cat/tests/main.nf.test.snap index ae9344df6f05..9af1b19ff9e7 100644 --- a/modules/nf-core/samtools/cat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/cat/tests/main.nf.test.snap @@ -14,14 +14,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8" + "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:35.044644556" + "timestamp": "2024-09-16T07:47:51.511914861" }, "bams_bam": { "content": [ @@ -58,13 +58,13 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,9b9451947b5de303ed028cf6513be3e8" + "versions.yml:md5,cd29ae344fb0bf5635527e1cb7a7d95f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:29.652817652" + "timestamp": "2024-09-16T08:47:50.783194958" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/collate/main.nf b/modules/nf-core/samtools/collate/main.nf index 748fc4020d0a..a0d831ff2784 100644 --- a/modules/nf-core/samtools/collate/main.nf +++ b/modules/nf-core/samtools/collate/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COLLATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collate/tests/main.nf.test.snap b/modules/nf-core/samtools/collate/tests/main.nf.test.snap index 8645f3b69dfc..4d2213695a7d 100644 --- a/modules/nf-core/samtools/collate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collate/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "cram_fasta_versions": { "content": [ [ - "versions.yml:md5,b88681026fe2f488e3704e6726464d26" + "versions.yml:md5,354d4c20293fa674e56f96d5f7db6580" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:11.322474854" + "timestamp": "2024-09-16T07:48:41.845649492" }, "bam_cram": { "content": [ @@ -82,13 +82,13 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,b88681026fe2f488e3704e6726464d26" + "versions.yml:md5,354d4c20293fa674e56f96d5f7db6580" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:04.384976938" + "timestamp": "2024-09-16T07:48:29.622364238" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf index 599c1b78ab09..8b70ebd34524 100644 --- a/modules/nf-core/samtools/collatefastq/main.nf +++ b/modules/nf-core/samtools/collatefastq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COLLATEFASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap b/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap index 3618619eadd9..26f5293699c4 100644 --- a/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/collatefastq/tests/main.nf.test.snap @@ -17,14 +17,14 @@ ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-27T08:53:29.440496728" + "timestamp": "2024-09-16T07:50:35.483719031" }, "human - bam - single_end": { "content": [ @@ -38,14 +38,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T13:36:44.978865568" + "timestamp": "2024-09-16T07:49:31.667042764" }, "human - bam - paired_end -stub": { "content": [ @@ -62,14 +62,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:12:21.528678233" + "timestamp": "2024-09-16T07:50:04.607920717" }, "human - cram - stub": { "content": [ @@ -86,14 +86,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:13:01.876034822" + "timestamp": "2024-09-16T07:50:25.354607106" }, "human - cram": { "content": [ @@ -110,14 +110,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T09:23:07.374415578" + "timestamp": "2024-09-16T07:49:43.12646213" }, "human - bam - paired_end - interleaved": { "content": [ @@ -137,14 +137,14 @@ ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T12:02:17.198640965" + "timestamp": "2024-09-16T07:49:53.799565712" }, "human - bam - single_end - stub": { "content": [ @@ -158,14 +158,14 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T10:12:39.204428667" + "timestamp": "2024-09-16T07:50:15.487972669" }, "human - bam - paired_end": { "content": [ @@ -182,13 +182,13 @@ ] ], [ - "versions.yml:md5,87af9bcdd32d550e7b1e2b995b5fa4aa" + "versions.yml:md5,6359bf4b480f99e14e14b9e7dcb2fd5a" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-17T13:31:43.988112588" + "timestamp": "2024-09-16T07:49:19.805942524" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index 5a85438e08a8..699c05ce8b66 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::samtools=1.20" + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/consensus/main.nf b/modules/nf-core/samtools/consensus/main.nf index 3339580682bc..6f66c5ae409a 100644 --- a/modules/nf-core/samtools/consensus/main.nf +++ b/modules/nf-core/samtools/consensus/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONSENSUS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_1': - 'biocontainers/samtools:1.20--h50ea8bc_1' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -37,7 +37,7 @@ process SAMTOOLS_CONSENSUS { cat <<-END_VERSIONS > versions.yml "${task.process}": - samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ @@ -54,7 +54,7 @@ process SAMTOOLS_CONSENSUS { cat <<-END_VERSIONS > versions.yml "${task.process}": - samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS """ } diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test b/modules/nf-core/samtools/consensus/tests/main.nf.test index bf321106a8d6..85163731d56c 100644 --- a/modules/nf-core/samtools/consensus/tests/main.nf.test +++ b/modules/nf-core/samtools/consensus/tests/main.nf.test @@ -16,8 +16,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ]) """ } @@ -39,9 +38,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) """ } } @@ -62,9 +59,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ]) """ } } @@ -87,9 +82,7 @@ nextflow_process { """ input[0] = Channel.of([ [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) - ]) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), ]) """ } } diff --git a/modules/nf-core/samtools/consensus/tests/main.nf.test.snap b/modules/nf-core/samtools/consensus/tests/main.nf.test.snap index afdc8617e8d1..6afeb5c3fe9f 100644 --- a/modules/nf-core/samtools/consensus/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/consensus/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:50.610585" + "timestamp": "2024-09-17T09:30:20.800066273" }, "sarscov2 - bam - stub": { "content": [ @@ -65,7 +65,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:54.651067" + "timestamp": "2024-09-17T09:30:38.211253068" }, "sarscov2 - bam - fasta": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -130,15 +130,15 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:42.303778" + "timestamp": "2024-09-17T09:29:47.601535754" }, "sarscov2 - bam - fastq": { "content": [ @@ -159,7 +159,7 @@ ], "3": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ], "fasta": [ [ @@ -177,14 +177,14 @@ ], "versions": [ - "versions.yml:md5,ae15c6f399e5f044212309e7b838cf69" + "versions.yml:md5,930b28ec23c0dafc0dae204dc9f4f13b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T13:48:46.516552" + "timestamp": "2024-09-17T09:30:06.666785126" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 03b7b5259db9..cf9253d10f2a 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 513629022bd5..a021254e8baa 100644 --- a/modules/nf-core/samtools/convert/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/convert/tests/main.nf.test.snap @@ -22,26 +22,26 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:34.618037105" + "timestamp": "2024-09-16T07:52:35.516411351" }, "bam_to_cram_versions": { "content": [ [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:29.165839679" + "timestamp": "2024-09-16T07:52:24.694454205" }, "stub": { "content": [ @@ -71,7 +71,7 @@ ] ], "4": [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ], "bai": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,b1040cd80ce16abb9b2c2902b62d5fcd" + "versions.yml:md5,5bc6eb42ab2a1ea6661f8ee998467ad6" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:40.258233921" + "timestamp": "2024-09-16T07:52:45.799885099" }, "bam_to_cram_index": { "content": [ diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/coverage/main.nf b/modules/nf-core/samtools/coverage/main.nf index af8438eafd6d..e386132fd840 100644 --- a/modules/nf-core/samtools/coverage/main.nf +++ b/modules/nf-core/samtools/coverage/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_COVERAGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap index 63e260514b40..b9ddb18df5a7 100644 --- a/modules/nf-core/samtools/coverage/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/coverage/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:47.4359515" + "timestamp": "2024-09-16T07:53:42.773351407" }, "test_samtools_coverage_bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:36.39684853" + "timestamp": "2024-09-16T07:53:22.798338025" }, "test_samtools_coverage_cram": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ], "coverage": [ [ @@ -94,14 +94,14 @@ ] ], "versions": [ - "versions.yml:md5,16dec2ad2e9aa7cc174e86b03ec99984" + "versions.yml:md5,9c876b9db54dc710c87c404e4b28243c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:41:42.036690983" + "timestamp": "2024-09-16T07:53:32.409876082" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/cramsize/environment.yml b/modules/nf-core/samtools/cramsize/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/cramsize/environment.yml +++ b/modules/nf-core/samtools/cramsize/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/cramsize/main.nf b/modules/nf-core/samtools/cramsize/main.nf index c5ba5e037232..1e1b378aef32 100644 --- a/modules/nf-core/samtools/cramsize/main.nf +++ b/modules/nf-core/samtools/cramsize/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CRAMSIZE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(cram) diff --git a/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap b/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap index 834fe42484a2..39aa62365a2f 100644 --- a/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/cramsize/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ], "size": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-03T13:38:57.726189593" + "timestamp": "2024-09-16T07:54:30.618612676" }, "human - cram": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ], "size": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,2814b0d0507520469838cbceb7516836" + "versions.yml:md5,5327ab7fae1c6edda8ddcf3d7f7d51b2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-03T13:38:46.273448099" + "timestamp": "2024-09-16T07:54:20.179335064" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/depth/main.nf b/modules/nf-core/samtools/depth/main.nf index c6fc529f7869..3af598d6c234 100644 --- a/modules/nf-core/samtools/depth/main.nf +++ b/modules/nf-core/samtools/depth/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_DEPTH { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta1), path(bam) diff --git a/modules/nf-core/samtools/depth/tests/main.nf.test.snap b/modules/nf-core/samtools/depth/tests/main.nf.test.snap index eea108d33510..f5523cbf7656 100644 --- a/modules/nf-core/samtools/depth/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/depth/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ], "tsv": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:57:20.065271" + "timestamp": "2024-09-16T07:55:28.207892316" }, "test-samtools-depth": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ], "tsv": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7e29632bc14d18f38d63e78a08a73175" + "versions.yml:md5,8a21701d45a94582920fea7e0ba15eec" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:57:13.724175" + "timestamp": "2024-09-16T07:55:17.233534429" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/dict/main.nf b/modules/nf-core/samtools/dict/main.nf index 52be415f0b76..707a72e48378 100644 --- a/modules/nf-core/samtools/dict/main.nf +++ b/modules/nf-core/samtools/dict/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_DICT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/dict/tests/main.nf.test.snap b/modules/nf-core/samtools/dict/tests/main.nf.test.snap index 66d7b1fcff5c..ca039e7cd8a6 100644 --- a/modules/nf-core/samtools/dict/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/dict/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d" + "versions.yml:md5,6903afebec7d19e8beeb0f903a782a2c" ], "dict": [ [ @@ -24,27 +24,27 @@ ] ], "versions": [ - "versions.yml:md5,47f9e889ed1e779cb54e61d707a7135d" + "versions.yml:md5,6903afebec7d19e8beeb0f903a782a2c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-18T09:43:30.509703257" + "timestamp": "2024-09-16T07:57:07.279372555" }, "sarscov2 - fasta": { "content": [ "@HD\tVN:1.0\tSO:unsorted", [ - "versions.yml:md5,0af6b2d2d6d9d96bc5abe98b99b91446" + "versions.yml:md5,f6b1fc0172793465c9e43110de9f3a4f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-30T12:12:31.201483952" + "timestamp": "2024-09-16T07:56:55.930509023" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index bdcdbc954df0..28c0a81cf797 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3223b72bc6ea..1bbb3ec2b075 100644 --- a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -36,15 +36,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:14.779784761" + "timestamp": "2024-09-16T07:57:47.450887871" }, "test_samtools_faidx_bgzip": { "content": [ @@ -71,7 +71,7 @@ ] ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -95,15 +95,15 @@ ] ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:20.256633877" + "timestamp": "2024-09-16T07:58:04.804905659" }, "test_samtools_faidx_fasta": { "content": [ @@ -124,7 +124,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -142,15 +142,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:25.632577273" + "timestamp": "2024-09-16T07:58:23.831268154" }, "test_samtools_faidx_stub_fasta": { "content": [ @@ -171,7 +171,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ [ @@ -189,15 +189,15 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:31.058424849" + "timestamp": "2024-09-16T07:58:35.600243706" }, "test_samtools_faidx_stub_fai": { "content": [ @@ -218,7 +218,7 @@ ], "3": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ], "fa": [ @@ -236,14 +236,14 @@ ], "versions": [ - "versions.yml:md5,2db78952923a61e05d50b95518b21856" + "versions.yml:md5,6bbe80a2e14bd61202ca63e12d66027f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:36.479929617" + "timestamp": "2024-09-16T07:58:54.705460167" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fasta/main.nf b/modules/nf-core/samtools/fasta/main.nf index 056f2f4ec915..1c42141a3dc8 100644 --- a/modules/nf-core/samtools/fasta/main.nf +++ b/modules/nf-core/samtools/fasta/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FASTA { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fasta/tests/main.nf.test.snap b/modules/nf-core/samtools/fasta/tests/main.nf.test.snap index 36cdb60e8cda..6c26c7e8b4f2 100644 --- a/modules/nf-core/samtools/fasta/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fasta/tests/main.nf.test.snap @@ -8,27 +8,27 @@ "test_singleton.fasta.gz", "test_other.fasta.gz", [ - "versions.yml:md5,169b03a7e4a82c620276542932c1312d" + "versions.yml:md5,da649728a4a937a64cb8865ebc9ace81" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:51:59.909648" + "timestamp": "2024-09-16T07:59:47.290462747" }, "test-samtools-fasta-interleave": { "content": [ ">ERR5069949.2151832/1", "test_other.fasta.gz", [ - "versions.yml:md5,169b03a7e4a82c620276542932c1312d" + "versions.yml:md5,da649728a4a937a64cb8865ebc9ace81" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:52:04.127593" + "timestamp": "2024-09-16T07:59:59.597655297" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/fastq/main.nf b/modules/nf-core/samtools/fastq/main.nf index 6796c02b6825..136744d5aadc 100644 --- a/modules/nf-core/samtools/fastq/main.nf +++ b/modules/nf-core/samtools/fastq/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FASTQ { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap index 1ba09d3a3bac..10e5cd3d77ff 100644 --- a/modules/nf-core/samtools/fastq/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fastq/tests/main.nf.test.snap @@ -93,26 +93,26 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:40.362380302" + "timestamp": "2024-09-16T08:00:41.44921616" }, "bam_verinterleave_sions": { "content": [ [ - "versions.yml:md5,3a8725ed574091b661fbc64754bfcef1" + "versions.yml:md5,11e074d69900de5a7dfdbe1fb4e789fd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:45.632731997" + "timestamp": "2024-09-16T08:00:56.47781168" }, "bam_singleton": { "content": [ diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/fixmate/main.nf b/modules/nf-core/samtools/fixmate/main.nf index 6d29ae2da74f..c8169fcba540 100644 --- a/modules/nf-core/samtools/fixmate/main.nf +++ b/modules/nf-core/samtools/fixmate/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FIXMATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap b/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap index e9507d5d054f..a178a78ca769 100644 --- a/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/fixmate/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,57175fc36f563ce7907bc6d1c0dd1625" + "versions.yml:md5,d1afb9aa7c14a683e2a0b8a43daa5d31" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:45.339827663" + "timestamp": "2024-09-16T08:01:53.33860034" }, "bam": { "content": [ diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/flagstat/main.nf b/modules/nf-core/samtools/flagstat/main.nf index 754d84b73fc7..4a49972747d5 100644 --- a/modules/nf-core/samtools/flagstat/main.nf +++ b/modules/nf-core/samtools/flagstat/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FLAGSTAT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap index 23989c612099..04c3852b26cc 100644 --- a/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/flagstat/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:28.002887" + "timestamp": "2024-09-16T08:02:58.866491759" }, "BAM": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ], "flagstat": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f606681ef971cbb548a4d9e3fbabdbc2" + "versions.yml:md5,108a155f2d4a99f50bf3176904208d27" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:13.330971" + "timestamp": "2024-09-16T08:02:47.383332837" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/getrg/main.nf b/modules/nf-core/samtools/getrg/main.nf index 8f41ad3d4aca..fdd29470543a 100644 --- a/modules/nf-core/samtools/getrg/main.nf +++ b/modules/nf-core/samtools/getrg/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_GETRG { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/getrg/tests/main.nf.test.snap b/modules/nf-core/samtools/getrg/tests/main.nf.test.snap index 338d5e7711f3..36e1130f7c53 100644 --- a/modules/nf-core/samtools/getrg/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/getrg/tests/main.nf.test.snap @@ -5,13 +5,13 @@ "@RG\tID:1\tLB:lib1\tPL:ILLUMINA\tSM:test\tPU:barcode1" ], [ - "versions.yml:md5,b2f2aff0694b71ae5d2225d85bbfba9d" + "versions.yml:md5,40cf98b3daaf262b18e889ea734dbc40" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:28:18.826853" + "timestamp": "2024-09-16T08:11:06.35329516" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/idxstats/main.nf b/modules/nf-core/samtools/idxstats/main.nf index 2ea2a5ccdeda..c4b5a0a3f538 100644 --- a/modules/nf-core/samtools/idxstats/main.nf +++ b/modules/nf-core/samtools/idxstats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IDXSTATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap index a5ac8104e684..2cc89a3b8334 100644 --- a/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/idxstats/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:56.180093" + "timestamp": "2024-09-16T08:11:56.466856235" }, "bam": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ], "idxstats": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7acbcb2a8ec6436ba7b2916d3ff13351" + "versions.yml:md5,c8d7394830c3c1e5be150589571534fb" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:17:41.408704" + "timestamp": "2024-09-16T08:11:46.311550359" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/import/main.nf b/modules/nf-core/samtools/import/main.nf index 954a8052003e..e0a51c03371a 100644 --- a/modules/nf-core/samtools/import/main.nf +++ b/modules/nf-core/samtools/import/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_IMPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b9ea6..311756102d35 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199cea7d..72d65e81af3a 100644 --- a/modules/nf-core/samtools/index/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -18,7 +18,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -36,15 +36,15 @@ ] ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:53.9057" + "timestamp": "2024-09-16T08:21:25.261127166" }, "crai - stub": { "content": [ @@ -65,7 +65,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -83,15 +83,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:45.931558" + "timestamp": "2024-09-16T08:21:12.653194876" }, "bai - stub": { "content": [ @@ -112,7 +112,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -130,28 +130,28 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:34.807525" + "timestamp": "2024-09-16T08:21:01.854932651" }, "csi": { "content": [ "test.paired_end.sorted.bam.csi", [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:52:55.688799" + "timestamp": "2024-09-16T08:20:51.485364222" }, "crai": { "content": [ @@ -172,7 +172,7 @@ ] ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ @@ -190,15 +190,15 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:17.609533" + "timestamp": "2024-09-16T08:20:40.518873972" }, "bai": { "content": [ @@ -219,7 +219,7 @@ ], "3": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ], "bai": [ [ @@ -237,14 +237,14 @@ ], "versions": [ - "versions.yml:md5,802c9776d9c5e95314e888cf18e96d77" + "versions.yml:md5,5e09a6fdf76de396728f877193d72315" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:51:04.16585" + "timestamp": "2024-09-16T08:20:21.184050361" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/markdup/main.nf b/modules/nf-core/samtools/markdup/main.nf index 9129c55b2f55..8453bf82bae1 100644 --- a/modules/nf-core/samtools/markdup/main.nf +++ b/modules/nf-core/samtools/markdup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MARKDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/markdup/tests/main.nf.test b/modules/nf-core/samtools/markdup/tests/main.nf.test new file mode 100644 index 000000000000..acfbd1c166e4 --- /dev/null +++ b/modules/nf-core/samtools/markdup/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process SAMTOOLS_MARKDUP" + script "../main.nf" + process "SAMTOOLS_MARKDUP" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/fixmate" + tag "samtools/sort" + tag "samtools/markdup" + + test("sarscov2 - bam") { + setup { + run("SAMTOOLS_FIXMATE") { + script "../../fixmate/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), + ] + """ + } + } + run("SAMTOOLS_SORT") { + script "../../sort/main.nf" + process { + """ + input[0] = SAMTOOLS_FIXMATE.out.bam + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + } + when { + process { + """ + input[0] = SAMTOOLS_SORT.out.bam + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + input[1] = [ + [ id:'fasta' ], + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/markdup/tests/main.nf.test.snap b/modules/nf-core/samtools/markdup/tests/main.nf.test.snap new file mode 100644 index 000000000000..4e7cbf5ead54 --- /dev/null +++ b/modules/nf-core/samtools/markdup/tests/main.nf.test.snap @@ -0,0 +1,96 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:46:57.510270753" + }, + "sarscov2 - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,e73ea77e3857e7c6b0e6db2ec660361f" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.markdup.bam:md5,e73ea77e3857e7c6b0e6db2ec660361f" + ] + ], + "cram": [ + + ], + "sam": [ + + ], + "versions": [ + "versions.yml:md5,4ce5394244e549f97b8250b7dfad71ba" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:51:17.068686604" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/markdup/nextflow.config b/modules/nf-core/samtools/markdup/tests/nextflow.config similarity index 60% rename from tests/modules/nf-core/samtools/markdup/nextflow.config rename to modules/nf-core/samtools/markdup/tests/nextflow.config index 0d7fb4f5597d..1a2b52b98880 100644 --- a/tests/modules/nf-core/samtools/markdup/nextflow.config +++ b/modules/nf-core/samtools/markdup/tests/nextflow.config @@ -1,24 +1,14 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: SAMTOOLS_COLLATE { ext.prefix = { "${meta.id}.collate" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_FIXMATE { ext.prefix = { "${meta.id}.fixmate" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_SORT { ext.prefix = { "${meta.id}.sorted" } - publishDir = [ enabled: false ] } - withName: SAMTOOLS_MARKDUP { ext.prefix = { "${meta.id}.markdup" } } - } diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 693b1d80f400..34da4c7c8703 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input_files, stageAs: "?/*") diff --git a/modules/nf-core/samtools/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 17bc846fa280..0a41e01af635 100644 --- a/modules/nf-core/samtools/merge/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/merge/tests/main.nf.test.snap @@ -80,14 +80,14 @@ "bam_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:35.851936597" + "timestamp": "2024-09-16T09:16:30.476887194" }, "bams_csi": { "content": [ @@ -124,14 +124,14 @@ "bams_stub_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:41.405707643" + "timestamp": "2024-09-16T09:16:52.203823961" }, "bam_cram": { "content": [ @@ -158,14 +158,14 @@ "bams_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:45:51.695689923" + "timestamp": "2024-09-16T08:29:57.524363148" }, "crams_bam": { "content": [ @@ -182,14 +182,14 @@ "crams_versions": { "content": [ [ - "versions.yml:md5,84dab54b9812780df48f5cecef690c34" + "versions.yml:md5,d51d18a97513e370e43f0c891c51dfc4" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:46:30.185392319" + "timestamp": "2024-09-16T09:16:06.977096207" }, "bam_csi": { "content": [ diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf index b51f96d369ad..a45c6045b192 100644 --- a/modules/nf-core/samtools/mpileup/main.nf +++ b/modules/nf-core/samtools/mpileup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MPILEUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(intervals) path fasta diff --git a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap index 76b2086b40b3..fb6b6f1b7d00 100644 --- a/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/mpileup/tests/main.nf.test.snap @@ -2,26 +2,26 @@ "bam_bed_versions": { "content": [ [ - "versions.yml:md5,449485eab74a465dc9023760be2c12a1" + "versions.yml:md5,0ad5d578348ec8f358197302530db925" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:41.535946155" + "timestamp": "2024-09-16T09:20:04.969588285" }, "bam_bed_fasta_versions": { "content": [ [ - "versions.yml:md5,449485eab74a465dc9023760be2c12a1" + "versions.yml:md5,0ad5d578348ec8f358197302530db925" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:46.787790118" + "timestamp": "2024-09-16T09:20:30.887599345" }, "bam_bed_mpileup": { "content": [ diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/reheader/main.nf b/modules/nf-core/samtools/reheader/main.nf index 2ffe8de2be84..063854206f25 100644 --- a/modules/nf-core/samtools/reheader/main.nf +++ b/modules/nf-core/samtools/reheader/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_REHEADER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0': - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0': + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(bam) @@ -41,7 +41,7 @@ process SAMTOOLS_REHEADER { """ touch ${prefix}.bam - ccat <<-END_VERSIONS > versions.yml + cat <<-END_VERSIONS > versions.yml "${task.process}": samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') END_VERSIONS diff --git a/modules/nf-core/samtools/reheader/tests/chrdel.config b/modules/nf-core/samtools/reheader/tests/chrdel.config new file mode 100644 index 000000000000..7b5da49a40b8 --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/chrdel.config @@ -0,0 +1,6 @@ +process { + withName: SAMTOOLS_REHEADER { + ext.args = "--command 'sed -E \"s/^(@SQ.*)(\\tSN:)chr/\\1\\2/\"'" + ext.prefix = { "${meta.id}_chrDel" } + } +} diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test b/modules/nf-core/samtools/reheader/tests/main.nf.test new file mode 100644 index 000000000000..53142525d15d --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process SAMTOOLS_REHEADER" + script "../main.nf" + process "SAMTOOLS_REHEADER" + + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/reheader" + + test("homo_sapiens - chrdel") { + config "./chrdel.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - rgdel") { + config "./rgdel.config" + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/samtools/reheader/tests/main.nf.test.snap b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap new file mode 100644 index 000000000000..885ee35041b5 --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "homo_sapiens - chrdel": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_chrDel.bam:md5,957d2d542fb9bbd6511df9c0b5069ce4" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test_chrDel.bam:md5,957d2d542fb9bbd6511df9c0b5069ce4" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:28:17.577422205" + }, + "homo_sapiens - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:26:34.99215454" + }, + "homo_sapiens - rgdel": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_rgDel.bam:md5,02e7512a76fd9df1905ee90558365b0c" + ] + ], + "1": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test_rgDel.bam:md5,02e7512a76fd9df1905ee90558365b0c" + ] + ], + "versions": [ + "versions.yml:md5,3ffd4092d9f7ad731794ab8691ea79af" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T08:23:30.403448169" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/reheader/tests/rgdel.config b/modules/nf-core/samtools/reheader/tests/rgdel.config new file mode 100644 index 000000000000..03a2dc8554f3 --- /dev/null +++ b/modules/nf-core/samtools/reheader/tests/rgdel.config @@ -0,0 +1,6 @@ +process { + withName: SAMTOOLS_REHEADER { + ext.args = "--command 'grep -v ^@RG'" + ext.prefix = { "${meta.id}_rgDel" } + } +} diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/sormadup/main.nf b/modules/nf-core/samtools/sormadup/main.nf index 9b39fd9532ae..e8ac9b1c7ee0 100644 --- a/modules/nf-core/samtools/sormadup/main.nf +++ b/modules/nf-core/samtools/sormadup/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORMADUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input) @@ -37,7 +37,6 @@ process SAMTOOLS_SORMADUP { """ samtools cat \\ - --threads $task.cpus \\ $args \\ ${input} \\ | \\ diff --git a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap index c4a5a6399cb2..0a38f7f0c37d 100644 --- a/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sormadup/tests/main.nf.test.snap @@ -30,7 +30,7 @@ ] ], "5": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ], "bam": [ [ @@ -60,15 +60,15 @@ ] ], "versions": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:23.721871158" + "timestamp": "2024-09-16T08:56:24.200237922" }, "sarscov2 - bam": { "content": [ @@ -79,7 +79,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,810247d7c843e3cb54872d97ed9df4a9" + "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" ] ], "1": [ @@ -101,7 +101,7 @@ ] ], "5": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ], "bam": [ [ @@ -109,7 +109,7 @@ "id": "test", "single_end": false }, - "test.bam:md5,810247d7c843e3cb54872d97ed9df4a9" + "test.bam:md5,e3fd51b4f67e7415fdf301e9f148b9cf" ] ], "crai": [ @@ -131,14 +131,14 @@ ] ], "versions": [ - "versions.yml:md5,25489d4ff726fa409219b51c519cfac5" + "versions.yml:md5,ad563b12da6299eec5c39564782d0814" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:44:18.300807204" + "timestamp": "2024-09-16T08:56:12.101922642" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index 8e019099c0f7..acfd9252ce4a 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_SORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta) , path(bam) @@ -32,7 +32,6 @@ process SAMTOOLS_SORT { """ samtools cat \\ - --threads $task.cpus \\ ${bam} \\ | \\ samtools sort \\ diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index da38d5d15c5d..2d6b29004325 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -20,14 +20,14 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:19:37.196205" + "timestamp": "2024-09-16T08:49:58.207549273" }, "bam - stub": { "content": [ @@ -57,7 +57,7 @@ ] ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ [ @@ -84,15 +84,15 @@ ] ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:46.580756" + "timestamp": "2024-09-16T08:50:08.630951018" }, "cram - stub": { "content": [ @@ -122,7 +122,7 @@ ], "4": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ], "bam": [ @@ -149,15 +149,15 @@ ], "versions": [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:57:30.505698" + "timestamp": "2024-09-16T08:50:19.061912443" }, "bam": { "content": [ @@ -167,7 +167,7 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,21c992d59615936b99f2ad008aa54400" + "test.sorted.bam:md5,34aa85e86abefe637f7a4a9887f016fc" ] ], [ @@ -180,13 +180,13 @@ ] ], [ - "versions.yml:md5,7a360de20e1d7a6f15a5e8fbe0a9c062" + "versions.yml:md5,2659b187d681241451539d4c53500b9f" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T15:54:25.872954" + "timestamp": "2024-09-16T08:49:43.971158333" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf index 982bc28e7fb5..493525a9e0e6 100644 --- a/modules/nf-core/samtools/stats/main.nf +++ b/modules/nf-core/samtools/stats/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_STATS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap index 3828f37880a4..df507be7a361 100644 --- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,c9d39b38c22de2057fc2f89949090975" + "test.stats:md5,a27fe55e49a341f92379bb20a65c6a06" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:24.885816" + "timestamp": "2024-09-16T09:29:16.767396182" }, "bam - stub": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -59,15 +59,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:20:39.310713" + "timestamp": "2024-09-16T09:29:29.721580274" }, "cram - stub": { "content": [ @@ -82,7 +82,7 @@ ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -94,15 +94,15 @@ ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:21:04.771199" + "timestamp": "2024-09-16T09:29:53.567964304" }, "bam": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "1": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ], "stats": [ [ @@ -125,18 +125,18 @@ "id": "test", "single_end": false }, - "test.stats:md5,d522a1fa016b259d6a55620ae53dcd63" + "test.stats:md5,d53a2584376d78942839e9933a34d11b" ] ], "versions": [ - "versions.yml:md5,b3b70b126f867fdbb7dcea5e36e49d4a" + "versions.yml:md5,15b91d8c0e0440332e0fe4df80957043" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T14:19:06.645466" + "timestamp": "2024-09-16T09:28:50.73610604" } } \ No newline at end of file diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index da2df5e43a40..09ad4c10750e 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::samtools=1.21 + - bioconda::htslib=1.21 diff --git a/modules/nf-core/samtools/view/main.nf b/modules/nf-core/samtools/view/main.nf index dc611448c3d2..37e05cec8874 100644 --- a/modules/nf-core/samtools/view/main.nf +++ b/modules/nf-core/samtools/view/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_VIEW { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 6bcce9fea70f..29e7aeb08ebd 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -56,14 +56,14 @@ "bam_stub_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:20.390692583" + "timestamp": "2024-09-16T09:26:24.461775464" }, "cram_to_bam_index_cram": { "content": [ @@ -169,6 +169,16 @@ }, "timestamp": "2024-02-12T19:37:56.490286" }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_csi": { "content": [ [ @@ -208,14 +218,14 @@ "cram_to_bam_index_qname_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:15.007493874" + "timestamp": "2024-09-16T09:25:51.953436682" }, "cram_to_bam_bam": { "content": [ @@ -240,14 +250,14 @@ "cram_to_bam_index_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:09.472376824" + "timestamp": "2024-09-16T09:25:14.475388399" }, "cram_to_bam_bai": { "content": [ @@ -264,14 +274,14 @@ "cram_to_bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:43:04.080050906" + "timestamp": "2024-09-16T09:24:49.673441798" }, "cram_bam": { "content": [ @@ -355,37 +365,17 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, - "cram_to_bam_index_qname_unselected": { - "content": [ - "test.unselected.bam" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.322874" - }, - "cram_to_bam_index_qname_unselected_csi": { - "content": [ - "test.unselected.bam.csi" - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.04.3" - }, - "timestamp": "2024-02-12T19:38:23.328458" - }, "bam_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-28T15:42:52.978954857" + "timestamp": "2024-09-16T09:23:27.151650338" }, "cram_to_bam_index_qname_cram": { "content": [ @@ -450,14 +440,24 @@ "cram_versions": { "content": [ [ - "versions.yml:md5,6cd41a9a3b4a95271ec011ea990a2838" + "versions.yml:md5,176db5ec46b965219604bcdbb3ef9e07" ] ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:24:12.95416913" + }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "23.04.3" }, - "timestamp": "2024-05-28T15:42:58.400776109" + "timestamp": "2024-02-12T19:38:23.322874" }, "bam_sam": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap index e0c32a77e3ae..ccb965763673 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap @@ -7,15 +7,15 @@ "id": "test", "single_end": false }, - "test.stats:md5,34e1f13bd6e6b78bb8a589560222e343" + "test.stats:md5,498621f92e86d55e4f7ae93170e6e733" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T07:42:00.089356713" + "timestamp": "2024-09-16T08:04:02.179870196" }, "test_bam_dedup_stats_samtools_umicollapse_flagstats": { "content": [ @@ -47,18 +47,18 @@ ] ], [ - "versions.yml:md5,15f852de3d9e3fb11c786d15873c5d16", + "versions.yml:md5,20605eb79c410c0ed179ba660d82f75b", + "versions.yml:md5,23617661d2c899996bee2b05db027e25", "versions.yml:md5,268e43f34038d4c6146ed050630f95b4", - "versions.yml:md5,543112ba38e0fae7ae41be77cf1e0791", - "versions.yml:md5,7f6271d4e25dc8c739f28a15399787db", - "versions.yml:md5,d241a309a3e0eecfe1d3fe6efa65515c" + "versions.yml:md5,e02a62a393a833778e16542eeed0d148", + "versions.yml:md5,ef00762e264b99ac45713dc0dedf4060" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-29T07:42:00.053427512" + "timestamp": "2024-09-16T08:04:02.126366857" }, "test_bam_dedup_stats_samtools_umicollapse_idxstats": { "content": [ diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap index 4fd70b5f326f..d39f9129b9a4 100644 --- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap @@ -6,7 +6,7 @@ { "id": "test" }, - "test.stats:md5,09d1bd8f10e000921202f7ea1cd0679e" + "test.stats:md5,84891a894010aeb882c4092db9248d2c" ] ], [ @@ -26,18 +26,18 @@ ] ], [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T11:53:11.53709" + "timestamp": "2024-09-16T08:04:23.444693448" }, "sarscov2_bam_bai - stub": { "content": [ @@ -67,7 +67,7 @@ ] ], "3": [ - + ], "4": [ [ @@ -94,10 +94,10 @@ ] ], "7": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ], "bai": [ @@ -117,7 +117,7 @@ ] ], "csi": [ - + ], "deduplog": [ [ @@ -152,18 +152,18 @@ ] ], "versions": [ - "versions.yml:md5,32b4a349a563fb5b01cf0688ae3ca860", - "versions.yml:md5,803d3f4d3992a7a597a09cf330bd46a4", - "versions.yml:md5,9b7824114bf90d4b60110ddaf149f1db", - "versions.yml:md5,f0864f64f8ebb81826a1cf5c14b77e69", + "versions.yml:md5,2bf4310f1d49429016f5633f965e9ed0", + "versions.yml:md5,306b85f2109aeac87f1bf0eed94e6940", + "versions.yml:md5,db76f947845712952426efae5356018f", + "versions.yml:md5,eb35d8fd0745ef0ebacb9e26d4124e1d", "versions.yml:md5,f4935d4e563646266cc6bb4d75d0fb7d" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T16:34:35.959581" + "timestamp": "2024-09-16T08:04:43.790052381" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index aecaef9350a2..093d9c8c3967 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -5,20 +5,20 @@ "test.cram.crai:md5,cb5268070f99cdd0d86f43613e5fc7db", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", - "test.stats:md5,372a7d9d9081aa009b21343a913beb14", + "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:50:25.483402093" + "timestamp": "2024-09-16T08:06:04.991702832" }, "sarscov2 - bam - stub": { "content": [ @@ -87,11 +87,11 @@ ] ], "9": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ [ @@ -157,19 +157,19 @@ ] ], "versions": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:40:02.492073" + "timestamp": "2024-09-16T08:06:20.672273462" }, "homo_sapiens - cram - stub": { "content": [ @@ -232,11 +232,11 @@ ] ], "9": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -296,19 +296,19 @@ ] ], "versions": [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:40:24.423583" + "timestamp": "2024-09-16T08:06:36.739909544" }, "sarscov2 - bam": { "content": [ @@ -316,19 +316,19 @@ "test.bam.bai:md5,be9485a644813773fb893a0a6b9b977c", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", - "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574", + "test.stats:md5,ba007b13981dad548358c7c957d41e12", [ - "versions.yml:md5,0d170c963555870ac9a0d438bf6c2f93", - "versions.yml:md5,3729819c49e6d8eed9ada247e5d77de1", - "versions.yml:md5,a62ca6eb27e59dd6f03a93fa8656e656", + "versions.yml:md5,39f93ad916207c307cdb142959a19e95", + "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", + "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", - "versions.yml:md5,fcf804c605f455127f2449403d70390c" + "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:50:01.597322113" + "timestamp": "2024-09-16T08:05:46.507645441" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap index b7f4da177eea..c3c9a0492efa 100644 --- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap @@ -25,22 +25,22 @@ "id": "test", "single_end": false }, - "test.stats:md5,d32de3b3716a11039cef2367c3c1a56e" + "test.stats:md5,2fe0f3a7a1f07906061c1dadb62e0d05" ] ], [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:02:44.34964" + "timestamp": "2024-09-16T08:26:24.36986488" }, "test_bam_sort_stats_samtools_paired_end": { "content": [ @@ -68,22 +68,22 @@ "id": "test", "single_end": false }, - "test.stats:md5,cca83e4fc9406fc3875b5e60055d6574" + "test.stats:md5,ba007b13981dad548358c7c957d41e12" ] ], [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:03:02.583095" + "timestamp": "2024-09-16T08:26:38.683996037" }, "test_bam_sort_stats_samtools_single_end - stub": { "content": [ @@ -137,11 +137,11 @@ ] ], "6": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ], "bai": [ [ @@ -192,19 +192,19 @@ ] ], "versions": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:03:22.328703" + "timestamp": "2024-09-16T08:07:18.896460047" }, "test_bam_sort_stats_samtools_paired_end - stub": { "content": [ @@ -258,11 +258,11 @@ ] ], "6": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ], "bai": [ [ @@ -313,18 +313,18 @@ ] ], "versions": [ - "versions.yml:md5,494b5530a1aa29fd5867cf655bebbfe1", - "versions.yml:md5,9fcb0cd845bfb1f89d83201bb20649b4", - "versions.yml:md5,bacc323ec4055d6f69f07a09089772d1", - "versions.yml:md5,ce946e97097c6a9ccf834a3f91f6da30", - "versions.yml:md5,d6c8dae685f1b7d050165fc15c7a20b5" + "versions.yml:md5,032c89015461d597fcc5a5331b619d0a", + "versions.yml:md5,416c5e4a374c61167db999b0e400e3cf", + "versions.yml:md5,721391fd94c417808516480c9451c6fd", + "versions.yml:md5,9e12386b91a2977d23292754e3bcb522", + "versions.yml:md5,c294c162aeb09862cc5e55b602647452" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:03:38.833662" + "timestamp": "2024-09-16T08:07:39.028688324" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap index a3ddcc5ce4f3..8ca22526384c 100644 --- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap @@ -30,9 +30,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -62,17 +62,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:20:06.699297" + "timestamp": "2024-09-16T08:08:35.660286921" }, "test_bam_stats_samtools_single_end - stub": { "content": [ @@ -105,9 +105,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -137,17 +137,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:57.708621" + "timestamp": "2024-09-16T08:08:24.220305512" }, "test_bam_stats_samtools_paired_end_cram - stub": { "content": [ @@ -180,9 +180,9 @@ ] ], "3": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ], "flagstat": [ [ @@ -212,17 +212,17 @@ ] ], "versions": [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:20:17.051493" + "timestamp": "2024-09-16T08:08:54.206770141" }, "test_bam_stats_samtools_single_end": { "content": [ @@ -250,20 +250,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,4a0c429c661d6aa0b60acb9309da642d" + "test.stats:md5,291bb2393ec947140d12d42c2795b222" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:25.801394" + "timestamp": "2024-09-16T08:07:49.731645858" }, "test_bam_stats_samtools_paired_end": { "content": [ @@ -291,20 +291,20 @@ "id": "test", "single_end": true }, - "test.stats:md5,7afd486ad6abb9a2a3dac90c99e1d87b" + "test.stats:md5,8140d69cdedd77570ca1d7618a744e16" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:36.158768" + "timestamp": "2024-09-16T08:08:01.421996172" }, "test_bam_stats_samtools_paired_end_cram": { "content": [ @@ -332,19 +332,19 @@ "id": "test", "single_end": false }, - "test.stats:md5,16b59a1f2c99d9fe30f711adc3ebe32d" + "test.stats:md5,1622856127bafd6cdbadee9cd64ec9b7" ] ], [ - "versions.yml:md5,3c485730f712b115bcdc235e7294133b", - "versions.yml:md5,90f593a26a2d53e0f0345df7888f448e", - "versions.yml:md5,9ae003814e63a0907d52eec64d5d3ca3" + "versions.yml:md5,73c55059ed478cd2f9cd93dd3185da3a", + "versions.yml:md5,80d8653e01575b3c381d87073f672fb5", + "versions.yml:md5,cb889532237a2f3d813978ac14a12d51" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:19:46.625907" + "timestamp": "2024-09-16T08:08:12.640915756" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap index 8ff1e9c51878..2c6d8787ba17 100644 --- a/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_subsampledepth_samtools/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "subsample_fraction": 0.06201800538763442, "depth": 2 }, - "NA12878.bam:md5,c998482010b83365a4889c3fa75ac578", + "NA12878.bam:md5,f9f41668c064cb54051f77a18bd6a258", "NA12878.bam.csi:md5,0b4abd161cdcc2b51571c9cc651df354" ], [ @@ -18,7 +18,7 @@ "subsample_fraction": 0.12403601077526884, "depth": 4 }, - "NA12878.bam:md5,d6045df32f7c77d5c863b2068739faa9", + "NA12878.bam:md5,766247cca7d1ccff1352ecc3d47fe4be", "NA12878.bam.csi:md5,3f8f9a17463b6c2391c632681d3f253a" ], [ @@ -27,7 +27,7 @@ "subsample_fraction": 0.062137851766009305, "depth": 2 }, - "NA19401.bam:md5,6b144e7adc1f9e6711aea0e4772c5937", + "NA19401.bam:md5,dd327e50a1d4ba3a8ccaa07a587a2ecf", "NA19401.bam.csi:md5,36c29896003f2de5306ff427a969058c" ], [ @@ -36,14 +36,14 @@ "subsample_fraction": 0.12427570353201861, "depth": 4 }, - "NA19401.bam:md5,3b0d20e5f44952135a547c6230117460", - "NA19401.bam.csi:md5,b44701d7d4de827cc1b83aaeb397deaf" + "NA19401.bam:md5,f678431058d8b4963f09fa3431681756", + "NA19401.bam.csi:md5,14a9e8d58a46360917263c22c07dea41" ] ], "1": [ - "versions.yml:md5,8019e4c6fa3c1ddea25d64d6bfe5651f", + "versions.yml:md5,0b62e253d214b752ae075e2f90d5deaa", "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb", - "versions.yml:md5,f134df55b5047c5a8222ca04cf5ec501" + "versions.yml:md5,fb8f3d6cc806f7d5965e184c4d42fbeb" ], "bam_subsampled": [ [ @@ -52,7 +52,7 @@ "subsample_fraction": 0.06201800538763442, "depth": 2 }, - "NA12878.bam:md5,c998482010b83365a4889c3fa75ac578", + "NA12878.bam:md5,f9f41668c064cb54051f77a18bd6a258", "NA12878.bam.csi:md5,0b4abd161cdcc2b51571c9cc651df354" ], [ @@ -61,7 +61,7 @@ "subsample_fraction": 0.12403601077526884, "depth": 4 }, - "NA12878.bam:md5,d6045df32f7c77d5c863b2068739faa9", + "NA12878.bam:md5,766247cca7d1ccff1352ecc3d47fe4be", "NA12878.bam.csi:md5,3f8f9a17463b6c2391c632681d3f253a" ], [ @@ -70,7 +70,7 @@ "subsample_fraction": 0.062137851766009305, "depth": 2 }, - "NA19401.bam:md5,6b144e7adc1f9e6711aea0e4772c5937", + "NA19401.bam:md5,dd327e50a1d4ba3a8ccaa07a587a2ecf", "NA19401.bam.csi:md5,36c29896003f2de5306ff427a969058c" ], [ @@ -79,14 +79,14 @@ "subsample_fraction": 0.12427570353201861, "depth": 4 }, - "NA19401.bam:md5,3b0d20e5f44952135a547c6230117460", - "NA19401.bam.csi:md5,b44701d7d4de827cc1b83aaeb397deaf" + "NA19401.bam:md5,f678431058d8b4963f09fa3431681756", + "NA19401.bam.csi:md5,14a9e8d58a46360917263c22c07dea41" ] ], "versions": [ - "versions.yml:md5,8019e4c6fa3c1ddea25d64d6bfe5651f", + "versions.yml:md5,0b62e253d214b752ae075e2f90d5deaa", "versions.yml:md5,b31618773ed8a31f8635bca3da001eeb", - "versions.yml:md5,f134df55b5047c5a8222ca04cf5ec501" + "versions.yml:md5,fb8f3d6cc806f7d5965e184c4d42fbeb" ] }, [ @@ -125,9 +125,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-24T11:40:16.846985786" + "timestamp": "2024-09-16T07:55:54.476774933" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap index 408dabff07b1..f5a872982369 100644 --- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap @@ -34,7 +34,7 @@ "id": "test", "single_end": true }, - "test.stats:md5,845655ccfd1fd701b9f692f8db9508af" + "test.stats:md5,0ebab7bf6149e6378b263997d7073067" ] ], [ @@ -47,19 +47,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:06.813423" + "timestamp": "2024-09-16T08:27:35.808393107" }, "sarscov2 - bam - single_end - stub": { "content": [ @@ -134,12 +134,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -211,20 +211,20 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:23.861012" + "timestamp": "2024-09-16T08:10:09.451605417" }, "sarscov2 - bam - paired_end": { "content": [ @@ -261,7 +261,7 @@ "id": "test", "single_end": false }, - "test.stats:md5,603fa8c9e0e9eb3769498fc989a29250" + "test.stats:md5,74b78cbd41df459e1037735f714cda4f" ] ], [ @@ -274,19 +274,19 @@ ] ], [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:36:25.071168" + "timestamp": "2024-09-16T08:28:01.671969576" }, "sarscov2 - bam - paired_end - stub": { "content": [ @@ -361,12 +361,12 @@ ] ], "9": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ], "bai": [ [ @@ -438,19 +438,19 @@ ] ], "versions": [ - "versions.yml:md5,2d9432e15956fe71fe0ba811547acea6", - "versions.yml:md5,5fcbed7fee2404be4ecee6efab5914b8", - "versions.yml:md5,6b9d9eed13bf074965d1623a7e8a1741", - "versions.yml:md5,7767a57d88fff540ce475902df2e9e0a", + "versions.yml:md5,60b3d72afae0af5e6ba9d522ed2a865d", + "versions.yml:md5,6d9f7a6b7da221197ec81a78012dd306", + "versions.yml:md5,9bb4be2b6931086977d43355fd7c9edb", "versions.yml:md5,b4ccce0351e5718d36600858452dd4b1", - "versions.yml:md5,bb6710ee58b84a1ed212f9c599d84066" + "versions.yml:md5,e5ba15fd38b21e5c3050edc8cf2ab665", + "versions.yml:md5,e65b217d1cb47f1c163fdc37023c0909" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T19:36:44.894976" + "timestamp": "2024-09-16T08:10:28.136547114" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 07e2e0108a20..b9c06ca0132d 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -587,12 +587,6 @@ rtgtools/format: rtgtools/vcfeval: - modules/nf-core/rtgtools/vcfeval/** - tests/modules/nf-core/rtgtools/vcfeval/** -samtools/markdup: - - modules/nf-core/samtools/markdup/** - - tests/modules/nf-core/samtools/markdup/** -samtools/reheader: - - modules/nf-core/samtools/reheader/** - - tests/modules/nf-core/samtools/reheader/** scramble/clusteranalysis: - modules/nf-core/scramble/clusteranalysis/** - tests/modules/nf-core/scramble/clusteranalysis/** diff --git a/tests/modules/nf-core/samtools/markdup/main.nf b/tests/modules/nf-core/samtools/markdup/main.nf deleted file mode 100644 index 304180a1b4e7..000000000000 --- a/tests/modules/nf-core/samtools/markdup/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_COLLATE } from '../../../../../modules/nf-core/samtools/collate/main.nf' -include { SAMTOOLS_FIXMATE } from '../../../../../modules/nf-core/samtools/fixmate/main.nf' -include { SAMTOOLS_SORT } from '../../../../../modules/nf-core/samtools/sort/main.nf' -include { SAMTOOLS_MARKDUP } from '../../../../../modules/nf-core/samtools/markdup/main.nf' - -workflow test_samtools_markdup { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - fasta = [ - [ id:'fasta' ], // meta map - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - - SAMTOOLS_COLLATE ( input, [[],[]] ) - SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam ) - SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam, fasta ) - SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, fasta ) - -} diff --git a/tests/modules/nf-core/samtools/markdup/test.yml b/tests/modules/nf-core/samtools/markdup/test.yml deleted file mode 100644 index 0a365fa78f50..000000000000 --- a/tests/modules/nf-core/samtools/markdup/test.yml +++ /dev/null @@ -1,8 +0,0 @@ -- name: samtools markdup test_samtools_markdup - command: nextflow run ./tests/modules/nf-core/samtools/markdup -entry test_samtools_markdup -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/markdup/nextflow.config - tags: - - samtools/markdup - - samtools - files: - - path: output/samtools/test.markdup.bam - - path: output/samtools/versions.yml diff --git a/tests/modules/nf-core/samtools/reheader/main.nf b/tests/modules/nf-core/samtools/reheader/main.nf deleted file mode 100644 index 1cf6af1f235f..000000000000 --- a/tests/modules/nf-core/samtools/reheader/main.nf +++ /dev/null @@ -1,26 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_RGDEL} from '../../../../../modules/nf-core/samtools/reheader/main.nf' -include { SAMTOOLS_REHEADER as SAMTOOLS_REHEADER_CHRDEL} from '../../../../../modules/nf-core/samtools/reheader/main.nf' - -workflow test_samtools_reheader_chrdel { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - - SAMTOOLS_REHEADER_CHRDEL ( input ) -} - -workflow test_samtools_reheader_rgdel { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) - ] - - SAMTOOLS_REHEADER_RGDEL ( input ) -} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/reheader/nextflow.config b/tests/modules/nf-core/samtools/reheader/nextflow.config deleted file mode 100644 index 7a7320f19988..000000000000 --- a/tests/modules/nf-core/samtools/reheader/nextflow.config +++ /dev/null @@ -1,13 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: SAMTOOLS_REHEADER_CHRDEL { - ext.args = "--command 'sed -E \"s/^(@SQ.*)(\\tSN:)chr/\\1\\2/\"'" - ext.prefix = { "${meta.id}_chrDel" } - } - withName: SAMTOOLS_REHEADER_RGDEL { - ext.args = "--command 'grep -v ^@RG'" - ext.prefix = { "${meta.id}_rgDel" } - } - -} \ No newline at end of file diff --git a/tests/modules/nf-core/samtools/reheader/test.yml b/tests/modules/nf-core/samtools/reheader/test.yml deleted file mode 100644 index b35b79ab484c..000000000000 --- a/tests/modules/nf-core/samtools/reheader/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: samtools reheader test_samtools_reheader_chrdel - command: nextflow run ./tests/modules/nf-core/samtools/reheader -entry test_samtools_reheader_chrdel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/reheader/nextflow.config - tags: - - samtools/reheader - - samtools - files: - - path: output/samtools/test_chrDel.bam - - path: output/samtools/versions.yml - -- name: samtools reheader test_samtools_reheader_rgdel - command: nextflow run ./tests/modules/nf-core/samtools/reheader -entry test_samtools_reheader_rgdel -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/samtools/reheader/nextflow.config - tags: - - samtools/reheader - - samtools - files: - - path: output/samtools/test_rgDel.bam - - path: output/samtools/versions.yml From ba8aac9d0b2f34811800bafab168b638cf2ff3cc Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Wed, 18 Sep 2024 14:32:19 +0200 Subject: [PATCH 069/486] Add SVDB build (#6660) * Add SVDB build * Add SVDB build * Add SVDB build --- modules/nf-core/svdb/build/environment.yml | 5 + modules/nf-core/svdb/build/main.nf | 48 ++++++++ modules/nf-core/svdb/build/meta.yml | 38 ++++++ modules/nf-core/svdb/build/tests/main.nf.test | 111 ++++++++++++++++++ .../svdb/build/tests/main.nf.test.snap | 94 +++++++++++++++ modules/nf-core/svdb/build/tests/tags.yml | 2 + 6 files changed, 298 insertions(+) create mode 100644 modules/nf-core/svdb/build/environment.yml create mode 100644 modules/nf-core/svdb/build/main.nf create mode 100644 modules/nf-core/svdb/build/meta.yml create mode 100644 modules/nf-core/svdb/build/tests/main.nf.test create mode 100644 modules/nf-core/svdb/build/tests/main.nf.test.snap create mode 100644 modules/nf-core/svdb/build/tests/tags.yml diff --git a/modules/nf-core/svdb/build/environment.yml b/modules/nf-core/svdb/build/environment.yml new file mode 100644 index 000000000000..cd35cf488a5b --- /dev/null +++ b/modules/nf-core/svdb/build/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::svdb=2.8.1 diff --git a/modules/nf-core/svdb/build/main.nf b/modules/nf-core/svdb/build/main.nf new file mode 100644 index 000000000000..db3055e26c9c --- /dev/null +++ b/modules/nf-core/svdb/build/main.nf @@ -0,0 +1,48 @@ +process SVDB_BUILD { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/svdb:2.8.1--py39h5371cbf_0': + 'biocontainers/svdb:2.8.1--py39h5371cbf_0' }" + + input: + tuple val(meta), path(input) + val(input_type) + + output: + tuple val(meta), path("*.db"), emit: db + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if (!input_type.matches('folder|files')) { error "Unrecognised input type. Options are: 'folder', 'files'" } + + """ + svdb \\ + --build \\ + --$input_type $input \\ + --prefix ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.db + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + svdb: \$( echo \$(svdb) | head -1 | sed 's/usage: SVDB-\\([0-9]\\.[0-9]\\.[0-9]\\).*/\\1/' ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/svdb/build/meta.yml b/modules/nf-core/svdb/build/meta.yml new file mode 100644 index 000000000000..c5c5a99265db --- /dev/null +++ b/modules/nf-core/svdb/build/meta.yml @@ -0,0 +1,38 @@ +name: svdb_build +description: Build a structural variant database +keywords: + - structural variants + - build + - svdb +tools: + - svdb: + description: structural variant database software + homepage: https://github.com/J35P312/SVDB + documentation: https://github.com/J35P312/SVDB/blob/master/README.md + licence: ["MIT"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF file(s) or folder + pattern: "*" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - db: + type: file + description: SVDB database +authors: + - "@fellen31" diff --git a/modules/nf-core/svdb/build/tests/main.nf.test b/modules/nf-core/svdb/build/tests/main.nf.test new file mode 100644 index 000000000000..ccf18f2b28bd --- /dev/null +++ b/modules/nf-core/svdb/build/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process SVDB_BUILD" + script "modules/nf-core/svdb/build/main.nf" + process "SVDB_BUILD" + tag "modules" + tag "modules_nfcore" + tag "svdb" + tag "svdb/build" + + test("one VCF - files") { + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.db.get(0).get(1)).name, + process.out.versions + ).match() } + ) + } + } + + test("two VCFs - files") { + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) + ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + file(process.out.db.get(0).get(1)).name, + process.out.versions + ).match() } + ) + } + } + + test("one VCF - files -stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true) ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("two VCFs - files -stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/sv_query.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true) + ] + ]) + input[1] = 'files' + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/svdb/build/tests/main.nf.test.snap b/modules/nf-core/svdb/build/tests/main.nf.test.snap new file mode 100644 index 000000000000..9a9929573cea --- /dev/null +++ b/modules/nf-core/svdb/build/tests/main.nf.test.snap @@ -0,0 +1,94 @@ +{ + "one VCF - files": { + "content": [ + "test.db", + [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:37:21.374511177" + }, + "two VCFs - files": { + "content": [ + "test.db", + [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:37:27.968892336" + }, + "two VCFs - files -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ], + "db": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T11:40:04.558825564" + }, + "one VCF - files -stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ], + "db": [ + [ + { + "id": "test" + }, + "test.db:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,171626910c11bd4ea32d2dc4255dbba8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T10:54:45.735248435" + } +} \ No newline at end of file diff --git a/modules/nf-core/svdb/build/tests/tags.yml b/modules/nf-core/svdb/build/tests/tags.yml new file mode 100644 index 000000000000..7eb9b2ab82f4 --- /dev/null +++ b/modules/nf-core/svdb/build/tests/tags.yml @@ -0,0 +1,2 @@ +svdb/query: + - modules/nf-core/svdb/build/** From 6453bce4cf3c43f455e7528bd4e12c4a10268904 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Wed, 18 Sep 2024 16:44:42 +0200 Subject: [PATCH 070/486] Tcoffee stub tests (#6555) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Fix align module test * Fix nf-tests * update typos * Update snaps * Update modules/nf-core/tcoffee/align/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/align/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/alncompare/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * update tetss * update tests align * update tests * update irmsd test * Update modules/nf-core/tcoffee/align/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/alncompare/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/irmsd/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/irmsd/tests/main.nf.test Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/seqreformat/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/tcs/main.nf Co-authored-by: Jose Espinosa-Carrasco * Update modules/nf-core/tcoffee/tcs/meta.yml Co-authored-by: Jose Espinosa-Carrasco * remove changes in consensus * fix * update snap * add * add tree test * rerun * test * test --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco Co-authored-by: Maxime U Garcia --- .../nf-core/fastme/tests/main.nf.test.snap | 20 --- modules/nf-core/tcoffee/align/main.nf | 2 + .../nf-core/tcoffee/align/tests/main.nf.test | 72 +++++++--- .../tcoffee/align/tests/main.nf.test.snap | 98 ++++--------- modules/nf-core/tcoffee/alncompare/main.nf | 2 + .../tcoffee/alncompare/tests/main.nf.test | 32 ++++- .../alncompare/tests/main.nf.test.snap | 37 +++++ .../tcoffee/consensus/tests/main.nf.test | 56 ++++---- .../tcoffee/consensus/tests/main.nf.test.snap | 50 ++++--- modules/nf-core/tcoffee/irmsd/main.nf | 6 +- modules/nf-core/tcoffee/irmsd/meta.yml | 8 ++ .../nf-core/tcoffee/irmsd/tests/main.nf.test | 87 +++++++----- .../tcoffee/irmsd/tests/main.nf.test.snap | 16 ++- modules/nf-core/tcoffee/seqreformat/main.nf | 2 + modules/nf-core/tcoffee/seqreformat/meta.yml | 2 +- .../tcoffee/seqreformat/tests/main.nf.test | 36 ++++- .../seqreformat/tests/main.nf.test.snap | 29 +++- modules/nf-core/tcoffee/tcs/environment.yml | 4 +- modules/nf-core/tcoffee/tcs/main.nf | 4 +- modules/nf-core/tcoffee/tcs/meta.yml | 5 + modules/nf-core/tcoffee/tcs/tests/lib.config | 2 + .../nf-core/tcoffee/tcs/tests/main.nf.test | 60 ++++++-- .../tcoffee/tcs/tests/main.nf.test.snap | 130 +++++------------- 23 files changed, 421 insertions(+), 339 deletions(-) diff --git a/modules/nf-core/fastme/tests/main.nf.test.snap b/modules/nf-core/fastme/tests/main.nf.test.snap index e892b351eae4..aa8ffbf7ff77 100644 --- a/modules/nf-core/fastme/tests/main.nf.test.snap +++ b/modules/nf-core/fastme/tests/main.nf.test.snap @@ -54,10 +54,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, "timestamp": "2024-03-19T10:03:04.842045" }, "versions": { @@ -66,10 +62,6 @@ "versions.yml:md5,0e7f28ae349efffa1ef75c2279e975b6" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, "timestamp": "2024-03-19T10:02:58.72899" }, "stats_boot": { @@ -90,10 +82,6 @@ "" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, "timestamp": "2024-03-19T10:09:35.813028" }, "setoxin - phylip - with_tree": { @@ -151,10 +139,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, "timestamp": "2024-03-19T10:02:51.77025" }, "setoxin - phylip - basic": { @@ -212,10 +196,6 @@ ] } ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.0" - }, "timestamp": "2024-03-19T10:02:44.598308" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf index a14964c92764..45be6226cb2a 100644 --- a/modules/nf-core/tcoffee/align/main.nf +++ b/modules/nf-core/tcoffee/align/main.nf @@ -57,6 +57,8 @@ process TCOFFEE_ALIGN { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' touch ${prefix}.aln${compress ? '.gz':''} cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test b/modules/nf-core/tcoffee/align/tests/main.nf.test index 4f136283d088..f0b1752ca8f6 100644 --- a/modules/nf-core/tcoffee/align/tests/main.nf.test +++ b/modules/nf-core/tcoffee/align/tests/main.nf.test @@ -11,7 +11,7 @@ nextflow_process { tag "famsa/guidetree" tag "untar" - test("fasta - align_sequence") { + test("align_sequence - compressed - seatoxin") { config "./sequence.config" @@ -19,7 +19,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] input[2] = [[:],[],[]] @@ -31,13 +31,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.alignment).match("alignment")}, - { assert snapshot(process.out.versions).match("versions_uncomp") } + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }, ) } } - test("fasta - align_sequence - uncompressed") { + test("align_sequence - uncompressed - seatoxin") { config "./sequence.config" @@ -45,7 +45,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] input[2] = [[:],[],[]] @@ -57,13 +57,13 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.alignment).match("alignment - uncompressed")}, - { assert snapshot(process.out.versions).match("versions_comp") } + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") }, ) } } - test("sarscov2 - fasta - align_with_guide_tree") { + test("align_with_guide_tree - uncompressed - seatoxin") { config "./tree.config" @@ -74,7 +74,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] """ @@ -86,7 +86,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/alignment/informative_sites.fas', checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]} input[2] = [ [:], [], [] ] @@ -98,14 +98,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.alignment).match("alignment_guidetree")}, - { assert snapshot(process.out.versions).match("versions_guidetree") } + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }, ) } } - test("fasta - align_with_structure") { + test("align_with_structure - uncompressed - seatoxin") { config "./structure.config" @@ -116,7 +116,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) ] """ @@ -128,7 +128,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [ [:], [] ] input[2] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], [] ,file(dir).listFiles().collect()]} @@ -148,7 +148,7 @@ nextflow_process { } - test("fasta - align_with_lib") { + test("align_with_lib - seatoxin") { config "./lib.config" @@ -156,7 +156,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] input[2] = [[:],[],[]] @@ -168,10 +168,40 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.alignment).match("alignment - lib") }, - { assert path(process.out.lib.get(0).get(1)).getText().contains("1ahl") }, - { assert snapshot(process.out.versions).match("versions_lib") } + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }, + { assert snapshot(process.out.versions).match() + } ) } } + + test("align_sequence - uncompressed - seatoxin - stub") { + options "-stub" + config "./sequence.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[],[]] + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.alignment, + process.out.versions + ).match() + } + ) + } + } + } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap index dfef40a73527..ecf8eadbd13c 100644 --- a/modules/nf-core/tcoffee/align/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/align/tests/main.nf.test.snap @@ -6,125 +6,77 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, "timestamp": "2024-02-28T19:00:28.712838" }, - "versions_lib": { + "align_sequence - uncompressed - seatoxin": { "content": [ [ "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-19T14:04:06.031557" + "timestamp": "2024-09-16T10:38:34.006567221" }, - "alignment - uncompressed": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.aln:md5,bd1db08ad04514cc6d1334598c1a6ef0" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-28T18:59:54.582504" - }, - "versions_comp": { + "align_sequence - compressed - seatoxin": { "content": [ [ "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T18:59:54.593312" + "timestamp": "2024-09-16T10:38:18.99603304" }, - "versions_guidetree": { + "align_with_guide_tree - uncompressed - seatoxin": { "content": [ [ "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T19:00:10.618213" + "timestamp": "2024-09-16T10:38:48.044669392" }, - "alignment - lib": { + "align_with_lib - seatoxin": { "content": [ [ - [ - { - "id": "test" - }, - "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0" - ] + "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-19T13:57:39.653762" + "timestamp": "2024-09-16T10:47:34.909457138" }, - "alignment": { + "align_sequence - uncompressed - seatoxin - stub": { "content": [ [ [ { "id": "test" }, - "test.aln.gz:md5,bd1db08ad04514cc6d1334598c1a6ef0" + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-28T18:59:35.169119" - }, - "versions_uncomp": { - "content": [ + ], [ "versions.yml:md5,fb187c9186b50a8076d08cd3be3c1b70" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" - }, - "timestamp": "2024-02-28T18:59:35.2062" - }, - "alignment_guidetree": { - "content": [ - [ - [ - { - "id": "test" - }, - "test.aln.gz:md5,93bc8adfcd88f7913718eacc13da8e4a" - ] - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-28T19:00:10.611489" + "timestamp": "2024-09-16T12:55:10.267649283" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/alncompare/main.nf b/modules/nf-core/tcoffee/alncompare/main.nf index 043158a75ad1..e902120f468e 100644 --- a/modules/nf-core/tcoffee/alncompare/main.nf +++ b/modules/nf-core/tcoffee/alncompare/main.nf @@ -53,6 +53,8 @@ process TCOFFEE_ALNCOMPARE { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' touch "${prefix}.scores" cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test index 225a4f124655..66e5f204cbd7 100644 --- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test +++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test @@ -6,7 +6,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "tcoffee" - tag "tcoffee/alncompare" + tag "tcoffee/alncompare" test("seatoxin") { @@ -15,12 +15,36 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true), - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true), + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] """ } - + + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + test("seatoxin - stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true), + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + ] + """ + } + } then { diff --git a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap index d1fd92e4304b..20fd7a888779 100644 --- a/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/alncompare/tests/main.nf.test.snap @@ -1,4 +1,37 @@ { + "seatoxin - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d" + ], + "scores": [ + [ + { + "id": "test" + }, + "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,438507517a1a831c7b7a1571b1fdd98d" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:48:00.328461809" + }, "seatoxin": { "content": [ { @@ -26,6 +59,10 @@ ] } ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, "timestamp": "2024-01-22T17:08:59.494237269" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test b/modules/nf-core/tcoffee/consensus/tests/main.nf.test index 78aa567bf2df..5f013e3f9e7f 100644 --- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test +++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test @@ -8,20 +8,20 @@ nextflow_process { tag "modules_nfcore" tag "tcoffee" tag "tcoffee/consensus" - tag "tcoffee/align" + tag "magus/align" tag "pigz" - tag "famsa/guidetree" + tag "clustalo/guidetree" tag "famsa/align" config "./sequence.config" setup { - run("FAMSA_GUIDETREE") { - script "../../../famsa/guidetree/main.nf" + run("CLUSTALO_GUIDETREE") { + script "../../../clustalo/guidetree/main.nf" process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] """ } @@ -31,7 +31,7 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] input[2] = false @@ -39,28 +39,27 @@ nextflow_process { """ } } - run("TCOFFEE_ALIGN") { - script "../../../tcoffee/align/main.nf" + run("MAGUS_ALIGN") { + script "../../../magus/align/main.nf" process { """ - input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + input[0] = [ [ id:'test2' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] - input[2] = [[:],[],[]] - input[3] = false + input[2] = false """ } - } + } } test("consensus - no tree - uncompressed - seatoxin ") { - + when { process { """ - msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple() + msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas input[1] = [[:],[]] input[2] = false @@ -71,41 +70,32 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.alignment, - process.out.versions - ).match() - } + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") } ) } } - test("consensus - tree - compressed- seatoxin") { - + test("consensus - tree - compressed- seatoxin") { when { process { """ - msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple() + msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas - input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]} + input[1] = CLUSTALO_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]} input[2] = true """ } } - then { assertAll( { assert process.success }, - { assert snapshot( - process.out.alignment, - process.out.versions - ).match() - } + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") } ) } } - test("consensus - stub") { options "-stub" @@ -113,7 +103,7 @@ nextflow_process { when { process { """ - msas = FAMSA_ALIGN.out.alignment.mix(TCOFFEE_ALIGN.out.alignment).groupTuple() + msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() input[0] = msas input[1] = [[:],[]] input[2] = false @@ -128,5 +118,5 @@ nextflow_process { ) } } - + } diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap index a0fe4f992ac7..ed50562d0e63 100644 --- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap @@ -2,23 +2,26 @@ "consensus - no tree - uncompressed - seatoxin ": { "content": [ [ - [ - { - "id": "test" - }, - "consensus.aln:md5,ed7fb1f7b7a9cd66e9b0c9d60d1b0e52" - ] - ], - [ + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ] ], - "timestamp": "2024-09-04T13:17:59.621521" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T13:54:43.924522245" }, "consensus - stub": { "content": [ { "0": [ + [ + { + "id": "test2" + }, + "consensus.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ], [ { "id": "test" @@ -27,9 +30,16 @@ ] ], "1": [ + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ], "alignment": [ + [ + { + "id": "test2" + }, + "consensus.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ], [ { "id": "test" @@ -38,26 +48,28 @@ ] ], "versions": [ + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ] } ], - "timestamp": "2024-09-04T13:18:15.69498" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T13:55:25.155000209" }, "consensus - tree - compressed- seatoxin": { "content": [ [ - [ - { - "id": "test" - }, - "consensus.aln.gz:md5,ed7fb1f7b7a9cd66e9b0c9d60d1b0e52" - ] - ], - [ + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ] ], - "timestamp": "2024-09-04T13:18:08.240517" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T13:55:03.627733582" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/irmsd/main.nf b/modules/nf-core/tcoffee/irmsd/main.nf index 95e6b61efb4f..be6b6a11bc57 100644 --- a/modules/nf-core/tcoffee/irmsd/main.nf +++ b/modules/nf-core/tcoffee/irmsd/main.nf @@ -8,8 +8,8 @@ process TCOFFEE_IRMSD { 'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }" input: - tuple val(meta), file (msa) - tuple val(meta2), file(template), file(structures) + tuple val(meta), path (msa) + tuple val(meta2), path(template), path(structures) output: tuple val(meta), path ("${prefix}.irmsd"), emit: irmsd @@ -44,6 +44,8 @@ process TCOFFEE_IRMSD { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${msa.baseName}" """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' touch ${prefix}.irmsd cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml index f55fca748cfd..e13e7ddadf34 100644 --- a/modules/nf-core/tcoffee/irmsd/meta.yml +++ b/modules/nf-core/tcoffee/irmsd/meta.yml @@ -27,10 +27,18 @@ input: type: file description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. pattern: "*.{aln,fa,fasta,fas}{.gz,}" + + - meta2: + type: map + description: | + Groovy Map containing information about the structures + e.g. [ id:'test', ... ] + - template: type: file description: Template file matching the structures to the sequences in the alignment. pattern: "*" + - structures: type: directory description: Directory containing the structures file matching the sequences in the alignment in PDB format diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test index 55a574a46162..dfb68629535c 100644 --- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test +++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test @@ -10,31 +10,43 @@ nextflow_process { tag "untar" tag "pigz/compress" - test("seatoxin") { + setup { - setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) + ] - run("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) - ] + """ + } + } - """ - } + run("PIGZ_COMPRESS") { + script "../../../pigz/compress/main.nf" + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + ] + + """ } } + } + + test("seatoxin") { when { process { """ input[0] = [ [ id:'test' ], // meta map - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] - input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} + input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} """ } @@ -51,38 +63,37 @@ nextflow_process { test("seatoxin - compressed") { - setup { - - run("UNTAR") { - script "../../../untar/main.nf" - process { - """ - input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) - ] - - """ - } + when { + process { + """ + input[0] = PIGZ_COMPRESS.out.archive + input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} + """ } - run("PIGZ_COMPRESS") { - script "../../../pigz/compress/main.nf" - process { - """ - input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) - ] + } - """ - } - } + then { + assertAll( + { assert process.success }, + { assert path(process.out.irmsd.get(0).get(1)).getText().contains("1ahl") } + ) } + } + + test("seatoxin - uncompressed - stub") { + + options "-stub" + when { process { """ - input[0] = PIGZ_COMPRESS.out.archive - input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + ] + input[1] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/templates/seatoxin-ref_template.txt", checkIfExists: true) ,file(dir).listFiles().collect()]} """ } @@ -91,7 +102,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert path(process.out.irmsd.get(0).get(1)).getText().contains("1ahl") } + { assert snapshot(process.out).match()} ) } diff --git a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap index c036642f18af..909d678c5caf 100644 --- a/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/irmsd/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "seatoxin": { + "seatoxin - uncompressed - stub": { "content": [ { "0": [ @@ -7,25 +7,29 @@ { "id": "test" }, - "setoxin.irmsd:md5,a8f49fb2621cdc9fe39690a813ad0ca5" + "setoxin.irmsd:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ - "versions.yml:md5,60646e38ef71127e3736a06c91c2983f" + "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6" ], "irmsd": [ [ { "id": "test" }, - "setoxin.irmsd:md5,a8f49fb2621cdc9fe39690a813ad0ca5" + "setoxin.irmsd:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ - "versions.yml:md5,60646e38ef71127e3736a06c91c2983f" + "versions.yml:md5,95ade8ac867efd9e18f850bb55b7c9b6" ] } ], - "timestamp": "2023-12-13T12:26:46.827121" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T10:15:36.874290895" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/seqreformat/main.nf b/modules/nf-core/tcoffee/seqreformat/main.nf index c4c31f835f87..04617b01ffd2 100644 --- a/modules/nf-core/tcoffee/seqreformat/main.nf +++ b/modules/nf-core/tcoffee/seqreformat/main.nf @@ -38,6 +38,8 @@ process TCOFFEE_SEQREFORMAT { def args = task.ext.args ?: '' prefix = task.ext.prefix ?: "${meta.id}" """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' touch "${prefix}.txt" cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml index 9c7d9ce99164..0571c7d875dc 100644 --- a/modules/nf-core/tcoffee/seqreformat/meta.yml +++ b/modules/nf-core/tcoffee/seqreformat/meta.yml @@ -19,7 +19,7 @@ input: Groovy Map containing sample information e.g. `[ id:'test' ]` - - fasta: + - infile: type: file description: Input file to be reformatted pattern: "*" diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test index 7a5492c51abc..1510e92075b8 100644 --- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test +++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test @@ -9,13 +9,13 @@ nextflow_process { tag "tcoffee" tag "tcoffee/seqreformat" - test("sarscov2 - bam") { + test("seatoxin") { when { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] """ } @@ -25,8 +25,36 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.formatted_file).match("formatted_file")}, - { assert snapshot(process.out.versions).match("versions") } + { assert snapshot( + process.out.formatted_file, + process.out.versions + ).match() + } + ) + } + } + + test("seatoxin - stub") { + options "-stub" + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + """ + } + } + + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.formatted_file, + process.out.versions + ).match() + } ) } } diff --git a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap index 150102ee3a87..185f24d8f55e 100644 --- a/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/seqreformat/tests/main.nf.test.snap @@ -1,23 +1,42 @@ { - "formatted_file": { + "seatoxin - stub": { "content": [ [ [ { "id": "test" }, - "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562" + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + [ + "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14" ] ], - "timestamp": "2023-11-28T11:56:22.705185493" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:53:55.165479364" }, - "versions": { + "seatoxin": { "content": [ + [ + [ + { + "id": "test" + }, + "test.txt:md5,fcd4691daf120c88ec5def7ac06fb562" + ] + ], [ "versions.yml:md5,68fb841e6e44274d430a1382bb0bbd14" ] ], - "timestamp": "2023-11-28T11:56:22.717235196" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T09:53:33.814075197" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml index 615d140e6bb7..26a17e709832 100644 --- a/modules/nf-core/tcoffee/tcs/environment.yml +++ b/modules/nf-core/tcoffee/tcs/environment.yml @@ -1,8 +1,6 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::t-coffee=13.46.0.919e8c6b" + - bioconda::t-coffee=13.46.0.919e8c6b - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/tcs/main.nf b/modules/nf-core/tcoffee/tcs/main.nf index 0c50f52a2331..9080a3174793 100644 --- a/modules/nf-core/tcoffee/tcs/main.nf +++ b/modules/nf-core/tcoffee/tcs/main.nf @@ -8,7 +8,7 @@ process TCOFFEE_TCS { 'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }" input: - tuple val(meta), path(msa) + tuple val(meta) , path(msa) tuple val(meta2), path(lib) output: @@ -63,6 +63,8 @@ process TCOFFEE_TCS { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' touch ${prefix}.tcs touch ${prefix}.scores diff --git a/modules/nf-core/tcoffee/tcs/meta.yml b/modules/nf-core/tcoffee/tcs/meta.yml index a28efad0ab87..7a13e79a8b61 100644 --- a/modules/nf-core/tcoffee/tcs/meta.yml +++ b/modules/nf-core/tcoffee/tcs/meta.yml @@ -29,6 +29,11 @@ input: type: file description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. pattern: "*.{aln,fa,fasta,fas}{.gz,}" + - meta2: + type: map + description: | + Groovy Map containing library information + e.g. [ id:'test', ... ] - lib: type: file description: lib file containing the alignment library of the given msa. diff --git a/modules/nf-core/tcoffee/tcs/tests/lib.config b/modules/nf-core/tcoffee/tcs/tests/lib.config index 56712f637983..610250ce2352 100644 --- a/modules/nf-core/tcoffee/tcs/tests/lib.config +++ b/modules/nf-core/tcoffee/tcs/tests/lib.config @@ -1,5 +1,7 @@ process { + withName: "TCOFFEE_ALIGN"{ ext.args = { "-output fasta_aln -out_lib sample_lib1.tc_lib" } } + } diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test b/modules/nf-core/tcoffee/tcs/tests/main.nf.test index 35636fff0755..d66a2cdaa319 100644 --- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test +++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test @@ -10,14 +10,14 @@ nextflow_process { tag "pigz/compress" tag "tcoffee/align" - test("tcs - msa") { + test("tcs - seatoxin") { when { process { """ input[0] = [ - [ id:'test'], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + [ id:'test'], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] input[1] = [ [ id:'test'], @@ -30,13 +30,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") }, + { assert snapshot(process.out.versions).match() + } ) } } - test("tcs - msa - compressed") { + test("tcs - seatoxin - compressed") { setup { run("PIGZ_COMPRESS") { @@ -44,12 +46,12 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] """ } - } + } } when { @@ -67,12 +69,14 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") }, + { assert snapshot(process.out.versions).match() + } ) } } - test("tcs - msa - lib") { + test("tcs - seatoxin - lib") { config "./lib.config" @@ -82,33 +86,63 @@ nextflow_process { process { """ input[0] = [ [ id:'test' ], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) ] input[1] = [[:],[]] input[2] = [[:],[],[]] input[3] = true """ } - } + } } when { process { """ input[0] = [ - [ id:'test'], - file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + [ id:'test'], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) ] input[1] = TCOFFEE_ALIGN.out.lib.map { it -> [[ id:'test' ], it[1]] } """ } } + then { + assertAll( + { assert process.success }, + { assert path(process.out.tcs.get(0).get(1)).getText().contains("1ahl") }, + { assert snapshot(process.out.versions).match() + } + ) + } + } + + test("tcs - seatoxin - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test'], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin.ref", checkIfExists: true) + ] + input[1] = [ + [ id:'test'], + [] + ] + """ + } + } + then { assertAll( { assert process.success }, { assert snapshot(process.out).match() } ) } + } } diff --git a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap index 8f6fca132c44..80da751875b3 100644 --- a/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/tcs/tests/main.nf.test.snap @@ -1,54 +1,17 @@ { - "tcs - msa - lib": { + "tcs - seatoxin - compressed": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" - ] - ], - "2": [ - "versions.yml:md5,99775735c64e1ae150252a3b09576e91" - ], - "scores": [ - [ - { - "id": "test" - }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" - ] - ], - "tcs": [ - [ - { - "id": "test" - }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" - ] - ], - "versions": [ - "versions.yml:md5,99775735c64e1ae150252a3b09576e91" - ] - } + [ + "versions.yml:md5,99775735c64e1ae150252a3b09576e91" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-19T17:52:51.096817" + "timestamp": "2024-09-16T13:13:16.017532678" }, - "tcs - msa": { + "tcs - seatoxin - stub": { "content": [ { "0": [ @@ -56,7 +19,7 @@ { "id": "test" }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" + "test.tcs:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "1": [ @@ -64,7 +27,7 @@ { "id": "test" }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" + "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "2": [ @@ -75,7 +38,7 @@ { "id": "test" }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" + "test.scores:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "tcs": [ @@ -83,7 +46,7 @@ { "id": "test" }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" + "test.tcs:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "versions": [ @@ -92,58 +55,33 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-19T12:47:34.828638" + "timestamp": "2024-09-16T09:59:35.62776554" }, - "tcs - msa - compressed": { + "tcs - seatoxin - lib": { "content": [ - { - "0": [ - [ - { - "id": "test" - }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" - ] - ], - "1": [ - [ - { - "id": "test" - }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" - ] - ], - "2": [ - "versions.yml:md5,99775735c64e1ae150252a3b09576e91" - ], - "scores": [ - [ - { - "id": "test" - }, - "test.scores:md5,25576b8e2fef74953d28f4e3df689d93" - ] - ], - "tcs": [ - [ - { - "id": "test" - }, - "test.tcs:md5,d6467c4c358a9fe2d21b5d6d3e128cdb" - ] - ], - "versions": [ - "versions.yml:md5,99775735c64e1ae150252a3b09576e91" - ] - } + [ + "versions.yml:md5,99775735c64e1ae150252a3b09576e91" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-16T13:13:32.306127259" + }, + "tcs - seatoxin": { + "content": [ + [ + "versions.yml:md5,99775735c64e1ae150252a3b09576e91" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-19T17:37:52.408687" + "timestamp": "2024-09-16T13:13:00.253922777" } } \ No newline at end of file From 749d72f162cb1493dca66b454064ed201de2cd95 Mon Sep 17 00:00:00 2001 From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com> Date: Wed, 18 Sep 2024 16:50:17 +0200 Subject: [PATCH 071/486] Added nf-test for bedtools/intersect (#6658) * migrate bedtools/intersect to nftest * changed test file paths --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../bedtools/intersect/tests/main.nf.test | 90 ++++++++++++++++ .../intersect/tests/main.nf.test.snap | 101 ++++++++++++++++++ .../bedtools/intersect/tests/nextflow.config | 5 + .../nf-core/bedtools/intersect/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - .../nf-core/bedtools/intersect/main.nf | 27 ----- .../bedtools/intersect/nextflow.config | 14 --- .../nf-core/bedtools/intersect/test.yml | 17 --- 8 files changed, 198 insertions(+), 61 deletions(-) create mode 100644 modules/nf-core/bedtools/intersect/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/intersect/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/intersect/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/intersect/tests/tags.yml delete mode 100644 tests/modules/nf-core/bedtools/intersect/main.nf delete mode 100644 tests/modules/nf-core/bedtools/intersect/nextflow.config delete mode 100644 tests/modules/nf-core/bedtools/intersect/test.yml diff --git a/modules/nf-core/bedtools/intersect/tests/main.nf.test b/modules/nf-core/bedtools/intersect/tests/main.nf.test new file mode 100644 index 000000000000..cd77094679db --- /dev/null +++ b/modules/nf-core/bedtools/intersect/tests/main.nf.test @@ -0,0 +1,90 @@ +nextflow_process { + + name "Test Process BEDTOOLS_INTERSECT" + script "../main.nf" + process "BEDTOOLS_INTERSECT" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/intersect" + + test("sarscov2 - bed - bed") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + + input[1] = [[:], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/baits.bed', checkIfExists: true) + ] + + input[1] = [[:], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test2.bed', checkIfExists: true) + ] + + input[1] = [[:], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bedtools/intersect/tests/main.nf.test.snap b/modules/nf-core/bedtools/intersect/tests/main.nf.test.snap new file mode 100644 index 000000000000..b748dd499e4a --- /dev/null +++ b/modules/nf-core/bedtools/intersect/tests/main.nf.test.snap @@ -0,0 +1,101 @@ +{ + "sarscov2 - bam - bam": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bam:md5,738324efe2b1e442ceb6539a630c3fe6" + ] + ], + "1": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ], + "intersect": [ + [ + { + "id": "test" + }, + "test_out.bam:md5,738324efe2b1e442ceb6539a630c3fe6" + ] + ], + "versions": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T20:55:57.454847668" + }, + "sarscov2 - bed - bed": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,afcbf01c2f2013aad71dbe8e34f2c15c" + ] + ], + "1": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ], + "intersect": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,afcbf01c2f2013aad71dbe8e34f2c15c" + ] + ], + "versions": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T20:55:49.072132931" + }, + "sarscov2 - bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ], + "intersect": [ + [ + { + "id": "test" + }, + "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,42ba439339672f4a9193f0f0fe7a7f64" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T20:56:06.259192552" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/intersect/tests/nextflow.config b/modules/nf-core/bedtools/intersect/tests/nextflow.config new file mode 100644 index 000000000000..f1f9e6937fb4 --- /dev/null +++ b/modules/nf-core/bedtools/intersect/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BEDTOOLS_INTERSECT { + ext.prefix = { "${meta.id}_out" } + } +} diff --git a/modules/nf-core/bedtools/intersect/tests/tags.yml b/modules/nf-core/bedtools/intersect/tests/tags.yml new file mode 100644 index 000000000000..6219cc40b59f --- /dev/null +++ b/modules/nf-core/bedtools/intersect/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/intersect: + - "modules/nf-core/bedtools/intersect/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index b9c06ca0132d..d9519ace74a7 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -40,9 +40,6 @@ bbmap/align: bcftools/convert: - modules/nf-core/bcftools/convert/** - tests/modules/nf-core/bcftools/convert/** -bedtools/intersect: - - modules/nf-core/bedtools/intersect/** - - tests/modules/nf-core/bedtools/intersect/** bedtools/unionbedg: - modules/nf-core/bedtools/unionbedg/** - tests/modules/nf-core/bedtools/unionbedg/** diff --git a/tests/modules/nf-core/bedtools/intersect/main.nf b/tests/modules/nf-core/bedtools/intersect/main.nf deleted file mode 100644 index 1b924bb5c97c..000000000000 --- a/tests/modules/nf-core/bedtools/intersect/main.nf +++ /dev/null @@ -1,27 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_INTERSECT } from '../../../../../modules/nf-core/bedtools/intersect/main.nf' -include { BEDTOOLS_INTERSECT as BEDTOOLS_INTERSECT_BAM } from '../../../../../modules/nf-core/bedtools/intersect/main.nf' - -workflow test_bedtools_intersect { - input = [ - [ id:'test' ], - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test2_bed'], checkIfExists: true) - ] - - - BEDTOOLS_INTERSECT ( input, [[:],[]] ) -} - -workflow test_bedtools_intersect_bam { - input = [ - [ id:'test' ], - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true) - ] - - BEDTOOLS_INTERSECT_BAM ( input, [[:],[]] ) -} diff --git a/tests/modules/nf-core/bedtools/intersect/nextflow.config b/tests/modules/nf-core/bedtools/intersect/nextflow.config deleted file mode 100644 index 8343cd665206..000000000000 --- a/tests/modules/nf-core/bedtools/intersect/nextflow.config +++ /dev/null @@ -1,14 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: BEDTOOLS_INTERSECT { - ext.prefix = { "${meta.id}_out" } - } - - withName: BEDTOOLS_INTERSECT_BAM { - ext.prefix = { "${meta.id}_out" } - ext.suffix = "bam" - } - -} diff --git a/tests/modules/nf-core/bedtools/intersect/test.yml b/tests/modules/nf-core/bedtools/intersect/test.yml deleted file mode 100644 index fc96a00b71e9..000000000000 --- a/tests/modules/nf-core/bedtools/intersect/test.yml +++ /dev/null @@ -1,17 +0,0 @@ -- name: bedtools intersect test_bedtools_intersect - command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config - tags: - - bedtools - - bedtools/intersect - files: - - path: output/bedtools/test_out.bed - md5sum: afcbf01c2f2013aad71dbe8e34f2c15c - -- name: bedtools intersect test_bedtools_intersect_bam - command: nextflow run ./tests/modules/nf-core/bedtools/intersect -entry test_bedtools_intersect_bam -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/intersect/nextflow.config - tags: - - bedtools - - bedtools/intersect - files: - - path: output/bedtools/test_out.bam - md5sum: 738324efe2b1e442ceb6539a630c3fe6 From cc9eb897e5bc339eedc1dfb007cc42fecd1b1582 Mon Sep 17 00:00:00 2001 From: Leon Hafner <60394289+LeonHafner@users.noreply.github.com> Date: Thu, 19 Sep 2024 00:12:05 +0200 Subject: [PATCH 072/486] Added nf-test for bedtools/unionbedg (#6665) migrate bedtools/unionbedg to nf-test --- .../bedtools/unionbedg/tests/main.nf.test | 100 +++++++++++++++++ .../unionbedg/tests/main.nf.test.snap | 101 ++++++++++++++++++ .../bedtools/unionbedg/tests/nextflow.config | 5 + .../nf-core/bedtools/unionbedg/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - .../nf-core/bedtools/unionbedg/main.nf | 30 ------ .../bedtools/unionbedg/nextflow.config | 9 -- .../nf-core/bedtools/unionbedg/test.yml | 19 ---- 8 files changed, 208 insertions(+), 61 deletions(-) create mode 100644 modules/nf-core/bedtools/unionbedg/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/unionbedg/tests/main.nf.test.snap create mode 100644 modules/nf-core/bedtools/unionbedg/tests/nextflow.config create mode 100644 modules/nf-core/bedtools/unionbedg/tests/tags.yml delete mode 100644 tests/modules/nf-core/bedtools/unionbedg/main.nf delete mode 100644 tests/modules/nf-core/bedtools/unionbedg/nextflow.config delete mode 100644 tests/modules/nf-core/bedtools/unionbedg/test.yml diff --git a/modules/nf-core/bedtools/unionbedg/tests/main.nf.test b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test new file mode 100644 index 000000000000..8ae4d3e656d9 --- /dev/null +++ b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test @@ -0,0 +1,100 @@ +nextflow_process { + + name "Test Process BEDTOOLS_UNIONBEDG" + script "../main.nf" + process "BEDTOOLS_UNIONBEDG" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/unionbedg" + + test("sarscov2 - bedgraph - bed") { + + when { + process { + """ + input[0] = [ + [ id:'test_out' ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bedgraph/test.bedgraph', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + ] + + input[1] = [[:], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bedgraph - bed - empty") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test_out' ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bedgraph/test.bedgraph', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + ] + + input[1] = [ + [ id: 'genome' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.sizes', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bedgraph - bed - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test_out' ], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bedgraph/test.bedgraph', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + ] + + input[1] = [[:], []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/bedtools/unionbedg/tests/main.nf.test.snap b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test.snap new file mode 100644 index 000000000000..7cece9e3e14d --- /dev/null +++ b/modules/nf-core/bedtools/unionbedg/tests/main.nf.test.snap @@ -0,0 +1,101 @@ +{ + "sarscov2 - bedgraph - bed - empty": { + "content": [ + { + "0": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,9f9d3a2615603091ac6b0949b53533e3" + ] + ], + "1": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ], + "bed": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,9f9d3a2615603091ac6b0949b53533e3" + ] + ], + "versions": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T21:49:33.613535314" + }, + "sarscov2 - bedgraph - bed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ], + "bed": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T21:49:43.199400399" + }, + "sarscov2 - bedgraph - bed": { + "content": [ + { + "0": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,b75de1183347c4e7c73db4597079e302" + ] + ], + "1": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ], + "bed": [ + [ + { + "id": "test_out" + }, + "test_out.bed:md5,b75de1183347c4e7c73db4597079e302" + ] + ], + "versions": [ + "versions.yml:md5,743ce25c5e7c7ee5bd8464fc3af1f141" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-18T21:49:24.761740365" + } +} \ No newline at end of file diff --git a/modules/nf-core/bedtools/unionbedg/tests/nextflow.config b/modules/nf-core/bedtools/unionbedg/tests/nextflow.config new file mode 100644 index 000000000000..16b7fd6aacb8 --- /dev/null +++ b/modules/nf-core/bedtools/unionbedg/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: BEDTOOLS_UNIONBEDG { + ext.args = '-empty' + } +} diff --git a/modules/nf-core/bedtools/unionbedg/tests/tags.yml b/modules/nf-core/bedtools/unionbedg/tests/tags.yml new file mode 100644 index 000000000000..b73b3ddf3640 --- /dev/null +++ b/modules/nf-core/bedtools/unionbedg/tests/tags.yml @@ -0,0 +1,2 @@ +bedtools/unionbedg: + - "modules/nf-core/bedtools/unionbedg/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index d9519ace74a7..c5ede631186f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -40,9 +40,6 @@ bbmap/align: bcftools/convert: - modules/nf-core/bcftools/convert/** - tests/modules/nf-core/bcftools/convert/** -bedtools/unionbedg: - - modules/nf-core/bedtools/unionbedg/** - - tests/modules/nf-core/bedtools/unionbedg/** biohansel: - modules/nf-core/biohansel/** - tests/modules/nf-core/biohansel/** diff --git a/tests/modules/nf-core/bedtools/unionbedg/main.nf b/tests/modules/nf-core/bedtools/unionbedg/main.nf deleted file mode 100644 index 9e534196b8e4..000000000000 --- a/tests/modules/nf-core/bedtools/unionbedg/main.nf +++ /dev/null @@ -1,30 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { BEDTOOLS_UNIONBEDG } from '../../../../../modules/nf-core/bedtools/unionbedg/main.nf' -include { BEDTOOLS_UNIONBEDG as BEDTOOLS_UNIONBEDG_EMPTY } from '../../../../../modules/nf-core/bedtools/unionbedg/main.nf' - -workflow test_bedtools_unionbedg { - - input = [ [ id:'test_output' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - ] - - BEDTOOLS_UNIONBEDG ( input, [[:],[]] ) -} - -workflow test_bedtools_unionbedg_empty { - - input = [ [ id:'test_output' ], // meta map - [ file(params.test_data['sarscov2']['illumina']['test_bedgraph'], checkIfExists: true), - file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) - ] - ] - sizes = [ [ id: 'genome' ], - file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true) ] - -BEDTOOLS_UNIONBEDG_EMPTY ( input, sizes ) -} diff --git a/tests/modules/nf-core/bedtools/unionbedg/nextflow.config b/tests/modules/nf-core/bedtools/unionbedg/nextflow.config deleted file mode 100644 index e988e4511373..000000000000 --- a/tests/modules/nf-core/bedtools/unionbedg/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: BEDTOOLS_UNIONBEDG_EMPTY { - ext.args = '-empty' - } - -} diff --git a/tests/modules/nf-core/bedtools/unionbedg/test.yml b/tests/modules/nf-core/bedtools/unionbedg/test.yml deleted file mode 100644 index caf03baf8d3f..000000000000 --- a/tests/modules/nf-core/bedtools/unionbedg/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: "bedtools unionbedg test_bedtools_unionbedg" - command: nextflow run ./tests/modules/nf-core/bedtools/unionbedg -entry test_bedtools_unionbedg -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/unionbedg/nextflow.config - tags: - - "bedtools" - - "bedtools/unionbedg" - files: - - path: "output/bedtools/test_output.bed" - md5sum: b75de1183347c4e7c73db4597079e302 - - path: "output/bedtools/versions.yml" - -- name: "bedtools unionbedg test_bedtools_unionbedg_empty" - command: nextflow run ./tests/modules/nf-core/bedtools/unionbedg -entry test_bedtools_unionbedg_empty -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/bedtools/unionbedg/nextflow.config - tags: - - "bedtools" - - "bedtools/unionbedg" - files: - - path: "output/bedtools/test_output.bed" - md5sum: 9f9d3a2615603091ac6b0949b53533e3 - - path: "output/bedtools/versions.yml" From bb8b9216efd4a578bd3c47505bafc10869d6271d Mon Sep 17 00:00:00 2001 From: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Date: Thu, 19 Sep 2024 15:00:59 +0200 Subject: [PATCH 073/486] Adjusting SnpEff modules (#6667) * Retiring snpeff_genome. (Just using snpeff_db.) * Fix stub in snpeff/download (again) * fix * Fixing test and updating snapshot --- modules/nf-core/snpeff/download/main.nf | 10 +++++----- modules/nf-core/snpeff/download/tests/main.nf.test | 4 ++-- .../nf-core/snpeff/download/tests/main.nf.test.snap | 2 +- modules/nf-core/snpeff/snpeff/tests/main.nf.test | 4 ++-- modules/nf-core/snpeff/snpeff/tests/nextflow.config | 3 +-- 5 files changed, 11 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/snpeff/download/main.nf b/modules/nf-core/snpeff/download/main.nf index f1f77dd13d0c..e42259337dc6 100644 --- a/modules/nf-core/snpeff/download/main.nf +++ b/modules/nf-core/snpeff/download/main.nf @@ -8,7 +8,7 @@ process SNPEFF_DOWNLOAD { 'biocontainers/snpeff:5.1--hdfd78af_2' }" input: - tuple val(meta), val(genome), val(cache_version) + tuple val(meta), val(snpeff_db) output: tuple val(meta), path('snpeff_cache'), emit: cache @@ -28,7 +28,7 @@ process SNPEFF_DOWNLOAD { """ snpEff \\ -Xmx${avail_mem}M \\ - download ${genome}.${cache_version} \\ + download ${snpeff_db} \\ -dataDir \${PWD}/snpeff_cache \\ ${args} @@ -41,10 +41,10 @@ process SNPEFF_DOWNLOAD { stub: """ - mkdir -p snpeff_cache/${genome}.${cache_version} + mkdir -p snpeff_cache/${snpeff_db} - touch snpeff_cache/${genome}.${cache_version}/sequence.I.bin - touch snpeff_cache/${genome}.${cache_version}/sequence.bin + touch snpeff_cache/${snpeff_db}/sequence.I.bin + touch snpeff_cache/${snpeff_db}/sequence.bin cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test b/modules/nf-core/snpeff/download/tests/main.nf.test index e067366ef187..ef547c6f2e91 100644 --- a/modules/nf-core/snpeff/download/tests/main.nf.test +++ b/modules/nf-core/snpeff/download/tests/main.nf.test @@ -15,7 +15,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"WBcel235.105" ], "WBcel235", "105" ] + input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] """ } @@ -34,7 +34,7 @@ nextflow_process { when { process { """ - input[0] = [ [ id:"WBcel235.105" ], "WBcel235", "105" ] + input[0] = [ [ id:"WBcel235.105" ], "WBcel235.105" ] """ } diff --git a/modules/nf-core/snpeff/download/tests/main.nf.test.snap b/modules/nf-core/snpeff/download/tests/main.nf.test.snap index accafe7dc8ea..5bccdd8ad31e 100644 --- a/modules/nf-core/snpeff/download/tests/main.nf.test.snap +++ b/modules/nf-core/snpeff/download/tests/main.nf.test.snap @@ -40,7 +40,7 @@ "nf-test": "0.8.4", "nextflow": "24.04.4" }, - "timestamp": "2024-08-29T14:31:59.051736" + "timestamp": "2024-09-19T12:48:45.183665736" }, "test-snpeff-download": { "content": [ diff --git a/modules/nf-core/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test index 803ff02cbc1e..2be0b7d72c78 100644 --- a/modules/nf-core/snpeff/snpeff/tests/main.nf.test +++ b/modules/nf-core/snpeff/snpeff/tests/main.nf.test @@ -18,7 +18,7 @@ nextflow_process { script "../../download/main.nf" process { """ - input[0] = Channel.of([[id:params.snpeff_genome + '.' + params.snpeff_cache_version], params.snpeff_genome, params.snpeff_cache_version]) + input[0] = Channel.of([[id:params.snpeff_db], params.snpeff_db]) """ } } @@ -31,7 +31,7 @@ nextflow_process { [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) ]) - input[1] = params.snpeff_genome + '.' + params.snpeff_cache_version + input[1] = params.snpeff_db input[2] = SNPEFF_DOWNLOAD.out.cache """ } diff --git a/modules/nf-core/snpeff/snpeff/tests/nextflow.config b/modules/nf-core/snpeff/snpeff/tests/nextflow.config index d31ebf6b7c6e..a950a0475dd7 100644 --- a/modules/nf-core/snpeff/snpeff/tests/nextflow.config +++ b/modules/nf-core/snpeff/snpeff/tests/nextflow.config @@ -1,4 +1,3 @@ params { - snpeff_cache_version = "105" - snpeff_genome = "WBcel235" + snpeff_db = "WBcel235.105" } From a5c02a8c0f6db792c5420aec5a66f75024da4b17 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Thu, 19 Sep 2024 15:48:36 +0200 Subject: [PATCH 074/486] Add kalign task.cpus flag (#6668) fix --- modules/nf-core/kalign/align/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf index e1601e15baaa..5d575dc71ea9 100644 --- a/modules/nf-core/kalign/align/main.nf +++ b/modules/nf-core/kalign/align/main.nf @@ -26,6 +26,7 @@ process KALIGN_ALIGN { unpigz -cdf $fasta | \\ kalign \\ $args \\ + -n ${task.cpus} \\ -o ${write_output} cat <<-END_VERSIONS > versions.yml From 039499d18495bd544367ff9bb46e87ebff26362c Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 20 Sep 2024 06:22:27 +0100 Subject: [PATCH 075/486] chore(deps): update actions/setup-node digest to 0a44ba7 (#6670) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/fix-linting.yml | 2 +- .github/workflows/test.yml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index 1b636925f239..c0c0e4bd36e8 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -32,7 +32,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 + - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4a44189f3e8a..c8dc9cbc5180 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -45,7 +45,7 @@ jobs: uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - name: Install NodeJS - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 + uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 with: node-version: "20" @@ -60,7 +60,7 @@ jobs: steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 + - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 with: node-version: "20" From 24b38175e0a63065ff3a2f851ad7e9eaf3c4412f Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Fri, 20 Sep 2024 10:59:39 +0200 Subject: [PATCH 076/486] new module : jvarkit/vcffilterjdk (#6621) * vcffilterdjdk * update params * update params * oppsss tag and TODO * target/region * answers to review * f...g space * fix conda problem https://nfcore.slack.com/archives/CJRH30T6V/p1726233311260959 * add test+bed * reset polyx * prevent test exception md5sum for empty file * update main.nf.test * update meta.yml * remove suggestion --------- Co-authored-by: James A. Fellows Yates --- .../jvarkit/vcffilterjdk/environment.yml | 8 ++ modules/nf-core/jvarkit/vcffilterjdk/main.nf | 88 +++++++++++++ modules/nf-core/jvarkit/vcffilterjdk/meta.yml | 118 +++++++++++++++++ .../jvarkit/vcffilterjdk/tests/main.nf.test | 119 ++++++++++++++++++ .../vcffilterjdk/tests/main.nf.test.snap | 45 +++++++ .../vcffilterjdk/tests/nextflow.config | 5 + .../jvarkit/vcffilterjdk/tests/tags.yml | 2 + 7 files changed, 385 insertions(+) create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/environment.yml create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/main.nf create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/meta.yml create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test.snap create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/tests/nextflow.config create mode 100644 modules/nf-core/jvarkit/vcffilterjdk/tests/tags.yml diff --git a/modules/nf-core/jvarkit/vcffilterjdk/environment.yml b/modules/nf-core/jvarkit/vcffilterjdk/environment.yml new file mode 100644 index 000000000000..bc3950656688 --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::jvarkit=2024.08.25" + - "bioconda:bcftools=1.20" diff --git a/modules/nf-core/jvarkit/vcffilterjdk/main.nf b/modules/nf-core/jvarkit/vcffilterjdk/main.nf new file mode 100644 index 000000000000..3b10a1f9cc29 --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/main.nf @@ -0,0 +1,88 @@ +process JVARKIT_VCFFILTERJDK { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(regions_file) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(dict) + tuple val(meta5), path(code) + tuple val(meta6), path(pedigree) + + output: + tuple val(meta), path("*.${extension}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args1 = task.ext.args1 ?: '' + def args2 = task.ext.args2 ?: '' + def args3 = task.ext.args3 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def script_file = code ? "--script \"${code}\"" : "" + def pedigree_file = pedigree ? " --pedigree \"${pedigree}\" " : "" + def regions_cmd = regions_file ? (tbi ? " --regions-file" : " --targets-file") + " \"${regions_file}\" " : "" + + extension = getVcfExtension(args3); /* custom function, see below */ + + if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + mkdir -p TMP + + bcftools view \\ + -O v \\ + ${regions_cmd} \\ + ${args1} \\ + "${vcf}" |\\ + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcffilterjdk \\ + ${pedigree_file} \\ + ${script_file} \\ + ${args2} |\\ + bcftools view \\ + --output "${prefix}.${extension}" \\ + ${args3} + + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def args3 = task.ext.args3 ?: '' + extension = getVcfExtension(args3); /* custom function, see below */ + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.${extension}" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} + + + +// Custom Function to get VCF extension +String getVcfExtension(String args) { + return args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf"; +} diff --git a/modules/nf-core/jvarkit/vcffilterjdk/meta.yml b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml new file mode 100644 index 000000000000..f4bce92102c3 --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml @@ -0,0 +1,118 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "jvarkit_vcffilterjdk" +description: Filtering VCF with dynamically-compiled java expressions +keywords: + - vcf + - bcf + - filter + - variant + - java + - script +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.1093/bioinformatics/btx734 " + licence: ["MIT License"] + args_id: "$args2" + + - "bcftools": + description: | + View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF + homepage: "http://samtools.github.io/bcftools/bcftools.html" + documentation: "http://www.htslib.org/doc/bcftools.html" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: ["$args1", "$args3"] +input: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test_reference' ] + - vcf: + type: file + description: Input VCF/BCF file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - tbi: + type: file + description: Optional VCF/BCF index file + pattern: "*.{tbi,csi}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{bed,bed.gz,txt,tsv}" + - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: Fasta reference file + pattern: "*.fasta" + - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Fasta file index + pattern: "*.fasta.fai" + - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - meta5: + type: map + description: | + Groovy Map containing code information + e.g. [ id:'test_reference' ] + - code: + type: file + description: File containing custom user code . May be empty if script if provided via `task.ext.args2`. + pattern: "*.{code,script,txt,tsv,java,js}" + - meta6: + type: map + description: | + Groovy Map containing pedigree information + e.g. [ id:'test_reference' ] + - pedigree: + type: file + description: Optional jvarkit pedigree. + pattern: "*.{tsv,ped,pedigree}" +output: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - csi: + type: file + description: Default VCF file index + pattern: "*.csi" + - tbi: + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test new file mode 100644 index 000000000000..2dc0a762f1fe --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test @@ -0,0 +1,119 @@ +// nf-core modules test jvarkit/vcffilterjdk +nextflow_process { + + name "Test Process JVARKIT_VCFFILTERJDK" + script "../main.nf" + process "JVARKIT_VCFFILTERJDK" + config "./nextflow.config" + + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/vcffilterjdk" + + test("sarscov2 - vcf") { + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [] , []] + input[5] = [ [] , []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]).vcf.variantsMD5, + process.out.versions + ).match() + } + ) + } + + } + + + + test("sarscov2 - vcf+bed") { + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [] , []] + input[5] = [ [] , []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.vcf[0][1]).exists() }, + { assert snapshot(process.out.versions).match() + } + ) + } + } + + + + + test("sarscov2 - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] + ] + input[1] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + input[2] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ] + input[3] = [ [:] , file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ] + input[4] = [ [] , []] + input[5] = [ [] , []] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.vcf[0][1]), + process.out.versions + ).match() + } + ) + } + + } + + +} diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test.snap new file mode 100644 index 000000000000..484f303b8f18 --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/main.nf.test.snap @@ -0,0 +1,45 @@ +{ + "sarscov2 - vcf": { + "content": [ + "335cdc0f8c403378e1e9d75c41c3736f", + [ + "versions.yml:md5,3601751995727e2ee7102d8ef18e5304" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + + + "sarscov2 - vcf+bed": { + "content": [ + [ + "versions.yml:md5,3601751995727e2ee7102d8ef18e5304" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + + + "sarscov2 - vcf - stub": { + "content": [ + "vcf_test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "versions.yml:md5,3601751995727e2ee7102d8ef18e5304" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + } + +} diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/nextflow.config b/modules/nf-core/jvarkit/vcffilterjdk/tests/nextflow.config new file mode 100644 index 000000000000..9c4e8e90690c --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: JVARKIT_VCFFILTERJDK { + ext.args2=" --expression 'return variant.getStart()%2==1;' " + } +} diff --git a/modules/nf-core/jvarkit/vcffilterjdk/tests/tags.yml b/modules/nf-core/jvarkit/vcffilterjdk/tests/tags.yml new file mode 100644 index 000000000000..da105badc903 --- /dev/null +++ b/modules/nf-core/jvarkit/vcffilterjdk/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/vcffilterjdk: + - "modules/nf-core/jvarkit/vcffilterjdk/**" From 666652151335353eef2fcd58880bcef5bc2928e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 20 Sep 2024 14:38:14 +0200 Subject: [PATCH 077/486] Batch update of modules (#6674) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Conda remove defaults channel - structural changes (#5847) * Update `branch_update_staging` (#6657) * Added nf-test for seroba/run (#6372) * Added nf-test for sequenzautils/gcwiggle (#6373) * Added nf-test for sequenzautils/gcwiggle * Added stub and locked python version as per container * Added nf-test for segemehl/index (#6375) * Added nf-test for raven (#6378) * Added nf-test for scramble/clusteridentifier (#6376) * Added nf-test for pydamage/analyze (#6379) * Added nf-test for spring/compress (#6366) * Added nf-test for survivor/merge (#6364) * Added nf-test for gatk4/splitintervals (#6302) * Added nf-test for gatk4/splitintervals * Added stub test * Added nf-test for picard/scatterintervalsbyns (#6291) * Added nf-test for picard/scatterintervalsbyns * Added stub test * Update pre-commit hook python-jsonschema/check-jsonschema to v0.29.2 (#5938) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for pureclip (#6380) * Added nf-test for pureclip * Updated power assertion * Added nf-test for snippy/run (#6368) * Added nf-test for snippy/run * Explicitly tell snippy how much RAM we have * Only snap for vcf_csi * Actually update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * remove defaults from utils_nextflow_pipeline (again) (#6382) * Swap samtools collatefastq to nf-test (#5754) * Swap to nftest * Update output channels to not snap empty ones * Add too many stubs * Update stub definition * Add nf-test to metaphlan (#6139) * add nf-test to metaphlan * add config file * Remove metaphlan/metaphlan form pytest from config * Remove ypyest files * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/metaphlan/metaphlan/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * update nf-test * update snapshot for metaphlan subworkflow * update metaphaln/mergemetaphlan * Update metaphlan/metaphlan assertions * Add stub and fix tests * Update subworkflow * Try adding docker.runOptions * Actually commit the second config * Try adding no-same-owner * add config to docker * remove enable docker from config * Update snapshot --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * added trio options (#6164) * added trio options * added trio options * added trio options * added trio options * added trio options * added additional optional trio output * add addtional trio output in meta * remove pytest * removed redundant channles * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/main.nf Co-authored-by: Mahesh Binzer-Panchal * Update modules/nf-core/merquryfk/merquryfk/meta.yml Co-authored-by: Mahesh Binzer-Panchal * some changes * corrected meta * removed environment.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Mahesh Binzer-Panchal * New sections for further module info (#5876) new sections for further module info * Cafe (#6209) * First commit * Complete main.nf * meta.yml * First try test * Failed nf tests * working test * working tests * Make Prettier * fix * With snapshot * sn * fix doi * Add new emitted results and snapshot a result that does not have a time stamp or random model likelihood * Not working with cafe snapshot * Working tests * Add new output variables to meta.yml * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add meta id (not working) * revert local files checks * back to s3 * Without channel of * Attempt to input data in test more verbose. Still not working * remove def * Fix version output in stub * With data on test-datasets * Fix test with variable pvalues, which was not reproducible * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add paths to new modules location data * Update modules/nf-core/cafe/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix input test data paths --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for dshbio/exportsegments (#6398) * Added nf-test for dshbio/filtergff3 (#6399) * Added nf-test for bioawk (#6384) * Added nf-test for snpdists (#6417) * Added nf-test for slimfastq (#6418) * Added nf-test for snpsift/split (#6416) * Updated nf-test for strelka/germline (#6415) Updated nf-test for strelka/germline * Added nf-test for svtyper/svtyper (#6414) * Added nf-test for cdhit/cdhitest (#6388) * Added nf-test for emboss/cons (#6402) * Added nf-test for eido/validate (#6401) * Added nf-test for eido/validate * Fixed assertions * Added nf-test for vg/deconstruct (#6410) * Added nf-test for wgsim (#6409) * Added nf-test for gamma/gamma (#6408) * Added nf-test for ffq (#6407) * Added nf-test for vcflib/vcfbreakmulti (#6411) * Added nf-test for cnvkit/access (#6391) * Added nf-test for cooler/digest (#6395) * Added nf-test for clonalframeml (#6390) * Added nf-test for expansionhunterdenovo/profile (#6405) * Foldmason (#6355) * Add foldmason * Add test * fix prettier * fix prettier * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update main.nf * Update main.nf.test * Update meta.yml * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/foldmason/easymsa/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add stub run tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add tbi index as an output to lofreq callparallel (#6427) Add tbi as an output to lofreq callparallel Co-authored-by: fmartinez * Update lofreq callparallel (#6429) * Add tbi as an output to lofreq callparallel * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update nf-test in lofreq callparallel * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/lofreq/callparallel/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update nf-test in lofreq callparallel --------- Co-authored-by: fmartinez Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * remove slashy strings from multiqc (#6431) * Added nf-test for cooler/makebins (#6396) * Added nf-test for seacr/callpeak (#6421) * Added nf-test for ectyper (#6400) * Added nf-test for shasum (#6419) * Fastqfilter (#6235) * First commit * Completed nf-test * Cleaned main.nf * Removed line in meta.yml * Modified meta.yml * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/vsearch/fastqfilter/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added snapshot for lines in log test.log * made meta.yml prettier * Simplified version extraction --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for preseq/ccurve (#6423) * Added nf-test for emmtyper (#6403) * Added nf-test for cnvpytor/importreaddepth (#6394) * Added nf-test for cnvpytor/importreaddepth * Updated tool ver and snapshot * Locked numpy version * Added nf-test for cnvpytor/callcnvs (#6393) * Added nf-test for circexplorer2/annotate (#6389) * Added nf-test for plink/bcf (#6425) * Added nf-test for biobambam/bammerge (#6385) * Added nf-test for fasttree (#6406) * Added nf-test for fasttree * Update modules/nf-core/fasttree/meta.yml * Update modules/nf-core/fasttree/meta.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for bwameth/index (#6387) * Added nf-test for bwameth/index * Updated tool ver and snapshot * Update modules/nf-core/bwameth/index/tests/main.nf.test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for epang/place (#6404) * Added nf-test for epang/place * Fixed assertion * Added stub and updated power assertion * Added nf-test for biscuit/vcf2bed (#6434) * Added nf-test for sickle (#6440) * Added nf-test for peka (#6446) * Added nf-test for gfatools/gfa2fa (#6451) * Added nf-test for panaroo/run (#6450) * Added nf-test for plasmidfinder (#6444) * Added nf-test for gffcompare (#6452) * Added nf-test for elprep/split (#6459) * Update tests and fix compression (#6463) * Update tests and fix compression * fix * Added nf-test for tbprofiler/profile (#6437) * Added nf-test for varlociraptor/estimatealignmentproperties (#6436) * Deleted pytest of filtlong (#6456) Deleted pytest files for filtlong * Added nf-test for cnvkit/genemetrics (#6392) * Added nf-test for dshbio/splitgff3 (#6461) * Added nf-test for gappa/examineassign (#6455) * Added nf-test for gappa/examineheattree (#6453) * Added nf-test for stadeniolib/scramble (#6438) * Added nf-test for plink/vcf (#6443) * Added nf-test for sequenzautils/bam2seqz (#6441) * Added nf-test for sequenzautils/bam2seqz * Locked python version * Added nf-test for pmdtools/filter (#6424) * Added nf-test for pmdtools/filter * Added stub and conda version trap * Locked samtools * Added nf-test for pindel/pindel (#6445) * Added nf-test for pindel/pindel * Fixed linting issues * Added nf-test for vt/normalize (#6435) * Added nf-test for dshbio/filterbed (#6462) * Added nf-test for dshbio/filterbed * Fixed nf-test * Added nf-test for snpeff/download (#6439) * Added nf-test for snpeff/download * Fixed linting issues * Added nf-test for plasmidid (#6433) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for entrezdirect/esummary (#6458) * Added nf-test for entrezdirect/esummary * Updated snapshot * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.3 (#6467) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Remove redundant rowname assignment (#6466) gene_info is derived from transcript_info, which only contains the columns "gene_id", "gene_name", but not "tx". Thus, the rownames assignment was not doing anything. Fortunately, the row names were not needed downstream regardless. * Update actions/setup-python digest to f677139 (#6471) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for scimap/mcmicro (#6442) * Added nf-test for scimap/mcmicro * Fixed typos * Removed module from nf-test/conda * Added nf-test for gfatools/stat (#6493) * Added nf-test for lissero (#6491) * Added nf-test for kleborate (#6492) * Added nf-test for qcat (#6422) * Added nf-test for qcat * Added stub and conda version trap * Added nf-test for maxbin2 (#6488) * Added nf-test for meningotype (#6487) * Added nf-test for methyldackel/mbias (#6485) * Added nf-test for mobsuite/recon (#6482) * Added nf-test for mobsuite/recon * Locked conda versions * Version bump * Added nf-test for purecn/normaldb (#6281) * Added nf-test for purecn/normaldb * Adjust environment * Add optparse * Try newer version from conda forge * Try adding r-utils too * Added wave containers, dynamic versioning and updated snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for msisensor2/scan (#6481) * Added nf-test for mykrobe/predict (#6479) * Added nf-test for mykrobe/predict * Fixed snapshot * Added nf-test for pasty (#6475) * Added nf-test for picard/collectinsertsizemetrics (#6473) * Added nf-test for nextgenmap (#6477) * Added nf-test for platypus (#6472) * Cleaned pytest files of porechop/abi (#6470) Cleaned pytest files for porechop/abi * Added nf-test for pbptyper (#6474) * Added nf-test for mash/dist (#6489) * Added nf-test for mtnucratio (#6480) * Added nf-test for nanolyse (#6478) * Added nf-test for nanolyse * Fixed snapshot * Added nf-test for paftools/sam2paf (#6476) * Added nf-test for snpsift/dbnsfp (#6469) * Added nf-test for eido/convert (#6460) * Added nf-test for eido/convert * Version bump and wave containers * Bump/wisecondorx (#6464) * bump wisecondorx to v1.2.9 * fix tests * Added nf-test for miniprot/index (#6483) * Added nf-test for fastawindows (#6457) * Added nf-test for fastawindows * Added stub and test * Added nf-test for gatk4/splitcram (#6303) * Added nf-test for hicap (#6495) * Added nf-test for vg/construct (#6468) * Added nf-test for paragraph/vcf2paragraph (#6448) * Added nf-test for paragraph/vcf2paragraph * Added version lock and trap --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for ngmaster (#6270) * Added nf-test for ngmaster * Added stub and version lock for python * Added nf-test for pbbam/pbmerge (#6447) * Added nf-test for pbbam/pbmerge * Updated modules, deprecation message and conda versions trap --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Added nf-test for biscuit/index (#6386) * Added nf-test for biscuit/index * Added stub and updated snapshot * Added stub and nf-test for qc * Added stub and nf-test for pileup * Added stub and nf-test for epiread --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for macrel/contigs (#6490) * Added nf-test for macrel/contigs * Version bump and snapshot update * Added nf-test for metaphlan/makedb (#6486) * Added nf-test for metaphlan/makedb * Updated power assertion * Version bump and snapshot update --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> * Added nf-test for lofreq/call (#6501) * Added nf-test for miranda (#6498) * Added nf-test for snapaligner/index (#6496) * Added nf-test for transdecoder/longorf (#6413) * Migrate renovate config (#6117) * chore(config): migrate config .github/renovate.json5 * Update .github/renovate.json5 Co-authored-by: Matthias Hörtenhuber --------- Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber * Added nf-test for mcroni (#6499) Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Bump sniffles and add missing inputs/outputs (#6503) * Bump sniffles and add missing inputs/outputs * Update modules/nf-core/sniffles/main.nf Co-authored-by: Maxime U Garcia * Update modules/nf-core/sniffles/meta.yml Co-authored-by: Maxime U Garcia --------- Co-authored-by: Maxime U Garcia * Added nf-test for vg/index (#6534) * Added nf-test for gvcftools/extractvariants (#6524) * No ".list" file is generated by this module (#6348) Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * remove "--outdir ." from fastq_screen bash command (#6247) * remove "--outdir ." from fastq_screen bash command fixes issue #6246 * adding optional fastqscreen output: fastq of nohits * fixing test.snap in fastqscreen module * fix linting fastqscreen/fastqscreen * Try pinning gdgraph, adding fastq test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Added nf-test for dshbio/splitbed (#6516) * updated ensemblvep modules and added nf-tests (#6538) * updating ensemblvep modules * fix tests --------- Co-authored-by: Lucpen * Add `mirTrace` module (#6507) * generate mirtrace module * fix linting * update tests and fix linting * update tests * update tests * Added nf-test for staphopiasccmec (#6535) * Added nf-test for ivar/trim (#6531) * Added nf-test for ivar/trim * Simplified version capture and added a trap * Version bump * Added nf-test for igv/js (#6529) * Added nf-test for icountmini/segment (#6528) * Added nf-test for hpsuissero (#6527) * Added nf-test for haplocheck (#6525) * Added nf-test for graphmap2/index (#6523) * Added nf-test for gappa/examinegraft (#6519) * Added nf-test for genmap/index (#6520) * Added nf-test for cnvkit/target (#6512) * Added nf-test for biobambam/bammarkduplicates2 (#6508) * Added nf-test for cooler/dump (#6514) * Added nf-test for cooler/dump * version bump * Added nf-test for goat/taxonsearch (#6522) * Added nf-test for goat/taxonsearch * Added suggested changes * Update actions/upload-artifact digest to 5076954 (#6540) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for getorganelle/config (#6521) * Added nf-test for calder2 (#6509) * Added nf-test for calder2 * Version bump * Added nf-test for mashtree (#6500) * Added nf-test for mashtree * Updated power assertions * Added nf-test for cellrangerarc/mkgtf (#6510) * Added nf-test for cellrangerarc/mkgtf * Excluded from conda profile * Added nf-test for cmseq/polymut (#6511) * Added nf-test for ismapper (#6530) * fix bug (#6541) * mcstaging/imc2mc (#6506) * create module * update meta.yml * add main.nf * add nextflow.config file * adding tests * finish tests * add conda exception in nf-test section of test.yml * change main.nf.test --------- Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * mcstaging/phenoimager2mc (#6143) * create initial module * added nextflow.config file * add test.snap * adapt main.nf to module * adapt meta.yml file * deleted env file * adapted nf.test * add test data specifications to test_data.config * added single files to test data * adapt input to file list, nor working yet * adapted to linting req, 3 warnings remain * successful tests, linting and prettier * ran test again for snapshot file * addressed minor comments in meta.yml * remove comment * remove conda test * adapt snapshot versions output and delete old snapshots * delete comment * add stub test * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Update modules/nf-core/mcstaging/phenoimager2mc/tests/main.nf.test Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> --------- Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> * Add index output to bcftools reheader (#6542) * wgsim: add seed option, add stub, update test, match readsimulator pipeline (#6544) * add seed option, add stub, update test, match readsimulator * Apply suggestions from code review Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * change version assessment and hand seed via args * add versions md5 --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Added nf-test for estsfs (#6518) * Added nf-test for vrhyme/vrhyme (#6533) * Added nf-test for vrhyme/vrhyme * Locked dependency versions * Updated power assertions * Added nf-test for crumble (#6515) * Added nf-test for crumble * Now BAM is the default output format * Added nf-test for nanocomp (#6497) * Added nf-test for nanocomp * Updated power assertions * Fix gene table row naming in tximeta/tximport (#6551) Update tximport.r * Added nf-test for methyldackel/extract (#6549) * Added nf-test for methyldackel/extract * Version bump * Update motus/profile and add nf-test (#6212) * add nf-test to motus/profile * add stub runs to all tests * Update main.nf.test * Update main.nf.test.snap * Remove donwload db in stub run in main.nf.test * Try moving setups to just test (not stubs, as these don't need database download executed again) * update snapshot to fix conda nf-test instability --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * Add tcoffee consensus module (#6539) * Add tcoffee consensus module * Add tcoffee consensus module * update snap * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update main.nf.test * Update main.nf * Update main.nf * test * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf * Update main.nf.test * Update modules/nf-core/tcoffee/consensus/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update tests * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * fix typos * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/tcoffee/consensus/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Add bcftools/plugintag2tag (#6547) Add bcftools/pluginstag2tag * Added nf-test for bwameth/align (#6550) * Added nf-test for bwameth/align * Update modules/nf-core/bwameth/align/tests/main.nf.test * update single-end test assert * print version yml * ignore syntax warning during version capture * Simplified the version extraction --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Sateesh * Added nf-test for msisensorpro/scan (#6561) * nf-test + update to genotypegvcfs (#6553) * nf-test + update to genotypegvcfs * fix linting * review comments * fix old typo * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/genotypegvcfs/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Added nf-test for pirate (#6560) * Added nf-test for minia (#6564) * Added nf-test for purecn/intervalfile (#6558) * Added nf-test for haplogrep2/classify (#6572) * Added nf-test for hmmer/hmmfetch (#6574) * Added nf-test for mapdamage2 (#6578) * Added nf-test for biobambam/bamsormadup (#6579) * Fix wrong array definition in env schema (#6585) * new tool: jvarkit/vcfpolyx (#6580) * vcfpolyx, 1st commit * vcfpolyx * vcfployx, tests ok * fix env and meta ? * remove tab * remove ws * [automated] Fix linting with Prettier * fix conda ? * remove defaults * fix meta info * I hate myslef, fix warnings * add type to meta * fix snap md5 * fix meta3/meta4 https://github.com/nf-core/modules/pull/6580#discussion_r1745494016 * fix https://github.com/nf-core/modules/pull/6580#discussion_r1745463698 * Update modules/nf-core/jvarkit/vcfpolyx/main.nf Co-authored-by: Maxime U Garcia --------- Co-authored-by: nf-core-bot Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Sort bcftools merge inputs, add index output and nf-test conversion (#6586) * Sort inputs and nf-test conversion * update snapshot * update mirtrace (#6593) * Orthofinder (#6288) * working with orthofinder continue feature * Working resume test * With existing data from datasets and chose stable expected outputs. * updated snap shot (sorted) * fix test to have untar-ed workdir dir input * Fix folder direction * Add new output inputs to yml * fix tag * working conda on gitpod * force diamond install to 2.1.9 * Removed defaults --------- Co-authored-by: Usman Rashid * Added nf-test for homer/annotatepeaks (#6573) * Added nf-test for homer/annotatepeaks * Removed defaults * Added nf-test for emboss/revseq (#6581) * Added nf-test for emboss/revseq * Removed defaults * Added nf-test for hapibd (#6575) * Added nf-test for hapibd * Removed defaults * Added nf-test for hypo (#6571) * Added nf-test for hypo * Removed defaults * Added nf-test for hmmer/hmmbuild (#6576) * Added nf-test for hmmer/hmmbuild * Removed defaults * Added nf-test for legsta (#6566) * Added nf-test for legsta * Removed defaults * Added nf-test for cnvkit/call (#6582) * Added nf-test for cnvkit/call * Removed defaults * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.4 (#6592) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Added nf-test for gubbins (#6598) * Added nf-test for gubbins * Version bump * Updated test names * Added nf-test for goleft/indexsplit (#6595) * Added nf-test for graphtyper/vcfconcatenate (#6596) * Added nf-test for geoquery/getgeo (#6594) * Added nf-test for geoquery/getgeo * Version bump and stub * Added versions trap * Locked r-base version * Updated power assertions * Fix bcftools merge for one sample (#6591) * Added nf-test for ivar/consensus (#6568) * Added nf-test for ivar/consensus * Verion bump * Added nf-test for circexplorer2/parse (#6577) * Added nf-test for circexplorer2/parse * Updated power assertion * Added nf-test for mmseqs/databases (#6563) * Added nf-test for mmseqs/databases * Updated power assertion * Removed defaults * Now sorting list * Bgzip and tabix paraphase (#6543) * Bgzip and tabix paraphase * Fixed snapshot size and added threads * remove defaults channel * fix tests * Added nf-test for ivar/variants (#6567) * Added nf-test for ivar/variants * Simplified version extraction * Version bump --------- Co-authored-by: Joon Klaps * Added nf-test for gfaffix (#6597) * Added nf-test for gfaffix * Version bump * Fixed linting * Fixed versions * version fix * Added nf-test for idr (#6570) * Added nf-test for idr * removed defaults * Added nf-test for gunc/downloaddb (#6599) * Added nf-test for metabat2/jgisummarizebamcontigdepths (#6565) * Added nf-test for metabat2/jgisummarizebamcontigdepths * Removed defaults * Added nf-test for krona/ktupdatetaxonomy (#6569) * Added nf-test for krona/ktupdatetaxonomy * Removed defaults * Updated power assertion * Mega conda environment update: Remove `name` and `defaults` (#6600) * Remove defaults channel from all modules * Remove 'name' from conda environment files * Update conda environment schema * Remove defaults from env template and GHA CI * Update Prettier in GHA test.yml workflow to match pre-commit version * Remove whitespace from environment.yml files * hmmsearch, rank and output fasta (#6601) * New subworkflow fasta_hmmsearch_rank_fastas * Add euk and mito SSU rRNA to tests * More tests * Fix trailing whitespace * Pre commit all files (#6604) * GitHub Actions: Always run pre-commit with all files. * First attempt at pre-commit on all files, automatic fixes * Ruff lint: DecryptionTimeout -> DecryptionTimeoutError * Ruff: disable block in template that uses Nextflow variables * Module meta.yml licenses - arrays in strings should not be in strings * License arrays: formatting * Add keywords to module meta files that were too short * Misc module meta.yml fixes * Wrap string licenses as arrays * Type: string instead of value * Fix more meta types * More types, keywords * Apply suggestions from code review Co-authored-by: Mahesh Binzer-Panchal * Boolean flag types --------- Co-authored-by: Mahesh Binzer-Panchal * Added nf-test for elprep/filter (#6517) * Added nf-test for elprep/filter * Updated power assertion * Now emitting logs --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for blat (#6603) Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added nf-test for quast (#6554) * Added nf-test for quast * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/quast/tests/main.nf.test Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Tests for each optional input and removed pytest * Removed "ref, nogff" test --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * bcftools csq (#6605) * bcftools csq * fix lint / format * env.yml * move fun at bottom * Update modules/nf-core/bcftools/csq/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Add module and subworkflow mirtop (#6587) * add mirtop gff module * add mirtop/counts module * add mirtop/export module * add mirtop/stats module * update yml * add bam_stats_mirna_mirtop subworkflow * add required dependencies * update test * update subworkflow test * update yml and output files * fix tag linting issue? * fix linting * run prettier * try to solve conda issue * add a compatible pandas * fix linting * update failing ci mirtop/gff test * Added nf-test for angsd/contamination (#6602) * Added nf-test for angsd/contamination * Swap container version * Update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Phil Ewels * Add support for pip dependencies and force version pinning in conda (#6588) * Add support for pip dependencies and force version pinning in conda * [automated] Fix linting with Prettier --------- Co-authored-by: nf-core-bot * Add `seqcluster` module (#6614) * add seqcluster module * run prettier * Update modules/nf-core/seqcluster/collapse/environment.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/main.nf Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/tests/main.nf.test Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Update modules/nf-core/seqcluster/collapse/meta.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> * Add PREFIX to SPADES warnings log (#6615) * Update main.nf * Update main.nf.test.snap * Update actions/setup-java digest to 2dfa201 (#6617) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update GTDBTK/CLASSIFYWF: Fix bash failing if nothing to move in output directory (#6618) * Fix bash failing if nothing to move in output directory (which is a valid behaviour) * HarshilAlignmentTM * Fix fq/generate (#6610) Update snapshot, add stub * Fix `seqcluster` (#6616) * change test data with smrnaseq data and fix fastq capturing * point to nf-core repo * add pairhmm threads to haplotypecaller (#6620) * Nextclade vers bump (#6356) * Update environment.yml * Update main.nf Updated containers to 3.8.2 * Update meta.yml * Update main.nf * Create nf-test.config * Create main.nf.test nf-test module * Create main.nf.test.snap * Create nextflow.config * Update main.nf fixing biocontainer issue * Update meta.yml * nextclade version bump from 2.12 to 3.8.2 * Update meta.yml * Update test.yml regenerated test.yml * Update modules/nf-core/nextclade/datasetget/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nextclade/run/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Delete tests/modules/nf-core/nextclade/run/test.yml deleted * Delete modules/nf-core/nextclade/run/tests/nextflow.config Deleting * Delete modules/nf-core/nextclade/run/nf-test.config * Delete modules/nf-core/nextclade/datasetget/tests/nextflow.config * Delete modules/nf-core/nextclade/datasetget/nf-test.config * Update main.nf.test * Update main.nf.test making tag adhere to guidelines * Update main.nf.test add params block [this mainly because I couldn't run the test locally without it) * Update main.nf.test.snap * Update main.nf.test * Update main.nf.test add stub * Update main.nf.test * Update tests/config/pytest_modules.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update pytest_modules.yml * Delete tests/modules/nf-core/nextclade/datasetget/main.nf * Delete tests/modules/nf-core/nextclade/datasetget/test.yml * Delete tests/modules/nf-core/nextclade/run/main.nf * Update main.nf.test add stub to nextclade/datasetget test * Delete tests/modules/nf-core/nextclade/datasetget/nextflow.config * Update snapshot * Update meta.yml * Update main.nf.test updated main.nf.test * Update main.nf.test.snap * Add stubs and swap to only snapshoting part of the json * Update modules/nf-core/nextclade/datasetget/main.nf --------- Co-authored-by: shahirnm Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add optional config mode in `mirtrace/qc` (#6623) * add optional config file * update mirtrace/qc * new module gatk/variants2table (#6619) * gatk/variants2table * Update modules/nf-core/gatk4/variantstotable/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix for https://github.com/nf-core/modules/pull/6619 * add optional file arguments This is a suggestion to add additional optional file arguments per the modules guidelines: https://nf-co.re/docs/guidelines/components/modules#required-and-optional-input-files These suggestions are untested. I did not add the [gatk_config_file](https://gatk.broadinstitute.org/hc/en-us/articles/360036896892-VariantsToTable#--gatk-config-file) argument. My current opinion is that the type of settings this would control are best set elsewhere. * update add args, update tests * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/gatk4/variantstotable/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * fix md5 --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Chase Mateusiak * Split deepvariant 3 (#6172) * Move DeepVariant into a subcommand module rundeepvariant, preparing for split modules The test snapshot is updated because the process name in the version file changed. * Add a split DeepVariant workflow with individual processes for each step * Remove hash unique ID and fix input structure issue * Fixes for call_variants outputing sharded file * Fix test * Remove --channels insert_size, which is only applicable for short read data The channels should be specified in the pipeline config * Replace the model type value input with ext.args config * Fix tests: should run twice for two samples in input channel * Fix linting issues and input channel description * Fix formatting of md files Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Corrections / imrpovements from @fellen31 review * Check tfrecord file names * Updating conda skipping options, because the paths have changed * Add deprecation warning for top-level process and test for the deprecated process * also skip conda for the new deprecated module --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia * 4451 add vcf2maf nf test (#4463) * add nf-test case for vcf2maf without VEP * add VEP test case for vcf2maf nf-test * update linting for vcf2maf * fix prettier for vcf2maf * remove pytest files for vcf2maf * remove vcf2maf from pytest modules yml * add modules/nf-core/vcf2maf/tests/tags.yml * add line count to vcf2maf test * add line number and versions contents yaml to vcf2maf test * remove alternate container from vcf2maf testing and use the same container for testing with or without VEP * update modules/nf-core/vcf2maf/tests/main.nf.test * update modules/nf-core/vcf2maf/tests/main.nf.test * Update and fix tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add conda declaration to nf-test * Remove output in snapshot * Add versions to snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> * Update mirtop modules and subworkflow (#6635) * add arity to mirtop/gff * add prefix to mirtop output * update tests and snapshots * update yml * Add bcftools/pluginimputeinfo (#6624) * Add bcftools/pluginimputeinfo * Remove TODO * Change label * Update meta.yml --------- Co-authored-by: James A. Fellows Yates * Get HISAT2 version from CLI (#6634) fix: Get version from cli * Fix tximport summarizedexperiment (#6638) * SummarizedExperiment: don't sanitise column names * tximport: explicitly disable name sanitisation * MEGAHIT: Add support for multi-libraries, export log (#6632) * Add support for coassembly, export log * Fix formatting * teensy bit more * New module jvarkit/wgscoverageplotter (#6633) * wgscoverageplotter * Apply suggestions from code review Co-authored-by: Maxime U Garcia * fix meta * change snap * fix tags * fix env.yml * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Maxime U Garcia Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add openmsthirdparty/cometadapter (#6627) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * Update output to use type dir for compatibility with tes. (#6645) Update output to use type dir for commpatibility with tes. * Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.5 (#6642) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * minor changes to fastq preprocessing (#6643) * minor changes to fastq preprocessing * Update main.nf * Update bcftools/pluginimputeinfo meta.yml (#6646) Update meta.yml * Fix GTDBTK version calling in stub test (#6649) Use the proper version calling now implemented * flye: fix nf-test, update module (#6613) * fix nf-test, update module * Update nextflow.config * Update nextflow.config * update test * small hifi dataset * remove raw tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add module openms/idmassaccuracy (#6647) * Setup cometadapter module * cometadapter draft * finalize tests * remove defaults * enclosing input as channel * replace collect with map * add channel of again * fix input channles by joining them * update correct snapshot * fix lint * fix snapshots, comet writes timestamps in output file * prettier * Update environment.yml * strip out suffix version tag, which differs between container and conda * move to version content check instead of hash * align conda version and container version tag * add idmassaccuracy module * shorten version parsing --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Stop nf-test complaining about missing dependency (#6652) * Finish filepaths * Fix tags * Added nf-test for untarfiles (#6412) * Added nf-test for untarfiles * Matched conda versions with docker/singularity using wave containers * Changed test name * Added deprecation message * Remove custom params in GTDBTK/CLASSIFYWF (#6651) * Use the proper version calling now implemented * Remove custom params * Fix test * Add UPP (#6546) * Add UPP * fix lint * Update UPP * fix prettier * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/upp/align/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * fixes * update * update tests * update * update * Update modules/nf-core/upp/align/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Usman Rashid Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: James A. Fellows Yates Co-authored-by: YSims Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com> Co-authored-by: Luisa Santus Co-authored-by: Francisco Martínez Co-authored-by: fmartinez Co-authored-by: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Co-authored-by: Pieter Moris <13552343+pmoris@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Ömer An Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Lucía Peña-Pérez Co-authored-by: Lucpen Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: MargotCh <55975768+MargotCh@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Chiara Schiller <94467188+chiarasch@users.noreply.github.com> Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Jonathan Manning Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Eric Wei Co-authored-by: Sateesh Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Co-authored-by: nf-core-bot Co-authored-by: Joon Klaps Co-authored-by: Daniel Lundin Co-authored-by: Nur M Shahir Co-authored-by: shahirnm Co-authored-by: Chase Mateusiak Co-authored-by: Marius Bjørnstad Co-authored-by: Stephen Kelly Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Venkat Malladi Co-authored-by: Júlia Mir Pedrol * update JSON schema for modules meta.yml (#5837) * update JSON schema for modules meta.yml * add identifier and ontologies to the modules meta.yml JSON schema * remove qualifier --------- Co-authored-by: Phil Ewels * Bulk update meta yml modules (#6015) * Update Abricate to include (missing) additional optional input channel and add stub (#5849) * Add missing optional input channel to abricate * Update abricate module to include missing optional input path * Update modules/nf-core/abricate/run/tests/main.nf.test Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Fix linting * Update modules/nf-core/abricate/run/main.nf * Get downstream module test --------- Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> * Fix custom/catadditionalfasta (#5851) * Update environment.yml * Update main.nf * update to samtools 1.20 (#5852) * update to samtools 1.20 * keep samtools 1.19.2 for now * update snapshot * [automated] Fix linting with Prettier * keep 1.20 afterall * update snapshot --------- Co-authored-by: nf-core-bot * Update input params for bwameme (#5853) * update recipe * update rthreads * update tests * Update meta.yml * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.10 (#5857) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * `--output-unselected` option in `samtools view` (#2674) * add unoutput option * trying to fix emit * CI fixed, tests still incorrect * Fixed the checksums * Fixed the syntax * Call this "unselected" rather than "unoutput" * Alignment rocks * bugfix: the variable needs to be visible by the output declaration * bugfix: this was not the regular file name * Updated the test case * fixup! Alignment rocks * Updated the meta.yml --------- Co-authored-by: Matthieu Muffato * stubs and test for rnaseq modules - part I (#5854) * stubs and test for bbmap_bbsplit * add test for index * add stubs for custom/catadditionalfasta * add stubs for fq/subsample * add stubs for hisat2/extractsplicesites * update fastq_align_hisat2 snapshot * add stubs for hisat2/build * add stubs for hisat2/align * more stubs bbmap/bbsplit * add stubs for preseq/lcextrap * more stubs for fq/subsample * proper stubs for hisat2/align * remove old snaps * Remove CUTUPFASTA from pytests * Revert "Remove CUTUPFASTA from pytests" This reverts commit 0fa8c1bd400ddc4c80c94cbb59f131d8a43f57b3. * Bump concoct/cutupfasta version, add stub, add nf-test (#5864) * Bump concoct/cutupfasta version, add stub, add nf-test * Fix linting * Adding meta to multivcfanalyzer, updating test to nf-test (#5773) * Adding meta to multivcfanalyzer, updating test to nf-test * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * fix meta.yml * Add sort to vcfs * Add tab to tags * add checks for files due to failing md5 sums across docker,conda,singularity --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Concoct/concoctcoveragetable modules updates (#5868) * Bump concoct/cutupfasta version, add stub, add nf-test * Bump conda build, add stub and nf-test for CONCOT/concoctcoveragetable * Remove pytest entry --------- Co-authored-by: Aida Andrades Valtueña * Added stub logic and test to fastq_fastqc_umitools_fastp (#5858) * Added stub logic and test to fastq_fastqc_umitools_fastp * Now emitting trimmed reads * Adding input value-channel for controlling spring-decompress cmd and output (#5850) * Enable single fastq.gz-output from spring/decompress by setting meta.single_end or meta.one_strand * Controlling output with value-channel write_one_fastq_gz * Update modules/nf-core/spring/decompress/meta.yml Co-authored-by: Maxime U Garcia * nf-test for spring/decompress * Trying to please linter * Trying to please linter --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Maxime U Garcia * Update stranger (#5717) * everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * mapAD: fix `versions.yml` emission (#5874) mapAD: fix `version.yml` emission * add stub and stub test to chromap, change test names (#5872) * add stub and stub test to chromap, change test names * add stub and stub test to chromap, change test names * change setup * move setup out of test * move * produce stub files (#5875) * chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.28.6 (#5878) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * update peddy tests (#5880) update peddy * Update main.nf (#5870) * Update main.nf VEP html report is missing when publishing results because by default vep html file is `_summary.html` instead of `.summary.html`. This changes just adjust the module to the vep defaults to avoid the issue. * Updated html pattern in VEP to be more generic * bump MultiQC version (#5884) bump MQC * Bump shinyngs modules (#5881) * Bump shinyngs modules * Bump versions for snapshot * Update CONCOCT module(s): conda build bump, stub, and nf-test (#5869) * Version update, stub, nf-test for concoct/concoct * Bump version, add nf-test, stub to concoct/mergecutupclustering * nf-test, stub, and version conda build version bump for concoct/extrafastabins * Remove a superfluous config and specify a used one * Update modules/nf-core/concoct/extractfastabins/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Remove superfluous config file * Clean up code * Repair all stub tests that were empty --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * `fasta_binning_concoct` subworkflow: do not fail on join (#5824) * fix: do not fail on mismatch for samples not binned with concoct * Migrate to pytest * Improved Harshil alignment --------- Co-authored-by: James A. Fellows Yates * new module: datavzrd (#5883) * Generated structure for new module * Implemented module * Added semi-functional tests * Cleaned tests - test don't work yet * fix main, start nf-test * add new test data * fix linting * try to assert folders * fix tests * change output to prefix * change to prefix * update to prefix --------- Co-authored-by: vickylaram * samtools/reheader: Fix bug causing output name to be incorrectly evaluated (#5887) Fix bug causing output name to be incorrectly evaluated * nf-test for snpsites (#5284) * nf-test for snpsites * remove old pytest * Delete modules/nf-core/snpsites/tests/nextflow.config * Update modules/nf-core/snpsites/tests/main.nf.test Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * Update assert Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * renamed test Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * reverted the input * updated input...again Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * fixed typo Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> * Regenerate snapshot and fix linting --------- Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added prefix to gunzip and while keeping the default name as `archive.toString() - '.gz'` (#5879) * Added prefix to gunzip * Fixed linting issues in fargene and leviosam2/lift * Removed unstable liftoff/conda * add dedicated output channel for trimmomatic stderr log (needed for multiqc) (#5501) * created new output channel capturing stderr of trimmomatic * updated output channel for trimmomatic * Add stub test and update snapshots * Add stub and update tests * Fix linting and add tee --------- Co-authored-by: John Palmer Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * `ariba/getref` port to nf-test, add meta to tuple and stub (#5877) * port to nf-test, add meta to tuple and stub * modify meta and fix tags * change from each to tuple * Pass annotation files to last-dotplot (#5885) * Pass annotation files to last-dotplot The annotation of the target (plotted horizontally) genome is passed as a new channel. The annotation of the query (plotted vertically) genome is passed as a new component of the first channel. This is because this module typically loops on a list of alignments of various query genomes (from samplesheet) to a single target genome. The annotation files are called `annot_a` and `annot_b` because they are passed to the `-a` and `-b` arguments of `last-dotplot`. * Put arguments on separate lines. * Add meta map and reorder channels. * Test with dummy annotation files. Thanks @SPPearce for the hint. * Add meta to bowtie build (#3848) * Add meta to bowtie build * Swap fastq ngscheckmate tests * Swap to nf-test * Remove spurious changes to bowtie2 * Actually revert bowtie2 * Add the rest of bowtie2 * Again * Revert bowtie2 changes * Swap to meta.id as prefix * Swap bowtie align to nftest * Update tests * Use nft-bam * Update modules/nf-core/bowtie/build/tests/main.nf.test Co-authored-by: Mahesh Binzer-Panchal * Swap to testdata path * Update modules/nf-core/ngscheckmate/patterngenerator/main.nf * Swap index finding to $ * Fix vafncm test * Update meta * Remove bam header md5sum * Update fastq test * Update paired bam test * Delete modules/nf-core/bowtie/align/tests/nextflow.config --------- Co-authored-by: Mahesh Binzer-Panchal * nf-test for pilon (#5293) * nf-test for pilon * linting for license * Add stub and extra test * Swap to testdata_base_path * Add missing END_VERSIONS and alignment * Add optional outputs to stub --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Bump phantompeakqualtools 1.2.2 (#5889) * Add stub section * Update yml * Add nf-test * Get rid of pytest * Make lint happy * Update tests * Update tests to make lint happy * update tests * Make lint happy * Using the same version as CI of nf-test locally might be a good idea * Use wave images * Make lint happy * Simplify tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added variance filtering to custom/matrixfilter (#5358) * Added variant filtering to matrix filter * Corrected indentation * Simplified function in single conditional block * fixed line indentation * Fixed whitespace * Fixed logic * line wrapping change * added whitespace around comments * [automated] Fix linting with Prettier * remove trailing whitespace * Update matrixfilter.R * Remove whitespace --------- Co-authored-by: Jonathan Manning Co-authored-by: nf-core-bot Co-authored-by: Jonathan Manning Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update md5sum module to be able to take multiple files (#3610) * Fix version string spurious text in singularity tests * Add config for subworkflow * Update md5sum module to work with multiple files * linting * Fix stub * Add option to generate single file * Update modules/nf-core/md5sum/main.nf Co-authored-by: Matthieu Muffato * Simplify versions processing --------- Co-authored-by: Matthieu Muffato * Add share to find path (#5899) * build: Bump deepvariant to 1.6.1 (#5801) * build: Bump deepvariant to 1.6.1 * interim dir not allowed to be a dot in 1.6 * Update modules/nf-core/deepvariant/main.nf Co-authored-by: Maxime U Garcia * hack: Hard code version https://github.com/google/deepvariant/issues/830 --------- Co-authored-by: Felix Lenner Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia * bump somalier/extract and somalier/relate version (#5894) * bump version * nf-test migratino * revert ancestry * fix linting * Update snap * fix unicode space --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Added evigene/tr2aacds (#5898) * Added evigene/tr2aacds * Sorted file list and added activation script * Fixed issues raised by feedback * correct president stub (#5904) * correct president stub * Large update to module * Update prefix and meta --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix EClint errors (#5907) Fix EClint * New module: nanoq (#5896) * Add the new module nanoq * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * define the output_format * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * update the stub run with gzip * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/nanoq/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Foldseek: createdb and easysearch modules version bump + stub nf-tests added (#5906) * foldseek/createdb version bump, added stub nf-test * foldseek/easysearch version bump, stub nf-test added * test.snap for createdb added * sourmash/compare stub, nf-test, snapshot (#4665) * sourmash/compare stub, nf-test, snapshot * Add sort * Add a sort * Update snap * Try sort inside the module * Add meta to output and change formatting on test --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * adding chewbbaca/createschema module (#4512) * adding chewbbaca/createschema module * updated for handling a mix of uncompressed and compressed files * update the formatting * update the formatting * updated module to emit meta * updated test.yml * update pytest * clean the meta.yml * clean the meta.yml * clean the meta.yml * replaced conda package with environment.yml file * py-test to nf-test migration * add stub and update tests, snapshot * updated stub * update stub test * update stub test * bump the version * update * updating container version * updated test snapshot * updated nf-test snapshot * added libmamba to environment file * Fix tests and linting * Update modules/nf-core/chewbbaca/createschema/main.nf Co-authored-by: Jose Espinosa-Carrasco * Apply suggestions from code review Co-authored-by: Jose Espinosa-Carrasco --------- Co-authored-by: Gisela Gabernet Co-authored-by: Sateesh Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco * stubs and test for rnaseq modules - part II (#5861) * add stubs for rsem * add stubs for rseqc * add stubs for subread/featurecounts * add stubs for trimgalore * add stubs for ucsc/bedclip * add stubs and more tests for umitools/extract * update snap * update snapshot for umitools/extract * fix umitools/extract tests * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * affy/justrma add stub, nf-test and snapshot (#4651) * affy/justrma add stub, nf-test and snapshot * Update snapshot and environment * Update snap * Update modules/nf-core/affy/justrma/main.nf Co-authored-by: James A. Fellows Yates * Swap test data file paths, fix config, update snaps and stub --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: James A. Fellows Yates * Bump fgbio versions and swap to nftest (#5624) * Convert callduplex and callmolecular to nftest and update version * Convert zipperbams * Convert groupreadsbyumi * Convert sortbam and add stubs * Convert filterconsensusreads * Update snapshot * Update modules/nf-core/fgbio/callmolecularconsensusreads/main.nf * Add collision checks, swap test data paths * Fix conda version and linting * Apply suggestions from code review Co-authored-by: Nils Homer * Update modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml Co-authored-by: Nils Homer * Update duplex snap --------- Co-authored-by: Nils Homer Co-authored-by: Maxime U Garcia * Added pbtk/pbindex (#5901) * Added pbtk/pbindex * Removed prefix * Added agat/spfilterfeaturefromkilllist (#5771) * Added agat/spfilterfeaturefromkilllist * Added AGAT config * Included test with agat config * bump stranger to 0.9.1 (#5910) bump stranger * Update nft-bam to v0.3.0 (#5912) * Add stubs for rnaseq subworkflows - part I (#5911) * fix stub and add tests + single snapshot * add stub * fix stub * snapshot versions + better snap for stub * add versions to snapshot + add tests for stub * Add stub tests + single snapshot * Add stub tests + single snapshot * maxime sorted * Add stub tests + single snapshot * Add stub tests * Add stub tests + single snapshot * code polish + update snap * update snapshot using nft-bam * Add stubs for rnaseq subworkflows - part II (#5913) * Add stub tests + single snapshot * Add stub tests + single snapshot * fix stub and update tests for kallisto modules * Add stub tests + single snapshot * Add stub tests + single snapshot * bcftools isec input can be bcf or bcf.gz as well as vcf.gz (#5685) * bcftools isec input can be bcf or bcf.gz as well as vcf.gz * Add stub and stub test * Update tests * Update meta.yml * Add stub to name of stub test * Update meta * Update tests Changes: - exclude .tbi files from snapshot due to failing conda tests - update main.nf.test.snap - specificy path type of the output * Update tests again Changes: - include versions - sort file name list for consistent order - update snapshot --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> * Add stubs for rnaseq subworkflows - part III (#5921) * do not snapshot input * do not snapshot input * Add stubs for rnaseq subworkflows - part IV (#5922) do not snapshot input with stub * mulled biocontainer for vardict-java and htslib (#5920) * vardict-java bgzip mulled container * update bioconda env * code polishing Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Update modules/nf-core/vardictjava/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * args3 for bgzip * args3 * Update snap * removed whitespace --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Add same file clash check to bioawk (#5926) * Update pre-commit hook astral-sh/ruff-pre-commit to v0.5.1 (#5893) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update actions/upload-artifact digest to 0b2256b (#5927) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * dysgu==1.6.4_version update (#5928) * all_files_update * Update environment.yml * update_meta.yml * input==input_bam * update_snapshot * meta.yml,tags.yml update * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * Update modules/nf-core/dysgu/meta.yml Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * update_author --------- Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * ADD argNorm module (#5905) * ADD argnorm module * ENH correct pattern for 'hamronized' input * ENH specify hamronization command in script * ENH don't pass 'hamronized' as val * Fixed trailing whitespace * "single_end" is not relevant in this module * alignment * "db_args" to avoid any confusion with the input channel * Added a test to check $tool is provided * Implemented the stub mode * Added a test for the missing database * Reordered the arguments to match the script --------- Co-authored-by: Matthieu Muffato * Sentieon license server - testing (#5856) * test it out * ci: Add license_message script https://github.com/nf-core/sarek/issues/1380 https://github.com/DonFreed/docker-actions-test?tab=readme-ov-file * test: Add tests for sentieon bwamem Because the pytest-workflow tests are taking so long * Add scratch from meeting * Clean up sentieon secrets * ci: Fix Nextflow secrets setup * fix(sentieon): Remove encryption key because it won't get used * fix # * ci: Fix when to setup secrets * feat: Add sentieon auth mech secret * chore(sentieon): Remove bwamem pytest-workflow tests * fix: Spike in with environment variables * fix: Add SENTIEON_AUTH_DATA in env file The reason for this is because when we require it in the module it fails. That doesn't make sense for normal Sentieon users. They don't care, this is more of a GitHub actions thing. * docs(sentieon): Make this a README * test: Add local testing setup * test: Remove publishDir * style: Remove sentieon/bwamem * fix: Change comments to prints for debugging and better reporting * fix: Add a quote? * chore: Remove unnecessary variable * debug: Print variables * Fix typo Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> * chore: Clean up code * docs: Write up all the learnings from Sentieon * style: Run prettier * style: Add tags for nf-core lint * docs: Clean up notes Co-authored-by: maxulysse * chore: Add @DonFreed as maintainer --------- Co-authored-by: Edmund Miller Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: maxulysse * Fix Sentieon CI (#5934) * ci: Remove setting secrets in pytest-workflow * ci: Add a longer note about conditionals https://docs.github.com/en/actions/security-guides/using-secrets-in-github-actions#using-secrets-in-a-workflow Secrets cannot be directly referenced in if: conditionals. Instead, consider setting secrets as job-level environment variables, then referencing the environment variables to conditionally run steps in the job. For more information, see "Contexts" and jobs..steps[*].if. * ci: Check for secrets in env Because if this is coming from a fork it will fail * disable conda setup when not using a conda profile (#5935) * stubs and test for rnaseq modules - part III (#5925) * improve bbmap_split stub * update stub tests * improve stub * single snapshot * fix stub + add stub tests * fix stub + add stub tests * fix stub * restore tags * fix stub + better stub tests * fix snapshot * NARFMAP segfault (#4895) * test(narfmap): Add segfault test * fix(narfmap): Clean up log error * test(narfmap): Should segfault * chore(narfmap): Bump to 1.4.2 * test(narfmap): Mark test as passing https://github.com/edmundmiller/NARFMAP/issues/10 * style: Add extra tag for nf-core/lint * test: Update all the snapshot declarations * chore: Add a TODO for poddar's test * narfmap cleanup (#5937) * chore: Add Note about issue * test: Remove bam name Co-authored-by: maxulysse --------- Co-authored-by: maxulysse * Add CRAM/index support to NARFMAP (#5946) * feat: Add cram/index support to narfmap * chore: Remove singularity image comment * test: Update tests for CRAM * Update actions/setup-node digest to 1e60f62 (#5947) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Fix bcftools plugin split (#5942) * bump bclconvert (#5952) * bump bclconvert * fix snapshots * bump multiqc (#5950) * bump multiqc * update snapshot * chore: bump picard (#5948) * bump picard * fix hsmetrics test * fix markduplicates * fix extractfingerprints * fix addorreplacereadgroups * fix crosscheckfingerprints * Add prefix to output file for barrnap (#5919) * Add prefix to output file * Update barrnap to nf-test * Update tags.yml * Add missing bracket and run test * Correct format of license * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/barrnap/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Review suggestions * Prettier * Update meta.yml * Update tests --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * chore(deps): update actions/setup-python digest to 39cd149 (#5961) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * LAST alignment statistics for MultiQC (#5902) * last train modified to output multiqc * Report alignment length and percent similarity, for MultiQC. * Update snapshot file. * Document the new channels * Fix indentation * Update test results. * Give a longer suffix for better MultiQC search patterns. --------- Co-authored-by: Mohammed Mahdi * Update lofreq somatic and callparallel (#5931) * update lofreq callparallel and somatic ssh * [automated] Fix linting with Prettier * suggestions * remove files tests * label lofreq somatic * Update modules/nf-core/lofreq/callparallel/main.nf Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> * port lofreq/callparallel to nf-test * Swap to nftest * update paths * add meta * Update main.nf * modify main * update paths * fix small errors * Update modules/nf-core/lofreq/somatic/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update main.nf.test.snap --------- Co-authored-by: AitorOP Co-authored-by: nf-core-bot Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Francisco Martínez Co-authored-by: Famke Bäuerle Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update dupradar.r according to new MultiQC (>=v1.22) config values (#5943) Update dupradar.r according to new MultiQC config values. Co-authored-by: Matthias Zepper * Update the module: nanoq (#5964) * update nanoq module * update nf-test * Update Glimpse2 phase (#5944) * Update Glimpse2 phase * Fix label * Update snapshot * Update modules/nf-core/glimpse2/phase/main.nf Co-authored-by: Maxime U Garcia * Update meta.yml --------- Co-authored-by: LouisLeNezet Co-authored-by: Maxime U Garcia Co-authored-by: Maxime U Garcia * Update dupradar test snapshot (#5966) * Update dupradar test snapshot * Dummy commit to try and trigger nf-test in ci * Revert "Dummy commit to try and trigger nf-test in ci" This reverts commit 130f9988c7041df8203aa74fb7307451c5fb0dda. * stubs and test for rnaseq modules - part IV (#5939) * fix stubs and add stub tests * fix linting * fix some linting * fix linting * better comment * change container * update snapshots * improve untar stubs * update snapshots * update snapshots * update env * better * use seqera containers * quay.io * proper usage * update snapshots * keep ubuntu for now * update tests and snap * update test and snapshot * update test and snapshot * Add new input to multiqc module for use with --rename_samples (#5973) * Add new input to multiqc module for use with --rename_samples * Update tests * update meta.yml * Add provision for sample_names * port `gridss/gridss` to nf-test (#5933) * port * remove pytest files * fix meta * Update meta.yml * fix indentation * update test with bam plugin * fix indents, try other test * remove --assembly flag for now --------- Co-authored-by: Maxime U Garcia * by remove the 2>&1 to avoid the warning message. (#5974) * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.2 (#5975) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Handle empty files (#5720) * fix: emit all fastqs, remove global log file * fix: remove rg parseing * fix(subworkflow/bcl_demultiplex): remove rg parsing, output empty fastqs, remove log file * test: update snaps * lint: traill\ing whitespace * feat: include read group parsing and empty file check in single closure * test: update snapshot * fix: lint final new line * fix: lint trailing whitespace * fix: add branch and emit empty fastq channel * tests: update snaps * lint: trailing whitespace * fix: filter bool and add test * test: update snaps * test: assert empty file exist * test: assert empty file exist * test: check file exists, update snap * Update test.yml * Update test.yml * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * ci: debug nf-test failure * lint: fix lint --------- Co-authored-by: khazen@clearnotehealth.com <--unset> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * new module: custom_gtffilter (#5965) * Add basic gtffilter implementation * Add gtffilter stub * Add gtffilter meta map * Update gtffilter meta.yml * Fix gtffilter formatting * Add first gtffilter tests * Fix problems in gtffilter module defintion * Add gtffilter nf-test snapshot * Add support for gzipped inputs to gtffilter * Add gtffilter gzip stub * Update nf-test definition for gtffilter * Add meta2 to fasta input Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Add fasta meta map to gtffilter test definitions * Add gtffilter MIT license text --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * Fix gtffilter output definition (#5977) * Added agat/spmergeannotations (#5772) * Added agat/spmergeannotations * Added tests with config * Rename preprocess rnaseq (#5959) * Edit content with subworkflow name * Rename subworkflow folder * Readd subworkflow with old name, with deprecation * remove rogue word * Appease eclint * Remove test suite for deprecated subworkflow * Using Seqera containers for Sentieon to avoid LD_LIBRARY errors (#5823) * Using seqera containers for sentieon * update containers for sentieon modules with quay.io registry --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: maxulysse * Swap unzip to nf-test (continuation of 5357) (#5897) * unzip stub, nf-test, snap * Revert "unzip stub, nf-test, snap" This reverts commit dec35aa305e243cb87024ab27f4f7e2b2f1c7a19. * Reapply "unzip stub, nf-test, snap" This reverts commit e0d708e51ccf89d293a583a4bd32c3a84e25949a. * added minimal required tests for process and stub * added snapshot * simplify snapshot input in stub test Co-authored-by: Matthias Hörtenhuber * remove unneeded stub files * migrate pytest for unzipfiles * add snapshot file for script block * added stub * added stub and stub test * updated stub snapshot for unzip * remove unneeded test config * Update snaps and malt * Update malt for linting * Fix linting for maltextract * Swap test-data paths for malt modules * Update modules/nf-core/maltextract/tests/main.nf.test --------- Co-authored-by: Sateesh Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Matthias Hörtenhuber Co-authored-by: Maxime U Garcia * Improve strandedness derivation in rnaseq preprocessing swf (#5982) * Improve strandedness devivation * Add missing params to nf-test * RNAseq preprocessing: rrna sequences make more sense as a channel of FASTAs, port tests (#5988) * rrna sequences make more sense as a channel of FASTAs * Also update tests * Add function test to swf * Fix up subworkflow function testing * [Upgrade] Normalize input of lofreq-viterbi to match other lofreq modules (#5989) * add meta2 to input fasta channel * update snapshot; nothing new but timestamp * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/lofreq/viterbi/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Add module fgbio/collectduplexseqmetrics (#5960) * Initial commit * Rerun nf-test * Change assertion for duplex_qc output * Add ggplot2 to version.yml * Update snapshot * Correct conda packages version * Add Seqfu/derep (#5958) * add-usearch-unoise3 * add seqfu/derep * Delete modules/nf-core/usearch/unoise3/environment.yml * Delete modules/nf-core/usearch/unoise3/main.nf * remove files * update metadata * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update modules/nf-core/seqfu/derep/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix dataset in -stub * Clarify description * Update modules/nf-core/seqfu/derep/meta.yml Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * check for pre-existing output file && update test * Update main.nf --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * modify valCutoff funtion in propr.R (#5995) Co-authored-by: Cristina Araiz * liftoff: Re-added conda environment (#5981) * liftoff: Readded conda environment * Added liftoff to env file * Cleaned up env file * chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.5.3 (#5996) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * Update: `CIRCULARMAPPER_CIRCULARGENERATOR` (#5997) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * rename elongation factor for consistency with other CM module --------- Co-authored-by: James A. Fellows Yates * Update: `CIRCULARMAPPER_REALIGNSAMFILE` (#5998) * Fix output naming, add req argument to input * add new input to nf-test * update nf-test due to changes in upstream module inputs * update snapshots * add metas to other input channels * update tests according to changes in module inputs. * add meta to elongation factor channel for consistency with other CM module * update nf-test to include new meta * rename metas * Add stub and test to lofreq/indelqual (#5941) * Add stub and test to lofreq/indelqual * Add author * new test setup using --migrate-pytest and PR feedback * Update main.nf.test * Update meta.yml * Update main.nf * add snap; del pytest * Update meta.yml * Update main.nf.test * Update meta.yml * update test * minor fix in stub test * Update tabix and add threads (#5999) * Update tabix and add threads * fix linting * Remove problematic ifEmpty() from rnaseq preprocessing (#6000) * Refactor Sentieon (#5945) * refactor: Clean up the logic and let Sentieon figure it out * refactor: Remove Sentieon license server IP check * fix: Add a -n * Try accessing secrets in the module? * fix: Use Nextflow for if statement * update snapshot * update snapshot * extend logic to all main.nf * ci: Add Sentieon logic to pytest-workflow * test(sentieon): Add env section to every config * Revert "ci: Add Sentieon logic to pytest-workflow" This reverts commit 76884d2a3d9dc9dfbc31b788026e0ac6ee7decaf. * test: Remove pytest_modules for sentieon --------- Co-authored-by: maxulysse * ltrharvest: Added test to verify graceful handling of no ltr input (#5978) * ltrharvest: Added test to verify graceful handling of no ltr input * Updated test data paths * Fixed test data path * Removed unstable items from snapshot * Updated snapshotting logic * ltrfinder: Added test to verify graceful handling of no ltr input (#5979) * ltrretriever/ltrretriever: Added test to verify graceful handling of … (#5980) * ltrretriever/ltrretriever: Added test to verify graceful handling of no ltr input * Removed unstable items from snapshot * update nf-test t0 0.9.0 (#6010) * Fix keyword meta (#6011) * Updated mkfastq module (#5984) * Updated mkfastq module * Combined input channels * Updated main.nf.test and snap --------- Co-authored-by: zxBIB Schcolnicov Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> * bulk update of meta.yml modules structure * update meta.yml files automatically with manual curation for missing information --------- Co-authored-by: James A. Fellows Yates Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: nf-core-bot Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Priyanka Surana Co-authored-by: Matthieu Muffato Co-authored-by: Aida Andrades Valtueña Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Usman Rashid Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Christian Heide <11767963+jch-13@users.noreply.github.com> Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Raquel Manzano <36073691+RaqManzano@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Jonathan Manning Co-authored-by: Maxime Borry Co-authored-by: vickylaram Co-authored-by: Tyler Chafin Co-authored-by: Thanh Lee Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: John Palmer <32370730+jpalmer37@users.noreply.github.com> Co-authored-by: John Palmer Co-authored-by: Charles Plessy Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Jose Espinosa-Carrasco Co-authored-by: thomgiles Co-authored-by: Jonathan Manning Co-authored-by: Matthieu Muffato Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Felix Lenner Co-authored-by: paulwolk <60699553+paulwolk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Zohaib Anwar Co-authored-by: Gisela Gabernet Co-authored-by: Sateesh Co-authored-by: Nils Homer Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: RuthEberhardt <37174225+RuthEberhardt@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> Co-authored-by: eolaniru <149598276+eolaniru@users.noreply.github.com> Co-authored-by: poddarharsh15 <45700858+poddarharsh15@users.noreply.github.com> Co-authored-by: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Co-authored-by: Edmund Miller Co-authored-by: maxulysse Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Mohammed Mahdi Co-authored-by: AitorPeseta <119889829+AitorPeseta@users.noreply.github.com> Co-authored-by: AitorOP Co-authored-by: Francisco Martínez Co-authored-by: Famke Bäuerle Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Co-authored-by: Matthias Zepper Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet Co-authored-by: JIANHONG OU Co-authored-by: Kyle Hazen <41054023+k1sauce@users.noreply.github.com> Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Matthias Hörtenhuber Co-authored-by: Thomas Krannich Co-authored-by: Georgia Kesisoglou <73076971+georgiakes@users.noreply.github.com> Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: caraiz2001 <105276325+caraiz2001@users.noreply.github.com> Co-authored-by: Cristina Araiz Co-authored-by: Thiseas C. Lamnidis Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com> Co-authored-by: zxBIB Schcolnicov Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> * allow identifier to be an empty string * run prettier * fixed indentation errors * fix meta.yml of missing modules --------- Co-authored-by: Phil Ewels Co-authored-by: Usman Rashid Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: James A. Fellows Yates Co-authored-by: YSims Co-authored-by: Mahesh Binzer-Panchal Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com> Co-authored-by: Chris Wyatt <9978862+chriswyatt1@users.noreply.github.com> Co-authored-by: Luisa Santus Co-authored-by: Francisco Martínez Co-authored-by: fmartinez Co-authored-by: FernandoDuarteF <123090819+FernandoDuarteF@users.noreply.github.com> Co-authored-by: Pieter Moris <13552343+pmoris@users.noreply.github.com> Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Co-authored-by: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Co-authored-by: Matthias Hörtenhuber Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Ömer An Co-authored-by: Franziska Bonath <41994400+FranBonath@users.noreply.github.com> Co-authored-by: Maxime U Garcia Co-authored-by: Lucía Peña-Pérez Co-authored-by: Lucpen Co-authored-by: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Co-authored-by: MargotCh <55975768+MargotCh@users.noreply.github.com> Co-authored-by: Krešimir Beštak <86408271+kbestak@users.noreply.github.com> Co-authored-by: Chiara Schiller <94467188+chiarasch@users.noreply.github.com> Co-authored-by: Miguel A. Ibarra-Arellano Co-authored-by: Krešimir Beštak Co-authored-by: Jonathan Manning Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Co-authored-by: Eric Wei Co-authored-by: Sateesh Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Co-authored-by: nf-core-bot Co-authored-by: Joon Klaps Co-authored-by: Daniel Lundin Co-authored-by: Nur M Shahir Co-authored-by: shahirnm Co-authored-by: Chase Mateusiak Co-authored-by: Marius Bjørnstad Co-authored-by: Stephen Kelly Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com> Co-authored-by: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Co-authored-by: Venkat Malladi Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> Co-authored-by: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Co-authored-by: Priyanka Surana Co-authored-by: Matthieu Muffato Co-authored-by: Aida Andrades Valtueña Co-authored-by: Anders Sune Pedersen <37172585+asp8200@users.noreply.github.com> Co-authored-by: Christian Heide <11767963+jch-13@users.noreply.github.com> Co-authored-by: Raquel Manzano <36073691+RaqManzano@users.noreply.github.com> Co-authored-by: Maxime Borry Co-authored-by: vickylaram Co-authored-by: Tyler Chafin Co-authored-by: Thanh Lee Co-authored-by: Joon Klaps <61584065+Joon-Klaps@users.noreply.github.com> Co-authored-by: John Palmer <32370730+jpalmer37@users.noreply.github.com> Co-authored-by: John Palmer Co-authored-by: Charles Plessy Co-authored-by: Jose Espinosa-Carrasco Co-authored-by: thomgiles Co-authored-by: Jonathan Manning Co-authored-by: Matthieu Muffato Co-authored-by: Felix Lenner Co-authored-by: paulwolk <60699553+paulwolk@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Zohaib Anwar Co-authored-by: Gisela Gabernet Co-authored-by: Nils Homer Co-authored-by: RuthEberhardt <37174225+RuthEberhardt@users.noreply.github.com> Co-authored-by: Theresa Störiko Co-authored-by: Theresa Störiko <73145457+tstoeriko@users.noreply.github.com> Co-authored-by: eolaniru <149598276+eolaniru@users.noreply.github.com> Co-authored-by: poddarharsh15 <45700858+poddarharsh15@users.noreply.github.com> Co-authored-by: Vedanth Ramji <86137377+Vedanth-Ramji@users.noreply.github.com> Co-authored-by: Edmund Miller Co-authored-by: maxulysse Co-authored-by: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Co-authored-by: Mohammed Mahdi Co-authored-by: AitorPeseta <119889829+AitorPeseta@users.noreply.github.com> Co-authored-by: AitorOP Co-authored-by: Famke Bäuerle Co-authored-by: Matthias Zepper <6963520+MatthiasZepper@users.noreply.github.com> Co-authored-by: Matthias Zepper Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Co-authored-by: LouisLeNezet Co-authored-by: JIANHONG OU Co-authored-by: Kyle Hazen <41054023+k1sauce@users.noreply.github.com> Co-authored-by: Nico Trummer <52698566+nictru@users.noreply.github.com> Co-authored-by: Jenny Leopoldina Smith Co-authored-by: Thomas Krannich Co-authored-by: Georgia Kesisoglou <73076971+georgiakes@users.noreply.github.com> Co-authored-by: Andrea Telatin <15690844+telatin@users.noreply.github.com> Co-authored-by: caraiz2001 <105276325+caraiz2001@users.noreply.github.com> Co-authored-by: Cristina Araiz Co-authored-by: Thiseas C. Lamnidis Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com> Co-authored-by: zxBIB Schcolnicov --- modules/meta-schema.json | 127 +-- modules/nf-core/abacas/meta.yml | 63 +- modules/nf-core/abricate/run/meta.yml | 54 +- modules/nf-core/abricate/summary/meta.yml | 45 +- modules/nf-core/abritamr/run/meta.yml | 98 ++- modules/nf-core/adapterremoval/meta.yml | 155 ++-- .../nf-core/adapterremovalfixprefix/meta.yml | 51 +- modules/nf-core/admixture/meta.yml | 97 ++- modules/nf-core/affy/justrma/meta.yml | 90 +- .../nf-core/agat/convertspgff2gtf/meta.yml | 51 +- .../nf-core/agat/convertspgff2tsv/meta.yml | 40 +- .../nf-core/agat/convertspgxf2gxf/meta.yml | 51 +- modules/nf-core/agat/spaddintrons/meta.yml | 52 +- .../agat/spfilterfeaturefromkilllist/meta.yml | 69 +- .../nf-core/agat/spmergeannotations/meta.yml | 65 +- modules/nf-core/agat/spstatistics/meta.yml | 40 +- modules/nf-core/agat/sqstatbasic/meta.yml | 40 +- modules/nf-core/agrvate/meta.yml | 56 +- modules/nf-core/ale/meta.yml | 59 +- modules/nf-core/allelecounter/meta.yml | 70 +- modules/nf-core/ampcombi/environment.yml | 5 +- modules/nf-core/ampcombi/meta.yml | 205 +++-- modules/nf-core/ampcombi2/cluster/meta.yml | 52 +- modules/nf-core/ampcombi2/complete/meta.yml | 42 +- .../nf-core/ampcombi2/parsetables/meta.yml | 214 +++-- modules/nf-core/ampir/meta.yml | 88 +- modules/nf-core/amplify/predict/meta.yml | 55 +- modules/nf-core/amps/meta.yml | 62 +- modules/nf-core/amrfinderplus/run/meta.yml | 80 +- modules/nf-core/amrfinderplus/update/meta.yml | 25 +- modules/nf-core/angsd/contamination/meta.yml | 65 +- modules/nf-core/angsd/docounts/meta.yml | 125 ++- modules/nf-core/angsd/gl/meta.yml | 83 +- modules/nf-core/annotsv/annotsv/meta.yml | 155 ++-- .../annotsv/installannotations/meta.yml | 17 +- .../nf-core/anota2seq/anota2seqrun/meta.yml | 331 ++++--- .../nf-core/antismash/antismashlite/meta.yml | 269 ++++-- .../antismashlitedownloaddatabases/meta.yml | 60 +- modules/nf-core/arcashla/extract/meta.yml | 93 +- modules/nf-core/argnorm/meta.yml | 70 +- modules/nf-core/aria2/meta.yml | 48 +- modules/nf-core/ariba/getref/meta.yml | 37 +- modules/nf-core/ariba/run/meta.yml | 52 +- modules/nf-core/arriba/arriba/meta.yml | 187 ++-- modules/nf-core/arriba/download/meta.yml | 21 +- modules/nf-core/art/illumina/meta.yml | 100 ++- modules/nf-core/artic/guppyplex/meta.yml | 46 +- modules/nf-core/artic/minion/meta.yml | 231 +++-- modules/nf-core/ascat/meta.yml | 220 +++-- modules/nf-core/ashlar/meta.yml | 49 +- modules/nf-core/assemblyscan/meta.yml | 45 +- modules/nf-core/ataqv/ataqv/meta.yml | 119 ++- modules/nf-core/ataqv/mkarv/meta.yml | 30 +- modules/nf-core/atlas/call/meta.yml | 106 +-- modules/nf-core/atlas/pmd/meta.yml | 134 +-- modules/nf-core/atlas/recal/meta.yml | 84 +- modules/nf-core/atlas/splitmerge/meta.yml | 97 ++- .../gtf2featureannotation/meta.yml | 85 +- modules/nf-core/authentict/deam2cont/meta.yml | 77 +- modules/nf-core/backsub/meta.yml | 87 +- modules/nf-core/bacphlip/meta.yml | 60 +- modules/nf-core/bakta/bakta/meta.yml | 184 ++-- .../nf-core/bakta/baktadbdownload/meta.yml | 17 +- modules/nf-core/bam2fastx/bam2fastq/meta.yml | 61 +- modules/nf-core/bamaligncleaner/meta.yml | 45 +- modules/nf-core/bamclipper/meta.yml | 80 +- modules/nf-core/bamcmp/meta.yml | 74 +- .../nf-core/bamstats/generalstats/meta.yml | 50 +- modules/nf-core/bamtofastq10x/meta.yml | 56 +- modules/nf-core/bamtools/convert/meta.yml | 48 +- modules/nf-core/bamtools/split/meta.yml | 48 +- modules/nf-core/bamtools/stats/meta.yml | 48 +- modules/nf-core/bamutil/trimbam/meta.yml | 65 +- modules/nf-core/bandage/image/meta.yml | 55 +- modules/nf-core/barrnap/meta.yml | 55 +- modules/nf-core/bases2fastq/meta.yml | 127 ++- modules/nf-core/basicpy/meta.yml | 53 +- modules/nf-core/bbmap/align/meta.yml | 72 +- modules/nf-core/bbmap/bbduk/meta.yml | 70 +- modules/nf-core/bbmap/bbmerge/meta.yml | 97 ++- modules/nf-core/bbmap/bbnorm/meta.yml | 61 +- modules/nf-core/bbmap/bbsplit/meta.yml | 125 +-- modules/nf-core/bbmap/clumpify/meta.yml | 62 +- modules/nf-core/bbmap/filterbyname/meta.yml | 88 +- modules/nf-core/bbmap/index/meta.yml | 30 +- modules/nf-core/bbmap/pileup/meta.yml | 63 +- modules/nf-core/bbmap/sendsketch/meta.yml | 53 +- modules/nf-core/bcftools/annotate/meta.yml | 91 +- modules/nf-core/bcftools/call/meta.yml | 111 ++- modules/nf-core/bcftools/concat/meta.yml | 81 +- modules/nf-core/bcftools/consensus/meta.yml | 67 +- modules/nf-core/bcftools/convert/meta.yml | 174 ++-- modules/nf-core/bcftools/csq/meta.yml | 116 +-- modules/nf-core/bcftools/filter/meta.yml | 69 +- modules/nf-core/bcftools/index/meta.yml | 65 +- modules/nf-core/bcftools/isec/meta.yml | 56 +- modules/nf-core/bcftools/merge/meta.yml | 123 +-- modules/nf-core/bcftools/mpileup/meta.yml | 109 ++- modules/nf-core/bcftools/norm/meta.yml | 102 ++- .../bcftools/pluginimputeinfo/meta.yml | 119 ++- .../nf-core/bcftools/pluginscatter/meta.yml | 127 +-- modules/nf-core/bcftools/pluginsplit/meta.yml | 124 +-- .../nf-core/bcftools/plugintag2tag/meta.yml | 106 ++- modules/nf-core/bcftools/query/meta.yml | 82 +- modules/nf-core/bcftools/reheader/meta.yml | 91 +- modules/nf-core/bcftools/roh/meta.yml | 95 +- modules/nf-core/bcftools/sort/meta.yml | 71 +- modules/nf-core/bcftools/split/meta.yml | 51 +- modules/nf-core/bcftools/stats/meta.yml | 124 ++- modules/nf-core/bcftools/view/meta.yml | 114 +-- modules/nf-core/bcl2fastq/meta.yml | 115 ++- modules/nf-core/bclconvert/meta.yml | 115 ++- modules/nf-core/beagle5/beagle/meta.yml | 98 ++- modules/nf-core/bedgovcf/meta.yml | 74 +- modules/nf-core/bedops/convert2bed/meta.yml | 49 +- modules/nf-core/bedops/gtf2bed/meta.yml | 43 +- modules/nf-core/bedtools/bamtobed/meta.yml | 43 +- modules/nf-core/bedtools/closest/meta.yml | 65 +- modules/nf-core/bedtools/complement/meta.yml | 55 +- modules/nf-core/bedtools/coverage/meta.yml | 68 +- modules/nf-core/bedtools/genomecov/meta.yml | 72 +- modules/nf-core/bedtools/getfasta/meta.yml | 54 +- modules/nf-core/bedtools/groupby/meta.yml | 53 +- modules/nf-core/bedtools/intersect/meta.yml | 70 +- modules/nf-core/bedtools/jaccard/meta.yml | 72 +- modules/nf-core/bedtools/makewindows/meta.yml | 48 +- modules/nf-core/bedtools/map/meta.yml | 70 +- modules/nf-core/bedtools/maskfasta/meta.yml | 54 +- modules/nf-core/bedtools/merge/meta.yml | 46 +- modules/nf-core/bedtools/multiinter/meta.yml | 56 +- modules/nf-core/bedtools/shift/meta.yml | 56 +- modules/nf-core/bedtools/slop/meta.yml | 49 +- modules/nf-core/bedtools/sort/meta.yml | 53 +- modules/nf-core/bedtools/split/meta.yml | 48 +- modules/nf-core/bedtools/subtract/meta.yml | 54 +- modules/nf-core/bedtools/unionbedg/meta.yml | 63 +- modules/nf-core/bioawk/meta.yml | 53 +- .../biobambam/bammarkduplicates2/meta.yml | 55 +- modules/nf-core/biobambam/bammerge/meta.yml | 65 +- .../nf-core/biobambam/bamsormadup/meta.yml | 95 +- modules/nf-core/biohansel/meta.yml | 77 +- modules/nf-core/biscuit/align/meta.yml | 71 +- .../nf-core/biscuit/biscuitblaster/meta.yml | 73 +- modules/nf-core/biscuit/bsconv/meta.yml | 58 +- modules/nf-core/biscuit/epiread/meta.yml | 64 +- modules/nf-core/biscuit/index/meta.yml | 24 +- modules/nf-core/biscuit/mergecg/meta.yml | 54 +- modules/nf-core/biscuit/pileup/meta.yml | 95 +- modules/nf-core/biscuit/qc/meta.yml | 65 +- modules/nf-core/biscuit/vcf2bed/meta.yml | 44 +- modules/nf-core/bismark/align/meta.yml | 79 +- .../bismark/coverage2cytosine/meta.yml | 75 +- modules/nf-core/bismark/deduplicate/meta.yml | 55 +- .../bismark/genomepreparation/meta.yml | 21 +- .../bismark/methylationextractor/meta.yml | 99 ++- modules/nf-core/bismark/report/meta.yml | 67 +- modules/nf-core/bismark/summary/meta.yml | 55 +- modules/nf-core/blast/blastdbcmd/meta.yml | 82 +- modules/nf-core/blast/blastn/meta.yml | 61 +- modules/nf-core/blast/blastp/meta.yml | 100 ++- modules/nf-core/blast/makeblastdb/meta.yml | 43 +- modules/nf-core/blast/tblastn/meta.yml | 61 +- modules/nf-core/blast/updateblastdb/meta.yml | 41 +- modules/nf-core/blat/meta.yml | 67 +- modules/nf-core/bowtie/align/meta.yml | 89 +- modules/nf-core/bowtie/build/meta.yml | 41 +- modules/nf-core/bowtie2/align/meta.yml | 159 ++-- modules/nf-core/bowtie2/build/meta.yml | 41 +- modules/nf-core/bracken/bracken/meta.yml | 75 +- modules/nf-core/bracken/build/meta.yml | 61 +- .../bracken/combinebrackenoutputs/meta.yml | 49 +- modules/nf-core/busco/busco/meta.yml | 172 ++-- modules/nf-core/busco/generateplot/meta.yml | 27 +- modules/nf-core/bwa/aln/meta.yml | 65 +- modules/nf-core/bwa/index/meta.yml | 41 +- modules/nf-core/bwa/mem/environment.yml | 4 +- modules/nf-core/bwa/mem/meta.yml | 111 ++- modules/nf-core/bwa/sampe/meta.yml | 72 +- modules/nf-core/bwa/samse/meta.yml | 72 +- modules/nf-core/bwamem2/index/meta.yml | 41 +- modules/nf-core/bwamem2/mem/environment.yml | 4 +- modules/nf-core/bwamem2/mem/meta.yml | 137 +-- modules/nf-core/bwameme/index/meta.yml | 45 +- modules/nf-core/bwameme/mem/meta.yml | 151 ++-- modules/nf-core/bwameth/align/meta.yml | 51 +- modules/nf-core/bwameth/index/meta.yml | 21 +- modules/nf-core/cadd/meta.yml | 60 +- modules/nf-core/cafe/meta.yml | 80 +- modules/nf-core/calder2/meta.yml | 55 +- modules/nf-core/canu/meta.yml | 155 ++-- modules/nf-core/cat/cat/meta.yml | 39 +- modules/nf-core/cat/fastq/meta.yml | 43 +- modules/nf-core/cdhit/cdhit/meta.yml | 55 +- modules/nf-core/cdhit/cdhitest/meta.yml | 57 +- modules/nf-core/celesta/meta.yml | 93 +- modules/nf-core/cellbender/merge/meta.yml | 59 +- .../cellbender/removebackground/meta.yml | 159 ++-- modules/nf-core/cellpose/meta.yml | 68 +- modules/nf-core/cellranger/count/meta.yml | 70 +- modules/nf-core/cellranger/mkfastq/meta.yml | 87 +- modules/nf-core/cellranger/mkgtf/meta.yml | 30 +- modules/nf-core/cellranger/mkref/meta.yml | 44 +- modules/nf-core/cellranger/mkvdjref/meta.yml | 57 +- modules/nf-core/cellranger/multi/meta.yml | 222 +++-- modules/nf-core/cellranger/vdj/meta.yml | 59 +- modules/nf-core/cellrangerarc/count/meta.yml | 61 +- .../nf-core/cellrangerarc/mkfastq/meta.yml | 44 +- modules/nf-core/cellrangerarc/mkgtf/meta.yml | 30 +- modules/nf-core/cellrangerarc/mkref/meta.yml | 66 +- modules/nf-core/cellrangeratac/count/meta.yml | 52 +- .../nf-core/cellrangeratac/mkfastq/meta.yml | 44 +- modules/nf-core/cellrangeratac/mkref/meta.yml | 62 +- modules/nf-core/cellsnp/modea/meta.yml | 142 +-- modules/nf-core/centrifuge/build/meta.yml | 90 +- .../nf-core/centrifuge/centrifuge/meta.yml | 119 ++- modules/nf-core/centrifuge/kreport/meta.yml | 55 +- modules/nf-core/checkm/lineagewf/meta.yml | 91 +- modules/nf-core/checkm/qa/meta.yml | 86 +- .../nf-core/checkm2/databasedownload/meta.yml | 25 +- modules/nf-core/checkm2/predict/meta.yml | 76 +- modules/nf-core/checkqc/meta.yml | 57 +- .../nf-core/checkv/downloaddatabase/meta.yml | 17 +- modules/nf-core/checkv/endtoend/meta.yml | 114 ++- .../nf-core/checkv/updatedatabase/meta.yml | 51 +- .../nf-core/chewbbaca/createschema/meta.yml | 90 +- modules/nf-core/chopper/meta.yml | 53 +- modules/nf-core/chromap/chromap/meta.yml | 151 ++-- modules/nf-core/chromap/index/meta.yml | 43 +- modules/nf-core/chromograph/meta.yml | 150 ++-- .../nf-core/circexplorer2/annotate/meta.yml | 59 +- modules/nf-core/circexplorer2/parse/meta.yml | 49 +- .../circularmapper/circulargenerator/meta.yml | 95 +- .../circularmapper/realignsamfile/meta.yml | 95 +- modules/nf-core/clame/meta.yml | 112 ++- modules/nf-core/clippy/meta.yml | 77 +- modules/nf-core/clonalframeml/meta.yml | 117 ++- modules/nf-core/clustalo/align/meta.yml | 73 +- modules/nf-core/clustalo/guidetree/meta.yml | 47 +- modules/nf-core/cmseq/polymut/meta.yml | 70 +- modules/nf-core/cnvkit/access/meta.yml | 63 +- modules/nf-core/cnvkit/antitarget/meta.yml | 43 +- modules/nf-core/cnvkit/batch/meta.yml | 191 ++-- modules/nf-core/cnvkit/call/meta.yml | 56 +- modules/nf-core/cnvkit/export/meta.yml | 47 +- modules/nf-core/cnvkit/genemetrics/meta.yml | 63 +- modules/nf-core/cnvkit/reference/meta.yml | 45 +- modules/nf-core/cnvkit/target/meta.yml | 61 +- modules/nf-core/cnvnator/cnvnator/meta.yml | 122 +-- modules/nf-core/cnvnator/convert2vcf/meta.yml | 48 +- modules/nf-core/cnvpytor/callcnvs/meta.yml | 50 +- modules/nf-core/cnvpytor/histogram/meta.yml | 50 +- .../nf-core/cnvpytor/importreaddepth/meta.yml | 72 +- modules/nf-core/cnvpytor/partition/meta.yml | 51 +- modules/nf-core/cnvpytor/view/meta.yml | 83 +- modules/nf-core/cobrameta/meta.yml | 240 +++-- .../nf-core/cobs/classicconstruct/meta.yml | 67 +- .../nf-core/cobs/compactconstruct/meta.yml | 67 +- modules/nf-core/concoct/concoct/meta.yml | 117 ++- .../concoct/concoctcoveragetable/meta.yml | 63 +- modules/nf-core/concoct/cutupfasta/meta.yml | 66 +- .../nf-core/concoct/extractfastabins/meta.yml | 54 +- .../concoct/mergecutupclustering/meta.yml | 45 +- modules/nf-core/conifer/meta.yml | 51 +- .../controlfreec/assesssignificance/meta.yml | 63 +- modules/nf-core/controlfreec/freec/meta.yml | 307 +++---- .../nf-core/controlfreec/freec2bed/meta.yml | 48 +- .../controlfreec/freec2circos/meta.yml | 48 +- .../nf-core/controlfreec/makegraph/meta.yml | 86 +- .../nf-core/controlfreec/makegraph2/meta.yml | 82 +- modules/nf-core/cooler/balance/meta.yml | 51 +- modules/nf-core/cooler/cload/meta.yml | 68 +- modules/nf-core/cooler/digest/meta.yml | 39 +- modules/nf-core/cooler/dump/meta.yml | 51 +- modules/nf-core/cooler/makebins/meta.yml | 38 +- modules/nf-core/cooler/merge/meta.yml | 45 +- modules/nf-core/cooler/zoomify/meta.yml | 45 +- modules/nf-core/coreograph/meta.yml | 82 +- modules/nf-core/crabz/compress/meta.yml | 50 +- modules/nf-core/crabz/decompress/meta.yml | 50 +- .../nf-core/crisprcleanr/normalize/meta.yml | 62 +- modules/nf-core/crumble/meta.yml | 93 +- modules/nf-core/csvtk/concat/meta.yml | 61 +- modules/nf-core/csvtk/join/meta.yml | 48 +- modules/nf-core/csvtk/split/meta.yml | 64 +- .../custom/catadditionalfasta/meta.yml | 89 +- .../custom/dumpsoftwareversions/meta.yml | 36 +- .../custom/getchromsizes/environment.yml | 3 +- modules/nf-core/custom/getchromsizes/meta.yml | 67 +- modules/nf-core/custom/gtffilter/meta.yml | 69 +- modules/nf-core/custom/matrixfilter/meta.yml | 143 ++- .../custom/sratoolsncbisettings/meta.yml | 20 +- .../nf-core/custom/tabulartogseacls/meta.yml | 58 +- .../nf-core/custom/tabulartogseagct/meta.yml | 50 +- modules/nf-core/custom/tx2gene/meta.yml | 84 +- modules/nf-core/cutadapt/meta.yml | 57 +- modules/nf-core/cutesv/meta.yml | 72 +- modules/nf-core/damageprofiler/meta.yml | 69 +- modules/nf-core/dastool/dastool/meta.yml | 198 +++-- .../dastool/fastatocontig2bin/meta.yml | 56 +- .../nf-core/dastool/scaffolds2bin/meta.yml | 56 +- modules/nf-core/datavzrd/meta.yml | 48 +- modules/nf-core/decoupler/decoupler/meta.yml | 96 +- modules/nf-core/dedup/meta.yml | 87 +- modules/nf-core/deeparg/downloaddata/meta.yml | 23 +- modules/nf-core/deeparg/predict/meta.yml | 106 ++- modules/nf-core/deepbgc/download/meta.yml | 20 +- modules/nf-core/deepbgc/pipeline/meta.yml | 173 ++-- modules/nf-core/deepcell/mesmer/meta.yml | 62 +- modules/nf-core/deeptmhmm/meta.yml | 100 ++- .../nf-core/deeptools/bamcoverage/meta.yml | 90 +- .../nf-core/deeptools/computematrix/meta.yml | 72 +- .../deeptools/multibamsummary/meta.yml | 64 +- .../deeptools/plotcorrelation/meta.yml | 89 +- .../deeptools/plotfingerprint/meta.yml | 84 +- .../nf-core/deeptools/plotheatmap/meta.yml | 67 +- modules/nf-core/deeptools/plotpca/meta.yml | 69 +- .../nf-core/deeptools/plotprofile/meta.yml | 68 +- .../nf-core/deepvariant/callvariants/meta.yml | 40 +- .../nf-core/deepvariant/makeexamples/meta.yml | 142 +-- modules/nf-core/deepvariant/meta.yml | 171 ++-- .../deepvariant/postprocessvariants/meta.yml | 151 ++-- .../deepvariant/rundeepvariant/meta.yml | 170 ++-- modules/nf-core/delly/call/meta.yml | 133 +-- modules/nf-core/demuxem/meta.yml | 112 +-- modules/nf-core/deseq2/differential/meta.yml | 235 +++-- modules/nf-core/diamond/blastp/meta.yml | 161 ++-- modules/nf-core/diamond/blastx/meta.yml | 173 ++-- modules/nf-core/diamond/cluster/meta.yml | 53 +- modules/nf-core/diamond/makedb/meta.yml | 68 +- modules/nf-core/dragmap/align/environment.yml | 4 +- modules/nf-core/dragmap/align/meta.yml | 128 ++- modules/nf-core/dragmap/hashtable/meta.yml | 41 +- modules/nf-core/dragonflye/meta.yml | 105 ++- .../nf-core/dshbio/exportsegments/meta.yml | 43 +- modules/nf-core/dshbio/filterbed/meta.yml | 43 +- modules/nf-core/dshbio/filtergff3/meta.yml | 43 +- modules/nf-core/dshbio/splitbed/meta.yml | 43 +- modules/nf-core/dshbio/splitgff3/meta.yml | 43 +- modules/nf-core/duphold/meta.yml | 92 +- modules/nf-core/dupradar/meta.yml | 147 ++-- modules/nf-core/dysgu/meta.yml | 94 +- modules/nf-core/ectyper/meta.yml | 69 +- modules/nf-core/eggnogmapper/meta.yml | 103 ++- modules/nf-core/eido/convert/meta.yml | 35 +- modules/nf-core/eido/validate/meta.yml | 39 +- .../eigenstratsnpcoverage/meta.yml | 79 +- modules/nf-core/eklipse/meta.yml | 85 +- modules/nf-core/elprep/filter/meta.yml | 220 +++-- modules/nf-core/elprep/merge/meta.yml | 50 +- modules/nf-core/elprep/split/meta.yml | 50 +- modules/nf-core/emboss/cons/meta.yml | 48 +- modules/nf-core/emboss/revseq/meta.yml | 46 +- modules/nf-core/emboss/seqret/meta.yml | 55 +- modules/nf-core/emmtyper/meta.yml | 45 +- modules/nf-core/endorspy/meta.yml | 65 +- modules/nf-core/ensemblvep/download/meta.yml | 56 +- modules/nf-core/ensemblvep/filtervep/meta.yml | 52 +- modules/nf-core/ensemblvep/vep/meta.yml | 148 ++-- modules/nf-core/entrezdirect/esearch/meta.yml | 53 +- .../nf-core/entrezdirect/esummary/meta.yml | 57 +- modules/nf-core/entrezdirect/xtract/meta.yml | 61 +- modules/nf-core/epang/place/meta.yml | 95 +- modules/nf-core/epang/split/meta.yml | 61 +- modules/nf-core/estsfs/meta.yml | 84 +- modules/nf-core/evigene/tr2aacds/meta.yml | 56 +- modules/nf-core/expansionhunter/meta.yml | 133 +-- .../expansionhunterdenovo/merge/meta.yml | 90 +- .../expansionhunterdenovo/profile/meta.yml | 116 +-- modules/nf-core/falco/meta.yml | 64 +- modules/nf-core/famsa/align/meta.yml | 71 +- modules/nf-core/famsa/guidetree/meta.yml | 44 +- modules/nf-core/faqcs/meta.yml | 124 ++- modules/nf-core/fargene/meta.yml | 235 +++-- modules/nf-core/fastani/meta.yml | 54 +- modules/nf-core/fastavalidator/meta.yml | 56 +- modules/nf-core/fastawindows/meta.yml | 97 ++- modules/nf-core/fastk/fastk/meta.yml | 71 +- modules/nf-core/fastk/histex/meta.yml | 45 +- modules/nf-core/fastk/merge/meta.yml | 86 +- modules/nf-core/fastme/meta.yml | 94 +- modules/nf-core/fastp/meta.yml | 138 +-- modules/nf-core/fastqc/meta.yml | 57 +- modules/nf-core/fastqscan/meta.yml | 45 +- .../fastqscreen/buildfromindex/meta.yml | 33 +- .../nf-core/fastqscreen/fastqscreen/meta.yml | 90 +- modules/nf-core/fasttree/meta.yml | 31 +- modules/nf-core/fastx/collapser/meta.yml | 57 +- modules/nf-core/fcs/fcsadaptor/meta.yml | 91 +- modules/nf-core/fcs/fcsgx/meta.yml | 66 +- modules/nf-core/ffq/meta.yml | 29 +- .../fgbio/callduplexconsensusreads/meta.yml | 66 +- .../callmolecularconsensusreads/meta.yml | 59 +- .../fgbio/collectduplexseqmetrics/meta.yml | 135 ++- modules/nf-core/fgbio/fastqtobam/meta.yml | 55 +- .../fgbio/filterconsensusreads/meta.yml | 87 +- .../nf-core/fgbio/groupreadsbyumi/meta.yml | 74 +- modules/nf-core/fgbio/sortbam/meta.yml | 50 +- modules/nf-core/fgbio/zipperbams/meta.yml | 103 +-- modules/nf-core/filtlong/meta.yml | 70 +- modules/nf-core/flash/meta.yml | 69 +- modules/nf-core/flye/meta.yml | 117 ++- modules/nf-core/foldcomp/compress/meta.yml | 50 +- modules/nf-core/foldcomp/decompress/meta.yml | 50 +- modules/nf-core/foldmason/easymsa/meta.yml | 70 +- .../nf-core/foldseek/createdb/environment.yml | 1 + modules/nf-core/foldseek/createdb/meta.yml | 45 +- .../foldseek/easysearch/environment.yml | 1 + modules/nf-core/foldseek/easysearch/meta.yml | 72 +- modules/nf-core/fq/generate/meta.yml | 35 +- modules/nf-core/fq/lint/meta.yml | 37 +- modules/nf-core/fq/subsample/meta.yml | 48 +- modules/nf-core/fqtk/meta.yml | 80 +- modules/nf-core/freebayes/meta.yml | 178 ++-- modules/nf-core/freyja/boot/meta.yml | 98 ++- modules/nf-core/freyja/demix/meta.yml | 71 +- modules/nf-core/freyja/update/meta.yml | 38 +- modules/nf-core/freyja/variants/meta.yml | 63 +- modules/nf-core/galah/meta.yml | 87 +- modules/nf-core/gamma/gamma/meta.yml | 89 +- modules/nf-core/gangstr/meta.yml | 106 ++- modules/nf-core/ganon/buildcustom/meta.yml | 80 +- modules/nf-core/ganon/classify/meta.yml | 117 ++- modules/nf-core/ganon/report/meta.yml | 58 +- modules/nf-core/ganon/table/meta.yml | 50 +- modules/nf-core/gappa/examineassign/meta.yml | 101 ++- modules/nf-core/gappa/examinegraft/meta.yml | 46 +- .../nf-core/gappa/examineheattree/meta.yml | 106 ++- modules/nf-core/gatk/indelrealigner/meta.yml | 141 +-- .../gatk/realignertargetcreator/meta.yml | 134 +-- .../nf-core/gatk/unifiedgenotyper/meta.yml | 180 ++-- .../gatk4/addorreplacereadgroups/meta.yml | 105 ++- .../nf-core/gatk4/annotateintervals/meta.yml | 185 ++-- modules/nf-core/gatk4/applybqsr/meta.yml | 101 ++- modules/nf-core/gatk4/applyvqsr/meta.yml | 107 ++- modules/nf-core/gatk4/asereadcounter/meta.yml | 128 +-- .../nf-core/gatk4/baserecalibrator/meta.yml | 99 ++- .../nf-core/gatk4/bedtointervallist/meta.yml | 59 +- .../gatk4/calculatecontamination/meta.yml | 61 +- .../gatk4/calibratedragstrmodel/meta.yml | 95 +- .../nf-core/gatk4/cnnscorevariants/meta.yml | 119 +-- .../nf-core/gatk4/collectreadcounts/meta.yml | 136 +-- .../nf-core/gatk4/collectsvevidence/meta.yml | 163 ++-- modules/nf-core/gatk4/combinegvcfs/meta.yml | 78 +- .../gatk4/composestrtablefile/meta.yml | 45 +- .../gatk4/condensedepthevidence/meta.yml | 91 +- .../createreadcountpanelofnormals/meta.yml | 48 +- .../gatk4/createsequencedictionary/meta.yml | 37 +- .../createsomaticpanelofnormals/meta.yml | 104 ++- .../nf-core/gatk4/denoisereadcounts/meta.yml | 75 +- .../determinegermlinecontigploidy/meta.yml | 112 +-- .../gatk4/estimatelibrarycomplexity/meta.yml | 69 +- modules/nf-core/gatk4/fastqtosam/meta.yml | 50 +- .../nf-core/gatk4/filterintervals/meta.yml | 90 +- .../nf-core/gatk4/filtermutectcalls/meta.yml | 162 ++-- .../gatk4/filtervarianttranches/meta.yml | 110 ++- .../nf-core/gatk4/gatherbqsrreports/meta.yml | 43 +- .../gatk4/gatherpileupsummaries/meta.yml | 46 +- .../nf-core/gatk4/genomicsdbimport/meta.yml | 139 +-- modules/nf-core/gatk4/genotypegvcfs/meta.yml | 170 ++-- .../nf-core/gatk4/germlinecnvcaller/meta.yml | 107 ++- .../nf-core/gatk4/getpileupsummaries/meta.yml | 128 +-- .../nf-core/gatk4/haplotypecaller/meta.yml | 178 ++-- .../nf-core/gatk4/indexfeaturefile/meta.yml | 43 +- .../nf-core/gatk4/intervallisttobed/meta.yml | 42 +- .../nf-core/gatk4/intervallisttools/meta.yml | 51 +- .../gatk4/learnreadorientationmodel/meta.yml | 37 +- .../gatk4/leftalignandtrimvariants/meta.yml | 99 ++- .../gatk4/markduplicates/environment.yml | 3 +- modules/nf-core/gatk4/markduplicates/meta.yml | 121 ++- .../nf-core/gatk4/mergebamalignment/meta.yml | 77 +- .../nf-core/gatk4/mergemutectstats/meta.yml | 45 +- modules/nf-core/gatk4/mergevcfs/meta.yml | 66 +- modules/nf-core/gatk4/mutect2/meta.yml | 175 ++-- .../postprocessgermlinecnvcalls/meta.yml | 104 ++- .../gatk4/preprocessintervals/meta.yml | 128 +-- modules/nf-core/gatk4/printreads/meta.yml | 131 +-- .../nf-core/gatk4/printsvevidence/meta.yml | 108 ++- modules/nf-core/gatk4/reblockgvcf/meta.yml | 104 +-- modules/nf-core/gatk4/revertsam/meta.yml | 37 +- modules/nf-core/gatk4/samtofastq/meta.yml | 37 +- modules/nf-core/gatk4/selectvariants/meta.yml | 73 +- modules/nf-core/gatk4/shiftfasta/meta.yml | 151 ++-- modules/nf-core/gatk4/sitedepthtobaf/meta.yml | 105 ++- modules/nf-core/gatk4/splitcram/meta.yml | 48 +- modules/nf-core/gatk4/splitintervals/meta.yml | 98 ++- .../nf-core/gatk4/splitncigarreads/meta.yml | 105 +-- modules/nf-core/gatk4/svannotate/meta.yml | 105 ++- modules/nf-core/gatk4/svcluster/meta.yml | 102 ++- .../nf-core/gatk4/variantfiltration/meta.yml | 110 +-- .../gatk4/variantrecalibrator/meta.yml | 132 +-- .../nf-core/gatk4/variantstotable/meta.yml | 123 +-- modules/nf-core/gatk4spark/applybqsr/meta.yml | 101 ++- .../gatk4spark/baserecalibrator/meta.yml | 99 ++- .../gatk4spark/markduplicates/meta.yml | 99 ++- modules/nf-core/gawk/meta.yml | 56 +- modules/nf-core/gecco/run/meta.yml | 117 ++- .../nf-core/gem2/gem2bedmappability/meta.yml | 82 +- modules/nf-core/gem2/gemindexer/meta.yml | 63 +- modules/nf-core/gem2/gemmappability/meta.yml | 55 +- modules/nf-core/gem3/gem3indexer/meta.yml | 60 +- modules/nf-core/gem3/gem3mapper/meta.yml | 72 +- modules/nf-core/genescopefk/meta.yml | 122 ++- modules/nf-core/genmap/index/meta.yml | 43 +- modules/nf-core/genmap/map/meta.yml | 97 ++- modules/nf-core/genmod/annotate/meta.yml | 45 +- modules/nf-core/genmod/compound/meta.yml | 45 +- modules/nf-core/genmod/models/meta.yml | 60 +- modules/nf-core/genmod/score/meta.yml | 60 +- modules/nf-core/genomad/download/meta.yml | 18 +- modules/nf-core/genomad/endtoend/meta.yml | 196 +++-- modules/nf-core/genomescope2/meta.yml | 136 ++- modules/nf-core/genotyphi/parse/meta.yml | 48 +- modules/nf-core/genrich/meta.yml | 133 +-- modules/nf-core/geofetch/meta.yml | 39 +- modules/nf-core/geoquery/getgeo/meta.yml | 57 +- modules/nf-core/getorganelle/config/meta.yml | 35 +- .../nf-core/getorganelle/fromreads/meta.yml | 72 +- modules/nf-core/gfaffix/meta.yml | 55 +- modules/nf-core/gfastats/meta.yml | 101 ++- modules/nf-core/gfatools/gfa2fa/meta.yml | 46 +- modules/nf-core/gfatools/stat/meta.yml | 46 +- modules/nf-core/gffcompare/meta.yml | 173 ++-- modules/nf-core/gffread/meta.yml | 84 +- modules/nf-core/gget/gget/meta.yml | 63 +- modules/nf-core/glimpse/chunk/meta.yml | 65 +- modules/nf-core/glimpse/concordance/meta.yml | 169 ++-- modules/nf-core/glimpse/ligate/meta.yml | 63 +- modules/nf-core/glimpse/phase/meta.yml | 122 +-- modules/nf-core/glimpse/sample/meta.yml | 48 +- modules/nf-core/glimpse2/chunk/meta.yml | 105 +-- modules/nf-core/glimpse2/concordance/meta.yml | 228 +++-- modules/nf-core/glimpse2/ligate/meta.yml | 56 +- modules/nf-core/glimpse2/phase/meta.yml | 177 ++-- .../nf-core/glimpse2/splitreference/meta.yml | 91 +- modules/nf-core/glnexus/meta.yml | 42 +- modules/nf-core/gmmdemux/meta.yml | 163 ++-- modules/nf-core/gnu/sort/meta.yml | 39 +- modules/nf-core/gnu/split/meta.yml | 45 +- modules/nf-core/goat/taxonsearch/meta.yml | 57 +- modules/nf-core/goleft/indexcov/meta.yml | 132 ++- modules/nf-core/goleft/indexsplit/meta.yml | 70 +- modules/nf-core/gprofiler2/gost/meta.yml | 171 ++-- modules/nf-core/grabix/check/meta.yml | 31 +- modules/nf-core/graphmap2/align/meta.yml | 59 +- modules/nf-core/graphmap2/index/meta.yml | 25 +- modules/nf-core/graphtyper/genotype/meta.yml | 106 ++- .../graphtyper/vcfconcatenate/meta.yml | 60 +- modules/nf-core/gridss/gridss/meta.yml | 83 +- .../gridss/gridssgenerateponbedpe/meta.yml | 131 +-- .../gridss/gridsssomaticfilter/meta.yml | 77 +- modules/nf-core/gsea/gsea/meta.yml | 319 ++++--- modules/nf-core/gstama/collapse/meta.yml | 164 ++-- modules/nf-core/gstama/merge/meta.yml | 95 +- modules/nf-core/gstama/polyacleanup/meta.yml | 74 +- modules/nf-core/gt/gff3/meta.yml | 59 +- modules/nf-core/gt/gff3validator/meta.yml | 56 +- modules/nf-core/gt/ltrharvest/meta.yml | 81 +- modules/nf-core/gt/stat/meta.yml | 47 +- modules/nf-core/gt/suffixerator/meta.yml | 50 +- modules/nf-core/gtdbtk/classifywf/meta.yml | 175 ++-- modules/nf-core/gtfsort/meta.yml | 30 +- modules/nf-core/gubbins/meta.yml | 93 +- modules/nf-core/gunc/downloaddb/meta.yml | 31 +- modules/nf-core/gunc/mergecheckm/meta.yml | 56 +- modules/nf-core/gunc/run/meta.yml | 70 +- modules/nf-core/gunzip/meta.yml | 37 +- .../gvcftools/extractvariants/meta.yml | 51 +- .../nf-core/hamronization/abricate/meta.yml | 87 +- .../hamronization/amrfinderplus/meta.yml | 87 +- .../nf-core/hamronization/deeparg/meta.yml | 87 +- .../nf-core/hamronization/fargene/meta.yml | 87 +- modules/nf-core/hamronization/rgi/meta.yml | 84 +- .../nf-core/hamronization/summarize/meta.yml | 53 +- modules/nf-core/hapibd/meta.yml | 95 +- modules/nf-core/haplocheck/meta.yml | 60 +- modules/nf-core/haplogrep2/classify/meta.yml | 51 +- modules/nf-core/happy/ftxpy/meta.yml | 104 +-- modules/nf-core/happy/happy/meta.yml | 287 +++--- modules/nf-core/happy/prepy/meta.yml | 89 +- modules/nf-core/happy/sompy/meta.yml | 189 ++-- modules/nf-core/hicap/meta.yml | 88 +- modules/nf-core/hicexplorer/hicpca/meta.yml | 64 +- modules/nf-core/hifiasm/meta.yml | 198 +++-- modules/nf-core/hisat2/align/meta.yml | 107 ++- modules/nf-core/hisat2/build/meta.yml | 83 +- .../hisat2/extractsplicesites/meta.yml | 49 +- modules/nf-core/hlala/preparegraph/meta.yml | 31 +- modules/nf-core/hlala/typing/meta.yml | 125 ++- modules/nf-core/hmmcopy/gccounter/meta.yml | 49 +- modules/nf-core/hmmcopy/generatemap/meta.yml | 50 +- modules/nf-core/hmmcopy/mapcounter/meta.yml | 52 +- modules/nf-core/hmmcopy/readcounter/meta.yml | 56 +- modules/nf-core/hmmer/eslalimask/meta.yml | 133 +-- modules/nf-core/hmmer/eslreformat/meta.yml | 49 +- modules/nf-core/hmmer/hmmalign/meta.yml | 56 +- modules/nf-core/hmmer/hmmbuild/meta.yml | 53 +- modules/nf-core/hmmer/hmmfetch/meta.yml | 77 +- modules/nf-core/hmmer/hmmrank/environment.yml | 4 +- modules/nf-core/hmmer/hmmrank/meta.yml | 50 +- modules/nf-core/hmmer/hmmsearch/meta.yml | 110 ++- modules/nf-core/hmtnote/annotate/meta.yml | 44 +- modules/nf-core/homer/annotatepeaks/meta.yml | 74 +- modules/nf-core/homer/findpeaks/meta.yml | 45 +- .../homer/maketagdirectory/environment.yml | 7 +- .../nf-core/homer/maketagdirectory/meta.yml | 66 +- modules/nf-core/homer/makeucscfile/meta.yml | 43 +- modules/nf-core/homer/pos2bed/meta.yml | 42 +- modules/nf-core/hpsuissero/meta.yml | 45 +- modules/nf-core/htseq/count/meta.yml | 71 +- modules/nf-core/htsnimtools/vcfcheck/meta.yml | 87 +- modules/nf-core/humid/meta.yml | 109 ++- modules/nf-core/hypo/meta.yml | 78 +- modules/nf-core/ichorcna/createpon/meta.yml | 86 +- modules/nf-core/ichorcna/run/meta.yml | 224 +++-- modules/nf-core/icountmini/metagene/meta.yml | 53 +- modules/nf-core/icountmini/peaks/meta.yml | 52 +- modules/nf-core/icountmini/segment/meta.yml | 53 +- modules/nf-core/icountmini/sigxls/meta.yml | 66 +- modules/nf-core/icountmini/summary/meta.yml | 74 +- modules/nf-core/idemux/meta.yml | 67 +- modules/nf-core/idr/meta.yml | 53 +- modules/nf-core/igv/js/meta.yml | 75 +- modules/nf-core/igvreports/meta.yml | 101 ++- modules/nf-core/ilastik/multicut/meta.yml | 90 +- .../ilastik/pixelclassification/meta.yml | 68 +- modules/nf-core/instrain/compare/meta.yml | 111 ++- modules/nf-core/instrain/profile/meta.yml | 145 +-- modules/nf-core/interproscan/meta.yml | 83 +- modules/nf-core/iphop/download/meta.yml | 15 +- modules/nf-core/iphop/predict/meta.yml | 77 +- modules/nf-core/iqtree/meta.yml | 489 +++++++---- modules/nf-core/islandpath/meta.yml | 51 +- modules/nf-core/ismapper/meta.yml | 64 +- modules/nf-core/isoseq/cluster/meta.yml | 166 ++-- modules/nf-core/isoseq/refine/meta.yml | 102 ++- modules/nf-core/isoseq3/tag/meta.yml | 70 +- modules/nf-core/ivar/consensus/meta.yml | 85 +- modules/nf-core/ivar/trim/meta.yml | 71 +- modules/nf-core/ivar/variants/meta.yml | 92 +- modules/nf-core/jasminesv/environment.yml | 3 +- modules/nf-core/jasminesv/meta.yml | 110 +-- .../nf-core/jupyternotebook/environment.yml | 3 +- modules/nf-core/jupyternotebook/meta.yml | 73 +- modules/nf-core/jvarkit/vcffilterjdk/meta.yml | 178 ++-- .../nf-core/jvarkit/vcfpolyx/environment.yml | 1 - modules/nf-core/jvarkit/vcfpolyx/meta.yml | 137 +-- .../jvarkit/wgscoverageplotter/meta.yml | 106 +-- modules/nf-core/kaiju/kaiju/meta.yml | 62 +- modules/nf-core/kaiju/kaiju2krona/meta.yml | 51 +- modules/nf-core/kaiju/kaiju2table/meta.yml | 58 +- modules/nf-core/kaiju/mergeoutputs/meta.yml | 67 +- modules/nf-core/kaiju/mkfmi/meta.yml | 46 +- modules/nf-core/kalign/align/meta.yml | 52 +- modules/nf-core/kallisto/index/meta.yml | 47 +- modules/nf-core/kallisto/quant/meta.yml | 128 +-- .../nf-core/kallistobustools/count/meta.yml | 102 ++- modules/nf-core/kallistobustools/ref/meta.yml | 80 +- modules/nf-core/kat/hist/meta.yml | 110 ++- .../nf-core/khmer/normalizebymedian/meta.yml | 43 +- modules/nf-core/khmer/uniquekmers/meta.yml | 39 +- modules/nf-core/kleborate/meta.yml | 51 +- modules/nf-core/kmcp/compute/meta.yml | 62 +- modules/nf-core/kmcp/index/meta.yml | 60 +- modules/nf-core/kmcp/merge/meta.yml | 48 +- modules/nf-core/kmcp/profile/meta.yml | 55 +- modules/nf-core/kmcp/search/meta.yml | 54 +- modules/nf-core/kofamscan/meta.yml | 70 +- modules/nf-core/kraken2/add/meta.yml | 70 +- modules/nf-core/kraken2/build/meta.yml | 53 +- .../nf-core/kraken2/buildstandard/meta.yml | 26 +- modules/nf-core/kraken2/kraken2/meta.yml | 121 +-- .../krakentools/combinekreports/meta.yml | 52 +- .../krakentools/extractkrakenreads/meta.yml | 83 +- .../krakentools/kreport2krona/meta.yml | 49 +- modules/nf-core/krakenuniq/build/meta.yml | 60 +- modules/nf-core/krakenuniq/download/meta.yml | 36 +- .../krakenuniq/preloadedkrakenuniq/meta.yml | 146 ++-- modules/nf-core/krona/kronadb/meta.yml | 25 +- .../nf-core/krona/ktimporttaxonomy/meta.yml | 62 +- modules/nf-core/krona/ktimporttext/meta.yml | 53 +- .../nf-core/krona/ktupdatetaxonomy/meta.yml | 25 +- modules/nf-core/last/dotplot/meta.yml | 87 +- modules/nf-core/last/lastal/meta.yml | 74 +- modules/nf-core/last/lastdb/meta.yml | 48 +- modules/nf-core/last/mafconvert/meta.yml | 150 ++-- modules/nf-core/last/mafswap/meta.yml | 47 +- modules/nf-core/last/postmask/meta.yml | 47 +- modules/nf-core/last/split/meta.yml | 59 +- modules/nf-core/last/train/meta.yml | 66 +- modules/nf-core/learnmsa/align/meta.yml | 51 +- modules/nf-core/leehom/meta.yml | 131 ++- modules/nf-core/legsta/meta.yml | 45 +- modules/nf-core/leviosam2/index/meta.yml | 52 +- modules/nf-core/leviosam2/lift/meta.yml | 65 +- modules/nf-core/liftoff/meta.yml | 94 +- modules/nf-core/lima/meta.yml | 213 +++-- modules/nf-core/limma/differential/meta.yml | 136 +-- modules/nf-core/lissero/meta.yml | 45 +- modules/nf-core/lofreq/alnqual/meta.yml | 56 +- modules/nf-core/lofreq/call/meta.yml | 62 +- modules/nf-core/lofreq/callparallel/meta.yml | 113 +-- modules/nf-core/lofreq/filter/meta.yml | 51 +- modules/nf-core/lofreq/indelqual/meta.yml | 67 +- modules/nf-core/lofreq/somatic/meta.yml | 108 +-- modules/nf-core/lofreq/viterbi/meta.yml | 71 +- modules/nf-core/longphase/haplotag/meta.yml | 139 +-- .../nf-core/longphase/phase/environment.yml | 7 +- modules/nf-core/longphase/phase/meta.yml | 123 +-- modules/nf-core/ltrfinder/meta.yml | 60 +- modules/nf-core/ltrharvest/meta.yml | 59 +- modules/nf-core/ltrretriever/lai/meta.yml | 88 +- .../ltrretriever/ltrretriever/meta.yml | 142 +-- modules/nf-core/macrel/contigs/meta.yml | 102 ++- modules/nf-core/macs2/callpeak/meta.yml | 95 +- modules/nf-core/macs3/callpeak/meta.yml | 114 ++- modules/nf-core/mafft/meta.yml | 153 ++-- modules/nf-core/mageck/count/meta.yml | 74 +- modules/nf-core/mageck/mle/meta.yml | 84 +- modules/nf-core/mageck/test/meta.yml | 95 +- modules/nf-core/magus/align/meta.yml | 89 +- modules/nf-core/magus/guidetree/meta.yml | 51 +- modules/nf-core/malt/build/meta.yml | 52 +- modules/nf-core/malt/run/meta.yml | 73 +- modules/nf-core/maltextract/meta.yml | 58 +- .../nf-core/manta/convertinversion/meta.yml | 79 +- modules/nf-core/manta/germline/meta.yml | 175 ++-- modules/nf-core/manta/somatic/meta.yml | 215 +++-- modules/nf-core/manta/tumoronly/meta.yml | 175 ++-- modules/nf-core/mapad/index/meta.yml | 45 +- modules/nf-core/mapad/map/meta.yml | 111 +-- modules/nf-core/mapdamage2/meta.yml | 257 ++++-- modules/nf-core/mash/dist/meta.yml | 53 +- modules/nf-core/mash/screen/meta.yml | 57 +- modules/nf-core/mash/sketch/meta.yml | 53 +- modules/nf-core/mashmap/meta.yml | 66 +- modules/nf-core/mashtree/meta.yml | 57 +- modules/nf-core/maxbin2/meta.yml | 147 +++- modules/nf-core/maxquant/lfq/meta.yml | 66 +- modules/nf-core/mcquant/meta.yml | 87 +- modules/nf-core/mcroni/meta.yml | 60 +- modules/nf-core/mcstaging/imc2mc/meta.yml | 54 +- .../nf-core/mcstaging/phenoimager2mc/meta.yml | 51 +- modules/nf-core/md5sum/meta.yml | 50 +- modules/nf-core/medaka/meta.yml | 56 +- modules/nf-core/megahit/meta.yml | 123 ++- modules/nf-core/megan/daa2info/meta.yml | 63 +- modules/nf-core/megan/rma2info/meta.yml | 63 +- modules/nf-core/meningotype/meta.yml | 48 +- modules/nf-core/merfin/hist/meta.yml | 121 +-- modules/nf-core/merqury/hapmers/meta.yml | 115 ++- modules/nf-core/merqury/merqury/meta.yml | 235 +++-- modules/nf-core/merquryfk/katcomp/meta.yml | 129 ++- modules/nf-core/merquryfk/katgc/meta.yml | 113 ++- modules/nf-core/merquryfk/merquryfk/meta.yml | 271 ++++-- modules/nf-core/merquryfk/ploidyplot/meta.yml | 113 ++- modules/nf-core/meryl/count/meta.yml | 53 +- modules/nf-core/meryl/histogram/meta.yml | 49 +- modules/nf-core/meryl/unionsum/meta.yml | 49 +- .../jgisummarizebamcontigdepths/meta.yml | 53 +- modules/nf-core/metabat2/metabat2/meta.yml | 107 ++- modules/nf-core/metaeuk/easypredict/meta.yml | 93 +- modules/nf-core/metamaps/classify/meta.yml | 151 ++-- modules/nf-core/metamaps/mapdirectly/meta.yml | 91 +- modules/nf-core/metaphlan/makedb/meta.yml | 18 +- .../metaphlan/mergemetaphlantables/meta.yml | 48 +- modules/nf-core/metaphlan/metaphlan/meta.yml | 93 +- .../metaphlan3/mergemetaphlantables/meta.yml | 48 +- .../nf-core/metaphlan3/metaphlan3/meta.yml | 93 +- modules/nf-core/methyldackel/extract/meta.yml | 79 +- modules/nf-core/methyldackel/mbias/meta.yml | 67 +- modules/nf-core/midas/run/meta.yml | 64 +- .../nf-core/mindagap/duplicatefinder/meta.yml | 52 +- modules/nf-core/mindagap/mindagap/meta.yml | 53 +- modules/nf-core/minia/meta.yml | 67 +- modules/nf-core/miniasm/meta.yml | 68 +- modules/nf-core/minimap2/align/meta.yml | 115 +-- modules/nf-core/minimap2/index/meta.yml | 43 +- modules/nf-core/miniprot/align/meta.yml | 67 +- modules/nf-core/miniprot/index/meta.yml | 43 +- modules/nf-core/miranda/meta.yml | 51 +- modules/nf-core/mirtop/counts/meta.yml | 83 +- modules/nf-core/mirtop/export/meta.yml | 107 ++- modules/nf-core/mirtop/gff/meta.yml | 80 +- modules/nf-core/mirtop/stats/meta.yml | 63 +- modules/nf-core/mirtrace/qc/meta.yml | 128 ++- .../mitohifi/findmitoreference/meta.yml | 46 +- modules/nf-core/mitohifi/mitohifi/meta.yml | 236 +++-- modules/nf-core/mlst/meta.yml | 45 +- modules/nf-core/mmseqs/cluster/meta.yml | 43 +- modules/nf-core/mmseqs/createdb/meta.yml | 46 +- modules/nf-core/mmseqs/createindex/meta.yml | 49 +- modules/nf-core/mmseqs/createtsv/meta.yml | 81 +- modules/nf-core/mmseqs/databases/meta.yml | 26 +- modules/nf-core/mmseqs/easysearch/meta.yml | 63 +- modules/nf-core/mmseqs/linclust/meta.yml | 43 +- modules/nf-core/mmseqs/search/meta.yml | 64 +- modules/nf-core/mmseqs/taxonomy/meta.yml | 52 +- .../nf-core/mmseqs/tsv2exprofiledb/meta.yml | 37 +- modules/nf-core/mobsuite/recon/meta.yml | 85 +- modules/nf-core/modkit/pileup/meta.yml | 120 +-- modules/nf-core/molkartgarage/clahe/meta.yml | 57 +- modules/nf-core/mosdepth/meta.yml | 214 +++-- modules/nf-core/motus/downloaddb/meta.yml | 31 +- modules/nf-core/motus/merge/meta.yml | 71 +- modules/nf-core/motus/profile/meta.yml | 99 ++- modules/nf-core/msisensor/msi/meta.yml | 124 +-- modules/nf-core/msisensor/scan/meta.yml | 48 +- modules/nf-core/msisensor2/msi/meta.yml | 103 ++- modules/nf-core/msisensor2/scan/meta.yml | 36 +- .../nf-core/msisensorpro/msisomatic/meta.yml | 127 +-- modules/nf-core/msisensorpro/scan/meta.yml | 52 +- modules/nf-core/mtmalign/align/meta.yml | 67 +- modules/nf-core/mtnucratio/meta.yml | 70 +- modules/nf-core/mudskipper/bulk/meta.yml | 82 +- modules/nf-core/mudskipper/index/meta.yml | 34 +- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/meta.yml | 91 +- modules/nf-core/multivcfanalyzer/meta.yml | 260 ++++-- modules/nf-core/mummer/meta.yml | 54 +- modules/nf-core/muscle/meta.yml | 120 ++- modules/nf-core/muscle5/super5/meta.yml | 59 +- modules/nf-core/mygene/meta.yml | 67 +- modules/nf-core/mykrobe/predict/meta.yml | 65 +- modules/nf-core/nanocomp/meta.yml | 232 +++-- modules/nf-core/nanofilt/meta.yml | 67 +- modules/nf-core/nanolyse/meta.yml | 62 +- modules/nf-core/nanomonsv/parse/meta.yml | 135 ++- modules/nf-core/nanoplot/meta.yml | 82 +- modules/nf-core/nanoq/meta.yml | 73 +- modules/nf-core/narfmap/align/environment.yml | 5 +- modules/nf-core/narfmap/align/meta.yml | 79 +- modules/nf-core/narfmap/hashtable/meta.yml | 41 +- modules/nf-core/ncbigenomedownload/meta.yml | 212 +++-- modules/nf-core/ncbitools/vecscreen/meta.yml | 63 +- modules/nf-core/nextclade/datasetget/meta.yml | 40 +- modules/nf-core/nextclade/run/meta.yml | 177 ++-- modules/nf-core/nextgenmap/meta.yml | 61 +- modules/nf-core/ngmaster/meta.yml | 48 +- modules/nf-core/ngmerge/meta.yml | 72 +- modules/nf-core/ngsbits/samplegender/meta.yml | 99 ++- modules/nf-core/ngscheckmate/fastq/meta.yml | 72 +- modules/nf-core/ngscheckmate/ncm/meta.yml | 133 +-- .../ngscheckmate/patterngenerator/meta.yml | 84 +- modules/nf-core/ngscheckmate/vafncm/meta.yml | 94 +- modules/nf-core/nonpareil/curve/meta.yml | 49 +- modules/nf-core/nonpareil/nonpareil/meta.yml | 98 ++- .../nonpareil/nonpareilcurvesr/meta.yml | 90 +- modules/nf-core/nonpareil/set/meta.yml | 49 +- modules/nf-core/nucmer/meta.yml | 69 +- modules/nf-core/oatk/meta.yml | 297 ++++--- modules/nf-core/odgi/build/meta.yml | 46 +- modules/nf-core/odgi/draw/meta.yml | 53 +- modules/nf-core/odgi/layout/meta.yml | 64 +- modules/nf-core/odgi/sort/meta.yml | 48 +- modules/nf-core/odgi/squeeze/meta.yml | 43 +- modules/nf-core/odgi/stats/meta.yml | 57 +- modules/nf-core/odgi/unchop/meta.yml | 45 +- modules/nf-core/odgi/view/meta.yml | 45 +- modules/nf-core/odgi/viz/meta.yml | 45 +- modules/nf-core/oncocnv/meta.yml | 99 ++- modules/nf-core/openms/decoydatabase/meta.yml | 48 +- modules/nf-core/openms/idfilter/meta.yml | 58 +- .../nf-core/openms/idmassaccuracy/meta.yml | 81 +- modules/nf-core/openms/idmerger/meta.yml | 54 +- modules/nf-core/openms/idripper/meta.yml | 53 +- .../nf-core/openms/idscoreswitcher/meta.yml | 57 +- .../nf-core/openms/peakpickerhires/meta.yml | 53 +- .../nf-core/openms/peptideindexer/meta.yml | 64 +- .../openmsthirdparty/cometadapter/meta.yml | 70 +- modules/nf-core/optitype/meta.yml | 65 +- modules/nf-core/orthofinder/meta.yml | 81 +- modules/nf-core/paftools/sam2paf/meta.yml | 38 +- modules/nf-core/pairix/meta.yml | 47 +- modules/nf-core/pairtools/dedup/meta.yml | 55 +- modules/nf-core/pairtools/flip/meta.yml | 49 +- modules/nf-core/pairtools/merge/meta.yml | 43 +- modules/nf-core/pairtools/parse/meta.yml | 63 +- modules/nf-core/pairtools/restrict/meta.yml | 55 +- modules/nf-core/pairtools/select/meta.yml | 55 +- modules/nf-core/pairtools/sort/meta.yml | 43 +- modules/nf-core/pairtools/split/meta.yml | 57 +- modules/nf-core/pairtools/stats/meta.yml | 43 +- modules/nf-core/panacus/histgrowth/meta.yml | 83 +- modules/nf-core/panacus/visualize/meta.yml | 48 +- modules/nf-core/panaroo/run/meta.yml | 57 +- modules/nf-core/pangolin/meta.yml | 35 +- modules/nf-core/parabricks/applybqsr/meta.yml | 96 +- modules/nf-core/parabricks/dbsnp/meta.yml | 66 +- .../nf-core/parabricks/deepvariant/meta.yml | 84 +- modules/nf-core/parabricks/fq2bam/meta.yml | 134 +-- .../nf-core/parabricks/genotypegvcf/meta.yml | 68 +- .../parabricks/haplotypecaller/meta.yml | 85 +- modules/nf-core/parabricks/indexgvcf/meta.yml | 41 +- .../nf-core/parabricks/mutectcaller/meta.yml | 130 +-- modules/nf-core/paraclu/meta.yml | 53 +- modules/nf-core/paragraph/idxdepth/meta.yml | 103 ++- modules/nf-core/paragraph/multigrmpy/meta.yml | 131 +-- .../nf-core/paragraph/vcf2paragraph/meta.yml | 54 +- modules/nf-core/paraphase/meta.yml | 144 +-- modules/nf-core/pasty/meta.yml | 69 +- modules/nf-core/pbbam/pbmerge/meta.yml | 61 +- modules/nf-core/pbccs/meta.yml | 116 ++- modules/nf-core/pbptyper/meta.yml | 68 +- modules/nf-core/pbtk/bam2fastq/meta.yml | 60 +- modules/nf-core/pbtk/pbindex/meta.yml | 52 +- modules/nf-core/pear/meta.yml | 76 +- modules/nf-core/peddy/meta.yml | 100 ++- modules/nf-core/peka/meta.yml | 146 +++- modules/nf-core/phantompeakqualtools/meta.yml | 73 +- .../pharokka/installdatabases/meta.yml | 16 +- modules/nf-core/pharokka/pharokka/meta.yml | 126 ++- modules/nf-core/phispy/meta.yml | 184 ++-- modules/nf-core/phyloflash/meta.yml | 64 +- .../picard/addorreplacereadgroups/meta.yml | 105 ++- .../nf-core/picard/bedtointervallist/meta.yml | 63 +- modules/nf-core/picard/cleansam/meta.yml | 48 +- .../nf-core/picard/collecthsmetrics/meta.yml | 128 +-- .../picard/collectinsertsizemetrics/meta.yml | 59 +- .../picard/collectmultiplemetrics/meta.yml | 97 ++- .../picard/collectrnaseqmetrics/meta.yml | 75 +- .../nf-core/picard/collectwgsmetrics/meta.yml | 97 ++- .../picard/createsequencedictionary/meta.yml | 45 +- .../picard/crosscheckfingerprints/meta.yml | 102 +-- .../picard/extractfingerprint/meta.yml | 78 +- modules/nf-core/picard/fastqtosam/meta.yml | 48 +- .../nf-core/picard/filtersamreads/meta.yml | 61 +- .../picard/fixmateinformation/meta.yml | 45 +- modules/nf-core/picard/liftovervcf/meta.yml | 102 ++- .../nf-core/picard/markduplicates/meta.yml | 116 ++- modules/nf-core/picard/mergesamfiles/meta.yml | 43 +- .../positionbaseddownsamplesam/meta.yml | 75 +- .../nf-core/picard/renamesampleinvcf/meta.yml | 45 +- .../picard/scatterintervalsbyns/meta.yml | 90 +- modules/nf-core/picard/sortsam/meta.yml | 53 +- modules/nf-core/picard/sortvcf/meta.yml | 84 +- modules/nf-core/pigz/compress/meta.yml | 49 +- modules/nf-core/pigz/uncompress/meta.yml | 46 +- modules/nf-core/pilon/meta.yml | 143 +-- modules/nf-core/pindel/pindel/meta.yml | 191 ++-- modules/nf-core/pints/caller/meta.yml | 101 ++- modules/nf-core/pirate/meta.yml | 57 +- modules/nf-core/plasmidfinder/meta.yml | 96 +- modules/nf-core/plasmidid/meta.yml | 135 ++- modules/nf-core/platypus/meta.yml | 123 +-- modules/nf-core/plink/bcf/meta.yml | 72 +- modules/nf-core/plink/epistasis/meta.yml | 170 ++-- modules/nf-core/plink/exclude/meta.yml | 96 +- modules/nf-core/plink/extract/meta.yml | 96 +- modules/nf-core/plink/fastepistasis/meta.yml | 170 ++-- modules/nf-core/plink/gwas/meta.yml | 153 ++-- modules/nf-core/plink/hwe/meta.yml | 108 +-- modules/nf-core/plink/indep/meta.yml | 101 ++- modules/nf-core/plink/indeppairwise/meta.yml | 104 ++- modules/nf-core/plink/ld/meta.yml | 153 ++-- modules/nf-core/plink/recode/meta.yml | 353 +++++--- modules/nf-core/plink/vcf/meta.yml | 69 +- modules/nf-core/plink2/extract/meta.yml | 93 +- modules/nf-core/plink2/score/meta.yml | 69 +- modules/nf-core/plink2/vcf/meta.yml | 81 +- modules/nf-core/pmdtools/filter/meta.yml | 67 +- modules/nf-core/pneumocat/meta.yml | 64 +- modules/nf-core/poolsnp/meta.yml | 163 ++-- modules/nf-core/popscle/demuxlet/meta.yml | 79 +- modules/nf-core/popscle/dscpileup/meta.yml | 111 ++- modules/nf-core/popscle/freemuxlet/meta.yml | 119 ++- modules/nf-core/porechop/abi/meta.yml | 63 +- modules/nf-core/porechop/porechop/meta.yml | 57 +- modules/nf-core/preseq/ccurve/meta.yml | 65 +- modules/nf-core/preseq/lcextrap/meta.yml | 63 +- modules/nf-core/president/meta.yml | 112 ++- modules/nf-core/presto/filterseq/meta.yml | 65 +- modules/nf-core/pretextmap/meta.yml | 74 +- modules/nf-core/pretextsnapshot/meta.yml | 45 +- modules/nf-core/prinseqplusplus/meta.yml | 92 +- modules/nf-core/prodigal/meta.yml | 93 +- modules/nf-core/prokka/meta.yml | 191 ++-- modules/nf-core/propr/grea/meta.yml | 74 +- modules/nf-core/propr/logratio/meta.yml | 64 +- modules/nf-core/propr/propd/meta.yml | 120 ++- modules/nf-core/propr/propr/meta.yml | 111 ++- modules/nf-core/proteinortho/meta.yml | 68 +- .../proteus/readproteingroups/environment.yml | 7 +- .../proteus/readproteingroups/meta.yml | 139 +-- modules/nf-core/pureclip/meta.yml | 117 +-- .../nf-core/purecn/coverage/environment.yml | 3 +- modules/nf-core/purecn/coverage/meta.yml | 113 ++- modules/nf-core/purecn/intervalfile/meta.yml | 90 +- modules/nf-core/purecn/normaldb/meta.yml | 124 ++- modules/nf-core/purecn/run/environment.yml | 3 +- modules/nf-core/purecn/run/meta.yml | 213 +++-- modules/nf-core/purgedups/calcuts/meta.yml | 60 +- modules/nf-core/purgedups/getseqs/meta.yml | 68 +- modules/nf-core/purgedups/histplot/meta.yml | 57 +- modules/nf-core/purgedups/pbcstat/meta.yml | 63 +- modules/nf-core/purgedups/purgedups/meta.yml | 76 +- modules/nf-core/purgedups/splitfa/meta.yml | 48 +- modules/nf-core/pycoqc/meta.yml | 56 +- modules/nf-core/pydamage/analyze/meta.yml | 53 +- modules/nf-core/pydamage/filter/meta.yml | 45 +- modules/nf-core/pyrodigal/meta.yml | 98 ++- modules/nf-core/qcat/meta.yml | 46 +- modules/nf-core/qualimap/bamqc/meta.yml | 51 +- modules/nf-core/qualimap/bamqccram/meta.yml | 67 +- modules/nf-core/qualimap/rnaseq/meta.yml | 61 +- modules/nf-core/quartonotebook/meta.yml | 124 +-- modules/nf-core/quast/meta.yml | 118 ++- modules/nf-core/quilt/quilt/meta.yml | 211 +++-- modules/nf-core/racon/meta.yml | 64 +- modules/nf-core/rapidnj/meta.yml | 42 +- modules/nf-core/rasusa/meta.yml | 55 +- modules/nf-core/raven/meta.yml | 57 +- modules/nf-core/raxmlng/meta.yml | 38 +- .../repeatmodeler/builddatabase/meta.yml | 47 +- .../repeatmodeler/repeatmodeler/meta.yml | 74 +- modules/nf-core/resfinder/run/meta.yml | 266 +++--- modules/nf-core/rgi/cardannotation/meta.yml | 43 +- modules/nf-core/rgi/main/meta.yml | 109 ++- modules/nf-core/rhocall/annotate/meta.yml | 77 +- modules/nf-core/rhocall/viz/meta.yml | 72 +- modules/nf-core/ribotish/predict/meta.yml | 205 +++-- modules/nf-core/ribotish/quality/meta.yml | 113 +-- .../nf-core/ribotricer/detectorfs/meta.yml | 188 ++-- .../nf-core/ribotricer/prepareorfs/meta.yml | 58 +- modules/nf-core/ribowaltz/meta.yml | 191 ++-- modules/nf-core/rmarkdownnotebook/meta.yml | 93 +- modules/nf-core/roary/meta.yml | 57 +- modules/nf-core/rrnatranscripts/meta.yml | 25 +- .../nf-core/rsem/calculateexpression/meta.yml | 120 ++- .../nf-core/rsem/preparereference/meta.yml | 40 +- modules/nf-core/rseqc/bamstat/meta.yml | 37 +- .../nf-core/rseqc/inferexperiment/meta.yml | 45 +- modules/nf-core/rseqc/innerdistance/meta.yml | 89 +- .../nf-core/rseqc/junctionannotation/meta.yml | 117 ++- .../nf-core/rseqc/junctionsaturation/meta.yml | 56 +- .../nf-core/rseqc/readdistribution/meta.yml | 45 +- .../nf-core/rseqc/readduplication/meta.yml | 74 +- modules/nf-core/rseqc/tin/meta.yml | 64 +- modules/nf-core/rtgtools/format/meta.yml | 69 +- modules/nf-core/rtgtools/pedfilter/meta.yml | 52 +- modules/nf-core/rtgtools/rocplot/meta.yml | 63 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 249 ++++-- modules/nf-core/rtn/tni/meta.yml | 76 +- modules/nf-core/sageproteomics/sage/meta.yml | 132 +-- modules/nf-core/salmon/index/meta.yml | 27 +- modules/nf-core/salmon/quant/meta.yml | 94 +- modules/nf-core/salsa2/meta.yml | 95 +- modules/nf-core/sam2lca/analyze/meta.yml | 89 +- modules/nf-core/sambamba/flagstat/meta.yml | 45 +- modules/nf-core/sambamba/markdup/meta.yml | 57 +- modules/nf-core/samblaster/meta.yml | 45 +- .../samtools/ampliconclip/environment.yml | 5 +- .../nf-core/samtools/ampliconclip/meta.yml | 89 +- .../nf-core/samtools/bam2fq/environment.yml | 5 +- modules/nf-core/samtools/bam2fq/meta.yml | 65 +- .../nf-core/samtools/calmd/environment.yml | 5 +- modules/nf-core/samtools/calmd/meta.yml | 58 +- modules/nf-core/samtools/cat/environment.yml | 5 +- modules/nf-core/samtools/cat/meta.yml | 56 +- .../nf-core/samtools/collate/environment.yml | 5 +- modules/nf-core/samtools/collate/meta.yml | 74 +- .../samtools/collatefastq/environment.yml | 4 +- .../nf-core/samtools/collatefastq/meta.yml | 125 ++- .../samtools/consensus/environment.yml | 3 +- modules/nf-core/samtools/consensus/meta.yml | 70 +- .../nf-core/samtools/convert/environment.yml | 5 +- modules/nf-core/samtools/convert/meta.yml | 111 ++- .../nf-core/samtools/coverage/environment.yml | 5 +- modules/nf-core/samtools/coverage/meta.yml | 85 +- modules/nf-core/samtools/cramsize/meta.yml | 43 +- .../nf-core/samtools/depth/environment.yml | 4 +- modules/nf-core/samtools/depth/meta.yml | 68 +- modules/nf-core/samtools/dict/environment.yml | 5 +- modules/nf-core/samtools/dict/meta.yml | 43 +- modules/nf-core/samtools/faidx/meta.yml | 85 +- .../nf-core/samtools/fasta/environment.yml | 4 +- modules/nf-core/samtools/fasta/meta.yml | 90 +- .../nf-core/samtools/fastq/environment.yml | 5 +- modules/nf-core/samtools/fastq/meta.yml | 90 +- .../nf-core/samtools/fixmate/environment.yml | 5 +- modules/nf-core/samtools/fixmate/meta.yml | 51 +- .../nf-core/samtools/flagstat/environment.yml | 5 +- modules/nf-core/samtools/flagstat/meta.yml | 54 +- .../nf-core/samtools/getrg/environment.yml | 4 +- modules/nf-core/samtools/getrg/meta.yml | 38 +- .../nf-core/samtools/idxstats/environment.yml | 5 +- modules/nf-core/samtools/idxstats/meta.yml | 51 +- .../nf-core/samtools/import/environment.yml | 4 +- modules/nf-core/samtools/import/meta.yml | 70 +- .../nf-core/samtools/index/environment.yml | 5 +- modules/nf-core/samtools/index/meta.yml | 68 +- .../nf-core/samtools/markdup/environment.yml | 5 +- modules/nf-core/samtools/markdup/meta.yml | 83 +- .../nf-core/samtools/merge/environment.yml | 5 +- modules/nf-core/samtools/merge/meta.yml | 117 ++- .../nf-core/samtools/mpileup/environment.yml | 5 +- modules/nf-core/samtools/mpileup/meta.yml | 59 +- .../nf-core/samtools/reheader/environment.yml | 5 +- modules/nf-core/samtools/reheader/meta.yml | 46 +- .../nf-core/samtools/sormadup/environment.yml | 5 +- modules/nf-core/samtools/sormadup/meta.yml | 115 ++- modules/nf-core/samtools/sort/environment.yml | 5 +- modules/nf-core/samtools/sort/meta.yml | 99 ++- .../nf-core/samtools/stats/environment.yml | 5 +- modules/nf-core/samtools/stats/meta.yml | 69 +- modules/nf-core/samtools/view/environment.yml | 5 +- modules/nf-core/samtools/view/meta.yml | 163 ++-- .../samtools/view/tests/main.nf.test.snap | 20 + modules/nf-core/scimap/mcmicro/meta.yml | 57 +- modules/nf-core/scimap/spatiallda/meta.yml | 82 +- modules/nf-core/scoary/meta.yml | 61 +- .../nf-core/scramble/clusteranalysis/meta.yml | 92 +- .../scramble/clusteridentifier/meta.yml | 61 +- modules/nf-core/seacr/callpeak/meta.yml | 59 +- modules/nf-core/segemehl/align/meta.yml | 123 +-- modules/nf-core/segemehl/index/meta.yml | 26 +- .../nf-core/semibin/singleeasybin/meta.yml | 107 ++- modules/nf-core/sentieon/applyvarcal/meta.yml | 126 +-- modules/nf-core/sentieon/bwaindex/meta.yml | 41 +- modules/nf-core/sentieon/bwamem/meta.yml | 99 ++- .../sentieon/collectvcmetrics/meta.yml | 153 ++-- .../nf-core/sentieon/coveragemetrics/meta.yml | 189 ++-- modules/nf-core/sentieon/datametrics/meta.yml | 154 ++-- modules/nf-core/sentieon/dedup/meta.yml | 164 ++-- .../nf-core/sentieon/dnamodelapply/meta.yml | 119 +-- modules/nf-core/sentieon/dnascope/meta.yml | 213 ++--- modules/nf-core/sentieon/gvcftyper/meta.yml | 130 +-- modules/nf-core/sentieon/haplotyper/meta.yml | 167 ++-- modules/nf-core/sentieon/qualcal/meta.yml | 174 ++-- modules/nf-core/sentieon/readwriter/meta.yml | 116 ++- modules/nf-core/sentieon/tnfilter/meta.yml | 140 +-- .../nf-core/sentieon/tnhaplotyper2/meta.yml | 258 +++--- modules/nf-core/sentieon/tnscope/meta.yml | 199 +++-- modules/nf-core/sentieon/varcal/meta.yml | 123 ++- modules/nf-core/sentieon/wgsmetrics/meta.yml | 107 +-- modules/nf-core/seqcluster/collapse/meta.yml | 55 +- modules/nf-core/seqfu/derep/meta.yml | 50 +- modules/nf-core/seqfu/stats/meta.yml | 67 +- modules/nf-core/seqkit/concat/meta.yml | 49 +- modules/nf-core/seqkit/fq2fa/meta.yml | 52 +- modules/nf-core/seqkit/fx2tab/meta.yml | 46 +- modules/nf-core/seqkit/grep/meta.yml | 67 +- modules/nf-core/seqkit/pair/meta.yml | 60 +- modules/nf-core/seqkit/replace/meta.yml | 48 +- modules/nf-core/seqkit/rmdup/meta.yml | 59 +- modules/nf-core/seqkit/seq/meta.yml | 47 +- modules/nf-core/seqkit/sliding/meta.yml | 46 +- modules/nf-core/seqkit/sort/meta.yml | 44 +- modules/nf-core/seqkit/split2/meta.yml | 43 +- modules/nf-core/seqkit/stats/meta.yml | 54 +- modules/nf-core/seqkit/tab2fx/meta.yml | 43 +- modules/nf-core/seqsero2/meta.yml | 69 +- modules/nf-core/seqtk/cutn/meta.yml | 47 +- modules/nf-core/seqtk/mergepe/meta.yml | 52 +- modules/nf-core/seqtk/rename/meta.yml | 49 +- modules/nf-core/seqtk/sample/meta.yml | 54 +- modules/nf-core/seqtk/seq/meta.yml | 50 +- modules/nf-core/seqtk/subseq/meta.yml | 50 +- modules/nf-core/seqtk/trim/meta.yml | 51 +- .../sequencetools/pileupcaller/meta.yml | 111 ++- .../nf-core/sequenzautils/bam2seqz/meta.yml | 78 +- .../nf-core/sequenzautils/gcwiggle/meta.yml | 53 +- modules/nf-core/seqwish/induce/meta.yml | 51 +- modules/nf-core/seroba/run/meta.yml | 63 +- modules/nf-core/severus/meta.yml | 269 ++++-- modules/nf-core/sexdeterrmine/meta.yml | 68 +- modules/nf-core/sgdemux/meta.yml | 123 ++- modules/nf-core/shapeit5/ligate/meta.yml | 61 +- modules/nf-core/shapeit5/phasecommon/meta.yml | 137 +-- modules/nf-core/shapeit5/phaserare/meta.yml | 122 +-- modules/nf-core/shapeit5/switch/meta.yml | 118 +-- modules/nf-core/shasta/meta.yml | 77 +- modules/nf-core/shasum/meta.yml | 45 +- modules/nf-core/shigatyper/meta.yml | 57 +- modules/nf-core/shigeifinder/meta.yml | 48 +- modules/nf-core/shinyngs/app/meta.yml | 107 +-- .../shinyngs/staticdifferential/meta.yml | 103 ++- .../shinyngs/staticexploratory/meta.yml | 212 +++-- .../shinyngs/validatefomcomponents/meta.yml | 136 +-- modules/nf-core/shovill/meta.yml | 92 +- modules/nf-core/sickle/meta.yml | 97 ++- modules/nf-core/simpleaf/index/meta.yml | 102 ++- modules/nf-core/simpleaf/quant/meta.yml | 123 +-- modules/nf-core/sistr/meta.yml | 86 +- modules/nf-core/slimfastq/meta.yml | 45 +- modules/nf-core/smncopynumbercaller/meta.yml | 69 +- modules/nf-core/smoothxg/meta.yml | 56 +- modules/nf-core/smoove/call/meta.yml | 95 +- modules/nf-core/snakemake/meta.yml | 78 +- modules/nf-core/snapaligner/align/meta.yml | 79 +- modules/nf-core/snapaligner/index/meta.yml | 58 +- modules/nf-core/sniffles/meta.yml | 120 ++- modules/nf-core/snippy/core/meta.yml | 112 ++- modules/nf-core/snippy/run/meta.yml | 252 ++++-- modules/nf-core/snpdists/meta.yml | 43 +- modules/nf-core/snpeff/download/meta.yml | 44 +- modules/nf-core/snpeff/snpeff/meta.yml | 96 +- modules/nf-core/snpsift/annotate/meta.yml | 81 +- modules/nf-core/snpsift/dbnsfp/meta.yml | 82 +- modules/nf-core/snpsift/split/meta.yml | 48 +- modules/nf-core/snpsites/meta.yml | 39 +- modules/nf-core/somalier/ancestry/meta.yml | 92 +- modules/nf-core/somalier/extract/meta.yml | 109 +-- modules/nf-core/somalier/relate/meta.yml | 85 +- modules/nf-core/sortmerna/meta.yml | 121 +-- modules/nf-core/sourmash/compare/meta.yml | 102 ++- modules/nf-core/sourmash/gather/meta.yml | 152 ++-- modules/nf-core/sourmash/index/meta.yml | 54 +- modules/nf-core/sourmash/sketch/meta.yml | 52 +- modules/nf-core/sourmash/taxannotate/meta.yml | 61 +- modules/nf-core/spaceranger/count/meta.yml | 132 +-- modules/nf-core/spaceranger/mkgtf/meta.yml | 27 +- modules/nf-core/spaceranger/mkref/meta.yml | 41 +- modules/nf-core/spades/meta.yml | 186 ++-- modules/nf-core/spatyper/meta.yml | 61 +- modules/nf-core/splitubam/meta.yml | 48 +- modules/nf-core/spotiflow/meta.yml | 54 +- modules/nf-core/spring/compress/meta.yml | 56 +- modules/nf-core/spring/decompress/meta.yml | 58 +- modules/nf-core/sratools/fasterqdump/meta.yml | 71 +- modules/nf-core/sratools/prefetch/meta.yml | 72 +- modules/nf-core/srst2/srst2/meta.yml | 118 ++- modules/nf-core/ssuissero/meta.yml | 45 +- modules/nf-core/stadeniolib/scramble/meta.yml | 82 +- modules/nf-core/staphopiasccmec/meta.yml | 45 +- modules/nf-core/star/align/environment.yml | 5 +- modules/nf-core/star/align/meta.yml | 246 ++++-- .../star/genomegenerate/environment.yml | 3 +- modules/nf-core/star/genomegenerate/meta.yml | 57 +- modules/nf-core/star/starsolo/meta.yml | 139 ++- modules/nf-core/staramr/search/meta.yml | 156 ++-- modules/nf-core/stardist/meta.yml | 53 +- modules/nf-core/stecfinder/meta.yml | 48 +- modules/nf-core/stitch/meta.yml | 216 +++-- modules/nf-core/stranger/meta.yml | 66 +- modules/nf-core/strelka/germline/meta.yml | 125 +-- modules/nf-core/strelka/somatic/meta.yml | 158 ++-- modules/nf-core/stringtie/merge/meta.yml | 38 +- modules/nf-core/stringtie/stringtie/meta.yml | 89 +- .../nf-core/subread/featurecounts/meta.yml | 68 +- .../summarizedexperiment/meta.yml | 112 +-- modules/nf-core/survivor/bedpetovcf/meta.yml | 43 +- modules/nf-core/survivor/filter/meta.yml | 74 +- modules/nf-core/survivor/merge/meta.yml | 89 +- modules/nf-core/survivor/simsv/meta.yml | 143 +-- modules/nf-core/survivor/stats/meta.yml | 63 +- modules/nf-core/svaba/meta.yml | 364 +++++--- .../nf-core/svanalyzer/svbenchmark/meta.yml | 166 ++-- modules/nf-core/svdb/build/meta.yml | 46 +- modules/nf-core/svdb/merge/environment.yml | 6 +- modules/nf-core/svdb/merge/meta.yml | 52 +- modules/nf-core/svdb/query/meta.yml | 88 +- modules/nf-core/svtk/baftest/meta.yml | 72 +- modules/nf-core/svtk/countsvtypes/meta.yml | 48 +- modules/nf-core/svtk/rdtest2vcf/meta.yml | 77 +- modules/nf-core/svtk/standardize/meta.yml | 69 +- modules/nf-core/svtk/vcf2bed/meta.yml | 56 +- modules/nf-core/svtyper/svtyper/meta.yml | 117 ++- modules/nf-core/svtyper/svtypersso/meta.yml | 98 ++- modules/nf-core/svync/meta.yml | 64 +- modules/nf-core/tabix/bgzip/environment.yml | 3 +- modules/nf-core/tabix/bgzip/meta.yml | 53 +- .../nf-core/tabix/bgziptabix/environment.yml | 3 +- modules/nf-core/tabix/bgziptabix/meta.yml | 70 +- modules/nf-core/tabix/tabix/meta.yml | 55 +- modules/nf-core/tailfindr/meta.yml | 51 +- modules/nf-core/taxonkit/name2taxid/meta.yml | 59 +- modules/nf-core/taxpasta/merge/meta.yml | 83 +- modules/nf-core/taxpasta/standardise/meta.yml | 68 +- modules/nf-core/tbprofiler/profile/meta.yml | 96 +- modules/nf-core/tcoffee/align/meta.yml | 113 +-- modules/nf-core/tcoffee/alncompare/meta.yml | 61 +- modules/nf-core/tcoffee/consensus/meta.yml | 80 +- modules/nf-core/tcoffee/irmsd/meta.yml | 68 +- modules/nf-core/tcoffee/seqreformat/meta.yml | 52 +- modules/nf-core/tcoffee/tcs/environment.yml | 4 +- modules/nf-core/tcoffee/tcs/meta.yml | 86 +- modules/nf-core/thermorawfileparser/meta.yml | 50 +- modules/nf-core/tiara/tiara/meta.yml | 77 +- modules/nf-core/tiddit/cov/meta.yml | 77 +- modules/nf-core/tiddit/sv/meta.yml | 99 ++- modules/nf-core/tidk/explore/meta.yml | 63 +- modules/nf-core/tidk/plot/meta.yml | 47 +- modules/nf-core/tidk/search/meta.yml | 65 +- modules/nf-core/topas/gencons/meta.yml | 140 ++- modules/nf-core/toulligqc/meta.yml | 82 +- modules/nf-core/transdecoder/longorf/meta.yml | 95 +- modules/nf-core/transdecoder/predict/meta.yml | 98 ++- modules/nf-core/trimgalore/meta.yml | 101 ++- modules/nf-core/trimmomatic/meta.yml | 93 +- modules/nf-core/trinity/meta.yml | 59 +- modules/nf-core/trust4/meta.yml | 170 +++- modules/nf-core/truvari/bench/meta.yml | 210 +++-- modules/nf-core/truvari/consistency/meta.yml | 45 +- modules/nf-core/truvari/segment/meta.yml | 45 +- modules/nf-core/trycycler/cluster/meta.yml | 58 +- modules/nf-core/trycycler/subsample/meta.yml | 53 +- modules/nf-core/tsebra/meta.yml | 93 +- modules/nf-core/tximeta/tximport/meta.yml | 198 +++-- modules/nf-core/ucsc/bedclip/meta.yml | 48 +- .../nf-core/ucsc/bedgraphtobigwig/meta.yml | 53 +- modules/nf-core/ucsc/bedtobigbed/meta.yml | 61 +- .../ucsc/bigwigaverageoverbed/meta.yml | 53 +- modules/nf-core/ucsc/gtftogenepred/meta.yml | 55 +- modules/nf-core/ucsc/liftover/meta.yml | 65 +- modules/nf-core/ucsc/wigtobigwig/meta.yml | 45 +- modules/nf-core/ultra/align/environment.yml | 3 +- modules/nf-core/ultra/align/meta.yml | 72 +- modules/nf-core/ultra/index/meta.yml | 44 +- modules/nf-core/ultra/pipeline/meta.yml | 59 +- modules/nf-core/ultraplex/meta.yml | 70 +- modules/nf-core/umicollapse/meta.yml | 94 +- modules/nf-core/umitools/dedup/meta.yml | 118 ++- modules/nf-core/umitools/extract/meta.yml | 64 +- modules/nf-core/umitools/group/meta.yml | 99 ++- .../nf-core/umitools/prepareforrsem/meta.yml | 70 +- modules/nf-core/unicycler/meta.yml | 81 +- modules/nf-core/universc/meta.yml | 46 +- modules/nf-core/untar/meta.yml | 43 +- modules/nf-core/untarfiles/meta.yml | 43 +- modules/nf-core/unzip/meta.yml | 46 +- modules/nf-core/unzipfiles/meta.yml | 46 +- modules/nf-core/upd/meta.yml | 46 +- modules/nf-core/upp/align/meta.yml | 70 +- modules/nf-core/vardictjava/meta.yml | 98 ++- modules/nf-core/variantbam/meta.yml | 48 +- .../varlociraptor/callvariants/meta.yml | 114 ++- .../estimatealignmentproperties/meta.yml | 86 +- .../nf-core/varlociraptor/preprocess/meta.yml | 147 ++-- modules/nf-core/vcf2cytosure/meta.yml | 110 +-- modules/nf-core/vcf2db/meta.yml | 53 +- modules/nf-core/vcf2maf/meta.yml | 55 +- modules/nf-core/vcfanno/meta.yml | 86 +- modules/nf-core/vcflib/vcfbreakmulti/meta.yml | 56 +- modules/nf-core/vcflib/vcffilter/meta.yml | 51 +- modules/nf-core/vcflib/vcffixup/meta.yml | 56 +- modules/nf-core/vcflib/vcfuniq/meta.yml | 56 +- modules/nf-core/vcftools/meta.yml | 822 +++++++++++++----- modules/nf-core/velocyto/meta.yml | 79 +- .../nf-core/verifybamid/verifybamid/meta.yml | 158 ++-- .../nf-core/verifybamid/verifybamid2/meta.yml | 169 ++-- modules/nf-core/vg/construct/meta.yml | 94 +- modules/nf-core/vg/deconstruct/meta.yml | 64 +- modules/nf-core/vg/index/meta.yml | 58 +- modules/nf-core/viennarna/rnacofold/meta.yml | 62 +- modules/nf-core/viennarna/rnafold/meta.yml | 55 +- modules/nf-core/viennarna/rnalfold/meta.yml | 29 +- modules/nf-core/vireo/meta.yml | 111 +-- .../nf-core/vrhyme/extractunbinned/meta.yml | 63 +- modules/nf-core/vrhyme/linkbins/meta.yml | 48 +- modules/nf-core/vrhyme/vrhyme/environment.yml | 7 +- modules/nf-core/vrhyme/vrhyme/meta.yml | 86 +- modules/nf-core/vsearch/cluster/meta.yml | 175 +++- modules/nf-core/vsearch/dereplicate/meta.yml | 58 +- modules/nf-core/vsearch/fastqfilter/meta.yml | 54 +- modules/nf-core/vsearch/sintax/meta.yml | 48 +- modules/nf-core/vsearch/sort/meta.yml | 58 +- .../nf-core/vsearch/usearchglobal/meta.yml | 169 ++-- modules/nf-core/vt/decompose/meta.yml | 54 +- modules/nf-core/vt/normalize/meta.yml | 111 +-- modules/nf-core/wfmash/meta.yml | 84 +- modules/nf-core/wgsim/meta.yml | 45 +- modules/nf-core/whamg/meta.yml | 95 +- modules/nf-core/windowmasker/convert/meta.yml | 47 +- .../nf-core/windowmasker/mkcounts/meta.yml | 45 +- modules/nf-core/windowmasker/ustat/meta.yml | 63 +- modules/nf-core/wisecondorx/convert/meta.yml | 90 +- modules/nf-core/wisecondorx/gender/meta.yml | 57 +- modules/nf-core/wisecondorx/newref/meta.yml | 45 +- modules/nf-core/wisecondorx/predict/meta.yml | 147 ++-- modules/nf-core/wittyer/meta.yml | 97 ++- modules/nf-core/xengsort/index/meta.yml | 65 +- modules/nf-core/xz/compress/meta.yml | 52 +- modules/nf-core/xz/decompress/meta.yml | 50 +- modules/nf-core/yahs/meta.yml | 87 +- modules/nf-core/yak/count/meta.yml | 47 +- modules/nf-core/yara/index/meta.yml | 40 +- modules/nf-core/yara/mapper/meta.yml | 78 +- modules/nf-core/zip/meta.yml | 44 +- 1378 files changed, 65225 insertions(+), 46375 deletions(-) diff --git a/modules/meta-schema.json b/modules/meta-schema.json index 0b855d76d07c..977ee1b624dd 100644 --- a/modules/meta-schema.json +++ b/modules/meta-schema.json @@ -38,40 +38,8 @@ "type": "array", "description": "Input channels for the module", "items": { - "type": "object", - "patternProperties": { - ".*": { - "type": "object", - "properties": { - "type": { - "type": "string", - "description": "Type of the input channel", - "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] - }, - "description": { - "type": "string", - "description": "Description of the input channel" - }, - "pattern": { - "type": "string", - "description": "Pattern of the input channel, given in Java glob syntax" - }, - "default": { - "type": ["string", "number", "boolean", "array", "object"], - "description": "Default value for the input channel" - }, - "enum": { - "type": "array", - "description": "List of allowed values for the input channel", - "items": { - "type": ["string", "number", "boolean", "array", "object"] - }, - "uniqueItems": true - } - }, - "required": ["type", "description"] - } - } + "type": "array", + "items": { "$ref": "#/definitions/elementProperties" } } }, "output": { @@ -79,35 +47,7 @@ "description": "Output channels for the module", "items": { "type": "object", - "patternProperties": { - ".*": { - "type": "object", - "properties": { - "type": { - "type": "string", - "description": "Type of the output channel", - "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] - }, - "description": { - "type": "string", - "description": "Description of the output channel" - }, - "pattern": { - "type": "string", - "description": "Pattern of the input channel, given in Java glob syntax" - }, - "enum": { - "type": "array", - "description": "List of allowed values for the output channel", - "items": { - "type": ["string", "number", "boolean", "array", "object"] - }, - "uniqueItems": true - } - }, - "required": ["type", "description"] - } - } + "items": { "$ref": "#/definitions/elementProperties" } } }, "tools": { @@ -160,6 +100,19 @@ "minItems": 1, "uniqueItems": true, "message": "Licence must be an array of one or more entries, e.g. [\"MIT\"]" + }, + "identifier": { + "description": "bio.tools identifier of the tool", + "anyOf": [ + { + "type": "string", + "pattern": "^biotools:.*$" + }, + { + "type": "string", + "maxLength": 0 + } + ] } }, "required": ["description"], @@ -182,5 +135,53 @@ } } }, + "definitions": { + "elementProperties": { + "type": "object", + "patternProperties": { + ".*": { + "type": "object", + "properties": { + "type": { + "type": "string", + "description": "Type of the channel element", + "enum": ["map", "file", "directory", "string", "integer", "float", "boolean", "list"] + }, + "description": { + "type": "string", + "description": "Description of the channel" + }, + "pattern": { + "type": "string", + "description": "Pattern of the channel, given in Java glob syntax" + }, + "enum": { + "type": "array", + "description": "List of allowed values for the channel", + "items": { + "type": ["string", "number", "boolean", "array", "object"] + }, + "uniqueItems": true + }, + "ontologies": { + "type": "array", + "description": "List of ontologies for the channel", + "uniqueItems": true, + "items": { + "type": "object", + "patternProperties": { + ".*": { + "type": "string", + "pattern": "^(http|https)://.*" + } + } + } + } + }, + "required": ["type", "description"] + } + } + } + }, "required": ["name", "description", "keywords", "authors", "output", "tools"] } diff --git a/modules/nf-core/abacas/meta.yml b/modules/nf-core/abacas/meta.yml index bef9868c8bda..9cbbef0143ce 100644 --- a/modules/nf-core/abacas/meta.yml +++ b/modules/nf-core/abacas/meta.yml @@ -14,40 +14,43 @@ tools: documentation: http://abacas.sourceforge.net/documentation.html doi: "10.1093/bioinformatics/btp347" licence: ["GPL v2-or-later"] + identifier: biotools:abacas input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - scaffold: - type: file - description: Fasta file containing scaffold - pattern: "*.{fasta,fa}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Fasta file containing scaffold + pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: file - description: | - List containing abacas output files - [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps', - 'test.abacas.gaps.tab', 'test.abacas.nucmer.delta', - 'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling', - 'test.abacas.tab', 'test.abacas.unused.contigs.out', - 'test.abacas.MULTIFASTA.fa' ] - pattern: "*.{abacas}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abacas*": + type: file + description: | + List containing abacas output files + [ 'test.abacas.bin', 'test.abacas.fasta', 'test.abacas.gaps', + 'test.abacas.gaps.tab', 'test.abacas.nucmer.delta', + 'test.abacas.nucmer.filtered.delta', 'test.abacas.nucmer.tiling', + 'test.abacas.tab', 'test.abacas.unused.contigs.out', + 'test.abacas.MULTIFASTA.fa' ] + pattern: "*.{abacas}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/abricate/run/meta.yml b/modules/nf-core/abricate/run/meta.yml index 927c21f60f99..dce78f3c704f 100644 --- a/modules/nf-core/abricate/run/meta.yml +++ b/modules/nf-core/abricate/run/meta.yml @@ -11,34 +11,38 @@ tools: documentation: https://github.com/tseemann/abricate tool_dev_url: https://github.com/tseemann/abricate licence: ["GPL v2"] + identifier: biotools:ABRicate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: FASTA, GenBank or EMBL formatted file - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" - - databasedir: - type: directory - description: Optional location of local copy of database files, possibly with custom databases set up with `abricate --setupdb` - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: FASTA, GenBank or EMBL formatted file + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + - - databasedir: + type: directory + description: Optional location of local copy of database files, possibly with + custom databases set up with `abricate --setupdb` + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Tab-delimited report of results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited report of results + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/abricate/summary/meta.yml b/modules/nf-core/abricate/summary/meta.yml index 71f1ac276058..041537761247 100644 --- a/modules/nf-core/abricate/summary/meta.yml +++ b/modules/nf-core/abricate/summary/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/tseemann/abricate tool_dev_url: https://github.com/tseemann/abricate licence: ["GPL v2"] + identifier: biotools:ABRicate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reports: - type: file - description: FASTA, GenBank or EMBL formatted file - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reports: + type: file + description: FASTA, GenBank or EMBL formatted file + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Tab-delimited report of aggregated results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited report of aggregated results + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/abritamr/run/meta.yml b/modules/nf-core/abritamr/run/meta.yml index a3262a9a2a6f..57fefad91c63 100644 --- a/modules/nf-core/abritamr/run/meta.yml +++ b/modules/nf-core/abritamr/run/meta.yml @@ -1,54 +1,88 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "abritamr_run" -description: A NATA accredited tool for reporting the presence of antimicrobial resistance genes in bacterial genomes +description: A NATA accredited tool for reporting the presence of antimicrobial resistance + genes in bacterial genomes keywords: - bacteria - fasta - antibiotic resistance tools: - "abritamr": - description: "A pipeline for running AMRfinderPlus and collating results into functional classes" + description: "A pipeline for running AMRfinderPlus and collating results into + functional classes" homepage: "https://github.com/MDU-PHL/abritamr" documentation: "https://github.com/MDU-PHL/abritamr" tool_dev_url: "https://github.com/MDU-PHL/abritamr" doi: "10.1038/s41467-022-35713-4" licence: ["GPL v3"] + identifier: biotools:abritamr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Assembled contigs in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Assembled contigs in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - matches: - type: file - description: Tab-delimited file, with a row per sequence, and columns representing functional drug classes - pattern: "*.summary_matches.txt" + - meta: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + functional drug classes + pattern: "*.summary_matches.txt" + - ${prefix}.summary_matches.txt: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + functional drug classes + pattern: "*.summary_matches.txt" - partials: - type: file - description: Tab-delimited file, with a row per sequence, and columns representing partial hits to functional drug classes - pattern: "*.summary_partials.txt" + - meta: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + partial hits to functional drug classes + pattern: "*.summary_partials.txt" + - ${prefix}.summary_partials.txt: + type: file + description: Tab-delimited file, with a row per sequence, and columns representing + partial hits to functional drug classes + pattern: "*.summary_partials.txt" - virulence: - type: string - description: Tab-delimited file, with a row per sequence, and columns representing AMRFinderPlus virulence gene classification - pattern: "*.summary_virulence.txt" - - txt: - type: string - description: Tab-delimited file, combining non-empty summary files - pattern: "*.abritamr.txt" + - meta: + type: string + description: Tab-delimited file, with a row per sequence, and columns representing + AMRFinderPlus virulence gene classification + pattern: "*.summary_virulence.txt" + - ${prefix}.summary_virulence.txt: + type: string + description: Tab-delimited file, with a row per sequence, and columns representing + AMRFinderPlus virulence gene classification + pattern: "*.summary_virulence.txt" - out: - type: string - description: raw output from AMRFinder plus (per sequence) - pattern: "*.amrfinder.txt" + - meta: + type: string + description: raw output from AMRFinder plus (per sequence) + pattern: "*.amrfinder.txt" + - ${prefix}.amrfinder.out: + type: string + description: raw output from AMRFinder plus (per sequence) + pattern: "*.amrfinder.txt" + - txt: + - meta: + type: string + description: Tab-delimited file, combining non-empty summary files + pattern: "*.abritamr.txt" + - ${prefix}.abritamr.txt: + type: string + description: Tab-delimited file, combining non-empty summary files + pattern: "*.abritamr.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/adapterremoval/meta.yml b/modules/nf-core/adapterremoval/meta.yml index 2deb613b5a11..e4859571cd5a 100644 --- a/modules/nf-core/adapterremoval/meta.yml +++ b/modules/nf-core/adapterremoval/meta.yml @@ -11,67 +11,120 @@ tools: homepage: https://github.com/MikkelSchubert/adapterremoval documentation: https://adapterremoval.readthedocs.io licence: ["GPL v3"] + identifier: biotools:adapterremoval input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - adapterlist: - type: file - description: Optional text file containing list of adapters to look for for removal with one adapter per line. Otherwise will look for default adapters (see AdapterRemoval man page), or can be modified to remove user-specified adapters via ext.args. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - adapterlist: + type: file + description: Optional text file containing list of adapters to look for for + removal with one adapter per line. Otherwise will look for default adapters + (see AdapterRemoval man page), or can be modified to remove user-specified + adapters via ext.args. output: - singles_truncated: - type: file - description: | - Adapter trimmed FastQ files of either single-end reads, or singleton - 'orphaned' reads from merging of paired-end data (i.e., one of the pair - was lost due to filtering thresholds). - pattern: "*.truncated.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed FastQ files of either single-end reads, or singleton + 'orphaned' reads from merging of paired-end data (i.e., one of the pair + was lost due to filtering thresholds). + pattern: "*.truncated.fastq.gz" + - ${prefix}.truncated.fastq.gz: + type: file + description: | + Adapter trimmed FastQ files of either single-end reads, or singleton + 'orphaned' reads from merging of paired-end data (i.e., one of the pair + was lost due to filtering thresholds). + pattern: "*.truncated.fastq.gz" - discarded: - type: file - description: | - Adapter trimmed FastQ files of reads that did not pass filtering - thresholds. - pattern: "*.discarded.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed FastQ files of reads that did not pass filtering + thresholds. + pattern: "*.discarded.fastq.gz" + - ${prefix}.discarded.fastq.gz: + type: file + description: | + Adapter trimmed FastQ files of reads that did not pass filtering + thresholds. + pattern: "*.discarded.fastq.gz" - paired_truncated: - type: file - description: | - Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge - with their respective R{1,2} pair due to long templates. The respective pair - is stored in 'pair{1,2}_truncated'. - pattern: "*.pair{1,2}.truncated.fastq.gz" + - meta: + type: file + description: | + Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge + with their respective R{1,2} pair due to long templates. The respective pair + is stored in 'pair{1,2}_truncated'. + pattern: "*.pair{1,2}.truncated.fastq.gz" + - ${prefix}.pair{1,2}.truncated.fastq.gz: + type: file + description: | + Adapter trimmed R{1,2} FastQ files of paired-end reads that did not merge + with their respective R{1,2} pair due to long templates. The respective pair + is stored in 'pair{1,2}_truncated'. + pattern: "*.pair{1,2}.truncated.fastq.gz" - collapsed: - type: file - description: | - Collapsed FastQ of paired-end reads that successfully merged with their - respective R1 pair but were not trimmed. - pattern: "*.collapsed.fastq.gz" + - meta: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair but were not trimmed. + pattern: "*.collapsed.fastq.gz" + - ${prefix}.collapsed.fastq.gz: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair but were not trimmed. + pattern: "*.collapsed.fastq.gz" - collapsed_truncated: - type: file - description: | - Collapsed FastQ of paired-end reads that successfully merged with their - respective R1 pair and were trimmed of adapter due to sufficient overlap. - pattern: "*.collapsed.truncated.fastq.gz" + - meta: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair and were trimmed of adapter due to sufficient overlap. + pattern: "*.collapsed.truncated.fastq.gz" + - ${prefix}.collapsed.truncated.fastq.gz: + type: file + description: | + Collapsed FastQ of paired-end reads that successfully merged with their + respective R1 pair and were trimmed of adapter due to sufficient overlap. + pattern: "*.collapsed.truncated.fastq.gz" - paired_interleaved: - type: file - description: | - Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads - pattern: "*.paired.fastq.gz" + - meta: + type: file + description: | + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads + pattern: "*.paired.fastq.gz" + - ${prefix}.paired.fastq.gz: + type: file + description: | + Write paired-end reads to a single file, interleaving mate 1 and mate 2 reads + pattern: "*.paired.fastq.gz" - settings: - type: file - description: AdapterRemoval log file - pattern: "*.settings" + - meta: + type: file + description: AdapterRemoval log file + pattern: "*.settings" + - "*.settings": + type: file + description: AdapterRemoval log file + pattern: "*.settings" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/adapterremovalfixprefix/meta.yml b/modules/nf-core/adapterremovalfixprefix/meta.yml index fe3a0f7006e7..f9ecdb6d6990 100644 --- a/modules/nf-core/adapterremovalfixprefix/meta.yml +++ b/modules/nf-core/adapterremovalfixprefix/meta.yml @@ -1,40 +1,45 @@ name: adapterremovalfixprefix -description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read names are in the output. For use with DeDup. +description: Fixes prefixes from AdapterRemoval2 output to make sure no clashing read + names are in the output. For use with DeDup. keywords: - adapterremoval - fastq - dedup tools: - adapterremovalfixprefix: - description: Fixes adapter removal prefixes to make sure no clashing read names are in the output. + description: Fixes adapter removal prefixes to make sure no clashing read names + are in the output. homepage: https://github.com/apeltzer/AdapterRemovalFixPrefix tool_dev_url: https://github.com/apeltzer/AdapterRemovalFixPrefix doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file from AdapterRemoval2 - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file from AdapterRemoval2 + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fixed_fastq: - type: file - description: FASTQ file with fixed read prefixes for DeDup - pattern: "*.{fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: FASTQ file with fixed read prefixes for DeDup + pattern: "*.{fq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/admixture/meta.yml b/modules/nf-core/admixture/meta.yml index 06aa57ff752f..bbb72fef0a43 100644 --- a/modules/nf-core/admixture/meta.yml +++ b/modules/nf-core/admixture/meta.yml @@ -1,5 +1,7 @@ name: "admixture" -description: ADMIXTURE is a program for estimating ancestry in a model-based manner from large autosomal SNP genotype datasets, where the individuals are unrelated (for example, the individuals in a case-control association study). +description: ADMIXTURE is a program for estimating ancestry in a model-based manner + from large autosomal SNP genotype datasets, where the individuals are unrelated + (for example, the individuals in a case-control association study). keywords: - ancestry - population genetics @@ -8,51 +10,70 @@ keywords: - gwas tools: - "admixture": - description: "ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets." + description: "ADMIXTURE is a software tool for maximum likelihood estimation of + individual ancestries from multilocus SNP genotype datasets." homepage: "https://dalexander.github.io/admixture/" documentation: "https://dalexander.github.io/admixture/admixture-manual.pdf" doi: "10.1101/gr.094052.109" licence: ["Free for Academic Use"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed_ped_geno: - type: file - description: One of PLINK ".bed" file or PLINK ".ped" or EIGENSTRAT ".geno" file. If you provide ".bed" then you need to provide ".bim" and "fam" files. If you provide ".ped" or ".geno" then you need to provide a ".map" file and an empty channel. - pattern: "*.{bed}" - - bim_map: - type: file - description: Mandatory accompanying file. One of PLINK ".bim" file or PLINK ".map" file. Provide ".bim" if ".bed" is the input. Provide ".map" if ".ped" or ".geno" is the input. - pattern: "*.{bim}" - - fam: - type: file - description: PLINK ".fam" file. Mandatory if you provide ".bed" as input. Replace with an empty channel if input is ".ped" or ".geno". - pattern: "*.{fam}" - - K: - type: integer - description: Belief of the number of ancestral populations. - pattern: "{*}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed_ped_geno: + type: file + description: One of PLINK ".bed" file or PLINK ".ped" or EIGENSTRAT ".geno" + file. If you provide ".bed" then you need to provide ".bim" and "fam" files. + If you provide ".ped" or ".geno" then you need to provide a ".map" file and + an empty channel. + pattern: "*.{bed}" + - bim_map: + type: file + description: Mandatory accompanying file. One of PLINK ".bim" file or PLINK + ".map" file. Provide ".bim" if ".bed" is the input. Provide ".map" if ".ped" + or ".geno" is the input. + pattern: "*.{bim}" + - fam: + type: file + description: PLINK ".fam" file. Mandatory if you provide ".bed" as input. Replace + with an empty channel if input is ".ped" or ".geno". + pattern: "*.{fam}" + - - K: + type: integer + description: Belief of the number of ancestral populations. + pattern: "{*}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ancestry_fractions: - type: file - description: Space-delimited files containing ancestry fractions. The output filenames have the number of populations (K) that was assumed for the analysis. - pattern: "*.{Q}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Q": + type: file + description: Space-delimited files containing ancestry fractions. The output + filenames have the number of populations (K) that was assumed for the analysis. + pattern: "*.{Q}" - allele_frequencies: - type: file - description: Space-delimited files containing the allele frequencies of the inferred ancestral populations. The output filenames have the number of populations (K) that was assumed for the analysis. - pattern: "*.{P}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.P": + type: file + description: Space-delimited files containing the allele frequencies of the + inferred ancestral populations. The output filenames have the number of populations + (K) that was assumed for the analysis. + pattern: "*.{P}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/affy/justrma/meta.yml b/modules/nf-core/affy/justrma/meta.yml index cd9b6d6cbec9..54a7beeeeef6 100644 --- a/modules/nf-core/affy/justrma/meta.yml +++ b/modules/nf-core/affy/justrma/meta.yml @@ -13,46 +13,66 @@ tools: tool_dev_url: "https://github.com/Bioconductor/affy" doi: "10.1093/bioinformatics/btg405" licence: ["LGPL >=2.0"] + identifier: biotools:affy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata and CEL file names - - celfiles_dir: - type: list - description: Path to a directory containing CEL files - pattern: "*.{CEL,CEL.gz}" - - description: - type: file - description: | - Optional description file in MIAME format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata and CEL file names + - celfiles_dir: + type: list + description: Path to a directory containing CEL files + pattern: "*.{CEL,CEL.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - description: + type: file + description: | + Optional description file in MIAME format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - rds: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.rds": + type: file + description: Serialised ExpressionSet object + pattern: "*.rds" - expression: - type: file - description: TSV-format intensity matrix - pattern: "matrix.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*matrix.tsv": + type: file + description: TSV-format intensity matrix + pattern: "matrix.tsv" - annotation: - type: file - description: TSV-format annotation table - pattern: "*.annotation.tsv" - - rds: - type: file - description: Serialised ExpressionSet object - pattern: "*.rds" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.annotation.tsv": + type: file + description: TSV-format annotation table + pattern: "*.annotation.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/agat/convertspgff2gtf/meta.yml b/modules/nf-core/agat/convertspgff2gtf/meta.yml index ab39f019b4ec..5330167c08f1 100644 --- a/modules/nf-core/agat/convertspgff2gtf/meta.yml +++ b/modules/nf-core/agat/convertspgff2gtf/meta.yml @@ -8,35 +8,48 @@ keywords: - conversion tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - output_gtf: - type: file - description: Annotation file in GTF format - pattern: "*.{gtf}" + - meta: + type: file + description: Annotation file in GTF format + pattern: "*.{gtf}" + - "*.agat.gtf": + type: file + description: Annotation file in GTF format + pattern: "*.{gtf}" - log: - type: file - description: Log file of the conversion process - pattern: "*.{log}" + - meta: + type: file + description: Log file of the conversion process + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of the conversion process + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/convertspgff2tsv/meta.yml b/modules/nf-core/agat/convertspgff2tsv/meta.yml index 83078787b733..31f0986837e0 100644 --- a/modules/nf-core/agat/convertspgff2tsv/meta.yml +++ b/modules/nf-core/agat/convertspgff2tsv/meta.yml @@ -9,31 +9,39 @@ keywords: - tsv tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - tsv: - type: file - description: Annotation file in TSV format - pattern: "*.{gtf}" + - meta: + type: file + description: Annotation file in TSV format + pattern: "*.{gtf}" + - "*.tsv": + type: file + description: Annotation file in TSV format + pattern: "*.{gtf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/agat/convertspgxf2gxf/meta.yml b/modules/nf-core/agat/convertspgxf2gxf/meta.yml index 0ef9881400ab..d9468ec47eb0 100644 --- a/modules/nf-core/agat/convertspgxf2gxf/meta.yml +++ b/modules/nf-core/agat/convertspgxf2gxf/meta.yml @@ -8,35 +8,48 @@ keywords: - conversion tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gxf: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gxf: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - output_gff: - type: file - description: Cleaned annotation file in GFF3 format - pattern: "*.{gff}" + - meta: + type: file + description: Cleaned annotation file in GFF3 format + pattern: "*.{gff}" + - "*.agat.gff": + type: file + description: Cleaned annotation file in GFF3 format + pattern: "*.{gff}" - log: - type: file - description: Log file of the conversion process - pattern: "*.{log}" + - meta: + type: file + description: Log file of the conversion process + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of the conversion process + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/spaddintrons/meta.yml b/modules/nf-core/agat/spaddintrons/meta.yml index 666e60376221..03f17b9f9d29 100644 --- a/modules/nf-core/agat/spaddintrons/meta.yml +++ b/modules/nf-core/agat/spaddintrons/meta.yml @@ -6,37 +6,43 @@ keywords: - introns tools: - agat: - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/NBISweden/AGAT" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Input gtf/gff file - pattern: "*.{gff,gff3,gtf}" - - config: - type: file - description: Optional input agat config file - pattern: "*.{yaml,yml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Input gtf/gff file + pattern: "*.{gff,gff3,gtf}" + - - config: + type: file + description: Optional input agat config file + pattern: "*.{yaml,yml}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output gff3 file with introns - pattern: "*.gff" - + - meta: + type: file + description: Output gff3 file with introns + pattern: "*.gff" + - ${output}: + type: file + description: Output gff3 file with introns + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml b/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml index d408fe7fe3b2..d6c8dbb783ac 100644 --- a/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml +++ b/modules/nf-core/agat/spfilterfeaturefromkilllist/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "agat_spfilterfeaturefromkilllist" description: | @@ -13,47 +12,49 @@ keywords: - feature tools: - "agat": - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_kill_list.html" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - gff: - type: file - description: Input GFF3 file that will be read - pattern: "*.{gff,gff3}" - - kill_list: - type: file - description: Kill list. One value per line. - pattern: "*.txt" - - config: - type: file - description: | - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). - pattern: "*.yaml" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff: + type: file + description: Input GFF3 file that will be read + pattern: "*.{gff,gff3}" + - - kill_list: + type: file + description: Kill list. One value per line. + pattern: "*.txt" + - - config: + type: file + description: | + Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently). + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output GFF file. - pattern: "*.gff" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ] + - "*.gff": + type: file + description: Output GFF file. + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/agat/spmergeannotations/meta.yml b/modules/nf-core/agat/spmergeannotations/meta.yml index afa9ddd0e7d9..fd5083b70e58 100644 --- a/modules/nf-core/agat/spmergeannotations/meta.yml +++ b/modules/nf-core/agat/spmergeannotations/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "agat_spmergeannotations" description: | @@ -10,44 +9,48 @@ keywords: - combine tools: - "agat": - description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene annotations in any GTF/GFF format." + description: "Another Gff Analysis Toolkit (AGAT). Suite of tools to handle gene + annotations in any GTF/GFF format." homepage: "https://agat.readthedocs.io/en/latest/" documentation: "https://agat.readthedocs.io/en/latest/tools/agat_sp_merge_annotations.html" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gffs: - type: list - description: A list of GFFs to merge - pattern: "[ *.{gff,gff3} ]" - - config: - type: file - description: | - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, - otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml - locally type: "agat config --expose". The --config option gives you the possibility to use your - own AGAT config file (located elsewhere or named differently). - pattern: "*.yaml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gffs: + type: list + description: A list of GFFs to merge + pattern: "[ *.{gff,gff3} ]" + - - config: + type: file + description: | + Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, + otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml + locally type: "agat config --expose". The --config option gives you the possibility to use your + own AGAT config file (located elsewhere or named differently). + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: Output GFF file. - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff": + type: file + description: Output GFF file. + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/agat/spstatistics/meta.yml b/modules/nf-core/agat/spstatistics/meta.yml index c6cb21dda308..a2f897b8a64f 100644 --- a/modules/nf-core/agat/spstatistics/meta.yml +++ b/modules/nf-core/agat/spstatistics/meta.yml @@ -8,31 +8,39 @@ keywords: - statistics tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - stats_txt: - type: file - description: Output of Statistics execution - pattern: "*.{txt}" + - meta: + type: file + description: Output of Statistics execution + pattern: "*.{txt}" + - "*.txt": + type: file + description: Output of Statistics execution + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agat/sqstatbasic/meta.yml b/modules/nf-core/agat/sqstatbasic/meta.yml index aba57e896ae2..b813a4a8169a 100644 --- a/modules/nf-core/agat/sqstatbasic/meta.yml +++ b/modules/nf-core/agat/sqstatbasic/meta.yml @@ -8,31 +8,39 @@ keywords: - statistics tools: - agat: - description: "AGAT is a toolkit for manipulation and getting information from GFF/GTF files" + description: "AGAT is a toolkit for manipulation and getting information from + GFF/GTF files" homepage: "https://github.com/NBISweden/AGAT" documentation: "https://agat.readthedocs.io/" tool_dev_url: "https://github.com/NBISweden/AGAT" doi: "10.5281/zenodo.3552717" licence: ["GPL v3"] + identifier: biotools:AGAT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: Annotation file in GFF3/GTF format - pattern: "*.{gff, gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: Annotation file in GFF3/GTF format + pattern: "*.{gff, gtf}" output: - stats_txt: - type: file - description: Output of Statistics execution - pattern: "*.{txt}" + - meta: + type: file + description: Output of Statistics execution + pattern: "*.{txt}" + - "*.txt": + type: file + description: Output of Statistics execution + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/agrvate/meta.yml b/modules/nf-core/agrvate/meta.yml index 0e11d8b296a5..8b45db819142 100644 --- a/modules/nf-core/agrvate/meta.yml +++ b/modules/nf-core/agrvate/meta.yml @@ -1,44 +1,50 @@ name: agrvate -description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants +description: Rapid identification of Staphylococcus aureus agr locus type and agr + operon variants keywords: - fasta - virulence - Staphylococcus aureus tools: - agrvate: - description: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. + description: Rapid identification of Staphylococcus aureus agr locus type and + agr operon variants. homepage: https://github.com/VishnuRaghuram94/AgrVATE documentation: https://github.com/VishnuRaghuram94/AgrVATE tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE licence: ["MIT"] + identifier: biotools:agrvate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A Staphylococcus aureus fasta file. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A Staphylococcus aureus fasta file. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary: - type: file - description: A summary of the agrvate assessement - pattern: "*-summary.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${fasta.baseName}-results/${fasta.baseName}-summary.tab: + type: file + description: A summary of the agrvate assessement + pattern: "*-summary.tab" - results_dir: - type: directory - description: Results of the agrvate assessement - pattern: "*-results" + - ${fasta.baseName}-results: + type: directory + description: Results of the agrvate assessement + pattern: "*-results" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/ale/meta.yml b/modules/nf-core/ale/meta.yml index 6191741e1ea0..6ada6fa314c4 100644 --- a/modules/nf-core/ale/meta.yml +++ b/modules/nf-core/ale/meta.yml @@ -1,4 +1,3 @@ ---- name: "ale" description: "ALE: assembly likelihood estimator." keywords: @@ -7,44 +6,44 @@ keywords: - evaluation tools: - "ale": - description: "ALE is a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies." + description: "ALE is a generic assembly likelihood evaluation framework for assessing + the accuracy of genome and metagenome assemblies." documentation: "https://portal.nersc.gov/dna/RD/Adv-Seq/ALE-doc/index.html#document-install" tool_dev_url: "https://github.com/sc932/ALE" doi: "10.1093/bioinformatics/bts723" licence: ["NCSA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - asm: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fa}" - - - bam: - type: file - description: BAM file containing sorted read mappings - pattern: "*.{bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - asm: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fa}" + - bam: + type: file + description: BAM file containing sorted read mappings + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - ale: - type: file - description: Output TXT file containing ALE results - pattern: "*_ALEoutput.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_ALEoutput.txt": + type: file + description: Output TXT file containing ALE results + pattern: "*_ALEoutput.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rodtheo" maintainers: diff --git a/modules/nf-core/allelecounter/meta.yml b/modules/nf-core/allelecounter/meta.yml index 751b9f97b448..fce9123d704e 100644 --- a/modules/nf-core/allelecounter/meta.yml +++ b/modules/nf-core/allelecounter/meta.yml @@ -6,46 +6,50 @@ keywords: - coverage tools: - allelecounter: - description: Takes a file of locations and a [cr|b]am file and generates a count of coverage of each allele at that location (given any filter settings) + description: Takes a file of locations and a [cr|b]am file and generates a count + of coverage of each allele at that location (given any filter settings) homepage: https://github.com/cancerit/alleleCount documentation: https://github.com/cancerit/alleleCount tool_dev_url: https://github.com/cancerit/alleleCount licence: ["GPL 3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - loci: - type: file - description: loci file - pattern: "*.{tsv}" - - fasta: - type: file - description: Input genome fasta file. Required when passing CRAM files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - - loci: + type: file + description: loci file + pattern: "*.{tsv}" + - - fasta: + type: file + description: Input genome fasta file. Required when passing CRAM files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - allelecount: - type: file - description: Allele count file - pattern: "*.{alleleCount}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.alleleCount": + type: file + description: Allele count file + pattern: "*.{alleleCount}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fullama" - "@fbdtemme" diff --git a/modules/nf-core/ampcombi/environment.yml b/modules/nf-core/ampcombi/environment.yml index 21ec05e613ea..1e945daa712c 100644 --- a/modules/nf-core/ampcombi/environment.yml +++ b/modules/nf-core/ampcombi/environment.yml @@ -1,9 +1,8 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - bioconda::ampcombi=0.1.7 - - python=3.11 - pandas=1.5.2 + - python=3.11 diff --git a/modules/nf-core/ampcombi/meta.yml b/modules/nf-core/ampcombi/meta.yml index be104d1770b5..152d0b294ded 100644 --- a/modules/nf-core/ampcombi/meta.yml +++ b/modules/nf-core/ampcombi/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi" -description: A tool to parse and summarise results from antimicrobial peptides tools and present functional classification. +description: A tool to parse and summarise results from antimicrobial peptides tools + and present functional classification. keywords: - antimicrobial peptides - amps @@ -16,83 +16,164 @@ keywords: - DRAMP tools: - ampcombi: - description: "This tool parses the results of amp prediction tools into a single table and aligns the hits against a reference database of antimicrobial peptides for functional classifications." + description: "This tool parses the results of amp prediction tools into a single + table and aligns the hits against a reference database of antimicrobial peptides + for functional classifications." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - amp_input: - type: list - description: The path to the directory containing the results for the AMP tools for each sample processed or a list of files corresponding to each file generated by AMP tools. - pattern: "[*amptool.tsv, *amptool.tsv]" - - faa_input: - type: file - description: The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa - pattern: "*.faa" - - opt_amp_db: - type: directory - description: The path to the folder containing the fasta and tsv database files. - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_input: + type: list + description: The path to the directory containing the results for the AMP tools + for each sample processed or a list of files corresponding to each file generated + by AMP tools. + pattern: "[*amptool.tsv, *amptool.tsv]" + - - faa_input: + type: file + description: The path to the file corresponding to the respective protein fasta + files with '.faa' extension. File names have to contain the corresponding + sample name, i.e. sample_1.faa + pattern: "*.faa" + - - opt_amp_db: + type: directory + description: The path to the folder containing the fasta and tsv database files. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_dir: - type: directory - description: The output directory that contains the summary output and related alignment files for one sample. - pattern: "/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/: + type: directory + description: The output directory that contains the summary output and related + alignment files for one sample. + pattern: "/*" - txt: - type: file - description: An alignment file containing the results from the DIAMOND alignment step done on all AMP hits. - pattern: "/*/*_diamond_matches.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*diamond_matches.txt: + type: file + description: An alignment file containing the results from the DIAMOND alignment + step done on all AMP hits. + pattern: "/*/*_diamond_matches.txt" - csv: - type: file - description: A file containing the summary report of all predicted AMP hits from all AMP tools given as input and the corresponding taxonomic and functional classification from the alignment step. - pattern: "/*/*_ampcombi.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*ampcombi.csv: + type: file + description: A file containing the summary report of all predicted AMP hits + from all AMP tools given as input and the corresponding taxonomic and functional + classification from the alignment step. + pattern: "/*/*_ampcombi.csv" - faa: - type: file - description: A fasta file containing the amino acid sequences of all predicted AMP hits. - pattern: "/*/*_amp.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*amp.faa: + type: file + description: A fasta file containing the amino acid sequences of all predicted + AMP hits. + pattern: "/*/*_amp.faa" - summary_csv: - type: file - description: A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`. - pattern: "AMPcombi_summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - AMPcombi_summary.csv: + type: file + description: A file that concatenates all samples ampcombi summaries. This is + activated with `--complete_summary true`. + pattern: "AMPcombi_summary.csv" - summary_html: - type: file - description: A file that concatenates all samples ampcombi summaries. This is activated with `--complete_summary true`. - pattern: "AMPcombi_summary.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - AMPcombi_summary.html: + type: file + description: A file that concatenates all samples ampcombi summaries. This is + activated with `--complete_summary true`. + pattern: "AMPcombi_summary.html" - log: - type: file - description: A log file that captures the standard output ina log file. Can be activated by `--log`. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: A log file that captures the standard output ina log file. Can + be activated by `--log`. + pattern: "*.log" - results_db: - type: directory - description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. - pattern: "/amp_ref_database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/: + type: directory + description: If the AMP reference database is not provided by the user using + the flag `--amp_database', by default the DRAMP database will be downloaded, + filtered and stored in this folder. + pattern: "/amp_ref_database" - results_db_dmnd: - type: file - description: AMP reference database converted to DIAMOND database format. - pattern: "/amp_ref_database/*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.dmnd: + type: file + description: AMP reference database converted to DIAMOND database format. + pattern: "/amp_ref_database/*.dmnd" - results_db_fasta: - type: file - description: AMP reference database fasta file, cleaned of diamond-uncompatible characters. - pattern: "/amp_ref_database/*.clean.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.clean.fasta: + type: file + description: AMP reference database fasta file, cleaned of diamond-uncompatible + characters. + pattern: "/amp_ref_database/*.clean.fasta" - results_db_tsv: - type: file - description: AMP reference database in tsv-format with two columns containing header and sequence. - pattern: "/amp_ref_database/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - amp_ref_database/*.tsv: + type: file + description: AMP reference database in tsv-format with two columns containing + header and sequence. + pattern: "/amp_ref_database/*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" - "@louperelo" diff --git a/modules/nf-core/ampcombi2/cluster/meta.yml b/modules/nf-core/ampcombi2/cluster/meta.yml index 60949dc34c69..2e37a0c2fade 100644 --- a/modules/nf-core/ampcombi2/cluster/meta.yml +++ b/modules/nf-core/ampcombi2/cluster/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_cluster" -description: A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables and ampcombi2/complete using MMseqs2 cluster. +description: A submodule that clusters the merged AMP hits generated from ampcombi2/parsetables + and ampcombi2/complete using MMseqs2 cluster. keywords: - antimicrobial peptides - amps @@ -12,36 +12,46 @@ keywords: - mmseqs2 tools: - ampcombi2/cluster: - description: "A tool for clustering all AMP hits found across many samples and supporting many AMP prediction tools." + description: "A tool for clustering all AMP hits found across many samples and + supporting many AMP prediction tools." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - summary_file: - type: file - description: A file corresponding to the Ampcombi_summary.tsv that is generated by running 'ampcombi complete'. It is a file containing all the merged AMP results from all samples and all tools. - pattern: "*.tsv" - + - - summary_file: + type: file + description: A file corresponding to the Ampcombi_summary.tsv that is generated + by running 'ampcombi complete'. It is a file containing all the merged AMP + results from all samples and all tools. + pattern: "*.tsv" output: - cluster_tsv: - type: file - description: A file containing all the results from the merged input table 'Ampcombi_summary.tsv', but also including the cluster id number. The clustering is done using MMseqs2 cluster. - pattern: "*.tsv" + - Ampcombi_summary_cluster.tsv: + type: file + description: A file containing all the results from the merged input table 'Ampcombi_summary.tsv', + but also including the cluster id number. The clustering is done using MMseqs2 + cluster. + pattern: "*.tsv" - rep_cluster_tsv: - type: file - description: A file containing the representative sequences of the clusters estimated by the tool. The clustering is done using MMseqs2 cluster. - pattern: "*.tsv" + - Ampcombi_summary_cluster_representative_seq.tsv: + type: file + description: A file containing the representative sequences of the clusters + estimated by the tool. The clustering is done using MMseqs2 cluster. + pattern: "*.tsv" - log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "*.log" + - Ampcombi_cluster.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampcombi2/complete/meta.yml b/modules/nf-core/ampcombi2/complete/meta.yml index e9ae632c644a..13a7468bc9b0 100644 --- a/modules/nf-core/ampcombi2/complete/meta.yml +++ b/modules/nf-core/ampcombi2/complete/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_complete" -description: A submodule that merges all output summary tables from ampcombi/parsetables in one summary file. +description: A submodule that merges all output summary tables from ampcombi/parsetables + in one summary file. keywords: - antimicrobial peptides - amps @@ -18,32 +18,38 @@ keywords: - DRAMP tools: - ampcombi2/complete: - description: "This merges the per sample AMPcombi summaries generated by running 'ampcombi2/parsetables'." + description: "This merges the per sample AMPcombi summaries generated by running + 'ampcombi2/parsetables'." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - summaries: - type: list - description: The path to the list of files corresponding to each sample as generated by ampcombi2/parsetables. - pattern: "[*_ampcombi.tsv, *_ampcombi.tsv]" - + - - summaries: + type: list + description: The path to the list of files corresponding to each sample as generated + by ampcombi2/parsetables. + pattern: "[*_ampcombi.tsv, *_ampcombi.tsv]" output: - tsv: - type: file - description: A file containing the complete AMPcombi summaries from all processed samples. - pattern: "*.tsv" + - Ampcombi_summary.tsv: + type: file + description: A file containing the complete AMPcombi summaries from all processed + samples. + pattern: "*.tsv" - log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "*.log" + - Ampcombi_complete.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampcombi2/parsetables/meta.yml b/modules/nf-core/ampcombi2/parsetables/meta.yml index eeea5586cd10..7159b1177396 100644 --- a/modules/nf-core/ampcombi2/parsetables/meta.yml +++ b/modules/nf-core/ampcombi2/parsetables/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ampcombi2_parsetables" -description: A submodule that parses and standardizes the results from various antimicrobial peptide identification tools. +description: A submodule that parses and standardizes the results from various antimicrobial + peptide identification tools. keywords: - antimicrobial peptides - amps @@ -18,89 +18,171 @@ keywords: - DRAMP tools: - ampcombi2/parsetables: - description: "A parsing tool to convert and summarise the outputs from multiple AMP detection tools in a standardized format." + description: "A parsing tool to convert and summarise the outputs from multiple + AMP detection tools in a standardized format." homepage: "https://github.com/Darcy220606/AMPcombi" documentation: "https://github.com/Darcy220606/AMPcombi" tool_dev_url: "https://github.com/Darcy220606/AMPcombi/tree/dev" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - amp_input: - type: list - description: The path to the directory containing the results for the AMP tools for each processed sample or a list of files corresponding to each file generated by AMP tools. - pattern: "[*amptool.tsv, *amptool.tsv]" - - faa_input: - type: file - description: The path to the file corresponding to the respective protein fasta files with '.faa' extension. File names have to contain the corresponding sample name, i.e. sample_1.faa - pattern: "*.faa" - - gbk_input: - type: file - description: The path to the file corresponding to the respective annotated files with either '.gbk' or '.gbff' extensions. File names must contain the corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample name. - pattern: "*.gbk" - - opt_amp_db: - type: directory - description: The path to the folder containing the fasta and tsv database files. - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_input: + type: list + description: The path to the directory containing the results for the AMP tools + for each processed sample or a list of files corresponding to each file generated + by AMP tools. + pattern: "[*amptool.tsv, *amptool.tsv]" + - - faa_input: + type: file + description: The path to the file corresponding to the respective protein fasta + files with '.faa' extension. File names have to contain the corresponding + sample name, i.e. sample_1.faa + pattern: "*.faa" + - - gbk_input: + type: file + description: The path to the file corresponding to the respective annotated + files with either '.gbk' or '.gbff' extensions. File names must contain the + corresponding sample name, i.e. sample_1.faa where "sample_1" is the sample + name. + pattern: "*.gbk" + - - opt_amp_db: + type: directory + description: The path to the folder containing the fasta and tsv database files. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - sample_dir: - type: directory - description: The output directory that contains the summary output and related alignment files for one sample. - pattern: "/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/: + type: directory + description: The output directory that contains the summary output and related + alignment files for one sample. + pattern: "/*" - contig_gbks: - type: directory - description: The output subdirectory that contains the gbk files containing the AMP hits for each sample. - pattern: "/*/contig_gbks" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/contig_gbks/: + type: directory + description: The output subdirectory that contains the gbk files containing + the AMP hits for each sample. + pattern: "/*/contig_gbks" - txt: - type: file - description: An alignment file containing the results from the DIAMOND alignment step done on all AMP hits. - pattern: "/*/*_diamond_matches.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_diamond_matches.txt: + type: file + description: An alignment file containing the results from the DIAMOND alignment + step done on all AMP hits. + pattern: "/*/*_diamond_matches.txt" - tsv: - type: file - description: A file containing the summary report of all predicted AMP hits from all AMP tools given as input, the corresponding taxonomic and functional classification from the alignment step and the estimated physiochemical properties. - pattern: "/*/*_ampcombi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_ampcombi.tsv: + type: file + description: A file containing the summary report of all predicted AMP hits + from all AMP tools given as input, the corresponding taxonomic and functional + classification from the alignment step and the estimated physiochemical properties. + pattern: "/*/*_ampcombi.tsv" - faa: - type: file - description: A fasta file containing the amino acid sequences of all predicted AMP hits. - pattern: "/*/*_amp.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_amp.faa: + type: file + description: A fasta file containing the amino acid sequences of all predicted + AMP hits. + pattern: "/*/*_amp.faa" - sample_log: - type: file - description: A log file that captures the standard output per sample in a log file. Can be activated by `--log`. - pattern: "/*/*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}/${meta.id}_ampcombi.log: + type: file + description: A log file that captures the standard output per sample in a log + file. Can be activated by `--log`. + pattern: "/*/*.log" - full_log: - type: file - description: A log file that captures the standard output for the entire process in a log file. Can be activated by `--log`. - pattern: "Ampcombi_parse_tables.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - Ampcombi_parse_tables.log: + type: file + description: A log file that captures the standard output for the entire process + in a log file. Can be activated by `--log`. + pattern: "Ampcombi_parse_tables.log" - results_db: - type: directory - description: If the AMP reference database is not provided by the user using the flag `--amp_database', by default the DRAMP database will be downloaded, filtered and stored in this folder. - pattern: "/amp_ref_database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/: + type: directory + description: If the AMP reference database is not provided by the user using + the flag `--amp_database', by default the DRAMP database will be downloaded, + filtered and stored in this folder. + pattern: "/amp_ref_database" - results_db_dmnd: - type: file - description: AMP reference database converted to DIAMOND database format. - pattern: "/amp_ref_database/*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.dmnd: + type: file + description: AMP reference database converted to DIAMOND database format. + pattern: "/amp_ref_database/*.dmnd" - results_db_fasta: - type: file - description: AMP reference database fasta file, cleaned of diamond-uncompatible characters. - pattern: "/amp_ref_database/*.clean.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.clean.fasta: + type: file + description: AMP reference database fasta file, cleaned of diamond-uncompatible + characters. + pattern: "/amp_ref_database/*.clean.fasta" - results_db_tsv: - type: file - description: AMP reference database in tsv-format with two columns containing header and sequence. - pattern: "/amp_ref_database/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - amp_ref_database/*.tsv: + type: file + description: AMP reference database in tsv-format with two columns containing + header and sequence. + pattern: "/amp_ref_database/*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/ampir/meta.yml b/modules/nf-core/ampir/meta.yml index 231cec54e2e2..571ddd86a57b 100644 --- a/modules/nf-core/ampir/meta.yml +++ b/modules/nf-core/ampir/meta.yml @@ -1,57 +1,69 @@ name: "ampir" -description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) from any given size protein dataset. ampir uses a supervised statistical machine learning approach to predict AMPs. +description: A fast and user-friendly method to predict antimicrobial peptides (AMPs) + from any given size protein dataset. ampir uses a supervised statistical machine + learning approach to predict AMPs. keywords: - ampir - amp - antimicrobial peptide prediction tools: - "ampir": - description: "A toolkit to predict antimicrobial peptides from protein sequences on a genome-wide scale." + description: "A toolkit to predict antimicrobial peptides from protein sequences + on a genome-wide scale." homepage: "https://github.com/Legana/ampir" documentation: "https://cran.r-project.org/web/packages/ampir/index.html" tool_dev_url: "https://github.com/Legana/ampir" doi: "10.1093/bioinformatics/btaa653" licence: ["GPL v2"] + identifier: biotools:ampir input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - faa: - type: file - description: FASTA file containing amino acid sequences - pattern: "*.{faa,fasta}" - - model: - type: string - description: Built-in model for AMP prediction - pattern: "{precursor,mature}" - - min_length: - type: integer - description: Minimum protein length for which predictions will be generated - pattern: "[0-9]+" - - min_probability: - type: float - description: Cut-off for AMP prediction - pattern: "[0-9].[0-9]+" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - faa: + type: file + description: FASTA file containing amino acid sequences + pattern: "*.{faa,fasta}" + - - model: + type: string + description: Built-in model for AMP prediction + pattern: "{precursor,mature}" + - - min_length: + type: integer + description: Minimum protein length for which predictions will be generated + pattern: "[0-9]+" + - - min_probability: + type: float + description: Cut-off for AMP prediction + pattern: "[0-9].[0-9]+" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - amps_faa: - type: file - description: File containing AMP predictions in amino acid FASTA format - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa": + type: file + description: File containing AMP predictions in amino acid FASTA format + pattern: "*.{faa}" - amps_tsv: - type: file - description: File containing AMP predictions in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: File containing AMP predictions in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/amplify/predict/meta.yml b/modules/nf-core/amplify/predict/meta.yml index 5ef93c831205..cbe19f3368eb 100644 --- a/modules/nf-core/amplify/predict/meta.yml +++ b/modules/nf-core/amplify/predict/meta.yml @@ -1,5 +1,6 @@ name: "amplify_predict" -description: AMPlify is an attentive deep learning model for antimicrobial peptide prediction. +description: AMPlify is an attentive deep learning model for antimicrobial peptide + prediction. keywords: - antimicrobial peptides - AMPs @@ -13,33 +14,37 @@ tools: tool_dev_url: "https://github.com/bcgsc/AMPlify" doi: "10.1186/s12864-022-08310-4" licence: ["GPL v3"] + identifier: biotools:amplify input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - faa: - type: file - description: amino acid sequences fasta - pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" - - model_dir: - type: directory - description: Directory of where models are stored (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - faa: + type: file + description: amino acid sequences fasta + pattern: "*.{fa,fa.gz,faa,faa.gz,fasta,fasta.gz}" + - - model_dir: + type: directory + description: Directory of where models are stored (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: amino acid sequences with prediction (AMP, non-AMP) and probability scores - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: amino acid sequences with prediction (AMP, non-AMP) and probability + scores + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/amps/meta.yml b/modules/nf-core/amps/meta.yml index de9a9da497e9..61194067fb81 100644 --- a/modules/nf-core/amps/meta.yml +++ b/modules/nf-core/amps/meta.yml @@ -25,40 +25,46 @@ tools: tool_dev_url: "https://github.com/keyfm/amps" doi: "10.1186/s13059-019-1903-0" licence: ["GPL >=3"] + identifier: "" input: - - maltextract_results: - type: directory - description: MaltExtract output directory - pattern: "results/" - - taxon_list: - type: file - description: List of target taxa to evaluate used in MaltExtract - pattern: "*.txt" - - filter: - type: string - description: The filter mode used in MaltExtract - pattern: "def_anc|default|scan|ancient|crawl" + - - maltextract_results: + type: directory + description: MaltExtract output directory + pattern: "results/" + - - taxon_list: + type: file + description: List of target taxa to evaluate used in MaltExtract + pattern: "*.txt" + - - filter: + type: string + description: The filter mode used in MaltExtract + pattern: "def_anc|default|scan|ancient|crawl" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Candidate summary heatmap in MultiQC compatible JSON format - pattern: "heatmap_overview_Wevid.json" + - results/heatmap_overview_Wevid.json: + type: file + description: Candidate summary heatmap in MultiQC compatible JSON format + pattern: "heatmap_overview_Wevid.json" - summary_pdf: - type: file - description: Candidate summary heatmap in PDF format - pattern: "heatmap_overview_Wevid.pdf" + - results/heatmap_overview_Wevid.pdf: + type: file + description: Candidate summary heatmap in PDF format + pattern: "heatmap_overview_Wevid.pdf" - tsv: - type: file - description: Candidate summary heatmap in TSV format - pattern: "heatmap_overview_Wevid.tsv" + - results/heatmap_overview_Wevid.tsv: + type: file + description: Candidate summary heatmap in TSV format + pattern: "heatmap_overview_Wevid.tsv" - candidate_pdfs: - type: directory - description: Directory of per sample output PDFs organised by reference - pattern: "pdf_candidate_profiles/" + - results/pdf_candidate_profiles/: + type: directory + description: Directory of per sample output PDFs organised by reference + pattern: "pdf_candidate_profiles/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/amrfinderplus/run/meta.yml b/modules/nf-core/amrfinderplus/run/meta.yml index 465927dffe63..d081a2bda094 100644 --- a/modules/nf-core/amrfinderplus/run/meta.yml +++ b/modules/nf-core/amrfinderplus/run/meta.yml @@ -6,50 +6,64 @@ keywords: - antibiotic resistance tools: - amrfinderplus: - description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences. + description: AMRFinderPlus finds antimicrobial resistance and other genes in protein + or nucleotide sequences. homepage: https://github.com/ncbi/amr/wiki documentation: https://github.com/ncbi/amr/wiki tool_dev_url: https://github.com/ncbi/amr doi: "10.1038/s41598-021-91456-0" licence: ["Public Domain"] + identifier: biotools:amrfinderplus input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - - db: - type: file - description: A compressed tarball of the AMRFinderPlus database to query - pattern: "*.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - db: + type: file + description: A compressed tarball of the AMRFinderPlus database to query + pattern: "*.tar.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: AMRFinder+ final report - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: AMRFinder+ final report + pattern: "*.tsv" - mutation_report: - type: file - description: Report of organism-specific point-mutations - pattern: "*-mutations.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-mutations.tsv: + type: file + description: Report of organism-specific point-mutations + pattern: "*-mutations.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - VER: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DBVER: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) authors: - "@rpetit3" - "@louperelo" diff --git a/modules/nf-core/amrfinderplus/update/meta.yml b/modules/nf-core/amrfinderplus/update/meta.yml index 7a9345d6fad8..574957e10ab2 100644 --- a/modules/nf-core/amrfinderplus/update/meta.yml +++ b/modules/nf-core/amrfinderplus/update/meta.yml @@ -6,27 +6,26 @@ keywords: - antibiotic resistance tools: - amrfinderplus: - description: AMRFinderPlus finds antimicrobial resistance and other genes in protein or nucleotide sequences. + description: AMRFinderPlus finds antimicrobial resistance and other genes in protein + or nucleotide sequences. homepage: https://github.com/ncbi/amr/wiki documentation: https://github.com/ncbi/amr/wiki tool_dev_url: https://github.com/ncbi/amr doi: "10.1038/s41598-021-91456-0" licence: ["Public Domain"] + identifier: biotools:amrfinderplus # this module does have any input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: The latest AMRFinder+ database in a compressed tarball - pattern: "*.tar.gz" + - amrfinderdb.tar.gz: + type: file + description: The latest AMRFinder+ database in a compressed tarball + pattern: "*.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/angsd/contamination/meta.yml b/modules/nf-core/angsd/contamination/meta.yml index ffe6428d6443..0bfb73d2a41b 100644 --- a/modules/nf-core/angsd/contamination/meta.yml +++ b/modules/nf-core/angsd/contamination/meta.yml @@ -1,5 +1,6 @@ name: "angsd_contamination" -description: A tool to estimate nuclear contamination in males based on heterozygosity in the female chromosome. +description: A tool to estimate nuclear contamination in males based on heterozygosity + in the female chromosome. keywords: - angsd - population genetics @@ -12,38 +13,42 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3", "MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - icounts: - type: file - description: Internal format for dumping binary single chrs. Useful for ANGSD contamination - pattern: "*.icnts.gz" - - meta2: - type: map - description: | - Groovy Map containing information related to the hapmap_file. - e.g. [ id:'test' ] - - hapmap_file: - type: file - description: A list of variable sites to look for heterozygosity. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - icounts: + type: file + description: Internal format for dumping binary single chrs. Useful for ANGSD + contamination + pattern: "*.icnts.gz" + - - meta2: + type: map + description: | + Groovy Map containing information related to the hapmap_file. + e.g. [ id:'test' ] + - hapmap_file: + type: file + description: A list of variable sites to look for heterozygosity. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Contamination estimation output. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Contamination estimation output. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jbv2" maintainers: diff --git a/modules/nf-core/angsd/docounts/meta.yml b/modules/nf-core/angsd/docounts/meta.yml index b1eec87da705..cbde98892f75 100644 --- a/modules/nf-core/angsd/docounts/meta.yml +++ b/modules/nf-core/angsd/docounts/meta.yml @@ -1,5 +1,6 @@ name: "angsd_docounts" -description: Calculates base frequency statistics across reference positions from BAM. +description: Calculates base frequency statistics across reference positions from + BAM. keywords: - angsd - population genetics @@ -13,58 +14,92 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3, MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of BAM or CRAM files - pattern: "*.{bam,cram}" - - bai: - type: file - description: List of BAM/CRAM index files - pattern: "*.{bai,csi}" - - minqfile: - type: file - description: File with individual quality score thresholds - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of BAM or CRAM files + pattern: "*.{bam,cram}" + - bai: + type: file + description: List of BAM/CRAM index files + pattern: "*.{bai,csi}" + - minqfile: + type: file + description: File with individual quality score thresholds + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth_sample: - type: file - description: Distribution of sequencing depths - pattern: "*.depthSample" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthSample": + type: file + description: Distribution of sequencing depths + pattern: "*.depthSample" - depth_global: - type: file - description: Distribution of sequencing depths - pattern: "*.depthGlobal" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthGlobal": + type: file + description: Distribution of sequencing depths + pattern: "*.depthGlobal" - qs: - type: file - description: Distribution of scores - pattern: "*.qs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qs": + type: file + description: Distribution of scores + pattern: "*.qs" - pos: - type: file - description: Various types of depth statistics (depending on value for -dumpCounts) - pattern: "*.pos.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pos.gz": + type: file + description: Various types of depth statistics (depending on value for -dumpCounts) + pattern: "*.pos.gz" - counts: - type: file - description: Various types of statistics (related to pos.gz) - pattern: "*.counts.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.counts.gz": + type: file + description: Various types of statistics (related to pos.gz) + pattern: "*.counts.gz" - icounts: - type: file - description: Internal format for dumping binary single chrs. Useful for ANGSD contamination - pattern: "*.icnts.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.icnts.gz": + type: file + description: Internal format for dumping binary single chrs. Useful for ANGSD + contamination + pattern: "*.icnts.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/angsd/gl/meta.yml b/modules/nf-core/angsd/gl/meta.yml index 168f615d5a2e..3951bbbf7129 100644 --- a/modules/nf-core/angsd/gl/meta.yml +++ b/modules/nf-core/angsd/gl/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "angsd_gl" description: Calculated genotype likelihoods from BAM files. @@ -14,49 +13,51 @@ tools: tool_dev_url: "https://github.com/ANGSD/angsd" doi: "10.1186/s12859-014-0356-4" licence: ["GPL v3", "MIT"] + identifier: biotools:angsd input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of BAM or CRAM files - pattern: "*.{bam,cram}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: A reference genome in FASTA format - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - error_file: - type: file - description: A file containing information about type specific errors. - pattern: "*.error.chunkunordered" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of BAM or CRAM files + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: A reference genome in FASTA format + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - error_file: + type: file + description: A file containing information about type specific errors. + pattern: "*.error.chunkunordered" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genotype_likelihood: - type: file - description: File containing genotype likelihoods per sample - pattern: "*.{glf,beagle}.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{glf,beagle}.gz": + type: file + description: File containing genotype likelihoods per sample + pattern: "*.{glf,beagle}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" - "@TCLamnidis" diff --git a/modules/nf-core/annotsv/annotsv/meta.yml b/modules/nf-core/annotsv/annotsv/meta.yml index f690f0aa123f..6458f2627c89 100644 --- a/modules/nf-core/annotsv/annotsv/meta.yml +++ b/modules/nf-core/annotsv/annotsv/meta.yml @@ -14,80 +14,97 @@ tools: tool_dev_url: "https://github.com/lgmgeo/AnnotSV" doi: 10.1093/bioinformatics/bty304 licence: ["GPL-3.0"] + identifier: biotools:AnnotSV input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sv_vcf: - type: file - description: A VCF or BED file containing the structural variants to be annotated - pattern: "*.{bed,vcf,vcf.gz}" - - sv_vcf_index: - type: file - description: OPTIONAL - The index for gzipped VCF files - pattern: "*.tbi" - - candidate_small_variants: - type: file - description: OPTIONAL - A file containing candidate small variants - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing annotations information - - annotations: - type: directory - description: | - The directory containing the annotations (URL to download this will be made available soon) - For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) - - meta3: - type: map - description: | - Groovy Map containing candidate genes information - - candidate_genes: - type: file - description: OPTIONAL - A file containing genes (either space-separated, tab-separated or line-break-separated) - pattern: "*.txt" - - meta4: - type: map - description: | - Groovy Map containing candidate false positive SNV information - - false_positive_snv: - type: file - description: OPTIONAL - A VCF file containing small variant candidates - pattern: "*.{vcf,vcf.gz}" - - meta5: - type: map - description: | - Groovy Map containing candidate gene transcripts information - - gene_transcripts: - type: file - description: OPTIONAL - A file containing the preferred gene transcripts to be used in priority during annotation (either space-separated or tab-separated) - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sv_vcf: + type: file + description: A VCF or BED file containing the structural variants to be annotated + pattern: "*.{bed,vcf,vcf.gz}" + - sv_vcf_index: + type: file + description: OPTIONAL - The index for gzipped VCF files + pattern: "*.tbi" + - candidate_small_variants: + type: file + description: OPTIONAL - A file containing candidate small variants + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing annotations information + - annotations: + type: directory + description: | + The directory containing the annotations (URL to download this will be made available soon) + For now this can be downloaded in the way defined in the repo (https://github.com/lgmgeo/AnnotSV#quick-installation) + - - meta3: + type: map + description: | + Groovy Map containing candidate genes information + - candidate_genes: + type: file + description: OPTIONAL - A file containing genes (either space-separated, tab-separated + or line-break-separated) + pattern: "*.txt" + - - meta4: + type: map + description: | + Groovy Map containing candidate false positive SNV information + - false_positive_snv: + type: file + description: OPTIONAL - A VCF file containing small variant candidates + pattern: "*.{vcf,vcf.gz}" + - - meta5: + type: map + description: | + Groovy Map containing candidate gene transcripts information + - gene_transcripts: + type: file + description: OPTIONAL - A file containing the preferred gene transcripts to + be used in priority during annotation (either space-separated or tab-separated) + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV file containing the annotated variants - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV file containing the annotated variants + pattern: "*.tsv" - unannotated_tsv: - type: file - description: OPTIONAL - TSV file containing the unannotated variants - pattern: "*.unannotated.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unannotated.tsv": + type: file + description: OPTIONAL - TSV file containing the unannotated variants + pattern: "*.unannotated.tsv" - vcf: - type: file - description: | - OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: | + OPTIONAL - A VCF file containing the annotated variants (created when `-vcf 1` is specified in the args) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/annotsv/installannotations/meta.yml b/modules/nf-core/annotsv/installannotations/meta.yml index a04c4f1d7fe4..a7b11d7011c1 100644 --- a/modules/nf-core/annotsv/installannotations/meta.yml +++ b/modules/nf-core/annotsv/installannotations/meta.yml @@ -12,15 +12,18 @@ tools: documentation: "https://lbgi.fr/AnnotSV/" tool_dev_url: "https://github.com/lgmgeo/AnnotSV" licence: ["GPL v3"] + identifier: biotools:AnnotSV output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotations: - type: file - description: A folder containing the annotations - pattern: "AnnotSV_annotations" + - AnnotSV_annotations: + type: file + description: A folder containing the annotations + pattern: "AnnotSV_annotations" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/anota2seq/anota2seqrun/meta.yml b/modules/nf-core/anota2seq/anota2seqrun/meta.yml index 67a8555b8dd9..3e864634066a 100644 --- a/modules/nf-core/anota2seq/anota2seqrun/meta.yml +++ b/modules/nf-core/anota2seq/anota2seqrun/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "anota2seq_anota2seqrun" -description: Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq +description: Generally applicable transcriptome-wide analysis of translational efficiency + using anota2seq keywords: - riboseq - rnaseq @@ -9,152 +9,233 @@ keywords: - differential tools: - "anota2seq": - description: "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq" + description: "Generally applicable transcriptome-wide analysis of translational + efficiency using anota2seq" homepage: "https://bioconductor.org/packages/release/bioc/html/anota2seq.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/anota2seq/inst/doc/anota2seq.pdf" doi: "10.18129/B9.bioc.anota2seq" licence: ["GPL v3"] + identifier: biotools:anota2seq input: - - meta: - type: map - description: | - Groovy Map containing contrast information. e.g. [ id:'contrast1', - blocking:'patient' ] - - sample_treatment_col: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - counts: - type: file - description: | - Raw TSV or CSV format expression matrix - + - - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - sample_treatment_col: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix output: - - meta: - type: map - description: | - Groovy Map containing contrast information. e.g. [ id:'contrast1', - blocking:'patient' ] - translated_mrna: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in RNA levels across conditions for Ribo-seq samples. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".translated_mRNA.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.translated_mRNA.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".translated_mRNA.anota2seq.results.tsv" - total_mrna: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in RNA levels across conditions for RNA-seq samples. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".total_mRNA.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.total_mRNA.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".total_mRNA.anota2seq.results.tsv" - translation: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - differences in translation across conditions, being differences in - translated RNA levels not explained by total RNA levels. See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".translation.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.translation.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + differences in translation across conditions, being differences in translated + RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".translation.anota2seq.results.tsv" - buffering: - type: file - description: anota2seq results for the 'translated mRNA' analysis, describing - buffering across conditions, being stable levels of translated RNA - (from riboseq samples) across conditions, despite changes in total - mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html - for description of output columns. - pattern: ".buffering.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.buffering.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'translated mRNA' analysis, describing + buffering across conditions, being stable levels of translated RNA (from riboseq + samples) across conditions, despite changes in total mRNA. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".buffering.anota2seq.results.tsv" - mrna_abundance: - type: file - description: anota2seq results for the 'mRNA abunance' analysis, describing changes - across conditions consistent between total mRNA and translated RNA - (RNA-seq and Riboseq samples). See - https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for - description of output columns. - pattern: ".mRNA_abundance.anota2seq.results.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.mRNA_abundance.anota2seq.results.tsv": + type: file + description: anota2seq results for the 'mRNA abunance' analysis, describing + changes across conditions consistent between total mRNA and translated RNA + (RNA-seq and Riboseq samples). See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html + for description of output columns. + pattern: ".mRNA_abundance.anota2seq.results.tsv" - rdata: - type: file - description: Serialised Anota2seqDataSet object - pattern: ".Anota2seqDataSet.rds" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.Anota2seqDataSet.rds": + type: file + description: Serialised Anota2seqDataSet object + pattern: ".Anota2seqDataSet.rds" - fold_change_plot: - type: file - description: | - A fold change plot in PNG format, from anota2seq's anota2seqPlotFC() - method. - pattern: ".fold_change.png" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.fold_change.png": + type: file + description: | + A fold change plot in PNG format, from anota2seq's anota2seqPlotFC() + method. + pattern: ".fold_change.png" - interaction_p_distribution_plot: - type: file - description: | - The distribution of p-values and adjusted p-values for the omnibus - interaction (both using densities and histograms). The second page of - the pdf displays the same plots but for the RVM statistics if RVM is - used. - pattern: ".interaction_p_distribution.pdf" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.interaction_p_distribution.pdf": + type: file + description: | + The distribution of p-values and adjusted p-values for the omnibus + interaction (both using densities and histograms). The second page of + the pdf displays the same plots but for the RVM statistics if RVM is + used. + pattern: ".interaction_p_distribution.pdf" - residual_distribution_summary_plot: - type: file - description: | - Summary plot for assessing normal distribution of regression residuals. - pattern: ".residual_distribution_summary.jpeg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.residual_distribution_summary.jpeg": + type: file + description: | + Summary plot for assessing normal distribution of regression residuals. + pattern: ".residual_distribution_summary.jpeg" - residual_vs_fitted_plot: - type: file - description: | - QC plot showing residuals against fitted values. - pattern: ".residual_vs_fitted.jpeg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.residual_vs_fitted.jpeg": + type: file + description: | + QC plot showing residuals against fitted values. + pattern: ".residual_vs_fitted.jpeg" - rvm_fit_for_all_contrasts_group_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), all - contrasts. - pattern: ".rvm_fit_for_all_contrasts_group.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_all_contrasts_group.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), all + contrasts. + pattern: ".rvm_fit_for_all_contrasts_group.jpg" - rvm_fit_for_interactions_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), for - interactions. - pattern: ".rvm_fit_for_interactions.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_interactions.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), for + interactions. + pattern: ".rvm_fit_for_interactions.jpg" - rvm_fit_for_omnibus_group_plot: - type: file - description: | - QC plot showing the CDF of variance (theoretical vs empirical), for - omnibus group. - pattern: ".rvm_fit_for_omnibus_group.jpg" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.rvm_fit_for_omnibus_group.jpg": + type: file + description: | + QC plot showing the CDF of variance (theoretical vs empirical), for + omnibus group. + pattern: ".rvm_fit_for_omnibus_group.jpg" - simulated_vs_obt_dfbetas_without_interaction_plot: - type: file - description: | - Bar graphs of the frequencies of outlier dfbetas using different - dfbetas thresholds. - pattern: ".simulated_vs_obt_dfbetas_without_interaction.pdf" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.simulated_vs_obt_dfbetas_without_interaction.pdf": + type: file + description: | + Bar graphs of the frequencies of outlier dfbetas using different + dfbetas thresholds. + pattern: ".simulated_vs_obt_dfbetas_without_interaction.pdf" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing contrast information. e.g. [ id:'contrast1', + blocking:'patient' ] + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/antismash/antismashlite/meta.yml b/modules/nf-core/antismash/antismashlite/meta.yml index 21f506bd846a..638283432c0e 100644 --- a/modules/nf-core/antismash/antismashlite/meta.yml +++ b/modules/nf-core/antismash/antismashlite/meta.yml @@ -23,110 +23,207 @@ tools: tool_dev_url: "https://github.com/antismash/antismash" doi: "10.1093/nar/gkab335" licence: ["AGPL v3"] + identifier: biotools:antismash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence_input: - type: file - description: nucleotide sequence file (annotated) - pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" - - databases: - type: directory - description: | - Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory - "data/databases") - pattern: "*/" - - antismash_dir: - type: directory - description: | - A local copy of an AntiSMASH installation folder. This is required when running with - docker and singularity (not required for conda), due to attempted 'modifications' of - files during database checks in the installation directory, something that cannot - be done in immutable docker/singularity containers. Therefore, a local installation - directory needs to be mounted (including all modified files from the downloading step) - to the container as a workaround. - pattern: "*/" - - gff: - type: file - description: Annotations in GFF3 format (only if sequence_input is in FASTA format) - pattern: "*.gff" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence_input: + type: file + description: nucleotide sequence file (annotated) + pattern: "*.{gbk, gb, gbff, genbank, embl, fasta, fna}" + - - databases: + type: directory + description: | + Downloaded AntiSMASH databases (e.g. in the AntiSMASH installation directory + "data/databases") + pattern: "*/" + - - antismash_dir: + type: directory + description: | + A local copy of an AntiSMASH installation folder. This is required when running with + docker and singularity (not required for conda), due to attempted 'modifications' of + files during database checks in the installation directory, something that cannot + be done in immutable docker/singularity containers. Therefore, a local installation + directory needs to be mounted (including all modified files from the downloading step) + to the container as a workaround. + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clusterblast_file: - type: file - description: Output of ClusterBlast algorithm - pattern: "clusterblast/*_c*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/clusterblast/*_c*.txt: + type: file + description: Output of ClusterBlast algorithm + pattern: "clusterblast/*_c*.txt" - html_accessory_files: - type: directory - description: Accessory files for the HTML output - pattern: "{css/,images/,js/}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/{css,images,js}: + type: directory + description: Accessory files for the HTML output + pattern: "{css/,images/,js/}" - knownclusterblast_html: - type: file - description: Tables with MIBiG hits in HTML format - pattern: "knownclusterblast/region*/ctg*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/region*/ctg*.html: + type: file + description: Tables with MIBiG hits in HTML format + pattern: "knownclusterblast/region*/ctg*.html" - knownclusterblast_dir: - type: directory - description: Directory with MIBiG hits - pattern: "knownclusterblast/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/: + type: directory + description: Directory with MIBiG hits + pattern: "knownclusterblast/" - knownclusterblast_txt: - type: file - description: Tables with MIBiG hits - pattern: "knownclusterblast/*_c*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblast/*_c*.txt: + type: file + description: Tables with MIBiG hits + pattern: "knownclusterblast/*_c*.txt" - svg_files_clusterblast: - type: file - description: SVG images showing the % identity of the aligned hits against their queries - pattern: "svg/clusterblast*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/svg/clusterblast*.svg: + type: file + description: SVG images showing the % identity of the aligned hits against their + queries + pattern: "svg/clusterblast*.svg" - svg_files_knownclusterblast: - type: file - description: SVG images showing the % identity of the aligned hits against their queries - pattern: "svg/knownclusterblast*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/svg/knownclusterblast*.svg: + type: file + description: SVG images showing the % identity of the aligned hits against their + queries + pattern: "svg/knownclusterblast*.svg" - gbk_input: - type: file - description: Nucleotide sequence and annotations in GenBank format; converted from input file - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gbk: + type: file + description: Nucleotide sequence and annotations in GenBank format; converted + from input file + pattern: "*.gbk" - json_results: - type: file - description: Nucleotide sequence and annotations in JSON format; converted from GenBank file (gbk_input) - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.json: + type: file + description: Nucleotide sequence and annotations in JSON format; converted from + GenBank file (gbk_input) + pattern: "*.json" - log: - type: file - description: Contains all the logging output that antiSMASH produced during its run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.log: + type: file + description: Contains all the logging output that antiSMASH produced during + its run + pattern: "*.log" - zip: - type: file - description: Contains a compressed version of the output folder in zip format - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.zip: + type: file + description: Contains a compressed version of the output folder in zip format + pattern: "*.zip" - gbk_results: - type: file - description: Nucleotide sequence and annotations in GenBank format; one file per antiSMASH hit - pattern: "*region*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*region*.gbk: + type: file + description: Nucleotide sequence and annotations in GenBank format; one file + per antiSMASH hit + pattern: "*region*.gbk" - clusterblastoutput: - type: file - description: Raw BLAST output of known clusters previously predicted by antiSMASH using the built-in ClusterBlast algorithm - pattern: "clusterblastoutput.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/clusterblastoutput.txt: + type: file + description: Raw BLAST output of known clusters previously predicted by antiSMASH + using the built-in ClusterBlast algorithm + pattern: "clusterblastoutput.txt" - html: - type: file - description: Graphical web view of results in HTML format - patterN: "index.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/index.html: + type: file + description: Graphical web view of results in HTML format + patterN: "index.html" - knownclusterblastoutput: - type: file - description: Raw BLAST output of known clusters of the MIBiG database - pattern: "knownclusterblastoutput.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/knownclusterblastoutput.txt: + type: file + description: Raw BLAST output of known clusters of the MIBiG database + pattern: "knownclusterblastoutput.txt" - json_sideloading: - type: file - description: Sideloaded annotations of protoclusters and/or subregions (see antiSMASH documentation "Annotation sideloading") - pattern: "regions.js" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/regions.js: + type: file + description: Sideloaded annotations of protoclusters and/or subregions (see + antiSMASH documentation "Annotation sideloading") + pattern: "regions.js" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml b/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml index 010c62678158..fdca8294b6d0 100644 --- a/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml +++ b/modules/nf-core/antismash/antismashlitedownloaddatabases/meta.yml @@ -1,5 +1,7 @@ name: antismash_antismashlitedownloaddatabases -description: antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters. This module downloads the antiSMASH databases for conda and docker/singularity runs. +description: antiSMASH allows the rapid genome-wide identification, annotation and + analysis of secondary metabolite biosynthesis gene clusters. This module downloads + the antiSMASH databases for conda and docker/singularity runs. keywords: - secondary metabolites - BGC @@ -22,36 +24,40 @@ tools: tool_dev_url: https://github.com/antismash/antismash doi: "10.1093/nar/gkab335" licence: ["AGPL v3"] + identifier: biotools:antismash input: - - database_css: - type: directory - description: | - antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "css" - - database_detection: - type: directory - description: | - antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "detection" - - database_modules: - type: directory - description: | - antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. - pattern: "modules" + - - database_css: + type: directory + description: | + antismash/outputs/html/css folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "css" + - - database_detection: + type: directory + description: | + antismash/detection folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "detection" + - - database_modules: + type: directory + description: | + antismash/modules folder which is being created during the antiSMASH database downloading step. These files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database in pipelines. + pattern: "modules" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: Download directory for antiSMASH databases - pattern: "antismash_db" + - antismash_db: + type: directory + description: Download directory for antiSMASH databases + pattern: "antismash_db" - antismash_dir: - type: directory - description: | - antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines. - pattern: "antismash_dir" + - antismash_dir: + type: directory + description: | + antismash installation folder which is being modified during the antiSMASH database downloading step. The modified files are normally downloaded by download-antismash-databases itself, and must be retrieved by the user by manually running the command with conda or a standalone installation of antiSMASH. Therefore we do not recommend using this module for production pipelines, but rather require users to specify their own local copy of the antiSMASH database and installation folder in pipelines. + pattern: "antismash_dir" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/arcashla/extract/meta.yml b/modules/nf-core/arcashla/extract/meta.yml index 6a85aad0f79b..381381d10e77 100644 --- a/modules/nf-core/arcashla/extract/meta.yml +++ b/modules/nf-core/arcashla/extract/meta.yml @@ -1,57 +1,82 @@ name: "arcashla_extract" -description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome 6 alternates. +description: Extracts reads mapped to chromosome 6 and any HLA decoys or chromosome + 6 alternates. keywords: - HLA - genotype - RNA-seq tools: - "arcashla": - description: "arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples." + description: "arcasHLA performs high resolution genotyping for HLA class I and + class II genes from RNA sequencing, supporting both paired and single-end samples." homepage: "https://github.com/RabadanLab/arcasHLA" documentation: "https://github.com/RabadanLab/arcasHLA" tool_dev_url: "https://github.com/RabadanLab/arcasHLA" doi: "10.1093/bioinformatics/btz474" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. If the BAM file is not indexed, this tool will run samtools index before extracting reads. - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. If the BAM file is not indexed, this tool will run samtools + index before extracting reads. + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - extracted_reads_fastq: - type: file - description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: FASTQ file(s) containing chromosome 6 reads and related HLA sequences + pattern: "*.fq.gz" - log: - type: file - description: Log file for run summary - pattern: "*.log" + - "*.log": + type: file + description: Log file for run summary + pattern: "*.log" - intermediate_sam: - type: file - description: Optional intermediate SAM file - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.sam: + type: file + description: Optional intermediate SAM file + pattern: "*.sam" - intermediate_bam: - type: file - description: Optional intermediate BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.bam: + type: file + description: Optional intermediate BAM file + pattern: "*.bam" - intermediate_sorted_bam: - type: file - description: Optional intermediate sorted BAM file - pattern: "*.sorted.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp_files/**.sorted.bam: + type: file + description: Optional intermediate sorted BAM file + pattern: "*.sorted.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-mohr" maintainers: diff --git a/modules/nf-core/argnorm/meta.yml b/modules/nf-core/argnorm/meta.yml index a977e86304cc..84842b9c5ca6 100644 --- a/modules/nf-core/argnorm/meta.yml +++ b/modules/nf-core/argnorm/meta.yml @@ -1,5 +1,6 @@ name: "argnorm" -description: Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD). +description: Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed + by CARD). keywords: - amr - antimicrobial resistance @@ -11,49 +12,48 @@ keywords: - drug categorization tools: - "argnorm": - description: "Normalize antibiotic resistance genes (ARGs) using the ARO ontology (developed by CARD)." + description: "Normalize antibiotic resistance genes (ARGs) using the ARO ontology + (developed by CARD)." homepage: "https://argnorm.readthedocs.io/en/latest/" documentation: "https://argnorm.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/BigDataBiology/argNorm" licence: ["MIT"] + identifier: biotools:argnorm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input_tsv: - type: file - description: ARG annotation output - pattern: "*.tsv" - - - tool: - type: string - description: ARG annotation tool used - pattern: "argsoap|abricate|deeparg|resfinder|amrfinderplus" - - - db: - type: string - description: Database used for ARG annotation - pattern: "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input_tsv: + type: file + description: ARG annotation output + pattern: "*.tsv" + - - tool: + type: string + description: ARG annotation tool used + pattern: "argsoap|abricate|deeparg|resfinder|amrfinderplus" + - - db: + type: string + description: Database used for ARG annotation + pattern: "sarg|ncbi|resfinder|deeparg|megares|argannot|resfinderfg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - tsv: - type: file - description: Normalized argNorm output - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Normalized argNorm output + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Vedanth-Ramji" maintainers: diff --git a/modules/nf-core/aria2/meta.yml b/modules/nf-core/aria2/meta.yml index 0908646aecd1..569e043acd1b 100644 --- a/modules/nf-core/aria2/meta.yml +++ b/modules/nf-core/aria2/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "aria2" description: CLI Download utility @@ -8,35 +7,40 @@ keywords: - http(s) tools: - "aria2": - description: "aria2 is a lightweight multi-protocol & multi-source, cross platform download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, BitTorrent and Metalink." + description: "aria2 is a lightweight multi-protocol & multi-source, cross platform + download utility operated in command-line. It supports HTTP/HTTPS, FTP, SFTP, + BitTorrent and Metalink." homepage: "https://aria2.github.io/" documentation: "https://aria2.github.io/manual/en/html/index.html" tool_dev_url: "https://github.com/aria2/aria2/" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - source_url: - type: string - description: Source URL to be downloaded - pattern: "{http,https}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - source_url: + type: string + description: Source URL to be downloaded + pattern: "{http,https}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - downloaded_file: - type: file - description: Downloaded file from source - pattern: "*.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $downloaded_file: + type: file + description: Downloaded file from source + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@leoisl" diff --git a/modules/nf-core/ariba/getref/meta.yml b/modules/nf-core/ariba/getref/meta.yml index bbdae6dec995..680126b3e0bd 100644 --- a/modules/nf-core/ariba/getref/meta.yml +++ b/modules/nf-core/ariba/getref/meta.yml @@ -13,24 +13,31 @@ tools: tool_dev_url: "https://github.com/sanger-pathogens/ariba" doi: "10.1099/mgen.0.000131" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - db_name: - type: string - description: A database to setup up for Ariba + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - db_name: + type: string + description: A database to setup up for Ariba output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: An Ariba prepared database - pattern: "*.tar.gz" + - meta: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" + - ${db_name}.tar.gz: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ariba/run/meta.yml b/modules/nf-core/ariba/run/meta.yml index bcd0b9e2d473..4fa1e0d452cb 100644 --- a/modules/nf-core/ariba/run/meta.yml +++ b/modules/nf-core/ariba/run/meta.yml @@ -13,29 +13,41 @@ tools: tool_dev_url: "https://github.com/sanger-pathogens/ariba" doi: "10.1099/mgen.0.000131" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Paired-end reads in FASTQ format - pattern: "*_R[1|2].{fastq.gz,fq.gz}" - - db: - type: file - description: An Ariba prepared database - pattern: "*.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Paired-end reads in FASTQ format + pattern: "*_R[1|2].{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - db: + type: file + description: An Ariba prepared database + pattern: "*.tar.gz" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: A directory of Ariba analysis outputs - pattern: "*" + - meta: + type: file + description: A directory of Ariba analysis outputs + pattern: "*" + - ${prefix}/*: + type: file + description: A directory of Ariba analysis outputs + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml index 11f744b54d6c..f230dda1fbe3 100644 --- a/modules/nf-core/arriba/arriba/meta.yml +++ b/modules/nf-core/arriba/arriba/meta.yml @@ -1,5 +1,6 @@ name: arriba_arriba -description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. +description: Arriba is a command-line tool for the detection of gene fusions from + RNA-Seq data. keywords: - fusion - arriba @@ -13,97 +14,107 @@ tools: tool_dev_url: https://github.com/suhrig/arriba doi: "10.1101/gr.257246.119" licence: ["MIT"] + identifier: biotools:Arriba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Assembly FASTA file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - blacklist: - type: file - description: Blacklist file - pattern: "*.{tsv}" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - known_fusions: - type: file - description: Known fusions file - pattern: "*.{tsv}" - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - structural_variants: - type: file - description: Structural variants file - pattern: "*.{tsv}" - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - tags: - type: file - description: Tags file - pattern: "*.{tsv}" - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - protein_domains: - type: file - description: Protein domains file - pattern: "*.{gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Assembly FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - blacklist: + type: file + description: Blacklist file + pattern: "*.{tsv}" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - known_fusions: + type: file + description: Known fusions file + pattern: "*.{tsv}" + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - structural_variants: + type: file + description: Structural variants file + pattern: "*.{tsv}" + - - meta7: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - tags: + type: file + description: Tags file + pattern: "*.{tsv}" + - - meta8: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - protein_domains: + type: file + description: Protein domains file + pattern: "*.{gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fusions: - type: file - description: File contains fusions which pass all of Arriba's filters. - pattern: "*.{fusions.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fusions.tsv": + type: file + description: File contains fusions which pass all of Arriba's filters. + pattern: "*.{fusions.tsv}" - fusions_fail: - type: file - description: File contains fusions that Arriba classified as an artifact or that are also observed in healthy tissue. - pattern: "*.{fusions.discarded.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fusions.discarded.tsv": + type: file + description: File contains fusions that Arriba classified as an artifact or + that are also observed in healthy tissue. + pattern: "*.{fusions.discarded.tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@praveenraj2018" - "@rannick" diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml index d32106163218..531c66c2f776 100644 --- a/modules/nf-core/arriba/download/meta.yml +++ b/modules/nf-core/arriba/download/meta.yml @@ -1,5 +1,6 @@ name: arriba_download -description: Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. +description: Arriba is a command-line tool for the detection of gene fusions from + RNA-Seq data. keywords: - fusion - arriba @@ -12,16 +13,18 @@ tools: tool_dev_url: https://github.com/suhrig/arriba doi: "10.1101/gr.257246.119" licence: ["MIT"] + identifier: biotools:Arriba output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reference: - type: directory - description: Folder with arriba references - pattern: "*" - + - "*": + type: directory + description: Folder with arriba references + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@peterpru" diff --git a/modules/nf-core/art/illumina/meta.yml b/modules/nf-core/art/illumina/meta.yml index b20df1cde874..e41db4869f05 100644 --- a/modules/nf-core/art/illumina/meta.yml +++ b/modules/nf-core/art/illumina/meta.yml @@ -1,5 +1,6 @@ name: "art_illumina" -description: Simulation tool to generate synthetic Illumina next-generation sequencing reads +description: Simulation tool to generate synthetic Illumina next-generation sequencing + reads keywords: - fastq - fasta @@ -7,51 +8,74 @@ keywords: - simulate tools: - "art": - description: "ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. " + description: "ART is a set of simulation tools to generate synthetic next-generation + sequencing reads. ART simulates sequencing reads by mimicking real sequencing + process with empirical error models or quality profiles summarized from large + recalibrated sequencing data. ART can also simulate reads using user own read + error model or quality profiles. " homepage: "https://www.niehs.nih.gov/research/resources/software/biostatistics/art/index.cfm" doi: "10.1093/bioinformatics/btr708" licence: ["GPL version 3 license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file of input DNA/RNA reference - pattern: "*.{fasta,fa}" - - sequencing_system: - type: string - description: The name of Illumina sequencing system of the built-in profile used for simulation - - fold_coverage: - type: integer - description: The fold of read coverage to be simulated or number of reads/read pairs generated for each amplicon - - read_length: - type: integer - description: The length of reads to be simulated + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file of input DNA/RNA reference + pattern: "*.{fasta,fa}" + - - sequencing_system: + type: string + description: The name of Illumina sequencing system of the built-in profile + used for simulation + - - fold_coverage: + type: integer + description: The fold of read coverage to be simulated or number of reads/read + pairs generated for each amplicon + - - read_length: + type: integer + description: The length of reads to be simulated output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Simulated reads - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: Simulated reads + pattern: "*.fq.gz" - aln: - type: file - description: OPTIONAL Alignment file of the simulated reads. Enabled by default, to disable, use -na/--noALN. - pattern: "*.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.aln": + type: file + description: OPTIONAL Alignment file of the simulated reads. Enabled by default, + to disable, use -na/--noALN. + pattern: "*.aln" - sam: - type: file - description: OPTIONAL Alignment file in SAM format of the simulated reads. Enabled with -sam/--samout. - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: OPTIONAL Alignment file in SAM format of the simulated reads. Enabled + with -sam/--samout. + pattern: "*.sam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/artic/guppyplex/meta.yml b/modules/nf-core/artic/guppyplex/meta.yml index 80a1d99907cb..de1c615010ab 100644 --- a/modules/nf-core/artic/guppyplex/meta.yml +++ b/modules/nf-core/artic/guppyplex/meta.yml @@ -6,35 +6,39 @@ keywords: - demultiplexed reads tools: - artic: - description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + description: ARTIC pipeline - a bioinformatics pipeline for working with virus + sequencing data sequenced with nanopore homepage: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics licence: ["MIT"] + identifier: biotools:artic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq_dir: - type: directory - description: Directory containing the fastq files with demultiplexed reads - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq_dir: + type: directory + description: Directory containing the fastq files with demultiplexed reads + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Aggregated FastQ files - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Aggregated FastQ files + pattern: "*.{fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/artic/minion/meta.yml b/modules/nf-core/artic/minion/meta.yml index 26ff4ad8576f..3c90d62272d0 100644 --- a/modules/nf-core/artic/minion/meta.yml +++ b/modules/nf-core/artic/minion/meta.yml @@ -7,110 +7,169 @@ keywords: - demultiplexed reads tools: - artic: - description: ARTIC pipeline - a bioinformatics pipeline for working with virus sequencing data sequenced with nanopore + description: ARTIC pipeline - a bioinformatics pipeline for working with virus + sequencing data sequenced with nanopore homepage: https://artic.readthedocs.io/en/latest/ documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics licence: ["MIT"] + identifier: biotools:artic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FastQ file containing reads - pattern: "*.{fastq.gz}" - - fast5_dir: - type: directory - description: Directory containing MinION FAST5 files - pattern: "*" - - sequencing_summary: - type: file - description: Path to Guppy sequencing summary - pattern: "*.{txt}" - - primer_scheme_fasta: - type: file - description: | - Sequence of the reference genome used in the scheme in FASTA format - pattern: "*.{reference.fasta}" - - primer_scheme_bed: - type: file - description: | - bed files containing coordinates of each primer in the scheme, - relative to the reference genome - pattern: "*.{scheme.bed}" - - medaka_model_file: - type: file - description: | - Medaka model file to use (if option --medaka is set) - pattern: "*.hdf5" - - medaka_model_string: - type: string - description: | - Medaka model string to use (if option --medaka is set) - pattern: "*" - - scheme: - type: string - description: Name of the primer scheme - - scheme_version: - type: string - description: Version of the primer scheme + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FastQ file containing reads + pattern: "*.{fastq.gz}" + - - fast5_dir: + type: directory + description: Directory containing MinION FAST5 files + pattern: "*" + - - sequencing_summary: + type: file + description: Path to Guppy sequencing summary + pattern: "*.{txt}" + - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.reference.fasta"': + type: file + description: Scheme reference file + - - '"primer-schemes/${scheme}/V${scheme_version}/${scheme}.scheme.bed"': + type: file + description: Scheme BED file + - - medaka_model_file: + type: file + description: | + Medaka model file to use (if option --medaka is set) + pattern: "*.hdf5" + - - medaka_model_string: + type: string + description: | + Medaka model string to use (if option --medaka is set) + pattern: "*" + - - scheme: + type: string + description: Name of the primer scheme + - - scheme_version: + type: string + description: Version of the primer scheme output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: file - description: Aggregated FastQ files - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*: + type: file + description: Aggregated FastQ files + pattern: "*.fastq.gz" - bam: - type: file - description: BAM file - pattern: "*.{sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sorted.bam: + type: file + description: BAM file + pattern: "*.{sorted.bam}" - bai: - type: file - description: BAM index file - pattern: "*.{sorted.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sorted.bam.bai: + type: file + description: BAM index file + pattern: "*.{sorted.bai}" - bam_trimmed: - type: file - description: BAM file with the primers left on - pattern: "*.{trimmed.rg.sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.trimmed.rg.sorted.bam: + type: file + description: BAM file with the primers left on + pattern: "*.{trimmed.rg.sorted.bam}" - bai_trimmed: - type: file - description: BAM index file of bam_trimmed - pattern: "*.{sorted.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.trimmed.rg.sorted.bam.bai: + type: file + description: BAM index file of bam_trimmed + pattern: "*.{sorted.bai}" - bam_primertrimmed: - type: file - description: BAM containing reads after primer-binding site trimming - pattern: "*.{trimmed.rg.sorted.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.primertrimmed.rg.sorted.bam: + type: file + description: BAM containing reads after primer-binding site trimming + pattern: "*.{trimmed.rg.sorted.bam}" - bai_primertrimmed: - type: file - description: BAM index file of bam_primertrimmed - pattern: "*.{primertrimmed.rg.sorted.bam.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.primertrimmed.rg.sorted.bam.bai: + type: file + description: BAM index file of bam_primertrimmed + pattern: "*.{primertrimmed.rg.sorted.bam.bai}" - fasta: - type: file - description: FAST file with consensus sequence - pattern: "*.{consensus.fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.consensus.fasta: + type: file + description: FAST file with consensus sequence + pattern: "*.{consensus.fasta}" - vcf: - type: file - description: VCF file containing detected variants passing quality filter - pattern: "*.{pass.vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.pass.vcf.gz: + type: file + description: VCF file containing detected variants passing quality filter + pattern: "*.{pass.vcf.gz}" - tbi: - type: file - description: VCF index - pattern: "*.{pass.vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.pass.vcf.gz.tbi: + type: file + description: VCF index + pattern: "*.{pass.vcf.gz.tbi}" - json: - type: file - description: JSON file for MultiQC - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file for MultiQC + pattern: "*.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/ascat/meta.yml b/modules/nf-core/ascat/meta.yml index 34ea2e51d99f..db7c92926a7c 100644 --- a/modules/nf-core/ascat/meta.yml +++ b/modules/nf-core/ascat/meta.yml @@ -6,105 +6,151 @@ keywords: - cram tools: - ascat: - description: ASCAT is a method to derive copy number profiles of tumour cells, accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour cell), expressed as multiples of haploid genomes from SNP array or massively parallel sequencing data, and calculates whole-genome allele-specific copy number profiles (the number of copies of both parental alleles for all SNP loci across the genome). + description: ASCAT is a method to derive copy number profiles of tumour cells, + accounting for normal cell admixture and tumour aneuploidy. ASCAT infers tumour + purity (the fraction of tumour cells) and ploidy (the amount of DNA per tumour + cell), expressed as multiples of haploid genomes from SNP array or massively + parallel sequencing data, and calculates whole-genome allele-specific copy number + profiles (the number of copies of both parental alleles for all SNP loci across + the genome). documentation: https://github.com/VanLoo-lab/ascat/tree/master/man tool_dev_url: https://github.com/VanLoo-lab/ascat doi: "10.1093/bioinformatics/btaa538" licence: ["GPL v3"] + identifier: biotools:ascat input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. (optional) parameters can be removed from the map, if they are not set. For default values, please check the documentation above. - - ``` - { - [ - "gender": "XX", - "genomeVersion": "hg19" - "purity": (optional), - "ploidy": (optional), - "gc_files": (optional), - "minCounts": (optional), - "BED_file": (optional) but recommended for WES, - "chrom_names": (optional), - "min_base_qual": (optional), - "min_map_qual": (optional), - "ref_fasta": (optional), - "skip_allele_counting_tumour": (optional), - "skip_allele_counting_normal": (optional) - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For modifying chromosome notation in bam files please follow https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/. - pattern: "*.{bam,cram}" - - index_normal: - type: file - description: index for normal_bam/cram - pattern: "*.{bai,crai}" - - input_tumor: - type: file - description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation - pattern: "*.{bam,cram}" - - index_tumor: - type: file - description: index for tumor_bam/cram - pattern: "*.{bai,crai}" - - allele_files: - type: file - description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS - - loci_files: - type: file - description: loci files for ASCAT WGS. Loci files without chromosome notation can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS Make sure the chromosome notation matches the bam/cram input files. To add the chromosome notation to loci files (hg19/hg38) if necessary, you can run this command `if [[ $(samtools view | head -n1 | cut -f3)\" == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; done; fi` - - bed_file: - type: file - description: Bed file for ASCAT WES (optional, but recommended for WES) - - fasta: - type: file - description: Reference fasta file (optional) - - gc_file: - type: file - description: GC correction file (optional) - Used to do logR correction of the tumour sample(s) with genomic GC content - - rt_file: - type: file - description: replication timing correction file (optional, provide only in combination with gc_file) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation For + modifying chromosome notation in bam files please follow + https://josephcckuo.wordpress.com/2016/11/17/modify-chromosome-notation-in-bam-file/. + pattern: "*.{bam,cram}" + - index_normal: + type: file + description: index for normal_bam/cram + pattern: "*.{bai,crai}" + - input_tumor: + type: file + description: BAM/CRAM file, must adhere to chr1, chr2, ...chrX notation + pattern: "*.{bam,cram}" + - index_tumor: + type: file + description: index for tumor_bam/cram + pattern: "*.{bai,crai}" + - - allele_files: + type: file + description: allele files for ASCAT WGS. Can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS + - - loci_files: + type: file + description: loci files for ASCAT WGS. Loci files without chromosome notation + can be downloaded here https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS + Make sure the chromosome notation matches the bam/cram input files. To add + the chromosome notation to loci files (hg19/hg38) if necessary, you can run + this command `if [[ $(samtools view | head -n1 | cut -f3)\" + == *\"chr\"* ]]; then for i in {1..22} X; do sed -i 's/^/chr/' G1000_loci_hg19_chr_${i}.txt; + done; fi` + - - bed_file: + type: file + description: Bed file for ASCAT WES (optional, but recommended for WES) + - - fasta: + type: file + description: Reference fasta file (optional) + - - gc_file: + type: file + description: GC correction file (optional) - Used to do logR correction of the + tumour sample(s) with genomic GC content + - - rt_file: + type: file + description: replication timing correction file (optional, provide only in combination + with gc_file) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - allelefreqs: - type: file - description: Files containing allee frequencies per chromosome - pattern: "*{alleleFrequencies_chr*.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*alleleFrequencies_chr*.txt": + type: file + description: Files containing allee frequencies per chromosome + pattern: "*{alleleFrequencies_chr*.txt}" + - bafs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*BAF.txt": + type: file + description: BAF file + - cnvs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnvs.txt": + type: file + description: CNV file + - logrs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*LogR.txt": + type: file + description: LogR file - metrics: - type: file - description: File containing quality metrics - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*metrics.txt": + type: file + description: File containing quality metrics + pattern: "*.{metrics.txt}" - png: - type: file - description: ASCAT plots - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*png": + type: file + description: ASCAT plots + pattern: "*.{png}" - purityploidy: - type: file - description: File with purity and ploidy data - pattern: "*.{purityploidy.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*purityploidy.txt": + type: file + description: File with purity and ploidy data + pattern: "*.{purityploidy.txt}" - segments: - type: file - description: File with segments data - pattern: "*.{segments.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*segments.txt": + type: file + description: File with segments data + pattern: "*.{segments.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aasNGC" - "@lassefolkersen" diff --git a/modules/nf-core/ashlar/meta.yml b/modules/nf-core/ashlar/meta.yml index f886a3d45d8c..221e2154aeab 100644 --- a/modules/nf-core/ashlar/meta.yml +++ b/modules/nf-core/ashlar/meta.yml @@ -11,30 +11,39 @@ tools: documentation: "https://labsyspharm.github.io/ashlar/" doi: "10.1093/bioinformatics/btac544" licence: ["MIT"] + identifier: biotools:ASHLAR input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - images: - type: file - description: Overlapping tile image data in formats from most commercial microscopes - pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - images: + type: file + description: Overlapping tile image data in formats from most commercial microscopes + pattern: "*.{ome.tiff,ome.tif,rcpnl,btf,nd2,tiff,tif,czi}" + - - opt_dfp: + type: file + description: Optional dark field image data + - - opt_ffp: + type: file + description: Optional flat field image data output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - tif: - type: file - description: A pyramidal, tiled OME-TIFF file created from input images. - pattern: "*.ome.tif" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.ome.tif": + type: file + description: A pyramidal, tiled OME-TIFF file created from input images. + pattern: "*.ome.tif" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@RobJY" - "@jmuhlich" diff --git a/modules/nf-core/assemblyscan/meta.yml b/modules/nf-core/assemblyscan/meta.yml index 4cf187798aa7..d8bcf06d7b80 100644 --- a/modules/nf-core/assemblyscan/meta.yml +++ b/modules/nf-core/assemblyscan/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/rpetit3/assembly-scan tool_dev_url: https://github.com/rpetit3/assembly-scan licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: FASTA file for a given assembly - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: FASTA file for a given assembly + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Assembly statistics in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Assembly statistics in JSON format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/ataqv/ataqv/meta.yml b/modules/nf-core/ataqv/ataqv/meta.yml index 227c9da8f514..25d566122663 100644 --- a/modules/nf-core/ataqv/ataqv/meta.yml +++ b/modules/nf-core/ataqv/ataqv/meta.yml @@ -6,64 +6,87 @@ keywords: - ataqv tools: - ataqv: - description: ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing. + description: ataqv is a toolkit for measuring and comparing ATAC-seq results. + It was written to help understand how well ATAC-seq assays have worked, and + to make it easier to spot differences that might be caused by library prep or + sequencing. homepage: https://github.com/ParkerLab/ataqv/blob/master/README.rst documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst tool_dev_url: https://github.com/ParkerLab/ataqv doi: "10.1016/j.cels.2020.02.009" licence: ["GPL v3"] + identifier: biotools:ataqv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file with the same prefix as bam file. Required if tss_file input is provided. - pattern: "*.bam.bai" - - peak_file: - type: file - description: A BED file of peaks called for alignments in the BAM file - pattern: "*.bed" - - organism: - type: string - description: The subject of the experiment, which determines the list of autosomes (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). - - mito_name: - type: string - description: Name of the mitochondrial sequence. - - tss_file: - type: file - description: A BED file of transcription start sites for the experiment organism. If supplied, a TSS enrichment score will be calculated according to the ENCODE data standards. This calculation requires that the BAM file of alignments be indexed. - pattern: "*.bed" - - excl_regs_file: - type: file - description: A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored. - pattern: "*.bed" - - autosom_ref_file: - type: file - description: A file containing autosomal reference names, one per line. The names must match the reference names in the alignment file exactly, or the metrics based on counts of autosomal alignments will be wrong. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file with the same prefix as bam file. Required if tss_file + input is provided. + pattern: "*.bam.bai" + - peak_file: + type: file + description: A BED file of peaks called for alignments in the BAM file + pattern: "*.bed" + - - organism: + type: string + description: The subject of the experiment, which determines the list of autosomes + (see "Reference Genome Configuration" section at https://github.com/ParkerLab/ataqv). + - - mito_name: + type: string + description: Name of the mitochondrial sequence. + - - tss_file: + type: file + description: A BED file of transcription start sites for the experiment organism. + If supplied, a TSS enrichment score will be calculated according to the ENCODE + data standards. This calculation requires that the BAM file of alignments + be indexed. + pattern: "*.bed" + - - excl_regs_file: + type: file + description: A BED file containing excluded regions. Peaks or TSS overlapping + these will be ignored. + pattern: "*.bed" + - - autosom_ref_file: + type: file + description: A file containing autosomal reference names, one per line. The + names must match the reference names in the alignment file exactly, or the + metrics based on counts of autosomal alignments will be wrong. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - json: - type: file - description: The JSON file to which metrics will be written. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ataqv.json": + type: file + description: The JSON file to which metrics will be written. - problems: - type: file - description: If given, problematic reads will be logged to a file per read group, with names derived from the read group IDs, with ".problems" appended. If no read groups are found, the reads will be written to one file named after the BAM file. - pattern: "*.problems" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.problems": + type: file + description: If given, problematic reads will be logged to a file per read group, + with names derived from the read group IDs, with ".problems" appended. If + no read groups are found, the reads will be written to one file named after + the BAM file. + pattern: "*.problems" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@i-pletenev" maintainers: diff --git a/modules/nf-core/ataqv/mkarv/meta.yml b/modules/nf-core/ataqv/mkarv/meta.yml index be4ff3ed519e..89576765ac48 100644 --- a/modules/nf-core/ataqv/mkarv/meta.yml +++ b/modules/nf-core/ataqv/mkarv/meta.yml @@ -8,25 +8,31 @@ keywords: - mkarv tools: - "ataqv": - description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. It was written to help understand how well ATAC-seq assays have worked, and to make it easier to spot differences that might be caused by library prep or sequencing." + description: "ataqv is a toolkit for measuring and comparing ATAC-seq results. + It was written to help understand how well ATAC-seq assays have worked, and + to make it easier to spot differences that might be caused by library prep or + sequencing." homepage: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" documentation: "https://github.com/ParkerLab/ataqv/blob/master/README.rst" tool_dev_url: "https://github.com/ParkerLab/ataqv" licence: ["GPL v3"] + identifier: biotools:ataqv input: - - json: - type: file - description: The JSON file with ataqv metrics - pattern: "*.json" + - - '"jsons/*"': + type: file + description: JSON files + pattern: "*.json" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: directory - description: Web application to visualize results in HTML format - pattern: "*.html" + - html: + type: directory + description: Web application to visualize results in HTML format + pattern: "*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjlang" maintainers: diff --git a/modules/nf-core/atlas/call/meta.yml b/modules/nf-core/atlas/call/meta.yml index a07bc6a7dd70..e5ff94d844e1 100644 --- a/modules/nf-core/atlas/call/meta.yml +++ b/modules/nf-core/atlas/call/meta.yml @@ -7,64 +7,70 @@ keywords: - population genetics tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A BAM/ file - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - fasta: - type: file - description: The reference FASTA file used to generate the BAM file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: The index of the FASTA file used for to generate the BAM file - pattern: "*.fai" - - recal: - type: file - description: Optional recalibration file from atlas recal function in text format - pattern: "*.txt" - - pmd: - type: file - description: Optional PMD file from atlas pmd function in text format - pattern: "*.txt" - - known_alleles: - type: file - description: Optional tab separated text file containing 1-based list of known alleles. See atlas call documentation. - pattern: "*.{txt.tsv}" - - method: - type: string - description: Which variant calling algorithm to use. Some may require additional parameters supplied via ext.args. Check atlas documentation. - pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A BAM/ file + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - pmd: + type: file + description: Optional PMD file from atlas pmd function in text format + pattern: "*.txt" + - recal: + type: file + description: Optional recalibration file from atlas recal function in text format + pattern: "*.txt" + - - fasta: + type: file + description: The reference FASTA file used to generate the BAM file + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: The index of the FASTA file used for to generate the BAM file + pattern: "*.fai" + - - known_alleles: + type: file + description: Optional tab separated text file containing 1-based list of known + alleles. See atlas call documentation. + pattern: "*.{txt.tsv}" + - - method: + type: string + description: Which variant calling algorithm to use. Some may require additional + parameters supplied via ext.args. Check atlas documentation. + pattern: "MLE|Bayesian|allelePresence|randomBase|majorityBase" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with variant calls - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with variant calls + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/atlas/pmd/meta.yml b/modules/nf-core/atlas/pmd/meta.yml index ed2ec3691bab..e7090bd9a13d 100644 --- a/modules/nf-core/atlas/pmd/meta.yml +++ b/modules/nf-core/atlas/pmd/meta.yml @@ -6,72 +6,96 @@ keywords: - bam tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Single input BAM file - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - fasta: - type: file - description: The reference genome provided as FASTA file - pattern: "*.fasta" - - fai: - type: file - description: The FAI file for the reference genome FASTA file - pattern: "*.fai" - - pool_rg_txt: - type: file - description: | - Optional. Provide the names of read groups that should be merged for PMD estimation. - All read groups that should be pooled listed on one line, separated by any white space. - Other read groups will be recalibrated separately. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Single input BAM file + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - pool_rg_txt: + type: file + description: | + Optional. Provide the names of read groups that should be merged for PMD estimation. + All read groups that should be pooled listed on one line, separated by any white space. + Other read groups will be recalibrated separately. + pattern: "*.txt" + - - fasta: + type: file + description: The reference genome provided as FASTA file + pattern: "*.fasta" + - - fai: + type: file + description: The FAI file for the reference genome FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - empiric: - type: file - description: A list of pmd patterns estimated with the empirical method for each readgroup - pattern: "*_PMD_input_Empiric.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_input_Empiric.txt": + type: file + description: A list of pmd patterns estimated with the empirical method for + each readgroup + pattern: "*_PMD_input_Empiric.txt" - exponential: - type: file - description: A list of pmd patterns estimated with the exponential method for each readgroup - pattern: "*_PMD_input_Exponential.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_input_Exponential.txt": + type: file + description: A list of pmd patterns estimated with the exponential method for + each readgroup + pattern: "*_PMD_input_Exponential.txt" - counts: - type: file - description: | - The counts of all possible transitions for each read position - (or up to a certain position, see specific command length) - pattern: "*_PMD_Table_counts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_Table_counts.txt": + type: file + description: | + The counts of all possible transitions for each read position + (or up to a certain position, see specific command length) + pattern: "*_PMD_Table_counts.txt" - table: - type: file - description: | - For all possible transitions the ratio of the transition counts, - which are taken from the _counts.txt table, over the total amount - of the base that was mutated, for each position and readgroup - pattern: "*_PMD_Table.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PMD_Table.txt": + type: file + description: | + For all possible transitions the ratio of the transition counts, + which are taken from the _counts.txt table, over the total amount + of the base that was mutated, for each position and readgroup + pattern: "*_PMD_Table.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@merszym" diff --git a/modules/nf-core/atlas/recal/meta.yml b/modules/nf-core/atlas/recal/meta.yml index 47b9c9afe6d5..68f3784d1972 100644 --- a/modules/nf-core/atlas/recal/meta.yml +++ b/modules/nf-core/atlas/recal/meta.yml @@ -6,51 +6,59 @@ keywords: - bias tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - empiric: - type: file - description: Optional txt file from PMD estimations (atlas/pmd) - pattern: "*.txt" - - alleles: - type: file - description: Optional bed file with known alleles - pattern: "*.bed" - - invariant_sites: - type: file - description: Optional bed file with invariant site coordinates - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - empiric: + type: file + description: Optional txt file from PMD estimations (atlas/pmd) + pattern: "*.txt" + - readgroups: + type: file + description: read groups + - - alleles: + type: file + description: Optional bed file with known alleles + pattern: "*.bed" + - - invariant_sites: + type: file + description: Optional bed file with invariant site coordinates + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - recal_patterns: - type: file - description: file containing the sequencing bias for each of the Read Group pools - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: file containing the sequencing bias for each of the Read Group + pools + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ltcrod" maintainers: diff --git a/modules/nf-core/atlas/splitmerge/meta.yml b/modules/nf-core/atlas/splitmerge/meta.yml index 24621b1901b9..d16a41bfeb63 100644 --- a/modules/nf-core/atlas/splitmerge/meta.yml +++ b/modules/nf-core/atlas/splitmerge/meta.yml @@ -7,58 +7,69 @@ keywords: - read group tools: - "atlas": - description: "ATLAS, a suite of methods to accurately genotype and estimate genetic diversity" + description: "ATLAS, a suite of methods to accurately genotype and estimate genetic + diversity" homepage: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" documentation: "https://bitbucket.org/wegmannlab/atlas/wiki/Home" tool_dev_url: "https://bitbucket.org/wegmannlab/atlas" doi: "10.1101/105346" licence: ["GPL v3"] + identifier: biotools:atlas_db input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Single input BAM file. - pattern: "*.bam" - - bai: - type: file - description: The BAI file for the input BAM file - pattern: "*.bai" - - read_group_settings: - type: file - description: | - TXT file containing the split and merge settings for - each readgroup. Each line consist of one readgroup, - single/double identifier and the maximum cycle number - of the sequencer. e.g. "RG1 single 100" - pattern: "*.txt" - - blacklist: - type: file - description: | - blacklist.txt (optional), A txt file with blacklisted read names - that should be ignored and just written to file, each on a new line - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Single input BAM file. + pattern: "*.bam" + - bai: + type: file + description: The BAI file for the input BAM file + pattern: "*.bai" + - read_group_settings: + type: file + description: | + TXT file containing the split and merge settings for + each readgroup. Each line consist of one readgroup, + single/double identifier and the maximum cycle number + of the sequencer. e.g. "RG1 single 100" + pattern: "*.txt" + - blacklist: + type: file + description: | + blacklist.txt (optional), A txt file with blacklisted read names + that should be ignored and just written to file, each on a new line + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: A BAM file with suffix_mergedReads.bam - pattern: "*_mergedReads.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_mergedReads.bam": + type: file + description: A BAM file with suffix_mergedReads.bam + pattern: "*_mergedReads.bam" - txt: - type: file - description: A file listing all reads that were filtered out in the merging process with suffix_ignoredReads.txt.gz - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: A file listing all reads that were filtered out in the merging + process with suffix_ignoredReads.txt.gz + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@merszym" maintainers: diff --git a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml index 3e34244e0384..d735b0707bc1 100644 --- a/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml +++ b/modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/meta.yml @@ -11,44 +11,61 @@ tools: documentation: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" tool_dev_url: "https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on input GTF file - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information in input FASTA file - e.g. [ id:'test' ] - - gtf: - type: file - description: gtf annotation file - pattern: "*.{gtf}" - - fasta: - type: file - description: | - An optional cDNA file for extracting meta info and/or filtering. - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing information on input GTF file + e.g. [ id:'test' ] + - gtf: + type: file + description: gtf annotation file + pattern: "*.{gtf}" + - - meta2: + type: map + description: | + Groovy Map containing information in input FASTA file + e.g. [ id:'test' ] + - fasta: + type: file + description: | + An optional cDNA file for extracting meta info and/or filtering. + pattern: "*.{gtf}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - feature_annotation: - type: file - description: TSV file with feature annotation - pattern: "*.{tsv}" + - meta: + type: file + description: TSV file with feature annotation + pattern: "*.{tsv}" + - "*.anno.tsv": + type: file + description: TSV file with feature annotation + pattern: "*.{tsv}" - filtered_cdna: - type: file - description: | - Where --parse-cdnas is specified in ext.args and an input fasta file is - provided, filtered sequences are output to the specified file. No file - will be output if this is not specified (for example for use of - --dummy-from-cdnas only). See documentation at - https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. - pattern: "*.{tsv}" + - meta: + type: file + description: | + Where --parse-cdnas is specified in ext.args and an input fasta file is + provided, filtered sequences are output to the specified file. No file + will be output if this is not specified (for example for use of + --dummy-from-cdnas only). See documentation at + https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. + pattern: "*.{tsv}" + - "*.fa.gz": + type: file + description: | + Where --parse-cdnas is specified in ext.args and an input fasta file is + provided, filtered sequences are output to the specified file. No file + will be output if this is not specified (for example for use of + --dummy-from-cdnas only). See documentation at + https://github.com/ebi-gene-expression-group/atlas-gene-annotation-manipulation. + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/authentict/deam2cont/meta.yml b/modules/nf-core/authentict/deam2cont/meta.yml index 0c05fbc46337..59bfb10f05fc 100644 --- a/modules/nf-core/authentict/deam2cont/meta.yml +++ b/modules/nf-core/authentict/deam2cont/meta.yml @@ -1,5 +1,6 @@ name: "authentict_deam2cont" -description: Use deamination patterns to estimate contamination in single-stranded libraries +description: Use deamination patterns to estimate contamination in single-stranded + libraries keywords: - authentict - ancientDNA @@ -9,44 +10,58 @@ keywords: - damage tools: - "authentict": - description: "Estimates present-day DNA contamination in ancient DNA single-stranded libraries." + description: "Estimates present-day DNA contamination in ancient DNA single-stranded + libraries." homepage: "https://github.com/StephanePeyregne/AuthentiCT" documentation: "https://github.com/StephanePeyregne/AuthentiCT" tool_dev_url: "https://github.com/StephanePeyregne/AuthentiCT" doi: "10.1186/s13059-020-02123-y" licence: ["GPL v3"] + identifier: biotools:authentict input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file (Mandatory) - pattern: "*.{bam,cram,sam}" - - config: - type: file - description: Optional AuthentiCT configuration text file - pattern: "*" - - positions: - type: file - description: Optional text file with positions that sequences should overlap - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file (Mandatory) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - config: + type: file + description: Optional AuthentiCT configuration text file + pattern: "*" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - positions: + type: file + description: Optional text file with positions that sequences should overlap + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Maximum likelihood estimates with associated standard errors - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Maximum likelihood estimates with associated standard errors + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scarlhoff" - "@StephanePeyregne" diff --git a/modules/nf-core/backsub/meta.yml b/modules/nf-core/backsub/meta.yml index b01dce6d935c..be82c9db987d 100644 --- a/modules/nf-core/backsub/meta.yml +++ b/modules/nf-core/backsub/meta.yml @@ -1,5 +1,6 @@ name: "backsub" -description: Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched `tif` images. +description: Pixel-by-pixel channel subtraction scaled by exposure times of pre-stitched + `tif` images. keywords: - background - cycif @@ -9,53 +10,59 @@ keywords: - highly_multiplexed_imaging tools: - "backsub": - description: "Module for pixel-by-pixel channel subtraction scaled by exposure times" + description: "Module for pixel-by-pixel channel subtraction scaled by exposure + times" homepage: "https://github.com/SchapiroLabor/Background_subtraction" documentation: "https://github.com/SchapiroLabor/Background_subtraction/blob/master/README.md" tool_dev_url: "https://github.com/SchapiroLabor/Background_subtraction" licence: ["MIT licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - image: - type: file - description: Multi-channel image file - pattern: "*.{tif,tiff}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - markerfile: - type: file - description: Marker file with channel names, exposure times, and specified background to subtract (and remove to exclude channels from output) - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - image: + type: file + description: Multi-channel image file + pattern: "*.{tif,tiff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - markerfile: + type: file + description: Marker file with channel names, exposure times, and specified background + to subtract (and remove to exclude channels from output) + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - backsub_tif: - type: file - description: Background corrected pyramidal ome.tif - pattern: "*.{tif}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.ome.tif": + type: file + description: Background corrected pyramidal ome.tif + pattern: "*.{tif}" - markerout: - type: file - description: Marker file adjusted to match the background corrected image - pattern: "*.{csv}" + - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.csv": + type: file + description: Marker file adjusted to match the background corrected image + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kbestak" maintainers: diff --git a/modules/nf-core/bacphlip/meta.yml b/modules/nf-core/bacphlip/meta.yml index 1bd8f68aad04..b6f008218dbb 100644 --- a/modules/nf-core/bacphlip/meta.yml +++ b/modules/nf-core/bacphlip/meta.yml @@ -15,34 +15,46 @@ tools: tool_dev_url: https://github.com/adamhockenberry/bacphlip doi: 10.7717/peerj.11396 licence: ["MIT"] + identifier: biotools:bacphlip input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing phage contigs/scaffolds/chromosomes (if it is a multi-FASTA file be sure to add the `--multi_fasta` argument) - pattern: "*.{fasta,fna,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing phage contigs/scaffolds/chromosomes (if it + is a multi-FASTA file be sure to add the `--multi_fasta` argument) + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bacphlip_results: - type: file - description: TSV file containing Temperate and Virulent scores for each phage sequence - pattern: "*.bacphlip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bacphlip": + type: file + description: TSV file containing Temperate and Virulent scores for each phage + sequence + pattern: "*.bacphlip" - hmmsearch_results: - type: file - description: TSV file containing binary output indicating gene presence/absence based on hmmsearch results - pattern: "*.hmmsearch.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hmmsearch.tsv": + type: file + description: TSV file containing binary output indicating gene presence/absence + based on hmmsearch results + pattern: "*.hmmsearch.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/bakta/bakta/meta.yml b/modules/nf-core/bakta/bakta/meta.yml index c0e53e2a3035..f947e61bcd14 100644 --- a/modules/nf-core/bakta/bakta/meta.yml +++ b/modules/nf-core/bakta/bakta/meta.yml @@ -12,76 +12,134 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] + identifier: biotools:bakta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - FASTA file to be annotated. Has to contain at least a non-empty string dummy value. - - db: - type: file - description: | - Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/'). - - proteins: - type: file - description: FASTA/GenBank file of trusted proteins to first annotate from (optional) - - prodigal_tf: - type: file - description: Training file to use for Prodigal (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + FASTA file to be annotated. Has to contain at least a non-empty string dummy value. + - - db: + type: file + description: | + Path to the Bakta database. Must have amrfinderplus database directory already installed within it (in a directory called 'amrfinderplus-db/'). + - - proteins: + type: file + description: FASTA/GenBank file of trusted proteins to first annotate from (optional) + - - prodigal_tf: + type: file + description: Training file to use for Prodigal (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: genome statistics and annotation summary - pattern: "*.txt" - - tsv: - type: file - description: annotations as simple human readble tab separated values - pattern: "*.tsv" - - gff: - type: file - description: annotations & sequences in GFF3 format - pattern: "*.gff3" - - gbff: - type: file - description: annotations & sequences in (multi) GenBank format - pattern: "*.gbff" - embl: - type: file - description: annotations & sequences in (multi) EMBL format - pattern: "*.embl" - - fna: - type: file - description: replicon/contig DNA sequences as FASTA - pattern: "*.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.embl: + type: file + description: annotations & sequences in (multi) EMBL format + pattern: "*.embl" - faa: - type: file - description: CDS/sORF amino acid sequences as FASTA - pattern: "*.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.faa: + type: file + description: CDS/sORF amino acid sequences as FASTA + pattern: "*.faa" - ffn: - type: file - description: feature nucleotide sequences as FASTA - pattern: "*.ffn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ffn: + type: file + description: feature nucleotide sequences as FASTA + pattern: "*.ffn" + - fna: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fna: + type: file + description: replicon/contig DNA sequences as FASTA + pattern: "*.fna" + - gbff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gbff: + type: file + description: annotations & sequences in (multi) GenBank format + pattern: "*.gbff" + - gff: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gff3: + type: file + description: annotations & sequences in GFF3 format + pattern: "*.gff3" - hypotheticals_tsv: - type: file - description: additional information on hypothetical protein CDS as simple human readble tab separated values - pattern: "*.hypotheticals.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hypotheticals.tsv: + type: file + description: additional information on hypothetical protein CDS as simple human + readble tab separated values + pattern: "*.hypotheticals.tsv" - hypotheticals_faa: - type: file - description: hypothetical protein CDS amino acid sequences as FASTA - pattern: "*.hypotheticals.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hypotheticals.faa: + type: file + description: hypothetical protein CDS amino acid sequences as FASTA + pattern: "*.hypotheticals.faa" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: annotations as simple human readble tab separated values + pattern: "*.tsv" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: genome statistics and annotation summary + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@oschwengers" diff --git a/modules/nf-core/bakta/baktadbdownload/meta.yml b/modules/nf-core/bakta/baktadbdownload/meta.yml index 21acacdac1f6..a0a3a4559dbd 100644 --- a/modules/nf-core/bakta/baktadbdownload/meta.yml +++ b/modules/nf-core/bakta/baktadbdownload/meta.yml @@ -15,15 +15,18 @@ tools: tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" licence: ["GPL v3"] + identifier: biotools:bakta output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: BAKTA database directory - pattern: "db*/" + - db*: + type: directory + description: BAKTA database directory + pattern: "db*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@jasmezz" diff --git a/modules/nf-core/bam2fastx/bam2fastq/meta.yml b/modules/nf-core/bam2fastx/bam2fastq/meta.yml index c7a884408de7..328931f41786 100644 --- a/modules/nf-core/bam2fastx/bam2fastq/meta.yml +++ b/modules/nf-core/bam2fastx/bam2fastq/meta.yml @@ -1,47 +1,50 @@ name: "bam2fastx_bam2fastq" -description: Conversion of PacBio BAM files into gzipped fastq files, including splitting of barcoded data +description: Conversion of PacBio BAM files into gzipped fastq files, including splitting + of barcoded data keywords: - bam2fastx - bam2fastq - pacbio tools: - "bam2fastx": - description: "Converting and demultiplexing of PacBio BAM files into gzipped fasta and fastq files" + description: "Converting and demultiplexing of PacBio BAM files into gzipped fasta + and fastq files" homepage: "https://github.com/PacificBiosciences/bam2fastx" documentation: "https://github.com/PacificBiosciences/bam2fastx" tool_dev_url: "https://github.com/PacificBiosciences/bam2fastx" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: PacBio BAM file - pattern: "*.bam" - - index: - type: file - description: PacBio BAM file index (.pbi) - pattern: "*.pbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: PacBio BAM file + pattern: "*.bam" + - index: + type: file + description: PacBio BAM file index (.pbi) + pattern: "*.pbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Gzipped FASTQ file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Gzipped FASTQ file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/bamaligncleaner/meta.yml b/modules/nf-core/bamaligncleaner/meta.yml index 1278aefb4330..0293aaaa3bb7 100644 --- a/modules/nf-core/bamaligncleaner/meta.yml +++ b/modules/nf-core/bamaligncleaner/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/maxibor/bamAlignCleaner tool_dev_url: https://github.com/maxibor/bamAlignCleaner licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bamclipper/meta.yml b/modules/nf-core/bamclipper/meta.yml index d857845b780c..0243c4880088 100644 --- a/modules/nf-core/bamclipper/meta.yml +++ b/modules/nf-core/bamclipper/meta.yml @@ -8,55 +8,57 @@ keywords: - bam tools: - "bamclipper": - description: "BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing" + description: "BAMClipper: removing primers from alignments to minimize false-negative + mutations in amplicon next-generation sequencing" homepage: "https://github.com/tommyau/bamclipper" documentation: "https://github.com/tommyau/bamclipper" tool_dev_url: "https://github.com/tommyau/bamclipper" doi: "10.1038/s41598-017-01703-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information `[ id:'sample1']` - - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - - bai: - type: file - description: BAI index of the input BAM file - pattern: "*.bam.bai" - - - bedpe: - type: file - description: BEDPE file of primer pair locations - pattern: "*.bed" - + - - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: BAI index of the input BAM file + pattern: "*.bam.bai" + - bedpe: + type: file + description: BEDPE file of primer pair locations + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Sorted BAM file containing clipped query sequences according to the given primer pair locations - pattern: "*.primerclipped.bam" - + - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - "*.primerclipped.bam": + type: file + description: Sorted BAM file containing clipped query sequences according to + the given primer pair locations + pattern: "*.primerclipped.bam" - bai: - type: file - description: "BAI index of the output BAM file" - pattern: "*.primerclipped.bam.bai" - + - meta: + type: map + description: | + Groovy Map containing sample information `[ id:'sample1']` + - "*.primerclipped.bam.bai": + type: file + description: "BAI index of the output BAM file" + pattern: "*.primerclipped.bam.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@krannich479" maintainers: diff --git a/modules/nf-core/bamcmp/meta.yml b/modules/nf-core/bamcmp/meta.yml index 1a83b7a57e8a..021652e850b6 100644 --- a/modules/nf-core/bamcmp/meta.yml +++ b/modules/nf-core/bamcmp/meta.yml @@ -1,5 +1,7 @@ name: bamcmp -description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary genome and a contamination genome. For instance, filtering out mouse reads from patient derived xenograft mouse models (PDX). +description: Bamcmp (Bam Compare) is a tool for assigning reads between a primary + genome and a contamination genome. For instance, filtering out mouse reads from + patient derived xenograft mouse models (PDX). keywords: - filter - xenograft @@ -9,39 +11,61 @@ keywords: - mouse tools: - bamcmp: - description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else reads which multimap to the contamination genome will be spuriously kept. + description: Bamcmp is a tool for deconvolving host and graft reads, using two + bam files. Reads should be mapped to two genomes, and the mapped, sorted bam + files supplied to the tool. It is highly recommended to use the "-s as" option + not the "-s mapq" option, else reads which multimap to the contamination genome + will be spuriously kept. homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp doi: "10.1158/1541-7786.MCR-16-0431" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - primary_aligned_bam: - type: file - description: BAM/CRAM/SAM file with the reads aligned to the primary genome (the one you want to keep) - pattern: "*.{bam,cram,sam}" - - contaminant_aligned_bam: - type: file - description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome (the one you want to filter out) - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - primary_aligned_bam: + type: file + description: BAM/CRAM/SAM file with the reads aligned to the primary genome + (the one you want to keep) + pattern: "*.{bam,cram,sam}" + - contaminant_aligned_bam: + type: file + description: BAM/CRAM/SAM file with the reads aligned to the contaminant genome + (the one you want to filter out) + pattern: "*.{bam,cram,sam}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - primary_filtered_bam: - type: file - description: Bam file containing the reads which align better to the primary genome. - pattern: "*.{bam,cram,sam}" + - meta: + type: file + description: Bam file containing the reads which align better to the primary + genome. + pattern: "*.{bam,cram,sam}" + - ${prefix}.bam: + type: file + description: Bam file containing the reads which align better to the primary + genome. + pattern: "*.{bam,cram,sam}" - contamination_bam: - type: file - description: Bam file containing the reads which align better to the contaminant genome. - pattern: "*.{bam,cram,sam}" + - meta: + type: file + description: Bam file containing the reads which align better to the contaminant + genome. + pattern: "*.{bam,cram,sam}" + - ${prefix2}.bam: + type: file + description: Bam file containing the reads which align better to the contaminant + genome. + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kmurat1" - "@sppearce" diff --git a/modules/nf-core/bamstats/generalstats/meta.yml b/modules/nf-core/bamstats/generalstats/meta.yml index a0921f4a3e33..664e2435b95b 100644 --- a/modules/nf-core/bamstats/generalstats/meta.yml +++ b/modules/nf-core/bamstats/generalstats/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bamstats_generalstats" description: write your description here @@ -13,34 +12,33 @@ tools: documentation: "https://github.com/guigolab/bamstats/" tool_dev_url: "https://github.com/guigolab" licence: ["BSD-3-clause"] + identifier: biotools:bamstats-ip input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: json containing bam statistics - pattern: "*.json" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.json": + type: file + description: json containing bam statistics + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@johnoooh" diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml index 2ac31a5cf827..ace49c251829 100644 --- a/modules/nf-core/bamtofastq10x/meta.yml +++ b/modules/nf-core/bamtofastq10x/meta.yml @@ -1,6 +1,8 @@ name: bamtofastq10x -description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis +description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell + Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used + as inputs to re-run analysis keywords: - bam @@ -10,38 +12,40 @@ keywords: tools: - bamtofastq10x: - description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis + description: Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, + Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that + can be used as inputs to re-run analysis homepage: https://github.com/10XGenomics/bamtofastq documentation: https://github.com/10XGenomics/bamtofastq tool_dev_url: https://github.com/10XGenomics/bamtofastq licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: fastq compressed file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: fastq compressed file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BlueBicycleBlog" maintainers: diff --git a/modules/nf-core/bamtools/convert/meta.yml b/modules/nf-core/bamtools/convert/meta.yml index 3cc8ae6aa899..a97d0e4ae8eb 100644 --- a/modules/nf-core/bamtools/convert/meta.yml +++ b/modules/nf-core/bamtools/convert/meta.yml @@ -1,5 +1,6 @@ name: bamtools_convert -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - bamtools/convert @@ -19,30 +20,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - data: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bed,fasta,fastq,json,pileup,sam,yaml}": + type: file + description: Output file + pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - out: - type: file - description: The data in the asked format (bed, fasta, fastq, json, pileup, sam, yaml) - pattern: "*.{bed,fasta,fastq,json,pileup,sam,yaml}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/bamtools/split/meta.yml b/modules/nf-core/bamtools/split/meta.yml index e42242bbd7ad..c580fbbae99e 100644 --- a/modules/nf-core/bamtools/split/meta.yml +++ b/modules/nf-core/bamtools/split/meta.yml @@ -1,5 +1,6 @@ name: bamtools_split -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - bamtools/split @@ -13,30 +14,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A list of one or more BAM files to merge and then split - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A list of one or more BAM files to merge and then split + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Several Bam files - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Several Bam files + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" - "@matthdsm" diff --git a/modules/nf-core/bamtools/stats/meta.yml b/modules/nf-core/bamtools/stats/meta.yml index 28db686fa549..952eab3e5bfc 100644 --- a/modules/nf-core/bamtools/stats/meta.yml +++ b/modules/nf-core/bamtools/stats/meta.yml @@ -1,5 +1,6 @@ name: "bamtools_stats" -description: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. +description: BamTools provides both a programmer's API and an end-user's toolkit for + handling BAM files. keywords: - bamtools - stats @@ -11,30 +12,33 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools licence: ["MIT"] + identifier: biotools:bamtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: File containing alignment statistics - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing alignment statistics + pattern: "*.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/bamutil/trimbam/meta.yml b/modules/nf-core/bamutil/trimbam/meta.yml index f40a7e5d71fd..ce603e76b3fc 100644 --- a/modules/nf-core/bamutil/trimbam/meta.yml +++ b/modules/nf-core/bamutil/trimbam/meta.yml @@ -1,5 +1,6 @@ name: bamutil_trimbam -description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’, or by soft clipping +description: trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and + quality to ‘!’, or by soft clipping keywords: - bam - trim @@ -8,42 +9,48 @@ keywords: - trimBam tools: - bamutil: - description: Programs that perform operations on SAM/BAM files, all built into a single executable, bam. + description: Programs that perform operations on SAM/BAM files, all built into + a single executable, bam. homepage: https://genome.sph.umich.edu/wiki/BamUtil documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam tool_dev_url: https://github.com/statgen/bamUtil doi: "10.1101/gr.176552.114" licence: ["GPL v3"] + identifier: biotools:bamutil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - trim_left: - type: integer - description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. - - trim_right: - type: integer - description: Number of bases to trim off the right-hand side of a read. Reverse strands are reversed before trimming. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - trim_left: + type: integer + description: Number of bases to trim off the right-hand side of a read. Reverse + strands are reversed before trimming. + - trim_right: + type: integer + description: Number of bases to trim off the right-hand side of a read. Reverse + strands are reversed before trimming. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Trimmed but unsorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Trimmed but unsorted BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bandage/image/meta.yml b/modules/nf-core/bandage/image/meta.yml index 94ce8a80ed6b..052780695e9c 100644 --- a/modules/nf-core/bandage/image/meta.yml +++ b/modules/nf-core/bandage/image/meta.yml @@ -12,34 +12,43 @@ tools: homepage: https://github.com/rrwick/Bandage documentation: https://github.com/rrwick/Bandage licence: ["GPL-3.0-or-later"] + identifier: biotools:bandage input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly graph in GFA 1.0 format - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly graph in GFA 1.0 format + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - png: - type: file - description: Bandage image in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: Bandage image in PNG format + pattern: "*.png" - svg: - type: file - description: Bandage image in SVG format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Bandage image in SVG format + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/barrnap/meta.yml b/modules/nf-core/barrnap/meta.yml index a683e712383c..7464c520eddb 100644 --- a/modules/nf-core/barrnap/meta.yml +++ b/modules/nf-core/barrnap/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "barrnap" description: barrnap uses a hmmer profile to find rrnas in reads or contig fasta files @@ -8,38 +7,42 @@ keywords: - removal tools: - "barrnap": - description: "Barrnap predicts the location of ribosomal RNA genes in genomes (bacteria, archaea, metazoan mitochondria and eukaryotes)." + description: "Barrnap predicts the location of ribosomal RNA genes in genomes + (bacteria, archaea, metazoan mitochondria and eukaryotes)." homepage: "https://github.com/tseemann/barrnap" documentation: "https://github.com/tseemann/barrnap" tool_dev_url: "https://github.com/tseemann/barrnap" licence: ["GPL v3"] + identifier: biotools:barrnap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq or fasta file nucleotides (it can be amino acids as well) - pattern: "*.{fna,fasta,faa,fastq}" - - dbname: - type: string - description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: fasta file + pattern: "*.fasta" + - dbname: + type: string + description: database to use(bacteria, archaea, eukaryota, metazoan mitochondria) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: gff file containing coordinates of genes - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.gff": + type: file + description: gff file containing coordinates of genes + pattern: "*.gff" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@danilodileo" maintainers: diff --git a/modules/nf-core/bases2fastq/meta.yml b/modules/nf-core/bases2fastq/meta.yml index 8de98e139080..dff90c1f3049 100644 --- a/modules/nf-core/bases2fastq/meta.yml +++ b/modules/nf-core/bases2fastq/meta.yml @@ -6,61 +6,102 @@ keywords: - fastq tools: - "bases2fastq": - description: "Demultiplexes sequencing data and converts base calls into FASTQ files for secondary analysis" + description: "Demultiplexes sequencing data and converts base calls into FASTQ + files for secondary analysis" homepage: "https://go.elementbiosciences.com/bases2fastq-download" documentation: "https://www.elementbiosciences.com/resources/user-guides/workflow/bases2fastq" licence: ["http://go.elembio.link/eula"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - run_manifest: - type: file - description: RunManifest file - pattern: "*.{csv}" - - run_dir: - type: directory - description: "Input run directory containing optionally containing a RunManifest.json if run_manifest is not supplied" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - run_manifest: + type: file + description: RunManifest file + pattern: "*.{csv}" + - run_dir: + type: directory + description: "Input run directory containing optionally containing a RunManifest.json + if run_manifest is not supplied" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "output/Samples/*/*_R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Samples/**/*_R*.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "output/Samples/*/*_R*.fastq.gz" - sample_json: - type: file - description: Demultiplexed sample stats - pattern: "output/Samples/*/*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Samples/**/*_stats.json: + type: file + description: Demultiplexed sample stats + pattern: "output/Samples/*/*.json" - qc_report: - type: file - description: QC HTML report - pattern: "output/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*.html: + type: file + description: QC HTML report + pattern: "output/*.html" - run_stats: - type: file - description: QC HTML report - pattern: "output/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/RunStats.json: + type: file + description: QC HTML report + pattern: "output/*.html" - generated_run_manifest: - type: file - description: Updated Run Manifest JSON from the run_manifest csv - pattern: "output/RunManifest.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/RunManifest.json: + type: file + description: Updated Run Manifest JSON from the run_manifest csv + pattern: "output/RunManifest.json" - metrics: - type: file - description: Sample metrics - pattern: "output/Metrics.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/Metrics.csv: + type: file + description: Sample metrics + pattern: "output/Metrics.csv" - unassigned: - type: file - description: Unassigned Sequences - pattern: "output/UnassignedSequences.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/UnassignedSequences.csv: + type: file + description: Unassigned Sequences + pattern: "output/UnassignedSequences.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/basicpy/meta.yml b/modules/nf-core/basicpy/meta.yml index 61e03566697c..b143f5db1166 100644 --- a/modules/nf-core/basicpy/meta.yml +++ b/modules/nf-core/basicpy/meta.yml @@ -1,5 +1,7 @@ name: "basicpy" -description: BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm. +description: BaSiCPy is a python package for background and shading correction of + optical microscopy images. It is developed based on the Matlab version of BaSiC + tool with major improvements in the algorithm. keywords: - illumiation_correction - background_correction @@ -7,36 +9,41 @@ keywords: - imaging tools: - "basicpy": - description: "BaSiCPy is a python package for background and shading correction of optical microscopy images. It is developed based on the Matlab version of BaSiC tool with major improvements in the algorithm." + description: "BaSiCPy is a python package for background and shading correction + of optical microscopy images. It is developed based on the Matlab version of + BaSiC tool with major improvements in the algorithm." homepage: "https://github.com/peng-lab/BaSiCPy" documentation: "https://basicpy.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/peng-lab/BaSiCPy" doi: 10.1038/ncomms14836 license: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - image: - type: file - description: Tiff file to be used for dark and flat field illumination correction - pattern: "*.{tiff,tif}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - image: + type: file + description: Tiff file to be used for dark and flat field illumination correction + pattern: "*.{tiff,tif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fields: - type: file - description: Tiff fields for dark and flat field illumination correction - pattern: "*.{tiff,tif}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tiff": + type: file + description: Tiff fields for dark and flat field illumination correction + pattern: "*.{tiff,tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/bbmap/align/meta.yml b/modules/nf-core/bbmap/align/meta.yml index a0bddba40109..38bd8e141b40 100644 --- a/modules/nf-core/bbmap/align/meta.yml +++ b/modules/nf-core/bbmap/align/meta.yml @@ -9,41 +9,55 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - ref: - type: file - description: | - Either "ref" a directory containing an index, the name of another directory - with a "ref" subdirectory containing an index or the name of a fasta formatted - nucleotide file containg the reference to map to. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - ref: + type: file + description: | + Either "ref" a directory containing an index, the name of another directory + with a "ref" subdirectory containing an index or the name of a fasta formatted + nucleotide file containg the reference to map to. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.{bam}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/bbmap/bbduk/meta.yml b/modules/nf-core/bbmap/bbduk/meta.yml index 9a1f05628600..5665a268033d 100644 --- a/modules/nf-core/bbmap/bbduk/meta.yml +++ b/modules/nf-core/bbmap/bbduk/meta.yml @@ -7,43 +7,53 @@ keywords: - fastq tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - contaminants: - type: file - description: | - Reference files containing adapter and/or contaminant sequences for sequence kmer matching + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - contaminants: + type: file + description: | + Reference files containing adapter and/or contaminant sequences for sequence kmer matching output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*fastq.gz" - log: - type: file - description: Bbduk log file - pattern: "*bbduk.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Bbduk log file + pattern: "*bbduk.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" maintainers: diff --git a/modules/nf-core/bbmap/bbmerge/meta.yml b/modules/nf-core/bbmap/bbmerge/meta.yml index 514412e8bee0..240c47407e9f 100644 --- a/modules/nf-core/bbmap/bbmerge/meta.yml +++ b/modules/nf-core/bbmap/bbmerge/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "bbmap_bbmerge" description: Merging overlapping paired reads into a single read. @@ -8,61 +7,69 @@ keywords: - overlap-based merging tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: | - List of input paired end fastq files - pattern: "*.{fastq,fq}.gz" - - - interleave: - type: boolean - description: | - Indicates whether the input paired reads are interleaved or not - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: | + List of input paired end fastq files + pattern: "*.{fastq,fq}.gz" + - - interleave: + type: boolean + description: | + Indicates whether the input paired reads are interleaved or not output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - merged: - type: file - description: merged reads - pattern: "*_merged.fastq" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_merged.fastq.gz": + type: file + description: merged reads + pattern: "*_merged.fastq" - unmerged: - type: file - description: unmerged reads - pattern: "*_unmerged.fastq" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_unmerged.fastq.gz": + type: file + description: unmerged reads + pattern: "*_unmerged.fastq" - ihist: - type: file - description: insert size histogram - pattern: "*_ihist.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_ihist.txt": + type: file + description: insert size histogram + pattern: "*_ihist.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: log file containing stdout and stderr from bbmerge.sh - pattern: "*.log" - + - "*.log": + type: file + description: log file containing stdout and stderr from bbmerge.sh + pattern: "*.log" authors: - "@guille0387" maintainers: diff --git a/modules/nf-core/bbmap/bbnorm/meta.yml b/modules/nf-core/bbmap/bbnorm/meta.yml index 052c5b534d65..e21f262a29a7 100644 --- a/modules/nf-core/bbmap/bbnorm/meta.yml +++ b/modules/nf-core/bbmap/bbnorm/meta.yml @@ -1,40 +1,55 @@ name: bbmap_bbnorm -description: BBNorm is designed to normalize coverage by down-sampling reads over high-depth areas of a genome, to result in a flat coverage distribution. +description: BBNorm is designed to normalize coverage by down-sampling reads over + high-depth areas of a genome, to result in a flat coverage distribution. keywords: - normalization - assembly - coverage tools: - bbmap: - description: "BBMap is a short read aligner, as well as various other bioinformatic tools." + description: "BBMap is a short read aligner, as well as various other bioinformatic + tools." homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" tool_dev_url: "https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/bbnorm-guide/" licence: ["BBMap - Bushnell B. - sourceforge.net/projects/bbmap/"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: fastq file - pattern: "*.{fastq,fq}(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: fastq file + pattern: "*.{fastq,fq}(.gz)?" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: fastq file - pattern: "*.{fastq, fq}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: fastq file + pattern: "*.{fastq, fq}.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@danilodileo" maintainers: diff --git a/modules/nf-core/bbmap/bbsplit/meta.yml b/modules/nf-core/bbmap/bbsplit/meta.yml index f4e0a5ed58e1..c34196e47702 100644 --- a/modules/nf-core/bbmap/bbsplit/meta.yml +++ b/modules/nf-core/bbmap/bbsplit/meta.yml @@ -8,64 +8,91 @@ keywords: - reference tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory to place generated index - pattern: "*" - - primary_ref: - type: file - description: Path to the primary reference - pattern: "*" - - other_ref_names: - type: list - description: List of other reference ids apart from the primary - - other_ref_paths: - type: list - description: Path to other references paths corresponding to "other_ref_names" - - only_build_index: - type: string - description: true = only build index; false = mapping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory to place generated index + pattern: "*" + - - primary_ref: + type: file + description: Path to the primary reference + pattern: "*" + - - other_ref_names: + type: list + description: List of other reference ids apart from the primary + - other_ref_paths: + type: list + description: Path to other references paths corresponding to "other_ref_names" + - - only_build_index: + type: string + description: true = only build index; false = mapping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory with index files - pattern: "bbsplit" + - bbsplit: + type: directory + description: Directory with index files + pattern: "bbsplit" - primary_fastq: - type: file - description: Output reads that map to the primary reference - pattern: "*primary*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*primary*fastq.gz": + type: file + description: Output reads that map to the primary reference + pattern: "*primary*fastq.gz" - all_fastq: - type: file - description: All reads mapping to any of the references - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: All reads mapping to any of the references + pattern: "*fastq.gz" - stats: - type: file - description: Tab-delimited text file containing mapping statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*txt": + type: file + description: Tab-delimited text file containing mapping statistics + pattern: "*.txt" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bbmap/clumpify/meta.yml b/modules/nf-core/bbmap/clumpify/meta.yml index ed333971d42a..7db435cd6332 100644 --- a/modules/nf-core/bbmap/clumpify/meta.yml +++ b/modules/nf-core/bbmap/clumpify/meta.yml @@ -7,39 +7,49 @@ keywords: - fastq tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ documentation: https://www.biostars.org/p/225338/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The reordered/clumped (and if necessary deduped) fastq reads - pattern: "*.clumped.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: The reordered/clumped (and if necessary deduped) fastq reads + pattern: "*.clumped.fastq.gz" - log: - type: file - description: Clumpify log file - pattern: "*clumpify.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Clumpify log file + pattern: "*clumpify.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamuanand" maintainers: diff --git a/modules/nf-core/bbmap/filterbyname/meta.yml b/modules/nf-core/bbmap/filterbyname/meta.yml index b99f46749060..b7b86419d98e 100644 --- a/modules/nf-core/bbmap/filterbyname/meta.yml +++ b/modules/nf-core/bbmap/filterbyname/meta.yml @@ -6,54 +6,62 @@ keywords: - filter tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/software-tools/bbtools/bb-tools-user-guide/clumpify-guide/ documentation: https://www.biostars.org/p/225338/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and - paired-end data, respectively. - - names_to_filter: - type: string - description: | - String containing names of reads to filter out of the fastq files. - - output_format: - type: string - description: | - String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2 - - interleaved_output: - type: boolean - description: | - Whether to produce an interleaved fastq output file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and + paired-end data, respectively. + - - names_to_filter: + type: string + description: | + String containing names of reads to filter out of the fastq files. + - - output_format: + type: string + description: | + String with the format of the output file, e.g. fastq.gz, fasta, fasta.bz2 + - - interleaved_output: + type: boolean + description: | + Whether to produce an interleaved fastq output file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*${output_format}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${output_format}": + type: file + description: The trimmed/modified fastq reads + pattern: "*${output_format}" - log: - type: file - description: filterbyname.sh log file - pattern: "*.filterbyname.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: filterbyname.sh log file + pattern: "*.filterbyname.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tokarevvasily" - "@sppearce" diff --git a/modules/nf-core/bbmap/index/meta.yml b/modules/nf-core/bbmap/index/meta.yml index c2dd342f562f..ab852b4196e0 100644 --- a/modules/nf-core/bbmap/index/meta.yml +++ b/modules/nf-core/bbmap/index/meta.yml @@ -1,29 +1,33 @@ name: bbmap_index -description: Creates an index from a fasta file, ready to be used by bbmap.sh in mapping mode. +description: Creates an index from a fasta file, ready to be used by bbmap.sh in mapping + mode. keywords: - map - index - fasta tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - fasta: - type: file - description: fasta formatted file with nucleotide sequences - pattern: "*.{fna,fa,fasta}" + - - fasta: + type: file + description: fasta formatted file with nucleotide sequences + pattern: "*.{fna,fa,fasta}" output: + - index: + - ref: + type: directory + description: Directory containing the index files - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - db: - type: directory - description: Directory with index files - pattern: "ref" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@daniellundin" maintainers: diff --git a/modules/nf-core/bbmap/pileup/meta.yml b/modules/nf-core/bbmap/pileup/meta.yml index 5620fd803a83..1ad776aed307 100644 --- a/modules/nf-core/bbmap/pileup/meta.yml +++ b/modules/nf-core/bbmap/pileup/meta.yml @@ -1,44 +1,55 @@ name: "bbmap_pileup" -description: Calculates per-scaffold or per-base coverage information from an unsorted sam or bam file. +description: Calculates per-scaffold or per-base coverage information from an unsorted + sam or bam file. keywords: - fasta - genome - coverage tools: - bbmap: - description: BBMap is a short read aligner, as well as various other bioinformatic tools. + description: BBMap is a short read aligner, as well as various other bioinformatic + tools. homepage: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: "https://github.com/BioInfoTools/BBMap/blob/master/sh/pileup.sh" licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Per-scaffold coverage info - pattern: "*.stats.txt" + - covstats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.txt": + type: file + description: Coverage statistics + pattern: "*.stats.txt" - hist: - type: file - description: "Histogram of # occurrences of each depth level" - pattern: "*.hist.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.txt": + type: file + description: "Histogram of # occurrences of each depth level" + pattern: "*.hist.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/bbmap/sendsketch/meta.yml b/modules/nf-core/bbmap/sendsketch/meta.yml index 76f3e9472ba9..fc27db517ef7 100644 --- a/modules/nf-core/bbmap/sendsketch/meta.yml +++ b/modules/nf-core/bbmap/sendsketch/meta.yml @@ -1,5 +1,6 @@ name: "bbmap_sendsketch" -description: Compares query sketches to reference sketches hosted on a remote server via the Internet. +description: Compares query sketches to reference sketches hosted on a remote server + via the Internet. keywords: - taxonomy - classification @@ -9,34 +10,40 @@ keywords: - fasta tools: - "bbmap": - description: "BBMap is a short read aligner, as well as various other bioinformatic tools." + description: "BBMap is a short read aligner, as well as various other bioinformatic + tools." homepage: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" documentation: "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/" licence: ["UC-LBL license (see package)"] + identifier: biotools:bbmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: file with nucleotide sequences - pattern: "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, fq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: file with nucleotide sequences + pattern: "*.{fna, fa, fasta, fa.gz, fasta.gz, fna.gz, fastq.gz, fastq, fq.gz, + fq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hits: - type: file - description: .txt file containing hits from a query seuqnce to various reference sequences output - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: .txt file containing hits from a query seuqnce to various reference + sequences output + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phanhung2" maintainers: diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 248eee0cefe8..5bfccd2bd8fa 100644 --- a/modules/nf-core/bcftools/annotate/meta.yml +++ b/modules/nf-core/bcftools/annotate/meta.yml @@ -13,49 +13,64 @@ tools: documentation: https://samtools.github.io/bcftools/bcftools.html#annotate doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Query VCF or BCF file, can be either uncompressed or compressed - - index: - type: file - description: Index of the query VCF or BCF file - - annotations: - type: file - description: Bgzip-compressed file with annotations - - annotations_index: - type: file - description: Index of the annotations file - - header_lines: - type: file - description: Contains lines to append to the output VCF header + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Query VCF or BCF file, can be either uncompressed or compressed + - index: + type: file + description: Index of the query VCF or BCF file + - annotations: + type: file + description: Bgzip-compressed file with annotations + - annotations_index: + type: file + description: Index of the annotations file + - - header_lines: + type: file + description: Contains lines to append to the output VCF header output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed annotated VCF file - pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Compressed annotated VCF file + pattern: "*{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/call/meta.yml b/modules/nf-core/bcftools/call/meta.yml index b5b46ac5833d..840a6355edf4 100644 --- a/modules/nf-core/bcftools/call/meta.yml +++ b/modules/nf-core/bcftools/call/meta.yml @@ -16,59 +16,74 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@LouisLeNezet" diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index eeeb20714eb4..b5d1f5b2cefd 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -13,44 +13,59 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbi: - type: list - description: | - List containing 2 or more index files (optional) - e.g. [ 'file1.tbi', 'file2.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbi: + type: list + description: | + List containing 2 or more index files (optional) + e.g. [ 'file1.tbi', 'file2.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF concatenated output file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF concatenated output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@nvnieuwk" diff --git a/modules/nf-core/bcftools/consensus/meta.yml b/modules/nf-core/bcftools/consensus/meta.yml index 5fd8567171fe..e9fa781517da 100644 --- a/modules/nf-core/bcftools/consensus/meta.yml +++ b/modules/nf-core/bcftools/consensus/meta.yml @@ -12,42 +12,45 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - mask: - type: file - description: BED file used for masking - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - mask: + type: file + description: BED file used for masking + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: FASTA reference consensus file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: FASTA reference consensus file + pattern: "*.{fasta,fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/convert/meta.yml b/modules/nf-core/bcftools/convert/meta.yml index 2c89112fff06..4f2a9f3fb3d9 100644 --- a/modules/nf-core/bcftools/convert/meta.yml +++ b/modules/nf-core/bcftools/convert/meta.yml @@ -7,83 +7,129 @@ keywords: - gvcf tools: - "bcftools": - description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." homepage: "https://samtools.github.io/bcftools/bcftools.html" documentation: "https://samtools.github.io/bcftools/bcftools.html#convert" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/gigascience/giab008" licence: ["GPL"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - The input format. Each format needs a seperate parameter to be specified in the `args`: - - GEN/SAMPLE file: `--gensample2vcf` - - gVCF file: `--gvcf2vcf` - - HAP/SAMPLE file: `--hapsample2vcf` - - HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf` - - TSV file: `--tsv2vcf` - pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}" - - input_index: - type: file - description: (Optional) The index for the input files, if needed - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: (Optional) The reference fasta, only needed for gVCF conversion - pattern: "*.{fa,fasta}" - - bed: - type: file - description: (Optional) The BED file containing the regions for the VCF file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + The input format. Each format needs a seperate parameter to be specified in the `args`: + - GEN/SAMPLE file: `--gensample2vcf` + - gVCF file: `--gvcf2vcf` + - HAP/SAMPLE file: `--hapsample2vcf` + - HAP/LEGEND/SAMPLE file: `--haplegendsample2vcf` + - TSV file: `--tsv2vcf` + pattern: "*.{gen,sample,g.vcf,hap,legend}{.gz,}" + - input_index: + type: file + description: (Optional) The index for the input files, if needed + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: (Optional) The reference fasta, only needed for gVCF conversion + pattern: "*.{fa,fasta}" + - - bed: + type: file + description: (Optional) The BED file containing the regions for the VCF file + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf_gz: - type: file - description: VCF merged output file (bgzipped) => when `--output-type z` is used - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF merged output file (bgzipped) => when `--output-type z` is + used + pattern: "*.vcf.gz" - vcf: - type: file - description: VCF merged output file => when `--output-type v` is used - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF merged output file => when `--output-type v` is used + pattern: "*.vcf" - bcf_gz: - type: file - description: BCF merged output file (bgzipped) => when `--output-type b` is used - pattern: "*.bcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF merged output file (bgzipped) => when `--output-type b` is + used + pattern: "*.bcf.gz" - bcf: - type: file - description: BCF merged output file => when `--output-type u` is used - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF merged output file => when `--output-type u` is used + pattern: "*.bcf" - hap: - type: file - description: hap format used by IMPUTE2 and SHAPEIT - pattern: "*.hap.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.gz": + type: file + description: hap format used by IMPUTE2 and SHAPEIT + pattern: "*.hap.gz" - legend: - type: file - description: legend format used by IMPUTE2 and SHAPEIT - pattern: "*.legend.gz" - - sample: - type: file - description: sample format used by IMPUTE2 and SHAPEIT - pattern: "*.samples" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.legend.gz": + type: file + description: legend format used by IMPUTE2 and SHAPEIT + pattern: "*.legend.gz" + - samples: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.samples": + type: file + description: samples format used by IMPUTE2 and SHAPEIT + pattern: "*.samples" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/csq/meta.yml b/modules/nf-core/bcftools/csq/meta.yml index a45d007c300a..7fb85ba020e7 100644 --- a/modules/nf-core/bcftools/csq/meta.yml +++ b/modules/nf-core/bcftools/csq/meta.yml @@ -17,63 +17,77 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#csq doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF/BCF file - pattern: "*.{vcf.gz,vcf,bcf}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - - fasta: - type: file - description: Fasta reference - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fai information - - fai: - type: file - description: Fasta index - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing gff3 information - - gff3: - type: file - description: GFF3 file - pattern: "*.{gff,gff.gz,gff3,gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: Fasta reference + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fai information + - fai: + type: file + description: Fasta index + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing gff3 information + - gff3: + type: file + description: GFF3 file + pattern: "*.{gff,gff.gz,gff3,gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF with annotation, bgzipped per default - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF with annotation, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index d67c0257a1cd..8ac594fc2225 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -12,38 +12,53 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/index/meta.yml b/modules/nf-core/bcftools/index/meta.yml index 0207d057f3fc..6897d1bd1212 100644 --- a/modules/nf-core/bcftools/index/meta.yml +++ b/modules/nf-core/bcftools/index/meta.yml @@ -8,40 +8,55 @@ keywords: - tbi tools: - bcftools: - description: BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations. + description: BCFtools is a set of utilities that manipulate variant calls in the + Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most + commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations. homepage: https://samtools.github.io/bcftools/ documentation: https://samtools.github.io/bcftools/howtos/index.html tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/gigascience/giab008" licence: ["MIT", "GPL-3.0-or-later"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file (optionally GZIPPED) - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file (optionally GZIPPED) + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - csi: - type: file - description: Default VCF file index file - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index file + pattern: "*.csi" - tbi: - type: file - description: Alternative VCF file index file for larger files (activated with -t parameter) - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index file for larger files (activated with + -t parameter) + pattern: "*.tbi" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bcftools/isec/meta.yml b/modules/nf-core/bcftools/isec/meta.yml index 7da88e19b7bb..9064a33323a5 100644 --- a/modules/nf-core/bcftools/isec/meta.yml +++ b/modules/nf-core/bcftools/isec/meta.yml @@ -15,36 +15,40 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - List containing 2 or more vcf/bcf files. These must be compressed and have an associated index. - e.g. [ 'file1.vcf.gz', 'file2.vcf' ] - - tbis: - type: list - description: | - List containing the tbi index files corresponding to the vcf/bcf input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + List containing 2 or more vcf/bcf files. These must be compressed and have an associated index. + e.g. [ 'file1.vcf.gz', 'file2.vcf' ] + - tbis: + type: list + description: | + List containing the tbi index files corresponding to the vcf/bcf input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Folder containing the set operations results perform on the vcf files - pattern: "${prefix}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '${prefix}", type: "dir': + type: directory + description: Folder containing the set operations results perform on the vcf + files + pattern: "${prefix}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/merge/meta.yml b/modules/nf-core/bcftools/merge/meta.yml index 2caf644e3a39..2cf09a1d4913 100644 --- a/modules/nf-core/bcftools/merge/meta.yml +++ b/modules/nf-core/bcftools/merge/meta.yml @@ -12,67 +12,78 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: file - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbis: - type: file - description: | - List containing the tbi index files corresponding to the vcfs input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: "(Optional) The fasta reference file (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: "(Optional) The fasta reference file index (only necessary for the `--gvcf FILE` parameter)" - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'genome' ] - - bed: - type: file - description: "(Optional) The bed regions to merge on" - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: file + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: "(Optional) The fasta reference file (only necessary for the `--gvcf + FILE` parameter)" + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: "(Optional) The fasta reference file index (only necessary for + the `--gvcf FILE` parameter)" + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: "(Optional) The bed regions to merge on" + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: merged output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf}{,.gz}": + type: file + description: merged output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: index of merged output - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: index of merged output + pattern: "*.{csi,tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/mpileup/meta.yml b/modules/nf-core/bcftools/mpileup/meta.yml index 65410ddd6618..febcb33f608e 100644 --- a/modules/nf-core/bcftools/mpileup/meta.yml +++ b/modules/nf-core/bcftools/mpileup/meta.yml @@ -12,56 +12,79 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - intervals: - type: file - description: Input intervals file. A file (commonly '.bed') containing regions to subset - - meta: - type: map - description: | - Groovy Map containing information about the genome fasta, e.g. [ id: 'sarscov2' ] - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - save_mpileup: - type: boolean - description: Save mpileup file generated by bcftools mpileup + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - intervals: + type: file + description: Input intervals file. A file (commonly '.bed') containing regions + to subset + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by bcftools mpileup output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF gzipped output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*vcf.gz": + type: file + description: VCF gzipped output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: tabix index file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*vcf.gz.tbi": + type: file + description: tabix index file + pattern: "*.{vcf.gz.tbi}" - stats: - type: file - description: Text output file containing stats - pattern: "*{stats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*stats.txt": + type: file + description: Text output file containing stats + pattern: "*{stats.txt}" - mpileup: - type: file - description: mpileup gzipped output for all positions - pattern: "{*.mpileup.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup.gz": + type: file + description: mpileup gzipped output for all positions + pattern: "{*.mpileup.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index a0cdeaf102e5..b6edeb4aae2b 100644 --- a/modules/nf-core/bcftools/norm/meta.yml +++ b/modules/nf-core/bcftools/norm/meta.yml @@ -13,54 +13,70 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf' - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: | - An optional index of the VCF file (for when the VCF is compressed) - pattern: "*.vcf.gz.tbi" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf' + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: | + An optional index of the VCF file (for when the VCF is compressed) + pattern: "*.vcf.gz.tbi" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: One of uncompressed VCF (.vcf), compressed VCF (.vcf.gz), compressed + BCF (.bcf.gz) or uncompressed BCF (.bcf) normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml index d944dae78170..8898ccd204b1 100644 --- a/modules/nf-core/bcftools/pluginimputeinfo/meta.yml +++ b/modules/nf-core/bcftools/pluginimputeinfo/meta.yml @@ -1,6 +1,6 @@ ---- name: "bcftools_pluginimputeinfo" -description: Adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. +description: Adds imputation information metrics to the INFO field based on selected + FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available. keywords: - impute-info - bcftools @@ -10,15 +10,24 @@ keywords: - vcf tools: - "bcftools": - description: "BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations." + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." homepage: "https://samtools.github.io/bcftools/howtos/index.html" documentation: "https://samtools.github.io/bcftools/bcftools.html" tool_dev_url: "https://github.com/samtools/bcftools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] args_id: "$args" + identifier: biotools:bcftools - "bcftools plugin impute-info": - description: "Bcftools plugins are tools that can be used with bcftools to manipulate variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds imputation information metrics to the INFO field based on selected FORMAT tags. Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available" + description: "Bcftools plugins are tools that can be used with bcftools to manipulate + variant calls in Variant Call Format (VCF) and BCF. The impute-info plugin adds + imputation information metrics to the INFO field based on selected FORMAT tags. + Only the IMPUTE2 INFO metric from FORMAT/GP tags is currently available" homepage: "https://samtools.github.io/bcftools/howtos/plugins.html" documentation: "https://samtools.github.io/bcftools/bcftools.html#plugin" tool_dev_url: "https://github.com/samtools/bcftools" @@ -26,55 +35,69 @@ tools: licence: ["MIT"] args_id: "$args2" + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF output file containing added INFO/INFO field - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF output file containing added INFO/INFO field + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eweizy" maintainers: diff --git a/modules/nf-core/bcftools/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 71805c0342de..5a31dacc0c4d 100644 --- a/modules/nf-core/bcftools/pluginscatter/meta.yml +++ b/modules/nf-core/bcftools/pluginscatter/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginscatter" description: Split VCF by chunks or regions, creating multiple VCFs. @@ -15,65 +14,81 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The input VCF to scatter - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - tbi: - type: file - description: Optional index of the input VCF - pattern: "*.tbi" - - sites_per_chunk: - type: integer - description: | - How many variants should be in each output file - Either this or `scatter` or `scatter_file` have to be given - - scatter: - type: string - description: | - A comma delimited list of regions to scatter into - Either this or `sites_per_chunk` or `scatter_file` have to be given - - scatter_file: - type: file - description: | - A file containing a region on each line with an optional second column containing the filename - Either this or `sites_per_chunk` or `scatter` have to be given - - regions: - type: file - description: Optional file containing the regions to work on - pattern: "*.bed" - - targets: - type: file - description: Optional file containing the regions to work on (but streams instead of index-jumping) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The input VCF to scatter + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: Optional index of the input VCF + pattern: "*.tbi" + - - sites_per_chunk: + type: integer + description: | + How many variants should be in each output file + Either this or `scatter` or `scatter_file` have to be given + - - scatter: + type: string + description: | + A comma delimited list of regions to scatter into + Either this or `sites_per_chunk` or `scatter_file` have to be given + - - scatter_file: + type: file + description: | + A file containing a region on each line with an optional second column containing the filename + Either this or `sites_per_chunk` or `scatter` have to be given + - - regions: + type: file + description: Optional file containing the regions to work on + pattern: "*.bed" + - - targets: + type: file + description: Optional file containing the regions to work on (but streams instead + of index-jumping) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scatter: - type: file - description: The resulting files of the scattering - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting files of the scattering + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/pluginsplit/meta.yml b/modules/nf-core/bcftools/pluginsplit/meta.yml index 64bfce0a89d9..41f766584fb6 100644 --- a/modules/nf-core/bcftools/pluginsplit/meta.yml +++ b/modules/nf-core/bcftools/pluginsplit/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "bcftools_pluginsplit" description: Split VCF by sample, creating single- or multi-sample VCFs. @@ -14,60 +13,83 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF file to split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + type: file + description: OPTIONAL - The index of the input VCF/BCF + pattern: "*.tbi" + - - samples: + type: file + description: | + A tab-separated file determining which samples should be in which output file + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file + Either this or a groups file should be given + pattern: "*" + - - groups: + type: file + description: | + A tab-separated file determining which samples should be in which output file(s) + column 1: The sample name(s) in the input file + column 2: The sample name(s) to use in the output file (use `-` to keep the original name) + column 3: The name of the output file(s) + Either this or a samples file should be given + pattern: "*" + - - regions: + type: file + description: A BED file containing regions to use + pattern: "*.bed" + - - targets: + type: file + description: A BED file containing regions to use (but streams rather than index-jumps) + pattern: "*.bed" +output: - vcf: - type: file - description: The VCF file to split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: The resulting VCF files from the split + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: OPTIONAL - The index of the input VCF/BCF - pattern: "*.tbi" - - samples: - type: file - description: | - A tab-separated file determining which samples should be in which output file - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file - Either this or a groups file should be given - pattern: "*" - - groups: - type: file - description: | - A tab-separated file determining which samples should be in which output file(s) - column 1: The sample name(s) in the input file - column 2: The sample name(s) to use in the output file (use `-` to keep the original name) - column 3: The name of the output file(s) - Either this or a samples file should be given - pattern: "*" - - regions: - type: file - description: A BED file containing regions to use - pattern: "*.bed" - - targets: - type: file - description: A BED file containing regions to use (but streams rather than index-jumps) - pattern: "*.bed" -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: TBI file + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf: - type: file - description: The resulting VCF files from the split - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bcftools/plugintag2tag/meta.yml b/modules/nf-core/bcftools/plugintag2tag/meta.yml index 5cbc772ce597..ad67d0cbdda7 100644 --- a/modules/nf-core/bcftools/plugintag2tag/meta.yml +++ b/modules/nf-core/bcftools/plugintag2tag/meta.yml @@ -1,6 +1,6 @@ ---- name: "bcftools_plugintag2tag" -description: Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized alleles, eg LPL,LAD. +description: Converts between similar tags, such as GL,PL,GP or QR,QA,QS or localized + alleles, eg LPL,LAD. keywords: - tag2tag - bcftools @@ -13,55 +13,69 @@ tools: documentation: https://samtools.github.io/bcftools/howtos/plugin.tag2tag.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eweizy" maintainers: diff --git a/modules/nf-core/bcftools/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml index 303ef61024cf..279b3205d6fb 100644 --- a/modules/nf-core/bcftools/query/meta.yml +++ b/modules/nf-core/bcftools/query/meta.yml @@ -1,5 +1,6 @@ name: bcftools_query -description: Extracts fields from VCF or BCF files and outputs them in user-defined format. +description: Extracts fields from VCF or BCF files and outputs them in user-defined + format. keywords: - query - variant calling @@ -13,48 +14,51 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be qeuried. - pattern: "*.{vcf.gz, vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be qeuried. + pattern: "*.{vcf.gz, vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. + pattern: "*.tbi" + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: BCFTools query output file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: BCFTools query output file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@drpatelh" diff --git a/modules/nf-core/bcftools/reheader/meta.yml b/modules/nf-core/bcftools/reheader/meta.yml index d903cc0f1365..47e5344cd5b5 100644 --- a/modules/nf-core/bcftools/reheader/meta.yml +++ b/modules/nf-core/bcftools/reheader/meta.yml @@ -12,51 +12,60 @@ tools: documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF/BCF file - pattern: "*.{vcf.gz,vcf,bcf}" - - header: - type: file - description: New header to add to the VCF - pattern: "*.{header.txt}" - - samples: - type: file - description: File containing sample names to update (one sample per line) - pattern: "*.{samples.txt}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Fasta index to update header sequences with - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF/BCF file + pattern: "*.{vcf.gz,vcf,bcf}" + - header: + type: file + description: New header to add to the VCF + pattern: "*.{header.txt}" + - samples: + type: file + description: File containing sample names to update (one sample per line) + pattern: "*.{samples.txt}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Fasta index to update header sequences with + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF with updated header, bgzipped per default - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF with updated header, bgzipped per default + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - index: - type: file - description: Index of VCF with updated header - pattern: "*.{csi,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: Index of VCF with updated header + pattern: "*.{csi,tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" - "@jemten" diff --git a/modules/nf-core/bcftools/roh/meta.yml b/modules/nf-core/bcftools/roh/meta.yml index ee928a8fa5e9..032148fa4af9 100644 --- a/modules/nf-core/bcftools/roh/meta.yml +++ b/modules/nf-core/bcftools/roh/meta.yml @@ -1,5 +1,6 @@ name: "bcftools_roh" -description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered. +description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites + are considered. keywords: - roh - biallelic @@ -7,53 +8,65 @@ keywords: - autozygosity tools: - "roh": - description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered." + description: "A program for detecting runs of homo/autozygosity. Only bi-allelic + sites are considered." homepage: https://www.htslib.org/ documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,.vcf.gz}" - - af_file: - type: file - description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." - - af_file_tbi: - type: file - description: "tbi index of af_file." - - genetic_map: - type: file - description: "Genetic map in the format required also by IMPUTE2." - - regions_file: - type: file - description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." - - samples_file: - type: file - description: "File of sample names to include or exclude if prefixed with '^'." - - targets_file: - type: file - description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,.vcf.gz}" + - tbi: + type: file + description: TBI file + patthern: "*.tbi" + - - af_file: + type: file + description: "Read allele frequencies from a tab-delimited file containing the + columns: CHROM\tPOS\tREF,ALT\tAF." + - af_file_tbi: + type: file + description: "tbi index of af_file." + - - genetic_map: + type: file + description: "Genetic map in the format required also by IMPUTE2." + - - regions_file: + type: file + description: "Regions can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." + - - samples_file: + type: file + description: "File of sample names to include or exclude if prefixed with '^'." + - - targets_file: + type: file + description: "Targets can be specified either on command line or in a VCF, BED, + or tab-delimited file (the default)." output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - roh: - type: file - description: Contains site-specific and/or per-region runs of homo/autozygosity calls. - pattern: "*.{roh}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roh": + type: file + description: Contains site-specific and/or per-region runs of homo/autozygosity + calls. + pattern: "*.{roh}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bcftools/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index dfbddcbac52c..f7a6eff17d94 100644 --- a/modules/nf-core/bcftools/sort/meta.yml +++ b/modules/nf-core/bcftools/sort/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file to be sorted - pattern: "*.{vcf.gz,vcf,bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file to be sorted + pattern: "*.{vcf.gz,vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: Sorted VCF file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Gwennid" maintainers: diff --git a/modules/nf-core/bcftools/split/meta.yml b/modules/nf-core/bcftools/split/meta.yml index 578b850f6349..4526696edbac 100644 --- a/modules/nf-core/bcftools/split/meta.yml +++ b/modules/nf-core/bcftools/split/meta.yml @@ -12,34 +12,37 @@ tools: tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed vcf file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Compressed vcf file index - pattern: "*.{tbi,csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed vcf file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Compressed vcf file index + pattern: "*.{tbi,csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - split_vcf: - type: file - description: Compressed vcf files per chromosome - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed vcf files per chromosome + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" - "@atrigila" diff --git a/modules/nf-core/bcftools/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index 7ea2103e3bd1..655a61c5f4fc 100644 --- a/modules/nf-core/bcftools/stats/meta.yml +++ b/modules/nf-core/bcftools/stats/meta.yml @@ -13,58 +13,86 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" - - tbi: - type: file - description: | - The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. - pattern: "*.tbi" - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' - - exons: - type: file - description: | - Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). - e.g. 'exons.tsv.gz' - - fasta: - type: file - description: | - Faidx indexed reference sequence file to determine INDEL context. - e.g. 'reference.fa' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" + - tbi: + type: file + description: | + The tab index for the VCF file to be inspected. Optional: only required when parameter regions is chosen. + pattern: "*.tbi" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. (VCF, BED or tab-delimited) + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon tbi index files) + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exons: + type: file + description: | + Tab-delimited file with exons for indel frameshifts (chr,beg,end; 1-based, inclusive, optionally bgzip compressed). + e.g. 'exons.tsv.gz' + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Faidx indexed reference sequence file to determine INDEL context. + e.g. 'reference.fa' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: Text output file containing stats - pattern: "*_{stats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*stats.txt": + type: file + description: Text output file containing stats + pattern: "*_{stats.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bcftools/view/meta.yml b/modules/nf-core/bcftools/view/meta.yml index 5eb1b196c0b9..aa7785f12225 100644 --- a/modules/nf-core/bcftools/view/meta.yml +++ b/modules/nf-core/bcftools/view/meta.yml @@ -1,5 +1,6 @@ name: bcftools_view -description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF +description: View, subset and filter VCF or BCF files by position and filtering expression. + Convert between VCF and BCF keywords: - variant calling - view @@ -13,59 +14,74 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:bcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF normalized output file + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/bcl2fastq/meta.yml b/modules/nf-core/bcl2fastq/meta.yml index a8c8efd85f7b..a30a33efce05 100644 --- a/modules/nf-core/bcl2fastq/meta.yml +++ b/modules/nf-core/bcl2fastq/meta.yml @@ -10,54 +10,91 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software" documentation: "https://support.illumina.com/content/dam/illumina-support/documents/documentation/software_documentation/bcl2fastq/bcl2fastq2-v2-20-software-guide-15051736-03.pdf" licence: ["ILLUMINA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - samplesheet: - type: file - description: "Input samplesheet" - pattern: "*.{csv}" - - run_dir: - type: file - description: | - Input run directory containing RunInfo.xml and BCL data - Could be a directory or a tar of the directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samplesheet: + type: file + description: "Input samplesheet" + pattern: "*.{csv}" + - run_dir: + type: file + description: | + Input run directory containing RunInfo.xml and BCL data + Could be a directory or a tar of the directory output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "**_S*_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" + - output/**_S[1-9]*_R?_00?.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" - fastq_idx: - type: file - description: Optional demultiplexed index FASTQ files - pattern: "**_S*_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" + - output/**_S[1-9]*_I?_00?.fastq.gz: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - output/**Undetermined_S0*_R?_00?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" - undetermined_idx: - type: file - description: Optional undetermined index FASTQ files - pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - output/**Undetermined_S0*_I?_00?.fastq.gz: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" - reports: - type: file - description: Demultiplexing Reports - pattern: "Reports/*" + - meta: + type: file + description: Demultiplexing Reports + pattern: "Reports/*" + - output/Reports: + type: file + description: Demultiplexing Reports + pattern: "Reports/*" - stats: - type: file - description: Statistics files - pattern: "Stats/*" + - meta: + type: file + description: Statistics files + pattern: "Stats/*" + - output/Stats: + type: file + description: Statistics files + pattern: "Stats/*" - interop: - type: file - description: Interop files - pattern: "*.{bin}" + - meta: + type: file + description: Interop files + pattern: "*.{bin}" + - InterOp/*.bin: + type: file + description: Interop files + pattern: "*.{bin}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/bclconvert/meta.yml b/modules/nf-core/bclconvert/meta.yml index c4acdb51c9a7..8687d7f62e54 100644 --- a/modules/nf-core/bclconvert/meta.yml +++ b/modules/nf-core/bclconvert/meta.yml @@ -10,54 +10,91 @@ tools: homepage: "https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html" documentation: "https://support-docs.illumina.com/SW/BCL_Convert/Content/SW/FrontPages/BCL_Convert.htm" licence: ["ILLUMINA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - samplesheet: - type: file - description: "Input samplesheet" - pattern: "*.{csv}" - - run_dir: - type: file - description: | - Input run directory containing RunInfo.xml and BCL data - Could be a directory or a tar of the directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - samplesheet: + type: file + description: "Input samplesheet" + pattern: "*.{csv}" + - run_dir: + type: file + description: | + Input run directory containing RunInfo.xml and BCL data + Could be a directory or a tar of the directory output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "**_S*_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" + - output/**_S[1-9]*_R?_00?.fastq.gz: + type: file + description: Demultiplexed sample FASTQ files + pattern: "**_S*_L00?_R?_00?.fastq.gz" - fastq_idx: - type: file - description: Optional demultiplexed index FASTQ files - pattern: "**_S*_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" + - output/**_S[1-9]*_I?_00?.fastq.gz: + type: file + description: Optional demultiplexed index FASTQ files + pattern: "**_S*_L00?_I?_00?.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" + - output/**Undetermined_S0*_R?_00?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_S0_L00?_R?_00?.fastq.gz" - undetermined_idx: - type: file - description: Optional undetermined index FASTQ files - pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - meta: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" + - output/**Undetermined_S0*_I?_00?.fastq.gz: + type: file + description: Optional undetermined index FASTQ files + pattern: "Undetermined_S0_L00?_I?_00?.fastq.gz" - reports: - type: file - description: Demultiplexing Reports - pattern: "Reports/*.{csv,xml}" + - meta: + type: file + description: Demultiplexing Reports + pattern: "Reports/*.{csv,xml}" + - output/Reports: + type: file + description: Demultiplexing Reports + pattern: "Reports/*.{csv,xml}" - logs: - type: file - description: Log files - pattern: "Logs/*.{log,txt}" + - meta: + type: file + description: Log files + pattern: "Logs/*.{log,txt}" + - output/Logs: + type: file + description: Log files + pattern: "Logs/*.{log,txt}" - interop: - type: file - description: Interop files - pattern: "*.{bin}" + - meta: + type: file + description: Interop files + pattern: "*.{bin}" + - '**/InterOp/*.bin", includeInputs: true': + type: file + description: Interop files + pattern: "*.{bin}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/beagle5/beagle/meta.yml b/modules/nf-core/beagle5/beagle/meta.yml index 51b9c6b69974..56793d1e7079 100644 --- a/modules/nf-core/beagle5/beagle/meta.yml +++ b/modules/nf-core/beagle5/beagle/meta.yml @@ -1,60 +1,74 @@ name: "beagle5_beagle" -description: Beagle v5.2 is a software package for phasing genotypes and for imputing ungenotyped markers. +description: Beagle v5.2 is a software package for phasing genotypes and for imputing + ungenotyped markers. keywords: - phasing - imputation - genotype tools: - "beagle5": - description: "Beagle is a software package for phasing genotypes and for imputing ungenotyped markers." + description: "Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers." homepage: "https://faculty.washington.edu/browning/beagle/b5_2.html" documentation: "https://faculty.washington.edu/browning/beagle/beagle_5.2_13Oct21.pdf" doi: "10.1016/j.ajhg.2021.08.005; doi:10.1016/j.ajhg.2018.07.015" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: target VCF input file to be imputed and or phased - pattern: "*.{vcf,vcf.gz}" - - ref: - type: file - description: reference panel in bref3 or VCF format - pattern: "*.{vcf,vcf.gz,bref3}" - - genmap: - type: file - description: a PLINK format genetic map with cM units - pattern: "*.{map,map.gz,map.zip}" - - exclsamples: - type: file - description: text file containing samples one sample per line to be excluded from the analysis - pattern: "*.*" - - exclmarkers: - type: file - description: text file containing markers one marker per line to be excluded from the analysis - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: target VCF input file to be imputed and or phased + pattern: "*.{vcf,vcf.gz}" + - - refpanel: + type: file + description: target reference panel + - - genmap: + type: file + description: a PLINK format genetic map with cM units + pattern: "*.{map,map.gz,map.zip}" + - - exclsamples: + type: file + description: text file containing samples one sample per line to be excluded + from the analysis + pattern: "*.*" + - - exclmarkers: + type: file + description: text file containing markers one marker per line to be excluded + from the analysis + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: bgzip compressed VCF file that contains phased non missing genotypes for all non reference samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: bgzip compressed VCF file that contains phased non missing genotypes + for all non reference samples + pattern: "*.vcf.gz" - log: - type: file - description: a summary of the analysis that includes the Beagle version, the command line arguments, and compute time. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: a summary of the analysis that includes the Beagle version, the + command line arguments, and compute time. + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" maintainers: diff --git a/modules/nf-core/bedgovcf/meta.yml b/modules/nf-core/bedgovcf/meta.yml index 406935eba504..6acbd65c14a9 100644 --- a/modules/nf-core/bedgovcf/meta.yml +++ b/modules/nf-core/bedgovcf/meta.yml @@ -1,4 +1,3 @@ ---- name: "bedgovcf" description: Convert a BED file to a VCF file according to a YAML config keywords: @@ -13,45 +12,46 @@ tools: documentation: "https://github.com/nvnieuwk/bedgovcf" tool_dev_url: "https://github.com/nvnieuwk/bedgovcf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: The BED file to convert to VCF - pattern: "*.bed" - - config: - type: file - description: The config file to use for the conversion - pattern: "*.{yml,yaml}" - - meta2: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The fasta index file - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: The BED file to convert to VCF + pattern: "*.bed" + - config: + type: file + description: The config file to use for the conversion + pattern: "*.{yml,yaml}" + - - meta2: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The fasta index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The converted VCF file - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The converted VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" diff --git a/modules/nf-core/bedops/convert2bed/meta.yml b/modules/nf-core/bedops/convert2bed/meta.yml index eea919650740..6d84c0316011 100644 --- a/modules/nf-core/bedops/convert2bed/meta.yml +++ b/modules/nf-core/bedops/convert2bed/meta.yml @@ -12,36 +12,33 @@ tools: tool_dev_url: "https://github.com/bedops" doi: "10.1093/bioinformatics/bts277" licence: ["GNU v2"] + identifier: biotools:bedops input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sorted BAM/GFF/GTF/GVF/PSL file - pattern: "*.{bam,gff,gtf,gvf,psl}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - in_file: + type: file + description: Input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bed: - type: file - description: Sorted BED file - pattern: "*.{bed}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bed": + type: file + description: Sorted BED file + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/bedops/gtf2bed/meta.yml b/modules/nf-core/bedops/gtf2bed/meta.yml index 2646b74a2f85..5fe3ad8bc4cf 100644 --- a/modules/nf-core/bedops/gtf2bed/meta.yml +++ b/modules/nf-core/bedops/gtf2bed/meta.yml @@ -6,33 +6,40 @@ keywords: - conversion tools: - gtf2bed: - description: The gtf2bed script converts 1-based, closed [start, end] Gene Transfer Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted data. + description: The gtf2bed script converts 1-based, closed [start, end] Gene Transfer + Format v2.2 (GTF2.2) to sorted, 0-based, half-open [start-1, end) extended BED-formatted + data. homepage: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html documentation: https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html tool_dev_url: https://github.com/bedops/bedops doi: 10.1093/bioinformatics/bts277 licence: ["GPL v2"] + identifier: biotools:bedops input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - gtf: - type: file - description: A reference file in GTF format - pattern: "*.{gtf,gtf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: A reference file in GTF format + pattern: "*.{gtf,gtf.gz}" output: - bed: - type: file - description: A reference file in BED format - pattern: "*.{bed}" + - meta: + type: file + description: A reference file in BED format + pattern: "*.{bed}" + - "*.bed": + type: file + description: A reference file in BED format + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidecarlson" diff --git a/modules/nf-core/bedtools/bamtobed/meta.yml b/modules/nf-core/bedtools/bamtobed/meta.yml index b6d149296df3..201718855d94 100644 --- a/modules/nf-core/bedtools/bamtobed/meta.yml +++ b/modules/nf-core/bedtools/bamtobed/meta.yml @@ -12,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing genomic intervals. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing genomic intervals. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/closest/meta.yml b/modules/nf-core/bedtools/closest/meta.yml index 4a9b390b1531..8b8998991605 100644 --- a/modules/nf-core/bedtools/closest/meta.yml +++ b/modules/nf-core/bedtools/closest/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_closest" -description: For each feature in A, finds the closest feature (upstream or downstream) in B. +description: For each feature in A, finds the closest feature (upstream or downstream) + in B. keywords: - bedtools - closest @@ -12,38 +13,42 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/closest.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_1: - type: file - description: The file to find the closest features of - pattern: "*.{bed,vcf,gff}(.gz)?" - - input_2: - type: list - description: The input file(s) to find the closest features from - pattern: "*.{bed,vcf,gff}(.gz)?" - - fasta_fai: - type: file - description: The index of the FASTA reference. Needed when the argument `--sorted` is used - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_1: + type: file + description: The file to find the closest features of + pattern: "*.{bed,vcf,gff}(.gz)?" + - input_2: + type: list + description: The input file(s) to find the closest features from + pattern: "*.{bed,vcf,gff}(.gz)?" + - - fasta_fai: + type: file + description: The index of the FASTA reference. Needed when the argument `--sorted` + is used + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: The resulting BED file containing the closest features - pattern: "*.{bed,vcf,gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: The resulting BED file containing the closest features + pattern: "*.{bed,vcf,gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/complement/meta.yml b/modules/nf-core/bedtools/complement/meta.yml index ee84bd79a417..b74cb95d74e8 100644 --- a/modules/nf-core/bedtools/complement/meta.yml +++ b/modules/nf-core/bedtools/complement/meta.yml @@ -1,5 +1,6 @@ name: bedtools_complement -description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. +description: Returns all intervals in a genome that are not covered by at least one + interval in the input BED/GFF/VCF file. keywords: - bed - gff @@ -13,34 +14,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - sizes: - type: file - description: File which defines the chromosome lengths for a given genome - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - sizes: + type: file + description: File which defines the chromosome lengths for a given genome + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file with all genomic intervals that are not covered by at least one record from the input file. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file with all genomic intervals that are not covered by at + least one record from the input file. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/coverage/meta.yml b/modules/nf-core/bedtools/coverage/meta.yml index 7c5648566a48..ea4d0ef4b5e9 100644 --- a/modules/nf-core/bedtools/coverage/meta.yml +++ b/modules/nf-core/bedtools/coverage/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_coverage" -description: computes both the depth and breadth of coverage of features in file B on the features in file A +description: computes both the depth and breadth of coverage of features in file B + on the features in file A keywords: - bedtools - coverage @@ -16,41 +17,44 @@ tools: tool_dev_url: "https://github.com/arq5x/bedtools2" doi: "10.1093/bioinformatics/btq033" licence: ["GPL v2", "MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_A: - type: file - description: BAM/BED/GFF/VCF file - pattern: "*.{bam,bed,gff,vcf}" - - input_B: - type: file - description: One or more BAM/BED/GFF/VCF file - pattern: "*.{bam,bed,gff,vcf}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order - in the input files for use with the -sorted option. - When `genome_file` is provided, `-sorted` option is added to the command. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_A: + type: file + description: BAM/BED/GFF/VCF file + pattern: "*.{bam,bed,gff,vcf}" + - input_B: + type: file + description: One or more BAM/BED/GFF/VCF file + pattern: "*.{bam,bed,gff,vcf}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order + in the input files for use with the -sorted option. + When `genome_file` is provided, `-sorted` option is added to the command. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing coverage of sequence alignments - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing coverage of sequence alignments + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/bedtools/genomecov/meta.yml b/modules/nf-core/bedtools/genomecov/meta.yml index 2b2385e3ea8a..41b1f8f491af 100644 --- a/modules/nf-core/bedtools/genomecov/meta.yml +++ b/modules/nf-core/bedtools/genomecov/meta.yml @@ -1,5 +1,6 @@ name: bedtools_genomecov -description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. +description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) + summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - bed - bam @@ -12,39 +13,50 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - scale: - type: integer - description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: integer + description: Number containing the scale factor for the output. Set to 1 to + disable. Setting to a value other than 1 will also get the -bg bedgraph output + format as this is required for this command switch + - - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and + chromosome sizes in the second column + - - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", + ".tab", etc.) It is set arbitrarily by the user and corresponds to the file + format which depends on arguments. + - - sort: + type: boolean + description: Sort the output output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genomecov: - type: file - description: Computed genome coverage file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Computed genome coverage file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/getfasta/meta.yml b/modules/nf-core/bedtools/getfasta/meta.yml index 41917fe3ffbc..bb38fa2591d9 100644 --- a/modules/nf-core/bedtools/getfasta/meta.yml +++ b/modules/nf-core/bedtools/getfasta/meta.yml @@ -1,5 +1,6 @@ name: bedtools_getfasta -description: extract sequences in a FASTA file based on intervals defined in a feature file. +description: extract sequences in a FASTA file based on intervals defined in a feature + file. keywords: - bed - fasta @@ -10,34 +11,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output fasta file with extracted sequences - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Output fasta file with extracted sequences + pattern: "*.{fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/groupby/meta.yml b/modules/nf-core/bedtools/groupby/meta.yml index bcbc561a0940..3be92b0778f7 100644 --- a/modules/nf-core/bedtools/groupby/meta.yml +++ b/modules/nf-core/bedtools/groupby/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: bedtools_groupby -description: Groups features in a BED file by given column(s) and computes summary statistics for each group to another column. +description: Groups features in a BED file by given column(s) and computes summary + statistics for each group to another column. keywords: - bed - groupby @@ -14,33 +14,36 @@ tools: homepage: https://bedtools.readthedocs.io/en/latest/ doi: 10.1093/bioinformatics/btq033 licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - summary_column: - type: integer - description: Column to be summarized (1-based) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - summary_col: + type: string + description: Column to summarize output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - bed: - type: file - description: Grouped by bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: Grouped by bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mashehu" maintainers: diff --git a/modules/nf-core/bedtools/intersect/meta.yml b/modules/nf-core/bedtools/intersect/meta.yml index 0939cb54a09b..45ecf377a1a5 100644 --- a/modules/nf-core/bedtools/intersect/meta.yml +++ b/modules/nf-core/bedtools/intersect/meta.yml @@ -10,43 +10,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - intervals2: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - intervals2: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - intersect: - type: file - description: File containing the description of overlaps found between the two features - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: File containing the description of overlaps found between the two + features + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/jaccard/meta.yml b/modules/nf-core/bedtools/jaccard/meta.yml index 2b5422841ffd..3ae68e58a964 100644 --- a/modules/nf-core/bedtools/jaccard/meta.yml +++ b/modules/nf-core/bedtools/jaccard/meta.yml @@ -14,43 +14,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_a: - type: file - description: VCF,GFF or BED file to use with the `-a` option - pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" - - input_b: - type: file - description: VCF,GFF or BED file to use with the `-b` option - pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" - - meta2: - type: map - description: | - Groovy Map containing genome file information - e.g. [ id:'test', single_end:false ] - - genome_file: - type: file - description: A file containing all the contigs of the genome used to create the input files - pattern: "*.{txt,sizes,fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_a: + type: file + description: VCF,GFF or BED file to use with the `-a` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - input_b: + type: file + description: VCF,GFF or BED file to use with the `-b` option + pattern: "*.{vcf,vcf.gz,bed,bed.gz,gff}" + - - meta2: + type: map + description: | + Groovy Map containing genome file information + e.g. [ id:'test', single_end:false ] + - genome_file: + type: file + description: A file containing all the contigs of the genome used to create + the input files + pattern: "*.{txt,sizes,fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file containing the results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing the results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/makewindows/meta.yml b/modules/nf-core/bedtools/makewindows/meta.yml index f89d71753df2..df047f663155 100644 --- a/modules/nf-core/bedtools/makewindows/meta.yml +++ b/modules/nf-core/bedtools/makewindows/meta.yml @@ -7,35 +7,39 @@ keywords: - chunking tools: - bedtools: - description: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + description: A set of tools for genomic analysis tasks, specifically enabling + genome arithmetic (merge, count, complement) on various file types. homepage: https://bedtools.readthedocs.io documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html doi: "10.1093/bioinformatics/btq033" licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - regions: - type: file - description: BED file OR Genome details file () - pattern: "*.{bed,tab,fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: BED file OR Genome details file () + pattern: "*.{bed,tab,fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file containing the windows - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file containing the windows + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" - "@nvnieuwk" diff --git a/modules/nf-core/bedtools/map/meta.yml b/modules/nf-core/bedtools/map/meta.yml index 0267f6ffecd5..4e56bb94cf11 100644 --- a/modules/nf-core/bedtools/map/meta.yml +++ b/modules/nf-core/bedtools/map/meta.yml @@ -12,43 +12,47 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/map.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - intervals2: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - intervals2: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mapped: - type: file - description: File containing the description of overlaps found between the features in A and the features in B, with statistics - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: File containing the description of overlaps found between the features + in A and the features in B, with statistics + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bedtools/maskfasta/meta.yml b/modules/nf-core/bedtools/maskfasta/meta.yml index 94f81aba7f42..2d976645fcd2 100644 --- a/modules/nf-core/bedtools/maskfasta/meta.yml +++ b/modules/nf-core/bedtools/maskfasta/meta.yml @@ -1,5 +1,6 @@ name: bedtools_maskfasta -description: masks sequences in a FASTA file based on intervals defined in a feature file. +description: masks sequences in a FASTA file based on intervals defined in a feature + file. keywords: - bed - fasta @@ -10,34 +11,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output masked fasta file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Output masked fasta file + pattern: "*.{fa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index d7463e3dbc00..6da542052b0d 100644 --- a/modules/nf-core/bedtools/merge/meta.yml +++ b/modules/nf-core/bedtools/merge/meta.yml @@ -1,5 +1,6 @@ name: bedtools_merge -description: combines overlapping or “book-ended” features in an interval file into a single feature which spans all of the combined features. +description: combines overlapping or “book-ended” features in an interval file into + a single feature which spans all of the combined features. keywords: - bed - merge @@ -11,30 +12,33 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/merge.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Overlapped bed file with combined features - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/multiinter/meta.yml b/modules/nf-core/bedtools/multiinter/meta.yml index e9a69cf3bab9..23d052da7922 100644 --- a/modules/nf-core/bedtools/multiinter/meta.yml +++ b/modules/nf-core/bedtools/multiinter/meta.yml @@ -1,5 +1,6 @@ name: "bedtools_multiinter" -description: Identifies common intervals among multiple (and subsets thereof) sorted BED/GFF/VCF files. +description: Identifies common intervals among multiple (and subsets thereof) sorted + BED/GFF/VCF files. keywords: - bedtools - multinterval @@ -12,34 +13,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/multiinter.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - beds: - type: list - description: List of files to be merged - pattern: "*.{bed,vcf,gff}" - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - beds: + type: list + description: List of files to be merged + pattern: "*.{bed,vcf,gff}" + - - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Common interval bed - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Common interval bed + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/bedtools/shift/meta.yml b/modules/nf-core/bedtools/shift/meta.yml index 57c8994ae80c..cf0719e898bd 100644 --- a/modules/nf-core/bedtools/shift/meta.yml +++ b/modules/nf-core/bedtools/shift/meta.yml @@ -14,34 +14,42 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt,.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt,.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Shift BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Shift BED file + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bedtools/slop/meta.yml b/modules/nf-core/bedtools/slop/meta.yml index 69116715bd83..762db534a5a5 100644 --- a/modules/nf-core/bedtools/slop/meta.yml +++ b/modules/nf-core/bedtools/slop/meta.yml @@ -1,5 +1,6 @@ name: bedtools_slop -description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) +description: Adds a specified number of bases in each direction (unique values may + be specified for either -l or -r) keywords: - bed - slopBed @@ -10,30 +11,36 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Slopped BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Slopped BED file + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/sort/meta.yml b/modules/nf-core/bedtools/sort/meta.yml index 7c915f5f9e83..313698f16041 100644 --- a/modules/nf-core/bedtools/sort/meta.yml +++ b/modules/nf-core/bedtools/sort/meta.yml @@ -11,35 +11,38 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BED/BEDGRAPH - pattern: "*.{bed|bedGraph}" - - genome_file: - type: file - description: | - Optional reference genome 2 column file that defines the expected chromosome order. - pattern: "*.{fai,txt,chromsizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" + - - genome_file: + type: file + description: | + Optional reference genome 2 column file that defines the expected chromosome order. + pattern: "*.{fai,txt,chromsizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: Sorted output file - pattern: "*.${extension}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Sorted output file + pattern: "*.${extension}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@sruthipsuresh" diff --git a/modules/nf-core/bedtools/split/meta.yml b/modules/nf-core/bedtools/split/meta.yml index 725bb9a20073..7e126d22e6ba 100644 --- a/modules/nf-core/bedtools/split/meta.yml +++ b/modules/nf-core/bedtools/split/meta.yml @@ -9,30 +9,36 @@ tools: description: "A powerful toolset for genome arithmetic" documentation: "https://bedtools.readthedocs.io/en/latest/content/tools/sort.html" licence: ["MIT", "GPL v2"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file + pattern: "*.bed" + - count: + type: integer + description: Number of lines per split file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - beds: - type: list - description: list of split BED files - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: list + description: list of split BED files + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/bedtools/subtract/meta.yml b/modules/nf-core/bedtools/subtract/meta.yml index 0226ff188467..ddf7d92db2d8 100644 --- a/modules/nf-core/bedtools/subtract/meta.yml +++ b/modules/nf-core/bedtools/subtract/meta.yml @@ -1,5 +1,6 @@ name: bedtools_subtract -description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. +description: Finds overlaps between two sets of regions (A and B), removes the overlaps + from A and reports the remaining portion of A. keywords: - bed - gff @@ -11,34 +12,37 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals1: - type: file - description: BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" - - intervals2: - type: file - description: BED/GFF/VCF - pattern: "*.{bed|gff|vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals1: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" + - intervals2: + type: file + description: BED/GFF/VCF + pattern: "*.{bed|gff|vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing the difference between the two sets of features - patters: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing the difference between the two sets of features + patters: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" maintainers: diff --git a/modules/nf-core/bedtools/unionbedg/meta.yml b/modules/nf-core/bedtools/unionbedg/meta.yml index ee73e8b51590..9fefd9203116 100644 --- a/modules/nf-core/bedtools/unionbedg/meta.yml +++ b/modules/nf-core/bedtools/unionbedg/meta.yml @@ -12,40 +12,43 @@ tools: A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html licence: ["MIT"] + identifier: biotools:bedtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: | - Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative - pattern: "*.{bedGraph,bedgraph}" - - meta2: - type: map - description: | - Groovy Map containing meta information for the reference chromosome sizes - e.g. [ id:'test' ] - - chrom_sizes: - type: file - description: Chromosome sizes file - pattern: "*{.sizes,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + Input BedGraph file: four column BED format, with 4th column with numerical values: integer or real, positive or negative + pattern: "*.{bedGraph,bedgraph}" + - - meta2: + type: map + description: | + Groovy Map containing meta information for the reference chromosome sizes + e.g. [ id:'test' ] + - chrom_sizes: + type: file + description: Chromosome sizes file + pattern: "*{.sizes,.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Combined BED file with values from all bedGraph files - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Combined BED file with values from all bedGraph files + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ekushele" maintainers: diff --git a/modules/nf-core/bioawk/meta.yml b/modules/nf-core/bioawk/meta.yml index 7af015821957..c691ac0c2a49 100644 --- a/modules/nf-core/bioawk/meta.yml +++ b/modules/nf-core/bioawk/meta.yml @@ -1,5 +1,6 @@ name: "bioawk" -description: Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats. +description: Bioawk is an extension to Brian Kernighan's awk, adding the support of + several common biological data formats. keywords: - bioawk - fastq @@ -14,32 +15,36 @@ tools: documentation: "https://github.com/lh3/bioawk" tool_dev_url: "https://github.com/lh3/bioawk" licence: ["Free software license (https://github.com/lh3/bioawk/blob/master/README.awk#L1)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input sequence biological sequence file (optionally gzipped) to be manipulated via program specified in `$args`. - pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input sequence biological sequence file (optionally gzipped) to + be manipulated via program specified in `$args`. + pattern: "*.{bed,gff,sam,vcf,fastq,fasta,tab,bed.gz,gff.gz,sam.gz,vcf.gz,fastq.gz,fasta.gz,tab.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: | - Manipulated and gzipped version of input sequence file following program specified in `args`. - File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: | + Manipulated and gzipped version of input sequence file following program specified in `args`. + File name will be what is specified in `$prefix`. Do not include `.gz` suffix in `$prefix`! Output files` will be gzipped for you! + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/biobambam/bammarkduplicates2/meta.yml b/modules/nf-core/biobambam/bammarkduplicates2/meta.yml index 567a0c7a12b5..60b263058402 100644 --- a/modules/nf-core/biobambam/bammarkduplicates2/meta.yml +++ b/modules/nf-core/biobambam/bammarkduplicates2/meta.yml @@ -12,34 +12,43 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - metrics: - type: file - description: Duplicate metrics file generated by biobambam - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by biobambam + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/biobambam/bammerge/meta.yml b/modules/nf-core/biobambam/bammerge/meta.yml index 144335913008..f9cdc2486676 100644 --- a/modules/nf-core/biobambam/bammerge/meta.yml +++ b/modules/nf-core/biobambam/bammerge/meta.yml @@ -12,37 +12,52 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List containing 1 or more bam files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List containing 1 or more bam files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Merged BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Merged BAM file + pattern: "*.bam" - bam_index: - type: file - description: BAM index file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM index file + pattern: "*" - checksum: - type: file - description: Checksum file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.md5": + type: file + description: Checksum file + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/biobambam/bamsormadup/meta.yml b/modules/nf-core/biobambam/bamsormadup/meta.yml index 88c95d651a4c..cfd09d875607 100644 --- a/modules/nf-core/biobambam/bamsormadup/meta.yml +++ b/modules/nf-core/biobambam/bamsormadup/meta.yml @@ -13,50 +13,71 @@ tools: documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md doi: 10.1186/1751-0473-9-13 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: List containing 1 or more bam files - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format (optional) - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: List containing 1 or more bam files + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format (optional) + pattern: "*.{fa,fasta,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.bam" - bam_index: - type: file - description: BAM index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.bai": + type: file + description: BAM index file + pattern: "*.bai" - cram: - type: file - description: CRAM file with duplicate reads marked/removed - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file with duplicate reads marked/removed + pattern: "*.cram" - metrics: - type: file - description: Duplicate metrics file generated by biobambam - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by biobambam + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/biohansel/meta.yml b/modules/nf-core/biohansel/meta.yml index 41aa8b6ee8e2..802cf8a10946 100644 --- a/modules/nf-core/biohansel/meta.yml +++ b/modules/nf-core/biohansel/meta.yml @@ -12,42 +12,57 @@ tools: tool_dev_url: "https://github.com/phac-nml/biohansel" doi: "10.1101/2020.01.10.902056" licence: ["Apache-2.0 license"] + identifier: biotools:biohansel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA or FASTQ - pattern: "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" - - scheme_metadata: - type: file - description: Scheme subtype metadata table - pattern: "*.{tab,tsv,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA or FASTQ + pattern: "*.{fasta.gz,fa.gz,fna.gz,fastq.gz,fq.gz}" + - - scheme_metadata: + type: file + description: Scheme subtype metadata table + pattern: "*.{tab,tsv,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - summary: - type: file - description: Tab-delimited subtyping summary output - pattern: "*summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-summary.txt: + type: file + description: Tab-delimited subtyping summary output + pattern: "*summary.txt" - kmer_results: - type: file - description: Tab-delimited subtyping kmer matching output - pattern: "*kmer-results.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-kmer-results.txt: + type: file + description: Tab-delimited subtyping kmer matching output + pattern: "*kmer-results.txt" - simple_summary: - type: file - description: A simple version of summary output - pattern: "*simple-summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-simple-summary.txt: + type: file + description: A simple version of summary output + pattern: "*simple-summary.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/biscuit/align/meta.yml b/modules/nf-core/biscuit/align/meta.yml index ba75da1c8ce0..645fc2c98a3f 100644 --- a/modules/nf-core/biscuit/align/meta.yml +++ b/modules/nf-core/biscuit/align/meta.yml @@ -1,5 +1,6 @@ name: biscuit_align -description: Aligns single- or paired-end reads from bisulfite-converted libraries to a reference genome using Biscuit. +description: Aligns single- or paired-end reads from bisulfite-converted libraries + to a reference genome using Biscuit. keywords: - biscuit - DNA methylation @@ -10,44 +11,54 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/alignment tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bai: - type: file - description: Output BAM index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Output BAM index + pattern: "*.{bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/biscuitblaster/meta.yml b/modules/nf-core/biscuit/biscuitblaster/meta.yml index 1aa16365f955..d64cc1c26941 100644 --- a/modules/nf-core/biscuit/biscuitblaster/meta.yml +++ b/modules/nf-core/biscuit/biscuitblaster/meta.yml @@ -1,5 +1,6 @@ name: biscuit_blaster -description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed BAM files using Biscuit +description: A fast, compact one-liner to produce duplicate-marked, sorted, and indexed + BAM files using Biscuit keywords: - biscuit - DNA methylation @@ -10,11 +11,13 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/biscuitblaster/ tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit - samblaster: description: | samblaster is a fast and flexible program for marking duplicates in read-id grouped paired-end SAM files. @@ -25,6 +28,7 @@ tools: tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] + identifier: biotools:biscuit - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -34,39 +38,48 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bai: - type: file - description: Output BAM index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Output BAM index + pattern: "*.{bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/bsconv/meta.yml b/modules/nf-core/biscuit/bsconv/meta.yml index 0db30255dfcf..75d9b2b79398 100644 --- a/modules/nf-core/biscuit/bsconv/meta.yml +++ b/modules/nf-core/biscuit/bsconv/meta.yml @@ -11,41 +11,45 @@ keywords: - filter tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-bsconv tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file contained mapped reads - - bai: - type: file - description: BAM file index - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file contained mapped reads + - bai: + type: file + description: BAM file index + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bsconv_bam: - type: file - description: Output BAM file containing filtered read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing filtered read alignments + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/epiread/meta.yml b/modules/nf-core/biscuit/epiread/meta.yml index e647957cedaf..8974f1d952ac 100644 --- a/modules/nf-core/biscuit/epiread/meta.yml +++ b/modules/nf-core/biscuit/epiread/meta.yml @@ -12,44 +12,48 @@ keywords: - bam tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/epiread_format/ tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Biscuit BAM file - - bai: - type: file - description: BAM index - - snp_bed: - type: file - description: BED file containing SNP information (optional) - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Biscuit BAM file + - bai: + type: file + description: BAM index + - snp_bed: + type: file + description: BED file containing SNP information (optional) + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - epiread_bed: - type: file - description: Gzipped BED file with methylation (and optionally SNV) information - pattern: "*.{epiread.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with methylation (and optionally SNV) information + pattern: "*.{epiread.bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/index/meta.yml b/modules/nf-core/biscuit/index/meta.yml index 549857e6d142..39a0bcf8d944 100644 --- a/modules/nf-core/biscuit/index/meta.yml +++ b/modules/nf-core/biscuit/index/meta.yml @@ -11,24 +11,28 @@ keywords: - fasta tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/alignment tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Biscuit genome index directory - pattern: "BiscuitIndex" + - BiscuitIndex/*.fa*: + type: directory + description: Biscuit genome index directory + pattern: "BiscuitIndex" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/mergecg/meta.yml b/modules/nf-core/biscuit/mergecg/meta.yml index 99570c81bf25..2084f43b9d61 100644 --- a/modules/nf-core/biscuit/mergecg/meta.yml +++ b/modules/nf-core/biscuit/mergecg/meta.yml @@ -10,39 +10,43 @@ keywords: - bed tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: | - Biscuit BED file (output of biscuit vcf2bed) - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: | + Biscuit BED file (output of biscuit vcf2bed) + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mergecg_bed: - type: file - description: Gzipped BED file with merged methylation information - pattern: "*.bed.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with merged methylation information + pattern: "*.bed.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/pileup/meta.yml b/modules/nf-core/biscuit/pileup/meta.yml index b32d564e6ac3..9f532797e437 100644 --- a/modules/nf-core/biscuit/pileup/meta.yml +++ b/modules/nf-core/biscuit/pileup/meta.yml @@ -1,5 +1,6 @@ name: biscuit_pileup -description: Computes cytosine methylation and callable SNV mutations, optionally in reference to a germline BAM to call somatic variants +description: Computes cytosine methylation and callable SNV mutations, optionally + in reference to a germline BAM to call somatic variants keywords: - bisulfite - DNA methylation @@ -11,57 +12,61 @@ keywords: - vcf tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/pileup.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_bams: - type: file - description: | - BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided - ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a - tumor BAM file is provided, exactly one normal (germline) BAM must be provided. - pattern: "*.{bam}" - - normal_bais: - type: file - description: BAM index file or files corresponding to the provided normal_bams - pattern: "*.{bai}" - - tumor_bam: - type: file - description: | - Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with - their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a - tumor BAM file is provided, exactly one normal BAM must be provided. - pattern: "*.{bam}" - - tumor_bai: - type: file - description: Optional. BAM index file corresponding to provided tumor_bam - pattern: "*.{bai}" - - index: - type: directory - description: Biscuit genome index directory (generated with 'biscuit index') - pattern: "BiscuitIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_bams: + type: file + description: | + BAM files to be analyzed. If no tumor_bam file is provided, any number of "normal" BAMs may be provided + ("normal" here is just a semantic issue, these BAMs could be from tumor or any other kind of tissue). If a + tumor BAM file is provided, exactly one normal (germline) BAM must be provided. + pattern: "*.{bam}" + - normal_bais: + type: file + description: BAM index file or files corresponding to the provided normal_bams + pattern: "*.{bai}" + - tumor_bam: + type: file + description: | + Optional. If a tumor BAM file is provided, pileup will run in "somatic" mode and will annotate variants with + their somatic state (present in tumor only, present in normal only, present in both, etc). Note that if a + tumor BAM file is provided, exactly one normal BAM must be provided. + pattern: "*.{bam}" + - tumor_bai: + type: file + description: Optional. BAM index file corresponding to provided tumor_bam + pattern: "*.{bai}" + - - index: + type: directory + description: Biscuit genome index directory (generated with 'biscuit index') + pattern: "BiscuitIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file with methylation information - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: vcf file with methylation information + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/qc/meta.yml b/modules/nf-core/biscuit/qc/meta.yml index 92199338c020..ab7500ba823a 100644 --- a/modules/nf-core/biscuit/qc/meta.yml +++ b/modules/nf-core/biscuit/qc/meta.yml @@ -11,37 +11,56 @@ keywords: - quality control tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/subcommand_help.html#biscuit-qc tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file produced using Biscuit + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file produced using Biscuit + - - index: + type: file + description: index file output: - biscuit_qc_reports: - type: file - description: | - Summary files containing the following information: - - CpG retention by position in read - - CpH retention by position in read - - Read duplication statistics - - Insert size distribution - - Distribution of mapping qualities - - Proportion of reads mapping to each strand - - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT - pattern: "*.txt" + - meta: + type: file + description: | + Summary files containing the following information: + - CpG retention by position in read + - CpH retention by position in read + - Read duplication statistics + - Insert size distribution + - Distribution of mapping qualities + - Proportion of reads mapping to each strand + - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT + pattern: "*.txt" + - "*.txt": + type: file + description: | + Summary files containing the following information: + - CpG retention by position in read + - CpH retention by position in read + - Read duplication statistics + - Insert size distribution + - Distribution of mapping qualities + - Proportion of reads mapping to each strand + - Read-averaged cytosine conversion rate for CpA, CpC, CpG, and CpT + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/biscuit/vcf2bed/meta.yml b/modules/nf-core/biscuit/vcf2bed/meta.yml index f03e62c3393d..76ee1cad11ca 100644 --- a/modules/nf-core/biscuit/vcf2bed/meta.yml +++ b/modules/nf-core/biscuit/vcf2bed/meta.yml @@ -12,34 +12,38 @@ keywords: - vcf tools: - biscuit: - description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification data + description: A utility for analyzing sodium bisulfite conversion-based DNA methylation/modification + data homepage: https://huishenlab.github.io/biscuit/ documentation: https://huishenlab.github.io/biscuit/docs/methylextraction.html tool_dev_url: https://github.com/huishenlab/biscuit licence: ["MIT"] + identifier: biotools:biscuit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Biscuit vcf file (output of biscuit pileup) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Biscuit vcf file (output of biscuit pileup) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Gzipped BED file with methylation or SNV information - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Gzipped BED file with methylation or SNV information + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@njspix" maintainers: diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml index 69fe455a4af5..e0a979b39e1c 100644 --- a/modules/nf-core/bismark/align/meta.yml +++ b/modules/nf-core/bismark/align/meta.yml @@ -19,43 +19,58 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - unmapped: - type: file - description: Output FastQ file(s) containing unmapped reads - pattern: "*.{fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - unmapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fq.gz": + type: file + description: Output FastQ file(s) containing unmapped reads + pattern: "*.{fq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml index db05862ca012..f35117f4f27e 100644 --- a/modules/nf-core/bismark/coverage2cytosine/meta.yml +++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml @@ -20,42 +20,57 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_file: - type: file - description: | - A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_file: + type: file + description: | + A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - coverage: - type: file - description: A file containing methylation calls per position. - pattern: "*.cov.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: A file containing methylation calls per position. + pattern: "*.cov.gz" - report: - type: file - description: Genomic cytosine context results. - pattern: "*report.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt.gz": + type: file + description: Genomic cytosine context results. + pattern: "*report.txt.gz" - summary: - type: file - description: Cyotosine context summary report. - pattern: "*cytosine_context_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cytosine_context_summary.txt": + type: file + description: Cyotosine context summary report. + pattern: "*cytosine_context_summary.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ewels" maintainers: diff --git a/modules/nf-core/bismark/deduplicate/meta.yml b/modules/nf-core/bismark/deduplicate/meta.yml index cb48f6b1e9a0..31ffeb945b16 100644 --- a/modules/nf-core/bismark/deduplicate/meta.yml +++ b/modules/nf-core/bismark/deduplicate/meta.yml @@ -21,34 +21,43 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Deduplicated output BAM file containing read alignments - pattern: "*.{deduplicated.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplicated.bam": + type: file + description: Deduplicated output BAM file containing read alignments + pattern: "*.{deduplicated.bam}" - report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.deduplication_report.txt": + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml index e7aa55290577..18ca34a9f8dc 100644 --- a/modules/nf-core/bismark/genomepreparation/meta.yml +++ b/modules/nf-core/bismark/genomepreparation/meta.yml @@ -21,19 +21,22 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - BismarkIndex: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/methylationextractor/meta.yml b/modules/nf-core/bismark/methylationextractor/meta.yml index ea13ae3a3fca..673cb1ca557e 100644 --- a/modules/nf-core/bismark/methylationextractor/meta.yml +++ b/modules/nf-core/bismark/methylationextractor/meta.yml @@ -20,50 +20,77 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" - - index: - type: directory - description: Bismark genome index directory - pattern: "BismarkIndex" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" + - - index: + type: directory + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: Bismark output file containing coverage and methylation metrics - pattern: "*.{bedGraph.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph.gz": + type: file + description: Bismark output file containing coverage and methylation metrics + pattern: "*.{bedGraph.gz}" - methylation_calls: - type: file - description: Bismark output file containing strand-specific methylation calls - pattern: "*.{txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Bismark output file containing strand-specific methylation calls + pattern: "*.{txt.gz}" - coverage: - type: file - description: Bismark output file containing coverage metrics - pattern: "*.{cov.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cov.gz": + type: file + description: Bismark output file containing coverage metrics + pattern: "*.{cov.gz}" - report: - type: file - description: Bismark splitting reports - pattern: "*_{splitting_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_splitting_report.txt": + type: file + description: Bismark splitting reports + pattern: "*_{splitting_report.txt}" - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{M-bias.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.M-bias.txt": + type: file + description: Text file containing methylation bias information + pattern: "*.{M-bias.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/report/meta.yml b/modules/nf-core/bismark/report/meta.yml index 8c57a09eb328..52fece5aeeb0 100644 --- a/modules/nf-core/bismark/report/meta.yml +++ b/modules/nf-core/bismark/report/meta.yml @@ -18,42 +18,45 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - align_report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*{splitting_report.txt}" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - align_report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*{splitting_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: Bismark reports - pattern: "*.{html,txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.{html,txt}": + type: file + description: Bismark reports + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bismark/summary/meta.yml b/modules/nf-core/bismark/summary/meta.yml index 6acf44e6cad8..907a2d706b6f 100644 --- a/modules/nf-core/bismark/summary/meta.yml +++ b/modules/nf-core/bismark/summary/meta.yml @@ -21,36 +21,39 @@ tools: documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs doi: 10.1093/bioinformatics/btr167 licence: ["GPL-3.0-or-later"] + identifier: biotools:bismark input: - - bam: - type: list - description: List of Bismark alignment BAM filenames - pattern: "*.bam" - - align_report: - type: file - description: Bismark alignment reports - pattern: "*report.txt" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.deduplication_report.txt" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*splitting_report.txt" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.txt" + - - bam: + type: list + description: List of Bismark alignment BAM filenames + pattern: "*.bam" + - - align_report: + type: file + description: Bismark alignment reports + pattern: "*report.txt" + - - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.deduplication_report.txt" + - - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*splitting_report.txt" + - - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.txt" output: - summary: - type: file - description: Bismark summary - pattern: "*.{html,txt}" + - "*report.{html": + type: file + description: Bismark summary + pattern: "*.{html,txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/blast/blastdbcmd/meta.yml b/modules/nf-core/blast/blastdbcmd/meta.yml index 1c2f90e1ab8c..4518833cc918 100644 --- a/modules/nf-core/blast/blastdbcmd/meta.yml +++ b/modules/nf-core/blast/blastdbcmd/meta.yml @@ -14,47 +14,57 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - entry: - type: string - description: Entry identifier of sequence in database. It cannot be used along with entry_batch - - entry_batch: - type: file - description: | - File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: Input BLAST-indexed database - pattern: "*.{fa.*,fasta.*}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - entry: + type: string + description: Entry identifier of sequence in database. It cannot be used along + with entry_batch + - entry_batch: + type: file + description: | + File with a list of entry identifiers of sequences in database (one identifier per line). It cannot be used along with entry + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: Input BLAST-indexed database + pattern: "*.{fa.*,fasta.*}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Output fasta file (default format) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Output fasta file (default format) + pattern: "*.{fasta}" - text: - type: file - description: | - Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`) - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: | + Output text file (generic format if fasta not used, i.e. `--outfmt` is supplied to `ext.args`) + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/blast/blastn/meta.yml b/modules/nf-core/blast/blastn/meta.yml index a0d64dd6b4b7..0f5e41bb7ccb 100644 --- a/modules/nf-core/blast/blastn/meta.yml +++ b/modules/nf-core/blast/blastn/meta.yml @@ -13,39 +13,42 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: File containing blastn hits - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing blastn hits + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/blast/blastp/meta.yml b/modules/nf-core/blast/blastp/meta.yml index 5fe7c5de5cd2..27052a2d098e 100644 --- a/modules/nf-core/blast/blastp/meta.yml +++ b/modules/nf-core/blast/blastp/meta.yml @@ -1,5 +1,6 @@ name: blast_blastp -description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino acid (protein) query sequence against a protein database +description: BLASTP (Basic Local Alignment Search Tool- Protein) compares an amino + acid (protein) query sequence against a protein database keywords: - fasta - blast @@ -13,53 +14,68 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `xml` corresponds to BLAST xml format. - `tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format. - pattern: "xml|tsv|csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `xml` corresponds to BLAST xml format. + `tsv` corresponds to BLAST tabular format. `csv` corresponds to BLAST comma separated format. + pattern: "xml|tsv|csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - xml: - type: file - description: File containing blastp hits in XML format - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.xml": + type: file + description: File containing blastp hits in XML format + pattern: "*.{xml}" - tsv: - type: file - description: File containing blastp hits in tabular format - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: File containing blastp hits in tabular format + pattern: "*.{tsv}" - csv: - type: file - description: File containing blastp hits in comma separated format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.csv": + type: file + description: File containing blastp hits in comma separated format + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/blast/makeblastdb/meta.yml b/modules/nf-core/blast/makeblastdb/meta.yml index 9ed63901bf0b..826e62e1501b 100644 --- a/modules/nf-core/blast/makeblastdb/meta.yml +++ b/modules/nf-core/blast/makeblastdb/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - db: - type: directory - description: Output directory containing blast database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}: + type: directory + description: Output directory containing blast database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/blast/tblastn/meta.yml b/modules/nf-core/blast/tblastn/meta.yml index 7dff4fff0936..6055742c055c 100644 --- a/modules/nf-core/blast/tblastn/meta.yml +++ b/modules/nf-core/blast/tblastn/meta.yml @@ -13,39 +13,42 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: directory - description: Directory containing the blast database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: directory + description: Directory containing the blast database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: File containing blastn hits - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing blastn hits + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@gq2" diff --git a/modules/nf-core/blast/updateblastdb/meta.yml b/modules/nf-core/blast/updateblastdb/meta.yml index 4b836b48ecb4..b5dc782b94a8 100644 --- a/modules/nf-core/blast/updateblastdb/meta.yml +++ b/modules/nf-core/blast/updateblastdb/meta.yml @@ -13,29 +13,32 @@ tools: documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'mito', single_end:false ] - - name: - type: string - description: Name of the NCBI BLAST database to be downloaded + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'mito', single_end:false ] + - name: + type: string + description: Name of the NCBI BLAST database to be downloaded output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'mito', single_end:false ] - db: - type: directory - description: Output directory containing blast database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'mito', single_end:false ] + - prefix: + type: directory + description: Output directory containing blast database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/blat/meta.yml b/modules/nf-core/blat/meta.yml index 25deca1aea3a..70a92c9b4b77 100644 --- a/modules/nf-core/blat/meta.yml +++ b/modules/nf-core/blat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "blat" description: Queries a sequence subject @@ -8,44 +7,48 @@ keywords: - search tools: - "blat": - description: "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA and cross-species protein alignments." + description: "BLAT is a bioinformatics software tool which performs rapid mRNA/DNA + and cross-species protein alignments." homepage: "https://kentinformatics.com/" documentation: "https://kentinformatics.com/documentation" doi: "10.1101/gr.229202" licence: ["Free for academic, nonprofit and personal use"] + identifier: biotools:blat input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - query: - type: file - description: Sequence file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" - - meta2: - type: map - description: | - Groovy Map containing subject information - e.g. `[ id:'test', single_end:false ]` - - subject: - type: file - description: Sequence file - pattern: "*.{fa,nib,2bit}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - query: + type: file + description: Sequence file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,nib,2bit}" + - - meta2: + type: map + description: | + Groovy Map containing subject information + e.g. `[ id:'test', single_end:false ]` + - subject: + type: file + description: Sequence file + pattern: "*.{fa,nib,2bit}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - psl: - type: file - description: Search results - pattern: "*.{psl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.psl": + type: file + description: Search results + pattern: "*.{psl}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d-jch" maintainers: diff --git a/modules/nf-core/bowtie/align/meta.yml b/modules/nf-core/bowtie/align/meta.yml index 7c7e82374766..7b346802370e 100644 --- a/modules/nf-core/bowtie/align/meta.yml +++ b/modules/nf-core/bowtie/align/meta.yml @@ -16,47 +16,64 @@ tools: documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] + identifier: biotools:bowtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'sarscov2' ] - - index: - type: file - description: Bowtie genome index files - pattern: "*.ebwt" - - save_unaligned: - type: boolean - description: Whether to save fastq files containing the reads which did not align. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'sarscov2' ] + - index: + type: file + description: Bowtie genome index files + pattern: "*.ebwt" + - - save_unaligned: + type: boolean + description: Whether to save fastq files containing the reads which did not + align. output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: file + description: Log file + pattern: "*.log" + - "*.out": + type: file + description: Log file + pattern: "*.log" + - fastq: + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/bowtie/build/meta.yml b/modules/nf-core/bowtie/build/meta.yml index dd48004f2941..a878a5b70381 100644 --- a/modules/nf-core/bowtie/build/meta.yml +++ b/modules/nf-core/bowtie/build/meta.yml @@ -14,29 +14,32 @@ tools: documentation: http://bowtie-bio.sourceforge.net/manual.shtml arxiv: arXiv:1303.3997 licence: ["Artistic-2.0"] + identifier: biotools:bowtie input: - - meta: - type: map - description: | - Groovy Map containing information about the genome fasta - e.g. [ id:'test' ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing information about the genome fasta + e.g. [ id:'test' ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing nformation about the genome fasta - e.g. [ id:'test' ] - index: - type: file - description: Folder containing bowtie genome index files - pattern: "*.ebwt" + - meta: + type: map + description: | + Groovy Map containing nformation about the genome fasta + e.g. [ id:'test' ] + - bowtie: + type: file + description: Folder containing bowtie genome index files + pattern: "*.ebwt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/bowtie2/align/meta.yml b/modules/nf-core/bowtie2/align/meta.yml index 38610e0ed593..f841f7812854 100644 --- a/modules/nf-core/bowtie2/align/meta.yml +++ b/modules/nf-core/bowtie2/align/meta.yml @@ -16,77 +16,114 @@ tools: documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.ebwt" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Bowtie2 genome fasta file - pattern: "*.fasta" - - save_unaligned: - type: boolean - description: | - Save reads that do not map to the reference (true) or discard them (false) - (default: false) - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Bowtie2 genome fasta file + pattern: "*.fasta" + - - save_unaligned: + type: boolean + description: | + Save reads that do not map to the reference (true) or discard them (false) + (default: false) + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.sam" + - meta: + type: file + description: Output SAM file containing read alignments + pattern: "*.sam" + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.sam" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.bam" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.bam" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.bam" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.cram" + - meta: + type: file + description: Output CRAM file containing read alignments + pattern: "*.cram" + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.cram" - csi: - type: file - description: Output SAM/BAM index for large inputs - pattern: "*.csi" + - meta: + type: file + description: Output SAM/BAM index for large inputs + pattern: "*.csi" + - "*.csi": + type: file + description: Output SAM/BAM index for large inputs + pattern: "*.csi" - crai: - type: file - description: Output CRAM index - pattern: "*.crai" + - meta: + type: file + description: Output CRAM index + pattern: "*.crai" + - "*.crai": + type: file + description: Output CRAM index + pattern: "*.crai" - log: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: file + description: Aligment log + pattern: "*.log" + - "*.log": + type: file + description: Aligment log + pattern: "*.log" - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bowtie2/build/meta.yml b/modules/nf-core/bowtie2/build/meta.yml index 2d6879919075..2729a92ec67f 100644 --- a/modules/nf-core/bowtie2/build/meta.yml +++ b/modules/nf-core/bowtie2/build/meta.yml @@ -15,29 +15,32 @@ tools: documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml doi: 10.1038/nmeth.1923 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Bowtie2 genome index files - pattern: "*.bt2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - bowtie2: + type: file + description: Bowtie2 genome index files + pattern: "*.bt2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/bracken/bracken/meta.yml b/modules/nf-core/bracken/bracken/meta.yml index b7ff4489f56c..85a267efc65d 100644 --- a/modules/nf-core/bracken/bracken/meta.yml +++ b/modules/nf-core/bracken/bracken/meta.yml @@ -7,44 +7,61 @@ keywords: - kraken2 tools: - bracken: - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_report: - type: file - description: TSV file with six columns coming from kraken2 output - pattern: "*.{tsv}" - - database: - type: file - description: Directory containing the kraken2/Bracken files for analysis - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_report: + type: file + description: TSV file with six columns coming from kraken2 output + pattern: "*.{tsv}" + - - database: + type: file + description: Directory containing the kraken2/Bracken files for analysis + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reports: - type: file - description: TSV output report of the re-estimated abundances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" + - bracken_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.{tsv}" - txt: - type: file - description: TXT file of bracken corrected results of Kraken2 report output - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - bracken_kraken_style_report: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/bracken/build/meta.yml b/modules/nf-core/bracken/build/meta.yml index 2bce245a27fb..b921941e7f28 100644 --- a/modules/nf-core/bracken/build/meta.yml +++ b/modules/nf-core/bracken/build/meta.yml @@ -1,4 +1,3 @@ ---- name: "bracken_build" description: Extends a Kraken2 database to be compatible with Bracken keywords: @@ -8,39 +7,51 @@ keywords: - build tools: - "bracken": - description: "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample." + description: "Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample." homepage: "https://ccb.jhu.edu/software/bracken/" documentation: "https://ccb.jhu.edu/software/bracken/" tool_dev_url: "https://github.com/jenniferlu717/Bracken/" doi: "10.7717/peerj-cs.104 " licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - kraken2db: - type: directory - description: A Kraken2 database directory - pattern: "*/" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - kraken2db: + type: directory + description: A Kraken2 database directory + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: A Kraken2 database directory with required bracken files in side - pattern: "*/" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "kraken2db , includeInputs: true": + type: directory + description: A Kraken2 database directory with required bracken files in side + pattern: "*/" + - bracken_files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '${kraken2db}/database*", includeInputs: true': + type: directory + description: Bracken files required to extend the Kraken2 database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml index 426d00992184..9dba2e43c239 100644 --- a/modules/nf-core/bracken/combinebrackenoutputs/meta.yml +++ b/modules/nf-core/bracken/combinebrackenoutputs/meta.yml @@ -7,36 +7,41 @@ keywords: - reporting tools: - "bracken": - description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. + description: Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly + accurate statistical method that computes the abundance of species in DNA sequences + from a metagenomics sample. homepage: https://ccb.jhu.edu/software/bracken/ documentation: https://ccb.jhu.edu/software/bracken/index.shtml?t=manual tool_dev_url: https://github.com/jenniferlu717/Bracken doi: "10.7717/peerj-cs.104" licence: ["GPL v3"] + identifier: biotools:bracken input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: List of output files from bracken - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: List of output files from bracken + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined output in table format - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Combined output in table format + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/busco/busco/meta.yml b/modules/nf-core/busco/busco/meta.yml index 29745d2c1d2a..7cb6d69c1846 100644 --- a/modules/nf-core/busco/busco/meta.yml +++ b/modules/nf-core/busco/busco/meta.yml @@ -7,81 +7,135 @@ keywords: - proteome tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleic or amino acid sequence file in FASTA format. - pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" - - mode: - type: string - description: The mode to run Busco in. One of genome, proteins, or transcriptome - pattern: "{genome,proteins,transcriptome}" - - lineage: - type: string - description: The BUSCO lineage to use, or "auto" to automatically select lineage - - busco_lineages_path: - type: directory - description: Path to local BUSCO lineages directory. - - config_file: - type: file - description: Path to BUSCO config file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleic or amino acid sequence file in FASTA format. + pattern: "*.{fasta,fna,fa,fasta.gz,fna.gz,fa.gz}" + - - mode: + type: string + description: The mode to run Busco in. One of genome, proteins, or transcriptome + pattern: "{genome,proteins,transcriptome}" + - - lineage: + type: string + description: The BUSCO lineage to use, or "auto" to automatically select lineage + - - busco_lineages_path: + type: directory + description: Path to local BUSCO lineages directory. + - - config_file: + type: file + description: Path to BUSCO config file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - batch_summary: - type: file - description: Summary of all sequence files analyzed - pattern: "*-busco.batch_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco.batch_summary.txt": + type: file + description: Summary of all sequence files analyzed + pattern: "*-busco.batch_summary.txt" - short_summaries_txt: - type: file - description: Short Busco summary in plain text format - pattern: "short_summary.*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.txt: + type: file + description: Short Busco summary in plain text format + pattern: "short_summary.*.txt" - short_summaries_json: - type: file - description: Short Busco summary in JSON format - pattern: "short_summary.*.json" - - busco_dir: - type: directory - description: BUSCO lineage specific output - pattern: "*-busco" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - short_summary.*.json: + type: file + description: Short Busco summary in JSON format + pattern: "short_summary.*.json" - full_table: - type: file - description: Full BUSCO results table - pattern: "full_table.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/full_table.tsv": + type: file + description: Full BUSCO results table + pattern: "full_table.tsv" - missing_busco_list: - type: file - description: List of missing BUSCOs - pattern: "missing_busco_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/missing_busco_list.tsv": + type: file + description: List of missing BUSCOs + pattern: "missing_busco_list.tsv" - single_copy_proteins: - type: file - description: Fasta file of single copy proteins (transcriptome mode) - pattern: "single_copy_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/single_copy_proteins.faa": + type: file + description: Fasta file of single copy proteins (transcriptome mode) + pattern: "single_copy_proteins.faa" - seq_dir: - type: directory - description: BUSCO sequence directory - pattern: "busco_sequences" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/run_*/busco_sequences": + type: directory + description: BUSCO sequence directory + pattern: "busco_sequences" - translated_dir: - type: directory - description: Six frame translations of each transcript made by the transcriptome mode - pattern: "translated_dir" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco/*/translated_proteins": + type: directory + description: Six frame translations of each transcript made by the transcriptome + mode + pattern: "translated_dir" + - busco_dir: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-busco": + type: directory + description: BUSCO lineage specific output + pattern: "*-busco" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@charles-plessy" diff --git a/modules/nf-core/busco/generateplot/meta.yml b/modules/nf-core/busco/generateplot/meta.yml index 796f32b43cbc..72ad2c92252e 100644 --- a/modules/nf-core/busco/generateplot/meta.yml +++ b/modules/nf-core/busco/generateplot/meta.yml @@ -9,26 +9,31 @@ keywords: - quality control tools: - busco: - description: BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB. + description: BUSCO provides measures for quantitative assessment of genome assembly, + gene set, and transcriptome completeness based on evolutionarily informed expectations + of gene content from near-universal single-copy orthologs selected from OrthoDB. homepage: https://busco.ezlab.org/ documentation: https://busco.ezlab.org/busco_userguide.html tool_dev_url: https://gitlab.com/ezlab/busco doi: "10.1007/978-1-4939-9173-0_14" licence: ["MIT"] + identifier: biotools:busco input: - - short_summary_txt: - type: file - description: One or more short summary txt files from BUSCO - pattern: "short_summary.*.txt" + - - short_summary_txt: + type: file + description: One or more short summary txt files from BUSCO + pattern: "short_summary.*.txt" output: - png: - type: file - description: A summary plot in png format - pattern: "*.png" + - "*.png": + type: file + description: A summary plot in png format + pattern: "*.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/bwa/aln/meta.yml b/modules/nf-core/bwa/aln/meta.yml index ef2e6582dbbe..40aabe86f992 100644 --- a/modules/nf-core/bwa/aln/meta.yml +++ b/modules/nf-core/bwa/aln/meta.yml @@ -18,40 +18,43 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sai: - type: file - description: Single or paired SA coordinate files - pattern: "*.sai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sai": + type: file + description: Single or paired SA coordinate files + pattern: "*.sai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwa/index/meta.yml b/modules/nf-core/bwa/index/meta.yml index 6bbc87a640b1..4884bca2ab9f 100644 --- a/modules/nf-core/bwa/index/meta.yml +++ b/modules/nf-core/bwa/index/meta.yml @@ -14,29 +14,32 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bwa: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml index 24f7f4436a6e..ef7b966c0fa9 100644 --- a/modules/nf-core/bwa/mem/environment.yml +++ b/modules/nf-core/bwa/mem/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bwa=0.7.18 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.20 - htslib=1.20.0 + - samtools=1.20 diff --git a/modules/nf-core/bwa/mem/meta.yml b/modules/nf-core/bwa/mem/meta.yml index b126dd86a8a2..37467d2912ae 100644 --- a/modules/nf-core/bwa/mem/meta.yml +++ b/modules/nf-core/bwa/mem/meta.yml @@ -17,55 +17,82 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml arxiv: arXiv:1303.3997 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fasta,fa}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fa}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - csi: - type: file - description: Optional index file for BAM file - pattern: "*.{csi}" + - meta: + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" + - "*.csi": + type: file + description: Optional index file for BAM file + pattern: "*.{csi}" - crai: - type: file - description: Optional index file for CRAM file - pattern: "*.{crai}" + - meta: + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" + - "*.crai": + type: file + description: Optional index file for CRAM file + pattern: "*.{crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@jeremy1805" diff --git a/modules/nf-core/bwa/sampe/meta.yml b/modules/nf-core/bwa/sampe/meta.yml index fa96499fcab9..42041963a9c7 100644 --- a/modules/nf-core/bwa/sampe/meta.yml +++ b/modules/nf-core/bwa/sampe/meta.yml @@ -19,43 +19,47 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ files specified alongside meta in input channel. - pattern: "*.{fastq,fq}.gz" - - sai: - type: file - description: SAI file specified alongside meta and reads in input channel. - pattern: "*.sai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ files specified alongside meta in input channel. + pattern: "*.{fastq,fq}.gz" + - sai: + type: file + description: SAI file specified alongside meta and reads in input channel. + pattern: "*.sai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from + BWA_INDEX + pattern: "bwa/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwa/samse/meta.yml b/modules/nf-core/bwa/samse/meta.yml index 45c396a3913a..cd284575233f 100644 --- a/modules/nf-core/bwa/samse/meta.yml +++ b/modules/nf-core/bwa/samse/meta.yml @@ -19,43 +19,47 @@ tools: documentation: https://bio-bwa.sourceforge.net/bwa.shtml doi: "10.1093/bioinformatics/btp324" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ files specified alongside meta in input channel. - pattern: "*.{fastq,fq}.gz" - - sai: - type: file - description: SAI file specified alongside meta and reads in input channel. - pattern: "*.sai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ files specified alongside meta in input channel. + pattern: "*.{fastq,fq}.gz" + - sai: + type: file + description: SAI file specified alongside meta and reads in input channel. + pattern: "*.sai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from + BWA_INDEX + pattern: "bwa/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/bwamem2/index/meta.yml b/modules/nf-core/bwamem2/index/meta.yml index c14a109252b5..74f54ef0d8e5 100644 --- a/modules/nf-core/bwamem2/index/meta.yml +++ b/modules/nf-core/bwamem2/index/meta.yml @@ -13,29 +13,32 @@ tools: homepage: https://github.com/bwa-mem2/bwa-mem2 documentation: https://github.com/bwa-mem2/bwa-mem2#usage licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bwamem2: + type: file + description: BWA genome index files + pattern: "*.{0123,amb,ann,bwt.2bit.64,pac}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml index 633712cf1412..7e0b5a34795f 100644 --- a/modules/nf-core/bwamem2/mem/environment.yml +++ b/modules/nf-core/bwamem2/mem/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bwa-mem2=2.2.1 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.19.2 - htslib=1.19.1 + - samtools=1.19.2 diff --git a/modules/nf-core/bwamem2/mem/meta.yml b/modules/nf-core/bwamem2/mem/meta.yml index 931f712943d4..c6333ca171dc 100644 --- a/modules/nf-core/bwamem2/mem/meta.yml +++ b/modules/nf-core/bwamem2/mem/meta.yml @@ -17,69 +17,96 @@ tools: documentation: http://www.htslib.org/doc/samtools.html arxiv: arXiv:1303.3997 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta,fna}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - crai: - type: file - description: Index file for CRAM file - pattern: "*.{crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" - csi: - type: file - description: Index file for BAM file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for BAM file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/bwameme/index/meta.yml b/modules/nf-core/bwameme/index/meta.yml index 2db1d3a82b70..e0cb04a630f4 100644 --- a/modules/nf-core/bwameme/index/meta.yml +++ b/modules/nf-core/bwameme/index/meta.yml @@ -12,32 +12,33 @@ tools: documentation: https://github.com/kaist-ina/BWA-MEME#getting-started doi: "10.1093/bioinformatics/btac137" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fasta: - type: file - description: Input genome fasta file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: BWA-MEME genome index files - pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bwameme: + type: file + description: BWA-MEME genome index files + pattern: "*.{0123,amb,ann,pac,pos_packed,suffixarray_uint64,suffixarray_uint64_L0_PARAMETERS,suffixarray_uint64_L1_PARAMETERS,suffixarray_uint64_L2_PARAMETERS}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameme/mem/meta.yml b/modules/nf-core/bwameme/mem/meta.yml index e5d28db259d5..070aefebfed5 100644 --- a/modules/nf-core/bwameme/mem/meta.yml +++ b/modules/nf-core/bwameme/mem/meta.yml @@ -18,78 +18,103 @@ tools: documentation: https://github.com/kaist-ina/BWA-MEME#getting-started doi: "10.1093/bioinformatics/btac137" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta,fna}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" - - mbuffer: - type: integer - description: memory for mbuffer in megabytes (default 3072) - - sort_threads: - type: integer - description: number of threads to used during samtools sort (default 2). - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" + - - mbuffer: + type: integer + description: memory for mbuffer in megabytes (default 3072) + - - samtools_threads: + type: integer + description: number of threads for samtools (default 2) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Output SAM file containing read alignments - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - cram: - type: file - description: Output CRAM file containing read alignments - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" - crai: - type: file - description: Index file for CRAM file - pattern: "*.{crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" - csi: - type: file - description: Index file for BAM file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for BAM file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/bwameth/align/meta.yml b/modules/nf-core/bwameth/align/meta.yml index a5338e4e7ea4..6cd78268d11f 100644 --- a/modules/nf-core/bwameth/align/meta.yml +++ b/modules/nf-core/bwameth/align/meta.yml @@ -21,34 +21,37 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: directory - description: Directory containing bwameth genome index + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: directory + description: Directory containing bwameth genome index output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/bwameth/index/meta.yml b/modules/nf-core/bwameth/index/meta.yml index 1836d2a2910a..d92273c4d7e0 100644 --- a/modules/nf-core/bwameth/index/meta.yml +++ b/modules/nf-core/bwameth/index/meta.yml @@ -17,19 +17,22 @@ tools: documentation: https://github.com/brentp/bwa-meth arxiv: arXiv:1401.1129 licence: ["MIT"] + identifier: "" input: - - fasta: - type: file - description: Input genome fasta file + - - fasta: + type: file + description: Input genome fasta file output: - index: - type: directory - description: Directory containing bwameth genome index - pattern: "index" + - bwameth: + type: directory + description: Directory containing bwameth genome index + pattern: "index" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/cadd/meta.yml b/modules/nf-core/cadd/meta.yml index 230ed9c0f2ec..751bea454c0c 100644 --- a/modules/nf-core/cadd/meta.yml +++ b/modules/nf-core/cadd/meta.yml @@ -1,5 +1,6 @@ name: "cadd" -description: CADD is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. +description: CADD is a tool for scoring the deleteriousness of single nucleotide variants + as well as insertion/deletions variants in the human genome. keywords: - cadd - annotate @@ -13,36 +14,39 @@ tools: doi: "10.1093/nar/gky1016" licence: - Restricted. Free for non-commercial users. + identifier: biotools:cadd_phred input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Input file for annotation in vcf or vcf.gz format - pattern: "*.{vcf,vcf.gz}" - - annotation_dir: - type: file - description: | - Path to folder containing the vcf files with precomputed CADD scores. - This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Input file for annotation in vcf or vcf.gz format + pattern: "*.{vcf,vcf.gz}" + - - annotation_dir: + type: file + description: | + Path to folder containing the vcf files with precomputed CADD scores. + This folder contains the uncompressed files that would otherwise be in data/annotation folder as described in https://github.com/kircherlab/CADD-scripts/#manual-installation. + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Annotated tsv file - pattern: "*.{tsv,tsv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv.gz": + type: file + description: Annotated tsv file + pattern: "*.{tsv,tsv.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cafe/meta.yml b/modules/nf-core/cafe/meta.yml index cc1e696c9dac..6dc7c83c6aaa 100644 --- a/modules/nf-core/cafe/meta.yml +++ b/modules/nf-core/cafe/meta.yml @@ -12,49 +12,57 @@ tools: tool_dev_url: "https://github.com/hahnlab/CAFE5" doi: "10.1093/bioinformatics/btaa1027" licence: ["IU OPEN SOURCE LICENSE (see https://github.com/hahnlab/CAFE5/blob/master/LICENSE)"] + identifier: biotools:CaFE_Calculation_of_Free_Energy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - infile: - type: file - description: Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue or OrthoFinder) - pattern: "*.{txt,tsv,tab}" - - tree: - type: file - description: Newick formatted tree - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - infile: + type: file + description: Gene counts table (from OrthoMCL, SwiftOrtho, FastOrtho, OrthAgogue + or OrthoFinder) + pattern: "*.{txt,tsv,tab}" + - - tree: + type: file + description: Newick formatted tree + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cafe: - type: directory - description: A folder with all the cafe output + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${prefix}: + type: directory + description: A folder with all the cafe output + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - cafe_base_count: - type: file - description: File containing counts of genes per orthogroup - pattern: "*_count.tab" + - $prefix/*_count.tab: + type: file + description: File containing counts of genes per orthogroup + pattern: "*_count.tab" - cafe_significant_trees: - type: file - description: File containing significant trees (newick format) - pattern: "*.tre" + - $prefix/*.tre: + type: file + description: File containing significant trees (newick format) + pattern: "*.tre" - cafe_report: - type: file - description: File containing the final report from cafe - pattern: "*_report.cafe" + - $prefix/*_report.cafe: + type: file + description: File containing the final report from cafe + pattern: "*_report.cafe" - cafe_results: - type: file - description: File containing the main result files from cafe - pattern: "*results.txt" + - $prefix/*results.txt: + type: file + description: File containing the main result files from cafe + pattern: "*results.txt" authors: - "@chriswyatt1" maintainers: diff --git a/modules/nf-core/calder2/meta.yml b/modules/nf-core/calder2/meta.yml index 24758928eec2..e4d13266de9d 100644 --- a/modules/nf-core/calder2/meta.yml +++ b/modules/nf-core/calder2/meta.yml @@ -15,31 +15,44 @@ tools: tool_dev_url: "https://github.com/CSOgroup/CALDER2" doi: "10.1038/s41467-021-22666-3" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool.mcool}" - - resolution: - type: integer - description: In case a .mcool file is provided, which resolution level to use for the analysis + - - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool.mcool}" + - - resolution: + type: integer + description: In case a .mcool file is provided, which resolution level to use + for the analysis output: - - meta: - type: map - description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output_folder: - type: directory - description: Output folder containing sub-compartment (.tsv/.bed) and domain boundaries calls (.bed) + - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - ${prefix}/: + type: directory + description: Output folder containing sub-compartment (.tsv/.bed) and domain + boundaries calls (.bed) - intermediate_data_folder: - type: directory - description: Output folder containing intermediate data produced during the computation + - meta: + type: map + description: Groovy Map containing sample information. E.g. [ id:'test', single_end:false + ] + - ${prefix}/intermediate_data/: + type: directory + description: Output folder containing intermediate data produced during the + computation + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucananni93" maintainers: diff --git a/modules/nf-core/canu/meta.yml b/modules/nf-core/canu/meta.yml index afcaa55b9e9c..706c8f267028 100644 --- a/modules/nf-core/canu/meta.yml +++ b/modules/nf-core/canu/meta.yml @@ -1,5 +1,6 @@ name: "canu" -description: Accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads. +description: Accurate assembly of segmental duplications, satellites, and allelic + variants from high-fidelity long reads. keywords: - Assembly - pacbio @@ -7,72 +8,122 @@ keywords: - nanopore tools: - "canu": - description: "Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing." + description: "Canu is a fork of the Celera Assembler designed for high-noise single-molecule + sequencing." homepage: "https://canu.readthedocs.io/en/latest/index.html#" documentation: "https://canu.readthedocs.io/en/latest/tutorial.html" tool_dev_url: "https://github.com/marbl/canu" doi: "10.1101/gr.215087.116" licence: ["GPL v2 and others"] + identifier: biotools:canu input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:true ] - - reads: - type: file - description: fasta/fastq file - pattern: "*.{fasta,fastq}" - - mode: - type: string - description: Canu mode depending on the input data (source and error rate) - pattern: "-pacbio|-nanopore|-pacbio-hifi" - - genomesize: - type: string - description: An estimate of the size of the genome. Common suffices are allowed, for example, 3.7m or 2.8g - pattern: "[g|m|k]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:true ] + - reads: + type: file + description: fasta/fastq file + pattern: "*.{fasta,fastq}" + - - mode: + type: string + description: Canu mode depending on the input data (source and error rate) + pattern: "-pacbio|-nanopore|-pacbio-hifi" + - - genomesize: + type: string + description: An estimate of the size of the genome. Common suffices are allowed, + for example, 3.7m or 2.8g + pattern: "[g|m|k]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Most of the analysis reported during assembly - pattern: "*.report" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.report": + type: file + description: Most of the analysis reported during assembly + pattern: "*.report" - assembly: - type: file - description: Everything which could be assembled and is the full assembly, including both unique, repetitive, and bubble elements. - pattern: "*.contigs.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fasta.gz": + type: file + description: Everything which could be assembled and is the full assembly, including + both unique, repetitive, and bubble elements. + pattern: "*.contigs.fasta" - contigs: - type: file - description: Reads and low-coverage contigs which could not be incorporated into the primary assembly. - pattern: "*.unassembled.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unassembled.fasta.gz": + type: file + description: Reads and low-coverage contigs which could not be incorporated + into the primary assembly. + pattern: "*.unassembled.fasta" - corrected_reads: - type: file - description: The reads after correction. - pattern: "*.correctedReads.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.correctedReads.fasta.gz": + type: file + description: The reads after correction. + pattern: "*.correctedReads.fasta.gz" - corrected_trimmed_reads: - type: file - description: The corrected reads after overlap based trimming - pattern: "*.trimmedReads.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmedReads.fasta.gz": + type: file + description: The corrected reads after overlap based trimming + pattern: "*.trimmedReads.fasta.gz" - metadata: - type: file - description: (undocumented) - pattern: "*.contigs.layout" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout": + type: file + description: (undocumented) + pattern: "*.contigs.layout" - contig_position: - type: file - description: The position of each read in a contig - pattern: "*.contigs.layout.readToTig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout.readToTig": + type: file + description: The position of each read in a contig + pattern: "*.contigs.layout.readToTig" - contig_info: - type: file - description: A list of the contigs, lengths, coverage, number of reads and other metadata. Essentially the same information provided in the FASTA header line. - pattern: "*.contigs.layout.tigInfo" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.layout.tigInfo": + type: file + description: A list of the contigs, lengths, coverage, number of reads and other + metadata. Essentially the same information provided in the FASTA header line. + pattern: "*.contigs.layout.tigInfo" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/cat/cat/meta.yml b/modules/nf-core/cat/cat/meta.yml index 00a8db0bca81..81778a06710c 100644 --- a/modules/nf-core/cat/cat/meta.yml +++ b/modules/nf-core/cat/cat/meta.yml @@ -9,25 +9,32 @@ tools: description: Just concatenation documentation: https://man7.org/linux/man-pages/man1/cat.1.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files_in: - type: file - description: List of compressed / uncompressed files - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files_in: + type: file + description: List of compressed / uncompressed files + pattern: "*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - file_out: - type: file - description: Concatenated file. Will be gzipped if file_out ends with ".gz" - pattern: "${file_out}" + - meta: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - ${prefix}: + type: file + description: Concatenated file. Will be gzipped if file_out ends with ".gz" + pattern: "${file_out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" - "@FriederikeHanssen" diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml index db4ac3c79af5..91ff2fb5f64d 100644 --- a/modules/nf-core/cat/fastq/meta.yml +++ b/modules/nf-core/cat/fastq/meta.yml @@ -10,30 +10,33 @@ tools: The cat utility reads files sequentially, writing them to the standard output. documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files to be concatenated. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/cdhit/cdhit/meta.yml b/modules/nf-core/cdhit/cdhit/meta.yml index fa3f204acc14..faa25b29114b 100644 --- a/modules/nf-core/cdhit/cdhit/meta.yml +++ b/modules/nf-core/cdhit/cdhit/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/weizhongli/cdhit" doi: "10.1093/bioinformatics/btl158" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta file of sequences to be clustered - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta file of sequences to be clustered + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: fasta file of the representative sequences for each cluster - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: fasta file of the representative sequences for each cluster + pattern: "*.{fasta}" - clusters: - type: file - description: List of clusters - pattern: "*.{clstr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clstr": + type: file + description: List of clusters + pattern: "*.{clstr}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@timslittle" - "@Puumanamana" diff --git a/modules/nf-core/cdhit/cdhitest/meta.yml b/modules/nf-core/cdhit/cdhitest/meta.yml index c6b2dfc82b01..0a0e55af5cde 100644 --- a/modules/nf-core/cdhit/cdhitest/meta.yml +++ b/modules/nf-core/cdhit/cdhitest/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/weizhongli/cdhit" doi: "10.1093/bioinformatics/btl158" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta or fastq file of sequences to be clustered - pattern: "*.{fasta,fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta or fastq file of sequences to be clustered + pattern: "*.{fasta,fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: fasta or fastq file of the representative sequences for each cluster - pattern: "*.{fasta,fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fq}": + type: file + description: fasta or fastq file of the representative sequences for each cluster + pattern: "*.{fasta,fastq}" - clusters: - type: file - description: List of clusters - pattern: "*.{clstr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clstr": + type: file + description: List of clusters + pattern: "*.{clstr}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/celesta/meta.yml b/modules/nf-core/celesta/meta.yml index 9d6cae71840b..50f57670ba0a 100644 --- a/modules/nf-core/celesta/meta.yml +++ b/modules/nf-core/celesta/meta.yml @@ -1,6 +1,7 @@ ---- name: "celesta" -description: Unsupervised machine learning for cell type identification in multiplexed imaging using protein expression and cell neighborhood information without ground truth +description: Unsupervised machine learning for cell type identification in multiplexed + imaging using protein expression and cell neighborhood information without ground + truth keywords: - highly_multiplexed_imaging - cell_type_identification @@ -10,55 +11,65 @@ keywords: - machine_learning tools: - "celesta": - description: "Automate unsupervised machine learning cell type identification using both protein expressions and cell spatial neighborhood information" + description: "Automate unsupervised machine learning cell type identification + using both protein expressions and cell spatial neighborhood information" homepage: https://github.com/SchapiroLabor/mcmicro-celesta documentation: https://github.com/SchapiroLabor/mcmicro-celesta/blob/main/README.md tool_dev_url: "https://github.com/plevritis-lab/CELESTA" doi: "10.1038/s41592-022-01498-z" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - img_data: - type: file - description: "Quantification table with single cells as rows, markers (e.g. CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as columns" - pattern: "*.csv" - - signature: - type: file - description: "Signature Matrix containing the definition of cell types according to markers" - pattern: "*.csv" - - high_thresholds: - type: file - description: "csv file with user-defined probability high thresholds for anchor cell (row 1) and index cell (row 2) definition" - pattern: "*.csv" - - low_thresholds: - type: file - description: "optional csv file with user-defined probability low thresholds for anchor cell (row 1) and index cell (row 2) definition" - pattern: "*.csv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - img_data: + type: file + description: "Quantification table with single cells as rows, markers (e.g. + CD3 or CD8 but names do not have to match exactly) and X/Y coordinates as + columns" + pattern: "*.csv" + - - signature: + type: file + description: "Signature Matrix containing the definition of cell types according + to markers" + pattern: "*.csv" + - - high_thresholds: + type: file + description: "csv file with user-defined probability high thresholds for anchor + cell (row 1) and index cell (row 2) definition" + pattern: "*.csv" + - - low_thresholds: + type: file + description: "optional csv file with user-defined probability low thresholds + for anchor cell (row 1) and index cell (row 2) definition" + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - celltypes: - type: file - description: File with final celltype annotations concatenated to the original input quantification, due to the mechanism its non-deterministic - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*results.csv": + type: file + description: File with final celltype annotations concatenated to the original + input quantification, due to the mechanism its non-deterministic + pattern: "*.csv" - quality: - type: file - description: File with final calculated marker probabilities for inspection, non-deterministic - pattern: "*.csv" - + - "*quality.csv": + type: file + description: File with final calculated marker probabilities for inspection, + non-deterministic + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LukasHats" - "@ArozHada" diff --git a/modules/nf-core/cellbender/merge/meta.yml b/modules/nf-core/cellbender/merge/meta.yml index 333ad6a69c44..97f2c0e64797 100644 --- a/modules/nf-core/cellbender/merge/meta.yml +++ b/modules/nf-core/cellbender/merge/meta.yml @@ -1,42 +1,51 @@ name: cellbender_merge -description: Module to use CellBender to remove ambient RNA from single-cell RNA-seq data +description: Module to use CellBender to remove ambient RNA from single-cell RNA-seq + data keywords: - single-cell - scRNA-seq - ambient RNA removal tools: - cellbender: - description: CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. + description: CellBender is a software package for eliminating technical artifacts + from high-throughput single-cell RNA sequencing (scRNA-seq) data. documentation: https://cellbender.readthedocs.io/en/latest/ tool_dev_url: https://github.com/broadinstitute/CellBender licence: ["BSD-3-Clause"] + identifier: biotools:CellBender input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - filtered: - type: file - description: AnnData file containing filtered data (without empty droplets) - pattern: "*.h5ad" - - unfiltered: - type: file - description: AnnData file containing unfiltered data (with empty droplets) - pattern: "*.h5ad" - - cellbender_h5: - type: file - description: CellBender h5 file containing ambient RNA estimates - pattern: "*.h5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - filtered: + type: file + description: AnnData file containing filtered data (without empty droplets) + pattern: "*.h5ad" + - unfiltered: + type: file + description: AnnData file containing unfiltered data (with empty droplets) + pattern: "*.h5ad" + - cellbender_h5: + type: file + description: CellBender h5 file containing ambient RNA estimates + pattern: "*.h5" output: - h5ad: - type: file - description: AnnData file containing decontaminated counts as `adata.X` - pattern: "*.h5ad" + - meta: + type: file + description: AnnData file containing decontaminated counts as `adata.X` + pattern: "*.h5ad" + - ${prefix}.h5ad: + type: file + description: AnnData file containing decontaminated counts as `adata.X` + pattern: "*.h5ad" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/cellbender/removebackground/meta.yml b/modules/nf-core/cellbender/removebackground/meta.yml index d70fa3fda1da..b037bf5c724d 100644 --- a/modules/nf-core/cellbender/removebackground/meta.yml +++ b/modules/nf-core/cellbender/removebackground/meta.yml @@ -1,74 +1,135 @@ name: cellbender_removebackground -description: Module to use CellBender to estimate ambient RNA from single-cell RNA-seq data +description: Module to use CellBender to estimate ambient RNA from single-cell RNA-seq + data keywords: - single-cell - scRNA-seq - ambient RNA removal tools: - cellbender: - description: CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data. + description: CellBender is a software package for eliminating technical artifacts + from high-throughput single-cell RNA sequencing (scRNA-seq) data. documentation: https://cellbender.readthedocs.io/en/latest/ tool_dev_url: https://github.com/broadinstitute/CellBender licence: ["BSD-3-Clause"] + identifier: biotools:CellBender input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - h5ad: - type: file - description: AnnData file containing unfiltered data (with empty droplets) - pattern: "*.h5ad" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - h5ad: + type: file + description: AnnData file containing unfiltered data (with empty droplets) + pattern: "*.h5ad" output: - h5: - type: file - description: Full count matrix as an h5 file, with background RNA removed. This file contains all the original droplet barcodes. - pattern: "*.h5" + - meta: + type: file + description: Full count matrix as an h5 file, with background RNA removed. This + file contains all the original droplet barcodes. + pattern: "*.h5" + - ${prefix}.h5: + type: file + description: Full count matrix as an h5 file, with background RNA removed. This + file contains all the original droplet barcodes. + pattern: "*.h5" - filtered_h5: - type: file - description: | - Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. - pattern: "*.h5" + - meta: + type: file + description: | + Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. + pattern: "*.h5" + - ${prefix}_filtered.h5: + type: file + description: | + Full count matrix as an h5 file, with background RNA removed. This file contains only the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. + pattern: "*.h5" - posterior_h5: - type: file - description: | - The full posterior probability of noise counts. This is not normally used downstream. - pattern: "*.h5" + - meta: + type: file + description: | + The full posterior probability of noise counts. This is not normally used downstream. + pattern: "*.h5" + - ${prefix}_posterior.h5: + type: file + description: | + The full posterior probability of noise counts. This is not normally used downstream. + pattern: "*.h5" - barcodes: - type: file - description: | - CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | - Barcodes are written in plain text. This information is also contained in each of the above outputs, | - but is included as a separate output for convenient use in certain downstream applications. - pattern: "*.csv" + - meta: + type: file + description: | + CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | + Barcodes are written in plain text. This information is also contained in each of the above outputs, | + but is included as a separate output for convenient use in certain downstream applications. + pattern: "*.csv" + - ${prefix}_cell_barcodes.csv: + type: file + description: | + CSV file containing all the droplet barcodes which were determined to have a > 50% posterior probability of containing cells. | + Barcodes are written in plain text. This information is also contained in each of the above outputs, | + but is included as a separate output for convenient use in certain downstream applications. + pattern: "*.csv" - metrics: - type: file - description: | - Metrics describing the run, potentially to be used to flag problematic runs | - when using CellBender as part of a large-scale automated pipeline. - pattern: "*.csv" + - meta: + type: file + description: | + Metrics describing the run, potentially to be used to flag problematic runs | + when using CellBender as part of a large-scale automated pipeline. + pattern: "*.csv" + - ${prefix}_metrics.csv: + type: file + description: | + Metrics describing the run, potentially to be used to flag problematic runs | + when using CellBender as part of a large-scale automated pipeline. + pattern: "*.csv" - report: - type: file - description: | - HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. - pattern: "*.html" + - meta: + type: file + description: | + HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. + pattern: "*.html" + - ${prefix}_report.html: + type: file + description: | + HTML report including plots and commentary, along with any warnings or suggestions for improved parameter settings. + pattern: "*.html" - pdf: - type: file - description: PDF file that provides a standard graphical summary of the inference procedure. - pattern: "*.pdf" + - meta: + type: file + description: PDF file that provides a standard graphical summary of the inference + procedure. + pattern: "*.pdf" + - ${prefix}.pdf: + type: file + description: PDF file that provides a standard graphical summary of the inference + procedure. + pattern: "*.pdf" - log: - type: file - description: Log file produced by the cellbender remove-background run. - pattern: "*.log" + - meta: + type: file + description: Log file produced by the cellbender remove-background run. + pattern: "*.log" + - ${prefix}.log: + type: file + description: Log file produced by the cellbender remove-background run. + pattern: "*.log" - checkpoint: - type: file - description: Checkpoint file which contains the trained model and the full posterior. - pattern: "*.ckpt" + - meta: + type: file + description: Checkpoint file which contains the trained model and the full posterior. + pattern: "*.ckpt" + - ckpt.tar.gz: + type: file + description: Checkpoint file which contains the trained model and the full posterior. + pattern: "*.ckpt" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/cellpose/meta.yml b/modules/nf-core/cellpose/meta.yml index 433d52044699..5397944baba5 100644 --- a/modules/nf-core/cellpose/meta.yml +++ b/modules/nf-core/cellpose/meta.yml @@ -6,44 +6,54 @@ keywords: - cellpose tools: - "cellpose": - description: "cellpose is an anatomical segmentation algorithm written in Python 3 by Carsen Stringer and Marius Pachitariu" + description: "cellpose is an anatomical segmentation algorithm written in Python + 3 by Carsen Stringer and Marius Pachitariu" homepage: "https://github.com/MouseLand/cellpose" documentation: "https://cellpose.readthedocs.io/en/latest/command.html" tool_dev_url: "https://github.com/MouseLand/cellpose" doi: 10.1038/s41592-022-01663-4 licence: ["BSD 3-Clause"] + identifier: biotools:cellpose input: - - meta: - type: map - description: | - Groovy Map containing sample information - (sample id) - - image: - type: file - description: tif file for ready for segmentation - pattern: "*.{tif,tiff}" - - model: - type: file - description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop approach. + - - meta: + type: map + description: | + Groovy Map containing sample information + (sample id) + - image: + type: file + description: tif file for ready for segmentation + pattern: "*.{tif,tiff}" + - - model: + type: file + description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop + approach. output: - - meta: - type: map - description: | - Groovy Map containing sample information - [sample id] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mask: - type: file - description: labelled mask output from cellpose in tif format - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*masks.tif": + type: file + description: labelled mask output from cellpose in tif format + pattern: "*.{tif, tiff}" - flows: - type: file - description: cell flow output from cellpose - pattern: "*.{tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + [sample id] + - "*flows.tif": + type: file + description: cell flow output from cellpose + pattern: "*.{tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@josenimo" - "@FloWuenne" diff --git a/modules/nf-core/cellranger/count/meta.yml b/modules/nf-core/cellranger/count/meta.yml index 1f1768a857be..046faf9fd648 100644 --- a/modules/nf-core/cellranger/count/meta.yml +++ b/modules/nf-core/cellranger/count/meta.yml @@ -1,49 +1,61 @@ name: cellranger_count -description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. +description: Module to use Cell Ranger's pipelines analyze sequencing data produced + from Chromium Single Cell Gene Expression. keywords: - align - count - reference tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: - 10x Genomics EULA + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files. The order of the input files MUST be ["sample1 R1", "sample1 R2", "sample2, R1", - "sample2, R2", ...]. This can usually be achieved by sorting the input files by file name. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files. The order of the input files MUST be ["sample1 R1", "sample1 R2", "sample2, R1", + "sample2, R2", ...]. This can usually be achieved by sorting the input files by file name. - Background: 10x data is always paired-end with R1 containing cell barcode and UMI - and R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name - convention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically - renames files to match this convention based on the order of input files to avoid various - issues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module - throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part. - Renaming the files does not affect the results (see README.md for detailed tests). - pattern: "*{R1,R2}*.fastq.gz" - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + Background: 10x data is always paired-end with R1 containing cell barcode and UMI + and R2 containing the actual read sequence. Cell Ranger requires files to adhere to the following file-name + convention: `${Sample_Name}_S1_L00${Lane_Number}_${R1,R2}_001.fastq.gz`. This module automatically + renames files to match this convention based on the order of input files to avoid various + issues (see https://github.com/nf-core/scrnaseq/issues/241). To avoid mistakes, the module + throws an error if a pair of R1 and R2 fastq files does not have the same filename except for the "_R1"/"_R2" part. + Renaming the files does not affect the results (see README.md for detailed tests). + pattern: "*{R1,R2}*.fastq.gz" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - outs: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkfastq/meta.yml b/modules/nf-core/cellranger/mkfastq/meta.yml index 0077b069d68a..fa7af86b6736 100644 --- a/modules/nf-core/cellranger/mkfastq/meta.yml +++ b/modules/nf-core/cellranger/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellranger_mkfastq -description: Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkfastq command. +description: Module to create FASTQs needed by the 10x Genomics Cell Ranger tool. + Uses the cellranger mkfastq command. keywords: - reference - mkfastq @@ -8,29 +9,83 @@ keywords: - bcl2fastq tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: Sample sheet + pattern: "*.csv" + - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" output: - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - "*_outs/outs/fastq_path/**/*.fastq.gz": + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - undetermined_fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Undetermined*.fastq.gz": + type: file + description: Undetermined FastQ files + pattern: "Undetermined*.fastq.gz" + - reports: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Reports": + type: directory + description: Reports + pattern: "Reports" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/fastq_path/Stats": + type: directory + description: Stats + pattern: "Stats" + - interop: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_outs/outs/interop_path/*.bin": + type: file + description: InterOp files + pattern: "*.bin" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkgtf/meta.yml b/modules/nf-core/cellranger/mkgtf/meta.yml index 282fcff03122..ceaca540923c 100644 --- a/modules/nf-core/cellranger/mkgtf/meta.yml +++ b/modules/nf-core/cellranger/mkgtf/meta.yml @@ -1,30 +1,36 @@ name: cellranger_mkgtf -description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command. +description: Module to build a filtered GTF needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkgtf command. keywords: - reference - mkref - index tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellranger/mkref/meta.yml b/modules/nf-core/cellranger/mkref/meta.yml index bd8ad5a65ca8..f4f595636fcc 100644 --- a/modules/nf-core/cellranger/mkref/meta.yml +++ b/modules/nf-core/cellranger/mkref/meta.yml @@ -1,37 +1,43 @@ name: cellranger_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkref command. keywords: - reference - mkref - index tools: - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov licence: [10X Genomics EULA] + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/cellranger/mkvdjref/meta.yml b/modules/nf-core/cellranger/mkvdjref/meta.yml index c7d70dd1e853..23605d3f319a 100644 --- a/modules/nf-core/cellranger/mkvdjref/meta.yml +++ b/modules/nf-core/cellranger/mkvdjref/meta.yml @@ -1,5 +1,6 @@ name: cellranger_mkvdjref -description: Module to build the VDJ reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkvdjref command. +description: Module to build the VDJ reference needed by the 10x Genomics Cell Ranger + tool. Uses the cellranger mkvdjref command. keywords: - reference - mkvdjref @@ -9,36 +10,46 @@ keywords: - cellranger tools: - cellranger: - description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. + description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger + vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries + and performs sequence assembly and paired clonotype calling. It uses the Chromium + cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes + and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe + V(D)J Browser. homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/advanced/references licence: ["10x Genomics EULA"] + identifier: "" input: - - reference_name: - type: string - description: The name to give the new reference folder, e.g. `my_vdj_ref`. This flag is required - pattern: str - - genes: - type: file - description: Reference transcriptome GTF file (optional) - pattern: "*.gtf" - - fasta: - type: file - description: Reference genome FASTA file (optional) - pattern: "*.{fasta,fa}" - - seqs: - type: file - description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow (optional) - pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: Reference genome FASTA file (optional) + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference genome GTF file (optional) + pattern: "*.gtf" + - - seqs: + type: file + description: Reference genome FASTA file from the 10X Genomics fetch-imgt workflow + (optional) + pattern: "*.{fasta,fa}" + - - reference_name: + type: string + description: The name to give the new reference folder, e.g. `my_vdj_ref`. This + flag is required + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@klkeys" diff --git a/modules/nf-core/cellranger/multi/meta.yml b/modules/nf-core/cellranger/multi/meta.yml index 5ac3ebdbb87b..ccd329aecad9 100644 --- a/modules/nf-core/cellranger/multi/meta.yml +++ b/modules/nf-core/cellranger/multi/meta.yml @@ -1,5 +1,7 @@ name: "cellranger_multi" -description: Module to use Cell Ranger's pipelines to analyze sequencing data produced from various Chromium technologies, including Single Cell Gene Expression, Single Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing. +description: Module to use Cell Ranger's pipelines to analyze sequencing data produced + from various Chromium technologies, including Single Cell Gene Expression, Single + Cell Immune Profiling, Feature Barcoding, and Cell Multiplexing. keywords: - align - reference @@ -12,98 +14,150 @@ keywords: - crispr tools: - "cellranger": - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process + Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_cp licence: [10X Genomics EULA] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gex_fastqs: - type: file - description: FASTQ files for gene expression analysis - pattern: "*.fastq.gz" - - vdj_fastqs: - type: file - description: FASTQ files for V(D)J immunoprofiling analysis - pattern: "*.fastq.gz" - - ab_fastqs: - type: file - description: FASTQ files for antibody analysis - pattern: "*.fastq.gz" - - beam_fastqs: - type: file - description: FASTQ files for Barcode-Enabled Antigen Mapping (antigen analysis) - pattern: "*.fastq.gz" - - cmo_fastqs: - type: file - description: FASTQ files for cell multiplexing data - pattern: "*.fastq.gz" - - gex_reference: - type: directory - description: Folder containing Cellranger gene expression reference. Can also be a gzipped tarball - pattern: "*.tar.gz" - - gex_frna_probeset: - type: file - description: Fixed RNA profiling information containing custom probes in CSV format - pattern: "*.csv" - - gex_targetpanel: - type: file - description: Declaration of the target panel for Targeted Gene Expression analysis - pattern: "*.csv" - - vdj_reference: - type: directory - description: Folder containing Cellranger V(D)J reference. Can also be a gzipped tarball - pattern: "*.tar.gz" - - vdj_primer_index: - type: file - description: List of custom V(D)J inner enrichment primers - pattern: "*.csv" - - fb_reference: - type: file - description: The Feature Barcodes used for reference in Feature Barcoding Analysis - pattern: "*.csv" - - beam_antigen_panel: - type: file - description: The BEAM manifest in Feature Barcode CSV format - pattern: "*.csv" - - beam_control_panel: - type: file - description: The BEAM antigens set to control status, with corresponding MHC alleles, in Feature Barcode CSV format - pattern: "*.csv" - - cmo_reference: - type: file - description: Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` option in Cellranger - pattern: "*.csv" - - cmo_barcodes: - type: file - description: A CSV file appended to the Cellranger multi config linking samples to CMO IDs - pattern: "*.csv" - - cmo_barcode_assignment: - type: file - description: A CSV file that specifies the barcode-sample assignment in Cell Multiplexing analysis - pattern: "*.csv" - - frna_sampleinfo: - type: file - description: Sample information for fixed RNA analysis - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - - meta_gex: + type: map + description: | + Groovy Map containing sample information + - "gex_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_vdj: + type: map + description: | + Groovy Map containing sample information + - "vdj_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_ab: + type: map + description: | + Groovy Map containing sample information + - "ab_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_beam: + type: map + description: | + Groovy Map containing sample information + - "beam_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_cmo: + type: map + description: | + Groovy Map containing sample information + - "cmo_fastqs ": + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - meta_crispr: + type: map + description: | + Groovy Map containing sample information + - crispr_fastqs: + type: file + description: FASTQ files + pattern: "*.fastq.gz" + - - gex_reference: + type: directory + description: Folder containing Cellranger gene expression reference. Can also + be a gzipped tarball + pattern: "*.tar.gz" + - - gex_frna_probeset: + type: file + description: Fixed RNA profiling information containing custom probes in CSV + format + pattern: "*.csv" + - - gex_targetpanel: + type: file + description: Declaration of the target panel for Targeted Gene Expression analysis + pattern: "*.csv" + - - vdj_reference: + type: directory + description: Folder containing Cellranger V(D)J reference. Can also be a gzipped + tarball + pattern: "*.tar.gz" + - - vdj_primer_index: + type: file + description: List of custom V(D)J inner enrichment primers + pattern: "*.csv" + - - fb_reference: + type: file + description: The Feature Barcodes used for reference in Feature Barcoding Analysis + pattern: "*.csv" + - - beam_antigen_panel: + type: file + description: The BEAM manifest in Feature Barcode CSV format + pattern: "*.csv" + - - beam_control_panel: + type: file + description: The BEAM antigens set to control status, with corresponding MHC + alleles, in Feature Barcode CSV format + pattern: "*.csv" + - - cmo_reference: + type: file + description: Path to a custom Cell Multiplexing CSV reference IDs, or the `cmo-set` + option in Cellranger + pattern: "*.csv" + - - cmo_barcodes: + type: file + description: A CSV file appended to the Cellranger multi config linking samples + to CMO IDs + pattern: "*.csv" + - - cmo_barcode_assignment: + type: file + description: A CSV file that specifies the barcode-sample assignment in Cell + Multiplexing analysis + pattern: "*.csv" + - - frna_sampleinfo: + type: file + description: Sample information for fixed RNA analysis + pattern: "*.csv" + - - skip_renaming: + type: boolean + description: Skip renaming output: - config: - type: file - description: The resolved Cellranger multi config used for analysis - pattern: "cellranger_multi_config.csv" + - meta: + type: file + description: The resolved Cellranger multi config used for analysis + pattern: "cellranger_multi_config.csv" + - cellranger_multi_config.csv: + type: file + description: The resolved Cellranger multi config used for analysis + pattern: "cellranger_multi_config.csv" - outs: - type: file - description: Files containing the outputs of Cell Ranger - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@klkeys" maintainers: diff --git a/modules/nf-core/cellranger/vdj/meta.yml b/modules/nf-core/cellranger/vdj/meta.yml index 2bdafe5d167e..8fbd75e802b2 100644 --- a/modules/nf-core/cellranger/vdj/meta.yml +++ b/modules/nf-core/cellranger/vdj/meta.yml @@ -1,5 +1,6 @@ name: cellranger_vdj -description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Immune Profiling. +description: Module to use Cell Ranger's pipelines analyze sequencing data produced + from Chromium Single Cell Immune Profiling. keywords: - align - vdj @@ -9,35 +10,49 @@ keywords: - cellranger tools: - cellranger: - description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries and performs sequence assembly and paired clonotype calling. It uses the Chromium cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe V(D)J Browser. + description: Cell Ranger processes data from 10X Genomics Chromium kits. `cellranger + vdj` takes FASTQ files from `cellranger mkfastq` or `bcl2fastq` for V(D)J libraries + and performs sequence assembly and paired clonotype calling. It uses the Chromium + cellular barcodes and UMIs to assemble V(D)J transcripts per cell. Clonotypes + and CDR3 sequences are output as a `.vloupe` file which can be loaded into Loupe + V(D)J Browser. homepage: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger documentation: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj tool_dev_url: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/tutorial/tutorial-vdj licence: [10X Genomics EULA] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - - reference: - type: directory - description: Folder containing all the reference indices needed by Cell Ranger + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Cell Ranger output: - outs: - type: file - description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" + - "**/outs/**": + type: file + description: Files containing the outputs of Cell Ranger, see official 10X Genomics + documentation for a complete list + pattern: "${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/count/meta.yml b/modules/nf-core/cellrangerarc/count/meta.yml index 8bc73c6fff57..6aa9d1f163e9 100644 --- a/modules/nf-core/cellrangerarc/count/meta.yml +++ b/modules/nf-core/cellrangerarc/count/meta.yml @@ -1,39 +1,60 @@ name: cellrangerarc_count -description: Module to use Cell Ranger's ARC pipelines analyze sequencing data produced from Chromium Single Cell ARC. Uses the cellranger-arc count command. +description: Module to use Cell Ranger's ARC pipelines analyze sequencing data produced + from Chromium Single Cell ARC. Uses the cellranger-arc count command. keywords: - align - count - reference tools: - cellrangerarc: - description: Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell ARC data. + description: Cell Ranger ARC is a set of analysis pipelines that process Chromium + Single Cell ARC data. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - lib_csv: - type: file - description: | - Path to a 3-column CSV file declaring FASTQ paths, sample names and library types of input ATAC and GEX FASTQs. - - reference: - type: directory - description: Directory containing all the reference indices needed by Cell Ranger ARC + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_type: + type: string + description: The type of sample + - sub_sample: + type: string + description: The name of sub sample + - reads: + type: file + description: FASTQ files produced using Cell Ranger ARC + pattern: "*.fastq.gz" + - - reference: + type: directory + description: Directory containing all the reference indices needed by Cell Ranger + ARC output: - outs: - type: file - description: Files containing the outputs of Cell Ranger ARC - pattern: "${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger ARC + pattern: "${meta.id}/outs/*" + - ${meta.id}/outs/**: + type: file + description: Files containing the outputs of Cell Ranger ARC + pattern: "${meta.id}/outs/*" + - lib: + - ${meta.id}_lib.csv: + type: file + description: Library + pattern: "*_lib.csv" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkfastq/meta.yml b/modules/nf-core/cellrangerarc/mkfastq/meta.yml index e344e900e817..f57487cdf29b 100644 --- a/modules/nf-core/cellrangerarc/mkfastq/meta.yml +++ b/modules/nf-core/cellrangerarc/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellrangerarc_mkfastq -description: Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkfastq command. +description: Module to create fastqs needed by the 10x Genomics Cell Ranger Arc tool. + Uses the cellranger-arc mkfastq command. keywords: - reference - mkfastq @@ -8,30 +9,39 @@ keywords: - bcl2fastq tools: - cellrangerarc: - description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" + - - csv: + type: file + description: Sample sheet + pattern: "*.csv" output: - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + - fastq: + - ${bcl.getSimpleName(: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - /*.fastq.gz: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkgtf/meta.yml b/modules/nf-core/cellrangerarc/mkgtf/meta.yml index 5fadc3eff55a..8730f856fce1 100644 --- a/modules/nf-core/cellrangerarc/mkgtf/meta.yml +++ b/modules/nf-core/cellrangerarc/mkgtf/meta.yml @@ -1,31 +1,37 @@ name: cellrangerarc_mkgtf -description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkgtf command. +description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger + Arc tool. Uses the cellranger-arc mkgtf command. keywords: - reference - mkref - index tools: - cellrangerarc: - description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger Arc by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.filtered.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangerarc/mkref/meta.yml b/modules/nf-core/cellrangerarc/mkref/meta.yml index cf98e60ca10f..59dadcda1b06 100644 --- a/modules/nf-core/cellrangerarc/mkref/meta.yml +++ b/modules/nf-core/cellrangerarc/mkref/meta.yml @@ -1,46 +1,58 @@ name: cellrangerarc_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger Arc tool. Uses the cellranger-arc mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + Arc tool. Uses the cellranger-arc mkref command. keywords: - reference - mkref - index tools: - cellrangerarc: - description: Cell Ranger Arc is a set of analysis pipelines that process Chromium Single Cell Arc data. + description: Cell Ranger Arc is a set of analysis pipelines that process Chromium + Single Cell Arc data. homepage: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc documentation: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc tool_dev_url: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc licence: - 10x Genomics EULA + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - motifs: - type: file - description: Sequence motif file (e.g., from transcription factors) - pattern: "*.txt" - - reference_config: - type: file - description: JSON-like file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path - pattern: config - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - motifs: + type: file + description: Sequence motif file (e.g., from transcription factors) + pattern: "*.txt" + - - reference_config: + type: file + description: JSON-like file holding organism, genome, reference fasta path, + reference annotation gtf path, contigs that should be excluded and sequence + format motif file path + pattern: config + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder called like the reference_name containing all the reference indices needed by Cell Ranger Arc + - ${reference_name}: + type: directory + description: Folder called like the reference_name containing all the reference + indices needed by Cell Ranger Arc + - config: + - config: + type: file + description: Configuration file - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@heylf" diff --git a/modules/nf-core/cellrangeratac/count/meta.yml b/modules/nf-core/cellrangeratac/count/meta.yml index 2bdef7f60d98..fd2599cdfdb1 100644 --- a/modules/nf-core/cellrangeratac/count/meta.yml +++ b/modules/nf-core/cellrangeratac/count/meta.yml @@ -1,39 +1,49 @@ name: cellrangeratac_count -description: Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced from Chromium Single Cell ATAC. +description: Module to use Cell Ranger's ATAC pipelines analyze sequencing data produced + from Chromium Single Cell ATAC. keywords: - align - count - reference tools: - cellranger-atac: - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively, plus an additional FastQ for the barcodes - - reference: - type: directory - description: Directory containing all the reference indices needed by Cell Ranger ATAC + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively, plus an additional FastQ for the barcodes + - - reference: + type: directory + description: Directory containing all the reference indices needed by Cell Ranger + ATAC output: - outs: - type: file - description: Files containing the outputs of Cell Ranger ATAC - pattern: "sample-${meta.gem}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger ATAC + pattern: "sample-${meta.gem}/outs/*" + - ${meta.id}/outs/*: + type: file + description: Files containing the outputs of Cell Ranger ATAC + pattern: "sample-${meta.gem}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangeratac/mkfastq/meta.yml b/modules/nf-core/cellrangeratac/mkfastq/meta.yml index fcee368d1ac4..22441625c54b 100644 --- a/modules/nf-core/cellrangeratac/mkfastq/meta.yml +++ b/modules/nf-core/cellrangeratac/mkfastq/meta.yml @@ -1,5 +1,6 @@ name: cellrangeratac_mkfastq -description: Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkfastq command. +description: Module to create fastqs needed by the 10x Genomics Cell Ranger ATAC tool. + Uses the cellranger-atac mkfastq command. keywords: - reference - mkfastq @@ -8,29 +9,38 @@ keywords: - bcl2fastq tools: - cellranger-atac: - description: Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + description: Cell Ranger ATAC by 10x Genomics is a set of analysis pipelines that + process Chromium single-cell data to align reads, generate feature-barcode matrices, + perform clustering and other secondary analysis, and more. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" + - - csv: + type: file + description: Sample sheet + pattern: "*.csv" output: - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" + - fastq: + - ${bcl.getSimpleName(: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - /*.fastq.gz: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - "@ggabernet" - "@edmundmiller" diff --git a/modules/nf-core/cellrangeratac/mkref/meta.yml b/modules/nf-core/cellrangeratac/mkref/meta.yml index 4baed308375e..caa46127bd16 100644 --- a/modules/nf-core/cellrangeratac/mkref/meta.yml +++ b/modules/nf-core/cellrangeratac/mkref/meta.yml @@ -1,45 +1,53 @@ name: cellrangeratac_mkref -description: Module to build the reference needed by the 10x Genomics Cell Ranger ATAC tool. Uses the cellranger-atac mkref command. +description: Module to build the reference needed by the 10x Genomics Cell Ranger + ATAC tool. Uses the cellranger-atac mkref command. keywords: - reference - mkref - index tools: - cellranger-atac: - description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. + description: Cell Ranger ATAC is a set of analysis pipelines that process Chromium + Single Cell ATAC data. homepage: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac documentation: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac tool_dev_url: https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac licence: ["10x Genomics EULA"] + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - motifs: - type: file - description: Sequence motif file (e.g., of transcription factors) - pattern: "*.txt" - - reference_config: - type: file - description: JSON-like config file holding organism, genome, reference fasta path, reference annotation gtf path, contigs that should be excluded and sequence format motif file path - pattern: config - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - motifs: + type: file + description: Sequence motif file (e.g., of transcription factors) + pattern: "*.txt" + - - reference_config: + type: file + description: JSON-like config file holding organism, genome, reference fasta + path, reference annotation gtf path, contigs that should be excluded and sequence + format motif file path + pattern: config + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder called regarding reference_name containing all the reference indices needed by Cell Ranger ATAC + - ${reference_name}: + type: directory + description: Folder called regarding reference_name containing all the reference + indices needed by Cell Ranger ATAC - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@heylf" diff --git a/modules/nf-core/cellsnp/modea/meta.yml b/modules/nf-core/cellsnp/modea/meta.yml index bed1bc482bda..886e5300548d 100644 --- a/modules/nf-core/cellsnp/modea/meta.yml +++ b/modules/nf-core/cellsnp/modea/meta.yml @@ -1,7 +1,9 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cellsnp_modea" -description: Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs on single cells. You can use the mode A of cellsnp-lite after read alignment to obtain the snp x cell pileup UMI or read count matrices for each alleles of given or detected SNPs for droplet based single cell data. +description: Cellsnp-lite is a C/C++ tool for efficient genotyping bi-allelic SNPs + on single cells. You can use the mode A of cellsnp-lite after read alignment to + obtain the snp x cell pileup UMI or read count matrices for each alleles of given + or detected SNPs for droplet based single cell data. keywords: - genotyping - single cell @@ -15,65 +17,101 @@ tools: tool_dev_url: "https://github.com/single-cell-genetics/cellsnp-lite" doi: "10.1093/bioinformatics/btab358" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: A single BAM/SAM/CRAM file, e.g., from CellRanger. - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: The index of the BAM/CRAM file. - pattern: "*.{bai,crai}" - - region_vcf: - type: file - description: A optional vcf file listing all candidate SNPs for genotyping. - pattern: "*.{vcf, vcf.gz}" - - barcode: - type: file - description: A plain file listing all effective cell barcodes. - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: A single BAM/SAM/CRAM file, e.g., from CellRanger. + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: The index of the BAM/CRAM file. + pattern: "*.{bai,crai}" + - region_vcf: + type: file + description: A optional vcf file listing all candidate SNPs for genotyping. + pattern: "*.{vcf, vcf.gz}" + - barcode: + type: file + description: A plain file listing all effective cell barcodes. + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - base: - type: file - description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation (without GT). - pattern: "*.base.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.base.vcf.gz": + type: file + description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation + (without GT). + pattern: "*.base.vcf.gz" - cell: - type: file - description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation & genotype (GT) information for each cell or sample. - pattern: "*.cells.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.cells.vcf.gz": + type: file + description: A VCF file listing genotyped SNPs and aggregated AD & DP infomation + & genotype (GT) information for each cell or sample. + pattern: "*.cells.vcf.gz" - sample: - type: file - description: A TSV file listing cell barcodes or sample IDs. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.samples.tsv": + type: file + description: A TSV file listing cell barcodes or sample IDs. + pattern: "*.tsv" - allele_depth: - type: file - description: A file in “Matrix Market exchange formats”, containing the allele depths of the alternative (ALT) alleles. - pattern: "*.tag.AD.mtx" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.AD.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the allele + depths of the alternative (ALT) alleles. + pattern: "*.tag.AD.mtx" - depth_coverage: - type: file - description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of the reference and alternative alleles (REF + ALT). - pattern: "*.tag.DP.mtx" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.DP.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the sum + of allele depths of the reference and alternative alleles (REF + ALT). + pattern: "*.tag.DP.mtx" - depth_other: - type: file - description: A file in “Matrix Market exchange formats”, containing the sum of allele depths of all the alleles other than REF and ALT. - pattern: "*.tag.OTH.mtx" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tag.OTH.mtx": + type: file + description: A file in “Matrix Market exchange formats”, containing the sum + of allele depths of all the alleles other than REF and ALT. + pattern: "*.tag.OTH.mtx" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@wxicu" maintainers: diff --git a/modules/nf-core/centrifuge/build/meta.yml b/modules/nf-core/centrifuge/build/meta.yml index d193ce1e833d..65a34f6d7b07 100644 --- a/modules/nf-core/centrifuge/build/meta.yml +++ b/modules/nf-core/centrifuge/build/meta.yml @@ -13,56 +13,54 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - fasta: - type: file - description: Fasta file containing sequences to be used in centrifuge database. - pattern: "*.{fasta,fna}" - - - conversion_table: - type: file - description: A tab-separated file with sequence ID to taxonomy ID mapping - pattern: "*.{map}" - - - taxonomy_tree: - type: file - description: A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their parents - pattern: "*.{dmp}" - - - name_table: - type: file - description: A '|'-separated file mapping taxonomy IDs to a name. Typically names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific name - pattern: "*.{dmp}" - - - size_table: - type: file - description: Optional list of taxonomic IDs and lengths of the sequences belonging to the same taxonomic IDs. - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file containing sequences to be used in centrifuge database. + pattern: "*.{fasta,fna}" + - - conversion_table: + type: file + description: A tab-separated file with sequence ID to taxonomy ID mapping + pattern: "*.{map}" + - - taxonomy_tree: + type: file + description: A \t|\t-separated file mapping taxonomy. Typically nodes.dmp from + the NCBI taxonomy dump. Links taxonomy IDs to their parents + pattern: "*.{dmp}" + - - name_table: + type: file + description: A '|'-separated file mapping taxonomy IDs to a name. Typically + names.dmp from the NCBI taxonomy dump. Links taxonomy IDs to their scientific + name + pattern: "*.{dmp}" + - - size_table: + type: file + description: Optional list of taxonomic IDs and lengths of the sequences belonging + to the same taxonomic IDs. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cf: - type: file - description: Index files for the centrifuge database - pattern: "*.{cf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cf": + type: file + description: Index files for the centrifuge database + pattern: "*.{cf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sarah-buddle" - "@jfy133" diff --git a/modules/nf-core/centrifuge/centrifuge/meta.yml b/modules/nf-core/centrifuge/centrifuge/meta.yml index a06104e168a5..17329e93355d 100644 --- a/modules/nf-core/centrifuge/centrifuge/meta.yml +++ b/modules/nf-core/centrifuge/centrifuge/meta.yml @@ -12,59 +12,86 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Path to directory containing centrifuge database files - - save_unaligned: - type: boolean - description: If true unmapped fastq files are saved - - save_aligned: - type: boolean - description: If true mapped fastq files are saved + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Path to directory containing centrifuge database files + - - save_unaligned: + type: boolean + description: If true unmapped fastq files are saved + - - save_aligned: + type: boolean + description: If true mapped fastq files are saved output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: | - File containing a classification summary - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + File containing a classification summary + pattern: "*.{report.txt}" - results: - type: file - description: | - File containing classification results - pattern: "*.{results.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*results.txt": + type: file + description: | + File containing classification results + pattern: "*.{results.txt}" - sam: - type: file - description: | - Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s - pattern: "*.{sam,tab}" - - fastq_unmapped: - type: file - description: Unmapped fastq files - pattern: "*.unmapped.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{sam,tab}": + type: file + description: | + Optional output file containing read alignments (SAM format )or a table of per-read hit information (TAB)s + pattern: "*.{sam,tab}" - fastq_mapped: - type: file - description: Mapped fastq files - pattern: "*.mapped.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.fastq{,.1,.2}.gz": + type: file + description: Mapped fastq files + pattern: "*.mapped.fastq.gz" + - fastq_unmapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unmapped.fastq{,.1,.2}.gz": + type: file + description: Unmapped fastq files + pattern: "*.unmapped.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/centrifuge/kreport/meta.yml b/modules/nf-core/centrifuge/kreport/meta.yml index 5641152b675c..e195eebf90be 100644 --- a/modules/nf-core/centrifuge/kreport/meta.yml +++ b/modules/nf-core/centrifuge/kreport/meta.yml @@ -14,35 +14,38 @@ tools: documentation: https://ccb.jhu.edu/software/centrifuge/manual.shtml doi: 10.1101/gr.210641.116 licence: ["GPL v3"] + identifier: biotools:centrifuge input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: File containing the centrifuge classification report - pattern: "*.{txt}" - - db: - type: directory - description: Path to directory containing centrifuge database files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: File containing the centrifuge classification report + pattern: "*.{txt}" + - - db: + type: directory + description: Path to directory containing centrifuge database files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - kreport: - type: file - description: | - File containing kraken-style report from centrifuge - out files. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: | + File containing kraken-style report from centrifuge + out files. + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/checkm/lineagewf/meta.yml b/modules/nf-core/checkm/lineagewf/meta.yml index 239b8d2eba23..e32441d24752 100644 --- a/modules/nf-core/checkm/lineagewf/meta.yml +++ b/modules/nf-core/checkm/lineagewf/meta.yml @@ -1,5 +1,6 @@ name: checkm_lineagewf -description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. +description: CheckM provides a set of tools for assessing the quality of genomes recovered + from isolates, single cells, or metagenomes. keywords: - checkm - mag @@ -14,50 +15,68 @@ keywords: - genome bins tools: - checkm: - description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. + description: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes. homepage: https://ecogenomics.github.io/CheckM/ documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" licence: ["GPL v3"] + identifier: biotools:checkm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: One or a list of multiple FASTA files of each bin, with extension defined with the fasta_ext value - pattern: "*.{$fasta_ext}" - - fasta_ext: - type: string - description: The file-type extension suffix of the input FASTA files (e.g., fasta, fna, fa, fas) - - db: - type: directory - description: Optional directory pointing to checkM database to prevent re-downloading + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: One or a list of multiple FASTA files of each bin, with extension + defined with the fasta_ext value + pattern: "*.{$fasta_ext}" + - - fasta_ext: + type: string + description: The file-type extension suffix of the input FASTA files (e.g., + fasta, fna, fa, fas) + - - db: + type: directory + description: Optional directory pointing to checkM database to prevent re-downloading output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - checkm_output: - type: directory - description: CheckM output directory - pattern: "*/" - checkm_output: - type: file - description: Lineage markfer file - pattern: "lineage.ms" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}: + type: directory + description: CheckM output directory + pattern: "*/" + - marker_file: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/lineage.ms: + type: file + description: Lineage file + pattern: "*.ms" - checkm_tsv: - type: file - description: CheckM summary completeness statistics table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}.tsv: + type: file + description: CheckM summary completeness statistics table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/checkm/qa/meta.yml b/modules/nf-core/checkm/qa/meta.yml index 9f3d51ce62e5..cd41eaecf7f3 100644 --- a/modules/nf-core/checkm/qa/meta.yml +++ b/modules/nf-core/checkm/qa/meta.yml @@ -1,5 +1,6 @@ name: checkm_qa -description: CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. +description: CheckM provides a set of tools for assessing the quality of genomes recovered + from isolates, single cells, or metagenomes. keywords: - checkm - mag @@ -16,50 +17,63 @@ keywords: - quality assurnce tools: - checkm: - description: Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes. + description: Assess the quality of microbial genomes recovered from isolates, + single cells, and metagenomes. homepage: https://ecogenomics.github.io/CheckM/ documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" licence: ["GPL v3"] + identifier: biotools:checkm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - analysis_dir: - type: file - description: Directory containing output of checkm/analyze or checkm/lineage_wf etc. - pattern: "*" - - marker_file: - type: file - description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf - pattern: "*.ms" - - coverage_file: - type: file - description: File containing coverage of each sequence (generated by checkm coverage) - - exclude_marker_file: - type: file - description: File specifying markers to exclude from marker sets + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - analysis_dir: + type: file + description: Directory containing output of checkm/analyze or checkm/lineage_wf + etc. + pattern: "*" + - marker_file: + type: file + description: Marker file specified during checkm/analyze or produced by checkm/{lineage,taxonomy}_wf + pattern: "*.ms" + - coverage_file: + type: file + description: File containing coverage of each sequence (generated by checkm + coverage) + - - exclude_marker_file: + type: file + description: File specifying markers to exclude from marker sets output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: "Default completeness statistics in various formats, as specified with --out_format (excluding option: 9)" - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: "Default completeness statistics in various formats, as specified + with --out_format (excluding option: 9)" + pattern: "*.txt" - fasta: - type: file - description: Output in fasta format (only if --out_format 9) - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fasta: + type: file + description: Output in fasta format (only if --out_format 9) + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/checkm2/databasedownload/meta.yml b/modules/nf-core/checkm2/databasedownload/meta.yml index 4672a1dcca51..09c69c923f59 100644 --- a/modules/nf-core/checkm2/databasedownload/meta.yml +++ b/modules/nf-core/checkm2/databasedownload/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkm2_databasedownload" description: CheckM2 database download @@ -16,17 +15,23 @@ tools: homepage: "https://github.com/chklovski/CheckM2" doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] + identifier: "" output: - - meta: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test', version:1 ]` + - database: + - meta: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test', version:1 ]` + - checkm2_db_v${db_version}.dmnd: + type: file + description: CheckM2 database file + pattern: "checkm2_db_v*.dmnd" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@dialvarezs" diff --git a/modules/nf-core/checkm2/predict/meta.yml b/modules/nf-core/checkm2/predict/meta.yml index db17500e344d..48cc9fbccaad 100644 --- a/modules/nf-core/checkm2/predict/meta.yml +++ b/modules/nf-core/checkm2/predict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkm2_predict" description: CheckM2 bin quality prediction @@ -16,44 +15,51 @@ tools: homepage: "https://github.com/chklovski/CheckM2" doi: "10.1038/s41592-023-01940-w" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - dbmeta: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test', version:1 ]` - - fasta: - type: file - description: One or multiple FASTA files of each bin - pattern: "*.{fasta,fna,fa}" - - db: - type: file - description: CheckM2 database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: One or multiple FASTA files of each bin + pattern: "*.{fasta,fna,fa}" + - - dbmeta: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test', version:1 ]` + - db: + type: file + description: CheckM2 database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkm2_output: - type: directory - description: CheckM2 output directory - pattern: "${prefix}/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}: + type: directory + description: CheckM2 output directory + pattern: "${prefix}/" - checkm2_tsv: - type: file - description: CheckM2 summary completeness statistics table - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}/quality_report.tsv: + type: file + description: CheckM2 summary completeness statistics table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@dialvarezs" diff --git a/modules/nf-core/checkqc/meta.yml b/modules/nf-core/checkqc/meta.yml index 0c3d98ba916e..42d0017f6ba8 100644 --- a/modules/nf-core/checkqc/meta.yml +++ b/modules/nf-core/checkqc/meta.yml @@ -1,43 +1,50 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "checkqc" -description: A simple program to parse Illumina NGS data and check it for quality criteria +description: A simple program to parse Illumina NGS data and check it for quality + criteria keywords: - QC - Illumina - genomics tools: - "checkqc": - description: "A simple program to parse Illumina NGS data and check it for quality criteria." + description: "A simple program to parse Illumina NGS data and check it for quality + criteria." homepage: "https://github.com/Molmed/checkQC" documentation: "http://checkqc.readthedocs.io/en/latest/" doi: "10.21105/joss.00556" licence: ["GPL v3"] + identifier: "" input: - - run_dir: - type: file - description: | - Illumina sequencing run directory - Can be directory or a compressed tar (tar.gz) of the directory - - checkqc_config: - type: file - description: CheckQC configuration file - pattern: "*.{yml,yaml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - run_dir: + type: file + description: | + Illumina sequencing run directory + Can be directory or a compressed tar (tar.gz) of the directory + - - checkqc_config: + type: file + description: CheckQC configuration file + pattern: "*.{yml,yaml}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: CheckQC report in json format - pattern: "*checkqc_report.json" - - log: - type: file - description: CheckQC log in txt format - pattern: "*_log.txt" - + - meta: + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + - "*checkqc_report.json": + type: file + description: CheckQC report in json format + pattern: "*checkqc_report.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matrulda" diff --git a/modules/nf-core/checkv/downloaddatabase/meta.yml b/modules/nf-core/checkv/downloaddatabase/meta.yml index 1ca541507233..533ab8c69bf2 100644 --- a/modules/nf-core/checkv/downloaddatabase/meta.yml +++ b/modules/nf-core/checkv/downloaddatabase/meta.yml @@ -20,15 +20,18 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkv_db: - type: directory - description: directory pointing to database - pattern: "${prefix}/" + - ${prefix}/*: + type: directory + description: directory pointing to database + pattern: "${prefix}/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/checkv/endtoend/meta.yml b/modules/nf-core/checkv/endtoend/meta.yml index 2bb4d330ed32..a8a6deaf0e6f 100644 --- a/modules/nf-core/checkv/endtoend/meta.yml +++ b/modules/nf-core/checkv/endtoend/meta.yml @@ -18,53 +18,89 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta,fna,fa}" - - db: - type: directory - description: Directory pointing to checkV database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta,fna,fa}" + - - db: + type: directory + description: Directory pointing to checkV database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - quality_summary: - type: file - description: CheckV's main output containing integrated results from the three main modules (contamination, completeness, complete genomes) with overall quality of contigs - pattern: "${prefix}/quality_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/quality_summary.tsv: + type: file + description: CheckV's main output containing integrated results from the three + main modules (contamination, completeness, complete genomes) with overall + quality of contigs + pattern: "${prefix}/quality_summary.tsv" - completeness: - type: file - description: CheckV's detailed overview table on estimating completeness - pattern: "${prefix}/completeness.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/completeness.tsv: + type: file + description: CheckV's detailed overview table on estimating completeness + pattern: "${prefix}/completeness.tsv" - contamination: - type: file - description: CheckV's detailed overview table on estimating contamination - pattern: "${prefix}/contamination.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/contamination.tsv: + type: file + description: CheckV's detailed overview table on estimating contamination + pattern: "${prefix}/contamination.tsv" - complete_genomes: - type: file - description: CheckV's detailed overview table on the identified putative complete genomes - pattern: "${prefix}/complete_genomes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/complete_genomes.tsv: + type: file + description: CheckV's detailed overview table on the identified putative complete + genomes + pattern: "${prefix}/complete_genomes.tsv" - proviruses: - type: file - description: CheckV's extracted proviruses contigs - pattern: "${prefix}/proviruses.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/proviruses.fna: + type: file + description: CheckV's extracted proviruses contigs + pattern: "${prefix}/proviruses.fna" - viruses: - type: file - description: CheckV's extracted virus contigs - pattern: "${prefix}/viruses.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/viruses.fna: + type: file + description: CheckV's extracted virus contigs + pattern: "${prefix}/viruses.fna" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/checkv/updatedatabase/meta.yml b/modules/nf-core/checkv/updatedatabase/meta.yml index 2bed0c4cf028..fe411c63323b 100644 --- a/modules/nf-core/checkv/updatedatabase/meta.yml +++ b/modules/nf-core/checkv/updatedatabase/meta.yml @@ -18,32 +18,37 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/checkv/src/master/ doi: "10.1038/s41587-020-00774-7" licence: ["BSD License"] + identifier: biotools:checkv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - fasta: - type: file - description: fasta file containing additional sequences for the existing checkv database - pattern: "*.{fasta,fna,fa}" - - db: - type: directory - description: directory pointing to existing checkV database to avoid redownloading the database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - fasta: + type: file + description: fasta file containing additional sequences for the existing checkv + database + pattern: "*.{fasta,fna,fa}" + - - db: + type: directory + description: directory pointing to existing checkV database to avoid redownloading + the database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', bin:'1' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checkv_db: - type: directory - description: directory pointing to database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', bin:'1' ] + - ${prefix}/*: + type: directory + description: directory pointing to database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/chewbbaca/createschema/meta.yml b/modules/nf-core/chewbbaca/createschema/meta.yml index 1c7be66e2eaf..ef761f8a3955 100644 --- a/modules/nf-core/chewbbaca/createschema/meta.yml +++ b/modules/nf-core/chewbbaca/createschema/meta.yml @@ -12,55 +12,57 @@ tools: tool_dev_url: "https://github.com/B-UMMI/chewBBACA" doi: "10.1099/mgen.0.000166" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: directory - description: One or multiple FASTA files to create schema from - pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" - - - prodigal_tf: - type: file - description: File containing the prodigal training file - pattern: "*.ptf" - - - cds: - type: file - description: File containing the prodigal cds file - pattern: "*.cds" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: directory + description: One or multiple FASTA files to create schema from + pattern: "*.{fasta,fa,fas,fna,fasta.gz,fa.gz,fas.gz,fna.gz}" + - - prodigal_tf: + type: file + description: File containing the prodigal training file + pattern: "*.ptf" + - - cds: + type: file + description: File containing the prodigal cds file + pattern: "*.cds" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - schema: - type: directory - description: Schema directory - pattern: "*/" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - results/$meta.id: + type: directory + description: Schema directory + pattern: "*/" - cds_coordinates: - type: file - description: File containing the coordinates of the CDS in the input sample - pattern: "*_cds_coordinates.tsv" - + - results/cds_coordinates.tsv: + type: file + description: File containing the coordinates of the CDS in the input sample + pattern: "*_cds_coordinates.tsv" - invalid_cds: - type: file - description: File containing the list of alleles predicted by Prodigal that were excluded - pattern: "*_invalid_cds.txt" - + - results/invalid_cds.txt: + type: file + description: File containing the list of alleles predicted by Prodigal that + were excluded + pattern: "*_invalid_cds.txt" + - id_cds: + type: file + description: File containing the list of alleles predicted by Prodigal that + were excluded + pattern: "*_invalid_cds.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anwarMZ" diff --git a/modules/nf-core/chopper/meta.yml b/modules/nf-core/chopper/meta.yml index 9d8093d66bcb..916c865e8390 100644 --- a/modules/nf-core/chopper/meta.yml +++ b/modules/nf-core/chopper/meta.yml @@ -8,9 +8,11 @@ keywords: - qc tools: - "zcat": - description: "zcat uncompresses either a list of files on the command line or its standard input and writes the uncompressed data on standard output." + description: "zcat uncompresses either a list of files on the command line or + its standard input and writes the uncompressed data on standard output." documentation: "https://linux.die.net/man/1/zcat" args_id: "$args" + identifier: "" - "chopper": description: "A rust command line for filtering and trimming long reads." homepage: "https://github.com/wdecoster/chopper" @@ -19,34 +21,39 @@ tools: doi: "10.1093/bioinformatics/bty149" licence: ["MIT"] args_id: "$args2" + identifier: "" - "gzip": - description: "Gzip reduces the size of the named files using Lempel-Ziv coding (LZ77)." + description: "Gzip reduces the size of the named files using Lempel-Ziv coding + (LZ77)." documentation: "https://linux.die.net/man/1/gzip" args_id: "$args3" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FastQ with reads from long read sequencing e.g. PacBio or ONT - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FastQ with reads from long read sequencing e.g. PacBio or ONT + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Filtered and trimmed FastQ file - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered and trimmed FastQ file + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FynnFreyer" maintainers: diff --git a/modules/nf-core/chromap/chromap/meta.yml b/modules/nf-core/chromap/chromap/meta.yml index 140299ed6d4a..5eefb46169c3 100644 --- a/modules/nf-core/chromap/chromap/meta.yml +++ b/modules/nf-core/chromap/chromap/meta.yml @@ -21,77 +21,98 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing information for the fasta - e.g. [ id:'test' ] - - fasta: - type: file - description: | - The fasta reference file. - - meta3: - type: map - description: | - Groovy Map containing information for the index - e.g. [ id:'test' ] - - index: - type: file - description: | - Chromap genome index files (*.index) - - barcodes: - type: file - description: | - Cell barcode files - - whitelist: - type: file - description: | - Cell barcode whitelist file - - chr_order: - type: file - description: | - Custom chromosome order - - pairs_chr_order: - type: file - description: | - Natural chromosome order for pairs flipping + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing information for the fasta + e.g. [ id:'test' ] + - fasta: + type: file + description: | + The fasta reference file. + - - meta3: + type: map + description: | + Groovy Map containing information for the index + e.g. [ id:'test' ] + - index: + type: file + description: | + Chromap genome index files (*.index) + - - barcodes: + type: file + description: | + Cell barcode files + - - whitelist: + type: file + description: | + Cell barcode whitelist file + - - chr_order: + type: file + description: | + Custom chromosome order + - - pairs_chr_order: + type: file + description: | + Natural chromosome order for pairs flipping output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file - pattern: "*.bed.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: BED file + pattern: "*.bed.gz" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*.bam" - tagAlign: - type: file - description: tagAlign file - pattern: "*.tagAlign.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tagAlign.gz": + type: file + description: tagAlign file + pattern: "*.tagAlign.gz" - pairs: - type: file - description: pairs file - pattern: "*.pairs.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: pairs file + pattern: "*.pairs.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@joseespinosa" diff --git a/modules/nf-core/chromap/index/meta.yml b/modules/nf-core/chromap/index/meta.yml index 6559509ca11b..057847fd7266 100644 --- a/modules/nf-core/chromap/index/meta.yml +++ b/modules/nf-core/chromap/index/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Fasta reference file. + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Fasta reference file. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: file - description: Index file of the reference genome - pattern: "*.{index}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - "*.index": + type: file + description: Index file of the reference genome + pattern: "*.{index}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@joseespinosa" diff --git a/modules/nf-core/chromograph/meta.yml b/modules/nf-core/chromograph/meta.yml index 6540d9f077ed..4a986dbbb993 100644 --- a/modules/nf-core/chromograph/meta.yml +++ b/modules/nf-core/chromograph/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "chromograph" -description: Chromograph is a python package to create PNG images from genetics data such as BED and WIG files. +description: Chromograph is a python package to create PNG images from genetics data + such as BED and WIG files. keywords: - chromosome_visualization - bed @@ -9,83 +9,87 @@ keywords: - png tools: - "chromograph": - description: "Chromograph is a python package to create PNG images from genetics data such as BED and WIG files." + description: "Chromograph is a python package to create PNG images from genetics + data such as BED and WIG files." homepage: "https://github.com/Clinical-Genomics/chromograph" documentation: "https://github.com/Clinical-Genomics/chromograph/blob/master/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta6: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta7: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - autozyg: - type: file - description: Bed file containing the regions of autozygosity - - coverage: - type: file - description: Wig file containing the coverage information - - exome: - type: file - description: Bed file containing the coverage for exome. - - fracsnp: - type: file - description: Wig file containing the fraction of homozygous SNPs - - ideogram: - type: file - description: | - Bed file containing information necessary for ideogram plots. - Format ['chrom', 'start', 'end', 'name', 'gStain'] - - regions: - type: file - description: Bed file containing UPD regions - - sites: - type: file - description: Bed file containing UPD sites + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - autozyg: + type: file + description: Bed file containing the regions of autozygosity + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage: + type: file + description: Wig file containing the coverage information + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exome: + type: file + description: Bed file containing the coverage for exome. + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fracsnp: + type: file + description: Wig file containing the fraction of homozygous SNPs + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ideogram: + type: file + description: | + Bed file containing information necessary for ideogram plots. + Format ['chrom', 'start', 'end', 'name', 'gStain'] + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: Bed file containing UPD regions + - - meta7: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: Bed file containing UPD sites output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - plots: - type: file - description: Directory containing the plots in png format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Directory containing the plots in png format + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/circexplorer2/annotate/meta.yml b/modules/nf-core/circexplorer2/annotate/meta.yml index aac031ce3db1..20b853104eec 100644 --- a/modules/nf-core/circexplorer2/annotate/meta.yml +++ b/modules/nf-core/circexplorer2/annotate/meta.yml @@ -11,38 +11,41 @@ tools: documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" licence: ["MIT License"] + identifier: biotools:CIRCexplorer2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - junctions: - type: file - description: Reformatted junctions file - pattern: "*.{junction}" - - fasta: - type: file - description: Genome FASTA file - pattern: "*.{fa,fasta}" - - gene_annotation: - type: file - description: Reformatted GTF file for CIRCexplorer2 - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - junctions: + type: file + description: Reformatted junctions file + pattern: "*.{junction}" + - - fasta: + type: file + description: Genome FASTA file + pattern: "*.{fa,fasta}" + - - gene_annotation: + type: file + description: Reformatted GTF file for CIRCexplorer2 + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Annotated circRNA TXT file - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Annotated circRNA TXT file + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/circexplorer2/parse/meta.yml b/modules/nf-core/circexplorer2/parse/meta.yml index 83e6e9d35b4e..382c64f30991 100644 --- a/modules/nf-core/circexplorer2/parse/meta.yml +++ b/modules/nf-core/circexplorer2/parse/meta.yml @@ -1,5 +1,6 @@ name: "circexplorer2_parse" -description: CIRCexplorer2 parses fusion junction files from multiple aligners to prepare them for CIRCexplorer2 annotate. +description: CIRCexplorer2 parses fusion junction files from multiple aligners to + prepare them for CIRCexplorer2 annotate. keywords: - parse - circrna @@ -11,30 +12,34 @@ tools: documentation: "https://circexplorer2.readthedocs.io/en/latest/" doi: "10.1101/gr.202895.115" licence: ["MIT License"] + identifier: biotools:CIRCexplorer2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fusions: - type: file - description: BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) file. Aligner will be autodetected based on file suffix. - pattern: "*.{bam,junction,bed,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fusions: + type: file + description: BAM (BWA), BED (Segemehl), TXT (MapSplice), or Junction (STAR) + file. Aligner will be autodetected based on file suffix. + pattern: "*.{bam,junction,bed,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Standardized fusion junction file suitable for CIRCexplorer2 annotate module. - pattern: "*.{bam,cram,sam}" + - junction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/circularmapper/circulargenerator/meta.yml b/modules/nf-core/circularmapper/circulargenerator/meta.yml index baa39e74b90a..637b38d4d969 100644 --- a/modules/nf-core/circularmapper/circulargenerator/meta.yml +++ b/modules/nf-core/circularmapper/circulargenerator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "circularmapper_circulargenerator" description: A method to improve mappings on circular genomes, using the BWA mapper. @@ -8,56 +7,68 @@ keywords: - genomics tools: - "circulargenerator": - description: "Creating a modified reference genome, with an elongation of the an specified amount of bases" + description: "Creating a modified reference genome, with an elongation of the + an specified amount of bases" homepage: "https://github.com/apeltzer/CircularMapper" documentation: "https://github.com/apeltzer/CircularMapper/blob/master/docs/contents/userguide.rst" tool_dev_url: "https://github.com/apeltzer/CircularMapper" doi: "no DOI available" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - reference: - type: file - description: Genome fasta file - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - elongation_factor: - type: integer - description: The number of bases that the ends of the target chromosome in the reference genome should be elongated by - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'sample1' ]` - - target: - type: string - description: The name of the chromosome in the reference genome that should be elongated + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - reference: + type: file + description: Genome fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - elongation_factor: + type: integer + description: The number of bases that the ends of the target chromosome in the + reference genome should be elongated by + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'sample1' ]` + - target: + type: string + description: The name of the chromosome in the reference genome that should + be elongated output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Genome fasta file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_${elongation_factor}.fasta": + type: file + description: Genome fasta file + pattern: "*.fasta" - elongated: - type: file - description: File listing the chromosomes that were elongated - pattern: "*_elongated" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*${elongation_factor}_elongated": + type: file + description: File listing the chromosomes that were elongated + pattern: "*_elongated" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apalleja" - "@TCLamnidis" diff --git a/modules/nf-core/circularmapper/realignsamfile/meta.yml b/modules/nf-core/circularmapper/realignsamfile/meta.yml index 94f74069e562..52b2fdd5a33d 100644 --- a/modules/nf-core/circularmapper/realignsamfile/meta.yml +++ b/modules/nf-core/circularmapper/realignsamfile/meta.yml @@ -17,55 +17,60 @@ tools: tool_dev_url: "https://github.com/apeltzer/CircularMapper/" doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - fasta: - type: file - description: Input elongated genome fasta - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - elongation_factor: - type: integer - description: The elongation factor used when running circulargenerator, i.e. the number of bases that the ends of the target chromosome in the reference genome was elongated by - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - elongated_chr_list: - type: file - description: File listing the chromosomes that were elongated - pattern: "*_elongated" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Input elongated genome fasta + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - elongation_factor: + type: integer + description: The elongation factor used when running circulargenerator, i.e. + the number of bases that the ends of the target chromosome in the reference + genome was elongated by + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - elongated_chr_list: + type: file + description: File listing the chromosomes that were elongated + pattern: "*_elongated" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - bam: - type: file - description: Realigned BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_realigned.bam": + type: file + description: Realigned BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@shyama-mama" - "@jbv2" diff --git a/modules/nf-core/clame/meta.yml b/modules/nf-core/clame/meta.yml index 24e17af00f5f..c5a7f7635158 100644 --- a/modules/nf-core/clame/meta.yml +++ b/modules/nf-core/clame/meta.yml @@ -6,56 +6,92 @@ keywords: - genomics tools: - "clame": - description: "CLAME is a binning software for metagenomic reads. It immplements a fm-index search algorithm for nucleotide sequence alignment. Then it uses strongly connected component strategy to bin sequences with similar DNA composition." + description: "CLAME is a binning software for metagenomic reads. It immplements + a fm-index search algorithm for nucleotide sequence alignment. Then it uses + strongly connected component strategy to bin sequences with similar DNA composition." homepage: "https://github.com/andvides/CLAME" documentation: "https://github.com/andvides/CLAME" tool_dev_url: "https://github.com/andvides/CLAME" doi: "10.1186/s12864-018-5191-y" licence: ["GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Nucleotide sequences in FASTA format - pattern: "*.{fasta,fa,fna,faa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Nucleotide sequences in FASTA format + pattern: "*.{fasta,fa,fna,faa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Output fasta file for all the bins reported, optional since it will be created when bins can be found - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: Output fasta file for all the bins reported, optional since it + will be created when bins can be found + pattern: "*.{fasta}" - bins: - type: file - description: All bins reported - pattern: "*.{binning}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.binning": + type: file + description: All bins reported + pattern: "*.{binning}" - fm: - type: file - description: FM-index output - pattern: "*.{fm9}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fm9": + type: file + description: FM-index output + pattern: "*.{fm9}" - index: - type: file - description: 1st column contains the original name for each read, 2nd column the index used by CLAME - pattern: "*.{index}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.index": + type: file + description: 1st column contains the original name for each read, 2nd column + the index used by CLAME + pattern: "*.{index}" - links: - type: file - description: Histogram links by number of reads - pattern: "*.{links}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.links": + type: file + description: Histogram links by number of reads + pattern: "*.{links}" - result: - type: file - description: Adjacency list for the overlap detected by each read - pattern: "*.{result}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.result": + type: file + description: Adjacency list for the overlap detected by each read + pattern: "*.{result}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" diff --git a/modules/nf-core/clippy/meta.yml b/modules/nf-core/clippy/meta.yml index cdb9f00b8432..7ccd82660486 100644 --- a/modules/nf-core/clippy/meta.yml +++ b/modules/nf-core/clippy/meta.yml @@ -1,4 +1,3 @@ ---- name: clippy description: Runs the Clippy CLIP peak caller keywords: @@ -13,37 +12,59 @@ tools: tool_dev_url: "https://github.com/ulelab/clippy" doi: "10.7554/eLife.84034" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bed,bed.gz}" - - gtf: - type: file - description: A GTF file of genes to call peaks on - pattern: "*.{gtf}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bed,bed.gz}" + - - gtf: + type: file + description: A GTF file of genes to call peaks on + pattern: "*.{gtf}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" output: - peaks: - type: file - description: BED file of peaks called by Clippy - pattern: "*_broadPeaks.bed.gz" + - meta: + type: file + description: BED file of peaks called by Clippy + pattern: "*_broadPeaks.bed.gz" + - "*_Peaks.bed": + type: file + description: BED file of peaks called by Clippy + pattern: "*_broadPeaks.bed.gz" - summits: - type: file - description: BED file of peak summits called by Clippy - pattern: "*[0-9].bed.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: file + description: BED file of peak summits called by Clippy + pattern: "*[0-9].bed.gz" + - "*_Summits.bed": + type: file + description: BED file of peak summits called by Clippy + pattern: "*[0-9].bed.gz" + - intergenic_gtf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_intergenic_regions.gtf": + type: file + description: GTF file of intergenic regions + pattern: "*_intergenic_regions.gtf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@CharlotteAnne" diff --git a/modules/nf-core/clonalframeml/meta.yml b/modules/nf-core/clonalframeml/meta.yml index 5abe2cc52163..2696edd872a5 100644 --- a/modules/nf-core/clonalframeml/meta.yml +++ b/modules/nf-core/clonalframeml/meta.yml @@ -12,54 +12,87 @@ tools: tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML doi: "10.1371/journal.pcbi.1004041" licence: ["GPL v3"] + identifier: biotools:clonalframeml input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - msa: - type: file - description: A multiple seqeunce alignmnet in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - newick: - type: file - description: A Newick formated tree based on multiple sequence alignment - pattern: "*.{newick,treefile,dnd}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - newick: + type: file + description: A Newick formated tree based on multiple sequence alignment + pattern: "*.{newick,treefile,dnd}" + - msa: + type: file + description: A multiple seqeunce alignmnet in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - emsim: - type: file - description: Bootstrapped values for the three parameters R/theta, nu and delta - pattern: "*.emsim.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.emsim.txt": + type: file + description: Bootstrapped values for the three parameters R/theta, nu and delta + pattern: "*.emsim.txt" - em: - type: file - description: Point estimates for R/theta, nu, delta and the branch lengths - pattern: "*.em.txt" - - fasta: - type: file - description: Sequence reconstructed by maximum likelihood - pattern: "*.ML_sequence.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.em.txt": + type: file + description: Point estimates for R/theta, nu, delta and the branch lengths + pattern: "*.em.txt" + - status: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.importation_status.txt": + type: file + description: List of reconstructed recombination events + pattern: "*.importation_status.txt" - newick: - type: file - description: Tree with all nodes labelled - pattern: "*.labelled_tree.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.labelled_tree.newick": + type: file + description: Tree with all nodes labelled + pattern: "*.labelled_tree.newick" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ML_sequence.fasta": + type: file + description: Sequence reconstructed by maximum likelihood + pattern: "*.ML_sequence.fasta" - pos_ref: - type: file - description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta - pattern: "*.position_cross_reference.txt" - - status: - type: file - description: List of reconstructed recombination events - pattern: "*.importation_status.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.position_cross_reference.txt": + type: file + description: CSV mapping input sequence files to the sequences in the *.ML_sequence.fasta + pattern: "*.position_cross_reference.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/clustalo/align/meta.yml b/modules/nf-core/clustalo/align/meta.yml index 469b3a376916..c97ebf722e9d 100644 --- a/modules/nf-core/clustalo/align/meta.yml +++ b/modules/nf-core/clustalo/align/meta.yml @@ -6,52 +6,59 @@ keywords: - genomics tools: - "clustalo": - description: "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins" + description: "Latest version of Clustal: a multiple sequence alignment program + for DNA or proteins" homepage: "http://www.clustal.org/omega/" documentation: "http://www.clustal.org/omega/" tool_dev_url: "http://www.clustal.org/omega/" doi: "10.1038/msb.2011.75" licence: ["GPL v2"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in gzipped fasta format - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in gzipped fasta format + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@joseespinosa" diff --git a/modules/nf-core/clustalo/guidetree/meta.yml b/modules/nf-core/clustalo/guidetree/meta.yml index b8e02352a2f9..e006bad7866b 100644 --- a/modules/nf-core/clustalo/guidetree/meta.yml +++ b/modules/nf-core/clustalo/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "clustalo_guidetree" description: Renders a guidetree in clustalo @@ -8,36 +7,40 @@ keywords: - newick tools: - "clustalo": - description: "Latest version of Clustal: a multiple sequence alignment program for DNA or proteins" + description: "Latest version of Clustal: a multiple sequence alignment program + for DNA or proteins" homepage: "http://www.clustal.org/omega/" documentation: "http://www.clustal.org/omega/" tool_dev_url: "http://www.clustal.org/omega/" doi: "10.1038/msb.2011.75" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - tree: - type: file - description: Guide tree file in Newick format - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.dnd": + type: file + description: Guide tree file in Newick format + pattern: "*.{dnd}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/cmseq/polymut/meta.yml b/modules/nf-core/cmseq/polymut/meta.yml index 182a75e0b260..8c0f52a9a662 100644 --- a/modules/nf-core/cmseq/polymut/meta.yml +++ b/modules/nf-core/cmseq/polymut/meta.yml @@ -18,42 +18,46 @@ tools: documentation: https://github.com/SegataLab/cmseq tool_dev_url: https://github.com/SegataLab/cmseq licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - gff: - type: file - description: GFF file used to extract protein-coding genes - pattern: "*.gff" - - fasta: - type: file - description: Optional fasta file to run on a subset of references in the BAM file. - pattern: .{fa,fasta,fas,fna} + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - gff: + type: file + description: GFF file used to extract protein-coding genes + pattern: "*.gff" + - fasta: + type: file + description: Optional fasta file to run on a subset of references in the BAM + file. + pattern: .{fa,fasta,fas,fna} output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - polymut: - type: file - description: Polymut report in `.txt` format. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Polymut report in `.txt` format. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/cnvkit/access/meta.yml b/modules/nf-core/cnvkit/access/meta.yml index 259ae3471c1f..4627fe0abd00 100644 --- a/modules/nf-core/cnvkit/access/meta.yml +++ b/modules/nf-core/cnvkit/access/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_access -description: Calculate the sequence-accessible coordinates in chromosomes from the given reference genome, output as a BED file. +description: Calculate the sequence-accessible coordinates in chromosomes from the + given reference genome, output as a BED file. keywords: - cvnkit - access @@ -15,38 +16,42 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome FASTA. - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - exclude_bed: - type: file - description: Additional regions to exclude, in BED format. Can be used multiple times. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome FASTA. + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - exclude_bed: + type: file + description: Additional regions to exclude, in BED format. Can be used multiple + times. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing accessible regions. - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing accessible regions. + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/antitarget/meta.yml b/modules/nf-core/cnvkit/antitarget/meta.yml index d879092d33ae..13f12a10c0e5 100644 --- a/modules/nf-core/cnvkit/antitarget/meta.yml +++ b/modules/nf-core/cnvkit/antitarget/meta.yml @@ -15,30 +15,33 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - targets: - type: file - description: File containing genomic regions - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - targets: + type: file + description: File containing genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing off-target regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing off-target regions + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index f14efe553c32..30f7a1a29b88 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -12,94 +12,127 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tumor: - type: file - description: | - Input tumour sample bam file (or cram) - - normal: - type: file - description: | - Input normal sample bam file (or cram) - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: | - Input reference genome fasta index (optional, but recommended for cram_input) - - meta4: - type: map - description: | - Groovy Map containing information about target file - e.g. [ id:'test' ] - - targets: - type: file - description: | - Input target bed file - - meta5: - type: map - description: | - Groovy Map containing information about reference file - e.g. [ id:'test' ] - - reference: - type: file - description: | - Input reference cnn-file (only for germline and tumor-only running) - - panel_of_normals: - type: file - description: | - Input panel of normals file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tumor: + type: file + description: | + Input tumour sample bam file (or cram) + - normal: + type: file + description: | + Input normal sample bam file (or cram) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + Input reference genome fasta file (only needed for cram_input and/or when normal_samples are provided) + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: | + Input reference genome fasta index (optional, but recommended for cram_input) + - - meta4: + type: map + description: | + Groovy Map containing information about target file + e.g. [ id:'test' ] + - targets: + type: file + description: | + Input target bed file + - - meta5: + type: map + description: | + Groovy Map containing information about reference file + e.g. [ id:'test' ] + - reference: + type: file + description: | + Input reference cnn-file (only for germline and tumor-only running) + - - panel_of_normals: + type: file + description: | + Input panel of normals file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing genomic regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing genomic regions + pattern: "*.{bed}" - cnn: - type: file - description: File containing coverage information - pattern: "*.{cnn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnn": + type: file + description: File containing coverage information + pattern: "*.{cnn}" - cnr: - type: file - description: File containing copy number ratio information - pattern: "*.{cnr}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnr": + type: file + description: File containing copy number ratio information + pattern: "*.{cnr}" - cns: - type: file - description: File containing copy number segment information - pattern: "*.{cns}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cns": + type: file + description: File containing copy number segment information + pattern: "*.{cns}" - pdf: - type: file - description: File with plot of copy numbers or segments on chromosomes - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: File with plot of copy numbers or segments on chromosomes + pattern: "*.{pdf}" - png: - type: file - description: File with plot of bin-level log2 coverages and segmentation calls - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: File with plot of bin-level log2 coverages and segmentation calls + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@drpatelh" diff --git a/modules/nf-core/cnvkit/call/meta.yml b/modules/nf-core/cnvkit/call/meta.yml index 64dc336869fa..b3b4a4a78afa 100644 --- a/modules/nf-core/cnvkit/call/meta.yml +++ b/modules/nf-core/cnvkit/call/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_call -description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute integer copy number +description: Given segmented log2 ratio estimates (.cns), derive each segment’s absolute + integer copy number keywords: - cnvkit - bam @@ -12,34 +13,37 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cns: - type: file - description: CNVKit CNS file. - pattern: "*.cns" - - vcf: - type: file - description: Germline VCF file for BAF. - pattern: "*.vcf{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cns: + type: file + description: CNVKit CNS file. + pattern: "*.cns" + - vcf: + type: file + description: Germline VCF file for BAF. + pattern: "*.vcf{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - cns: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cns": + type: file + description: CNS file. + pattern: "*.cns" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: File containing copy number information in new format. - pattern: "*.{bed,vcf,cdt,jtv,seg,interval_count}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/export/meta.yml b/modules/nf-core/cnvkit/export/meta.yml index 836baa1b58ee..a573e03bac5a 100644 --- a/modules/nf-core/cnvkit/export/meta.yml +++ b/modules/nf-core/cnvkit/export/meta.yml @@ -1,5 +1,6 @@ name: cnvkit_export -description: Convert copy number ratio tables (.cnr files) or segments (.cns) to another format. +description: Convert copy number ratio tables (.cnr files) or segments (.cns) to another + format. keywords: - cnvkit - copy number @@ -11,30 +12,32 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cns: - type: file - description: CNVKit CNS file. - pattern: "*.cns" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cns: + type: file + description: CNVKit CNS file. + pattern: "*.cns" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${suffix}: + type: file + description: Output file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cns: - type: file - description: File containing copy number segment information - pattern: "*.{cns}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/genemetrics/meta.yml b/modules/nf-core/cnvkit/genemetrics/meta.yml index 4bef28c7d5e4..6b110accc234 100644 --- a/modules/nf-core/cnvkit/genemetrics/meta.yml +++ b/modules/nf-core/cnvkit/genemetrics/meta.yml @@ -12,34 +12,47 @@ tools: homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cnr: - type: file - description: CNR file - pattern: "*.cnr" - - cns: - type: file - description: CNS file [Optional] - pattern: "*.cns" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cnr: + type: file + description: CNR file + pattern: "*.cnr" + - cns: + type: file + description: CNS file [Optional] + pattern: "*.cns" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - txt: - type: file - description: TXT file - pattern: "*.txt" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file + pattern: "*.tsv" + - cnn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cnn": + type: file + description: CNN file + pattern: "*.cnn" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@marrip" diff --git a/modules/nf-core/cnvkit/reference/meta.yml b/modules/nf-core/cnvkit/reference/meta.yml index 8747893b6fb4..965a7b579534 100644 --- a/modules/nf-core/cnvkit/reference/meta.yml +++ b/modules/nf-core/cnvkit/reference/meta.yml @@ -15,33 +15,32 @@ tools: tool_dev_url: https://github.com/etal/cnvkit doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - fasta: - type: file - description: File containing reference genome - pattern: "*.{fasta}" - - targets: - type: file - description: File containing genomic regions - pattern: "*.{bed}" - - antitargets: - type: file - description: File containing off-target genomic regions - pattern: "*.{bed}" + - - fasta: + type: file + description: File containing reference genome + pattern: "*.{fasta}" + - - targets: + type: file + description: File containing genomic regions + pattern: "*.{bed}" + - - antitargets: + type: file + description: File containing off-target genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - cnn: - type: file - description: File containing a copy-number reference (required for CNV calling in tumor_only mode) - pattern: "*.{cnn}" + - "*.cnn": + type: file + description: File containing a copy-number reference (required for CNV calling + in tumor_only mode) + pattern: "*.{cnn}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvkit/target/meta.yml b/modules/nf-core/cnvkit/target/meta.yml index 1f0e31dc8ff0..94e1f57b1ab1 100644 --- a/modules/nf-core/cnvkit/target/meta.yml +++ b/modules/nf-core/cnvkit/target/meta.yml @@ -15,39 +15,42 @@ tools: tool_dev_url: "https://github.com/etal/cnvkit" doi: 10.1371/journal.pcbi.1004873 licence: ["Apache-2.0"] + identifier: biotools:cnvkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - baits: - type: file - description: BED or interval file listing the targeted regions. - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotation: - type: file - description: Use gene models from this file to assign names to the target regions. - pattern: "*.{txt,bed,gff3,pil}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - baits: + type: file + description: BED or interval file listing the targeted regions. + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - annotation: + type: file + description: Use gene models from this file to assign names to the target regions. + pattern: "*.{txt,bed,gff3,pil}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: File containing target regions - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: File containing target regions + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@priesgo" diff --git a/modules/nf-core/cnvnator/cnvnator/meta.yml b/modules/nf-core/cnvnator/cnvnator/meta.yml index 627b76b993de..7ad6b4068b84 100644 --- a/modules/nf-core/cnvnator/cnvnator/meta.yml +++ b/modules/nf-core/cnvnator/cnvnator/meta.yml @@ -1,5 +1,6 @@ name: "cnvnator_cnvnator" -description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage by mapped reads. +description: CNVnator is a command line tool for CNV/CNA analysis from depth-of-coverage + by mapped reads. keywords: - cnvnator - cnv @@ -11,65 +12,74 @@ tools: documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" licence: ["MIT"] + identifier: biotools:cnvnator input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.bam" - - root: - type: file - description: ROOT file - pattern: "*.root" - - fasta: - type: file - description: Path to a directory containing fasta files or a fasta file - pattern: "*.fa" - - fai: - type: file - description: Path to a fasta file index - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - root: + type: file + description: ROOT file + pattern: "*.root" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Path to a directory containing fasta files or a fasta file + pattern: "*.fa" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Path to a fasta file index + pattern: "*.fai" output: - - output_meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - root: - type: file - description: A ROOT file - pattern: "*.root" + - output_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.root: + type: file + description: A ROOT file + pattern: "*.root" - tab: - type: file - description: A tab file containing cnvnator calls - pattern: "*.tab" + - output_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.tab: + type: file + description: A tab file containing cnvnator calls + pattern: "*.tab" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvnator/convert2vcf/meta.yml b/modules/nf-core/cnvnator/convert2vcf/meta.yml index b7d269e04801..3d686c2f17f8 100644 --- a/modules/nf-core/cnvnator/convert2vcf/meta.yml +++ b/modules/nf-core/cnvnator/convert2vcf/meta.yml @@ -1,5 +1,6 @@ name: "cnvnator_convert2vcf" -description: convert2vcf.pl is command line tool to convert CNVnator calls to vcf format. +description: convert2vcf.pl is command line tool to convert CNVnator calls to vcf + format. keywords: - cnvnator - cnv @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/abyzovlab/CNVnator/blob/master/README.md" tool_dev_url: "https://github.com/abyzovlab/CNVnator" licence: ["MIT"] + identifier: biotools:cnvnator input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - calls: - type: file - description: A tab file containing CNVnator calls - pattern: "*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - calls: + type: file + description: A tab file containing CNVnator calls + pattern: "*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: CNVnator calls in vcf format - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: CNVnator calls in vcf format + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/cnvpytor/callcnvs/meta.yml b/modules/nf-core/cnvpytor/callcnvs/meta.yml index 25e22941c7ee..cdc96d8c0dcf 100644 --- a/modules/nf-core/cnvpytor/callcnvs/meta.yml +++ b/modules/nf-core/cnvpytor/callcnvs/meta.yml @@ -12,33 +12,37 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - pytor: - type: file - description: pytor file containing partitions of read depth histograms using mean-shift method - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - pytor: + type: file + description: pytor file containing partitions of read depth histograms using + mean-shift method + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: pytor files containing cnv calls - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor files containing cnv calls + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" maintainers: diff --git a/modules/nf-core/cnvpytor/histogram/meta.yml b/modules/nf-core/cnvpytor/histogram/meta.yml index e8fcedd47f6b..d53733b21324 100644 --- a/modules/nf-core/cnvpytor/histogram/meta.yml +++ b/modules/nf-core/cnvpytor/histogram/meta.yml @@ -12,33 +12,37 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor: - type: file - description: pytor file containing read depth data - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor: + type: file + description: pytor file containing read depth data + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: pytor file containing read depth histograms binned based on given bin size(s) - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor file containing read depth histograms binned based on given + bin size(s) + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/importreaddepth/meta.yml b/modules/nf-core/cnvpytor/importreaddepth/meta.yml index 660a7bdd77ab..0e1acff32855 100644 --- a/modules/nf-core/cnvpytor/importreaddepth/meta.yml +++ b/modules/nf-core/cnvpytor/importreaddepth/meta.yml @@ -1,5 +1,6 @@ name: cnvpytor_importreaddepth -description: command line tool for CNV/CNA analysis. This step imports the read depth data into a root pytor file. +description: command line tool for CNV/CNA analysis. This step imports the read depth + data into a root pytor file. keywords: - read depth - cnv @@ -13,42 +14,47 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input_file: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: bam file index - pattern: "*.{bai,crai}" - - fasta: - type: file - description: specifies reference genome file (only for cram file without reference genome) - pattern: "*.{fasta,fasta.gz,fa,fa.gz}" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input_file: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: bam file index + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: specifies reference genome file (only for cram file without reference + genome) + pattern: "*.{fasta,fasta.gz,fa,fa.gz}" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - pytor: - type: file - description: read depth root file in which read depth data binned to 100 base pair bins will be stored. - pattern: "*.{pytor}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.pytor": + type: file + description: read depth root file in which read depth data binned to 100 base + pair bins will be stored. + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/partition/meta.yml b/modules/nf-core/cnvpytor/partition/meta.yml index c9a04d305166..014e0d407026 100644 --- a/modules/nf-core/cnvpytor/partition/meta.yml +++ b/modules/nf-core/cnvpytor/partition/meta.yml @@ -12,33 +12,36 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor: - type: file - description: pytor file containing read depth data - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor: + type: file + description: pytor file containing read depth data + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - partitions: - type: file - description: pytor file containing partitions of read depth histograms using mean-shift method - pattern: "*.{pytor}" + - pytor: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ${pytor.baseName}.pytor: + type: file + description: pytor file + pattern: "*.{pytor}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cnvpytor/view/meta.yml b/modules/nf-core/cnvpytor/view/meta.yml index 7c2088b4c356..9cab351a26fe 100644 --- a/modules/nf-core/cnvpytor/view/meta.yml +++ b/modules/nf-core/cnvpytor/view/meta.yml @@ -12,44 +12,61 @@ tools: tool_dev_url: https://github.com/abyzovlab/CNVpytor doi: "10.1101/2021.01.27.428472v1" licence: ["MIT"] + identifier: biotools:cnvpytor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pytor_files: - type: file - description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files. - pattern: "*.{pytor}" - - bin_sizes: - type: string - description: list of binsizes separated by space e.g. "1000 10000" and "1000" - - output_format: - type: string - description: output format of the cnv calls. Valid entries are "tsv", "vcf", and "xls" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pytor_files: + type: file + description: pytor file containing cnv calls. To merge calls from multiple samples + use a list of files. + pattern: "*.{pytor}" + - - bin_sizes: + type: string + description: list of binsizes separated by space e.g. "1000 10000" and "1000" + - - output_format: + type: string + description: output format of the cnv calls. Valid entries are "tsv", "vcf", + and "xls" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - tsv: - type: file - description: tsv file containing cnv calls - pattern: "*.{tsv}" - vcf: - type: file - description: vcf file containing cnv calls - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: vcf file containing cnv calls + pattern: "*.{vcf}" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tsv": + type: file + description: tsv file containing cnv calls + pattern: "*.{tsv}" - xls: - type: file - description: xls file containing cnv calls - pattern: "*.{xls}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xls": + type: file + description: xls file containing cnv calls + pattern: "*.{xls}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sima-r" - "@ramprasadn" diff --git a/modules/nf-core/cobrameta/meta.yml b/modules/nf-core/cobrameta/meta.yml index 5885f079bc4f..1a5820d6c649 100644 --- a/modules/nf-core/cobrameta/meta.yml +++ b/modules/nf-core/cobrameta/meta.yml @@ -1,5 +1,6 @@ name: cobrameta -description: A tool to raise the quality of viral genomes assembled from short-read metagenomes via resolving and joining of contigs fragmented during de novo assembly. +description: A tool to raise the quality of viral genomes assembled from short-read + metagenomes via resolving and joining of contigs fragmented during de novo assembly. keywords: - cobra - contig @@ -10,111 +11,168 @@ keywords: - phage tools: - cobra-meta: - description: COBRA is a tool to get higher quality viral genomes assembled from metagenomes. + description: COBRA is a tool to get higher quality viral genomes assembled from + metagenomes. homepage: https://github.com/linxingchen/cobra documentation: https://github.com/linxingchen/cobra tool_dev_url: https://github.com/linxingchen/cobra doi: 10.1038/s41564-023-01598-2 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: | - Assembly file (contigs/scaffolds) in FASTA format - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" - - coverage: - type: file - description: | - TSV file with 2 columns containing 1) the contig/scaffold id and - 2) the coverage depth of the sequence specified in column 1 - pattern: "*.{tsv,txt}" - - query: - type: file - description: | - File containing the query contigs that the user wants COBRA to extend. This - can be provided in one-column TXT or FASTA format. (The IDs must match the IDs - in the `--fasta` file exactly) - pattern: "*.{txt,fasta}" - - bam: - type: file - description: | - Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly - to the resulting assembly FASTA - pattern: "*.{bam,cram,sam}" - - assembler: - type: string - description: The name of the tool used to assemble contigs - pattern: "{metaspades,megahit,idba}" - - mink: - type: integer - description: The minimum kmer size used to assemble contigs - pattern: "[0-9]+" - - maxk: - type: integer - description: The maximum kmer size used to assemble contigs - pattern: "[0-9]+" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: | + Assembly file (contigs/scaffolds) in FASTA format + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage: + type: file + description: | + TSV file with 2 columns containing 1) the contig/scaffold id and + 2) the coverage depth of the sequence specified in column 1 + pattern: "*.{tsv,txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: | + File containing the query contigs that the user wants COBRA to extend. This + can be provided in one-column TXT or FASTA format. (The IDs must match the IDs + in the `--fasta` file exactly) + pattern: "*.{txt,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Sorted BAM/CRAM/SAM file resulting from mapping reads used in assembly + to the resulting assembly FASTA + pattern: "*.{bam,cram,sam}" + - - assembler: + type: string + description: The name of the tool used to assemble contigs + pattern: "{metaspades,megahit,idba}" + - - mink: + type: integer + description: The minimum kmer size used to assemble contigs + pattern: "[0-9]+" + - - maxk: + type: integer + description: The maximum kmer size used to assemble contigs + pattern: "[0-9]+" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - extended_assemblies: - type: file - description: | - Gzipped FASTA file containing query contigs that are already circular - pattern: "${prefix}/COBRA_category_i_self_circular.fasta.gz" + - self_circular: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_i_self_circular.fasta.gz: + type: file + description: fasta file + pattern: "*/COBRA_category_i_self_circular.fasta.gz" - extended_circular: - type: file - description: | - Gzipped FASTA file containing query contigs that were joined and extended - into a circular genome - pattern: "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that were joined and extended + into a circular genome + pattern: "${prefix}/COBRA_category_ii-a_extended_circular_unique.fasta.gz" - extended_partial: - type: file - description: | - Gzipped FASTA file containing query contigs were joined and extended, but - not into circular sequences - pattern: "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs were joined and extended, but + not into circular sequences + pattern: "${prefix}/COBRA_category_ii-b_extended_partial_unique.fasta.gz" - extended_failed: - type: file - description: | - Gzipped FASTA file containing query contigs that could not be extended due - to COBRA rules - pattern: "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that could not be extended due + to COBRA rules + pattern: "${prefix}/COBRA_category_ii-c_extended_failed.fasta.gz" - orphan_end: - type: file - description: | - Gzipped FASTA file containing query contigs that do not shared the - "expected overlap length" with other contigs - pattern: "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" - - all_assemblies: - type: file - description: | - Gzipped FASTA file containing all FASTA outputs combined into one file - pattern: "${prefix}/COBRA_all_assemblies.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_category_iii_orphan_end.fasta.gz: + type: file + description: | + Gzipped FASTA file containing query contigs that do not shared the + "expected overlap length" with other contigs + pattern: "${prefix}/COBRA_category_iii_orphan_end.fasta.gz" + - all_cobra_assemblies: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_all_assemblies.fasta.gz: + type: file + description: Gzipped FASTA file containing all the assemblies generated by COBRA + pattern: "*/COBRA_all_assemblies.fasta.gz" - joining_summary: - type: file - description: | - TSV file containing information regarding COBRA's extension results - pattern: "${prefix}/COBRA_joining_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/COBRA_joining_summary.txt: + type: file + description: | + TSV file containing information regarding COBRA's extension results + pattern: "${prefix}/COBRA_joining_summary.txt" - log: - type: file - description: | - Log file containing the contents of each processing - pattern: "${prefix}/log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/log: + type: file + description: | + Log file containing the contents of each processing + pattern: "${prefix}/log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/cobs/classicconstruct/meta.yml b/modules/nf-core/cobs/classicconstruct/meta.yml index 07488abd277a..3f661b026684 100644 --- a/modules/nf-core/cobs/classicconstruct/meta.yml +++ b/modules/nf-core/cobs/classicconstruct/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cobs_classicconstruct" description: Builds a classic bloom filter COBS index @@ -15,45 +14,43 @@ tools: tool_dev_url: "https://github.com/iqbal-lab-org/cobs" doi: "10.1007/978-3-030-32686-9_21" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: | - The file or directory to be indexed. - COBS can read: - 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz), - 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz), - 3. "Multi-FASTA" and "Multi-FASTQ" files (*.mfasta, *.mfastq), - 4. McCortex files (*.ctx), - 5. or text files (*.txt). - You can either recursively scan a directory for all files matching any of these files, - or pass a *.list file which lists all paths COBS should index. - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: | + The file or directory to be indexed. + COBS can read: + 1. FASTA files (*.fa, *.fasta, *.fna, *.ffn, *.faa, *.frn, *.fa.gz, *.fasta.gz, *.fna.gz, *.ffn.gz, *.faa.gz, *.frn.gz), + 2. FASTQ files (*.fq, *.fastq, *.fq.gz., *.fastq.gz), + 3. "Multi-FASTA" and "Multi-FASTQ" files (*.mfasta, *.mfastq), + 4. McCortex files (*.ctx), + 5. or text files (*.txt). + You can either recursively scan a directory for all files matching any of these files, + or pass a *.list file which lists all paths COBS should index. + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - index: - type: file - description: The COBS classic index - pattern: "*.index.cobs_classic" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.index.cobs_classic": + type: file + description: The COBS classic index + pattern: "*.index.cobs_classic" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/cobs/compactconstruct/meta.yml b/modules/nf-core/cobs/compactconstruct/meta.yml index a9fc6c27c847..1f1dfa2e6ed1 100644 --- a/modules/nf-core/cobs/compactconstruct/meta.yml +++ b/modules/nf-core/cobs/compactconstruct/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "cobs_compactconstruct" description: Builds a compact bloom filter COBS index @@ -14,45 +13,43 @@ tools: documentation: "https://github.com/iqbal-lab-org/cobs" doi: "10.1007/978-3-030-32686-9_21" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - input: - type: file - description: | - The file or directory to be indexed. - COBS can read: - 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`), - 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`), - 3. "Multi-FASTA" and "Multi-FASTQ" files (`*.mfasta`, `*.mfastq`), - 4. McCortex files (`*.ctx`), - 5. or text files (`*.txt`). - You can either recursively scan a directory for all files matching any of these files, - or pass a `*.list` file which lists all paths COBS should index. - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - input: + type: file + description: | + The file or directory to be indexed. + COBS can read: + 1. FASTA files (`*.fa`, `*.fasta`, `*.fna`, `*.ffn`, `*.faa`, `*.frn`, `*.fa.gz`, `*.fasta.gz`, `*.fna.gz`, `*.ffn.gz`, `*.faa.gz`, `*.frn.gz`), + 2. FASTQ files (`*.fq`, `*.fastq`, `*.fq.gz.`, `*.fastq.gz`), + 3. "Multi-FASTA" and "Multi-FASTQ" files (`*.mfasta`, `*.mfastq`), + 4. McCortex files (`*.ctx`), + 5. or text files (`*.txt`). + You can either recursively scan a directory for all files matching any of these files, + or pass a `*.list` file which lists all paths COBS should index. + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - index: - type: file - description: The COBS compact index - pattern: "*.index.cobs_compact" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.index.cobs_compact": + type: file + description: The COBS compact index + pattern: "*.index.cobs_compact" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/concoct/concoct/meta.yml b/modules/nf-core/concoct/concoct/meta.yml index d92455cf8508..d47d1672c3b7 100644 --- a/modules/nf-core/concoct/concoct/meta.yml +++ b/modules/nf-core/concoct/concoct/meta.yml @@ -1,5 +1,6 @@ name: "concoct_concoct" -description: Unsupervised binning of metagenomic contigs by using nucleotide composition - kmer frequencies - and coverage data for multiple samples +description: Unsupervised binning of metagenomic contigs by using nucleotide composition + - kmer frequencies - and coverage data for multiple samples keywords: - contigs - fragment @@ -18,54 +19,88 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_file: - type: file - description: Subcontig coverage TSV table (typically generated with concoct_coverage_table.py) - pattern: "*.tsv" - - fasta: - type: file - description: FASTA file containing subcontigs (typically generated with cutup_fasta.py) - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_file: + type: file + description: Subcontig coverage TSV table (typically generated with concoct_coverage_table.py) + pattern: "*.tsv" + - fasta: + type: file + description: FASTA file containing subcontigs (typically generated with cutup_fasta.py) + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - args_txt: - type: file - description: File containing execution parameters - pattern: "*_args.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_args.txt": + type: file + description: File containing execution parameters + pattern: "*_args.txt" - clustering_csv: - type: file - description: CSV containing information which subcontig is assigned to which cluster - pattern: "*_clustering_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_clustering_gt1000.csv": + type: file + description: CSV containing information which subcontig is assigned to which + cluster + pattern: "*_clustering_gt1000.csv" - log_txt: - type: file - description: Log file of tool execution - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_log.txt": + type: file + description: Log file of tool execution + pattern: "*_log.txt" - original_data_csv: - type: file - description: Original CONCOCT GT1000 output - pattern: "*_original_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_original_data_gt1000.csv": + type: file + description: Original CONCOCT GT1000 output + pattern: "*_original_data_gt1000.csv" - pca_components_csv: - type: file - description: Untransformed PCA component values - pattern: "*_PCA_components_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PCA_components_data_gt1000.csv": + type: file + description: Untransformed PCA component values + pattern: "*_PCA_components_data_gt1000.csv" - pca_transformed_csv: - type: file - description: Transformed PCA compontent values - pattern: "*_PCA_transformed_data_gt1000.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PCA_transformed_data_gt1000.csv": + type: file + description: Transformed PCA compontent values + pattern: "*_PCA_transformed_data_gt1000.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/concoctcoveragetable/meta.yml b/modules/nf-core/concoct/concoctcoveragetable/meta.yml index 26b9793c9c8c..ce878eb6f048 100644 --- a/modules/nf-core/concoct/concoctcoveragetable/meta.yml +++ b/modules/nf-core/concoct/concoctcoveragetable/meta.yml @@ -17,38 +17,43 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file describing where each contig was cut up (typically output from CONCOCT's cut_up_fasta.py) - pattern: "*.bed" - - bamfiles: - type: file - description: A single or list of BAM files of reads mapped back to original contigs (prior cutting up) - pattern: "*.bam" - - baifiles: - type: file - description: A single or list of BAM index files (.bai) corresponding to BAM - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file describing where each contig was cut up (typically output + from CONCOCT's cut_up_fasta.py) + pattern: "*.bed" + - bamfiles: + type: file + description: A single or list of BAM files of reads mapped back to original + contigs (prior cutting up) + pattern: "*.bam" + - baifiles: + type: file + description: A single or list of BAM index files (.bai) corresponding to BAM + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Contig coverage table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Contig coverage table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/cutupfasta/meta.yml b/modules/nf-core/concoct/cutupfasta/meta.yml index 44a287233009..021466408470 100644 --- a/modules/nf-core/concoct/cutupfasta/meta.yml +++ b/modules/nf-core/concoct/cutupfasta/meta.yml @@ -16,37 +16,49 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: (Uncompressed) FASTA file containing contigs - pattern: "*.{fasta,fna,fa,fas}" - - bed: - type: boolean - description: Specify whether to generate a BED file describing where each contig was cut up + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: (Uncompressed) FASTA file containing contigs + pattern: "*.{fasta,fna,fa,fas}" + - - bed: + type: boolean + description: Specify whether to generate a BED file describing where each contig + was cut up output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Cut up fasta file in non-overlapping or overlapping parts of equal length. - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Cut up fasta file in non-overlapping or overlapping parts of equal + length. + pattern: "*.fasta" - bed: - type: file - description: Optional BED File containing locations on original contigs where they were cut up. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Optional BED File containing locations on original contigs where + they were cut up. + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/extractfastabins/meta.yml b/modules/nf-core/concoct/extractfastabins/meta.yml index a9ac00a304cb..4e6effda3a88 100644 --- a/modules/nf-core/concoct/extractfastabins/meta.yml +++ b/modules/nf-core/concoct/extractfastabins/meta.yml @@ -18,34 +18,38 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - original_fasta: - type: file - description: Original input FASTA file to CONOCT cut_up_fasta - pattern: "*.{fasta,fna,fa,fas}" - - csv: - type: boolean - description: Output table of merge_cutup_clustering with new cluster assignments - pattern: ".csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - original_fasta: + type: file + description: Original input FASTA file to CONOCT cut_up_fasta + pattern: "*.{fasta,fna,fa,fas}" + - csv: + type: boolean + description: Output table of merge_cutup_clustering with new cluster assignments + pattern: ".csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: FASTA files containing CONCOCT predicted bin clusters, named numerically by CONCOCT cluster ID in a directory called `fasta_bins` - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fa.gz: + type: file + description: FASTA files containing CONCOCT predicted bin clusters, named numerically + by CONCOCT cluster ID in a directory called `fasta_bins` + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/concoct/mergecutupclustering/meta.yml b/modules/nf-core/concoct/mergecutupclustering/meta.yml index e34a423c22bd..69a839928d43 100644 --- a/modules/nf-core/concoct/mergecutupclustering/meta.yml +++ b/modules/nf-core/concoct/mergecutupclustering/meta.yml @@ -17,30 +17,33 @@ tools: tool_dev_url: "https://github.com/BinPro/CONCOCT" doi: "10.1038/nmeth.3103" licence: ["FreeBSD"] + identifier: biotools:concoct input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - clustering_csv: - type: file - description: Input cutup clustering result. Typically *_gt1000.csv from concoct - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - clustering_csv: + type: file + description: Input cutup clustering result. Typically *_gt1000.csv from concoct + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Cluster assignments per contig part with concensus cluster - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Cluster assignments per contig part with concensus cluster + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/conifer/meta.yml b/modules/nf-core/conifer/meta.yml index d70ca4630fa5..795d8f85951c 100644 --- a/modules/nf-core/conifer/meta.yml +++ b/modules/nf-core/conifer/meta.yml @@ -12,34 +12,37 @@ tools: documentation: "https://github.com/Ivarz/Conifer" tool_dev_url: "https://github.com/Ivarz/Conifer" licence: ["BSD / BSD-2-Clause"] + identifier: biotools:conifer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kraken_result: - type: file - description: | - Raw Kraken2 standard output file - - kraken_taxon_db: - type: file - description: Kraken2 taxo.k2d database file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kraken_result: + type: file + description: | + Raw Kraken2 standard output file + - - kraken_taxon_db: + type: file + description: Kraken2 taxo.k2d database file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - score: - type: file - description: | - Conifer report file containing confidence scores of Kraken2 classified reads. - pattern: "*.score" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.score": + type: file + description: | + Conifer report file containing confidence scores of Kraken2 classified reads. + pattern: "*.score" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@icaromsc" - "@rpetit3" diff --git a/modules/nf-core/controlfreec/assesssignificance/meta.yml b/modules/nf-core/controlfreec/assesssignificance/meta.yml index b8cda6dd5055..8a6ab47edb94 100644 --- a/modules/nf-core/controlfreec/assesssignificance/meta.yml +++ b/modules/nf-core/controlfreec/assesssignificance/meta.yml @@ -1,5 +1,6 @@ name: controlfreec_assesssignificance -description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV output of FREEC +description: Add both Wilcoxon test and Kolmogorov-Smirnov test p-values to each CNV + output of FREEC keywords: - cna - cnv @@ -8,41 +9,49 @@ keywords: - tumor-only tools: - controlfreec/assesssignificance: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cnvs: - type: file - description: _CNVs file generated by FREEC - pattern: "*._CNVs" - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cnvs: + type: file + description: _CNVs file generated by FREEC + pattern: "*._CNVs" + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - p_value_txt: - type: file - description: CNV file containing p_values for each call - pattern: "*.p.value.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.p.value.txt": + type: file + description: CNV file containing p_values for each call + pattern: "*.p.value.txt" + - ue_txt: + type: file + description: CNV file containing p_values for each call + pattern: "*.p.value.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec/meta.yml b/modules/nf-core/controlfreec/freec/meta.yml index 1442bbe44a7c..6b35a38be729 100644 --- a/modules/nf-core/controlfreec/freec/meta.yml +++ b/modules/nf-core/controlfreec/freec/meta.yml @@ -1,5 +1,6 @@ name: controlfreec_freec -description: Copy number and genotype annotation from whole genome and whole exome sequencing data +description: Copy number and genotype annotation from whole genome and whole exome + sequencing data keywords: - cna - cnv @@ -8,172 +9,176 @@ keywords: - tumor-only tools: - controlfreec/freec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. - Parameters marked as (optional) can be removed from the map, if they are not set. All values must be surrounded by quotes, meta map parameters can be set with, i.e. `sex = meta.sex`: - For default values, please check the documentation above. - - ``` - { - [ - "general" :[ - "bedgraphoutput": (optional), - "breakpointthreshold": (optional), - "breakpointtype": (optional), - "coefficientofvariation": (optional), - "contamination": (optional), - "contaminationadjustment": (optional), - "degree": (optional), - "forcegccontentnormalization": (optional), - "gccontentprofile": (optional), - "intercept": (optional), - "mincnalength": (optional), - "minmappabilityperwindow": (optional), - "minexpectedgc": (optional), - "maxexpectedgc": (optional), - "minimalsubclonepresence": (optional), - "noisydata": (optional), - "ploidy": (optional), - "printNA": (optional), - "readcountthreshold": (optional), - "sex": (optional), - "step": (optional), - "telocentromeric": (optional), - "uniquematch": (optional), - "window": (optional) - ], - "control":[ - "inputformat": (required), - "mateorientation": (optional), - ], - "sample":[ - "inputformat": (required), - "mateorientation": (optional), - ], - "BAF":[ - "minimalcoverageperposition": (optional), - "minimalqualityperposition": (optional), - "shiftinquality": (optional) - ] - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mateFile_normal: - type: file - description: File with mapped reads - pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - - mateFile_tumor: - type: file - description: File with mapped reads - pattern: "*.{sam,bam,pileup(.gz),bowtie(.gz),eland(.gz),arachne(.gz),psl(.gz),bed(.gz)}" - - cpn_normal: - type: file - description: Raw copy number profiles (optional) - pattern: "*.cpn" - - cpn_tumor: - type: file - description: Raw copy number profiles (optional) - pattern: "*.cpn" - - minipileup_normal: - type: file - description: miniPileup file from previous run (optional) - pattern: "*.pileup" - - minipileup_tumor: - type: file - description: miniPileup file from previous run (optional) - pattern: "*.pileup" - - fasta: - type: file - description: Reference file (optional; required if args 'makePileup' is set) - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: Fasta index - pattern: "*.fai" - - snp_position: - type: file - description: Path to a BED or VCF file with SNP positions to create a mini pileup file from the initial BAM file provided in mateFile (optional) - pattern: "*.{bed,vcf}" - - known_snps: - type: file - description: File with known SNPs - pattern: "*.{vcf,vcf.gz}" - - known_snps_tbi: - type: file - description: Index of known_snps - pattern: "*.tbi" - - chr_directory: - type: file - description: Path to directory with chromosome fasta files (optional, required if gccontentprofile is not provided) - pattern: "*/" - - mappability: - type: file - description: Contains information of mappable positions (optional) - pattern: "*.gem" - - target_bed: - type: file - description: Sorted bed file containing capture regions (optional) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mpileup_normal: + type: file + description: miniPileup file + - mpileup_tumor: + type: file + description: miniPileup file + - cpn_normal: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - cpn_tumor: + type: file + description: Raw copy number profiles (optional) + pattern: "*.cpn" + - minipileup_normal: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - minipileup_tumor: + type: file + description: miniPileup file from previous run (optional) + pattern: "*.pileup" + - - fasta: + type: file + description: Reference file (optional; required if args 'makePileup' is set) + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: Fasta index + pattern: "*.fai" + - - snp_position: + type: file + description: Path to a BED or VCF file with SNP positions to create a mini pileup + file from the initial BAM file provided in mateFile (optional) + pattern: "*.{bed,vcf}" + - - known_snps: + type: file + description: File with known SNPs + pattern: "*.{vcf,vcf.gz}" + - - known_snps_tbi: + type: file + description: Index of known_snps + pattern: "*.tbi" + - - chr_directory: + type: file + description: Path to directory with chromosome fasta files (optional, required + if gccontentprofile is not provided) + pattern: "*/" + - - mappability: + type: file + description: Contains information of mappable positions (optional) + pattern: "*.gem" + - - target_bed: + type: file + description: Sorted bed file containing capture regions (optional) + pattern: "*.bed" + - - gccontent_profile: + type: file + description: File with GC-content profile output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: Bedgraph format for the UCSC genome browser - pattern: ".bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.BedGraph": + type: file + description: Bedgraph format for the UCSC genome browser + pattern: ".bedgraph" - control_cpn: - type: file - description: files with raw copy number profiles - pattern: "*_control.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_control.cpn": + type: file + description: files with raw copy number profiles + pattern: "*_control.cpn" - sample_cpn: - type: file - description: files with raw copy number profiles - pattern: "*_sample.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_sample.cpn": + type: file + description: files with raw copy number profiles + pattern: "*_sample.cpn" - gcprofile_cpn: - type: file - description: file with GC-content profile. - pattern: "GC_profile.*.cpn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - GC_profile.*.cpn: + type: file + description: file with GC-content profile. + pattern: "GC_profile.*.cpn" - BAF: - type: file - description: file B-allele frequencies for each possibly heterozygous SNP position - pattern: "*_BAF.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.txt": + type: file + description: file B-allele frequencies for each possibly heterozygous SNP position + pattern: "*_BAF.txt" - CNV: - type: file - description: file with coordinates of predicted copy number alterations. - pattern: "*_CNVs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_CNVs": + type: file + description: file with coordinates of predicted copy number alterations. + pattern: "*_CNVs" - info: - type: file - description: parsable file with information about FREEC run - pattern: "*_info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_info.txt": + type: file + description: parsable file with information about FREEC run + pattern: "*_info.txt" - ratio: - type: file - description: file with ratios and predicted copy number alterations for each window - pattern: "*_ratio.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.txt": + type: file + description: file with ratios and predicted copy number alterations for each + window + pattern: "*_ratio.txt" - config: - type: file - description: Config file used to run Control-FREEC - pattern: "config.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - config.txt: + type: file + description: Config file used to run Control-FREEC + pattern: "config.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec2bed/meta.yml b/modules/nf-core/controlfreec/freec2bed/meta.yml index b10c8ab377a5..e01f870f4dc4 100644 --- a/modules/nf-core/controlfreec/freec2bed/meta.yml +++ b/modules/nf-core/controlfreec/freec2bed/meta.yml @@ -8,36 +8,40 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Bed file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/freec2circos/meta.yml b/modules/nf-core/controlfreec/freec2circos/meta.yml index 2c6b77d611b7..5368c0429ea7 100644 --- a/modules/nf-core/controlfreec/freec2circos/meta.yml +++ b/modules/nf-core/controlfreec/freec2circos/meta.yml @@ -8,36 +8,40 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - circos: - type: file - description: Txt file - pattern: "*.circos.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.circos.txt": + type: file + description: Txt file + pattern: "*.circos.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/makegraph/meta.yml b/modules/nf-core/controlfreec/makegraph/meta.yml index 6f91db38aa40..f9dff86eeb87 100644 --- a/modules/nf-core/controlfreec/makegraph/meta.yml +++ b/modules/nf-core/controlfreec/makegraph/meta.yml @@ -8,52 +8,68 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" - - baf: - type: file - description: .BAF file generated by FREEC - pattern: "*.BAF" - - ploidy: - type: integer - description: Ploidy value for which graph should be created + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" + - baf: + type: file + description: .BAF file generated by FREEC + pattern: "*.BAF" + - ploidy: + type: integer + description: Ploidy value for which graph should be created output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png_baf: - type: file - description: Image of BAF plot - pattern: "*_BAF.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.png": + type: file + description: Image of BAF plot + pattern: "*_BAF.png" - png_ratio_log2: - type: file - description: Image of ratio log2 plot - pattern: "*_ratio.log2.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.log2.png": + type: file + description: Image of ratio log2 plot + pattern: "*_ratio.log2.png" - png_ratio: - type: file - description: Image of ratio plot - pattern: "*_ratio.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.png": + type: file + description: Image of ratio plot + pattern: "*_ratio.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/controlfreec/makegraph2/meta.yml b/modules/nf-core/controlfreec/makegraph2/meta.yml index 1325da4a8b96..6614b39ba909 100644 --- a/modules/nf-core/controlfreec/makegraph2/meta.yml +++ b/modules/nf-core/controlfreec/makegraph2/meta.yml @@ -8,51 +8,65 @@ keywords: - tumor-only tools: - controlfreec: - description: Copy number and genotype annotation from whole genome and whole exome sequencing data. + description: Copy number and genotype annotation from whole genome and whole exome + sequencing data. homepage: http://boevalab.inf.ethz.ch/FREEC documentation: http://boevalab.inf.ethz.ch/FREEC/tutorial.html tool_dev_url: https://github.com/BoevaLab/FREEC/ doi: "10.1093/bioinformatics/btq635" licence: ["GPL >=2"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ratio: - type: file - description: ratio file generated by FREEC - pattern: "*.ratio.txt" - - baf: - type: file - description: .BAF file generated by FREEC - pattern: "*.BAF" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ratio: + type: file + description: ratio file generated by FREEC + pattern: "*.ratio.txt" + - baf: + type: file + description: .BAF file generated by FREEC + pattern: "*.BAF" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png_baf: - type: file - description: Image of BAF plot - pattern: "*_BAF.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BAF.png": + type: file + description: Image of BAF plot + pattern: "*_BAF.png" - png_ratio_log2: - type: file - description: Image of ratio log2 plot - pattern: "*_ratio.log2.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.log2.png": + type: file + description: Image of ratio log2 plot + pattern: "*_ratio.log2.png" - png_ratio: - type: file - description: Image of ratio plot - pattern: "*_ratio.png" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_ratio.png": + type: file + description: Image of ratio plot + pattern: "*_ratio.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" diff --git a/modules/nf-core/cooler/balance/meta.yml b/modules/nf-core/cooler/balance/meta.yml index 9b8906387219..ace840ec5984 100644 --- a/modules/nf-core/cooler/balance/meta.yml +++ b/modules/nf-core/cooler/balance/meta.yml @@ -13,33 +13,36 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" - - resolution: - type: integer - description: Resolution + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" + - resolution: + type: integer + description: Resolution output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cool: - type: file - description: Output COOL file balancing weigths - pattern: "*.cool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: file + description: Output COOL file balancing weigths + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" - "@muffato" diff --git a/modules/nf-core/cooler/cload/meta.yml b/modules/nf-core/cooler/cload/meta.yml index fa5474aeb617..1bb9f7485a04 100644 --- a/modules/nf-core/cooler/cload/meta.yml +++ b/modules/nf-core/cooler/cload/meta.yml @@ -13,41 +13,45 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: Path to contacts (i.e. read pairs) file. - - index: - type: file - description: Path to index file of the contacts. - - cool_bin: - type: integer - description: Bins size in bp - - chromsizes: - type: file - description: Path to a chromsizes file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: Path to contacts (i.e. read pairs) file. + - index: + type: file + description: Path to index file of the contacts. + - cool_bin: + type: integer + description: Bins size in bp + - - chromsizes: + type: file + description: Path to a chromsizes file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "versions.yml" - cool: - type: file - description: Output COOL file path - pattern: "*.cool" - - cool_bin: - type: integer - description: Bins size in bp + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cool": + type: file + description: Output COOL file path + pattern: "*.cool" + - cool_bin: + type: file + description: Output COOL file path + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@muffato" diff --git a/modules/nf-core/cooler/digest/meta.yml b/modules/nf-core/cooler/digest/meta.yml index a52e21b0396b..e3ec3f079eac 100644 --- a/modules/nf-core/cooler/digest/meta.yml +++ b/modules/nf-core/cooler/digest/meta.yml @@ -12,27 +12,30 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - fasta: - type: file - description: Genome assembly FASTA file or folder containing FASTA files (uncompressed). - pattern: "*.{fasta,fa}" - - chromsizes: - type: file - description: Path to a chromsizes file. - - enzyme: - type: string - description: Name of restriction enzyme. e.g. CviQI. - documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html + - - fasta: + type: file + description: Genome assembly FASTA file or folder containing FASTA files (uncompressed). + pattern: "*.{fasta,fa}" + - - chromsizes: + type: file + description: Path to a chromsizes file. + - - enzyme: + type: string + description: Name of restriction enzyme. e.g. CviQI. + documentation: http://biopython.org/DIST/docs/cookbook/Restriction.html output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: A genome segmentation of restriction fragments as a BED file. - pattern: "*.{bed}" + - "*.bed": + type: file + description: A genome segmentation of restriction fragments as a BED file. + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/cooler/dump/meta.yml b/modules/nf-core/cooler/dump/meta.yml index 2f882aeb9839..e8150097e2bc 100644 --- a/modules/nf-core/cooler/dump/meta.yml +++ b/modules/nf-core/cooler/dump/meta.yml @@ -12,33 +12,36 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" - - resolution: - type: integer - description: Resolution + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" + - resolution: + type: integer + description: Resolution output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedpe: - type: file - description: Output text file - pattern: "*.bedpe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedpe": + type: file + description: Output text file + pattern: "*.bedpe" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@muffato" diff --git a/modules/nf-core/cooler/makebins/meta.yml b/modules/nf-core/cooler/makebins/meta.yml index 16e2c59815d8..73bc62577ed9 100644 --- a/modules/nf-core/cooler/makebins/meta.yml +++ b/modules/nf-core/cooler/makebins/meta.yml @@ -12,22 +12,34 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-Clause"] + identifier: "" input: - - chromsize: - type: file - description: Path to chromosome size file - - cool_bin: - type: integer - description: Resolution (bin size) in base pairs + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chromsizes: + type: file + description: Path to a chromsizes file. + - cool_bin: + type: integer + description: Resolution (bin size) in base pairs output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Genome segmentation at a fixed resolution as a BED file. - pattern: "*.bed" + - meta: + type: file + description: Genome segmentation at a fixed resolution as a BED file. + pattern: "*.bed" + - "*.bed": + type: file + description: Genome segmentation at a fixed resolution as a BED file. + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" - "@muffato" diff --git a/modules/nf-core/cooler/merge/meta.yml b/modules/nf-core/cooler/merge/meta.yml index 3ef7f16c45f0..d097b84dd107 100644 --- a/modules/nf-core/cooler/merge/meta.yml +++ b/modules/nf-core/cooler/merge/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - cool: - type: file - description: Path to COOL file - pattern: "*.cool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cool": + type: file + description: Path to COOL file + pattern: "*.cool" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/cooler/zoomify/meta.yml b/modules/nf-core/cooler/zoomify/meta.yml index d87aaf298a3b..3f928781b9a3 100644 --- a/modules/nf-core/cooler/zoomify/meta.yml +++ b/modules/nf-core/cooler/zoomify/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cool: - type: file - description: Path to COOL file - pattern: "*.{cool,mcool}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cool: + type: file + description: Path to COOL file + pattern: "*.{cool,mcool}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mcool: - type: file - description: Output mcool file - pattern: "*.mcool" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mcool": + type: file + description: Output mcool file + pattern: "*.mcool" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/coreograph/meta.yml b/modules/nf-core/coreograph/meta.yml index fa61fec708e0..4cf3b08ef2f9 100644 --- a/modules/nf-core/coreograph/meta.yml +++ b/modules/nf-core/coreograph/meta.yml @@ -1,5 +1,8 @@ name: "coreograph" -description: Great....yet another TMA dearray program. What does this one do? Coreograph uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray. It has been trained on 9 TMA slides of different sizes and tissue types. +description: Great....yet another TMA dearray program. What does this one do? Coreograph + uses UNet, a deep learning model, to identify complete/incomplete tissue cores on + a tissue microarray. It has been trained on 9 TMA slides of different sizes and + tissue types. keywords: - UNet - TMA dearray @@ -7,47 +10,66 @@ keywords: - Cores tools: - "coreograph": - description: "A TMA dearray porgram that uses UNet, a deep learning model, to identify complete/incomplete tissue cores on a tissue microarray." + description: "A TMA dearray porgram that uses UNet, a deep learning model, to + identify complete/incomplete tissue cores on a tissue microarray." homepage: "https://mcmicro.org/parameters/core.html#coreograph" documentation: "https://mcmicro.org/troubleshooting/tuning/coreograph.html" tool_dev_url: "https://github.com/HMS-IDAC/UNetCoreograph" doi: 10.1038/s41592-021-01308-y license: ["MIT License"] + identifier: "" input: - - image: - type: file - description: ome.tif/tif file - pattern: "*.{ome.tif,tif}" - - meta: - type: map - description: | - Groovy Map containing sample information + - - meta: + type: map + description: | + Groovy Map containing sample information + - image: + type: file + description: ome.tif/tif file + pattern: "*.{ome.tif,tif}" output: # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cores: - type: file - description: Complete/Incomplete tissue cores - pattern: "*.{tif}" + - meta: + type: file + description: Complete/Incomplete tissue cores + pattern: "*.{tif}" + - "*[0-9]*.tif": + type: file + description: Complete/Incomplete tissue cores + pattern: "*.{tif}" - masks: - type: file - description: Binary masks for the Complete/Incomplete tissue cores - pattern: "./masks/*.{tif}" + - meta: + type: file + description: Binary masks for the Complete/Incomplete tissue cores + pattern: "./masks/*.{tif}" + - ./masks/: + type: file + description: Binary masks for the Complete/Incomplete tissue cores + pattern: "./masks/*.{tif}" - tma_map: - type: file - description: A TMA map showing labels and outlines - pattern: "TMA_MAP.tif" + - meta: + type: file + description: A TMA map showing labels and outlines + pattern: "TMA_MAP.tif" + - TMA_MAP.tif: + type: file + description: A TMA map showing labels and outlines + pattern: "TMA_MAP.tif" - centroids: - type: file - description: A text file listing centroids of each core in format Y, X - pattern: "centroidsY-X.txt" - - meta: - type: map - description: | - Groovy Map containing sample information + - meta: + type: file + description: A text file listing centroids of each core in format Y, X + pattern: "centroidsY-X.txt" + - centroidsY-X.txt: + type: file + description: A text file listing centroids of each core in format Y, X + pattern: "centroidsY-X.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@arozhada" - "@MargotCh" diff --git a/modules/nf-core/crabz/compress/meta.yml b/modules/nf-core/crabz/compress/meta.yml index bd7cc8a6a879..6c69b81d343b 100644 --- a/modules/nf-core/crabz/compress/meta.yml +++ b/modules/nf-core/crabz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crabz_compress" description: Compress files with crabz @@ -13,37 +12,36 @@ tools: documentation: "https://github.com/sstadick/crabz" tool_dev_url: "https://github.com/sstadick/crabz" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - file: + type: file + description: File to be compressed + pattern: "*.*" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - archive: - type: file - description: The compressed file - pattern: "*.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gz": + type: file + description: The compressed file + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@camlloyd" maintainers: diff --git a/modules/nf-core/crabz/decompress/meta.yml b/modules/nf-core/crabz/decompress/meta.yml index 9072694c2a73..dd25233e8997 100644 --- a/modules/nf-core/crabz/decompress/meta.yml +++ b/modules/nf-core/crabz/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "crabz_decompress" description: Decompress files with crabz @@ -13,37 +12,36 @@ tools: documentation: "https://github.com/sstadick/crabz" tool_dev_url: "https://github.com/sstadick/crabz" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - archive: - type: file - description: File to be decompressed - pattern: "*.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - archive: + type: file + description: File to be decompressed + pattern: "*.gz" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - file: - type: file - description: The decompressed file - pattern: "*.*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.*": + type: file + description: The decompressed file + pattern: "*.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@camlloyd" maintainers: diff --git a/modules/nf-core/crisprcleanr/normalize/meta.yml b/modules/nf-core/crisprcleanr/normalize/meta.yml index f20492fd7449..28be35cd8940 100644 --- a/modules/nf-core/crisprcleanr/normalize/meta.yml +++ b/modules/nf-core/crisprcleanr/normalize/meta.yml @@ -7,40 +7,50 @@ keywords: - CRISPR tools: - "crisprcleanr": - description: "Analysis of CRISPR functional genomics, remove false positive due to CNVs." + description: "Analysis of CRISPR functional genomics, remove false positive due + to CNVs." homepage: "https://github.com/francescojm/CRISPRcleanR" documentation: "https://github.com/francescojm/CRISPRcleanR/blob/master/Quick_start.pdf" tool_dev_url: "https://github.com/francescojm/CRISPRcleanR/tree/v3.0.0" doi: "10.1186/s12864-018-4989-y" licence: ["MIT"] + identifier: biotools:crisprcleanr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_file: - type: file - description: sgRNA raw counts - pattern: "*.tsv" - - library_file: - type: file - description: sgRNA library - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_file: + type: file + description: sgRNA raw counts + pattern: "*.tsv" + - library_file: + type: file + description: sgRNA library + pattern: "*.tsv" + - - min_reads: + type: integer + description: Minimum number of reads + - - min_targeted_genes: + type: integer + description: Minimum number of targeted genes output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - norm_count_file: - type: file - description: normalized count file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_norm_table.tsv": + type: file + description: normalized count file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/crumble/meta.yml b/modules/nf-core/crumble/meta.yml index 66665f127f61..cc63012dd3a4 100644 --- a/modules/nf-core/crumble/meta.yml +++ b/modules/nf-core/crumble/meta.yml @@ -13,48 +13,69 @@ tools: tool_dev_url: "https://github.com/jkbonfield/crumble" doi: "10.1093/bioinformatics/bty608" licence: ["multiple BSD style licenses"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - keepbed: - type: file - description: BED file defining regions to keep quality - - bedout: - type: boolean - description: set to true to ouput suspicious regions to a BED file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - keepbed: + type: file + description: BED file defining regions to keep quality + - - bedout: + type: boolean + description: set to true to ouput suspicious regions to a BED file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: optional filtered/compressed BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: optional filtered/compressed BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/compressed CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: optional filtered/compressed CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/compressed SAM file - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: optional filtered/compressed SAM file + pattern: "*.{sam}" - bed: - type: file - description: optional suspicious regions BED file - pattern: "*{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: optional suspicious regions BED file + pattern: "*{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/csvtk/concat/meta.yml b/modules/nf-core/csvtk/concat/meta.yml index 5f53229cf640..27ffc1caf09c 100644 --- a/modules/nf-core/csvtk/concat/meta.yml +++ b/modules/nf-core/csvtk/concat/meta.yml @@ -11,38 +11,41 @@ tools: documentation: http://bioinf.shenwei.me/csvtk tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV formatted files - pattern: "*.{csv,tsv}" - - in_format: - type: string - description: Input format (csv, tab, or a delimiting character) - pattern: "*" - - out_format: - type: string - description: Output format (csv, tab, or a delimiting character) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" + - - in_format: + type: string + description: Input format (csv, tab, or a delimiting character) + pattern: "*" + - - out_format: + type: string + description: Output format (csv, tab, or a delimiting character) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "version.yml" - csv: - type: file - description: Concatenated CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${out_extension}: + type: file + description: Concatenated CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "version.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/csvtk/join/meta.yml b/modules/nf-core/csvtk/join/meta.yml index a75ec40f0362..d8671b176e72 100644 --- a/modules/nf-core/csvtk/join/meta.yml +++ b/modules/nf-core/csvtk/join/meta.yml @@ -1,5 +1,6 @@ name: csvtk_join -description: Join two or more CSV (or TSV) tables by selected fields into a single table +description: Join two or more CSV (or TSV) tables by selected fields into a single + table keywords: - join - tsv @@ -11,30 +12,33 @@ tools: documentation: http://bioinf.shenwei.me/csvtk tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV formatted files - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV formatted files + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "version.yml" - csv: - type: file - description: Joined CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${out_extension}: + type: file + description: Joined CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "version.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/csvtk/split/meta.yml b/modules/nf-core/csvtk/split/meta.yml index 6ff78aa0168b..fc2205068183 100644 --- a/modules/nf-core/csvtk/split/meta.yml +++ b/modules/nf-core/csvtk/split/meta.yml @@ -6,43 +6,47 @@ keywords: - tsv tools: - csvtk: - description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit that allows rapid data investigation and manipulation. + description: CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit + that allows rapid data investigation and manipulation. homepage: https://bioinf.shenwei.me/csvtk/ documentation: https://bioinf.shenwei.me/csvtk/ tool_dev_url: https://github.com/shenwei356/csvtk licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: CSV/TSV file - pattern: "*.{csv,tsv}" - - in_format: - type: string - description: Input format (csv, tab, or a delimiting character) - pattern: "*" - - out_format: - type: string - description: Output format (csv, tab, or a delimiting character) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: CSV/TSV file + pattern: "*.{csv,tsv}" + - - in_format: + type: string + description: Input format (csv, tab, or a delimiting character) + pattern: "*" + - - out_format: + type: string + description: Output format (csv, tab, or a delimiting character) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_csv: - type: file - description: Split CSV/TSV file - pattern: "*.{csv,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_extension}": + type: file + description: Split CSV/TSV file + pattern: "*.{csv,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@SusiJo" maintainers: diff --git a/modules/nf-core/custom/catadditionalfasta/meta.yml b/modules/nf-core/custom/catadditionalfasta/meta.yml index 8a9505d30a4a..e6c313d3999b 100644 --- a/modules/nf-core/custom/catadditionalfasta/meta.yml +++ b/modules/nf-core/custom/catadditionalfasta/meta.yml @@ -1,60 +1,67 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_catadditionalfasta" -description: Custom module to Add a new fasta file to an old one and update an associated GTF +description: Custom module to Add a new fasta file to an old one and update an associated + GTF keywords: - fasta - gtf - genomics tools: - "custom": - description: "Custom module to Add a new fasta file to an old one and update an associated GTF" + description: "Custom module to Add a new fasta file to an old one and update an + associated GTF" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/catadditionalfasta/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - - meta2: - type: map - description: | - Groovy Map containing additional fasta information - - fasta: - type: file - description: FASTA-format sequence file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: GTF-format annotation file for fasta - pattern: "*.gtf" - - add_fasta: - type: file - description: FASTA-format file of additional sequences - pattern: "*.fa" - - biotype: - type: string - description: Biotype to apply to new GTF entries - + - - meta: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: FASTA-format sequence file + pattern: "*.{fasta,fa}" + - gtf: + type: file + description: GTF-format annotation file for fasta + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing additional fasta information + - add_fasta: + type: file + description: FASTA-format file of additional sequences + pattern: "*.fa" + - - biotype: + type: string + description: Biotype to apply to new GTF entries output: - - meta: - type: map - description: | - Groovy Map containing fasta information - fasta: - type: file - description: FASTA-format combined sequence file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.fasta": + type: file + description: FASTA-format combined sequence file + pattern: "*.{fasta,fa}" - gtf: - type: file - description: GTF-format combined annotation file - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing fasta information + - "*/*.gtf": + type: file + description: GTF-format combined annotation file + pattern: "*.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index 5f15a5fde058..dc1e412fbcde 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,34 +1,40 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions -description: Custom module used to dump software versions within the nf-core pipeline template +description: Custom module used to dump software versions within the nf-core pipeline + template keywords: - custom - dump - version tools: - custom: - description: Custom module used to dump software versions within the nf-core pipeline template + description: Custom module used to dump software versions within the nf-core pipeline + template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools licence: ["MIT"] + identifier: "" input: - - versions: - type: file - description: YML file containing software versions - pattern: "*.yml" + - - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" output: - yml: - type: file - description: Standard YML file containing software versions - pattern: "software_versions.yml" + - software_versions.yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" - mqc_yml: - type: file - description: MultiQC custom content YML file containing software versions - pattern: "software_versions_mqc.yml" + - software_versions_mqc.yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index da2df5e43a40..b98cbb99092d 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.20 - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/custom/getchromsizes/meta.yml b/modules/nf-core/custom/getchromsizes/meta.yml index 529be07e4431..2a0e8da0a635 100644 --- a/modules/nf-core/custom/getchromsizes/meta.yml +++ b/modules/nf-core/custom/getchromsizes/meta.yml @@ -12,38 +12,53 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna,fas}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna,fas}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sizes: - type: file - description: File containing chromosome lengths - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: File containing chromosome lengths + pattern: "*.{sizes}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/custom/gtffilter/meta.yml b/modules/nf-core/custom/gtffilter/meta.yml index 2c8692218de4..672256494350 100644 --- a/modules/nf-core/custom/gtffilter/meta.yml +++ b/modules/nf-core/custom/gtffilter/meta.yml @@ -1,50 +1,53 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_gtffilter" -description: Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file +description: Filter a gtf file to keep only regions that are located on a chromosome + represented in a given fasta file keywords: - gtf - fasta - filter tools: - "gtffilter": - description: "Filter a gtf file to keep only regions that are located on a chromosome represented in a given fasta file" + description: "Filter a gtf file to keep only regions that are located on a chromosome + represented in a given fasta file" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/gtffilter/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fasta,fa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gtf: - type: file - description: Filtered GTF file - pattern: "*.{gtf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.${suffix}: + type: file + description: Filtered GTF file + pattern: "*.{gtf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nictru" maintainers: diff --git a/modules/nf-core/custom/matrixfilter/meta.yml b/modules/nf-core/custom/matrixfilter/meta.yml index 99d7ca4e864b..ce9601b580fe 100644 --- a/modules/nf-core/custom/matrixfilter/meta.yml +++ b/modules/nf-core/custom/matrixfilter/meta.yml @@ -1,5 +1,6 @@ name: "custom_matrixfilter" -description: filter a matrix based on a minimum value and numbers of samples that must pass. +description: filter a matrix based on a minimum value and numbers of samples that + must pass. keywords: - matrix - filter @@ -9,93 +10,67 @@ tools: - "matrixfilter": description: "filter a matrix based on a minimum value and numbers of samples" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/matrixfilter/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on matrix to be filtered, at a - minimum an id. e.g. [ id:'test' ] - - abundance: - type: file - description: | - Raw TSV or CSV format abundance matrix with features (e.g. - genes) by row and observations (e.g. samples) by column. All rownames - from the sample sheet should be present in the columns. - - samplesheet_meta: - type: map - description: | - Where samplesheet is provided, aroovy Map containing information on - sample sheet, at a minimum an id. e.g. [ id:'test' ] - - samplesheet: - type: file - description: | - Optional CSV or TSV format sample sheet with sample metadata. If - provided this is used to infer minimum passing samples from group sizes - present (see grouping_variable), but also to validate matrix columns. - If not provided, all numeric columns are selected. - - minimum_abundance: - type: float - description: | - Minimum abundance value, supplied via task.ext.args as --minimum_abundance - default: 1 - - minimum_samples: - type: integer - description: | - Minimum observations that must pass the threshold to retain - the row/ feature (e.g. gene). Supplied via task.ext.args as - --minimum_samples - default: 1 - - minimum_proportion: - type: float - description: | - A minimum proportion of observations that must pass the threshold. - Supplied via task.ext.args as --minimum_proportion. Overrides - minimum_samples - default: 0 - - grouping_variable: - type: string - description: | - Optionally supply a variable from the sample sheet that can be used to - define groups and derive a minimum group size upon which to base - minimum observation numbers. The rationale being to allow retention of - features that might be present in only one group. Supplied via - task.ext.args as --grouping_variable - - minimum_proportion_not_na: - type: float - description: | - A minimum proportion of observations that must have a numeric value (not be NA). - Supplied via task.ext.args as --minimum_proportion_not_na - default: 0.5 - - minimum_samples_not_na: - type: integer - description: | - Minimum observations that must have a numeric value (not be NA) to retain - the row/ feature (e.g. gene). Supplied via task.ext.args as - --minimum_samples_not_na. Overrides minimum_proportion_not_na - - most_variant_features: - type: integer - description: | - Variance filter for the number of row/ feature (e.g. gene) observations returned. - Supplied via task.ext.args as --most_variant_features - + - - meta: + type: map + description: | + Groovy Map containing information on matrix to be filtered, at a + minimum an id. e.g. [ id:'test' ] + - abundance: + type: file + description: | + Raw TSV or CSV format abundance matrix with features (e.g. + genes) by row and observations (e.g. samples) by column. All rownames + from the sample sheet should be present in the columns. + - - samplesheet_meta: + type: map + description: | + Where samplesheet is provided, aroovy Map containing information on + sample sheet, at a minimum an id. e.g. [ id:'test' ] + - samplesheet: + type: file + description: | + Optional CSV or TSV format sample sheet with sample metadata. If + provided this is used to infer minimum passing samples from group sizes + present (see grouping_variable), but also to validate matrix columns. + If not provided, all numeric columns are selected. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - filtered: - type: file - description: Filtered version of input matrix - pattern: "*.filtered.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*.filtered.tsv": + type: file + description: Filtered version of input matrix + pattern: "*.filtered.tsv" - tests: - type: file - description: Boolean matrix with pass/ fail status for each test on each feature - pattern: "*.tests.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*.tests.tsv": + type: file + description: Boolean matrix with pass/ fail status for each test on each feature + pattern: "*.tests.tsv" + - session_info: + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - R_sessionInfo.log: + type: file + description: Log file containing R session information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/sratoolsncbisettings/meta.yml b/modules/nf-core/custom/sratoolsncbisettings/meta.yml index 46a6cd329c27..2938a35dc84e 100644 --- a/modules/nf-core/custom/sratoolsncbisettings/meta.yml +++ b/modules/nf-core/custom/sratoolsncbisettings/meta.yml @@ -1,5 +1,6 @@ name: "custom_sratoolsncbisettings" -description: Test for the presence of suitable NCBI settings or create them on the fly. +description: Test for the presence of suitable NCBI settings or create them on the + fly. keywords: - NCBI - settings @@ -13,15 +14,18 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ncbi_settings: - type: file - description: An NCBI user settings file. - pattern: "*.mkfg" + - "*.mkfg": + type: file + description: An NCBI user settings file. + pattern: "*.mkfg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/custom/tabulartogseacls/meta.yml b/modules/nf-core/custom/tabulartogseacls/meta.yml index 2d1ec0b8d32a..e0d8c340a462 100644 --- a/modules/nf-core/custom/tabulartogseacls/meta.yml +++ b/modules/nf-core/custom/tabulartogseacls/meta.yml @@ -9,37 +9,41 @@ tools: - custom: description: "Make a GSEA class file (.cls) from tabular inputs" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseacls/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing metadata including an id, the sample sheet column - used to define groups, and optionally a separator to override defaults e.g. [ - id:'test', variable:'treatment', separator:',' ]. The way these values are - passed to the associated module parameters is then defined via an ext.args - specification for the process from the workflow, like: ext.args = { [ - "separator": "\t", "variable": "$meta.variable" ] } ('variable' is - compulsory here). - - samples: - type: file - description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row and variables by column. - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing metadata including an id, the sample sheet column + used to define groups, and optionally a separator to override defaults e.g. [ + id:'test', variable:'treatment', separator:',' ]. The way these values are + passed to the associated module parameters is then defined via an ext.args + specification for the process from the workflow, like: ext.args = { [ + "separator": "\t", "variable": "$meta.variable" ] } ('variable' is + compulsory here). + - samples: + type: file + description: Tabular (e.g. TSV/CSV) samples file with sample IDs by row and + variables by column. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing metadata e.g. [ id:'test', variable:'treatment', - separator:',' ] - cls: - type: file - description: | - A categorical class format file (.cls) as defined by the Broad - documentation at - https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats + - meta: + type: map + description: | + Groovy Map containing metadata e.g. [ id:'test', variable:'treatment', + separator:',' ] + - "*.cls": + type: file + description: | + A categorical class format file (.cls) as defined by the Broad + documentation at + https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Data_formats - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tabulartogseagct/meta.yml b/modules/nf-core/custom/tabulartogseagct/meta.yml index 4f4a806429c1..055cd9e4d320 100644 --- a/modules/nf-core/custom/tabulartogseagct/meta.yml +++ b/modules/nf-core/custom/tabulartogseagct/meta.yml @@ -1,37 +1,43 @@ name: "custom_tabulartogseagct" -description: Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA +description: Convert a TSV or CSV with features by row and observations by column + to a GCT format file as consumed by GSEA keywords: - gsea - gct - tabular tools: - tabulartogseagct: - description: "Convert a TSV or CSV with features by row and observations by column to a GCT format file as consumed by GSEA" + description: "Convert a TSV or CSV with features by row and observations by column + to a GCT format file as consumed by GSEA" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tabulartogseagct/main.nf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing matrix information - e.g. [ id:'test' ] - - tabular: - type: file - description: Tabular (e.g. TSV or CSV file) containing a numeric matrix with features (e.g. genes) by row and samples by column. - pattern: "*.{tsv,csv}" + - - meta: + type: map + description: | + Groovy Map containing matrix information + e.g. [ id:'test' ] + - tabular: + type: file + description: Tabular (e.g. TSV or CSV file) containing a numeric matrix with + features (e.g. genes) by row and samples by column. + pattern: "*.{tsv,csv}" output: - - meta: - type: map - description: | - Groovy Map containing matrix information - e.g. [ id:'test' ] - gct: - type: file - description: GCT format version of input TSV - pattern: "*.{gct}" + - meta: + type: map + description: | + Groovy Map containing matrix information + e.g. [ id:'test' ] + - "*.gct": + type: file + description: GCT format version of input TSV + pattern: "*.{gct}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/custom/tx2gene/meta.yml b/modules/nf-core/custom/tx2gene/meta.yml index d991bf1be95b..8254afa08dab 100644 --- a/modules/nf-core/custom/tx2gene/meta.yml +++ b/modules/nf-core/custom/tx2gene/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "custom_tx2gene" -description: Make a transcript/gene mapping from a GTF and cross-reference with transcript quantifications. +description: Make a transcript/gene mapping from a GTF and cross-reference with transcript + quantifications. keywords: - gene - gtf @@ -14,51 +14,51 @@ tools: check it against transcript quantifications" tool_dev_url: "https://github.com/nf-core/modules/blob/master/modules/nf-core/custom/tx2gene/main.nf" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" - - meta2: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - - id: - type: string - description: Gene ID attribute in the GTF file (default= gene_id) - - extra: - type: string - description: Extra gene attribute in the GTF file (default= gene_name) - + - - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" + - - meta2: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: file + description: quants file + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' + - - id: + type: string + description: Gene ID attribute in the GTF file (default= gene_id) + - - extra: + type: string + description: Extra gene attribute in the GTF file (default= gene_name) output: - - meta: - type: map - description: | - Groovy Map containing reference information related to the GTF file - e.g. `[ id:'yeast' ]` - tx2gene: - type: file - description: A transcript/ gene mapping table in TSV format - pattern: "*.tx2gene.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information related to the GTF file + e.g. `[ id:'yeast' ]` + - "*tx2gene.tsv": + type: file + description: A transcript/ gene mapping table in TSV format + pattern: "*.tx2gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/cutadapt/meta.yml b/modules/nf-core/cutadapt/meta.yml index 5ecfe27a9bb8..8844d86c8ca0 100644 --- a/modules/nf-core/cutadapt/meta.yml +++ b/modules/nf-core/cutadapt/meta.yml @@ -12,35 +12,44 @@ tools: documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: 10.14806/ej.17.1.200 licence: ["MIT"] + identifier: biotools:cutadapt input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trim.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*fastq.gz" - log: - type: file - description: cuatadapt log file - pattern: "*cutadapt.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: cuatadapt log file + pattern: "*cutadapt.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/cutesv/meta.yml b/modules/nf-core/cutesv/meta.yml index 480efafd0996..409fd1fc0108 100644 --- a/modules/nf-core/cutesv/meta.yml +++ b/modules/nf-core/cutesv/meta.yml @@ -6,48 +6,52 @@ keywords: - sv tools: - cutesv: - description: a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. + description: a clustering-and-refinement method to analyze the signatures to implement + sensitive SV detection. homepage: https://github.com/tjiangHIT/cuteSV documentation: https://github.com/tjiangHIT/cuteSV#readme tool_dev_url: https://github.com/tjiangHIT/cuteSV licence: ["MIT"] + identifier: biotools:cuteSV input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: | - Reference database in FASTA format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: Index of BAM file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: | + Reference database in FASTA format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: VCF file containing called variants from CuteSV - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: VCF file containing called variants from CuteSV + pattern: "*.vcf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-hakkaart" - "@yuukiiwa" diff --git a/modules/nf-core/damageprofiler/meta.yml b/modules/nf-core/damageprofiler/meta.yml index 7cf1a4a51461..0c3360e893bb 100644 --- a/modules/nf-core/damageprofiler/meta.yml +++ b/modules/nf-core/damageprofiler/meta.yml @@ -1,5 +1,6 @@ name: damageprofiler -description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage +description: A Java based tool to determine damage patterns on ancient DNA as a replacement + for mapDamage keywords: - damage - deamination @@ -13,43 +14,51 @@ keywords: - archaeogenetics tools: - damageprofiler: - description: A Java based tool to determine damage patterns on ancient DNA as a replacement for mapDamage + description: A Java based tool to determine damage patterns on ancient DNA as + a replacement for mapDamage homepage: https://github.com/Integrative-Transcriptomics/DamageProfiler documentation: https://damageprofiler.readthedocs.io/ tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler doi: "10.1093/bioinformatics/btab190" licence: ["GPL v3"] + identifier: biotools:damageprofiler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: OPTIONAL FASTA reference file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: OPTIONAL FASTA index file from samtools faidx - pattern: "*.{fai}" - - specieslist: - type: file - description: OPTIONAL text file with list of target reference headers - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: OPTIONAL FASTA reference file + pattern: "*.{fasta,fna,fa}" + - - fai: + type: file + description: OPTIONAL FASTA index file from samtools faidx + pattern: "*.{fai}" + - - specieslist: + type: file + description: OPTIONAL text file with list of target reference headers + pattern: "*.{txt}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: DamageProfiler results directory - pattern: "*/*" + - meta: + type: directory + description: DamageProfiler results directory + pattern: "*/*" + - ${prefix}: + type: directory + description: DamageProfiler results directory + pattern: "*/*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/dastool/dastool/meta.yml b/modules/nf-core/dastool/dastool/meta.yml index c661de8db6b5..7eab655a8426 100644 --- a/modules/nf-core/dastool/dastool/meta.yml +++ b/modules/nf-core/dastool/dastool/meta.yml @@ -20,81 +20,155 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - contigs: - type: file - description: fasta file - pattern: "*.{fa.gz,fas.gz,fasta.gz}" - - bins: - type: file - description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin" - pattern: "*.tsv" - - proteins: - type: file - description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo) - pattern: "*.{fa.gz,fas.gz,fasta.gz}" - - db_directory: - type: file - description: (optional) Directory of single copy gene database. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs: + type: file + description: fasta file + pattern: "*.{fa.gz,fas.gz,fasta.gz}" + - bins: + type: file + description: "FastaToContig2Bin tabular file generated with dastool/fastatocontig2bin" + pattern: "*.tsv" + - - proteins: + type: file + description: Predicted proteins in prodigal fasta format (>scaffoldID_geneNo) + pattern: "*.{fa.gz,fas.gz,fasta.gz}" + - - db_directory: + type: file + description: (optional) Directory of single copy gene database. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "versions.yml" - log: - type: file - description: Log file of the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file of the run + pattern: "*.log" - summary: - type: file - description: Summary of output bins including quality and completeness estimates - pattern: "*summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary.tsv": + type: file + description: Summary of output bins including quality and completeness estimates + pattern: "*summary.txt" - contig2bin: - type: file - description: Scaffolds to bin file of output bins - pattern: "*.contig2bin.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DASTool_contig2bin.tsv": + type: file + description: Scaffolds to bin file of output bins + pattern: "*.contig2bin.txt" - eval: - type: file - description: Quality and completeness estimates of input bin sets - pattern: "*.eval" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.eval": + type: file + description: Quality and completeness estimates of input bin sets + pattern: "*.eval" - bins: - type: file - description: Final refined bins in fasta format - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DASTool_bins/*.fa": + type: file + description: Final refined bins in fasta format + pattern: "*.fa" - pdfs: - type: file - description: Plots showing the amount of high quality bins and score distribution of bins per method - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Plots showing the amount of high quality bins and score distribution + of bins per method + pattern: "*.pdf" - fasta_proteins: - type: file - description: Output from prodigal if not already supplied - pattern: "*.proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidates.faa": + type: file + description: Output from prodigal if not already supplied + pattern: "*.proteins.faa" + - candidates_faa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa": + type: file + description: FAA file + pattern: "*.faa" - fasta_archaea_scg: - type: file - description: Results of archaeal single-copy-gene prediction - pattern: "*.archaea.scg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.archaea.scg": + type: file + description: Results of archaeal single-copy-gene prediction + pattern: "*.archaea.scg" - fasta_bacteria_scg: - type: file - description: Results of bacterial single-copy-gene prediction - pattern: "*.bacteria.scg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bacteria.scg": + type: file + description: Results of bacterial single-copy-gene prediction + pattern: "*.bacteria.scg" - b6: - type: file - description: Results in b6 format - pattern: "*.b6" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.b6": + type: file + description: Results in b6 format + pattern: "*.b6" - seqlength: - type: file - description: Summary of contig lengths - pattern: "*.seqlength" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.seqlength": + type: file + description: Summary of contig lengths + pattern: "*.seqlength" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/dastool/fastatocontig2bin/meta.yml b/modules/nf-core/dastool/fastatocontig2bin/meta.yml index bbecfd27ef76..97b140bb9741 100644 --- a/modules/nf-core/dastool/fastatocontig2bin/meta.yml +++ b/modules/nf-core/dastool/fastatocontig2bin/meta.yml @@ -1,5 +1,6 @@ name: dastool_fastatocontig2bin -description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format +description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin + format keywords: - binning - das tool @@ -20,33 +21,38 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta of list of fasta files recommended to be gathered via with .collect() of bins - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - - extension: - type: string - description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, if gzipped input. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta of list of fasta files recommended to be gathered via with + .collect() of bins + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - extension: + type: string + description: Fasta file extension (fa | fas | fasta | ...), without .gz suffix, + if gzipped input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastatocontig2bin: - type: file - description: tabular contig2bin file for DAS tool input - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: tabular contig2bin file for DAS tool input + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/dastool/scaffolds2bin/meta.yml b/modules/nf-core/dastool/scaffolds2bin/meta.yml index f57c50ab0176..2fcc05bdc1f1 100644 --- a/modules/nf-core/dastool/scaffolds2bin/meta.yml +++ b/modules/nf-core/dastool/scaffolds2bin/meta.yml @@ -1,5 +1,6 @@ name: dastool_scaffolds2bin -description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin format +description: Helper script to convert a set of bins in fasta format to tabular scaffolds2bin + format keywords: - binning - das tool @@ -20,33 +21,38 @@ tools: tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" licence: ["BSD"] + identifier: biotools:dastool input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta or list of fasta files recommended to be gathered via with .collect() of bins - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" - - extension: - type: string - description: Fasta file extension (fa | fas | fasta | ...), but without .gz suffix, even if gzipped input. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta or list of fasta files recommended to be gathered via with + .collect() of bins + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - extension: + type: string + description: Fasta file extension (fa | fas | fasta | ...), but without .gz + suffix, even if gzipped input. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds2bin: - type: file - description: tabular scaffolds2bin file for DAS tool input - pattern: "*.scaffolds2bin.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: tabular scaffolds2bin file for DAS tool input + pattern: "*.scaffolds2bin.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/datavzrd/meta.yml b/modules/nf-core/datavzrd/meta.yml index 8ac5f55d0d5c..44d6bd6932ed 100644 --- a/modules/nf-core/datavzrd/meta.yml +++ b/modules/nf-core/datavzrd/meta.yml @@ -1,44 +1,42 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "datavzrd" -description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables. +description: Datavzrd is a tool to create visual HTML reports from collections of + CSV/TSV tables. keywords: - visualisation - tsv - csv tools: - datavzrd: - description: Datavzrd is a tool to create visual HTML reports from collections of CSV/TSV tables. + description: Datavzrd is a tool to create visual HTML reports from collections + of CSV/TSV tables. homepage: https://datavzrd.github.io/ documentation: https://datavzrd.github.io/docs/index.html tool_dev_url: https://github.com/datavzrd/datavzrd licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - config_file: - type: file - description: configuration file used for visualisation - pattern: "*.{yml,yaml}" - - table: - type: file - description: file used for visualisation - pattern: "*.{tsv,csv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: directory - description: directory with HTML report of provided CSV/TSV files - pattern: "/output/" - + - meta: + type: directory + description: directory with HTML report of provided CSV/TSV files + pattern: "/output/" + - ${prefix}: + type: directory + description: directory with HTML report of provided CSV/TSV files + pattern: "/output/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vickylaram" - "@famosab" diff --git a/modules/nf-core/decoupler/decoupler/meta.yml b/modules/nf-core/decoupler/decoupler/meta.yml index 4188611897b7..8f502254188a 100644 --- a/modules/nf-core/decoupler/decoupler/meta.yml +++ b/modules/nf-core/decoupler/decoupler/meta.yml @@ -25,58 +25,62 @@ tools: tool_dev_url: "https://decoupler-py.readthedocs.io" doi: "10.1093/bioadv/vbac016" licence: ["GPL v3"] + identifier: biotools:decoupler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:‘test’, single_end ] - - mat: - type: file - description: | - Path to the matrix file (e.g. gene/protein expression, etc.). - Should be in in tab-separated format (`*.tab`) - pattern: "*.tsv" - - net: - type: file - description: | - The prior knowledge network linking the features of the - expression matrix to a process/component (e.g. gene set, - transcription factor, kinase, etc.) - pattern: "*.tsv" - - args: - type: string - description: | - Keyword arguments passed to `decoupler.decouple()` (see - documentation for more information here: - https://decoupler-py.readthedocs.io/en/latest/generated/decoupler.decouple.html#decoupler.decouple). - Arguments specific for a method must be specified with - the method name as a prefix e.g. `'gsea_batch_size'` - pattern: "{arg: val, ..., method_arg: val}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - mat: + type: file + description: | + Path to the matrix file (e.g. gene/protein expression, etc.). + Should be in in tab-separated format (`*.tab`) + pattern: "*.tsv" + - - net: + type: file + description: | + The prior knowledge network linking the features of the + expression matrix to a process/component (e.g. gene set, + transcription factor, kinase, etc.) + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:‘test’, single_end ] - dc_estimate: - type: file - description: | - The file containing the estimation results of the enrichment(s) - pattern: "*estimate__decoupler.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - "*estimate__decoupler.tsv": + type: file + description: | + The file containing the estimation results of the enrichment(s) + pattern: "*estimate__decoupler.tsv" - dc_pvals: - type: file - description: | - The file containing the p-value associated to the estimation - results of the enrichment(s) - pattern: "*pvals__decoupler.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:‘test’, single_end ] + - "*pvals__decoupler.tsv": + type: file + description: | + The file containing the p-value associated to the estimation + results of the enrichment(s) + pattern: "*pvals__decoupler.tsv" + - s: + type: file + description: | + The file containing the p-value associated to the estimation + results of the enrichment(s) + pattern: "*pvals__decoupler.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gabora" - "@vicpaton" diff --git a/modules/nf-core/dedup/meta.yml b/modules/nf-core/dedup/meta.yml index 3a6265878420..614236f22977 100644 --- a/modules/nf-core/dedup/meta.yml +++ b/modules/nf-core/dedup/meta.yml @@ -1,5 +1,6 @@ name: dedup -description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). +description: DeDup is a tool for read deduplication in paired-end read merging (e.g. + for ancient DNA experiments). keywords: - dedup - deduplication @@ -9,48 +10,70 @@ keywords: - bam tools: - dedup: - description: DeDup is a tool for read deduplication in paired-end read merging (e.g. for ancient DNA experiments). + description: DeDup is a tool for read deduplication in paired-end read merging + (e.g. for ancient DNA experiments). homepage: https://github.com/apeltzer/DeDup documentation: https://dedup.readthedocs.io/en/latest/ tool_dev_url: https://github.com/apeltzer/DeDup doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Deduplicated BAM file - pattern: "*_rmdup.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rmdup.bam": + type: file + description: Deduplicated BAM file + pattern: "*_rmdup.bam" - json: - type: file - description: JSON file for MultiQC - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file for MultiQC + pattern: "*.json" - hist: - type: file - description: Histogram data of amount of deduplication - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram data of amount of deduplication + pattern: "*.hist" - log: - type: file - description: Dedup log information - pattern: "*log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*log": + type: file + description: Dedup log information + pattern: "*log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deeparg/downloaddata/meta.yml b/modules/nf-core/deeparg/downloaddata/meta.yml index 65fb39039ed5..5df2887ba0e9 100644 --- a/modules/nf-core/deeparg/downloaddata/meta.yml +++ b/modules/nf-core/deeparg/downloaddata/meta.yml @@ -1,5 +1,6 @@ name: deeparg_downloaddata -description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes +description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes keywords: - download - database @@ -9,22 +10,26 @@ keywords: - prediction tools: - deeparg: - description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes + description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes homepage: https://github.com/gaarangoa/deeparg documentation: https://github.com/gaarangoa/deeparg tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] + identifier: "" # No input required for download module. output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing database required for deepARG. - pattern: "db/" + - db/: + type: directory + description: Directory containing database required for deepARG. + pattern: "db/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deeparg/predict/meta.yml b/modules/nf-core/deeparg/predict/meta.yml index d62c2c5fb26c..dbd63945dbb7 100644 --- a/modules/nf-core/deeparg/predict/meta.yml +++ b/modules/nf-core/deeparg/predict/meta.yml @@ -1,5 +1,6 @@ name: deeparg_predict -description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes +description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes keywords: - deeparg - antimicrobial resistance @@ -11,56 +12,81 @@ keywords: - metagenomes tools: - deeparg: - description: A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes + description: A deep learning based approach to predict Antibiotic Resistance Genes + (ARGs) from metagenomes homepage: https://github.com/gaarangoa/deeparg documentation: https://github.com/gaarangoa/deeparg tool_dev_url: https://github.com/gaarangoa/deeparg doi: "10.1186/s40168-018-0401-z" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file containing gene-like sequences - pattern: "*.{fasta,fa,fna}" - - model: - type: string - description: Which model to use, depending on input data. Either 'LS' or 'SS' for long or short sequences respectively - pattern: "LS|LS" - - db: - type: directory - description: Path to a directory containing the deepARG pre-built models - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file containing gene-like sequences + pattern: "*.{fasta,fa,fna}" + - model: + type: string + description: Which model to use, depending on input data. Either 'LS' or 'SS' + for long or short sequences respectively + pattern: "LS|LS" + - - db: + type: directory + description: Path to a directory containing the deepARG pre-built models + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - daa: - type: file - description: Sequences of ARG-like sequences from DIAMOND alignment - pattern: "*.align.daa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.align.daa": + type: file + description: Sequences of ARG-like sequences from DIAMOND alignment + pattern: "*.align.daa" - daa_tsv: - type: file - description: Alignments scores against ARG-like sequences from DIAMOND alignment - pattern: "*.align.daa.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.align.daa.tsv": + type: file + description: Alignments scores against ARG-like sequences from DIAMOND alignment + pattern: "*.align.daa.tsv" - arg: - type: file - description: Table containing sequences with an ARG-like probability of more than specified thresholds - pattern: "*.mapping.ARG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapping.ARG": + type: file + description: Table containing sequences with an ARG-like probability of more + than specified thresholds + pattern: "*.mapping.ARG" - potential_arg: - type: file - description: Table containing sequences with an ARG-like probability of less than specified thresholds, and requires manual inspection - pattern: "*.mapping.potential.ARG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapping.potential.ARG": + type: file + description: Table containing sequences with an ARG-like probability of less + than specified thresholds, and requires manual inspection + pattern: "*.mapping.potential.ARG" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/deepbgc/download/meta.yml b/modules/nf-core/deepbgc/download/meta.yml index 6444dd41d493..4551e9a00df5 100644 --- a/modules/nf-core/deepbgc/download/meta.yml +++ b/modules/nf-core/deepbgc/download/meta.yml @@ -1,5 +1,6 @@ name: "deepbgc_download" -description: Database download module for DeepBGC which detects BGCs in bacterial and fungal genomes using deep learning. +description: Database download module for DeepBGC which detects BGCs in bacterial + and fungal genomes using deep learning. keywords: - database - download @@ -19,15 +20,18 @@ tools: tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" licence: ["MIT"] + identifier: biotools:DeepBGC output: + - db: + - deepbgc_db/: + type: directory + description: Directory containing the DeepBGC database + pattern: "deepbgc_db/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - deepbgc_db: - type: directory - description: Contains reference database files - pattern: "deepbgc_db" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/deepbgc/pipeline/meta.yml b/modules/nf-core/deepbgc/pipeline/meta.yml index 5f939eaa4fd1..186c7d30c750 100644 --- a/modules/nf-core/deepbgc/pipeline/meta.yml +++ b/modules/nf-core/deepbgc/pipeline/meta.yml @@ -17,73 +17,138 @@ tools: tool_dev_url: "https://github.com/Merck/deepbgc" doi: "10.1093/nar/gkz654" licence: ["MIT"] + identifier: biotools:DeepBGC input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - genome: - type: file - description: FASTA/GenBank/Pfam CSV file - pattern: "*.{fasta,fa,fna,gbk,csv}" - - db: - type: directory - description: Database path + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - genome: + type: file + description: FASTA/GenBank/Pfam CSV file + pattern: "*.{fasta,fa,fna,gbk,csv}" + - - db: + type: directory + description: Database path output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - readme: - type: file - description: txt file containing description of output files - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/README.txt: + type: file + description: txt file containing description of output files + pattern: "*.{txt}" - log: - type: file - description: Log output of DeepBGC - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/LOG.txt: + type: file + description: Log output of DeepBGC + pattern: "*.{txt}" - json: - type: file - description: AntiSMASH JSON file for sideloading - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.antismash.json: + type: file + description: AntiSMASH JSON file for sideloading + pattern: "*.{json}" - bgc_gbk: - type: file - description: Sequences and features of all detected BGCs in GenBank format - pattern: "*.{bgc.gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.bgc.gbk: + type: file + description: Sequences and features of all detected BGCs in GenBank format + pattern: "*.{bgc.gbk}" - bgc_tsv: - type: file - description: Table of detected BGCs and their properties - pattern: "*.{bgc.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.bgc.tsv: + type: file + description: Table of detected BGCs and their properties + pattern: "*.{bgc.tsv}" - full_gbk: - type: file - description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain features) and BGCs (cluster features) - pattern: "*.{full.gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.full.gbk: + type: file + description: Fully annotated input sequence with proteins, Pfam domains (PFAM_domain + features) and BGCs (cluster features) + pattern: "*.{full.gbk}" - pfam_tsv: - type: file - description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) in genomic order, with BGC detection scores - pattern: "*.{pfam.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/${prefix}.pfam.tsv: + type: file + description: Table of Pfam domains (pfam_id) from given sequence (sequence_id) + in genomic order, with BGC detection scores + pattern: "*.{pfam.tsv}" - bgc_png: - type: file - description: Detected BGCs plotted by their nucleotide coordinates - pattern: "*.{bgc.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.bgc.png: + type: file + description: Detected BGCs plotted by their nucleotide coordinates + pattern: "*.{bgc.png}" - pr_png: - type: file - description: Precision-Recall curve based on predicted per-Pfam BGC scores - pattern: "*.{pr.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.pr.png: + type: file + description: Precision-Recall curve based on predicted per-Pfam BGC scores + pattern: "*.{pr.png}" - roc_png: - type: file - description: ROC curve based on predicted per-Pfam BGC scores - pattern: "*.{roc.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.roc.png: + type: file + description: ROC curve based on predicted per-Pfam BGC scores + pattern: "*.{roc.png}" - score_png: - type: file - description: BGC detection scores of each Pfam domain in genomic order - pattern: "*.{score.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/evaluation/${prefix}.score.png: + type: file + description: BGC detection scores of each Pfam domain in genomic order + pattern: "*.{score.png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" - "@jfy133" diff --git a/modules/nf-core/deepcell/mesmer/meta.yml b/modules/nf-core/deepcell/mesmer/meta.yml index dec360b9c388..0292aa79e7d1 100644 --- a/modules/nf-core/deepcell/mesmer/meta.yml +++ b/modules/nf-core/deepcell/mesmer/meta.yml @@ -12,42 +12,44 @@ tools: tool_dev_url: "https://githu/b.com/vanvalenlab/deepcell-tf" doi: 10.1038/s41587-021-01094-0 licence: ["APACHE2"] + identifier: biotools:deepcell input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - img: - type: file - description: Multichannel image file - pattern: "*.{tiff,tif,h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - membrane_img: - type: file - description: Optional membrane image to be provided separately. - pattern: "*.{tiff,tif,h5,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - img: + type: file + description: Multichannel image file + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - membrane_img: + type: file + description: Optional membrane image to be provided separately. + pattern: "*.{tiff,tif,h5,hdf5}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mask: - type: file - description: File containing the mask. - pattern: "*.{tif, tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tif": + type: file + description: File containing the mask. + pattern: "*.{tif, tiff}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" - "@chiarasch" diff --git a/modules/nf-core/deeptmhmm/meta.yml b/modules/nf-core/deeptmhmm/meta.yml index 5abcf1e306d0..dc51ec59b02d 100644 --- a/modules/nf-core/deeptmhmm/meta.yml +++ b/modules/nf-core/deeptmhmm/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: deeptmhmm description: A Deep Learning Model for Transmembrane Topology Prediction and Classification @@ -8,51 +7,84 @@ keywords: - classification tools: - deeptmhmm: - description: Deep Learning model for Transmembrane Helices protein domain prediction through the BioLib Python Client + description: Deep Learning model for Transmembrane Helices protein domain prediction + through the BioLib Python Client homepage: https://dtu.biolib.com/DeepTMHMM documentation: https://dtu.biolib.com/DeepTMHMM doi: 10.1101/2022.04.08.487609 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Predicted topologies (inside, outside, TMhelix) in general Feature Format Version 3 - pattern: "biolib_results/TMRs.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/TMRs.gff3: + type: file + description: Predicted topologies (inside, outside, TMhelix) in general Feature + Format Version 3 + pattern: "biolib_results/TMRs.gff3" - line3: - type: file - description: Predicted topologies and information of protein sequences in three lines (name, sequence, topology) - pattern: "biolib_results/predicted_topologies.3line" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/predicted_topologies.3line: + type: file + description: Predicted topologies and information of protein sequences in three + lines (name, sequence, topology) + pattern: "biolib_results/predicted_topologies.3line" - md: - type: file - description: Markdown results file - pattern: "biolib_results/deeptmhmm_results.md" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/deeptmhmm_results.md: + type: file + description: Markdown results file + pattern: "biolib_results/deeptmhmm_results.md" - csv: - type: file - description: CSV file with per-residue predictions for the likelihood of each amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, Inside, Outside or Signal (only when querying against genomic fasta) - pattern: "biolib_results/*_probs.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/*_probs.csv: + type: file + description: CSV file with per-residue predictions for the likelihood of each + amino acid being in structural regions such as Beta-sheet, Periplasm, Membrane, + Inside, Outside or Signal (only when querying against genomic fasta) + pattern: "biolib_results/*_probs.csv" - png: - type: file - description: Most likely topology probability line plots (only when querying against genomic fasta) - pattern: "biolib_results/plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - biolib_results/plot.png: + type: file + description: Most likely topology probability line plots (only when querying + against genomic fasta) + pattern: "biolib_results/plot.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/deeptools/bamcoverage/meta.yml b/modules/nf-core/deeptools/bamcoverage/meta.yml index 89cf05ff9033..c349bfb93197 100644 --- a/modules/nf-core/deeptools/bamcoverage/meta.yml +++ b/modules/nf-core/deeptools/bamcoverage/meta.yml @@ -1,57 +1,69 @@ name: deeptools_bamcoverage -description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. +description: This tool takes an alignment of reads or fragments as input (BAM file) + and generates a coverage track (bigWig or bedGraph) as output. keywords: - coverage - depth - track tools: - deeptools: - description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data + description: A set of user-friendly tools for normalization and visualzation of + deep-sequencing data homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html tool_dev_url: https://github.com/deeptools/deepTools/ doi: "10.1093/nar/gkw257" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference file the CRAM file was created with (required with CRAM input) - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference file (optional, but recommended) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Reference file the CRAM file was created with (required with CRAM + input) + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference file (optional, but recommended) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bigWig: - type: file - description: BigWig file - pattern: "*.bigWig" + - bigwig: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: BigWig file + pattern: "*.bigWig" - bedgraph: - type: file - description: Bedgraph file - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedgraph": + type: file + description: Bedgraph file + pattern: "*.bedgraph" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@SusiJo" diff --git a/modules/nf-core/deeptools/computematrix/meta.yml b/modules/nf-core/deeptools/computematrix/meta.yml index a48dec392628..1ab222081bb6 100644 --- a/modules/nf-core/deeptools/computematrix/meta.yml +++ b/modules/nf-core/deeptools/computematrix/meta.yml @@ -7,46 +7,56 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bigwig: - type: file - description: bigwig file containing genomic scores - pattern: "*.{bw,bigwig}" - - bed: - type: file - description: bed file containing genomic regions - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bigwig: + type: file + description: bigwig file containing genomic scores + pattern: "*.{bw,bigwig}" + - - bed: + type: file + description: bed file containing genomic regions + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - matrix: - type: file - description: | - gzipped matrix file needed by the plotHeatmap and plotProfile - deeptools utilities - pattern: "*.{computeMatrix.mat.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mat.gz": + type: file + description: | + gzipped matrix file needed by the plotHeatmap and plotProfile + deeptools utilities + pattern: "*.{computeMatrix.mat.gz}" - table: - type: file - description: | - tabular file containing the scores of the generated matrix - pattern: "*.{computeMatrix.vals.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mat.tab": + type: file + description: | + tabular file containing the scores of the generated matrix + pattern: "*.{computeMatrix.vals.mat.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jeremy1805" - "@edmundmiller" diff --git a/modules/nf-core/deeptools/multibamsummary/meta.yml b/modules/nf-core/deeptools/multibamsummary/meta.yml index 25362587b92b..035f7f02241e 100644 --- a/modules/nf-core/deeptools/multibamsummary/meta.yml +++ b/modules/nf-core/deeptools/multibamsummary/meta.yml @@ -7,44 +7,48 @@ keywords: - bin tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" - - labels: - type: string - description: User specified labels instead of default labels (file names). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or more BAM files + pattern: "*.{bam}" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" + - labels: + type: string + description: User specified labels instead of default labels (file names). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - matrix: - type: file - description: | - compressed numpy array of read coverage data used by plotCorrelation and plotPCA - deeptool utilities - pattern: "all_bam.bamSummary.npz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: | + compressed numpy array of read coverage data used by plotCorrelation and plotPCA + deeptool utilities + pattern: "all_bam.bamSummary.npz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotcorrelation/meta.yml b/modules/nf-core/deeptools/plotcorrelation/meta.yml index 4b32e7b7ef44..d82ae170508e 100644 --- a/modules/nf-core/deeptools/plotcorrelation/meta.yml +++ b/modules/nf-core/deeptools/plotcorrelation/meta.yml @@ -1,5 +1,6 @@ name: "deeptools_plotcorrelation" -description: Visualises sample correlations using a compressed matrix generated by mutlibamsummary or multibigwigsummary as input. +description: Visualises sample correlations using a compressed matrix generated by + mutlibamsummary or multibigwigsummary as input. keywords: - corrrelation - matrix @@ -7,53 +8,63 @@ keywords: - scatterplot tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - matrix: - type: file - description: | - compressed matrix file produced by - mutlibamsummary or multibigwigsummary - pattern: "*.{npz}" - - method: - type: string - description: | - Correlation coefficient to use for heatmap or scatterplot generation - pattern: "{spearman,pearson}" - - plot_type: - type: string - description: | - Type of output plot to display sample correlation - pattern: "{heatmap,scatterplot}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - matrix: + type: file + description: | + compressed matrix file produced by + mutlibamsummary or multibigwigsummary + pattern: "*.{npz}" + - - method: + type: string + description: | + Correlation coefficient to use for heatmap or scatterplot generation + pattern: "{spearman,pearson}" + - - plot_type: + type: string + description: | + Type of output plot to display sample correlation + pattern: "{heatmap,scatterplot}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotCorrelation.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotCorrelation.pdf}" - matrix: - type: file - description: | - Tab-separated file containing a matrix of pairwise correlations - pattern: "*.{plotCorrelation.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: | + Tab-separated file containing a matrix of pairwise correlations + pattern: "*.{plotCorrelation.mat.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotfingerprint/meta.yml b/modules/nf-core/deeptools/plotfingerprint/meta.yml index f8217440104b..d659f02cf722 100644 --- a/modules/nf-core/deeptools/plotfingerprint/meta.yml +++ b/modules/nf-core/deeptools/plotfingerprint/meta.yml @@ -7,50 +7,66 @@ keywords: - bam tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bams: + type: file + description: BAM files + pattern: "*.bam" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotFingerprint.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotFingerprint.pdf}" - matrix: - type: file - description: | - Output file summarizing the read counts per bin - pattern: "*.{plotFingerprint.raw.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.raw.txt": + type: file + description: | + Output file summarizing the read counts per bin + pattern: "*.{plotFingerprint.raw.txt}" - metrics: - type: file - description: | - file containing BAM file quality metrics - pattern: "*.{qcmetrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qcmetrics.txt": + type: file + description: | + file containing BAM file quality metrics + pattern: "*.{qcmetrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deeptools/plotheatmap/meta.yml b/modules/nf-core/deeptools/plotheatmap/meta.yml index 54ddeb0a0043..7c4828ca2fda 100644 --- a/modules/nf-core/deeptools/plotheatmap/meta.yml +++ b/modules/nf-core/deeptools/plotheatmap/meta.yml @@ -7,44 +7,51 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - matrix: - type: file - description: | - gzipped matrix file produced by deeptools_ - computematrix deeptools utility - pattern: "*.{mat.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - matrix: + type: file + description: | + gzipped matrix file produced by deeptools_ + computematrix deeptools utility + pattern: "*.{mat.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotHeatmap.pdf}" - - matrix: - type: file - description: | - File containing the matrix of values - used to generate the heatmap - pattern: "*.{plotHeatmap.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotHeatmap.pdf}" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: Output table - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deeptools/plotpca/meta.yml b/modules/nf-core/deeptools/plotpca/meta.yml index b04b60ccebca..ea999922695f 100644 --- a/modules/nf-core/deeptools/plotpca/meta.yml +++ b/modules/nf-core/deeptools/plotpca/meta.yml @@ -1,5 +1,6 @@ name: "deeptools_plotpca" -description: Generates principal component analysis (PCA) plot using a compressed matrix generated by multibamsummary or multibigwigsummary as input. +description: Generates principal component analysis (PCA) plot using a compressed + matrix generated by multibamsummary or multibigwigsummary as input. keywords: - PCA - matrix @@ -7,43 +8,53 @@ keywords: - bigwig tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - matrix: - type: file - description: | - compressed matrix file produced by - mutlibamsummary or multibigwigsummary - pattern: "*.{npz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - matrix: + type: file + description: | + compressed matrix file produced by + mutlibamsummary or multibigwigsummary + pattern: "*.{npz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotPCA.pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotPCA.pdf}" - tab: - type: file - description: | - Tab file containing data used to generate the PCA plot - pattern: "*.{plotPCA.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: | + Tab file containing data used to generate the PCA plot + pattern: "*.{plotPCA.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/nf-core/deeptools/plotprofile/meta.yml b/modules/nf-core/deeptools/plotprofile/meta.yml index f7f105055320..8056816a8d91 100644 --- a/modules/nf-core/deeptools/plotprofile/meta.yml +++ b/modules/nf-core/deeptools/plotprofile/meta.yml @@ -7,44 +7,52 @@ keywords: - matrix tools: - deeptools: - description: A set of user-friendly tools for normalization and visualization of deep-sequencing data + description: A set of user-friendly tools for normalization and visualization + of deep-sequencing data documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" licence: ["GPL v3"] + identifier: biotools:deeptools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - matrix: - type: file - description: | - gzipped matrix file produced by deeptools_ - computematrix deeptools utility - pattern: "*.{mat.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - matrix: + type: file + description: | + gzipped matrix file produced by deeptools_ + computematrix deeptools utility + pattern: "*.{mat.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - pdf: - type: file - description: | - Output figure containing resulting plot - pattern: "*.{plotProfile.pdf}" - - matrix: - type: file - description: | - File containing the matrix of values - used to generate the profile - pattern: "*.{plotProfile.mat.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: | + Output figure containing resulting plot + pattern: "*.{plotProfile.pdf}" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: Output table + pattern: "*.tab" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" - "@drpatelh" diff --git a/modules/nf-core/deepvariant/callvariants/meta.yml b/modules/nf-core/deepvariant/callvariants/meta.yml index db779c62ba04..4507192ca2f3 100644 --- a/modules/nf-core/deepvariant/callvariants/meta.yml +++ b/modules/nf-core/deepvariant/callvariants/meta.yml @@ -6,31 +6,39 @@ keywords: - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - make_examples_tfrecords: - type: file - description: The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process - pattern: "*.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - make_examples_tfrecords: + type: file + description: The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process + pattern: "*.gz" output: - call_variants_tfrecords: - type: list - description: | - Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. + - meta: + type: list + description: | + Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. + - ${prefix}.call-*-of-*.tfrecord.gz: + type: list + description: | + Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls. - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/makeexamples/meta.yml b/modules/nf-core/deepvariant/makeexamples/meta.yml index ab1d2e589a13..6fb9f1b81435 100644 --- a/modules/nf-core/deepvariant/makeexamples/meta.yml +++ b/modules/nf-core/deepvariant/makeexamples/meta.yml @@ -1,84 +1,98 @@ name: deepvariant_makeexamples -description: Transforms the input alignments to a format suitable for the deep neural network variant caller +description: Transforms the input alignments to a format suitable for the deep neural + network variant caller keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - intervals: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - pattern: "*.gzi" - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: Interval file for targeted regions + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + pattern: "*.gzi" + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - examples: - type: list - description: | - Tuple containing sample metadata and examples that can be used for calling + - meta: + type: list + description: | + Tuple containing sample metadata and examples that can be used for calling + - ${prefix}.examples.tfrecord-*-of-*.gz{,.example_info.json}: + type: list + description: | + Tuple containing sample metadata and examples that can be used for calling - gvcf: - type: list - description: | - Tuple containing sample metadata and the GVCF data in tfrecord format + - meta: + type: list + description: | + Tuple containing sample metadata and the GVCF data in tfrecord format + - ${prefix}.gvcf.tfrecord-*-of-*.gz: + type: list + description: | + Tuple containing sample metadata and the GVCF data in tfrecord format - versions: - type: file - description: File containing the DeepVariant software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing the DeepVariant software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/meta.yml b/modules/nf-core/deepvariant/meta.yml index 30c0285ae3ee..77dbf438c3fa 100644 --- a/modules/nf-core/deepvariant/meta.yml +++ b/modules/nf-core/deepvariant/meta.yml @@ -1,89 +1,120 @@ name: deepvariant -description: (DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: (DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses + a deep neural network to call genetic variants from next-generation DNA sequencing + data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - interval: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: file containing intervals + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Tabix index of compressed VCF file + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Tabix index of compressed GVCF file + pattern: "*.g.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/postprocessvariants/meta.yml b/modules/nf-core/deepvariant/postprocessvariants/meta.yml index 03a0a6b8235a..132a5263226f 100644 --- a/modules/nf-core/deepvariant/postprocessvariants/meta.yml +++ b/modules/nf-core/deepvariant/postprocessvariants/meta.yml @@ -1,86 +1,109 @@ name: deepvariant_postprocessvariants -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variant_calls_tfrecord_files: - type: file - description: | - One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS - pattern: "*.tfrecord.gz" - - gvcf_tfrecords: - type: file - description: | - Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output - pattern: "*.gz" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variant_calls_tfrecord_files: + type: file + description: | + One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS + pattern: "*.tfrecord.gz" + - gvcf_tfrecords: + type: file + description: | + Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output + pattern: "*.gz" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - vcf_tbi: - type: file - description: Index for VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Index for VCF + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index for GVCF - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Index for GVCF + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/deepvariant/rundeepvariant/meta.yml b/modules/nf-core/deepvariant/rundeepvariant/meta.yml index a6ee5499285e..29b45ff91739 100644 --- a/modules/nf-core/deepvariant/rundeepvariant/meta.yml +++ b/modules/nf-core/deepvariant/rundeepvariant/meta.yml @@ -1,89 +1,119 @@ name: deepvariant_rundeepvariant -description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data keywords: - variant calling - machine learning - neural network tools: - deepvariant: - description: DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data homepage: https://github.com/google/deepvariant documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "10.1038/nbt.4235" licence: ["BSD-3-clause"] + identifier: biotools:deepvariant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.bam/cram" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.bai/crai" - - interval: - type: file - description: Interval file for targeted regions - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gzi: - type: file - description: GZI index of reference fasta file - pattern: "*.gzi" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - par_bed: - type: file - description: BED file containing PAR regions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.bam/cram" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.bai/crai" + - intervals: + type: file + description: file containing intervals + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gzi: + type: file + description: GZI index of reference fasta file + pattern: "*.gzi" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - par_bed: + type: file + description: BED file containing PAR regions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - vcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf.gz.tbi: + type: file + description: Tabix index file of compressed VCF + pattern: "*.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz: + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" + - gvcf_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.g.vcf.gz.tbi: + type: file + description: Tabix index file of compressed GVCF + pattern: "*.g.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@ramprasadn" diff --git a/modules/nf-core/delly/call/meta.yml b/modules/nf-core/delly/call/meta.yml index cc378ffd62a7..ef7c238d6b65 100644 --- a/modules/nf-core/delly/call/meta.yml +++ b/modules/nf-core/delly/call/meta.yml @@ -7,73 +7,88 @@ keywords: - bcf tools: - delly: - description: Structural variant discovery by integrated paired-end and split-read analysis + description: Structural variant discovery by integrated paired-end and split-read + analysis homepage: https://github.com/dellytools/delly documentation: https://github.com/dellytools/delly/blob/master/README.md doi: "10.1093/bioinformatics/bts378" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate marked - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - vcf: - type: file - description: A BCF/VCF file to genotype with Delly. If this is supplied, the variant calling will be skipped - pattern: "*.{vcf.gz,bcf}" - - vcf_index: - type: file - description: The index of the BCF/VCF file - pattern: "*.{tbi,csi}" - - exclude_bed: - type: file - description: An optional bed file containing regions to exclude from the called VCF - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference fasta file to identify split-reads - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment must be sorted, indexed, and duplicate + marked + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - vcf: + type: file + description: A BCF/VCF file to genotype with Delly. If this is supplied, the + variant calling will be skipped + pattern: "*.{vcf.gz,bcf}" + - vcf_index: + type: file + description: The index of the BCF/VCF file + pattern: "*.{tbi,csi}" + - exclude_bed: + type: file + description: An optional bed file containing regions to exclude from the called + VCF + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file to identify split-reads + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bcf: - type: file - description: Called variants in BCF/VCF format. Specify either "bcf" or "vcf" in ext.suffix to define the output type - pattern: "*.{bcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{bcf,vcf.gz}": + type: file + description: Called variants in BCF/VCF format. Specify either "bcf" or "vcf" + in ext.suffix to define the output type + pattern: "*.{bcf,vcf.gz}" - csi: - type: file - description: A generated csi index that matches the bcf output (not generated for vcf files) - pattern: "*.{bcf.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{csi,tbi}": + type: file + description: A generated csi index that matches the bcf output (not generated + for vcf files) + pattern: "*.{bcf.csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@nvnieuwk" diff --git a/modules/nf-core/demuxem/meta.yml b/modules/nf-core/demuxem/meta.yml index 0aa94d1de600..2fb43f5780ef 100644 --- a/modules/nf-core/demuxem/meta.yml +++ b/modules/nf-core/demuxem/meta.yml @@ -1,73 +1,81 @@ name: "demuxem" -description: Demultiplexing cell nucleus hashing data, using the estimated antibody background probability. +description: Demultiplexing cell nucleus hashing data, using the estimated antibody + background probability. keywords: - demultiplexing - hashing-based deconvoltion - single-cell tools: - demuxem: - description: "DemuxEM is the demultiplexing module of Pegasus, which works on cell-hashing and nucleus-hashing genomics data." + description: "DemuxEM is the demultiplexing module of Pegasus, which works on + cell-hashing and nucleus-hashing genomics data." homepage: "https://demuxEM.readthedocs.io" documentation: "https://demuxEM.readthedocs.io" tool_dev_url: "https://github.com/lilab-bcb/pegasus/tree/master" doi: "10.1038/s41467-019-10756-2" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input_raw_gene_bc_matrices_h5: - type: string - description: | - Path to file containing input raw RNA expression matrix in 10x hdf5 format - pattern: "*.{h5}" - - input_hto_csv_file: - type: string - description: | - Path to file containing input HTO (antibody tag) count matrix in CSV format. - pattern: "*.{csv}" - - output_name: - type: string - description: | - Output name. All outputs will use it as the prefix. - - generate_gender_plot: - type: string - description: | - Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names. - - genome: - type: string - description: | - Reference genome name. If not provided, the tools infers it from the expression matrix file - - generate_diagnostic_plots: - type: string - description: | - Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input_raw_gene_bc_matrices_h5: + type: string + description: | + Path to file containing input raw RNA expression matrix in 10x hdf5 format + pattern: "*.{h5}" + - input_hto_csv_file: + type: string + description: | + Path to file containing input HTO (antibody tag) count matrix in CSV format. + pattern: "*.{csv}" + - - output_name: + type: string + description: | + Output name. All outputs will use it as the prefix. + - - generate_gender_plot: + type: string + description: | + Generate violin plots using gender-specific genes (e.g. Xist). It is a comma-separated list of gene names. + - - genome: + type: string + description: | + Reference genome name. If not provided, the tools infers it from the expression matrix file + - - generate_diagnostic_plots: + type: string + description: | + Generate diagnostic plots, including the background/signal between HTO counts, estimated background probabilities, HTO distributions. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample1' ] - zarr: - type: file - description: | - RNA expression matrix with demultiplexed sample identities in Zarr format. - pattern: "*_demux.zarr.zip" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*_demux.zarr.zip": + type: file + description: | + RNA expression matrix with demultiplexed sample identities in Zarr format. + pattern: "*_demux.zarr.zip" - out_zarr: - type: file - description: | - DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA. - pattern: "*.out.demuxEM.zarr.zip" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.out.demuxEM.zarr.zip": + type: file + description: | + DemuxEM-calculated results in Zarr format, containing two datasets, one for HTO and one for RNA. + pattern: "*.out.demuxEM.zarr.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/deseq2/differential/meta.yml b/modules/nf-core/deseq2/differential/meta.yml index 41fcc014f020..be8cec47cb1a 100644 --- a/modules/nf-core/deseq2/differential/meta.yml +++ b/modules/nf-core/deseq2/differential/meta.yml @@ -7,114 +7,167 @@ keywords: - deseq2 tools: - "deseq2": - description: "Differential gene expression analysis based on the negative binomial distribution" + description: "Differential gene expression analysis based on the negative binomial + distribution" homepage: "https://bioconductor.org/packages/release/bioc/html/DESeq2.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html" tool_dev_url: "https://github.com/mikelove/DESeq2" doi: "10.1186/s13059-014-0550-8" licence: ["LGPL >=3"] + identifier: biotools:deseq2 input: - - meta: - type: map - description: | - Groovy Map containing contrast information. This can be used at the - workflow level to pass optional parameters to the module, e.g. - [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: - '--blocking_variable $meta.blocking'. - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - counts: - type: file - description: | - Raw TSV or CSV format expression matrix as output from the nf-core - RNA-seq workflow - - meta3: - type: file - description: | - Meta map describing control genes, e.g. [ id: 'ERCC' ] - - control_genes_file: - type: file - description: | - Text file listing control genes, one per line - - meta4: - type: map - description: | - Groovy map containing study-wide metadata related to the transcript - lengths file - - transcript_lengths_file: - type: file - description: | - Optional file of transcript lengths, with the same sample columns as - counts. If supplied, lengths will be supplied to DESeq2 to correct for - differences in average transcript lengths across samples. - + - - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata + - counts: + type: file + description: | + Raw TSV or CSV format expression matrix as output from the nf-core + RNA-seq workflow + - - meta3: + type: file + description: | + Meta map describing control genes, e.g. [ id: 'ERCC' ] + - control_genes_file: + type: file + description: | + Text file listing control genes, one per line + - - meta4: + type: map + description: | + Groovy map containing study-wide metadata related to the transcript + lengths file + - transcript_lengths_file: + type: file + description: | + Optional file of transcript lengths, with the same sample columns as + counts. If supplied, lengths will be supplied to DESeq2 to correct for + differences in average transcript lengths across samples. output: - results: - type: file - description: TSV-format table of differential expression information as output by DESeq2 - pattern: "deseq2.results.tsv" + - meta: + type: file + description: TSV-format table of differential expression information as output + by DESeq2 + pattern: "deseq2.results.tsv" + - "*.deseq2.results.tsv": + type: file + description: TSV-format table of differential expression information as output + by DESeq2 + pattern: "deseq2.results.tsv" - dispersion_plot: - type: file - description: DESeq2 dispersion plot - pattern: "deseq2.dispersion.png" + - meta: + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" + - "*.deseq2.dispersion.png": + type: file + description: DESeq2 dispersion plot + pattern: "deseq2.dispersion.png" - rdata: - type: file - description: Serialised DESeq2 object - pattern: "dds.rld.rds" + - meta: + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" + - "*.dds.rld.rds": + type: file + description: Serialised DESeq2 object + pattern: "dds.rld.rds" - size_factors: - type: file - description: Size factors - pattern: "deseq2.sizefactors.tsv" + - meta: + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" + - "*.deseq2.sizefactors.tsv": + type: file + description: Size factors + pattern: "deseq2.sizefactors.tsv" - normalised_counts: - type: file - description: TSV-format counts matrix, normalised to size factors - pattern: "normalised_counts.tsv" + - meta: + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" + - "*.normalised_counts.tsv": + type: file + description: TSV-format counts matrix, normalised to size factors + pattern: "normalised_counts.tsv" - rlog_counts: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `rlog()`. - pattern: "rlog.tsv" + - meta: + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `rlog()`. + pattern: "rlog.tsv" + - "*.rlog.tsv": + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `rlog()`. + pattern: "rlog.tsv" - vst_counts: - type: file - description: | - Optional, TSV-format counts matrix, normalised to size factors, with - variance stabilisation applied via `vst()`. - pattern: "vst_counts.tsv" + - meta: + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `vst()`. + pattern: "vst_counts.tsv" + - "*.vst.tsv": + type: file + description: | + Optional, TSV-format counts matrix, normalised to size factors, with + variance stabilisation applied via `vst()`. + pattern: "vst_counts.tsv" - model: - type: file - description: TXT-format DESeq2 model - pattern: "deseq2.model.tsv" + - meta: + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" + - "*.deseq2.model.txt": + type: file + description: TXT-format DESeq2 model + pattern: "deseq2.model.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: file + description: dump of R SessionInfo + pattern: "*.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/diamond/blastp/meta.yml b/modules/nf-core/diamond/blastp/meta.yml index bab6801eaa2e..fbddfbd00f18 100644 --- a/modules/nf-core/diamond/blastp/meta.yml +++ b/modules/nf-core/diamond/blastp/meta.yml @@ -13,77 +13,116 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `blast` corresponds to - BLAST pairwise format. `xml` corresponds to BLAST xml format. - `txt` corresponds to to BLAST tabular format. `tsv` corresponds to - taxonomic classification format. - pattern: "blast|xml|txt|daa|sam|tsv|paf" - - blast_columns: - type: string - description: | - Optional space separated list of DIAMOND tabular BLAST output keywords - used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: - qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `blast` corresponds to + BLAST pairwise format. `xml` corresponds to BLAST xml format. + `txt` corresponds to to BLAST tabular format. `tsv` corresponds to + taxonomic classification format. + pattern: "blast|xml|txt|daa|sam|tsv|paf" + - - blast_columns: + type: string + description: | + Optional space separated list of DIAMOND tabular BLAST output keywords + used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: + qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - blast: - type: file - description: File containing blastp hits - pattern: "*.{blast}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.blast": + type: file + description: File containing blastp hits + pattern: "*.{blast}" - xml: - type: file - description: File containing blastp hits - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: File containing blastp hits + pattern: "*.{xml}" - txt: - type: file - description: File containing hits in tabular BLAST format. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing hits in tabular BLAST format. + pattern: "*.{txt}" - daa: - type: file - description: File containing hits DAA format - pattern: "*.{daa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.daa": + type: file + description: File containing hits DAA format + pattern: "*.{daa}" - sam: - type: file - description: File containing aligned reads in SAM format - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: File containing aligned reads in SAM format + pattern: "*.{sam}" - tsv: - type: file - description: Tab separated file containing taxonomic classification of hits - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab separated file containing taxonomic classification of hits + pattern: "*.{tsv}" - paf: - type: file - description: File containing aligned reads in pairwise mapping format format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: File containing aligned reads in pairwise mapping format format + pattern: "*.{paf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" - "@jfy133" diff --git a/modules/nf-core/diamond/blastx/meta.yml b/modules/nf-core/diamond/blastx/meta.yml index 17106548d6a8..a5c058758118 100644 --- a/modules/nf-core/diamond/blastx/meta.yml +++ b/modules/nf-core/diamond/blastx/meta.yml @@ -13,81 +13,126 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - meta2: - type: map - description: | - Groovy Map containing db information - e.g. [ id:'test2', single_end:false ] - - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" - - out_ext: - type: string - description: | - Specify the type of output file to be generated. `blast` corresponds to - BLAST pairwise format. `xml` corresponds to BLAST xml format. - `txt` corresponds to to BLAST tabular format. `tsv` corresponds to - taxonomic classification format. - pattern: "blast|xml|txt|daa|sam|tsv|paf" - - blast_columns: - type: string - description: | - Optional space separated list of DIAMOND tabular BLAST output keywords - used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: - qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing db information + e.g. [ id:'test2', single_end:false ] + - db: + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" + - - out_ext: + type: string + description: | + Specify the type of output file to be generated. `blast` corresponds to + BLAST pairwise format. `xml` corresponds to BLAST xml format. + `txt` corresponds to to BLAST tabular format. `tsv` corresponds to + taxonomic classification format. + pattern: "blast|xml|txt|daa|sam|tsv|paf" + - - blast_columns: + type: string + description: | + Optional space separated list of DIAMOND tabular BLAST output keywords + used for in conjunction with the 'txt' out_ext option (--outfmt 6). Options: + qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - blast: - type: file - description: File containing blastp hits - pattern: "*.{blast}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.blast": + type: file + description: File containing blastp hits + pattern: "*.{blast}" - xml: - type: file - description: File containing blastp hits - pattern: "*.{xml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: File containing blastp hits + pattern: "*.{xml}" - txt: - type: file - description: File containing hits in tabular BLAST format. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: File containing hits in tabular BLAST format. + pattern: "*.{txt}" - daa: - type: file - description: File containing hits DAA format - pattern: "*.{daa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.daa": + type: file + description: File containing hits DAA format + pattern: "*.{daa}" - sam: - type: file - description: File containing aligned reads in SAM format - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: File containing aligned reads in SAM format + pattern: "*.{sam}" - tsv: - type: file - description: Tab separated file containing taxonomic classification of hits - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab separated file containing taxonomic classification of hits + pattern: "*.{tsv}" - paf: - type: file - description: File containing aligned reads in pairwise mapping format format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: File containing aligned reads in pairwise mapping format format + pattern: "*.{paf}" - log: - type: file - description: Log file containing stdout information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" - "@jfy133" diff --git a/modules/nf-core/diamond/cluster/meta.yml b/modules/nf-core/diamond/cluster/meta.yml index 4858b240687b..49699cece328 100644 --- a/modules/nf-core/diamond/cluster/meta.yml +++ b/modules/nf-core/diamond/cluster/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "diamond_cluster" description: calculate clusters of highly similar sequences @@ -15,36 +14,36 @@ tools: tool_dev_url: "https://github.com/bbuchfink/diamond" doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3-or-later"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - db: - type: file - description: The input sequence database. Supported formats are FASTA and DIAMOND (.dmnd) format. - pattern: "*.{dmnd,fa,faa,fasta}(.gz)" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - db: + type: file + description: The input sequence database. Supported formats are FASTA and DIAMOND + (.dmnd) format. + pattern: "*.{dmnd,fa,faa,fasta}(.gz)" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tsv: - type: file - description: a 2-column tabular file with the representative accession as the first column and the member sequence accession as the second column - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: a 2-column tabular file with the representative accession as the + first column and the member sequence accession as the second column + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@itrujnara" maintainers: diff --git a/modules/nf-core/diamond/makedb/meta.yml b/modules/nf-core/diamond/makedb/meta.yml index fdcf032dba58..71de32eef867 100644 --- a/modules/nf-core/diamond/makedb/meta.yml +++ b/modules/nf-core/diamond/makedb/meta.yml @@ -13,42 +13,46 @@ tools: tool_dev_url: https://github.com/bbuchfink/diamond doi: "10.1038/s41592-021-01101-x" licence: ["GPL v3.0"] + identifier: biotools:diamond input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - taxonmap: - type: file - description: Optional mapping file of NCBI protein accession numbers to taxon ids (gzip compressed), required for taxonomy functionality. - pattern: "*.gz" - - taxonnodes: - type: file - description: Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality. - pattern: "*.dmp" - - taxonnames: - type: file - description: Optional NCBI taxonomy names.dmp file, required for taxonomy functionality. - pattern: "*.dmp" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - taxonmap: + type: file + description: Optional mapping file of NCBI protein accession numbers to taxon + ids (gzip compressed), required for taxonomy functionality. + pattern: "*.gz" + - - taxonnodes: + type: file + description: Optional NCBI taxonomy nodes.dmp file, required for taxonomy functionality. + pattern: "*.dmp" + - - taxonnames: + type: file + description: Optional NCBI taxonomy names.dmp file, required for taxonomy functionality. + pattern: "*.dmp" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - db: - type: file - description: File of the indexed DIAMOND database - pattern: "*.dmnd" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dmnd": + type: file + description: File of the indexed DIAMOND database + pattern: "*.dmnd" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" maintainers: diff --git a/modules/nf-core/dragmap/align/environment.yml b/modules/nf-core/dragmap/align/environment.yml index 2f1191b2ec6c..547e6f24a5f6 100644 --- a/modules/nf-core/dragmap/align/environment.yml +++ b/modules/nf-core/dragmap/align/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - dragmap=1.3.0 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.18 - pigz=2.8 + - samtools=1.18 diff --git a/modules/nf-core/dragmap/align/meta.yml b/modules/nf-core/dragmap/align/meta.yml index 2270bd3397d4..80f020f58f12 100644 --- a/modules/nf-core/dragmap/align/meta.yml +++ b/modules/nf-core/dragmap/align/meta.yml @@ -13,44 +13,104 @@ tools: documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - hashmap: - type: file - description: DRAGMAP hash table - pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta reference files - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - hashmap: + type: file + description: DRAGMAP hash table + pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: + type: file + description: Genome fasta reference files + pattern: "*.{fa,fasta,fna}" + - - sort_bam: + type: boolean + description: Sort the BAM file output: + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Output SAM file containing read alignments + pattern: "*.{sam}" - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file containing read alignments + pattern: "*.{cram}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Index file for CRAM file + pattern: "*.{crai}" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Index file for CRAM file + pattern: "*.{csi}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/dragmap/hashtable/meta.yml b/modules/nf-core/dragmap/hashtable/meta.yml index 1d1f92f52285..450a1e58e064 100644 --- a/modules/nf-core/dragmap/hashtable/meta.yml +++ b/modules/nf-core/dragmap/hashtable/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/Illumina/dragmap tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - hashmap: - type: file - description: DRAGMAP hash table - pattern: "*.{cmp,.bin,.txt}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - dragmap: + type: file + description: DRAGMAP hash table + pattern: "*.{cmp,.bin,.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/dragonflye/meta.yml b/modules/nf-core/dragonflye/meta.yml index 60ccad453413..0c5edd88a439 100644 --- a/modules/nf-core/dragonflye/meta.yml +++ b/modules/nf-core/dragonflye/meta.yml @@ -10,51 +10,78 @@ tools: homepage: https://github.com/rpetit3/dragonflye documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: | - Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome. - pattern: "*.fastq.gz" - - longreads: - type: file - description: Input Nanopore FASTQ file - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: | + Optional. List of FastQ files of short reads (paired-end data) that will be used to polish the draft genome. + pattern: "*.fastq.gz" + - longreads: + type: file + description: Input Nanopore FASTQ file + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: The final assembly produced by Dragonflye - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: The final assembly produced by Dragonflye + pattern: "*.fa" - log: - type: file - description: Full log file for bug reporting - pattern: "dragonflye.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dragonflye.log: + type: file + description: Full log file for bug reporting + pattern: "dragonflye.log" - raw_contigs: - type: file - description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven) - pattern: "{flye,miniasm,raven}.fasta" - - txt: - type: file - description: Assembly information output by Flye - pattern: "flye-info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{flye,miniasm,raven}.fasta": + type: file + description: Raw assembly produced by the assembler (Flye, Miniasm, or Raven) + pattern: "{flye,miniasm,raven}.fasta" - gfa: - type: file - description: Assembly graph produced by Miniasm, or Raven - pattern: "{flye,miniasm,raven}-unpolished.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{flye,miniasm,raven}-unpolished.gfa": + type: file + description: Assembly graph produced by Miniasm, or Raven + pattern: "{flye,miniasm,raven}-unpolished.gfa" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - flye-info.txt: + type: file + description: Assembly information output by Flye + pattern: "flye-info.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/dshbio/exportsegments/meta.yml b/modules/nf-core/dshbio/exportsegments/meta.yml index e0e837342050..c5ccac39a84f 100644 --- a/modules/nf-core/dshbio/exportsegments/meta.yml +++ b/modules/nf-core/dshbio/exportsegments/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly segments in uncompressed or compressed GFA 1.0 format - pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly segments in uncompressed or compressed GFA 1.0 format + pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Assembly segment sequences in gzipped FASTA format - pattern: "*.{fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: Assembly segment sequences in gzipped FASTA format + pattern: "*.{fa.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/filterbed/meta.yml b/modules/nf-core/dshbio/filterbed/meta.yml index 7e8abc8b25ad..0669239934d7 100644 --- a/modules/nf-core/dshbio/filterbed/meta.yml +++ b/modules/nf-core/dshbio/filterbed/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/filtergff3/meta.yml b/modules/nf-core/dshbio/filtergff3/meta.yml index 5b4da52e7874..2a3973a4dd43 100644 --- a/modules/nf-core/dshbio/filtergff3/meta.yml +++ b/modules/nf-core/dshbio/filtergff3/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff3.gz": + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/splitbed/meta.yml b/modules/nf-core/dshbio/splitbed/meta.yml index 91d37f0f220f..4ef53e7067ac 100644 --- a/modules/nf-core/dshbio/splitbed/meta.yml +++ b/modules/nf-core/dshbio/splitbed/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format to split - pattern: "*.{bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format to split + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Features in split gzipped BED formatted files - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed.gz": + type: file + description: Features in split gzipped BED formatted files + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/dshbio/splitgff3/meta.yml b/modules/nf-core/dshbio/splitgff3/meta.yml index 4de6614e1ffd..2e96c20cd6b2 100644 --- a/modules/nf-core/dshbio/splitgff3/meta.yml +++ b/modules/nf-core/dshbio/splitgff3/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://github.com/heuermh/dishevelled-bio documentation: https://github.com/heuermh/dishevelled-bio licence: ["LGPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format to split - pattern: "*.{gff3.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format to split + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gff3: - type: file - description: Features in split gzipped GFF3 formatted files - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff3.gz": + type: file + description: Features in split gzipped GFF3 formatted files + pattern: "*.{gff3.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml index 934fe8ed69c3..da4d166055f3 100644 --- a/modules/nf-core/duphold/meta.yml +++ b/modules/nf-core/duphold/meta.yml @@ -1,5 +1,9 @@ name: "duphold" -description: SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls. This can be used as additional information for filtering variants; for example we will be skeptical of deletion calls that do not have lower than average coverage compared to regions with similar gc-content. +description: SV callers like lumpy look at split-reads and pair distances to find + structural variants. This tool is a fast way to add depth information to those calls. + This can be used as additional information for filtering variants; for example we + will be skeptical of deletion calls that do not have lower than average coverage + compared to regions with similar gc-content. keywords: - sort - duphold @@ -7,52 +11,62 @@ keywords: - depth information tools: - "duphold": - description: "SV callers like lumpy look at split-reads and pair distances to find structural variants. This tool is a fast way to add depth information to those calls." + description: "SV callers like lumpy look at split-reads and pair distances to + find structural variants. This tool is a fast way to add depth information to + those calls." homepage: "https://github.com/brentp/duphold" documentation: "https://github.com/brentp/duphold" tool_dev_url: "https://github.com/brentp/duphold" doi: "10.1093/gigascience/giz040" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - aligment_file: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - aligment_file_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - sv_variants: - type: file - description: A variants file containing structural variants - pattern: "*.{vcf,bcf}(.gz)?" - - snp_variants: - type: file - description: A variants file containing SNPs - pattern: "*.{vcf,bcf}(.gz)?" - - snp_variants: - type: file - description: The index of the variants file containing SNPs - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_file: + type: file + description: file containing alignments + - alignement_index: + type: file + description: index of alignment file + - sv_variants: + type: file + description: A variants file containing structural variants + pattern: "*.{vcf,bcf}(.gz)?" + - snp_variants: + type: file + description: A variants file containing SNPs + pattern: "*.{vcf,bcf}(.gz)?" + - snp_variants_index: + type: file + description: index of snp variants file + - - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta,fna}" + - - fasta_fai: + type: file + description: Index of fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The output VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The output VCF + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/dupradar/meta.yml b/modules/nf-core/dupradar/meta.yml index 95960ae989da..a532519fea7b 100644 --- a/modules/nf-core/dupradar/meta.yml +++ b/modules/nf-core/dupradar/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "dupradar" description: Assessment of duplication rates in RNA-Seq datasets @@ -14,71 +13,109 @@ tools: tool_dev_url: "https://github.com/ssayols/dupRadar" doi: "10.1186/s12859-016-1276-2" licence: ["GPL v3"] + identifier: biotools:dupradar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'human' ] - - gtf: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file containing read alignments + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'human' ] + - gtf: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - scatter2d: - type: file - description: PDF duplication rate against total read count plot - pattern: "*_duprateExpDens.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpDens.pdf": + type: file + description: PDF duplication rate against total read count plot + pattern: "*_duprateExpDens.pdf" - boxplot: - type: file - description: | - PDF duplication rate ~ total reads per kilobase (RPK) boxplot - pattern: "*_duprateExpBoxplot.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_duprateExpBoxplot.pdf": + type: file + description: | + PDF duplication rate ~ total reads per kilobase (RPK) boxplot + pattern: "*_duprateExpBoxplot.pdf" - hist: - type: file - description: | - PDF expression histogram - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_expressionHist.pdf": + type: file + description: | + PDF expression histogram + pattern: "*.pdf" - dupmatrix: - type: file - description: | - Text file containing tags falling on the features described in the GTF - file - pattern: "*_dupMatrix.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dupMatrix.txt": + type: file + description: | + Text file containing tags falling on the features described in the GTF + file + pattern: "*_dupMatrix.txt" - intercept_slope: - type: file - description: | - Text file containing intercept and slope from dupRadar modelling - pattern: "*_intercept_slope.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_intercept_slope.txt": + type: file + description: | + Text file containing intercept and slope from dupRadar modelling + pattern: "*_intercept_slope.txt" - multiqc: - type: file - description: | - dupRadar files for passing to MultiQC - pattern: "*_multiqc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: | + dupRadar files for passing to MultiQC + pattern: "*_multiqc.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/dysgu/meta.yml b/modules/nf-core/dysgu/meta.yml index 67c6c70abf8c..227a41169dbf 100644 --- a/modules/nf-core/dysgu/meta.yml +++ b/modules/nf-core/dysgu/meta.yml @@ -1,6 +1,7 @@ name: dysgu -description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations. +description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It + is designed for accurate and efficient detection of structural variations. keywords: - structural variants - sv @@ -13,54 +14,61 @@ tools: tool_dev_url: https://github.com/kcleal/dysgu doi: "10.1093/nar/gkac039" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - input: - type: file - description: Input BAM file - pattern: "*.bam" - - index: - type: file - description: BAM index file - pattern: "*.bai" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - input: + type: file + description: Input BAM file + pattern: "*.bam" + - index: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample1' ] - vcf: - type: file - description: VCF file with identified structural variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.vcf.gz": + type: file + description: VCF file with identified structural variants + pattern: "*.{vcf.gz}" - tbi: - type: file - description: The index of the BCF/VCF file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample1' ] + - "*.vcf.gz.tbi": + type: file + description: The index of the BCF/VCF file + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@famosab" - "@poddarharsh15" diff --git a/modules/nf-core/ectyper/meta.yml b/modules/nf-core/ectyper/meta.yml index 58ae53b687f6..97accd7bb625 100644 --- a/modules/nf-core/ectyper/meta.yml +++ b/modules/nf-core/ectyper/meta.yml @@ -11,38 +11,53 @@ tools: documentation: https://github.com/phac-nml/ecoli_serotyping tool_dev_url: https://github.com/phac-nml/ecoli_serotyping licence: ["Apache 2"] + identifier: biotools:ectyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA formatted assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA formatted assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: ectyper log output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: ectyper log output + pattern: "*.log" - tsv: - type: file - description: ectyper serotyping results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: ectyper serotyping results in TSV format + pattern: "*.tsv" - txt: - type: file - description: Allele report generated from BLAST results - pattern: "*.tst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Allele report generated from BLAST results + pattern: "*.tst" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/eggnogmapper/meta.yml b/modules/nf-core/eggnogmapper/meta.yml index 95090a10c65d..8cf836d08741 100644 --- a/modules/nf-core/eggnogmapper/meta.yml +++ b/modules/nf-core/eggnogmapper/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "eggnogmapper" description: Fast genome-wide functional annotation through orthology assignment. @@ -14,55 +13,71 @@ tools: tool_dev_url: "https://github.com/eggnogdb/eggnog-mapper" doi: "10.1093/molbev/msab293" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - eggnog_db: - type: file - description: The eggnog database file (e.g. eggnog-mapper/data/eggnog.db) - pattern: "*.db" - - eggnog_data_dir: - type: directory - description: Directory containing eggnog database files (e.g. eggnog-mapper/data) - pattern: "*" - - meta2: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test' ]` - - eggnog_diamond_db: - type: file - description: The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd) - pattern: "*.dmnd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - eggnog_db: + type: file + description: The eggnog database file (e.g. eggnog-mapper/data/eggnog.db) + pattern: "*.db" + - - eggnog_data_dir: + type: directory + description: Directory containing eggnog database files (e.g. eggnog-mapper/data) + pattern: "*" + - - meta2: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test' ]` + - eggnog_diamond_db: + type: file + description: The eggnog Diamond protein database file (e.g. eggnog-mapper/data/eggnog_proteins.dmnd) + pattern: "*.dmnd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - annotations: - type: file - description: TSV with the results from the annotation phase - pattern: "*.emapper.annotations" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.annotations": + type: file + description: TSV with the results from the annotation phase + pattern: "*.emapper.annotations" - orthologs: - type: file - description: TSV with the results from parsing the hits, linking queries with seed orthologs (with commented metadata) - pattern: "*.emapper.seed_orthologs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.seed_orthologs": + type: file + description: TSV with the results from parsing the hits, linking queries with + seed orthologs (with commented metadata) + pattern: "*.emapper.seed_orthologs" - hits: - type: file - description: TSV with the results from the Diamond search phase - pattern: "*.emapper.hits" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.emapper.hits": + type: file + description: TSV with the results from the Diamond search phase + pattern: "*.emapper.hits" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/eido/convert/meta.yml b/modules/nf-core/eido/convert/meta.yml index 9c84140154f4..a7c292c69814 100644 --- a/modules/nf-core/eido/convert/meta.yml +++ b/modules/nf-core/eido/convert/meta.yml @@ -13,25 +13,30 @@ tools: documentation: "http://eido.databio.org/en/latest/" doi: "10.1093/gigascience/giab077" licence: ["BSD-2-Clause"] + identifier: biotools:eido-python-package input: - - samplesheet: - type: file - description: Nextflow samplesheet or PEP project - pattern: "*.{yaml,yml,csv}" - - format: - type: string - description: Extension of an output file - - pep_input_base_dir: - type: file - description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory. + - - samplesheet: + type: file + description: Nextflow samplesheet or PEP project + pattern: "*.{yaml,yml,csv}" + - - format: + type: string + description: Extension of an output file + - - pep_input_base_dir: + type: file + description: Optional path to the directory where files specified in a PEP config + file are stored. Any paths specified in the config will need to be relative + to this base directory. output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - samplesheet_converted: - type: file - description: PEP project or samplesheet converted to csv file + - ${prefix}.${format}: + type: file + description: PEP project or samplesheet converted to csv file authors: - "@rafalstepien" maintainers: diff --git a/modules/nf-core/eido/validate/meta.yml b/modules/nf-core/eido/validate/meta.yml index 3d895af29031..d5d4016ea017 100644 --- a/modules/nf-core/eido/validate/meta.yml +++ b/modules/nf-core/eido/validate/meta.yml @@ -13,27 +13,32 @@ tools: documentation: "http://eido.databio.org/en/latest/" doi: "10.1093/gigascience/giab077" licence: ["BSD-2-Clause"] + identifier: biotools:eido-python-package input: - - samplesheet: - type: file - description: Samplesheet or PEP file to be validated - pattern: "*.{yaml,yml,csv}" - - schema: - type: file - description: Schema that the samplesheet will be validated against - pattern: "*.{yaml,yml}" - - pep_input_base_dir: - type: file - description: Optional path to the directory where files specified in a PEP config file are stored. Any paths specified in the config will need to be relative to this base directory. + - - samplesheet: + type: file + description: Samplesheet or PEP file to be validated + pattern: "*.{yaml,yml,csv}" + - - schema: + type: file + description: Schema that the samplesheet will be validated against + pattern: "*.{yaml,yml}" + - - pep_input_base_dir: + type: file + description: Optional path to the directory where files specified in a PEP config + file are stored. Any paths specified in the config will need to be relative + to this base directory. output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: File containing validation log. - pattern: "*.log" + - "*.log": + type: file + description: File containing validation log. + pattern: "*.log" authors: - "@rafalstepien" maintainers: diff --git a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml index bb4c7f84b7fa..ac92ca85d3b1 100644 --- a/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml +++ b/modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/meta.yml @@ -1,5 +1,6 @@ name: "eigenstratdatabasetools_eigenstratsnpcoverage" -description: Provide the SNP coverage of each individual in an eigenstrat formatted dataset. +description: Provide the SNP coverage of each individual in an eigenstrat formatted + dataset. keywords: - coverage - eigenstrat @@ -8,46 +9,56 @@ keywords: - snps tools: - "eigenstratdatabasetools": - description: "A set of tools to compare and manipulate the contents of EingenStrat databases, and to calculate SNP coverage statistics in such databases." + description: "A set of tools to compare and manipulate the contents of EingenStrat + databases, and to calculate SNP coverage statistics in such databases." documentation: "https://github.com/TCLamnidis/EigenStratDatabaseTools/README.md" tool_dev_url: "https://github.com/TCLamnidis/EigenStratDatabaseTools" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - geno: - type: file - description: An Eigenstrat formatted genotype file - pattern: "*.{geno}" - - snp: - type: file - description: An Eigenstrat formatted snp file - pattern: "*.{snp}" - - ind: - type: file - description: An Eigenstrat formatted individual file - pattern: "*.{ind}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - geno: + type: file + description: An Eigenstrat formatted genotype file + pattern: "*.{geno}" + - snp: + type: file + description: An Eigenstrat formatted snp file + pattern: "*.{snp}" + - ind: + type: file + description: An Eigenstrat formatted individual file + pattern: "*.{ind}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV table with the number of covered SNPs per individual. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV table with the number of covered SNPs per individual. + pattern: "*.{tsv}" - json: - type: file - description: A json table with the number of covered SNPs per individual. - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: A json table with the number of covered SNPs per individual. + pattern: "*.{json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/eklipse/meta.yml b/modules/nf-core/eklipse/meta.yml index 0f5e88a88aa1..cf31919594c5 100644 --- a/modules/nf-core/eklipse/meta.yml +++ b/modules/nf-core/eklipse/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "eklipse" description: tool for detection and quantification of large mtDNA rearrangements. @@ -17,42 +16,62 @@ tools: tool_dev_url: "https://github.com/dooguypapua/eKLIPse/tree/master" doi: "10.1038/s41436-018-0350-8" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: MT BAM/SAM file - pattern: "*.{bam,sam}" - - bai: - type: file - description: MT BAM/SAM index file - pattern: "*.{bai,sai}" - - ref_gb: - type: file - description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb will be used - pattern: "*.{gb}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: MT BAM/SAM file + pattern: "*.{bam,sam}" + - bai: + type: file + description: MT BAM/SAM index file + pattern: "*.{bai,sai}" + - - ref_gb: + type: file + description: mtDNA reference genome in Genbank format, optional if empty NC_012920.1.gb + will be used + pattern: "*.{gb}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: csv file containing deletions - pattern: "*.{csv}" + - deletions: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*deletions.csv": + type: file + description: csv file with deletion information + pattern: "*deletions.csv" + - genes: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*genes.csv": + type: file + description: csv file with gene information + pattern: "*genes.csv" - circos: - type: file - description: png file with circos plot of mt - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: png file with circos plot of mt + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/elprep/filter/meta.yml b/modules/nf-core/elprep/filter/meta.yml index 01d76648e919..5ada70e4eb42 100644 --- a/modules/nf-core/elprep/filter/meta.yml +++ b/modules/nf-core/elprep/filter/meta.yml @@ -1,5 +1,6 @@ name: "elprep_filter" -description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant calling." +description: "Filter, sort and markdup sam/bam files, with optional BQSR and variant + calling." keywords: - sort - bam @@ -8,103 +9,156 @@ keywords: - variant calling tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input SAM/BAM file - pattern: "*.{bam,sam}" - - run_haplotypecaller: - type: boolean - description: Run variant calling on the input files. Needed to generate gvcf output. - - run_bqsr: - type: boolean - description: Run BQSR on the input files. Needed to generate recall metrics. - - reference_sequences: - type: file - description: Optional SAM header to replace existing header. - pattern: "*.sam" - - filter_regions_bed: - type: file - description: Optional BED file containing regions to filter. - pattern: "*.bed" - - reference_elfasta: - type: file - description: Elfasta file, required for BQSR and variant calling. - pattern: "*.elfasta" - - known_sites_elsites: - type: file - description: Optional elsites file containing known SNPs for BQSR. - pattern: "*.elsites" - - target_regions_bed: - type: file - description: Optional BED file containing target regions for BQSR and variant calling. - pattern: "*.bed" - - intermediate_bqsr_tables: - type: file - description: Optional list of BQSR tables, used when parsing files created by `elprep split` - pattern: "*.table" - - bqsr_tables_only: - type: boolean - description: Write intermediate BQSR tables, used when parsing files created by `elprep split`. - - get_activity_profile: - type: boolean - description: Get the activity profile calculated by the haplotypecaller to the given file in IGV format. - - get_assembly_regions: - type: boolean - description: Get the assembly regions calculated by haplotypecaller to the speficied file in IGV format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input SAM/BAM file + pattern: "*.{bam,sam}" + - - run_haplotypecaller: + type: boolean + description: Run variant calling on the input files. Needed to generate gvcf + output. + - - run_bqsr: + type: boolean + description: Run BQSR on the input files. Needed to generate recall metrics. + - - reference_sequences: + type: file + description: Optional SAM header to replace existing header. + pattern: "*.sam" + - - filter_regions_bed: + type: file + description: Optional BED file containing regions to filter. + pattern: "*.bed" + - - reference_elfasta: + type: file + description: Elfasta file, required for BQSR and variant calling. + pattern: "*.elfasta" + - - known_sites_elsites: + type: file + description: Optional elsites file containing known SNPs for BQSR. + pattern: "*.elsites" + - - target_regions_bed: + type: file + description: Optional BED file containing target regions for BQSR and variant + calling. + pattern: "*.bed" + - - intermediate_bqsr_tables: + type: file + description: Optional list of BQSR tables, used when parsing files created by + `elprep split` + pattern: "*.table" + - - bqsr_tables_only: + type: boolean + description: Write intermediate BQSR tables, used when parsing files created + by `elprep split`. + - - get_activity_profile: + type: boolean + description: Get the activity profile calculated by the haplotypecaller to the + given file in IGV format. + - - get_assembly_regions: + type: boolean + description: Get the assembly regions calculated by haplotypecaller to the speficied + file in IGV format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted, markdup, optionally BQSR BAM/SAM file - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: Sorted, markdup, optionally BQSR BAM/SAM file + pattern: "*.{bam,sam}" - logs: - type: list - description: Runtime log files - pattern: "elprep-*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - logs/elprep/elprep*: + type: list + description: Runtime log files + pattern: "elprep-*.log" - metrics: - type: file - description: Optional duplicate metrics file generated by elprep - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Optional duplicate metrics file generated by elprep + pattern: "*.{metrics.txt}" - recall: - type: file - description: Optional recall metrics file generated by elprep - pattern: "*.{recall}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recall": + type: file + description: Optional recall metrics file generated by elprep + pattern: "*.{recall}" - gvcf: - type: file - description: Optional GVCF output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Optional GVCF output file + pattern: "*.{vcf.gz}" - table: - type: file - description: Optional intermediate BQSR table output file - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Optional intermediate BQSR table output file + pattern: "*.{table}" - activity_profile: - type: file - description: Optional activity profile output file - pattern: "*.{activity_profile.igv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.activity_profile.igv": + type: file + description: Optional activity profile output file + pattern: "*.{activity_profile.igv}" - assembly_regions: - type: file - description: Optional activity regions output file - pattern: "*.{assembly_regions.igv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly_regions.igv": + type: file + description: Optional activity regions output file + pattern: "*.{assembly_regions.igv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/elprep/merge/meta.yml b/modules/nf-core/elprep/merge/meta.yml index ec7ec6de292e..ffb6b30120f4 100644 --- a/modules/nf-core/elprep/merge/meta.yml +++ b/modules/nf-core/elprep/merge/meta.yml @@ -6,37 +6,41 @@ keywords: - merge tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM/SAM chunks to merge - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM/SAM chunks to merge + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Merged BAM/SAM file - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: Merged BAM/SAM file + pattern: "*.{bam,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/elprep/split/meta.yml b/modules/nf-core/elprep/split/meta.yml index c3854146a953..c3ebc2970437 100644 --- a/modules/nf-core/elprep/split/meta.yml +++ b/modules/nf-core/elprep/split/meta.yml @@ -6,37 +6,41 @@ keywords: - chunk tools: - "elprep": - description: "elPrep is a high-performance tool for preparing .sam/.bam files for variant calling in sequencing pipelines. It can be used as a drop-in replacement for SAMtools/Picard/GATK4." + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." homepage: "https://github.com/ExaScience/elprep" documentation: "https://github.com/ExaScience/elprep" tool_dev_url: "https://github.com/ExaScience/elprep" doi: "10.1371/journal.pone.0244471" licence: ["AGPL v3"] + identifier: biotools:elprep input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM/SAM files - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM/SAM files + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: List of split BAM/SAM files - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/**.{bam,sam}: + type: file + description: List of split BAM/SAM files + pattern: "*.{bam,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/emboss/cons/meta.yml b/modules/nf-core/emboss/cons/meta.yml index 4be6d581a8c2..91e8aff89186 100644 --- a/modules/nf-core/emboss/cons/meta.yml +++ b/modules/nf-core/emboss/cons/meta.yml @@ -1,6 +1,7 @@ ---- name: "emboss_cons" -description: cons calculates a consensus sequence from a multiple sequence alignment. To obtain the consensus, the sequence weights and a scoring matrix are used to calculate a score for each amino acid residue or nucleotide at each position in the alignment. +description: cons calculates a consensus sequence from a multiple sequence alignment. + To obtain the consensus, the sequence weights and a scoring matrix are used to calculate + a score for each amino acid residue or nucleotide at each position in the alignment. keywords: - emboss - consensus @@ -15,30 +16,33 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Multiple sequence alignment (unzipped) - pattern: "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Multiple sequence alignment (unzipped) + pattern: "*.{fasta,fa,fas,fsa,seq,mpfa,aln,clustal,clw,msf,phy,phylip,stockholm,sto,msf,afa,afa,a}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - consensus: - type: file - description: Consensus sequence calculated from multiple sequence alignment - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: Consensus sequence calculated from multiple sequence alignment + pattern: "*.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/emboss/revseq/meta.yml b/modules/nf-core/emboss/revseq/meta.yml index 3019e7be6081..1ecdca5dc0ff 100644 --- a/modules/nf-core/emboss/revseq/meta.yml +++ b/modules/nf-core/emboss/revseq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "emboss_revseq" description: the revseq program from emboss reverse complements a nucleotide sequence @@ -14,30 +13,33 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sequences: - type: file - description: Input sequences - pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sequences: + type: file + description: Input sequences + pattern: "*.{fasta,fna,fa,fst,aln,phy}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - revseq: - type: file - description: File with reverse complemented sequences - pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - '*.${sequences.name - ~/.*\./}': + type: file + description: File with reverse complemented sequences + pattern: "*.{fasta,fna,fa,fst,aln,phy}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/emboss/seqret/meta.yml b/modules/nf-core/emboss/seqret/meta.yml index 4af9e11a3d38..dff9a6142117 100644 --- a/modules/nf-core/emboss/seqret/meta.yml +++ b/modules/nf-core/emboss/seqret/meta.yml @@ -1,5 +1,6 @@ name: "emboss_seqret" -description: Reads in one or more sequences, converts, filters, or transforms them and writes them out again +description: Reads in one or more sequences, converts, filters, or transforms them + and writes them out again keywords: - emboss - gff @@ -16,33 +17,37 @@ tools: tool_dev_url: "http://emboss.open-bio.org/" doi: "10.1016/s0168-9525(00)02024-2 " licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence: - type: file - description: Input sequence query - pattern: "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" - - out_ext: - type: string - description: File extension of the output file. Unless otherwise set by a flag in `ext.args`, the extension dictates the output file format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence: + type: file + description: Input sequence query + pattern: "*.{gff,em,gb,refseq,pir,swiss,sw,txt}" + - - out_ext: + type: string + description: File extension of the output file. Unless otherwise set by a flag + in `ext.args`, the extension dictates the output file format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - outseq: - type: file - description: Converted sequence file - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_ext}": + type: file + description: Converted sequence file + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/emmtyper/meta.yml b/modules/nf-core/emmtyper/meta.yml index 9ba56f679871..742498960fa9 100644 --- a/modules/nf-core/emmtyper/meta.yml +++ b/modules/nf-core/emmtyper/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/MDU-PHL/emmtyper tool_dev_url: https://github.com/MDU-PHL/emmtyper licence: ["GNU General Public v3 (GPL v3)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/endorspy/meta.yml b/modules/nf-core/endorspy/meta.yml index 4578998425b9..0c5490355ae9 100644 --- a/modules/nf-core/endorspy/meta.yml +++ b/modules/nf-core/endorspy/meta.yml @@ -1,5 +1,6 @@ name: "endorspy" -description: endorS.py calculates endogenous DNA from samtools flagstat files and print to screen +description: endorS.py calculates endogenous DNA from samtools flagstat files and + print to screen keywords: - endogenous DNA - ancient DNA @@ -7,41 +8,49 @@ keywords: - statistics tools: - "endorspy": - description: "endorS.py calculates percent on target and/or clonality from samtools flagstat files and print to screen" + description: "endorS.py calculates percent on target and/or clonality from samtools + flagstat files and print to screen" homepage: "https://github.com/aidaanva/endorS.py" documentation: "https://github.com/aidaanva/endorS.py" tool_dev_url: "https://github.com/aidaanva/endorS.py" doi: "10.7717/peerj.10947" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats_raw: - type: file - description: output of samtools flagstat in a txt file, assumes no quality filtering nor duplicate removal performed - - stats_qualityfiltered: - type: file - description: output of samtools flagstat in a txt file, assumes some form of quality or length filtering has been performed, must be provided with at least one of the options -r or -d - - stats_deduplicated: - type: file - description: output of samtools flagstat in a txt file, whereby duplicate removal has been performed on the input reads + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats_raw: + type: file + description: output of samtools flagstat in a txt file, assumes no quality filtering + nor duplicate removal performed + - stats_qualityfiltered: + type: file + description: output of samtools flagstat in a txt file, assumes some form of + quality or length filtering has been performed, must be provided with at least + one of the options -r or -d + - stats_deduplicated: + type: file + description: output of samtools flagstat in a txt file, whereby duplicate removal + has been performed on the input reads output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: file with the endogenous DNA calculation tailored for multiQC - pattern: "*_mqc.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_mqc.json": + type: file + description: file with the endogenous DNA calculation tailored for multiQC + pattern: "*_mqc.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aidaanva" maintainers: diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index a4277ad7a737..8da9621cbf0d 100644 --- a/modules/nf-core/ensemblvep/download/meta.yml +++ b/modules/nf-core/ensemblvep/download/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_download -description: Ensembl Variant Effect Predictor (VEP). The cache downloading options are controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The cache downloading options + are controlled through `task.ext.args`. keywords: - annotation - cache @@ -12,33 +13,40 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: string - description: | - Genome assembly - - species: - type: string - description: | - Specie - - cache_version: - type: string - description: | - cache version + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: string + description: | + Genome assembly + - species: + type: string + description: | + Specie + - cache_version: + type: string + description: | + cache version output: - cache: - type: file - description: cache - pattern: "*" + - meta: + type: file + description: cache + pattern: "*" + - prefix: + type: file + description: cache + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/ensemblvep/filtervep/meta.yml b/modules/nf-core/ensemblvep/filtervep/meta.yml index bde3aa165756..a73e3b7a7421 100644 --- a/modules/nf-core/ensemblvep/filtervep/meta.yml +++ b/modules/nf-core/ensemblvep/filtervep/meta.yml @@ -13,33 +13,37 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input: - type: file - description: VCF/TAB file annotated with vep - pattern: "*.{vcf,tab,tsv,txt}" - - feature_file: - type: file - description: File containing features on separate lines. To be used with --filter option. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: VCF/TAB file annotated with vep + pattern: "*.{vcf,tab,tsv,txt}" + - - feature_file: + type: file + description: File containing features on separate lines. To be used with --filter + option. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: VCF/TAB file - pattern: "*.{vcf,tab,txt,tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.${extension}": + type: file + description: VCF/TAB file + pattern: "*.{vcf,tab,txt,tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index d8ff8d144351..9288a93849fb 100644 --- a/modules/nf-core/ensemblvep/vep/meta.yml +++ b/modules/nf-core/ensemblvep/vep/meta.yml @@ -1,5 +1,6 @@ name: ensemblvep_vep -description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled through `task.ext.args`. +description: Ensembl Variant Effect Predictor (VEP). The output-file-format is controlled + through `task.ext.args`. keywords: - annotation - vcf @@ -13,75 +14,96 @@ tools: homepage: https://www.ensembl.org/info/docs/tools/vep/index.html documentation: https://www.ensembl.org/info/docs/tools/vep/script/index.html licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - custom_extra_files: - type: file - description: | - extra sample-specific files to be used with the `--custom` flag to be configured with ext.args - (optional) - - genome: - type: string - description: | - which genome to annotate with - - species: - type: string - description: | - which species to annotate with - - cache_version: - type: integer - description: | - which version of the cache to annotate with - - cache: - type: file - description: | - path to VEP cache (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: | - reference FASTA file (optional) - pattern: "*.{fasta,fa}" - - extra_files: - type: file - description: | - path to file(s) needed for plugins (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - custom_extra_files: + type: file + description: | + extra sample-specific files to be used with the `--custom` flag to be configured with ext.args + (optional) + - - genome: + type: string + description: | + which genome to annotate with + - - species: + type: string + description: | + which species to annotate with + - - cache_version: + type: integer + description: | + which version of the cache to annotate with + - - cache: + type: file + description: | + path to VEP cache (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: | + reference FASTA file (optional) + pattern: "*.{fasta,fa}" + - - extra_files: + type: file + description: | + path to file(s) needed for plugins (optional) output: - vcf: - type: file - description: | - annotated vcf (optional) - pattern: "*.ann.vcf.gz" + - meta: + type: file + description: | + annotated vcf (optional) + pattern: "*.ann.vcf.gz" + - "*.vcf.gz": + type: file + description: | + annotated vcf (optional) + pattern: "*.ann.vcf.gz" - tab: - type: file - description: | - tab file with annotated variants (optional) - pattern: "*.ann.tab.gz" + - meta: + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" + - "*.tab.gz": + type: file + description: | + tab file with annotated variants (optional) + pattern: "*.ann.tab.gz" - json: - type: file - description: | - json file with annotated variants (optional) - pattern: "*.ann.json.gz" + - meta: + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" + - "*.json.gz": + type: file + description: | + json file with annotated variants (optional) + pattern: "*.ann.json.gz" - report: - type: file - description: VEP report file - pattern: "*.html" + - "*.html": + type: file + description: VEP report file + pattern: "*.html" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@matthdsm" diff --git a/modules/nf-core/entrezdirect/esearch/meta.yml b/modules/nf-core/entrezdirect/esearch/meta.yml index e3e2ffedc908..4a972826f33b 100644 --- a/modules/nf-core/entrezdirect/esearch/meta.yml +++ b/modules/nf-core/entrezdirect/esearch/meta.yml @@ -20,34 +20,37 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - database: - type: string - description: Value must be a valid Entrez database name. - - term: - type: string - description: | - Entrez text query. All special characters must be URL encoded. - Spaces may be replaced by '+' signs. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - term: + type: string + description: | + Entrez text query. All special characters must be URL encoded. + Spaces may be replaced by '+' signs. + - - database: + type: string + description: Value must be a valid Entrez database name. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] + - xml: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xml": + type: file + description: XML file containing search results + pattern: "*.xml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - result_xml: - type: file - description: Query result text in XML format - pattern: "*.xml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/entrezdirect/esummary/meta.yml b/modules/nf-core/entrezdirect/esummary/meta.yml index 8f0dbd589e5f..36abbf02fd70 100644 --- a/modules/nf-core/entrezdirect/esummary/meta.yml +++ b/modules/nf-core/entrezdirect/esummary/meta.yml @@ -21,35 +21,40 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - database: - type: string - description: Value must be a valid Entrez database name ('assembly', etc). - - uid: - type: string - description: Unique Identifier (UID) of record in NCBI database. Cannot be used at the same time as uids_file - - uids_file: - type: file - description: Text file containing multiple UIDs. Cannot be used at the same time as uid. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - uid: + type: string + description: Unique Identifier (UID) of record in NCBI database. Cannot be used + at the same time as uids_file + - uids_file: + type: file + description: Text file containing multiple UIDs. Cannot be used at the same + time as uid. + - - database: + type: string + description: Value must be a valid Entrez database name ('assembly', etc). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xml: - type: file - description: Query result in XML format - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xml": + type: file + description: Query result in XML format + pattern: "*.xml" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/entrezdirect/xtract/meta.yml b/modules/nf-core/entrezdirect/xtract/meta.yml index 0b3cdd0321c6..0b220a5c328b 100644 --- a/modules/nf-core/entrezdirect/xtract/meta.yml +++ b/modules/nf-core/entrezdirect/xtract/meta.yml @@ -20,38 +20,41 @@ tools: tool_dev_url: https://www.ncbi.nlm.nih.gov/books/NBK25498/ doi: 10.1016/S0076-6879(96)66012-1 licence: ["PUBLIC DOMAIN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - xml_input: - type: file - description: XML text file containing query results from database. - - pattern: - type: string - description: String in xml_input that encloses element to search. - - element: - type: string - description: Space-delimited strings that will be converted to columns. - - sep: - type: string - description: Separator/delimiter between columns (for instance "," or "\t"). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - xml_input: + type: file + description: XML text file containing query results from database. + - - pattern: + type: string + description: String in xml_input that encloses element to search. + - - element: + type: string + description: Space-delimited strings that will be converted to columns. + - - sep: + type: string + description: Separator/delimiter between columns (for instance "," or "\t"). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Text file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - xtract_table: - type: file - description: TXT file containing columns searched from element. - pattern: "*.txt" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/epang/place/meta.yml b/modules/nf-core/epang/place/meta.yml index be90ceabfc4d..64fc1f590299 100644 --- a/modules/nf-core/epang/place/meta.yml +++ b/modules/nf-core/epang/place/meta.yml @@ -12,53 +12,66 @@ tools: tool_dev_url: "https://github.com/Pbdas/epa-ng" doi: "10.1093/sysbio/syy054" licence: ["GNU Affero General Public License v3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - queryaln: - type: file - description: aligned query sequences in any supported format including phylip and fasta, may be gzipped - pattern: "*" - - referencealn: - type: file - description: reference alignment in any supported format including phylip and fasta, may be gzipped - pattern: "*" - - referencetree: - type: file - description: newick file containing the reference tree in which query sequences will be placed - pattern: "*" - - bfastfile: - type: file - description: file argument to the --bfast parameter - pattern: "*" - - binaryfile: - type: file - description: file argument to the --binary parameter - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - queryaln: + type: file + description: aligned query sequences in any supported format including phylip + and fasta, may be gzipped + pattern: "*" + - referencealn: + type: file + description: reference alignment in any supported format including phylip and + fasta, may be gzipped + pattern: "*" + - referencetree: + type: file + description: newick file containing the reference tree in which query sequences + will be placed + pattern: "*" + - - bfastfile: + type: file + description: file argument to the --bfast parameter + pattern: "*" + - - binaryfile: + type: file + description: file argument to the --binary parameter + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - epang: - type: directory - description: directory in which EPA-NG was run + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ./.: + type: directory + description: directory in which EPA-NG was run - jplace: - type: file - description: gzipped file with placement information - pattern: "*.jplace.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.epa_result.jplace.gz": + type: file + description: gzipped file with placement information + pattern: "*.jplace.gz" - log: - type: file - description: log file from placement - pattern: "*.log" + - "*.epa_info.log": + type: file + description: log file from placement + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/epang/split/meta.yml b/modules/nf-core/epang/split/meta.yml index 21cb81ae217c..c91b1de5f531 100644 --- a/modules/nf-core/epang/split/meta.yml +++ b/modules/nf-core/epang/split/meta.yml @@ -12,37 +12,48 @@ tools: tool_dev_url: "https://github.com/Pbdas/epa-ng" doi: "10.1093/sysbio/syy054" licence: ["GNU Affero General Public License v3.0"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - refaln: - type: file - description: reference alignment in any supported format including phylip and fasta, may be gzipped - pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" - - fullaln: - type: file - description: full alignment in any supported format to split into reference and query alignments - pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - refaln: + type: file + description: reference alignment in any supported format including phylip and + fasta, may be gzipped + pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" + - fullaln: + type: file + description: full alignment in any supported format to split into reference + and query alignments + pattern: "*.{faa,fna,fa,fasta,fa,phy,aln,alnfaa,alnfna,alnfa,mfa,faa.gz,fna.gz,fa.gz,fasta.gz,fa.gz,phy.gz,aln.gz,alnfaa.gz,alnfna.gz,alnfa.gz,mfa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - query: - type: file - description: query sequence alignment in gzipped fasta format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*query.fasta.gz": + type: file + description: query sequence alignment in gzipped fasta format - reference: - type: file - description: reference sequence alignment in gzipped fasta format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*reference.fasta.gz": + type: file + description: reference sequence alignment in gzipped fasta format - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/estsfs/meta.yml b/modules/nf-core/estsfs/meta.yml index 9d3d0d80da17..a1582dc95b6a 100644 --- a/modules/nf-core/estsfs/meta.yml +++ b/modules/nf-core/estsfs/meta.yml @@ -1,4 +1,3 @@ ---- name: "estsfs" description: estimation of the unfolded site frequency spectrum keywords: @@ -7,47 +6,64 @@ keywords: - derived alleles tools: - "estsfs": - description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral state probabilities by maximum likelihood (ML)." + description: "est-sfs ( Keightley and Jackson, 2018) is a stand-alone implementation + of a method to infer the unfolded site frequency spectrum (the uSFS) and ancestral + state probabilities by maximum likelihood (ML)." homepage: "https://sourceforge.net/projects/est-usfs/" documentation: "https://sourceforge.net/projects/est-usfs/" tool_dev_url: "https://sourceforge.net/projects/est-usfs/files/est-sfs-release-2.04.tar.gz" doi: "10.1534/genetics.118.301120" licence: ["Free for Academic Use"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - e_config: - type: file - description: config file for est-sfs - pattern: "*.txt" - - data: - type: file - description: input data file for est-sfs - pattern: "*.txt" - - seed: - type: file - description: text file containing random number seed - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - e_config: + type: file + description: config file for est-sfs + pattern: "*.txt" + - data: + type: file + description: input data file for est-sfs + pattern: "*.txt" + - seed: + type: file + description: text file containing random number seed + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sfs_out: - type: file - description: output file consists of the comma-separated estimated uSFS vector - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${prefix}_sfs.txt: + type: file + description: output file consists of the comma-separated estimated uSFS vector + pattern: "*.txt" - pvalues_out: - type: file - description: this file contains the estimated ancestral state probabilities for each site - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${prefix}_pvalues.txt: + type: file + description: this file contains the estimated ancestral state probabilities + for each site + pattern: "*.txt" + - ues_out: + type: file + description: this file contains the estimated ancestral state probabilities + for each site + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" diff --git a/modules/nf-core/evigene/tr2aacds/meta.yml b/modules/nf-core/evigene/tr2aacds/meta.yml index 9642ed8bd665..6cc6f579ed35 100644 --- a/modules/nf-core/evigene/tr2aacds/meta.yml +++ b/modules/nf-core/evigene/tr2aacds/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "evigene_tr2aacds" description: Uses evigene/scripts/prot/tr2aacds.pl to filter a transcript assembly @@ -22,34 +21,43 @@ tools: tool_dev_url: "http://arthropods.eugenes.org/EvidentialGene/evigene/" doi: "10.7490/f1000research.1112594.1 " licence: ["Don Gilbert, gilbertd At indiana edu, 2018"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Transcript assembly in fasta format - pattern: "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Transcript assembly in fasta format + pattern: "*.{fsa,fa,fasta,fsa.gz,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - dropset: - type: directory - description: Directory containing dropped transcripts and associated files - pattern: "dropset" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - dropset: + type: directory + description: Directory containing dropped transcripts and associated files + pattern: "dropset" - okayset: - type: directory - description: Directory containing included transcripts and associated files - pattern: "okayset" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - okayset: + type: directory + description: Directory containing included transcripts and associated files + pattern: "okayset" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/expansionhunter/meta.yml b/modules/nf-core/expansionhunter/meta.yml index 698529dcc1b9..4d55fe260ed6 100644 --- a/modules/nf-core/expansionhunter/meta.yml +++ b/modules/nf-core/expansionhunter/meta.yml @@ -14,69 +14,84 @@ tools: documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md doi: "10.1093/bioinformatics/btz431" licence: ["Apache-2.0"] + identifier: biotools:ExpansionHunter input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome - pattern: "*.{fna,fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: Reference genome index - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - variant_catalog: - type: file - description: JSON file with repeat expansion sites to genotype - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome + pattern: "*.{fna,fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: Reference genome index + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - variant_catalog: + type: file + description: JSON file with repeat expansion sites to genotype + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', gender:'female' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - vcf: - type: file - description: VCF with repeat expansions - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*.vcf.gz": + type: file + description: VCF with repeat expansions + pattern: "*.vcf.gz" - json: - type: file - description: JSON with repeat expansions - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*.json.gz": + type: file + description: JSON with repeat expansions + pattern: "*.json.gz" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', gender:'female' ] + - "*_realigned.bam": + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" maintainers: diff --git a/modules/nf-core/expansionhunterdenovo/merge/meta.yml b/modules/nf-core/expansionhunterdenovo/merge/meta.yml index a7aa59fb4059..3d47ed8d0a2a 100644 --- a/modules/nf-core/expansionhunterdenovo/merge/meta.yml +++ b/modules/nf-core/expansionhunterdenovo/merge/meta.yml @@ -6,56 +6,60 @@ keywords: - str tools: - "expansionhunterdenovo": - description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." + description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting + novel expansions of short tandem repeats (STRs)." homepage: "https://github.com/Illumina/ExpansionHunterDenovo" documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md" tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo" licence: ["Apache License 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - manifest: - type: file - description: | - A tab-delimited file containing the sample name, whether it's case or control - and the paths to the corresponding STR profiles. - See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files - pattern: "*.{tsv,txt}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - manifest: + type: file + description: | + A tab-delimited file containing the sample name, whether it's case or control + and the paths to the corresponding STR profiles. + See here for an example: https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/06_Merging_profiles.md#manifest-files + pattern: "*.{tsv,txt}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_profiles: - type: file - description: The merged STR profiles - pattern: "*.multisample_profile.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.multisample_profile.json": + type: file + description: The merged STR profiles + pattern: "*.multisample_profile.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/expansionhunterdenovo/profile/meta.yml b/modules/nf-core/expansionhunterdenovo/profile/meta.yml index 68fac10a2a52..c3a15b9dfbc5 100644 --- a/modules/nf-core/expansionhunterdenovo/profile/meta.yml +++ b/modules/nf-core/expansionhunterdenovo/profile/meta.yml @@ -9,65 +9,81 @@ keywords: - cram tools: - "expansionhunterdenovo": - description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs)." + description: "ExpansionHunter Denovo (EHdn) is a suite of tools for detecting + novel expansions of short tandem repeats (STRs)." homepage: "https://github.com/Illumina/ExpansionHunterDenovo" documentation: "https://github.com/Illumina/ExpansionHunterDenovo/blob/master/documentation/00_Introduction.md" tool_dev_url: "https://github.com/Illumina/ExpansionHunterDenovo" licence: ["Apache License 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment_file: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - alignment_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The FASTA reference file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the FASTA reference file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_file: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - alignment_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The FASTA reference file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the FASTA reference file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - locus_tsv: - type: file - description: The locus TSV file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.locus.tsv": + type: file + description: The locus TSV file + pattern: "*.tsv" - motif_tsv: - type: file - description: The motif TSV file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.motif.tsv": + type: file + description: The motif TSV file + pattern: "*.tsv" - str_profile: - type: file - description: The JSON file containing the STR profile - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.str_profile.json": + type: file + description: The JSON file containing the STR profile + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/falco/meta.yml b/modules/nf-core/falco/meta.yml index 6201790ce43e..b2405f424329 100644 --- a/modules/nf-core/falco/meta.yml +++ b/modules/nf-core/falco/meta.yml @@ -7,43 +7,49 @@ keywords: - fastq tools: - fastqc: - description: "falco is a drop-in C++ implementation of FastQC to assess the quality of sequence reads." + description: "falco is a drop-in C++ implementation of FastQC to assess the quality + of sequence reads." homepage: "https://falco.readthedocs.io/" documentation: "https://falco.readthedocs.io/" licence: ["GPL v3"] + identifier: biotools:falco-rna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC like report - pattern: "*_{fastqc_report.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC like report + pattern: "*_{fastqc_report.html}" - txt: - type: file - description: falco report data - pattern: "*_{data.txt}" - - txt: - type: file - description: falco summary file - pattern: "*_{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: falco report data + pattern: "*_{data.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucacozzuto" maintainers: diff --git a/modules/nf-core/famsa/align/meta.yml b/modules/nf-core/famsa/align/meta.yml index 6acf3c210102..c12a99dcb3f8 100644 --- a/modules/nf-core/famsa/align/meta.yml +++ b/modules/nf-core/famsa/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "famsa_align" description: Aligns sequences using FAMSA @@ -14,42 +13,48 @@ tools: tool_dev_url: "https://github.com/refresh-bio/FAMSA" doi: "10.1038/srep33964" licence: ["GPL v3"] + identifier: biotools:famsa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is handled by passing '-gz' to FAMSA along with any other options specified in task.ext.args. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is handled + by passing '-gz' to FAMSA along with any other options specified in task.ext.args. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed, + depending on if compress is set to true or false + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/famsa/guidetree/meta.yml b/modules/nf-core/famsa/guidetree/meta.yml index 2bd4e798d643..a7b1454fc25a 100644 --- a/modules/nf-core/famsa/guidetree/meta.yml +++ b/modules/nf-core/famsa/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "famsa_guidetree" description: Renders a guidetree in famsa @@ -14,30 +13,33 @@ tools: tool_dev_url: "https://github.com/refresh-bio/FAMSA" doi: "10.1038/srep33964" licence: ["GPL v3"] + identifier: biotools:famsa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - tree: - type: file - description: Guide tree file in Newick format - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.dnd": + type: file + description: Guide tree file in Newick format + pattern: "*.{dnd}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/faqcs/meta.yml b/modules/nf-core/faqcs/meta.yml index cc0a87898770..9d8b6711ca1b 100644 --- a/modules/nf-core/faqcs/meta.yml +++ b/modules/nf-core/faqcs/meta.yml @@ -14,55 +14,95 @@ tools: tool_dev_url: https://github.com/LANL-Bioinformatics/FaQCs doi: "10.1186/s12859-014-0366-2" licence: ["GPLv3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: The trimmed/modified fastq reads - pattern: "*trimmed.fastq.gz" - - reads_fail: - type: file - description: Reads that failed the preprocessing (Optional with --discard args setting) - pattern: "*discard.fastq.gz" - - reads_unpaired: - type: file - description: Reads without matching mates in paired-end files (Optional) - pattern: "*trimmed.unpaired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmed.fastq.gz": + type: file + description: The trimmed/modified fastq reads + pattern: "*trimmed.fastq.gz" - stats: - type: file - description: trimming/qc text stats file - pattern: "*.stats.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.txt": + type: file + description: trimming/qc text stats file + pattern: "*.stats.txt" - debug: - type: directory - description: trimming/qc files from --debug option - pattern: "./debug" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ./debug: + type: directory + description: trimming/qc files from --debug option + pattern: "./debug" - statspdf: - type: file - description: trimming/qc pdf report file - pattern: "*_qc_report.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_qc_report.pdf": + type: file + description: trimming/qc pdf report file + pattern: "*_qc_report.pdf" + - reads_fail: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.discard.fastq.gz": + type: file + description: Reads that failed the preprocessing (Optional with --discard args + setting) + pattern: "*discard.fastq.gz" + - reads_unpaired: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.trimmed.unpaired.fastq.gz": + type: file + description: Reads without matching mates in paired-end files (Optional) + pattern: "*trimmed.unpaired.fastq.gz" - log: - type: file - description: fastq log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@sateeshperi" diff --git a/modules/nf-core/fargene/meta.yml b/modules/nf-core/fargene/meta.yml index 9fc5ce0f8ebe..e1bcc5ea18b1 100644 --- a/modules/nf-core/fargene/meta.yml +++ b/modules/nf-core/fargene/meta.yml @@ -1,5 +1,6 @@ name: fargene -description: tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. +description: tool that takes either fragmented metagenomic data or longer sequences + as input and predicts and delivers full-length antiobiotic resistance genes as output. keywords: - antibiotic resistance genes - ARGs @@ -8,94 +9,192 @@ keywords: - contigs tools: - fargene: - description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output + description: Fragmented Antibiotic Resistance Gene Identifier takes either fragmented + metagenomic data or longer sequences as input and predicts and delivers full-length + antiobiotic resistance genes as output homepage: https://github.com/fannyhb/fargene documentation: https://github.com/fannyhb/fargene tool_dev_url: https://github.com/fannyhb/fargene licence: ["MIT"] + identifier: biotools:fargene input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: uncompressed fasta file or paired-end fastq files containing either genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented metagenomic reads (fastq) - pattern: "*.{fasta}" - - hmm_model: - type: string - description: name of custom hidden markov model to be used [pre-defined class_a, class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, tet_enzyme] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: uncompressed fasta file or paired-end fastq files containing either + genomes or longer contigs as nucleotide or protein sequences (fasta) or fragmented + metagenomic reads (fastq) + pattern: "*.{fasta}" + - - hmm_model: + type: string + description: name of custom hidden markov model to be used [pre-defined class_a, + class_b_1_2, class_b_3, class_c, class_d_1, class_d_2, qnr, tet_efflux, tet_rpg, + tet_enzyme] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file + pattern: "*.{log}" - txt: - type: file - description: analysis summary text file - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/results_summary.txt: + type: file + description: analysis summary text file + pattern: "*.{txt}" - hmm: - type: file - description: output from hmmsearch (both single gene annotations + contigs) - pattern: "*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/hmmsearchresults/*.out: + type: file + description: output from hmmsearch (both single gene annotations + contigs) + pattern: "*.{out}" - hmm_genes: - type: file - description: output from hmmsearch (single gene annotations only) - pattern: "retrieved-*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/hmmsearchresults/retrieved-*.out: + type: file + description: output from hmmsearch (single gene annotations only) + pattern: "retrieved-*.{out}" - orfs: - type: file - description: open reading frames (ORFs) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/predicted-orfs.fasta: + type: file + description: open reading frames (ORFs) + pattern: "*.{fasta}" - orfs_amino: - type: file - description: protein translation of open reading frames (ORFs) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/predicted-orfs-amino.fasta: + type: file + description: protein translation of open reading frames (ORFs) + pattern: "*.{fasta}" - contigs: - type: file - description: (complete) contigs that passed the final full-length classification - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/retrieved-contigs.fasta: + type: file + description: (complete) contigs that passed the final full-length classification + pattern: "*.{fasta}" - contigs_pept: - type: file - description: parts of the contigs that passed the final classification step that aligned with the HMM, as amino acid sequences - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/retrieved-contigs-peptides.fasta: + type: file + description: parts of the contigs that passed the final classification step + that aligned with the HMM, as amino acid sequences + pattern: "*.{fasta}" - filtered: - type: file - description: sequences that passed the final classification step, but only the parts that where predicted by the HMM to be part of the gene - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/*filtered.fasta: + type: file + description: sequences that passed the final classification step, but only the + parts that where predicted by the HMM to be part of the gene + pattern: "*.{fasta}" - filtered_pept: - type: file - description: sequences from filtered.fasta, translated in the same frame as the gene is predicted to be located - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/predictedGenes/*filtered-peptides.fasta: + type: file + description: sequences from filtered.fasta, translated in the same frame as + the gene is predicted to be located + pattern: "*.{fasta}" - fragments: - type: file - description: All quality controlled retrieved fragments that were classified as positive, together with its read-pair, gathered in two files - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/retrievedFragments/all_retrieved_*.fastq: + type: file + description: All quality controlled retrieved fragments that were classified + as positive, together with its read-pair, gathered in two files + pattern: "*.{fastq}" - trimmed: - type: file - description: The quality controlled retrieved fragments from each input file. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/retrievedFragments/trimmedReads/*.fasta: + type: file + description: The quality controlled retrieved fragments from each input file. + pattern: "*.{fasta}" - spades: - type: directory - description: The output from the SPAdes assembly - pattern: "spades_assembly" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/spades_assembly/*: + type: directory + description: The output from the SPAdes assembly + pattern: "spades_assembly" - metagenome: - type: file - description: The FASTQ to FASTA converted input files from metagenomic reads. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/tmpdir/*.fasta: + type: file + description: The FASTQ to FASTA converted input files from metagenomic reads. + pattern: "*.{fasta}" - tmp: - type: file - description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/tmpdir/*.out: + type: file + description: The from FASTQ to FASTA converted input files and their translated + input sequences. Are only saved if option --store-peptides is used. + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml index cf505471f92f..59a82fc027ed 100644 --- a/modules/nf-core/fastani/meta.yml +++ b/modules/nf-core/fastani/meta.yml @@ -6,40 +6,44 @@ keywords: - ANI tools: - fastani: - description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). + description: FastANI is developed for fast alignment-free computation of whole-genome + Average Nucleotide Identity (ANI). homepage: https://github.com/ParBLiSS/FastANI documentation: https://github.com/ParBLiSS/FastANI tool_dev_url: https://github.com/ParBLiSS/FastANI doi: 10.1038/s41467-018-07641-9 licence: ["Apache-2.0"] + identifier: biotools:fastani input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query: - type: file - description: Fasta file(s) to be queried - pattern: "*.fasta" - - reference: - type: file - description: Fasta file(s) to be used as reference for the query - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: Fasta file(s) to be queried + pattern: "*.fasta" + - - reference: + type: file + description: Fasta file(s) to be used as reference for the query + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - ani: - type: file - description: Results of the query - pattern: "*.ani.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ani.txt": + type: file + description: Results of the query + pattern: "*.ani.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/fastavalidator/meta.yml b/modules/nf-core/fastavalidator/meta.yml index c5c4371c629e..94198e629d12 100644 --- a/modules/nf-core/fastavalidator/meta.yml +++ b/modules/nf-core/fastavalidator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastavalidator" description: | @@ -19,34 +18,43 @@ tools: tool_dev_url: "https://github.com/linsalrob/py_fasta_validator" doi: "10.5281/zenodo.5002710" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing file information - e.g. [ id:'test' ] - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing file information + e.g. [ id:'test' ] + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/nf-core/fastawindows/meta.yml b/modules/nf-core/fastawindows/meta.yml index 87f1d8b7dcf4..f8ee0043203a 100644 --- a/modules/nf-core/fastawindows/meta.yml +++ b/modules/nf-core/fastawindows/meta.yml @@ -7,49 +7,78 @@ keywords: - bed tools: - "fastawindows": - description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal level genome assemblies. The executable takes a fasta formatted file and calculates some statistics of interest in windows" + description: "fasta_windows is a tool written for Darwin Tree of Life chromosomal + level genome assemblies. The executable takes a fasta formatted file and calculates + some statistics of interest in windows" homepage: "https://github.com/tolkit/fasta_windows" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - freq: - type: file - description: TSV file with frequencies and statistics - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_freq_windows.tsv: + type: file + description: TSV file with frequencies and statistics + pattern: "*.{tsv}" - mononuc: - type: file - description: TSV file with mononucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_mononuc_windows.tsv: + type: file + description: TSV file with mononucleotide counts + pattern: "*.{tsv}" - dinuc: - type: file - description: TSV file with dinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_dinuc_windows.tsv: + type: file + description: TSV file with dinucleotide counts + pattern: "*.{tsv}" - trinuc: - type: file - description: TSV file with trinucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_trinuc_windows.tsv: + type: file + description: TSV file with trinucleotide counts + pattern: "*.{tsv}" - tetranuc: - type: file - description: TSV file with tetranucleotide counts - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fw_out/*_tetranuc_windows.tsv: + type: file + description: TSV file with tetranucleotide counts + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/fastk/fastk/meta.yml b/modules/nf-core/fastk/fastk/meta.yml index 3086aca51afc..4abc1033d320 100644 --- a/modules/nf-core/fastk/fastk/meta.yml +++ b/modules/nf-core/fastk/fastk/meta.yml @@ -10,39 +10,54 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" licence: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" - ktab: - type: file - description: A sorted table of all canonical k‑mers along with their counts. - pattern: "*.ktab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: A sorted table of all canonical k‑mers along with their counts. + pattern: "*.ktab" - prof: - type: file - description: A k‑mer count profile of each sequence in the input data set. - pattern: "*.prof" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: A k‑mer count profile of each sequence in the input data set. + pattern: "*.prof" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastk/histex/meta.yml b/modules/nf-core/fastk/histex/meta.yml index 6fcd6bd25729..1ce1bd01c1e3 100644 --- a/modules/nf-core/fastk/histex/meta.yml +++ b/modules/nf-core/fastk/histex/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - histogram: - type: file - description: A FastK histogram file - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A FastK histogram file + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: A formatted histogram file - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: A formatted histogram file + pattern: "*.hist" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastk/merge/meta.yml b/modules/nf-core/fastk/merge/meta.yml index 2a3c72429838..8bf2eda39d02 100644 --- a/modules/nf-core/fastk/merge/meta.yml +++ b/modules/nf-core/fastk/merge/meta.yml @@ -11,46 +11,58 @@ tools: homepage: "https://github.com/thegenemyers/FASTK" tool_dev_url: "https://github.com/thegenemyers/FASTK" license: ["https://github.com/thegenemyers/FASTK/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk_prof: - type: file - description: Histogram profile files from the program FastK (option -p) - pattern: "*.{prof,pidx}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hist: + type: file + description: FastK histogram file + - ktab: + type: file + description: FastK ktab file + - prof: + type: file + description: FastK prof file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: FastK histogram file + pattern: "*.hist" + - ktab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.ktab*", hidden: true': + type: file + description: FastK ktab file + pattern: "*.ktab" + - prof: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.{prof,pidx}*", hidden: true': + type: file + description: FastK prof file + pattern: "*.{prof,pidx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk_prof: - type: file - description: Histogram profile files from the program FastK (option -p) - pattern: "*.{prof,pidx}*" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/fastme/meta.yml b/modules/nf-core/fastme/meta.yml index 93e1dc671f6b..77ce44e6d097 100644 --- a/modules/nf-core/fastme/meta.yml +++ b/modules/nf-core/fastme/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastme" description: "Distance-based phylogeny with FastME" @@ -9,7 +8,8 @@ keywords: - distance-based tools: - "fastme": - description: "A comprehensive, accurate and fast distance-based phylogeny inference program." + description: "A comprehensive, accurate and fast distance-based phylogeny inference + program." homepage: "http://www.atgc-montpellier.fr/fastme" documentation: "http://www.atgc-montpellier.fr/fastme/usersguide.php" tool_dev_url: "https://gite.lirmm.fr/atgc/FastME/" @@ -17,44 +17,70 @@ tools: licence: ["GPL v3"] args_id: "$args" + identifier: biotools:fastme input: - - meta: - type: map - description: | - A Groovy map containing sample information, - e.g. [ id: "test" ] - - infile: - type: file - description: MSA or distance matrix in Phylip format - pattern: "*" - # note: I have omitted any specific extension as it is not standardized for those file types - - topo: - type: file - description: Initial tree topology in Newick format - pattern: "*.{nwk,dnd}" - + - - meta: + type: map + description: | + A Groovy map containing sample information, + e.g. [ id: "test" ] + - infile: + type: file + description: MSA or distance matrix in Phylip format + pattern: "*" + - initial_tree: + type: file + description: Initial tree output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - nwk: - type: file - description: Final phylogeny in Newick format - pattern: "*.nwk" + - meta: + type: file + description: Final phylogeny in Newick format + pattern: "*.nwk" + - "*.nwk": + type: file + description: Final phylogeny in Newick format + pattern: "*.nwk" - stats: - type: file - description: A text file with the statistics of the phylogeny - pattern: "*_stat.txt" + - meta: + type: file + description: A text file with the statistics of the phylogeny + pattern: "*_stat.txt" + - "*_stat.txt": + type: file + description: A text file with the statistics of the phylogeny + pattern: "*_stat.txt" - matrix: - type: file - description: Optional; the distance matrix in Phylip matrix format; it is generated if the -O option is passed in ext.args, although the provided file name will be overwritten - pattern: "*.matrix.phy" + - meta: + type: file + description: Optional; the distance matrix in Phylip matrix format; it is generated + if the -O option is passed in ext.args, although the provided file name will + be overwritten + pattern: "*.matrix.phy" + - "*.matrix.phy": + type: file + description: Optional; the distance matrix in Phylip matrix format; it is generated + if the -O option is passed in ext.args, although the provided file name will + be overwritten + pattern: "*.matrix.phy" - bootstrap: - type: file - description: A file containing all bootstrap trees in Newick format; it is generated if the -B option is passed in ext.args (and bootstrap is used), although the provided file name will be overwritten - pattern: "*.bootstrap" - + - meta: + type: file + description: A file containing all bootstrap trees in Newick format; it is generated + if the -B option is passed in ext.args (and bootstrap is used), although the + provided file name will be overwritten + pattern: "*.bootstrap" + - "*.bootstrap": + type: file + description: A file containing all bootstrap trees in Newick format; it is generated + if the -B option is passed in ext.args (and bootstrap is used), although the + provided file name will be overwritten + pattern: "*.bootstrap" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@itrujnara" maintainers: diff --git a/modules/nf-core/fastp/meta.yml b/modules/nf-core/fastp/meta.yml index 8dfecc1848c5..159404d08d34 100644 --- a/modules/nf-core/fastp/meta.yml +++ b/modules/nf-core/fastp/meta.yml @@ -11,66 +11,100 @@ tools: documentation: https://github.com/OpenGene/fastp doi: 10.1093/bioinformatics/bty560 licence: ["MIT"] + identifier: biotools:fastp input: - - meta: - type: map - description: | - Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. If you wish to run interleaved paired-end data, supply as single-end data - but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. - - adapter_fasta: - type: file - description: File in FASTA format containing possible adapters to remove. - pattern: "*.{fasta,fna,fas,fa}" - - discard_trimmed_pass: - type: boolean - description: Specify true to not write any reads that pass trimming thresholds. | - This can be used to use fastp for the output report only. - - save_trimmed_fail: - type: boolean - description: Specify true to save files that failed to pass trimming thresholds ending in `*.fail.fastq.gz` - - save_merged: - type: boolean - description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` + - - meta: + type: map + description: | + Groovy Map containing sample information. Use 'single_end: true' to specify single ended or interleaved FASTQs. Use 'single_end: false' for paired-end reads. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. If you wish to run interleaved paired-end data, supply as single-end data + but with `--interleaved_in` in your `modules.conf`'s `ext.args` for the module. + - - adapter_fasta: + type: file + description: File in FASTA format containing possible adapters to remove. + pattern: "*.{fasta,fna,fas,fa}" + - - discard_trimmed_pass: + type: boolean + description: Specify true to not write any reads that pass trimming thresholds. + | This can be used to use fastp for the output report only. + - - save_trimmed_fail: + type: boolean + description: Specify true to save files that failed to pass trimming thresholds + ending in `*.fail.fastq.gz` + - - save_merged: + type: boolean + description: Specify true to save all merged reads to a file ending in `*.merged.fastq.gz` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: The trimmed/modified/unmerged fastq reads - pattern: "*fastp.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastp.fastq.gz": + type: file + description: The trimmed/modified/unmerged fastq reads + pattern: "*fastp.fastq.gz" - json: - type: file - description: Results in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.json" - html: - type: file - description: Results in HTML format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format + pattern: "*.html" - log: - type: file - description: fastq log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: fastq log file + pattern: "*.log" - reads_fail: - type: file - description: Reads the failed the preprocessing - pattern: "*fail.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fail.fastq.gz": + type: file + description: Reads the failed the preprocessing + pattern: "*fail.fastq.gz" - reads_merged: - type: file - description: Reads that were successfully merged - pattern: "*.{merged.fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.merged.fastq.gz": + type: file + description: Reads that were successfully merged + pattern: "*.{merged.fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml index ee5507e06b62..4827da7af24e 100644 --- a/modules/nf-core/fastqc/meta.yml +++ b/modules/nf-core/fastqc/meta.yml @@ -16,35 +16,44 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ licence: ["GPL-2.0-only"] + identifier: biotools:fastqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/fastqscan/meta.yml b/modules/nf-core/fastqscan/meta.yml index 6cfe3de361ec..6c04aa556e93 100644 --- a/modules/nf-core/fastqscan/meta.yml +++ b/modules/nf-core/fastqscan/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/rpetit3/fastq-scan tool_dev_url: https://github.com/rpetit3/fastq-scan licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file - pattern: "*.{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file + pattern: "*.{fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted file of summary statistics - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted file of summary statistics + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/fastqscreen/buildfromindex/meta.yml b/modules/nf-core/fastqscreen/buildfromindex/meta.yml index 3d5cb9b12cb8..d92817fc13eb 100644 --- a/modules/nf-core/fastqscreen/buildfromindex/meta.yml +++ b/modules/nf-core/fastqscreen/buildfromindex/meta.yml @@ -7,28 +7,33 @@ keywords: - reference tools: - "fastqscreen": - description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect." + description: "FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition + of the library matches with what you expect." homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" documentation: "https://stevenwingett.github.io/FastQ-Screen/" tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip" doi: "10.5281/zenodo.5838377" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - genome_names: - type: string - description: List of names for each index - - indexes: - type: directory - description: Bowtie2 genome directories containing index files + - - genome_names: + type: string + description: List of names for each index + - - indexes: + type: directory + description: Bowtie2 genome directories containing index files output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" + - FastQ_Screen_Genomes: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fastqscreen/fastqscreen/meta.yml b/modules/nf-core/fastqscreen/fastqscreen/meta.yml index e0b0120df647..39c86b4f5860 100644 --- a/modules/nf-core/fastqscreen/fastqscreen/meta.yml +++ b/modules/nf-core/fastqscreen/fastqscreen/meta.yml @@ -9,52 +9,70 @@ keywords: - reference tools: - "fastqscreen": - description: "FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect." + description: "FastQ Screen allows you to screen a library of sequences in FastQ + format against a set of sequence databases so you can see if the composition + of the library matches with what you expect." homepage: "https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/" documentation: "https://stevenwingett.github.io/FastQ-Screen/" tool_dev_url: "https://github.com/StevenWingett/FastQ-Screen/archive/refs/tags/v0.15.3.zip" doi: "10.5281/zenodo.5838377" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - database: - type: directory - description: fastq screen database folder containing config file and index folders - pattern: "FastQ_Screen_Genomes" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - database: + type: directory + description: fastq screen database folder containing config file and index folders + pattern: "FastQ_Screen_Genomes" output: - - fastq_screen: - type: directory - description: Output fastq_screen file containing png, html, txt and no_hits_fastq files - pattern: "*.{_fq_screen}" + - txt: + - meta: + type: map + description: Groovy Map containing sample information + - "*.txt": + type: file + description: TXT file containing alignment statistics + pattern: "*.txt" - png: - type: file - description: PNG file with graphical representation of alignments - pattern: "*.png" + - meta: + type: map + description: Groovy Map containing sample information + - "*.png": + type: file + description: PNG file with graphical representation of alignments + pattern: "*.png" - html: - type: file - description: HTML file containing mapping results as a table and graphical representation - pattern: "*.html" - - txt: - type: file - description: TXT file containing alignment statistics - pattern: "*.txt" - - no_hits_fastq: - type: file - description: FastQ file containing reads that did not align to any database (optional) - pattern: "*_nohits.fastq" + - meta: + type: map + description: Groovy Map containing sample information + - "*.html": + type: file + description: HTML file containing mapping results as a table and graphical representation + pattern: "*.html" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: FastQ file containing reads that did not align to any database (optional) + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@snesic" - "@JPejovicApis" diff --git a/modules/nf-core/fasttree/meta.yml b/modules/nf-core/fasttree/meta.yml index 97622e590702..111bbc46afd3 100644 --- a/modules/nf-core/fasttree/meta.yml +++ b/modules/nf-core/fasttree/meta.yml @@ -1,29 +1,34 @@ name: fasttree -description: Produces a Newick format phylogeny from a multiple sequence alignment. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment. + Capable of bacterial genome size alignments. keywords: - phylogeny - newick - alignment tools: - fasttree: - description: FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences + description: FastTree infers approximately-maximum-likelihood phylogenetic trees + from alignments of nucleotide or protein sequences homepage: http://www.microbesonline.org/fasttree/ documentation: http://www.microbesonline.org/fasttree/#Usage licence: ["GPL v2"] + identifier: biotools:fasttree input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{tre}" + - "*.tre": + type: file + description: A phylogeny in Newick format + pattern: "*.{tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aunderwo" maintainers: diff --git a/modules/nf-core/fastx/collapser/meta.yml b/modules/nf-core/fastx/collapser/meta.yml index ad36701142c5..30b774b7de8e 100644 --- a/modules/nf-core/fastx/collapser/meta.yml +++ b/modules/nf-core/fastx/collapser/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "fastx_collapser" -description: Collapses identical sequences in a FASTQ/A file into a single sequence (while maintaining reads counts) +description: Collapses identical sequences in a FASTQ/A file into a single sequence + (while maintaining reads counts) keywords: - collapse - genomics @@ -9,42 +9,41 @@ keywords: - fastq tools: - "fastx": - description: "A collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing" + description: "A collection of command line tools for Short-Reads FASTA/FASTQ files + preprocessing" homepage: "http://hannonlab.cshl.edu/fastx_toolkit/" documentation: "http://hannonlab.cshl.edu/fastx_toolkit/commandline.html" tool_dev_url: "https://github.com/agordon/fastx_toolkit" licence: ["AGPL"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fastx: - type: file - description: Decompressed FASTA/FASTQ input file - pattern: "*.{fastq,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: Decompressed FASTA/FASTQ input file + pattern: "*.{fastq,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Collapsed FASTA file - pattern: "*.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.fasta: + type: file + description: Collapsed FASTA file + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/fcs/fcsadaptor/meta.yml b/modules/nf-core/fcs/fcsadaptor/meta.yml index 54fca1bb7b68..83cae5b78848 100644 --- a/modules/nf-core/fcs/fcsadaptor/meta.yml +++ b/modules/nf-core/fcs/fcsadaptor/meta.yml @@ -18,45 +18,72 @@ tools: documentation: "https://github.com/ncbi/fcs/wiki/FCS-adaptor" tool_dev_url: "https://github.com/ncbi/fcs" licence: ["United States Government Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: assembly fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: assembly fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cleaned_assembly: - type: file - description: Cleaned assembly in fasta format - pattern: "*.{cleaned_sequences.fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cleaned_sequences.fa.gz": + type: file + description: Cleaned assembly in fasta format + pattern: "*.{cleaned_sequences.fa.gz}" - adaptor_report: - type: file - description: Report of identified adaptors - pattern: "*.{fcs_adaptor_report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor_report.txt": + type: file + description: Report of identified adaptors + pattern: "*.{fcs_adaptor_report.txt}" - log: - type: file - description: Log file - pattern: "*.{fcs_adaptor.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fcs_adaptor.log": + type: file + description: Log file + pattern: "*.{fcs_adaptor.log}" - pipeline_args: - type: file - description: Run arguments - pattern: "*.{pipeline_args.yaml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pipeline_args.yaml": + type: file + description: Run arguments + pattern: "*.{pipeline_args.yaml}" - skipped_trims: - type: file - description: Skipped trim information - pattern: "*.{skipped_trims.jsonl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.skipped_trims.jsonl": + type: file + description: Skipped trim information + pattern: "*.{skipped_trims.jsonl}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d4straub" maintainers: diff --git a/modules/nf-core/fcs/fcsgx/meta.yml b/modules/nf-core/fcs/fcsgx/meta.yml index 0537d97c90d4..8e4786f9c318 100644 --- a/modules/nf-core/fcs/fcsgx/meta.yml +++ b/modules/nf-core/fcs/fcsgx/meta.yml @@ -1,5 +1,6 @@ name: "fcs_fcsgx" -description: Run FCS-GX on assembled genomes. The contigs of the assembly are searched against a reference database excluding the given taxid. +description: Run FCS-GX on assembled genomes. The contigs of the assembly are searched + against a reference database excluding the given taxid. keywords: - assembly - genomics @@ -18,36 +19,47 @@ tools: documentation: "https://github.com/ncbi/fcs/wiki/FCS-GX" tool_dev_url: "https://github.com/ncbi/fcs" license: ["United States Government Work"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'6973' ] - - assembly: - type: file - description: assembly fasta file - - database: - type: file - description: Files of the database downloaded from the ncbi server, https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/. All files of one db should be downloaded and given to the process as channel.collect(). The link contains 2 databases, test-only and all. Use all for pipeline usage and test-only for tests. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'6973' ] + - assembly: + type: file + description: assembly fasta file + - - gxdb: + type: file + description: The NCBI GenBank database to search against. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'9606' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fcs_gx_report: - type: file - description: Report containing the contig identifier and recommended action (EXCLUDE, TRIM, FIX, REVIEW) - pattern: "*.fcs_gx_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - out/*.fcs_gx_report.txt: + type: file + description: Report containing the contig identifier and recommended action + (EXCLUDE, TRIM, FIX, REVIEW) + pattern: "*.fcs_gx_report.txt" - taxonomy_report: - type: file - description: Report containing the contig identifier and mapped contaminant species - pattern: "*.taxonomy.rpt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - out/*.taxonomy.rpt: + type: file + description: Report containing the contig identifier and mapped contaminant + species + pattern: "*.taxonomy.rpt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tillenglert" maintainers: diff --git a/modules/nf-core/ffq/meta.yml b/modules/nf-core/ffq/meta.yml index d5f178738558..2bd95b86c83d 100644 --- a/modules/nf-core/ffq/meta.yml +++ b/modules/nf-core/ffq/meta.yml @@ -1,5 +1,6 @@ name: "ffq" -description: A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA. +description: A command line tool that makes it easier to find sequencing data from + the SRA / GEO / ENA. keywords: - SRA - ENA @@ -10,25 +11,29 @@ keywords: - databases tools: - "ffq": - description: "A command line tool that makes it easier to find sequencing data from the SRA / GEO / ENA." + description: "A command line tool that makes it easier to find sequencing data + from the SRA / GEO / ENA." homepage: https://github.com/pachterlab/ffq documentation: https://github.com/pachterlab/ffq#usage tool_dev_url: https://github.com/pachterlab/ffq doi: "10.1101/2022.05.18.492548" licence: ["MIT"] + identifier: "" input: - - ids: - type: list - description: List of supported database ids e.g. SRA / GEO / ENA + - - ids: + type: list + description: List of supported database ids e.g. SRA / GEO / ENA output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON file containing metadata for ids - pattern: "*.{json}" + - "*.json": + type: file + description: JSON file containing metadata for ids + pattern: "*.{json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml index 50bc48839079..0b733a5dff96 100644 --- a/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/callduplexconsensusreads/meta.yml @@ -1,47 +1,53 @@ name: "fgbio_callduplexconsensusreads" -description: Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences from reads generated from the same double-stranded source molecule. +description: Uses FGBIO CallDuplexConsensusReads to call duplex consensus sequences + from reads generated from the same double-stranded source molecule. keywords: - umi - duplex - fgbio tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/CallDuplexConsensusReads.html tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file, grouped by UMI - pattern: "*.{bam,sam}" - - min_reads: - type: string - description: Minimum number of raw/original reads to build each consensus read. Can be a space delimited list of 1-3 values. See fgbio documentation for more details. - - min_baseq: - type: integer - description: Ignore bases in raw reads that have Q below this value + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - grouped_bam: + type: file + description: Grouped BAM file + pattern: "*.bam" + - - min_reads: + type: string + description: Minimum number of raw/original reads to build each consensus read. Can + be a space delimited list of 1-3 values. See fgbio documentation for more + details. + - - min_baseq: + type: integer + description: Ignore bases in raw reads that have Q below this value output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: consensus BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: consensus BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml index b7246c4296c9..846c297b191d 100644 --- a/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/callmolecularconsensusreads/meta.yml @@ -10,38 +10,41 @@ tools: homepage: https://github.com/fulcrumgenomics/fgbio documentation: http://fulcrumgenomics.github.io/fgbio/ licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - grouped_bam: - type: file - description: | - The input SAM or BAM file, grouped by UMIs - pattern: "*.{bam,sam}" - - min_reads: - type: integer - description: Minimum number of original reads to build each consensus read. - - min_baseq: - type: integer - description: Ignore bases in raw reads that have Q below this value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - grouped_bam: + type: file + description: | + The input SAM or BAM file, grouped by UMIs + pattern: "*.{bam,sam}" + - - min_reads: + type: integer + description: Minimum number of original reads to build each consensus read. + - - min_baseq: + type: integer + description: Ignore bases in raw reads that have Q below this value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output SAM or BAM file to write consensus reads. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output SAM or BAM file to write consensus reads. + pattern: "*.{bam,sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sruthipsuresh" maintainers: diff --git a/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml index f7afa4b41016..4ef27fc4f2cd 100644 --- a/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml +++ b/modules/nf-core/fgbio/collectduplexseqmetrics/meta.yml @@ -1,4 +1,3 @@ ---- name: "fgbio_collectduplexseqmetrics" description: Collects a suite of metrics to QC duplex sequencing data. keywords: @@ -8,70 +7,112 @@ keywords: - duplex tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: "http://fulcrumgenomics.github.io/fgbio/" documentation: "http://fulcrumgenomics.github.io/fgbio/" tool_dev_url: "https://github.com/fulcrumgenomics/fgbio" licence: ["MIT"] + identifier: biotools:fgbio - "r-ggplot2": - description: "ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics. " + description: "ggplot2 is a system for declaratively creating graphics, based on + The Grammar of Graphics. " homepage: "https://ggplot2.tidyverse.org/" documentation: "https://ggplot2.tidyverse.org/" tool_dev_url: "https://github.com/tidyverse/ggplot2" licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - grouped_bam: - type: file - description: It has to be either 1)The exact BAM output by the GroupReadsByUmi tool (in the sort-order it was produced in) 2)A BAM file that has MI tags present on all reads (usually set by GroupReadsByUmi and has been sorted with SortBam into TemplateCoordinate order. - pattern: "*.bam" - - - interval_list: - type: file - description: Calculation of metrics may be restricted to a set of regions using the --intervals parameter. The file format is descripted here https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html - pattern: "*.{tsv|txt|interval_list}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - grouped_bam: + type: file + description: It has to be either 1)The exact BAM output by the GroupReadsByUmi + tool (in the sort-order it was produced in) 2)A BAM file that has MI tags + present on all reads (usually set by GroupReadsByUmi and has been sorted with + SortBam into TemplateCoordinate order. + pattern: "*.bam" + - - interval_list: + type: file + description: Calculation of metrics may be restricted to a set of regions using + the --intervals parameter. The file format is descripted here + https://samtools.github.io/htsjdk/javadoc/htsjdk/index.html?htsjdk/samtools/util/Interval.html + pattern: "*.{tsv|txt|interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - family_sizes: - type: file - description: Metrics on the frequency of different types of families of different sizes - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.family_sizes.txt": + type: file + description: Metrics on the frequency of different types of families of different + sizes + pattern: "*.txt" - duplex_family_sizes: - type: file - description: Metrics on the frequency of duplex tag families by the number of observations from each strand - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_family_sizes.txt": + type: file + description: Metrics on the frequency of duplex tag families by the number of + observations from each strand + pattern: "*.txt" - duplex_yield_metrics: - type: file - description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_yield_metrics.txt": + type: file + description: Summary QC metrics produced using 5%, 10%, 15%...100% of the data + pattern: "*.txt" - umi_counts: - type: file - description: Metrics on the frequency of observations of UMIs within reads and tag families - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.umi_counts.txt": + type: file + description: Metrics on the frequency of observations of UMIs within reads and + tag families + pattern: "*.txt" - duplex_qc: - type: file - description: A series of plots generated from the preceding metrics files for visualization - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_qc.pdf": + type: file + description: A series of plots generated from the preceding metrics files for + visualization + pattern: "*.pdf" - duplex_umi_counts: - type: file - description: Metrics on the frequency of observations of duplex UMIs within reads and tag families. - pattern: "*.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "**.duplex_umi_counts.txt": + type: file + description: Metrics on the frequency of observations of duplex UMIs within + reads and tag families. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@georgiakes" maintainers: diff --git a/modules/nf-core/fgbio/fastqtobam/meta.yml b/modules/nf-core/fgbio/fastqtobam/meta.yml index f26f29da299d..bce76cf8c0ac 100644 --- a/modules/nf-core/fgbio/fastqtobam/meta.yml +++ b/modules/nf-core/fgbio/fastqtobam/meta.yml @@ -7,34 +7,49 @@ keywords: - cram tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - reads: - type: file - description: pair of reads to be converted into BAM file - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: pair of reads to be converted into BAM file + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - version: - type: file - description: File containing software version - pattern: "*.{version.yml}" - bam: - type: file - description: Unaligned, unsorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Unaligned, unsorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Unaligned, unsorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Unaligned, unsorted CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" - "@matthdsm" diff --git a/modules/nf-core/fgbio/filterconsensusreads/meta.yml b/modules/nf-core/fgbio/filterconsensusreads/meta.yml index 0a0d62979b93..e1c044823781 100644 --- a/modules/nf-core/fgbio/filterconsensusreads/meta.yml +++ b/modules/nf-core/fgbio/filterconsensusreads/meta.yml @@ -1,5 +1,6 @@ name: "fgbio_filterconsensusreads" -description: Uses FGBIO FilterConsensusReads to filter consensus reads generated by CallMolecularConsensusReads or CallDuplexConsensusReads. +description: Uses FGBIO FilterConsensusReads to filter consensus reads generated by + CallMolecularConsensusReads or CallDuplexConsensusReads. keywords: - fgbio - filter @@ -8,54 +9,58 @@ keywords: - duplexumi tools: - "fgbio": - description: "A set of tools for working with genomic and high throughput sequencing data, including UMIs" + description: "A set of tools for working with genomic and high throughput sequencing + data, including UMIs" homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/FilterConsensusReads.html tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file containing genomic sequence information - pattern: "*.bam" - - min_reads: - type: integer - description: Minimum number of reads required to keep a consensus read - - min_baseq: - type: file - description: Minimum base quality to consider - - max_base_error_rate: - type: file - description: Maximum base error rate for a position before it is replaced with an N. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file containing genomic sequence information + pattern: "*.bam" + - - min_reads: + type: integer + description: Minimum number of reads required to keep a consensus read + - - min_baseq: + type: file + description: Minimum base quality to consider + - - max_base_error_rate: + type: file + description: Maximum base error rate for a position before it is replaced with + an N. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Filtered consensus BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Filtered consensus BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml index c8243f213866..3e525fd647d2 100644 --- a/modules/nf-core/fgbio/groupreadsbyumi/meta.yml +++ b/modules/nf-core/fgbio/groupreadsbyumi/meta.yml @@ -12,46 +12,56 @@ keywords: - fgbio tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file. Note: the MQ tag is required on reads with mapped mates (!) - pattern: "*.bam" - - strategy: - type: string - enum: ["Identity", "Edit", "Adjacency", "Paired"] - description: | - Reguired argument: defines the UMI assignment strategy. - Must be chosen among: Identity, Edit, Adjacency, Paired. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file. Note: the MQ tag is required on reads with mapped mates (!) + pattern: "*.bam" + - - strategy: + type: string + enum: ["Identity", "Edit", "Adjacency", "Paired"] + description: | + Reguired argument: defines the UMI assignment strategy. + Must be chosen among: Identity, Edit, Adjacency, Paired. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: UMI-grouped BAM - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: UMI-grouped BAM + pattern: "*.bam" - histogram: - type: file - description: A text file containing the tag family size counts - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*histogram.txt": + type: file + description: A text file containing the tag family size counts + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/fgbio/sortbam/meta.yml b/modules/nf-core/fgbio/sortbam/meta.yml index 61630d7a5973..26cbda22a501 100644 --- a/modules/nf-core/fgbio/sortbam/meta.yml +++ b/modules/nf-core/fgbio/sortbam/meta.yml @@ -1,5 +1,6 @@ name: fgbio_sortbam -description: Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. +description: Sorts a SAM or BAM file. Several sort orders are available, including + coordinate, queryname, random, and randomquery. keywords: - sort - bam @@ -10,32 +11,35 @@ tools: homepage: https://github.com/fulcrumgenomics/fgbio documentation: http://fulcrumgenomics.github.io/fgbio/ licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - bam: - type: file - description: | - The input SAM or BAM file to be sorted. - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - bam: + type: file + description: | + The input SAM or BAM file to be sorted. + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output SAM or BAM file. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output SAM or BAM file. + pattern: "*.{bam,sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sruthipsuresh" maintainers: diff --git a/modules/nf-core/fgbio/zipperbams/meta.yml b/modules/nf-core/fgbio/zipperbams/meta.yml index 8b7ca634cd59..553e9388f08e 100644 --- a/modules/nf-core/fgbio/zipperbams/meta.yml +++ b/modules/nf-core/fgbio/zipperbams/meta.yml @@ -1,5 +1,6 @@ name: "fgbio_zipperbams" -description: FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata into the output BAM +description: FGBIO tool to zip together an unmapped and mapped BAM to transfer metadata + into the output BAM keywords: - fgbio - umi @@ -8,62 +9,66 @@ keywords: - zipperbams tools: - fgbio: - description: A set of tools for working with genomic and high throughput sequencing data, including UMIs + description: A set of tools for working with genomic and high throughput sequencing + data, including UMIs homepage: http://fulcrumgenomics.github.io/fgbio/ documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio licence: ["MIT"] + identifier: biotools:fgbio input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mapped_bam: - type: file - description: mapped BAM/SAM file - pattern: "*.{bam,sam}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - unmapped_bam: - type: file - description: unmapped BAM file - pattern: "*.bam" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'GRCh38' ] - - fasta: - type: file - description: fasta file containing genomic sequence information - pattern: "*.{fasta,fa}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'GRCh38' ] - - dict: - type: file - description: dict file containing a sequence dictionary for the fasta file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - unmapped_bam: + type: file + description: unmapped BAM file + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mapped_bam: + type: file + description: mapped BAM/SAM file + pattern: "*.{bam,sam}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'GRCh38' ] + - fasta: + type: file + description: fasta file containing genomic sequence information + pattern: "*.{fasta,fa}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'GRCh38' ] + - dict: + type: file + description: dict file containing a sequence dictionary for the fasta file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Zipped BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Zipped BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/filtlong/meta.yml b/modules/nf-core/filtlong/meta.yml index 4a0f072a1b8d..804c1b0d3fc7 100644 --- a/modules/nf-core/filtlong/meta.yml +++ b/modules/nf-core/filtlong/meta.yml @@ -9,42 +9,54 @@ keywords: - short reads tools: - filtlong: - description: Filtlong is a tool for filtering long reads. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. + description: Filtlong is a tool for filtering long reads. It can take a set of + long reads and produce a smaller, better subset. It uses both read length (longer + is better) and read identity (higher is better) when choosing which reads pass + the filter. homepage: https://anaconda.org/bioconda/filtlong tool_dev_url: https://github.com/rrwick/Filtlong licence: ["GPL v3"] + identifier: biotools:filtlong input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: fastq file - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - longreads: - type: file - description: fastq file - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: fastq file + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - longreads: + type: file + description: fastq file + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Filtered (compressed) fastq file - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered (compressed) fastq file + pattern: "*.fastq.gz" - log: - type: file - description: Standard error logging file containing summary statistics - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Standard error logging file containing summary statistics + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d4straub" - "@sofstam" diff --git a/modules/nf-core/flash/meta.yml b/modules/nf-core/flash/meta.yml index 8253482ebcfb..e8d3ac21d962 100644 --- a/modules/nf-core/flash/meta.yml +++ b/modules/nf-core/flash/meta.yml @@ -11,39 +11,54 @@ tools: homepage: https://ccb.jhu.edu/software/FLASH/ doi: 10.1093/bioinformatics/btr507 licence: ["GPL v3+"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 2; i.e., paired-end data. - pattern: "*fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 2; i.e., paired-end data. + pattern: "*fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - merged: - type: file - description: The merged fastq reads - pattern: ".extendedFrags.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.extendedFrags.fastq.gz: + type: file + description: The merged fastq reads + pattern: ".extendedFrags.fastq.gz" - notcombined: - type: file - description: Not combined reads from flash - pattern: ".notCombined_*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.notCombined_*.fastq.gz: + type: file + description: Not combined reads from flash + pattern: ".notCombined_*.fastq.gz" - histogram: - type: file - description: HistogramNumeric histogram of merged read lengths. - pattern: ".hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hist: + type: file + description: HistogramNumeric histogram of merged read lengths. + pattern: ".hist" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Erkison" maintainers: diff --git a/modules/nf-core/flye/meta.yml b/modules/nf-core/flye/meta.yml index 4b030d9ec528..1e33c275de73 100644 --- a/modules/nf-core/flye/meta.yml +++ b/modules/nf-core/flye/meta.yml @@ -8,60 +8,95 @@ keywords: - single molecule tools: - "flye": - description: "Fast and accurate de novo assembler for single molecule sequencing reads" + description: "Fast and accurate de novo assembler for single molecule sequencing + reads" homepage: "https://github.com/fenderglass/Flye" documentation: "https://github.com/fenderglass/Flye/blob/flye/docs/USAGE.md" tool_dev_url: "https://github.com/fenderglass/Flye" doi: "10.1038/s41592-020-00971-x" licence: ["BSD-3-clause"] + identifier: biotools:Flye input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - reads: - type: file - description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ format. - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" - - mode: - type: string - description: Flye mode depending on the input data (source and error rate) - pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - reads: + type: file + description: Input reads from Oxford Nanopore or PacBio data in FASTA/FASTQ + format. + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + - - mode: + type: string + description: Flye mode depending on the input data (source and error rate) + pattern: "--pacbio-raw|--pacbio-corr|--pacbio-hifi|--nano-raw|--nano-corr|--nano-hq" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Assembled FASTA file - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "*.fasta.gz" - gfa: - type: file - description: Repeat graph in gfa format - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gfa.gz": + type: file + description: Repeat graph in gfa format + pattern: "*.gfa.gz" - gv: - type: file - description: Repeat graph in gv format - pattern: "*.gv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gv.gz": + type: file + description: Repeat graph in gv format + pattern: "*.gv.gz" - txt: - type: file - description: Extra information and statistics about resulting contigs - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.txt": + type: file + description: Extra information and statistics about resulting contigs + pattern: "*.txt" - log: - type: file - description: Flye log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: Flye log file + pattern: "*.log" - json: - type: file - description: Flye parameters - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: Flye parameters + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/foldcomp/compress/meta.yml b/modules/nf-core/foldcomp/compress/meta.yml index e924039651ad..cd45099ff085 100644 --- a/modules/nf-core/foldcomp/compress/meta.yml +++ b/modules/nf-core/foldcomp/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "foldcomp_compress" description: Efficient compression tool for protein structures @@ -8,37 +7,42 @@ keywords: - compression tools: - "foldcomp": - description: "Foldcomp: a library and format for compressing and indexing large protein structure sets" + description: "Foldcomp: a library and format for compressing and indexing large + protein structure sets" homepage: "https://github.com/steineggerlab/foldcomp" documentation: "https://github.com/steineggerlab/foldcomp" tool_dev_url: "https://github.com/steineggerlab/foldcomp" doi: "10.1093/bioinformatics/btad153" licence: ["GPL v3-or-later"] + identifier: biotools:foldcomp input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB or CIF format to compress (also works with folder input) - pattern: "*.{pdb,cif}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB or CIF format to compress (also works + with folder input) + pattern: "*.{pdb,cif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - fcz: - type: file - description: | - Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory) - pattern: "{*_fcz,*.fcz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*fcz": + type: file + description: | + Either single compressed protein structure (if input was file) or folder with all compressed protein structures (if input was directory) + pattern: "{*_fcz,*.fcz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/foldcomp/decompress/meta.yml b/modules/nf-core/foldcomp/decompress/meta.yml index 81800f0fd7de..6084220d3dac 100644 --- a/modules/nf-core/foldcomp/decompress/meta.yml +++ b/modules/nf-core/foldcomp/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldcomp_decompress" description: Decompression tool for foldcomp compressed structures @@ -8,36 +7,41 @@ keywords: - compression tools: - "foldcomp": - description: "Foldcomp: a library and format for compressing and indexing large protein structure sets" + description: "Foldcomp: a library and format for compressing and indexing large + protein structure sets" homepage: "https://github.com/steineggerlab/foldcomp" documentation: "https://github.com/steineggerlab/foldcomp" tool_dev_url: "https://github.com/steineggerlab/foldcomp" doi: "10.1093/bioinformatics/btad153" licence: ["GPL v3-or-later"] + identifier: biotools:foldcomp input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - fcz: - type: file - description: Foldcomp compressed protein structure(s) (also works with folder input) - pattern: "*{*,*.fcz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fcz: + type: file + description: Foldcomp compressed protein structure(s) (also works with folder + input) + pattern: "*{*,*.fcz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - pdb: - type: file - description: | - Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory) - pattern: "{*_pdb,*.pdb,*.cif}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "{*pdb,*.cif}": + type: file + description: | + Either single protein structure (if input was file) or folder with all decompressed protein structures (if input was directory) + pattern: "{*_pdb,*.pdb,*.cif}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/foldmason/easymsa/meta.yml b/modules/nf-core/foldmason/easymsa/meta.yml index e1b807888db8..cc00f44c58b2 100644 --- a/modules/nf-core/foldmason/easymsa/meta.yml +++ b/modules/nf-core/foldmason/easymsa/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "foldmason_easymsa" description: Aligns protein structures using foldmason @@ -15,40 +14,51 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldmason" doi: "10.1101/2024.08.01.606130" licence: ["GPL v3"] + identifier: biotools:foldmason input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - pdbs: - type: file - description: Input protein structures in PDB format. - pattern: "*.{pdb,mmcif}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pdbs: + type: file + description: Input protein structures in PDB format. + pattern: "*.{pdb,mmcif}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - msa_3di: - type: file - description: Fasta file containing the multiple sequence alignment with 3Di alphabet - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "${prefix}_3di.fa${compress ? '.gz' : ''}": + type: file + description: Fasta file containing the multiple sequence alignment with 3Di + alphabet + pattern: "*.{fa}" - msa_aa: - type: file - description: Fasta file containing the multiple sequence alignment with Amino Acid alphabet - pattern: "*.{fa}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "${prefix}_aa.fa${compress ? '.gz' : ''}": + type: file + description: Fasta file containing the multiple sequence alignment with Amino + Acid alphabet + pattern: "*.{fa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/foldseek/createdb/environment.yml b/modules/nf-core/foldseek/createdb/environment.yml index 5467561cf935..c59ddfe54d73 100644 --- a/modules/nf-core/foldseek/createdb/environment.yml +++ b/modules/nf-core/foldseek/createdb/environment.yml @@ -1,3 +1,4 @@ +name: foldseek_createdb channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldseek/createdb/meta.yml b/modules/nf-core/foldseek/createdb/meta.yml index 27d0a43f0572..f11e24c96ee9 100644 --- a/modules/nf-core/foldseek/createdb/meta.yml +++ b/modules/nf-core/foldseek/createdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldseek_createdb" description: Create a database from protein structures @@ -14,29 +13,33 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldseek" doi: "10.1038/s41587-023-01773-0" licence: ["GPL v3"] + identifier: biotools:foldseek input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB, mmCIF or mmJSON format (also works with folder input) - pattern: "*.{pdb,mmcif,mmjson}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB, mmCIF or mmJSON format (also works + with folder input) + pattern: "*.{pdb,mmcif,mmjson}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db: - type: directory - description: Directory containing pdb database files - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${meta.id}: + type: directory + description: Directory containing pdb database files + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/foldseek/easysearch/environment.yml b/modules/nf-core/foldseek/easysearch/environment.yml index 5467561cf935..c38d477d0c44 100644 --- a/modules/nf-core/foldseek/easysearch/environment.yml +++ b/modules/nf-core/foldseek/easysearch/environment.yml @@ -1,3 +1,4 @@ +name: foldseek_easysearch channels: - conda-forge - bioconda diff --git a/modules/nf-core/foldseek/easysearch/meta.yml b/modules/nf-core/foldseek/easysearch/meta.yml index d18cc01dbed4..c548213705c2 100644 --- a/modules/nf-core/foldseek/easysearch/meta.yml +++ b/modules/nf-core/foldseek/easysearch/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "foldseek_easysearch" -description: Search for protein structural hits against a foldseek database of protein structures +description: Search for protein structural hits against a foldseek database of protein + structures keywords: - protein - structure @@ -14,41 +14,45 @@ tools: tool_dev_url: "https://github.com/steineggerlab/foldseek" doi: "10.1038/s41587-023-01773-0" licence: ["GPL v3"] + identifier: biotools:foldseek input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - pdb: - type: file - description: Protein structure(s) in PDB, mmCIF or mmJSON format to compare against a foldseek database (also works with folder input) - pattern: "*.{pdb,mmcif,mmjson}" - - meta_db: - type: map - description: | - Groovy Map containing sample information for the foldseek db - e.g. `[ id:'test', single_end:false ]` - - db: - type: directory - description: foldseek database from protein structures - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pdb: + type: file + description: Protein structure(s) in PDB, mmCIF or mmJSON format to compare + against a foldseek database (also works with folder input) + pattern: "*.{pdb,mmcif,mmjson}" + - - meta_db: + type: map + description: | + Groovy Map containing sample information for the foldseek db + e.g. `[ id:'test', single_end:false ]` + - db: + type: directory + description: foldseek database from protein structures + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - aln: - type: file - description: | - Structural comparisons file output - Query, Target, Identity, Alignment length, Mismatches, Gap openings, - Query start, Query end, Target start, Target end, E-value, Bit score - pattern: "*.{m8}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${meta.id}.m8: + type: file + description: | + Structural comparisons file output + Query, Target, Identity, Alignment length, Mismatches, Gap openings, + Query start, Query end, Target start, Target end, E-value, Bit score + pattern: "*.{m8}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" diff --git a/modules/nf-core/fq/generate/meta.yml b/modules/nf-core/fq/generate/meta.yml index e8fcfce7294a..10e6cc0fa2fb 100644 --- a/modules/nf-core/fq/generate/meta.yml +++ b/modules/nf-core/fq/generate/meta.yml @@ -13,26 +13,29 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Random generated FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Random generated FASTQ files. + pattern: "*_R[12].fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/lint/meta.yml b/modules/nf-core/fq/lint/meta.yml index 96223bd05894..7240fb5796e1 100644 --- a/modules/nf-core/fq/lint/meta.yml +++ b/modules/nf-core/fq/lint/meta.yml @@ -11,25 +11,32 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file list - pattern: "*.fastq{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file list + pattern: "*.fastq{,.gz}" output: - lint: - type: file - description: Lint output - pattern: "*.fq_lint.txt" + - meta: + type: file + description: Lint output + pattern: "*.fq_lint.txt" + - "*.fq_lint.txt": + type: file + description: Lint output + pattern: "*.fq_lint.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fq/subsample/meta.yml b/modules/nf-core/fq/subsample/meta.yml index 6c5e87f3e852..7d91b0d9ada2 100644 --- a/modules/nf-core/fq/subsample/meta.yml +++ b/modules/nf-core/fq/subsample/meta.yml @@ -1,5 +1,6 @@ name: "fq_subsample" -description: fq subsample outputs a subset of records from single or paired FASTQ files. This requires a seed (--seed) to be set in ext.args. +description: fq subsample outputs a subset of records from single or paired FASTQ + files. This requires a seed (--seed) to be set in ext.args. keywords: - fastq - fq @@ -11,30 +12,33 @@ tools: documentation: "https://github.com/stjude-rust-labs/fq" tool_dev_url: "https://github.com/stjude-rust-labs/fq" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: FASTQ file - pattern: "*.{fq,fastq}{,.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: FASTQ file + pattern: "*.{fq,fastq}{,.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Randomly sampled FASTQ files. - pattern: "*_R[12].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Randomly sampled FASTQ files. + pattern: "*_R[12].fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/fqtk/meta.yml b/modules/nf-core/fqtk/meta.yml index 357b23ca22ba..db8063e71f18 100644 --- a/modules/nf-core/fqtk/meta.yml +++ b/modules/nf-core/fqtk/meta.yml @@ -10,43 +10,59 @@ tools: homepage: "https://github.com/fulcrumgenomics/fqtk" documentation: "https://github.com/fulcrumgenomics/fqtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sample_sheet: - type: file - description: Tsv file, with two columns sample_id and barcode - pattern: "*.{tsv}" - - fastq_readstructure_pairs: - type: map - description: List of lists i.e. [[, , ],...] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_sheet: + type: file + description: Tsv file, with two columns sample_id and barcode + pattern: "*.{tsv}" + - fastq_readstructure_pairs: + type: map + description: List of lists i.e. [[, , ],...] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed per-sample FASTQ files - pattern: "output/*R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*.fq.gz: + type: file + description: Demultiplexed per-sample FASTQ files + pattern: "output/*R*.fastq.gz" - metrics: - type: file - description: | - Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best - pattern: "output/demux-metrics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/demux-metrics.txt: + type: file + description: | + Demultiplexing summary stats; sample_id, barcode templates, frac_templates, ratio_to_mean, ratio_to_best + pattern: "output/demux-metrics.txt" - most_frequent_unmatched: - type: file - description: | - File containing unmatched fastq records - pattern: "output/unmatched*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/unmatched*.fq.gz: + type: file + description: | + File containing unmatched fastq records + pattern: "output/unmatched*.fq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nh13" - "@sam-white04" diff --git a/modules/nf-core/freebayes/meta.yml b/modules/nf-core/freebayes/meta.yml index 1803b2b31951..45fc61d5bd75 100644 --- a/modules/nf-core/freebayes/meta.yml +++ b/modules/nf-core/freebayes/meta.yml @@ -16,95 +16,101 @@ tools: tool_dev_url: https://github.com/freebayes/freebayes doi: "10.48550/arXiv.1207.3907" licence: ["MIT"] + identifier: biotools:freebayes input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_1: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_1_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai}" - - input_2: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_2_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai}" - - target_bed: - type: file - description: Optional - Limit analysis to targets listed in this BED-format FILE. - pattern: "*.bed" - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: reference fasta file - pattern: ".{fa,fa.gz,fasta,fasta.gz}" - - ref_idx_meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test_reference' ] - - fasta_fai: - type: file - description: reference fasta file index - pattern: "*.{fa,fasta}.fai" - - samples_meta: - type: map - description: | - Groovy Map containing meta information for the samples file. - e.g. [ id:'test_samples' ] - - samples: - type: file - description: Optional - Limit analysis to samples listed (one per line) in the FILE. - pattern: "*.txt" - - populations_meta: - type: map - description: | - Groovy Map containing meta information for the populations file. - e.g. [ id:'test_populations' ] - - populations: - type: file - description: Optional - Each line of FILE should list a sample and a population which it is part of. - pattern: "*.txt" - - cnv_meta: - type: map - description: | - Groovy Map containing meta information for the cnv file. - e.g. [ id:'test_cnv' ] - - cnv: - type: file - description: | - A copy number map BED file, which has either a sample-level ploidy: - sample_name copy_number - or a region-specific format: - seq_name start end sample_name copy_number - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_1: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_1_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - input_2: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_2_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: Optional - Limit analysis to targets listed in this BED-format + FILE. + pattern: "*.bed" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: reference fasta file + pattern: ".{fa,fa.gz,fasta,fasta.gz}" + - - ref_idx_meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test_reference' ] + - fasta_fai: + type: file + description: reference fasta file index + pattern: "*.{fa,fasta}.fai" + - - samples_meta: + type: map + description: | + Groovy Map containing meta information for the samples file. + e.g. [ id:'test_samples' ] + - samples: + type: file + description: Optional - Limit analysis to samples listed (one per line) in the + FILE. + pattern: "*.txt" + - - populations_meta: + type: map + description: | + Groovy Map containing meta information for the populations file. + e.g. [ id:'test_populations' ] + - populations: + type: file + description: Optional - Each line of FILE should list a sample and a population + which it is part of. + pattern: "*.txt" + - - cnv_meta: + type: map + description: | + Groovy Map containing meta information for the cnv file. + e.g. [ id:'test_cnv' ] + - cnv: + type: file + description: | + A copy number map BED file, which has either a sample-level ploidy: + sample_name copy_number + or a region-specific format: + seq_name start end sample_name copy_number + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@maxibor" - "@FriederikeHanssen" diff --git a/modules/nf-core/freyja/boot/meta.yml b/modules/nf-core/freyja/boot/meta.yml index f3d91b52de4f..3095a1f268df 100644 --- a/modules/nf-core/freyja/boot/meta.yml +++ b/modules/nf-core/freyja/boot/meta.yml @@ -1,5 +1,11 @@ name: "freyja_boot" -description: Bootstrap sample demixing by resampling each site based on a multinomial distribution of read depth across all sites, where the event probabilities were determined by the fraction of the total sample reads found at each site, followed by a secondary resampling at each site according to a multinomial distribution (that is, binomial when there was only one SNV at a site), where event probabilities were determined by the frequencies of each base at the site, and the number of trials is given by the sequencing depth. +description: Bootstrap sample demixing by resampling each site based on a multinomial + distribution of read depth across all sites, where the event probabilities were + determined by the fraction of the total sample reads found at each site, followed + by a secondary resampling at each site according to a multinomial distribution (that + is, binomial when there was only one SNV at a site), where event probabilities were + determined by the frequencies of each base at the site, and the number of trials + is given by the sequencing depth. keywords: - variants - fasta @@ -8,55 +14,67 @@ keywords: - bootstrapping tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" - - repeats: - type: integer - description: Number of bootstrap repeats to perform - - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" - - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - depths: + type: file + description: File containing depth of the variants + pattern: "*.depth.tsv" + - - repeats: + type: integer + description: Number of bootstrap repeats to perform + - - barcodes: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" + - - lineages_meta: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - lineages: - type: file - description: a csv file that includes the lineages present and their corresponding abundances - pattern: "*lineages.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lineages.csv": + type: file + description: a csv file that includes the lineages present and their corresponding + abundances + pattern: "*lineages.csv" - summarized: - type: file - description: a csv file that includes the lineages present but summarized by constellation and their corresponding abundances - pattern: "*summarized.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summarized.csv": + type: file + description: a csv file that includes the lineages present but summarized by + constellation and their corresponding abundances + pattern: "*summarized.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/demix/meta.yml b/modules/nf-core/freyja/demix/meta.yml index 141a155fd820..6b95e2e614ca 100644 --- a/modules/nf-core/freyja/demix/meta.yml +++ b/modules/nf-core/freyja/demix/meta.yml @@ -7,48 +7,53 @@ keywords: - wastewater tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" - - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" - - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - depths: + type: file + description: File containing depth of the variants + pattern: "*.depth.tsv" + - - barcodes: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" + - - lineages_meta: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - demix: - type: file - description: a tsv file that includes the lineages present, their corresponding abundances, and summarization by constellation - pattern: "*.demix.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: a tsv file that includes the lineages present, their corresponding + abundances, and summarization by constellation + pattern: "*.demix.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/update/meta.yml b/modules/nf-core/freyja/update/meta.yml index 1f5fc3c633e3..a61b0676f2c3 100644 --- a/modules/nf-core/freyja/update/meta.yml +++ b/modules/nf-core/freyja/update/meta.yml @@ -6,33 +6,39 @@ keywords: - UShER tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - db_name: - type: string - description: "The name of the database directory" + - - db_name: + type: string + description: "The name of the database directory" output: - barcodes: - type: file - description: File containing lineage defining barcodes - pattern: "*barcodes.csv" + - ${db_name}/usher_barcodes.csv: + type: file + description: File containing lineage defining barcodes + pattern: "*barcodes.csv" - lineages_topology: - type: file - description: File containing the lineage topology - pattern: "*lineages.yml" + - ${db_name}/lineages.yml: + type: file + description: File containing the lineage topology + pattern: "*lineages.yml" - lineages_meta: - type: file - description: File containing lineage metadata that correspond to barcodes - pattern: "*lineages.json" + - ${db_name}/curated_lineages.json: + type: file + description: File containing lineage metadata that correspond to barcodes + pattern: "*lineages.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/freyja/variants/meta.yml b/modules/nf-core/freyja/variants/meta.yml index 24f8d6936a3f..bccfb36fed02 100644 --- a/modules/nf-core/freyja/variants/meta.yml +++ b/modules/nf-core/freyja/variants/meta.yml @@ -6,44 +6,49 @@ keywords: - wastewater tools: - "freyja": - description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 samples and provides functionality to analyze lineage dynamics." + description: "Freyja recovers relative lineage abundances from mixed SARS-CoV-2 + samples and provides functionality to analyze lineage dynamics." homepage: "https://github.com/andersen-lab/Freyja" documentation: "https://github.com/andersen-lab/Freyja/wiki" tool_dev_url: "https://github.com/andersen-lab/Freyja" doi: "10.1038/s41586-022-05049-6" licence: ["BSD-2-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - variants: - type: file - description: File containing identified variants in a gff-like format - pattern: "*.variants.tsv" - - depths: - type: file - description: File containing depth of the variants - pattern: "*.depth.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.variants.tsv": + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" + - "*.depth.tsv": + type: file + description: File containing identified variants in a gff-like format + pattern: "*.variants.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/galah/meta.yml b/modules/nf-core/galah/meta.yml index 1a14d8a9f2b9..efadae5822a1 100644 --- a/modules/nf-core/galah/meta.yml +++ b/modules/nf-core/galah/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "galah" description: Cluster genome FASTA files by average nucleotide identity @@ -9,54 +8,64 @@ keywords: - metagenomics tools: - "galah": - description: "Galah aims to be a more scalable metagenome assembled genome (MAG) dereplication method." + description: "Galah aims to be a more scalable metagenome assembled genome (MAG) + dereplication method." homepage: "https://github.com/wwood/galah" documentation: "https://github.com/wwood/galah" tool_dev_url: "https://github.com/wwood/galah" doi: "10.1111/NODOI" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bins: - type: file - description: A list of fasta-formatted genomes for dereplication - pattern: "*.{fa,fna,fa.gz, etc}" - - qc_table: - type: file - description: | - (optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing - information on the completeness and contamination of the input genomes (13 columns), - or a 3-column csv with the header `genome,completeness,contamination`. - In both cases the first column should contain the names of the input genome files, - minus the last file extension - (i.e. if the genome is gzipped, the genome name should retain the .fasta extension). - pattern: "*.{csv,tsv}" - - qc_format: - type: string - description: Defines the type if input table in `qc_table`, if specified. - pattern: "checkm|genome_info" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bins: + type: file + description: A list of fasta-formatted genomes for dereplication + pattern: "*.{fa,fna,fa.gz, etc}" + - qc_table: + type: file + description: | + (optional) Either a (CheckM)[https://nf-co.re/modules/checkm_lineagewf] summary TSV containing + information on the completeness and contamination of the input genomes (13 columns), + or a 3-column csv with the header `genome,completeness,contamination`. + In both cases the first column should contain the names of the input genome files, + minus the last file extension + (i.e. if the genome is gzipped, the genome name should retain the .fasta extension). + pattern: "*.{csv,tsv}" + - qc_format: + type: string + description: Defines the type if input table in `qc_table`, if specified. + pattern: "checkm|genome_info" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - tsv: - type: file - description: TSV file in the format `representative_genome` \t `member_genome` - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: TSV file in the format `representative_genome` \t `member_genome` + pattern: "*.tsv" - dereplicated_bins: - type: file - description: The representative genomes following dereplication by galah. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}-dereplicated/*: + type: file + description: The representative genomes following dereplication by galah. + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/gamma/gamma/meta.yml b/modules/nf-core/gamma/gamma/meta.yml index 7eb3287359ea..f8c5f92e8274 100644 --- a/modules/nf-core/gamma/gamma/meta.yml +++ b/modules/nf-core/gamma/gamma/meta.yml @@ -13,46 +13,67 @@ tools: tool_dev_url: "https://github.com/rastanton/GAMMA" doi: "10.1093/bioinformatics/btab607" licence: ["Apache License 2.0"] + identifier: biotools:gamma input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - db: - type: file - description: Database in FASTA format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - db: + type: file + description: Database in FASTA format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gamma: - type: file - description: GAMMA file with annotated gene matches - pattern: "*.{gamma}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gamma": + type: file + description: GAMMA file with annotated gene matches + pattern: "*.{gamma}" - psl: - type: file - description: PSL file with all gene matches found - pattern: "*.{psl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psl": + type: file + description: PSL file with all gene matches found + pattern: "*.{psl}" - gff: - type: file - description: GFF file - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: GFF file + pattern: "*.{gff}" - fasta: - type: file - description: multifasta file of the gene matches - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: multifasta file of the gene matches + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@rastanton" diff --git a/modules/nf-core/gangstr/meta.yml b/modules/nf-core/gangstr/meta.yml index 963395337291..0d0919257845 100644 --- a/modules/nf-core/gangstr/meta.yml +++ b/modules/nf-core/gangstr/meta.yml @@ -1,5 +1,6 @@ name: "gangstr" -description: GangSTR is a tool for genome-wide profiling tandem repeats from short reads. +description: GangSTR is a tool for genome-wide profiling tandem repeats from short + reads. keywords: - gangstr - STR @@ -8,62 +9,71 @@ keywords: - vcf tools: - "gangstr": - description: "GangSTR is a tool for genome-wide profiling tandem repeats from short reads." + description: "GangSTR is a tool for genome-wide profiling tandem repeats from + short reads." homepage: "https://github.com/gymreklab/GangSTR" documentation: "https://github.com/gymreklab/GangSTR" tool_dev_url: "https://github.com/gymreklab/GangSTR" doi: "10.1093/nar/gkz501" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - aligment_files: - type: file - description: One or more sorted BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - alignment_indices: - type: file - description: The index/indices of the BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - ref_regions: - type: file - description: | - A reference set of regions to genotype in a BED-like format. The file should have following columns: - 1. The name of the chromosome on which the STR is located - 2. The start position of the STR on its chromosome - 3. The end position of the STR on its chromosome - 4. The motif length - 5. The repeat motif - pattern: "*.bed" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment_files: + type: file + description: Alignment files + - alignment_indices: + type: file + description: The index/indices of the BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - ref_regions: + type: file + description: | + A reference set of regions to genotype in a BED-like format. The file should have following columns: + 1. The name of the chromosome on which the STR is located + 2. The start position of the STR on its chromosome + 3. The end position of the STR on its chromosome + 4. The motif length + 5. The repeat motif + pattern: "*.bed" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The resulting VCF file containing the genotypes - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: The resulting VCF file containing the genotypes + pattern: "*.vcf" - samplestats: - type: file - description: A tab-delimited file containing statistics for each sample - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.samplestats.tab": + type: file + description: A tab-delimited file containing statistics for each sample + pattern: "*.tab" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ganon/buildcustom/meta.yml b/modules/nf-core/ganon/buildcustom/meta.yml index 7ddae1211bd8..538fd21306d9 100644 --- a/modules/nf-core/ganon/buildcustom/meta.yml +++ b/modules/nf-core/ganon/buildcustom/meta.yml @@ -9,49 +9,61 @@ keywords: - database tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - List of input FASTA files, or a directory containing input FASTA files. - Note you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`. - pattern: "*" - - taxonomy_files: - type: file - description: Pre-downloaded taxonomy files of input sequences. See ganon docs for formats - - genome_size_files: - type: file - description: Pre-downloaded NCBI or GTDB genome size files of input sequences. See ganon docs for formats - pattern: "{species_genome_size.txt.gz,*_metadata.tar.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + List of input FASTA files, or a directory containing input FASTA files. + Note you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`. + pattern: "*" + - - taxonomy_files: + type: file + description: Pre-downloaded taxonomy files of input sequences. See ganon docs + for formats + - - genome_size_files: + type: file + description: Pre-downloaded NCBI or GTDB genome size files of input sequences. + See ganon docs for formats + pattern: "{species_genome_size.txt.gz,*_metadata.tar.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: ganon database files - pattern: "*.{ibf,tax}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{hibf,ibf,tax}": + type: file + description: ganon database files + pattern: "*.{ibf,tax}" - info: - type: file - description: Copy of target info generated. Can be used for updating database. - pattern: "*info.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info.tsv": + type: file + description: Copy of target info generated. Can be used for updating database. + pattern: "*info.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/classify/meta.yml b/modules/nf-core/ganon/classify/meta.yml index 55a8eae6d05f..49f0572bc015 100644 --- a/modules/nf-core/ganon/classify/meta.yml +++ b/modules/nf-core/ganon/classify/meta.yml @@ -10,60 +10,95 @@ keywords: - classify tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastqs: - type: file - description: Single or paired FASTQ files, optionally gzipped - pattern: "*.{fq,fq.gz,fastq,fastq.gz}" - - db: - type: file - description: Ganon database files from build or build-custom - pattern: "*.{ibf,tax}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastqs: + type: file + description: Single or paired FASTQ files, optionally gzipped + pattern: "*.{fq,fq.gz,fastq,fastq.gz}" + - - db: + type: file + description: Ganon database files from build or build-custom + pattern: "*.{ibf,tax}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tre: - type: file - description: Full ganon report file - pattern: "*.tre" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tre": + type: file + description: Full ganon report file + pattern: "*.tre" - report: - type: file - description: Plain ganon report file with only targets with match - pattern: "*.rep" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rep": + type: file + description: Plain ganon report file with only targets with match + pattern: "*.rep" - one: - type: file - description: Information about a single (best) match of a given read after EM or LCA algorithms - pattern: "*.one" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.one": + type: file + description: Information about a single (best) match of a given read after EM + or LCA algorithms + pattern: "*.one" - all: - type: file - description: Information of all matches to a given read - pattern: "*.all" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.all": + type: file + description: Information of all matches to a given read + pattern: "*.all" - unc: - type: file - description: List of all reads without a hit - pattern: "*.unc" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unc": + type: file + description: List of all reads without a hit + pattern: "*.unc" - log: - type: file - description: Text file containing console output from ganon classify - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Text file containing console output from ganon classify + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/report/meta.yml b/modules/nf-core/ganon/report/meta.yml index c820e9c430ac..e282c82014a7 100644 --- a/modules/nf-core/ganon/report/meta.yml +++ b/modules/nf-core/ganon/report/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ganon_report" description: Generate a ganon report file from the output of ganon classify @@ -12,40 +11,45 @@ keywords: - report tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rep: - type: file - description: Input 'repo' files from ganon classify - pattern: "*.rep" - - db: - type: file - description: Ganon database files from build or build-custom - pattern: "*.{ibf,tax}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rep: + type: file + description: Input 'repo' files from ganon classify + pattern: "*.rep" + - - db: + type: file + description: Ganon database files from build or build-custom + pattern: "*.{ibf,tax}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tre: - type: file - description: Output ganon report containing taxonomic profile information. Formatting of contents depends on --output-format. - pattern: "*.tre" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tre": + type: file + description: Output ganon report containing taxonomic profile information. Formatting + of contents depends on --output-format. + pattern: "*.tre" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/ganon/table/meta.yml b/modules/nf-core/ganon/table/meta.yml index bf15f083591f..23abe6bdb19b 100644 --- a/modules/nf-core/ganon/table/meta.yml +++ b/modules/nf-core/ganon/table/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ganon_table" description: Generate a multi-sample report file from the output of ganon report runs @@ -13,36 +12,41 @@ keywords: - table tools: - "ganon": - description: "ganon classifies short DNA sequences against large sets of genomic reference sequences efficiently" + description: "ganon classifies short DNA sequences against large sets of genomic + reference sequences efficiently" homepage: "https://github.com/pirovc/ganon" documentation: "https://github.com/pirovc/ganon" tool_dev_url: "https://github.com/pirovc/ganon" doi: "10.1093/bioinformatics/btaa458" licence: ["MIT"] + identifier: biotools:ganon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tre: - type: file - description: A list of 'tre' files from ganon report - pattern: "*.tre" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tre: + type: file + description: A list of 'tre' files from ganon report + pattern: "*.tre" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Output ganon table containing taxonomic profile information of multiple samples. Formatting of contents depends on --output-format. - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Output ganon table containing taxonomic profile information of + multiple samples. Formatting of contents depends on --output-format. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gappa/examineassign/meta.yml b/modules/nf-core/gappa/examineassign/meta.yml index e70489e62650..12c1bfe62973 100644 --- a/modules/nf-core/gappa/examineassign/meta.yml +++ b/modules/nf-core/gappa/examineassign/meta.yml @@ -13,41 +13,86 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" + - taxonomy: + type: file + description: taxonomy file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - examineassign: - type: directory - description: Execution directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ./.: + type: directory + description: Execution directory - profile: - type: file - description: profile tsv file - pattern: "*profile.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*profile.tsv": + type: file + description: profile tsv file + pattern: "*profile.tsv" - labelled_tree: - type: file - description: labelled tree in newick format - pattern: "*labelled_tree.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*labelled_tree.newick": + type: file + description: labelled tree in newick format + pattern: "*labelled_tree.newick" - per_query: - type: file - description: per query taxonomy assignments in tsv format - pattern: "*per_query.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*per_query.tsv": + type: file + description: per query taxonomy assignments in tsv format + pattern: "*per_query.tsv" + - krona: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*krona.profile": + type: file + description: krona profile file + pattern: "*krona.profile" + - sativa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*sativa.tsv": + type: file + description: sativa output file + pattern: "*sativa.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gappa/examinegraft/meta.yml b/modules/nf-core/gappa/examinegraft/meta.yml index 195c3e440473..f24b732e01c0 100644 --- a/modules/nf-core/gappa/examinegraft/meta.yml +++ b/modules/nf-core/gappa/examinegraft/meta.yml @@ -12,30 +12,34 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - newick: - type: file - description: phylogenetic tree file in newick format - pattern: "*.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.newick": + type: file + description: phylogenetic tree file in newick format + pattern: "*.newick" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gappa/examineheattree/meta.yml b/modules/nf-core/gappa/examineheattree/meta.yml index 4e59d029e784..2e533d367649 100644 --- a/modules/nf-core/gappa/examineheattree/meta.yml +++ b/modules/nf-core/gappa/examineheattree/meta.yml @@ -13,50 +13,84 @@ tools: tool_dev_url: "https://github.com/lczech/gappa" doi: "10.1093/bioinformatics/btaa070" licence: ["GPL v3"] + identifier: biotools:GAPPA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - jplace: - type: file - description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped or not - pattern: "*.{jplace,jplace.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - jplace: + type: file + description: jplace file output from phylogenetic placement, e.g. EPA-NG, gzipped + or not + pattern: "*.{jplace,jplace.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - newick: - type: file - description: phylogenetic tree file in newick format - pattern: "*.newick" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.newick": + type: file + description: phylogenetic tree file in newick format + pattern: "*.newick" - nexus: - type: file - description: coloured phylogenetic tree file in nexus format - pattern: "*.nexus" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.nexus": + type: file + description: coloured phylogenetic tree file in nexus format + pattern: "*.nexus" - phyloxml: - type: file - description: coloured phylogenetic tree file in phyloxml format - pattern: "*.phyloxml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.phyloxml": + type: file + description: coloured phylogenetic tree file in phyloxml format + pattern: "*.phyloxml" - svg: - type: file - description: coloured phylogenetic tree file in svg format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svg": + type: file + description: coloured phylogenetic tree file in svg format + pattern: "*.svg" - colours: - type: file - description: colours used in plot - pattern: "*.colours.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.colours.txt": + type: file + description: colours used in plot + pattern: "*.colours.txt" - log: - type: file - description: log file from the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: log file from the run + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/gatk/indelrealigner/meta.yml b/modules/nf-core/gatk/indelrealigner/meta.yml index 31806e175f00..75639de1b63c 100644 --- a/modules/nf-core/gatk/indelrealigner/meta.yml +++ b/modules/nf-core/gatk/indelrealigner/meta.yml @@ -17,78 +17,81 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - intervals: - type: file - description: Intervals file created by gatk3 RealignerTargetCreator - pattern: "*.{intervals,list}" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing file meta-information for known_vcf. - e.g. [ id:'test', single_end:false ] - - known_vcf: - type: file - description: Optional input VCF file(s) with known indels - pattern: ".vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - intervals: + type: file + description: Intervals file created by gatk3 RealignerTargetCreator + pattern: "*.{intervals,list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] + - known_vcf: + type: file + description: Optional input VCF file(s) with known indels + pattern: ".vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted and indexed BAM file with local realignment around variants - pattern: "*.bam" - - bai: - type: file - description: Output BAM Index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted and indexed BAM file with local realignment around variants + pattern: "*.bam" + - "*.bai": + type: file + description: Sorted and indexed BAM file with local realignment around variants + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gatk/realignertargetcreator/meta.yml b/modules/nf-core/gatk/realignertargetcreator/meta.yml index 038b0007274d..789f0b2bf69e 100644 --- a/modules/nf-core/gatk/realignertargetcreator/meta.yml +++ b/modules/nf-core/gatk/realignertargetcreator/meta.yml @@ -1,5 +1,6 @@ name: "gatk_realignertargetcreator" -description: Generates a list of locations that should be considered for local realignment prior genotyping. +description: Generates a list of locations that should be considered for local realignment + prior genotyping. keywords: - bam - vcf @@ -18,70 +19,79 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing file meta-information for known_vcf. - e.g. [ id:'test', single_end:false ] - - known_vcf: - type: file - description: Optional input VCF file(s) with known indels - pattern: ".vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing file meta-information for known_vcf. + e.g. [ id:'test', single_end:false ] + - known_vcf: + type: file + description: Optional input VCF file(s) with known indels + pattern: ".vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - intervals: - type: file - description: File containg intervals that represent sites of extant and potential indels. - pattern: "*.intervals" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.intervals": + type: file + description: File containg intervals that represent sites of extant and potential + indels. + pattern: "*.intervals" + - s: + type: file + description: File containg intervals that represent sites of extant and potential + indels. + pattern: "*.intervals" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gatk/unifiedgenotyper/meta.yml b/modules/nf-core/gatk/unifiedgenotyper/meta.yml index 95ac33375ddb..27b95a0aaa49 100644 --- a/modules/nf-core/gatk/unifiedgenotyper/meta.yml +++ b/modules/nf-core/gatk/unifiedgenotyper/meta.yml @@ -15,97 +15,101 @@ tools: "BSD", "https://www.broadinstitute.org/gatk/about/#licensing", ] + identifier: biotools:gatk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted and indexed BAM/CRAM/SAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference file used to generate BAM file - pattern: ".{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of reference file used to generate BAM file - pattern: ".fai" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: GATK dict file for reference - pattern: ".dict" - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - pattern: "*.intervals" - - meta6: - type: map - description: | - Groovy Map containing file meta-information for the contamination file. - e.g. [ id:'test', single_end:false ] - - contamination: - type: file - description: Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove - pattern: "*" - - meta7: - type: map - description: | - Groovy Map containing file meta-information for the dbsnps file. - e.g. [ id:'test', single_end:false ] - - dbsnp: - type: file - description: VCF file containing known sites (optional) - pattern: "*" - - meta8: - type: map - description: | - Groovy Map containing file meta-information for the VCF comparison file. - e.g. [ id:'test', single_end:false ] - - comp: - type: file - description: Comparison VCF file (optional) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted and indexed BAM/CRAM/SAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file used to generate BAM file + pattern: ".{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference file used to generate BAM file + pattern: ".fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: GATK dict file for reference + pattern: ".dict" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + pattern: "*.intervals" + - - meta6: + type: map + description: | + Groovy Map containing file meta-information for the contamination file. + e.g. [ id:'test', single_end:false ] + - contamination: + type: file + description: Tab-separated file containing fraction of contamination in sequencing + data (per sample) to aggressively remove + pattern: "*" + - - meta7: + type: map + description: | + Groovy Map containing file meta-information for the dbsnps file. + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + pattern: "*" + - - meta8: + type: map + description: | + Groovy Map containing file meta-information for the VCF comparison file. + e.g. [ id:'test', single_end:false ] + - comp: + type: file + description: Comparison VCF file (optional) + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file containing called variants - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file containing called variants + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ilight1542" - "@jfy133" diff --git a/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml index d78081d5db9f..2f1f022320e1 100644 --- a/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/gatk4/addorreplacereadgroups/meta.yml @@ -16,56 +16,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/gatk4/annotateintervals/meta.yml b/modules/nf-core/gatk4/annotateintervals/meta.yml index 1c8e77ff1382..ee644c97b1d4 100644 --- a/modules/nf-core/gatk4/annotateintervals/meta.yml +++ b/modules/nf-core/gatk4/annotateintervals/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_annotateintervals" -description: Annotates intervals with GC content, mappability, and segmental-duplication content +description: Annotates intervals with GC content, mappability, and segmental-duplication + content keywords: - annotateintervals - annotation @@ -16,95 +17,105 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: One or more interval files to annotate - pattern: "*.{interval_list,list,bed}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: The sequence dictionary reference FASTA file - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - mappable_regions: - type: file - description: | - Optional - Umap single-read mappability track - The track should correspond to the appropriate read length and overlapping intervals must be merged - pattern: "*.bed(.gz)?" - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - mappable_regions_tbi: - type: file - description: Optional - The index of the gzipped umap single-read mappability track - pattern: "*.bed.gz.tbi" - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - segmental_duplication_regions: - type: file - description: Optional - Segmental-duplication track - pattern: "*.bed(.gz)?" - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - segmental_duplication_regions_tbi: - type: file - description: Optional - The index of the gzipped segmental-duplication track - pattern: "*.bed.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: One or more interval files to annotate + pattern: "*.{interval_list,list,bed}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: The sequence dictionary reference FASTA file + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - mappable_regions: + type: file + description: | + Optional - Umap single-read mappability track + The track should correspond to the appropriate read length and overlapping intervals must be merged + pattern: "*.bed(.gz)?" + - - meta6: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - mappable_regions_tbi: + type: file + description: Optional - The index of the gzipped umap single-read mappability + track + pattern: "*.bed.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - segmental_duplication_regions: + type: file + description: Optional - Segmental-duplication track + pattern: "*.bed(.gz)?" + - - meta8: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - segmental_duplication_regions_tbi: + type: file + description: Optional - The index of the gzipped segmental-duplication track + pattern: "*.bed.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotated_intervals: - type: file - description: The output TSV file with a SAM-style header containing the annotated intervals - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output TSV file with a SAM-style header containing the annotated + intervals + pattern: "*.tsv" + - s: + type: file + description: The output TSV file with a SAM-style header containing the annotated + intervals + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/applybqsr/meta.yml b/modules/nf-core/gatk4/applybqsr/meta.yml index ab9efea3f4b9..65d9c9e9a893 100644 --- a/modules/nf-core/gatk4/applybqsr/meta.yml +++ b/modules/nf-core/gatk4/applybqsr/meta.yml @@ -16,56 +16,65 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Recalibrated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Recalibrated CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/applyvqsr/meta.yml b/modules/nf-core/gatk4/applyvqsr/meta.yml index de5d6d067af9..ceedff621ed8 100644 --- a/modules/nf-core/gatk4/applyvqsr/meta.yml +++ b/modules/nf-core/gatk4/applyvqsr/meta.yml @@ -19,57 +19,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: file - description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator. - pattern: "*.vcf" - - vcf_tbi: - type: file - description: tabix index for the input vcf file. - pattern: "*.vcf.tbi" - - recal: - type: file - description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: "*.recal" - - recal_index: - type: file - description: Index file for the recalibration file. - pattern: ".recal.idx" - - tranches: - type: file - description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: ".tranches" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to be recalibrated, this should be the same file as used + for the first stage VariantRecalibrator. + pattern: "*.vcf" + - vcf_tbi: + type: file + description: tabix index for the input vcf file. + pattern: "*.vcf.tbi" + - recal: + type: file + description: Recalibration file produced when the input vcf was run through + VariantRecalibrator in stage 1. + pattern: "*.recal" + - recal_index: + type: file + description: Index file for the recalibration file. + pattern: ".recal.idx" + - tranches: + type: file + description: Tranches file produced when the input vcf was run through VariantRecalibrator + in stage 1. + pattern: ".tranches" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: compressed vcf file containing the recalibrated variants. - pattern: "*.vcf.gz" + - meta: + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of recalibrated vcf file. - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/asereadcounter/meta.yml b/modules/nf-core/gatk4/asereadcounter/meta.yml index 1adfaa813aed..799f9cbed940 100644 --- a/modules/nf-core/gatk4/asereadcounter/meta.yml +++ b/modules/nf-core/gatk4/asereadcounter/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_asereadcounter" -description: Calculates the allele-specific read counts for alle-specific expression analysis of RNAseq data +description: Calculates the allele-specific read counts for alle-specific expression + analysis of RNAseq data keywords: - allele-specific - asereadcounter @@ -15,72 +16,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: index file for input file - pattern: "*.{bai,crai}" - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" - - tbi: - type: file - description: index file for VCF file - pattern: "*.{vcf.gz.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - fasta: - type: file - description: fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - fai: - type: file - description: fasta index file - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - dict: - type: file - description: dictionary file - pattern: "*.{dict}" - - intervals: - type: file - description: interval file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: index file for BAM file + pattern: "*.{bai}" + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: index file for VCF file + pattern: "*.{vcf.gz.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - fasta: + type: file + description: fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - fai: + type: file + description: fasta index file + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - dict: + type: file + description: dictionary file + pattern: "*.{dict}" + - - intervals: + type: file + description: interval file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: output file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/gatk4/baserecalibrator/meta.yml b/modules/nf-core/gatk4/baserecalibrator/meta.yml index 8252b8c290dd..876b79603988 100644 --- a/modules/nf-core/gatk4/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4/baserecalibrator/meta.yml @@ -16,57 +16,60 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Recalibration table from BaseRecalibrator - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Recalibration table from BaseRecalibrator + pattern: "*.{table}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/bedtointervallist/meta.yml b/modules/nf-core/gatk4/bedtointervallist/meta.yml index 187da8850c7b..25348e16214a 100644 --- a/modules/nf-core/gatk4/bedtointervallist/meta.yml +++ b/modules/nf-core/gatk4/bedtointervallist/meta.yml @@ -15,34 +15,45 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bed: - type: file - description: Input bed file - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bed: + type: file + description: Input bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary + pattern: "*.dict" output: - interval_list: - type: file - description: gatk interval list file - pattern: "*.interval_list" + - meta: + type: file + description: gatk interval list file + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: gatk interval list file + pattern: "*.interval_list" + - _list: + type: file + description: gatk interval list file + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/calculatecontamination/meta.yml b/modules/nf-core/gatk4/calculatecontamination/meta.yml index b0ffe814c54b..ee90a4825299 100644 --- a/modules/nf-core/gatk4/calculatecontamination/meta.yml +++ b/modules/nf-core/gatk4/calculatecontamination/meta.yml @@ -17,33 +17,50 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - pileup: - type: file - description: File containing the pileups summary table of a tumor sample to be used to calculate contamination. - pattern: "*.pileups.table" - - matched: - type: file - description: File containing the pileups summary table of a normal sample that matches with the tumor sample specified in pileup argument. This is an optional input. - pattern: "*.pileups.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - pileup: + type: file + description: File containing the pileups summary table of a tumor sample to + be used to calculate contamination. + pattern: "*.pileups.table" + - matched: + type: file + description: File containing the pileups summary table of a normal sample that + matches with the tumor sample specified in pileup argument. This is an optional + input. + pattern: "*.pileups.table" output: - contamination: - type: file - description: File containing the contamination table. - pattern: "*.contamination.table" + - meta: + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" + - "*.contamination.table": + type: file + description: File containing the contamination table. + pattern: "*.contamination.table" - segmentation: - type: file - description: output table containing segmentation of tumor minor allele fractions (optional) - pattern: "*.segmentation.table" + - meta: + type: file + description: output table containing segmentation of tumor minor allele fractions + (optional) + pattern: "*.segmentation.table" + - "*.segmentation.table": + type: file + description: output table containing segmentation of tumor minor allele fractions + (optional) + pattern: "*.segmentation.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml b/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml index bf2ca2d7389f..cc19131b70b4 100644 --- a/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml +++ b/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml @@ -8,62 +8,65 @@ keywords: - calibratedragstrmodel tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360057441571-CalibrateDragstrModel-BETA- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bam_index: - type: file - description: index of the BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: BED file or interval list containing regions (optional) - pattern: "*.{bed,interval_list}" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: The sequence dictionary of the reference FASTA file - pattern: "*.dict" - - strtablefile: - type: file - description: The StrTableFile zip folder of the reference FASTA file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bam_index: + type: file + description: index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - dict: + type: file + description: The sequence dictionary of the reference FASTA file + pattern: "*.dict" + - - strtablefile: + type: file + description: The StrTableFile zip folder of the reference FASTA file + pattern: "*.zip" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - dragstr_model: - type: file - description: The DragSTR model - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The DragSTR model + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/cnnscorevariants/meta.yml b/modules/nf-core/gatk4/cnnscorevariants/meta.yml index 8a9d0f51c2a9..b55c9d999537 100644 --- a/modules/nf-core/gatk4/cnnscorevariants/meta.yml +++ b/modules/nf-core/gatk4/cnnscorevariants/meta.yml @@ -14,65 +14,74 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" - - aligned_input: - type: file - description: BAM/CRAM file from alignment (optional) - pattern: "*.{bam,cram}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - architecture: - type: file - description: Neural Net architecture configuration json file (optional) - pattern: "*.json" - - weights: - type: file - description: Keras model HD5 file with neural net weights. (optional) - pattern: "*.hd5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - aligned_input: + type: file + description: BAM/CRAM file from alignment (optional) + pattern: "*.{bam,cram}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - architecture: + type: file + description: Neural Net architecture configuration json file (optional) + pattern: "*.json" + - - weights: + type: file + description: Keras model HD5 file with neural net weights. (optional) + pattern: "*.hd5" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnn.vcf.gz": + type: file + description: Annotated VCF file + pattern: "*.vcf" - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cnn.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index 25fb8b8cf15d..cf8c7731d343 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_collectreadcounts" -description: Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. +description: Collects read counts at specified intervals. The count for each interval + is calculated by counting the number of read starts that lie in the interval. keywords: - collectreadcounts - bam @@ -7,75 +8,88 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: A file containing the specified intervals - pattern: "*.{bed,intervals}" - - fasta: - type: file - description: Optional - Reference FASTA - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Optional - Index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: Optional - Sequence dictionary of the reference FASTA file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - intervals: + type: file + description: A file containing the specified intervals + pattern: "*.{bed,intervals}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Optional - Reference FASTA + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: Optional - Index of the reference FASTA file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: Optional - Sequence dictionary of the reference FASTA file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hdf5: - type: file - description: The read counts in hdf5 format - pattern: "*.hdf5" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hdf5": + type: file + description: The read counts in hdf5 format + pattern: "*.hdf5" - tsv: - type: file - description: The read counts in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The read counts in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml index 264a58922d0f..2a8b6fc46433 100644 --- a/modules/nf-core/gatk4/collectsvevidence/meta.yml +++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml @@ -1,5 +1,8 @@ name: "gatk4_collectsvevidence" -description: Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. +description: Gathers paired-end and split read evidence files for use in the GATK-SV + pipeline. Output files are a file containing the location of and orientation of + read pairs marked as discordant, and a file containing the clipping location of + all soft clipped reads and the orientation of the clipping. keywords: - gatk4 - collectsvevidence @@ -12,74 +15,112 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: Index of the BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - site_depth_vcf: - type: file - description: Optional - input VCF of SNPs marking loci for site depths, needed for the site depths output - pattern: "*.vcf.gz" - - site_depth_vcf_index: - type: file - description: Optional - index of the VCF file, needed for the site depths output - pattern: "*.tbi" - - fasta: - type: file - description: Optional - reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Optional - index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - site_depth_vcf: + type: file + description: Optional - input VCF of SNPs marking loci for site depths, needed + for the site depths output + pattern: "*.vcf.gz" + - site_depth_vcf_tbi: + type: file + description: tbi index of the input VCF of SNPs marking loci for site + depths + pattern: "*.vcf.gz.tbi" + - - fasta: + type: file + description: Optional - reference FASTA file needed when the input is a CRAM + file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Optional - index of the reference FASTA file needed when the input + is a CRAM file + pattern: "*.fai" + - - dict: + type: file + description: Optional - sequence dictionary of the reference FASTA file needed + when the input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_read_evidence: - type: file - description: Output file for split read evidence - pattern: "*.sr.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sr.txt.gz": + type: file + description: Output file for split read evidence + pattern: "*.sr.txt.gz" - split_read_evidence_index: - type: file - description: Index of the output file for split read evidence - pattern: "*.sr.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sr.txt.gz.tbi": + type: file + description: Index of the output file for split read evidence + pattern: "*.sr.txt.gz.tbi" - paired_end_evidence: - type: file - description: Output file for paired end evidence - pattern: "*.pe.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pe.txt.gz": + type: file + description: Output file for paired end evidence + pattern: "*.pe.txt.gz" - paired_end_evidence_index: - type: file - description: Index of the output file for paired end evidence - pattern: "*.pe.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pe.txt.gz.tbi": + type: file + description: Index of the output file for paired end evidence + pattern: "*.pe.txt.gz.tbi" - site_depths: - type: file - description: Output file for site depths - pattern: "*.sd.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sd.txt.gz": + type: file + description: Output file for site depths + pattern: "*.sd.txt.gz" - site_depths_index: - type: file - description: Index of the output file for site depths - pattern: "*.sd.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sd.txt.gz.tbi": + type: file + description: Index of the output file for site depths + pattern: "*.sd.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/combinegvcfs/meta.yml b/modules/nf-core/gatk4/combinegvcfs/meta.yml index f13ddde7f6e8..c4fd646cf15b 100644 --- a/modules/nf-core/gatk4/combinegvcfs/meta.yml +++ b/modules/nf-core/gatk4/combinegvcfs/meta.yml @@ -1,5 +1,6 @@ name: gatk4_combinegvcfs -description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample gVCF file +description: Combine per-sample gVCF files produced by HaplotypeCaller into a multi-sample + gVCF file keywords: - gvcf - gatk4 @@ -8,47 +9,58 @@ keywords: - short variant discovery tools: - gatk4: - description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: Compressed VCF files - pattern: "*.vcf.gz" - - vcf_idx: - type: file - description: VCF Index file - pattern: "*.vcf.gz.idx" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: FASTA index file - pattern: "*.fasta.fai" - - dict: - type: file - description: FASTA dictionary file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: Compressed VCF files + pattern: "*.vcf.gz" + - vcf_idx: + type: file + description: VCF Index file + pattern: "*.vcf.gz.idx" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: FASTA index file + pattern: "*.fasta.fai" + - - dict: + type: file + description: FASTA dictionary file + pattern: "*.dict" output: - combined_gvcf: - type: file - description: Compressed Combined GVCF file - pattern: "*.combined.g.vcf.gz" + - meta: + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" + - "*.combined.g.vcf.gz": + type: file + description: Compressed Combined GVCF file + pattern: "*.combined.g.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/gatk4/composestrtablefile/meta.yml b/modules/nf-core/gatk4/composestrtablefile/meta.yml index 249aed2448e4..fd56c797cc80 100644 --- a/modules/nf-core/gatk4/composestrtablefile/meta.yml +++ b/modules/nf-core/gatk4/composestrtablefile/meta.yml @@ -1,5 +1,7 @@ name: "gatk4_composestrtablefile" -description: This tool looks for low-complexity STR sequences along the reference that are later used to estimate the Dragstr model during single sample auto calibration CalibrateDragstrModel. +description: This tool looks for low-complexity STR sequences along the reference + that are later used to estimate the Dragstr model during single sample auto calibration + CalibrateDragstrModel. keywords: - composestrtablefile - dragstr @@ -14,28 +16,31 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/4405451249819-ComposeSTRTableFile doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: index of the FASTA reference file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the FASTA reference file - pattern: "*.dict" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: index of the FASTA reference file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the FASTA reference file + pattern: "*.dict" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - str_table: - type: file - description: A zipped folder containing the STR table files - pattern: "*.zip" + - "*.zip": + type: file + description: A zipped folder containing the STR table files + pattern: "*.zip" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/condensedepthevidence/meta.yml b/modules/nf-core/gatk4/condensedepthevidence/meta.yml index dffb414bf461..b5c0207d83f7 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/meta.yml +++ b/modules/nf-core/gatk4/condensedepthevidence/meta.yml @@ -11,50 +11,61 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - depth_evidence: - type: file - description: The depth evidence file - pattern: "*.rd.txt.gz" - - depth_evidence_index: - type: file - description: The index of the depth evidence file - pattern: "*.rd.txt.gz.tbi" - - fasta: - type: file - description: Reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - depth_evidence: + type: file + description: The depth evidence file + pattern: "*.rd.txt.gz" + - depth_evidence_index: + type: file + description: The index of the depth evidence file + pattern: "*.rd.txt.gz.tbi" + - - fasta: + type: file + description: Reference FASTA file needed when the input is a CRAM file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference FASTA file needed when the input is a CRAM + file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the reference FASTA file needed when the + input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - condensed_evidence: - type: file - description: The condensed depth evidence - pattern: "*.rd.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rd.txt.gz": + type: file + description: The condensed depth evidence + pattern: "*.rd.txt.gz" - condensed_evidence_index: - type: file - description: The condensed depth evidence - pattern: "*.rd.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rd.txt.gz.tbi": + type: file + description: The condensed depth evidence + pattern: "*.rd.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml b/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml index ba01f630302f..cbbed8c0a157 100644 --- a/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml +++ b/modules/nf-core/gatk4/createreadcountpanelofnormals/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_createreadcountpanelofnormals" -description: Creates a panel of normals (PoN) for read-count denoising given the read counts for samples in the panel. +description: Creates a panel of normals (PoN) for read-count denoising given the read + counts for samples in the panel. keywords: - createreadcountpanelofnormals - gatk4 @@ -15,30 +16,33 @@ tools: doi: 10.1158/1538-7445.AM2017-3590 tool_dev_url: "https://github.com/broadinstitute/gatk" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - counts: - type: file - description: Read counts in hdf5 or tsv format. - pattern: "*.{hdf5,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - counts: + type: file + description: Read counts in hdf5 or tsv format. + pattern: "*.{hdf5,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pon: - type: file - description: Panel-of-normals file. - pattern: "*.{hdf5}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.hdf5": + type: file + description: Panel-of-normals file. + pattern: "*.{hdf5}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index f9d70be09826..7b5156bb3d4b 100644 --- a/modules/nf-core/gatk4/createsequencedictionary/meta.yml +++ b/modules/nf-core/gatk4/createsequencedictionary/meta.yml @@ -15,25 +15,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Input fasta file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Input fasta file + pattern: "*.{fasta,fa}" output: - dict: - type: file - description: gatk dictionary file - pattern: "*.{dict}" + - meta: + type: file + description: gatk dictionary file + pattern: "*.{dict}" + - "*.dict": + type: file + description: gatk dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml b/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml index 9c3ee192cc44..45d88c16a082 100644 --- a/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml +++ b/modules/nf-core/gatk4/createsomaticpanelofnormals/meta.yml @@ -1,5 +1,6 @@ name: gatk4_createsomaticpanelofnormals -description: Create a panel of normals contraining germline and artifactual sites for use with mutect2. +description: Create a panel of normals contraining germline and artifactual sites + for use with mutect2. keywords: - createsomaticpanelofnormals - gatk4 @@ -13,56 +14,67 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - genoomicsdb: - type: directory - description: genomicsDB workspace that contains the samples to create the somatic panel of normals with. - pattern: "*_genomicsDBworkspace" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - genomicsdb: + type: file + description: GenomicsDB database + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: panel of normal as compressed vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: panel of normal as compressed vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: panel of normal as compressed vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/denoisereadcounts/meta.yml b/modules/nf-core/gatk4/denoisereadcounts/meta.yml index f2bd853f52c1..367321ba2094 100644 --- a/modules/nf-core/gatk4/denoisereadcounts/meta.yml +++ b/modules/nf-core/gatk4/denoisereadcounts/meta.yml @@ -15,43 +15,52 @@ tools: doi: 10.1158/1538-7445.AM2017-3590 tool_dev_url: "https://github.com/broadinstitute/gatk" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - counts: - type: file - description: Read counts in hdf5 or tsv format. - pattern: "*.{hdf5,tsv}" - - pon: - type: file - description: Panel of normals file hdf5 or tsv format. - pattern: "*.{hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - counts: + type: file + description: Read counts in hdf5 or tsv format. + pattern: "*.{hdf5,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - pon: + type: file + description: Panel of normals file hdf5 or tsv format. + pattern: "*.{hdf5}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - standardized: - type: file - description: Standardized copy ratios file. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_standardizedCR.tsv": + type: file + description: Standardized copy ratios file. + pattern: "*.{tsv}" - denoised: - type: file - description: Denoised copy ratios file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_denoisedCR.tsv": + type: file + description: Denoised copy ratios file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 56eb40890646..828628b2834e 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_determinegermlinecontigploidy" -description: Determines the baseline contig ploidy for germline samples given counts data +description: Determines the baseline contig ploidy for germline samples given counts + data keywords: - copy number - counts @@ -15,59 +16,70 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - counts: - type: file - description: One or more count TSV files created with gatk/collectreadcounts - pattern: "*.tsv" - - bed: - type: file - description: Optional - A bed file containing the intervals to include in the process - pattern: "*.bed" - - exclude_beds: - type: file - description: Optional - One or more bed files containing intervals to exclude from the process - pattern: "*.bed" - - contig_ploidy_table: - type: file - description: The contig ploidy priors table - pattern: "*.tsv" - - ploidy_model: - type: directory - description: | - Optional - A folder containing the ploidy model. - When a model is supplied to tool will run in CASE mode. - pattern: '*-model/' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - counts: + type: file + description: One or more count TSV files created with gatk/collectreadcounts + pattern: "*.tsv" + - bed: + type: file + description: Optional - A bed file containing the intervals to include in the + process + pattern: "*.bed" + - exclude_beds: + type: file + description: Optional - One or more bed files containing intervals to exclude + from the process + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ploidy_model: + type: directory + description: | + Optional - A folder containing the ploidy model. + When a model is supplied to tool will run in CASE mode. + pattern: '*-model/' + - - contig_ploidy_table: + type: file + description: The contig ploidy priors table + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - calls: - type: directory - description: A folder containing the calls from the input files - pattern: "*-calls/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-calls: + type: directory + description: A folder containing the calls from the input files + pattern: "*-calls/" - model: - type: directory - description: | - A folder containing the model from the input files. - This will only be created in COHORT mode (when no model is supplied to the process). - pattern: "*-model/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-model: + type: directory + description: | + A folder containing the model from the input files. + This will only be created in COHORT mode (when no model is supplied to the process). + pattern: "*-model/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml index 2d5bddf6c9e2..4fb06a3a2e09 100644 --- a/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml +++ b/modules/nf-core/gatk4/estimatelibrarycomplexity/meta.yml @@ -13,42 +13,45 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: File containing metrics on the input files - pattern: "*.{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: File containing metrics on the input files + pattern: "*.{metrics}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/gatk4/fastqtosam/meta.yml b/modules/nf-core/gatk4/fastqtosam/meta.yml index 60658df00313..6d3e90786154 100644 --- a/modules/nf-core/gatk4/fastqtosam/meta.yml +++ b/modules/nf-core/gatk4/fastqtosam/meta.yml @@ -7,36 +7,44 @@ keywords: - gatk4 tools: - gatk4: - description: Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4) Developed in the Data Sciences Platform + at the Broad Institute, the toolkit offers a wide variety of tools with a primary + focus on variant discovery and genotyping. Its powerful processing engine and + high-performance computing features make it capable of taking on projects of + any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Converted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Converted BAM file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/gatk4/filterintervals/meta.yml b/modules/nf-core/gatk4/filterintervals/meta.yml index 425c0015a10f..87376ed6bcb5 100644 --- a/modules/nf-core/gatk4/filterintervals/meta.yml +++ b/modules/nf-core/gatk4/filterintervals/meta.yml @@ -6,53 +6,63 @@ keywords: - interval_list tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - intervals: - type: file - description: Processed interval list file (processed_intervals.interval_list) - pattern: "*.interval_list" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - read_counts: - type: file - description: Read counts input file - pattern: "*.{tsv, hdf5}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotated_intervals: - type: file - description: Annotated intervals TSV file (annotated_intervals.tsv). - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - intervals: + type: file + description: Processed interval list file (processed_intervals.interval_list) + pattern: "*.interval_list" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - read_counts: + type: file + description: Read counts input file + pattern: "*.{tsv, hdf5}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - annotated_intervals: + type: file + description: Annotated intervals TSV file (annotated_intervals.tsv). + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Filtered interval list file - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interval_list": + type: file + description: Filtered interval list file + pattern: "*.interval_list" + - _list: + type: file + description: Filtered interval list file + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/filtermutectcalls/meta.yml b/modules/nf-core/gatk4/filtermutectcalls/meta.yml index 736c83862559..9287277eb7ad 100644 --- a/modules/nf-core/gatk4/filtermutectcalls/meta.yml +++ b/modules/nf-core/gatk4/filtermutectcalls/meta.yml @@ -16,83 +16,103 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: compressed vcf file of mutect2calls - pattern: "*.vcf.gz" - - vcf_tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" - - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" - - orientationbias: - type: file - description: files containing artifact priors for input vcf. Optional input. - pattern: "*.artifact-prior.tar.gz" - - segmentation: - type: file - description: tables containing segmentation information for input vcf. Optional input. - pattern: "*.segmentation.table" - - table: - type: file - description: table(s) containing contamination data for input vcf. Optional input, takes priority over estimate. - pattern: "*.contamination.table" - - estimate: - type: float - description: estimation of contamination value as a double. Optional input, will only be used if table is not specified. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: compressed vcf file of mutect2calls + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - stats: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - orientationbias: + type: file + description: files containing artifact priors for input vcf. Optional input. + pattern: "*.artifact-prior.tar.gz" + - segmentation: + type: file + description: tables containing segmentation information for input vcf. Optional + input. + pattern: "*.segmentation.table" + - table: + type: file + description: table(s) containing contamination data for input vcf. Optional + input, takes priority over estimate. + pattern: "*.contamination.table" + - estimate: + type: float + description: estimation of contamination value as a double. Optional input, + will only be used if table is not specified. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - vcf: - type: file - description: file containing filtered mutect2 calls. - pattern: "*.vcf.gz" + - meta: + type: file + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: file containing filtered mutect2 calls. + pattern: "*.vcf.gz" - tbi: - type: file - description: tbi file that pairs with vcf. - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" + - "*.vcf.gz.tbi": + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" - stats: - type: file - description: file containing statistics of the filtermutectcalls run. - pattern: "*.filteringStats.tsv" + - meta: + type: file + description: file containing statistics of the filtermutectcalls run. + pattern: "*.filteringStats.tsv" + - "*.filteringStats.tsv": + type: file + description: file containing statistics of the filtermutectcalls run. + pattern: "*.filteringStats.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@maxulysse" diff --git a/modules/nf-core/gatk4/filtervarianttranches/meta.yml b/modules/nf-core/gatk4/filtervarianttranches/meta.yml index 9346d2b4a439..398bbb07c1d0 100644 --- a/modules/nf-core/gatk4/filtervarianttranches/meta.yml +++ b/modules/nf-core/gatk4/filtervarianttranches/meta.yml @@ -14,58 +14,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360051308071-FilterVariantTranches doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: a VCF file containing variants, must have info key:CNN_2D - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resources: - type: list - description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary - pattern: "*.vcf.gz" - - resources_index: - type: list - description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary - pattern: "*.vcf.gz" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: ".dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: a VCF file containing variants, must have info key:CNN_2D + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - intervals: + type: file + description: Intervals + - - resources: + type: list + description: resource A VCF containing known SNP and or INDEL sites. Can be + supplied as many times as necessary + pattern: "*.vcf.gz" + - - resources_index: + type: list + description: Index of resource VCF containing known SNP and or INDEL sites. + Can be supplied as many times as necessary + pattern: "*.vcf.gz" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: ".dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: VCF index file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml index b9f5bf5f8bab..587175b3a434 100644 --- a/modules/nf-core/gatk4/gatherbqsrreports/meta.yml +++ b/modules/nf-core/gatk4/gatherbqsrreports/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - table: - type: file - description: File(s) containing BQSR table(s) - pattern: "*.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - table: + type: file + description: File(s) containing BQSR table(s) + pattern: "*.table" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - table: - type: file - description: File containing joined BQSR table - pattern: "*.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: File containing joined BQSR table + pattern: "*.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml index 35381a3b5145..d8b29d210068 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/gatherpileupsummaries/meta.yml @@ -12,30 +12,36 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pileup: - type: file - description: Pileup files from gatk4/getpileupsummaries - pattern: "*.pileups.table" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pileup: + type: file + description: Pileup files from gatk4/getpileupsummaries + pattern: "*.pileups.table" + - - dict: + type: file + description: dictionary output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - table: - type: file - description: pileup summaries table file - pattern: "*.pileups.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pileups.table": + type: file + description: pileup summaries table file + pattern: "*.pileups.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/gatk4/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml index 11e565b1046d..174ae2eb0a88 100644 --- a/modules/nf-core/gatk4/genomicsdbimport/meta.yml +++ b/modules/nf-core/gatk4/genomicsdbimport/meta.yml @@ -1,5 +1,6 @@ name: gatk4_genomicsdbimport -description: merge GVCFs from multiple samples. For use in joint genotyping or somatic panel of normal creation. +description: merge GVCFs from multiple samples. For use in joint genotyping or somatic + panel of normal creation. keywords: - gatk4 - genomicsdb @@ -15,61 +16,99 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: either a list of vcf files to be used to create or update a genomicsdb, or a file that contains a map to vcf files to be used. - pattern: "*.vcf.gz" - - tbi: - type: list - description: list of tbi files that match with the input vcf files - pattern: "*.vcf.gz_tbi" - - wspace: - type: file - description: path to an existing genomicsdb to be used in update db mode or get intervals mode. This WILL NOT specify name of a new genomicsdb in create db mode. - pattern: "/path/to/existing/gendb" - - interval_file: - type: file - description: file containing the intervals to be used when creating the genomicsdb - pattern: "*.interval_list" - - interval_value: - type: string - description: if an intervals file has not been spcified, the value enetered here will be used as an interval via the "-L" argument - pattern: "example: chr1:1000-10000" - - run_intlist: - type: boolean - description: Specify whether to run get interval list mode, this option cannot be specified at the same time as run_updatewspace. - pattern: "true/false" - - run_updatewspace: - type: boolean - description: Specify whether to run update genomicsdb mode, this option takes priority over run_intlist. - pattern: "true/false" - - input_map: - type: boolean - description: Specify whether the vcf input is providing a list of vcf file(s) or a single file containing a map of paths to vcf files to be used to create or update a genomicsdb. - pattern: "*.sample_map" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: either a list of vcf files to be used to create or update a genomicsdb, + or a file that contains a map to vcf files to be used. + pattern: "*.vcf.gz" + - tbi: + type: list + description: list of tbi files that match with the input vcf files + pattern: "*.vcf.gz_tbi" + - interval_file: + type: file + description: file containing the intervals to be used when creating the genomicsdb + pattern: "*.interval_list" + - interval_value: + type: string + description: if an intervals file has not been spcified, the value enetered + here will be used as an interval via the "-L" argument + pattern: "example: chr1:1000-10000" + - wspace: + type: file + description: path to an existing genomicsdb to be used in update db mode or + get intervals mode. This WILL NOT specify name of a new genomicsdb in create + db mode. + pattern: "/path/to/existing/gendb" + - - run_intlist: + type: boolean + description: Specify whether to run get interval list mode, this option cannot + be specified at the same time as run_updatewspace. + pattern: "true/false" + - - run_updatewspace: + type: boolean + description: Specify whether to run update genomicsdb mode, this option takes + priority over run_intlist. + pattern: "true/false" + - - input_map: + type: boolean + description: Specify whether the vcf input is providing a list of vcf file(s) + or a single file containing a map of paths to vcf files to be used to create + or update a genomicsdb. + pattern: "*.sample_map" output: - genomicsdb: - type: directory - description: Directory containing the files that compose the genomicsdb workspace, this is only output for create mode, as update changes an existing db - pattern: "*/$prefix" + - meta: + type: directory + description: Directory containing the files that compose the genomicsdb workspace, + this is only output for create mode, as update changes an existing db + pattern: "*/$prefix" + - $prefix: + type: directory + description: Directory containing the files that compose the genomicsdb workspace, + this is only output for create mode, as update changes an existing db + pattern: "*/$prefix" - updatedb: - type: directory - description: Directory containing the files that compose the updated genomicsdb workspace, this is only output for update mode, and should be the same path as the input wspace. - pattern: "same/path/as/wspace" + - meta: + type: directory + description: Directory containing the files that compose the updated genomicsdb + workspace, this is only output for update mode, and should be the same path + as the input wspace. + pattern: "same/path/as/wspace" + - $updated_db: + type: directory + description: Directory containing the files that compose the updated genomicsdb + workspace, this is only output for update mode, and should be the same path + as the input wspace. + pattern: "same/path/as/wspace" - intervallist: - type: file - description: File containing the intervals used to generate the genomicsdb, only created by get intervals mode. - pattern: "*.interval_list" + - meta: + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" + - list: + type: file + description: File containing the intervals used to generate the genomicsdb, + only created by get intervals mode. + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/genotypegvcfs/meta.yml b/modules/nf-core/gatk4/genotypegvcfs/meta.yml index eb704364b483..0c1fe491fe03 100644 --- a/modules/nf-core/gatk4/genotypegvcfs/meta.yml +++ b/modules/nf-core/gatk4/genotypegvcfs/meta.yml @@ -14,91 +14,101 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - gVCF(.gz) file or a GenomicsDB - pattern: "*.{vcf,vcf.gz}" - - gvcf_index: - type: file - description: | - index of gvcf file, or empty when providing GenomicsDB - pattern: "*.{idx,tbi}" - - intervals: - type: file - description: Interval file with the genomic regions included in the library (optional) - - intervals_index: - type: file - description: Interval index file (optional) - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing fai information - e.g. [ id:'test' ] - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing dict information - e.g. [ id:'test' ] - - dict: - type: file - description: Reference fasta sequence dict file - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test' ] - - dbsnp: - type: file - description: dbSNP VCF file - pattern: "*.vcf.gz" - - meta6: - type: map - description: | - Groovy Map containing dbsnp tbi information - e.g. [ id:'test' ] - - dbsnp_tbi: - type: file - description: dbSNP VCF index file - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + gVCF(.gz) file or a GenomicsDB + pattern: "*.{vcf,vcf.gz}" + - gvcf_index: + type: file + description: | + index of gvcf file, or empty when providing GenomicsDB + pattern: "*.{idx,tbi}" + - intervals: + type: file + description: Interval file with the genomic regions included in the library + (optional) + - intervals_index: + type: file + description: Interval index file (optional) + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test' ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing dict information + e.g. [ id:'test' ] + - dict: + type: file + description: Reference fasta sequence dict file + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test' ] + - dbsnp: + type: file + description: dbSNP VCF file + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing dbsnp tbi information + e.g. [ id:'test' ] + - dbsnp_tbi: + type: file + description: dbSNP VCF index file + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Genotyped VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Genotyped VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Tbi index for VCF file + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@santiagorevale" - "@maxulysse" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml index d4715ff0f77d..a185d9d1091d 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml @@ -1,60 +1,85 @@ name: "gatk4_germlinecnvcaller" -description: Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy. +description: Calls copy-number variants in germline samples given their counts and + the output of DetermineGermlineContigPloidy. keywords: - gatk - germline contig ploidy - germlinecnvcaller tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: One or more count TSV files created with gatk/collectreadcounts - pattern: "*.tsv" - - intervals: - type: file - description: Optional - A bed file containing the intervals to include in the process - pattern: "*.bed" - - model: - type: directory - description: Optional - directory containing the model produced by germlinecnvcaller cohort mode - pattern: "*-cnv-model/*-model" - - ploidy: - type: directory - description: Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode - pattern: "*-calls" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tsv: + type: file + description: One or more count TSV files created with gatk/collectreadcounts + pattern: "*.tsv" + - intervals: + type: file + description: Optional - A bed file containing the intervals to include in the + process + pattern: "*.bed" + - ploidy: + type: directory + description: Directory containing ploidy calls produced by determinegermlinecontigploidy + case or cohort mode + pattern: "*-calls" + - model: + type: directory + description: Optional - directory containing the model produced by germlinecnvcaller + cohort mode + pattern: "*-cnv-model/*-model" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cohortcalls: - type: directory - description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode - pattern: "*-cnv-model/*-calls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-model/*-calls": + type: directory + description: Tar gzipped directory containing calls produced by germlinecnvcaller + case mode + pattern: "*-cnv-model/*-calls" - cohortmodel: - type: directory - description: Optional - Tar gzipped directory containing the model produced by germlinecnvcaller cohort mode - pattern: "*-cnv-model/*-model" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-model/*-model": + type: directory + description: Optional - Tar gzipped directory containing the model produced + by germlinecnvcaller cohort mode + pattern: "*-cnv-model/*-model" - casecalls: - type: directory - description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode - pattern: "*-cnv-calls/*-calls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cnv-calls/*-calls": + type: directory + description: Tar gzipped directory containing calls produced by germlinecnvcaller + case mode + pattern: "*-cnv-calls/*-calls" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/getpileupsummaries/meta.yml b/modules/nf-core/gatk4/getpileupsummaries/meta.yml index fab3c1435e5a..86b851e13a47 100644 --- a/modules/nf-core/gatk4/getpileupsummaries/meta.yml +++ b/modules/nf-core/gatk4/getpileupsummaries/meta.yml @@ -16,68 +16,78 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file to be summarised. - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM file index. - pattern: "*.{bai,crai}" - - intervals: - type: file - description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. - pattern: "*.interval_list" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - variants: - type: file - description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. - pattern: "*.vcf.gz" - - variants_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: BAM/CRAM file to be summarised. + pattern: "*.{bam,cram}" + - index: + type: file + description: Index file for the input BAM/CRAM file. + pattern: "*.{bam.bai,cram.crai}" + - intervals: + type: file + description: File containing specified sites to be used for the summary. If + this option is not specified, variants file is used instead automatically. + pattern: "*.interval_list" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - variants: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + Is also used as sites file if no separate sites file is specified. + pattern: "*.vcf.gz" + - - variants_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" output: - - pileup: - type: file - description: File containing the pileup summary table. - pattern: "*.pileups.table" + - table: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.pileups.table": + type: file + description: Table containing read counts for each site. + pattern: "*.pileups.table" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 703b99a09850..9d4a05e9144d 100644 --- a/modules/nf-core/gatk4/haplotypecaller/meta.yml +++ b/modules/nf-core/gatk4/haplotypecaller/meta.yml @@ -14,92 +14,108 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - dragstr_model: - type: file - description: Text file containing the DragSTR model of the used BAM/CRAM file (optional) - pattern: "*.txt" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - meta6: - type: map - description: | - Groovy Map containing dbsnp information - e.g. [ id:'test_dbsnp' ] - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - dragstr_model: + type: file + description: Text file containing the DragSTR model of the used BAM/CRAM file + (optional) + pattern: "*.txt" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - meta6: + type: map + description: | + Groovy Map containing dbsnp information + e.g. [ id:'test_dbsnp' ] + - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - bam: - type: file - description: Assembled haplotypes and locally realigned reads - pattern: "*.realigned.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.realigned.bam": + type: file + description: Assembled haplotypes and locally realigned reads + pattern: "*.realigned.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/indexfeaturefile/meta.yml b/modules/nf-core/gatk4/indexfeaturefile/meta.yml index 575c6038b3f6..cfc717d227bb 100644 --- a/modules/nf-core/gatk4/indexfeaturefile/meta.yml +++ b/modules/nf-core/gatk4/indexfeaturefile/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - feature_file: - type: file - description: VCF/BED file - pattern: "*.{vcf,vcf.gz,bed,bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - feature_file: + type: file + description: VCF/BED file + pattern: "*.{vcf,vcf.gz,bed,bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Index for VCF/BED file - pattern: "*.{tbi,idx}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tbi,idx}": + type: file + description: Index for VCF/BED file + pattern: "*.{tbi,idx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@santiagorevale" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttobed/meta.yml b/modules/nf-core/gatk4/intervallisttobed/meta.yml index 28d264dfef57..0779fa182234 100644 --- a/modules/nf-core/gatk4/intervallisttobed/meta.yml +++ b/modules/nf-core/gatk4/intervallisttobed/meta.yml @@ -13,30 +13,32 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - interval: - type: file - description: Interval list - pattern: "*.{interval,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: IntervalList file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/intervallisttools/meta.yml b/modules/nf-core/gatk4/intervallisttools/meta.yml index 748dccfc56b5..8ee15a2975f5 100644 --- a/modules/nf-core/gatk4/intervallisttools/meta.yml +++ b/modules/nf-core/gatk4/intervallisttools/meta.yml @@ -1,5 +1,6 @@ name: gatk4_intervallisttools -description: Splits the interval list file into unique, equally-sized interval files and place it under a directory +description: Splits the interval list file into unique, equally-sized interval files + and place it under a directory keywords: - bed - gatk4 @@ -15,30 +16,36 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - interval_list: - type: file - description: Interval list file - pattern: "*.interval_list" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: Interval file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Interval list files - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_split/*/*.interval_list": + type: file + description: Interval list files + pattern: "*.interval_list" + - _list: + type: file + description: Interval list files + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@praveenraj2018" maintainers: diff --git a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml index 4b73a51adbaf..fde7829c8d9e 100644 --- a/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml +++ b/modules/nf-core/gatk4/learnreadorientationmodel/meta.yml @@ -16,25 +16,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - f1r2: - type: list - description: list of f1r2 files to be used as input. - pattern: "*.f1r2.tar.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - f1r2: + type: list + description: list of f1r2 files to be used as input. + pattern: "*.f1r2.tar.gz" output: - artifactprior: - type: file - description: file containing artifact-priors to be used by filtermutectcalls - pattern: "*.tar.gz" + - meta: + type: file + description: file containing artifact-priors to be used by filtermutectcalls + pattern: "*.tar.gz" + - "*.tar.gz": + type: file + description: file containing artifact-priors to be used by filtermutectcalls + pattern: "*.tar.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" maintainers: diff --git a/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml b/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml index ace4d5031e74..176cc902f25a 100644 --- a/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml +++ b/modules/nf-core/gatk4/leftalignandtrimvariants/meta.yml @@ -16,55 +16,64 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be normalized - e.g. 'file1.vcf.gz' - - tbi: - type: file - description: | - Index of the vcf file to be normalized - e.g. 'file1.vcf.gz.tbi' - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be normalized + e.g. 'file1.vcf.gz' + - tbi: + type: file + description: | + Index of the vcf file to be normalized + e.g. 'file1.vcf.gz.tbi' + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Tbi index for VCF file + pattern: "*.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/gatk4/markduplicates/environment.yml b/modules/nf-core/gatk4/markduplicates/environment.yml index 9fe34eb36c88..3c73c17e4334 100644 --- a/modules/nf-core/gatk4/markduplicates/environment.yml +++ b/modules/nf-core/gatk4/markduplicates/environment.yml @@ -1,7 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - bioconda::gatk4=4.5.0.0 - - bioconda::samtools=1.19.2 - bioconda::htslib=1.19.1 + - bioconda::samtools=1.19.2 diff --git a/modules/nf-core/gatk4/markduplicates/meta.yml b/modules/nf-core/gatk4/markduplicates/meta.yml index b0f09d4b843d..4772c5f39aa0 100644 --- a/modules/nf-core/gatk4/markduplicates/meta.yml +++ b/modules/nf-core/gatk4/markduplicates/meta.yml @@ -1,5 +1,6 @@ name: gatk4_markduplicates -description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. +description: This tool locates and tags duplicate reads in a BAM or SAM file, where + duplicate reads are defined as originating from a single fragment of DNA. keywords: - bam - gatk4 @@ -7,60 +8,90 @@ keywords: - sort tools: - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta}" - - fasta_fai: - type: file - description: Fasta index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: Fasta file + pattern: "*.{fasta}" + - - fasta_fai: + type: file + description: Fasta index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Marked duplicates BAM file - pattern: "*.{bam}" - cram: - type: file - description: Marked duplicates CRAM file - pattern: "*.{cram}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*cram": + type: file + description: Marked duplicates CRAM file + pattern: "*.{cram}" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*bam": + type: file + description: Marked duplicates BAM file + pattern: "*.{bam}" - crai: - type: file - description: CRAM index file - pattern: "*.{cram.crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file + pattern: "*.{cram.crai}" + - bai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM index file + pattern: "*.{bam.bai}" - metrics: - type: file - description: Duplicate metrics file generated by GATK - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Duplicate metrics file generated by GATK + pattern: "*.{metrics.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ajodeh-juma" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4/mergebamalignment/meta.yml b/modules/nf-core/gatk4/mergebamalignment/meta.yml index af4a3f18b0a3..7bde9345947b 100644 --- a/modules/nf-core/gatk4/mergebamalignment/meta.yml +++ b/modules/nf-core/gatk4/mergebamalignment/meta.yml @@ -16,45 +16,52 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - aligned: - type: file - description: The aligned bam file - pattern: "*.{bam}" - - unaligned: - type: file - description: The unmaped bam file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - aligned: + type: file + description: The aligned bam file + pattern: "*.{bam}" + - unmapped: + type: file + description: The unmapped bam file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary output: - bam: - type: file - description: The merged bam file - pattern: "*.bam" + - meta: + type: file + description: The merged bam file + pattern: "*.bam" + - "*.bam": + type: file + description: The merged bam file + pattern: "*.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/mergemutectstats/meta.yml b/modules/nf-core/gatk4/mergemutectstats/meta.yml index 126952565763..09c8a5472091 100644 --- a/modules/nf-core/gatk4/mergemutectstats/meta.yml +++ b/modules/nf-core/gatk4/mergemutectstats/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Stats file - pattern: "*.{stats}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: + type: file + description: Stats file + pattern: "*.{stats}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Stats file - pattern: "*.vcf.gz.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.stats": + type: file + description: Stats file + pattern: "*.vcf.gz.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/gatk4/mergevcfs/meta.yml b/modules/nf-core/gatk4/mergevcfs/meta.yml index 996053fcc617..b4f61d780d95 100644 --- a/modules/nf-core/gatk4/mergevcfs/meta.yml +++ b/modules/nf-core/gatk4/mergevcfs/meta.yml @@ -14,38 +14,50 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: Two or more VCF files - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - dict: - type: file - description: Optional Sequence Dictionary as input - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: Two or more VCF files + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: Optional Sequence Dictionary as input + pattern: "*.dict" output: - vcf: - type: file - description: merged vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: merged vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: merged vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: index files for the merged vcf files - pattern: "*.tbi" + - meta: + type: file + description: index files for the merged vcf files + pattern: "*.tbi" + - "*.tbi": + type: file + description: index files for the merged vcf files + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/mutect2/meta.yml b/modules/nf-core/gatk4/mutect2/meta.yml index 21c928ed96b8..27fd63a243a5 100644 --- a/modules/nf-core/gatk4/mutect2/meta.yml +++ b/modules/nf-core/gatk4/mutect2/meta.yml @@ -17,88 +17,113 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - input: - type: list - description: list of BAM files, also able to take CRAM as an input - pattern: "*.{bam/cram}" - - input_index: - type: list - description: list of BAM file indexes, also able to take CRAM indexes as an input - pattern: "*.{bam.bai/cram.crai}" - - intervals: - type: file - description: Specify region the tools is run on. - pattern: ".{bed,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - germline_resource: - type: file - description: Population vcf of germline sequencing, containing allele fractions. - pattern: "*.vcf.gz" - - germline_resource_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" - - panel_of_normals: - type: file - description: vcf file to be used as a panel of normals. - pattern: "*.vcf.gz" - - panel_of_normals_tbi: - type: file - description: Index for the panel of normals. - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - input: + type: list + description: list of BAM files, also able to take CRAM as an input + pattern: "*.{bam/cram}" + - input_index: + type: list + description: list of BAM file indexes, also able to take CRAM indexes as an + input + pattern: "*.{bam.bai/cram.crai}" + - intervals: + type: file + description: Specify region the tools is run on. + pattern: ".{bed,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - germline_resource: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + pattern: "*.vcf.gz" + - - germline_resource_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + - - panel_of_normals: + type: file + description: vcf file to be used as a panel of normals. + pattern: "*.vcf.gz" + - - panel_of_normals_tbi: + type: file + description: Index for the panel of normals. + pattern: "*.vcf.gz.tbi" output: - vcf: - type: file - description: compressed vcf file - pattern: "*.vcf.gz" + - meta: + type: file + description: compressed vcf file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: compressed vcf file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of vcf file - pattern: "*vcf.gz.tbi" + - meta: + type: file + description: Index of vcf file + pattern: "*vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of vcf file + pattern: "*vcf.gz.tbi" - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" + - meta: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - "*.stats": + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" - f1r2: - type: file - description: file containing information to be passed to LearnReadOrientationModel (only outputted when tumor_normal_pair mode is run) - pattern: "*.f1r2.tar.gz" + - meta: + type: file + description: file containing information to be passed to LearnReadOrientationModel + (only outputted when tumor_normal_pair mode is run) + pattern: "*.f1r2.tar.gz" + - "*.f1r2.tar.gz": + type: file + description: file containing information to be passed to LearnReadOrientationModel + (only outputted when tumor_normal_pair mode is run) + pattern: "*.f1r2.tar.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml index a724da11c1a8..d090169ab071 100644 --- a/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml +++ b/modules/nf-core/gatk4/postprocessgermlinecnvcalls/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_postprocessgermlinecnvcalls" -description: Postprocesses the output of GermlineCNVCaller and generates VCFs and denoised copy ratios +description: Postprocesses the output of GermlineCNVCaller and generates VCFs and + denoised copy ratios keywords: - copy number - gatk4 @@ -14,50 +15,69 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593411-PostprocessGermlineCNVCalls doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ploidy: - type: directory - description: | - Optional - A folder containing the ploidy model. - When a model is supplied to tool will run in CASE mode. - pattern: "*-calls/" - - calls: - type: directory - description: A folder containing the calls from the input files - pattern: "*-cnv-calls/*-calls" - - model: - type: directory - description: | - A folder containing the model from the input files. - This will only be created in COHORT mode (when no model is supplied to the process). - pattern: "*-cnv-model/*-model" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - calls: + type: directory + description: A folder containing the calls from the input files + pattern: "*-cnv-calls/*-calls" + - model: + type: directory + description: | + A folder containing the model from the input files. + This will only be created in COHORT mode (when no model is supplied to the process). + pattern: "*-cnv-model/*-model" + - ploidy: + type: directory + description: | + Optional - A folder containing the ploidy model. + When a model is supplied to tool will run in CASE mode. + pattern: "*-calls/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - denoised: - type: file - description: Denoised copy ratio file - pattern: "*.vcf.gz" - - segments: - type: file - description: Segments VCF file - pattern: "*.vcf.gz" - intervals: - type: file - description: Intervals VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genotyped_intervals.vcf.gz": + type: file + description: Intervals VCF file + pattern: "*.vcf.gz" + - s: + type: file + description: Intervals VCF file + pattern: "*.vcf.gz" + - segments: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genotyped_segments.vcf.gz": + type: file + description: Segments VCF file + pattern: "*.vcf.gz" + - denoised: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_denoised.vcf.gz": + type: file + description: Denoised copy ratio file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" maintainers: diff --git a/modules/nf-core/gatk4/preprocessintervals/meta.yml b/modules/nf-core/gatk4/preprocessintervals/meta.yml index cf3f6ac43a04..0e1367487992 100644 --- a/modules/nf-core/gatk4/preprocessintervals/meta.yml +++ b/modules/nf-core/gatk4/preprocessintervals/meta.yml @@ -7,71 +7,83 @@ keywords: - preprocessintervals tools: - "gatk4": - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - intervals: - type: file - description: Interval file (bed or interval_list) with the genomic regions to be included from the analysis (optional) - pattern: "*.{bed,interval_list}" - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - exclude_intervals: - type: file - description: Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional) - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - intervals: + type: file + description: Interval file (bed or interval_list) with the genomic regions to + be included from the analysis (optional) + pattern: "*.{bed,interval_list}" + - - meta5: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - exclude_intervals: + type: file + description: Interval file (bed or interval_list) with the genomic regions to + be excluded from the analysis (optional) + pattern: "*.{bed,interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - interval_list: - type: file - description: Processed interval list file - pattern: "*.{bed,interval_list}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - "*.interval_list": + type: file + description: Processed interval list file + pattern: "*.{bed,interval_list}" + - _list: + type: file + description: Processed interval list file + pattern: "*.{bed,interval_list}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ryanjameskennedy" - "@ViktorHy" diff --git a/modules/nf-core/gatk4/printreads/meta.yml b/modules/nf-core/gatk4/printreads/meta.yml index aca7e18878ab..de8da7c56a3b 100644 --- a/modules/nf-core/gatk4/printreads/meta.yml +++ b/modules/nf-core/gatk4/printreads/meta.yml @@ -16,69 +16,84 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: reference fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: reference fasta index file - pattern: "*.{fai}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: reference fasta dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: reference fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: reference fasta index file + pattern: "*.{fai}" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: reference fasta dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: Sorted SAM file - pattern: "*.{sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: Sorted SAM file + pattern: "*.{sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/printsvevidence/meta.yml b/modules/nf-core/gatk4/printsvevidence/meta.yml index 6d24fe190277..3e3ad72d58e5 100644 --- a/modules/nf-core/gatk4/printsvevidence/meta.yml +++ b/modules/nf-core/gatk4/printsvevidence/meta.yml @@ -1,5 +1,9 @@ name: "gatk4_printsvevidence" -description: WARNING - this tool is still experimental and shouldn't be used in a production setting. Gathers paired-end and split read evidence files for use in the GATK-SV pipeline. Output files are a file containing the location of and orientation of read pairs marked as discordant, and a file containing the clipping location of all soft clipped reads and the orientation of the clipping. +description: WARNING - this tool is still experimental and shouldn't be used in a + production setting. Gathers paired-end and split read evidence files for use in + the GATK-SV pipeline. Output files are a file containing the location of and orientation + of read pairs marked as discordant, and a file containing the clipping location + of all soft clipped reads and the orientation of the clipping. keywords: - gatk4 - printsvevidence @@ -14,54 +18,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - evidence_files: - type: file - description: The evidence files created by CollectSVEvidence. They all need to be of the same type to print the SV evidence. - pattern: "*.{pe,sr,baf,rd}.txt(.gz)" - - evidence_indices: - type: file - description: The indices of the evidence files created by CollectSVEvidence - pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi" - - bed: - type: file - description: An optional BED file - pattern: "*.bed" - - fasta: - type: file - description: An optional reference FASTA file - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: An optional reference FASTA file index - pattern: "*.fai" - - dict: - type: file - description: The mandatory sequence dictionary file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - evidence_files: + type: file + description: The evidence files created by CollectSVEvidence. They all need + to be of the same type to print the SV evidence. + pattern: "*.{pe,sr,baf,rd}.txt(.gz)" + - evidence_indices: + type: file + description: The indices of the evidence files created by CollectSVEvidence + pattern: "*.{pe,sr,baf,rd}.txt(.gz).tbi" + - - bed: + type: file + description: An optional BED file + pattern: "*.bed" + - - fasta: + type: file + description: An optional reference FASTA file + pattern: "*.{fa,fasta}" + - - fasta_fai: + type: file + description: An optional reference FASTA file index + pattern: "*.fai" + - - dict: + type: file + description: The mandatory sequence dictionary file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - printed_evidence: - type: file - description: The output file containing the discordant read pairs or the soft clipped reads - pattern: "*.{pe,sr,baf,rd}.txt.gz" - - printed_evidence: - type: file - description: The index of the output file containing the discordant read pairs or the soft clipped reads - pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: The output file containing the discordant read pairs or the soft + clipped reads + pattern: "*.{pe,sr,baf,rd}.txt.gz" + - printed_evidence_index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz.tbi": + type: file + description: The index file of the output compressed text file containing the discordant read + pairs or the soft clipped reads + pattern: "*.{pe,sr,baf,rd}.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/reblockgvcf/meta.yml b/modules/nf-core/gatk4/reblockgvcf/meta.yml index 5a93f0f072f6..d02c24e7774d 100644 --- a/modules/nf-core/gatk4/reblockgvcf/meta.yml +++ b/modules/nf-core/gatk4/reblockgvcf/meta.yml @@ -14,59 +14,63 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcf: - type: file - description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or '-ERC BP_RESOLUTION' mode - pattern: "*.{vcf,gvcf}.gz" - - tbi: - type: file - description: Index of the GVCF file - pattern: "*.tbi" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcf: + type: file + description: GVCF file created using HaplotypeCaller using the '-ERC GVCF' or + '-ERC BP_RESOLUTION' mode + pattern: "*.{vcf,gvcf}.gz" + - tbi: + type: file + description: Index of the GVCF file + pattern: "*.tbi" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rb.g.vcf.gz": + type: file + description: The reblocked GVCF file + pattern: "*.rb.g.vcf.gz" + - "*.tbi": + type: file + description: Index of the reblocked GVCF file + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gvcf: - type: file - description: Filtered GVCF - pattern: "*rb.g.vcf.gz" - - tbi: - type: file - description: Index of the filtered GVCF - pattern: "*rb.g.vcf.gz.tbi" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/revertsam/meta.yml b/modules/nf-core/gatk4/revertsam/meta.yml index ac6c0d0f0e83..fb73b13f7479 100644 --- a/modules/nf-core/gatk4/revertsam/meta.yml +++ b/modules/nf-core/gatk4/revertsam/meta.yml @@ -14,25 +14,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: file - description: The input bam/sam file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: The input bam/sam file + pattern: "*.{bam,sam}" output: - bam: - type: file - description: The reverted bam/sam file - pattern: "*.reverted.bam" + - meta: + type: file + description: The reverted bam/sam file + pattern: "*.reverted.bam" + - "*.bam": + type: file + description: The reverted bam/sam file + pattern: "*.reverted.bam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/samtofastq/meta.yml b/modules/nf-core/gatk4/samtofastq/meta.yml index b61ef4fc9565..91a8e503f50d 100644 --- a/modules/nf-core/gatk4/samtofastq/meta.yml +++ b/modules/nf-core/gatk4/samtofastq/meta.yml @@ -14,25 +14,32 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: file - description: Input SAM/BAM file - pattern: "*.{bam,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: Input SAM/BAM file + pattern: "*.{bam,sam}" output: - fastq: - type: file - description: converted fastq file - pattern: "*.fastq" + - meta: + type: file + description: converted fastq file + pattern: "*.fastq" + - "*.fastq.gz": + type: file + description: converted fastq file + pattern: "*.fastq" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/selectvariants/meta.yml b/modules/nf-core/gatk4/selectvariants/meta.yml index 5bd0fc69aba0..5fd9c6f39a98 100644 --- a/modules/nf-core/gatk4/selectvariants/meta.yml +++ b/modules/nf-core/gatk4/selectvariants/meta.yml @@ -15,42 +15,51 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: VCF(.gz) file - pattern: "*.{vcf,vcf.gz}" - - vcf_idx: - type: list - description: VCF file index - pattern: "*.{idx,tbi}" - - intervals: - type: file - description: One or more genomic intervals over which to operate - pattern: ".intervals" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: VCF(.gz) file + pattern: "*.{vcf,vcf.gz}" + - vcf_idx: + type: list + description: VCF file index + pattern: "*.{idx,tbi}" + - intervals: + type: file + description: One or more genomic intervals over which to operate + pattern: ".intervals" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.selectvariants.vcf.gz" - - vcf_tbi: - type: list - description: VCF file index - pattern: "*.{idx,tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.selectvariants.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Tabix index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/shiftfasta/meta.yml b/modules/nf-core/gatk4/shiftfasta/meta.yml index c1ab0c2f1c88..28b2ac555b7c 100644 --- a/modules/nf-core/gatk4/shiftfasta/meta.yml +++ b/modules/nf-core/gatk4/shiftfasta/meta.yml @@ -17,64 +17,109 @@ tools: tool_dev_url: "https://github.com/broadinstitute/gatk" doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: index for fasta file - pattern: "*.{fai}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - dict: - type: file - description: sequence dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: index for fasta file + pattern: "*.{fai}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - dict: + type: file + description: sequence dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - shift_fa: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.fasta": + type: file + description: Shifted fasta file + pattern: "*.{fa,fasta}" + - shift_fai: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.fasta.fai": + type: file + description: Index file for the shifted fasta file + pattern: "*.{fai}" + - shift_back_chain: + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.back_chain": + type: file + description: The shiftback chain file to use when lifting over + pattern: "*.{back_chain}" - dict: - type: file - description: sequence dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*_shift.dict": + type: file + description: sequence dictionary file + pattern: "*.{dict}" - intervals: - type: file - description: Intervals file for the fasta file - pattern: "*.{intervals}" - - shift_back_chain: - type: file - description: The shiftback chain file to use when lifting over - pattern: "*.{back_chain}" - - shift_fa: - type: file - description: Shifted fasta file - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*.intervals": + type: file + description: Intervals file for the fasta file + pattern: "*.{intervals}" + - s: + type: file + description: Intervals file for the fasta file + pattern: "*.{intervals}" - shift_intervals: - type: file - description: Intervals file for the shifted fasta file - pattern: "*.{shifted.intervals}" + - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test' ] + - "*.shifted.intervals": + type: file + description: Intervals file for the shifted fasta file + pattern: "*.{shifted.intervals}" + - s: + type: file + description: Intervals file for the shifted fasta file + pattern: "*.{shifted.intervals}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gatk4/sitedepthtobaf/meta.yml b/modules/nf-core/gatk4/sitedepthtobaf/meta.yml index 2876fb9e2d15..fee4b33f97ee 100644 --- a/modules/nf-core/gatk4/sitedepthtobaf/meta.yml +++ b/modules/nf-core/gatk4/sitedepthtobaf/meta.yml @@ -12,58 +12,67 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - site_depths: - type: file - description: Files containing site depths - pattern: "*.sd.txt.gz" - - site_depths_indices: - type: file - description: The indices of the site depth files - pattern: "*.sd.txt.gz.tbi" - - vcf: - type: file - description: Input VCF of SNPs marking loci for site depths - pattern: "*.vcf.gz" - - tbi: - type: file - description: Index of the input VCF of SNPs marking loci for site depths - pattern: "*.vcf.gz.tbi" - - fasta: - type: file - description: The reference FASTA file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" - - dict: - type: file - description: The sequence dictionary of the reference FASTA file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - site_depths: + type: file + description: Files containing site depths + pattern: "*.sd.txt.gz" + - site_depths_indices: + type: file + description: The indices of the site depth files + pattern: "*.sd.txt.gz.tbi" + - - vcf: + type: file + description: Input VCF of SNPs marking loci for site depths + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of the input VCF of SNPs marking loci for site depths + pattern: "*.vcf.gz.tbi" + - - fasta: + type: file + description: The reference FASTA file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" + - - dict: + type: file + description: The sequence dictionary of the reference FASTA file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - baf: - type: file - description: The created BAF file - pattern: "*.baf.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.baf.txt.gz": + type: file + description: The created BAF file + pattern: "*.baf.txt.gz" - baf_tbi: - type: file - description: The index of the created BAF file - pattern: "*.baf.txt.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.baf.txt.gz.tbi": + type: file + description: The index of the created BAF file + pattern: "*.baf.txt.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/splitcram/meta.yml b/modules/nf-core/gatk4/splitcram/meta.yml index cb3005ee71bc..56b81b637022 100644 --- a/modules/nf-core/gatk4/splitcram/meta.yml +++ b/modules/nf-core/gatk4/splitcram/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_splitcram" -description: Splits CRAM files efficiently by taking advantage of their container based structure +description: Splits CRAM files efficiently by taking advantage of their container + based structure keywords: - cram - gatk4 @@ -15,30 +16,33 @@ tools: documentation: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cram: - type: file - description: The CRAM file to split - pattern: "*.cram" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: The CRAM file to split + pattern: "*.cram" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_crams: - type: file - description: A list of split CRAM files - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: A list of split CRAM files + pattern: "*.cram" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/splitintervals/meta.yml b/modules/nf-core/gatk4/splitintervals/meta.yml index c92bad8b5316..6a1b869b0d1a 100644 --- a/modules/nf-core/gatk4/splitintervals/meta.yml +++ b/modules/nf-core/gatk4/splitintervals/meta.yml @@ -13,57 +13,59 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - interval: - type: file - description: Interval list or BED - pattern: "*.{interval,interval_list,bed}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference FASTA - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference FASTA index - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Reference sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: Interval file + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference FASTA + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference FASTA index + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Reference sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bed: - type: file - description: A list of scattered interval lists - pattern: "*.interval_list" + - split_intervals: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "**.interval_list": + type: file + description: interval files + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/splitncigarreads/meta.yml b/modules/nf-core/gatk4/splitncigarreads/meta.yml index f813274671e4..6b05bef10b9f 100644 --- a/modules/nf-core/gatk4/splitncigarreads/meta.yml +++ b/modules/nf-core/gatk4/splitncigarreads/meta.yml @@ -14,59 +14,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bam: - type: list - description: BAM/SAM/CRAM file containing reads - pattern: "*.{bam,sam,cram}" - - bai: - type: list - description: BAI/SAI/CRAI index file (optional) - pattern: "*.{bai,sai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: list + description: BAM/SAM/CRAM file containing reads + pattern: "*.{bam,sam,cram}" + - bai: + type: list + description: BAI/SAI/CRAI index file (optional) + pattern: "*.{bai,sai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - bam: - type: file - description: Output file with split reads (BAM/SAM/CRAM) - pattern: "*.{bam,sam,cram}" + - meta: + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" + - "*.bam": + type: file + description: Output file with split reads (BAM/SAM/CRAM) + pattern: "*.{bam,sam,cram}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" maintainers: diff --git a/modules/nf-core/gatk4/svannotate/meta.yml b/modules/nf-core/gatk4/svannotate/meta.yml index 30a56f6fcb27..8f398a8372a8 100644 --- a/modules/nf-core/gatk4/svannotate/meta.yml +++ b/modules/nf-core/gatk4/svannotate/meta.yml @@ -1,5 +1,8 @@ name: "gatk4_svannotate" -description: Adds predicted functional consequence, gene overlap, and noncoding element overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, a GTF file containing primary or canonical transcripts, and a BED file containing noncoding elements. Output file is an annotated SV VCF. +description: Adds predicted functional consequence, gene overlap, and noncoding element + overlap annotations to SV VCF from GATK-SV pipeline. Input files are an SV VCF, + a GTF file containing primary or canonical transcripts, and a BED file containing + noncoding elements. Output file is an annotated SV VCF. keywords: - annotate - gatk4 @@ -14,54 +17,66 @@ tools: tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A VCF file created with a structural variant caller - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index file of the VCF - pattern: "*.vcf.gz.tbi" - - bed: - type: file - description: Regions to limit the analysis to - pattern: "*.bed" - - fasta: - type: file - description: Optional - reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Optional - index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Optional - sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A VCF file created with a structural variant caller + pattern: "*.vcf.gz" + - tbi: + type: file + description: The index file of the VCF + pattern: "*.vcf.gz.tbi" + - bed: + type: file + description: Regions to limit the analysis to + pattern: "*.bed" + - - fasta: + type: file + description: Optional - reference FASTA file needed when the input is a CRAM + file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Optional - index of the reference FASTA file needed when the input + is a CRAM file + pattern: "*.fai" + - - dict: + type: file + description: Optional - sequence dictionary of the reference FASTA file needed + when the input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotated_vcf: - type: file - description: The annotated structural variant VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The annotated structural variant VCF + pattern: "*.vcf.gz" - index: - type: file - description: The index of the VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the VCF + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/svcluster/meta.yml b/modules/nf-core/gatk4/svcluster/meta.yml index 8a772058e3e0..39d3e8876735 100644 --- a/modules/nf-core/gatk4/svcluster/meta.yml +++ b/modules/nf-core/gatk4/svcluster/meta.yml @@ -1,5 +1,6 @@ name: "gatk4_svcluster" -description: Clusters structural variants based on coordinates, event type, and supporting algorithms +description: Clusters structural variants based on coordinates, event type, and supporting + algorithms keywords: - gatk4 - structural variants @@ -15,54 +16,65 @@ tools: documentation: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: file - description: One or more VCF files created with a structural variant caller - pattern: "*.vcf.gz" - - indices: - type: file - description: Index files for the VCFs - pattern: "*.vcf.gz.tbi" - - ploidy_table: - type: file - description: The sample ploidy table - pattern: "*.tsv" - - fasta: - type: file - description: Reference FASTA file needed when the input is a CRAM file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference FASTA file needed when the input is a CRAM file - pattern: "*.fai" - - dict: - type: file - description: Sequence dictionary of the reference FASTA file needed when the input is a CRAM file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: file + description: One or more VCF files created with a structural variant caller + pattern: "*.vcf.gz" + - indices: + type: file + description: Index files for the VCFs + pattern: "*.vcf.gz.tbi" + - - ploidy_table: + type: file + description: The sample ploidy table + pattern: "*.tsv" + - - fasta: + type: file + description: Reference FASTA file needed when the input is a CRAM file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference FASTA file needed when the input is a CRAM + file + pattern: "*.fai" + - - dict: + type: file + description: Sequence dictionary of the reference FASTA file needed when the + input is a CRAM file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clustered_vcf: - type: file - description: The VCF containing the clustered VCFs - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The VCF containing the clustered VCFs + pattern: "*.vcf.gz" - clustered_vcf_index: - type: file - description: The index of the VCF containing the clustered VCFs - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the VCF containing the clustered VCFs + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gatk4/variantfiltration/meta.yml b/modules/nf-core/gatk4/variantfiltration/meta.yml index 11915a94ff12..8e23e205b078 100644 --- a/modules/nf-core/gatk4/variantfiltration/meta.yml +++ b/modules/nf-core/gatk4/variantfiltration/meta.yml @@ -15,60 +15,72 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: list - description: List of VCF(.gz) files - pattern: "*.{vcf,vcf.gz}" - - vcf_tbi: - type: list - description: List of VCF file indexes - pattern: "*.{idx,tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of fastea file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: list + description: List of VCF(.gz) files + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: list + description: List of VCF file indexes + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" output: - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" + - "*.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ramprasadn" diff --git a/modules/nf-core/gatk4/variantrecalibrator/meta.yml b/modules/nf-core/gatk4/variantrecalibrator/meta.yml index 39a415b61c78..72fcfd601c53 100644 --- a/modules/nf-core/gatk4/variantrecalibrator/meta.yml +++ b/modules/nf-core/gatk4/variantrecalibrator/meta.yml @@ -18,64 +18,92 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: input vcf file containing the variants to be recalibrated - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resource_vcf: - type: file - description: all resource vcf files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz" - - resource_tbi: - type: file - description: all resource tbi files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz.tbi" - - labels: - type: string - description: necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: input vcf file containing the variants to be recalibrated + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - - resource_vcf: + type: file + description: all resource vcf files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz" + - - resource_tbi: + type: file + description: all resource tbi files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz.tbi" + - - labels: + type: string + description: necessary arguments for GATK VariantRecalibrator. Specified to + directly match the resources provided. More information can be found at + https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - recal: - type: file - description: Output recal file used by ApplyVQSR - pattern: "*.recal" + - meta: + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" + - "*.recal": + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" - idx: - type: file - description: Index file for the recal output file - pattern: "*.idx" + - meta: + type: file + description: Index file for the recal output file + pattern: "*.idx" + - "*.idx": + type: file + description: Index file for the recal output file + pattern: "*.idx" - tranches: - type: file - description: Output tranches file used by ApplyVQSR - pattern: "*.tranches" + - meta: + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" + - "*.tranches": + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" - plots: - type: file - description: Optional output rscript file to aid in visualization of the input data and learned model. - pattern: "*plots.R" - - version: - type: file - description: File containing software versions - pattern: "*.versions.yml" + - meta: + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - "*plots.R": + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GCJMackenzie" - "@nickhsmith" diff --git a/modules/nf-core/gatk4/variantstotable/meta.yml b/modules/nf-core/gatk4/variantstotable/meta.yml index 80d31265c4f4..28ee57083f41 100644 --- a/modules/nf-core/gatk4/variantstotable/meta.yml +++ b/modules/nf-core/gatk4/variantstotable/meta.yml @@ -15,68 +15,75 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. - e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD'] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: Index of VCF file. - pattern: "*.{idx,tbi}" - - arguments_file: - type: file - description: "optional GATK arguments file" - pattern: "*.{txt,list,args,arguments}" - - include_intervals: - type: file - description: "optional GATK region file" - pattern: "*.{bed,bed.gz,interval,interval_list}" - - exclude_intervals: - type: file - description: "optional GATK exclude region file" - pattern: "*.{bed,bed.gz,interval,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of fasta file - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of fastea file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk. + e.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD'] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: Index of VCF file. + pattern: "*.{idx,tbi}" + - arguments_file: + type: file + description: "optional GATK arguments file" + pattern: "*.{txt,list,args,arguments}" + - include_intervals: + type: file + description: "optional GATK region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - exclude_intervals: + type: file + description: "optional GATK exclude region file" + pattern: "*.{bed,bed.gz,interval,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of fastea file + pattern: "*.dict" output: - table: - type: file - description: GATK output - pattern: "*.tsv" + - meta: + type: file + description: GATK output + pattern: "*.tsv" + - "*.tsv": + type: file + description: GATK output + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/gatk4spark/applybqsr/meta.yml b/modules/nf-core/gatk4spark/applybqsr/meta.yml index 4904568d2e77..609af2f45034 100644 --- a/modules/nf-core/gatk4spark/applybqsr/meta.yml +++ b/modules/nf-core/gatk4spark/applybqsr/meta.yml @@ -16,56 +16,65 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - bqsr_table: - type: file - description: Recalibration table from gatk4_baserecalibrator - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - bqsr_table: + type: file + description: Recalibration table from gatk4_baserecalibrator + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Recalibrated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Recalibrated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Recalibrated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Recalibrated CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4spark/baserecalibrator/meta.yml b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml index dd334a225f2d..abb0e1a65e1b 100644 --- a/modules/nf-core/gatk4spark/baserecalibrator/meta.yml +++ b/modules/nf-core/gatk4spark/baserecalibrator/meta.yml @@ -16,57 +16,60 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Recalibration table from BaseRecalibrator - pattern: "*.{table}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Recalibration table from BaseRecalibrator + pattern: "*.{table}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yocra3" - "@FriederikeHanssen" diff --git a/modules/nf-core/gatk4spark/markduplicates/meta.yml b/modules/nf-core/gatk4spark/markduplicates/meta.yml index 016a215b259c..fc8dee3dffb0 100644 --- a/modules/nf-core/gatk4spark/markduplicates/meta.yml +++ b/modules/nf-core/gatk4spark/markduplicates/meta.yml @@ -1,5 +1,6 @@ name: gatk4spark_markduplicates -description: This tool locates and tags duplicate reads in a BAM or SAM file, where duplicate reads are defined as originating from a single fragment of DNA. +description: This tool locates and tags duplicate reads in a BAM or SAM file, where + duplicate reads are defined as originating from a single fragment of DNA. keywords: - bam - gatk4spark @@ -7,52 +8,74 @@ keywords: - sort tools: - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the + toolkit offers a wide variety of tools with a primary focus on variant discovery + and genotyping. Its powerful processing engine and high-performance computing + features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fasta_fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Marked duplicates BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Marked duplicates BAM/CRAM file + pattern: "*.{bam,cram}" - bam_index: - type: file - description: Optional BAM index file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bai: + type: file + description: Optional BAM index file + pattern: "*.bai" + - metrics: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Metrics file + pattern: "*.metrics" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ajodeh-juma" - "@FriederikeHanssen" diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 2b6033b0b5e5..051700820dee 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -16,34 +16,40 @@ tools: documentation: "https://www.gnu.org/software/gawk/manual/" tool_dev_url: "https://www.gnu.org/prep/ftp.html" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: The input file - Specify the logic that needs to be executed on this file on the `ext.args2` or in the program file - pattern: "*" - - program_file: - type: file - description: Optional file containing logic for awk to execute. If you don't wish to use a file, you can use `ext.args2` to specify the logic. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file - Specify the logic that needs to be executed on + this file on the `ext.args2` or in the program file + pattern: "*" + - - program_file: + type: file + description: Optional file containing logic for awk to execute. If you don't + wish to use a file, you can use `ext.args2` to specify the logic. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: The output file - specify the name of this file using `ext.prefix` and the extension using `ext.suffix` - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${suffix}: + type: file + description: The output file - specify the name of this file using `ext.prefix` + and the extension using `ext.suffix` + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gecco/run/meta.yml b/modules/nf-core/gecco/run/meta.yml index a2f4a7266bb0..6a557ceaf55b 100644 --- a/modules/nf-core/gecco/run/meta.yml +++ b/modules/nf-core/gecco/run/meta.yml @@ -1,5 +1,7 @@ name: "gecco_run" -description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields (CRFs). +description: GECCO is a fast and scalable method for identifying putative novel Biosynthetic + Gene Clusters (BGCs) in genomic and metagenomic data using Conditional Random Fields + (CRFs). keywords: - bgc - detection @@ -13,53 +15,86 @@ tools: tool_dev_url: "https://github.com/zellerlab/GECCO" doi: "10.1101/2021.05.03.442509" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: A genomic file containing one or more sequences as input. Input type is any supported by Biopython (fasta, gbk, etc.) - pattern: "*" - - hmm: - type: file - description: Alternative HMM file(s) to use in HMMER format - pattern: "*.hmm" - - model_dir: - type: directory - description: Path to an alternative CRF (Conditional Random Fields) module to use + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: A genomic file containing one or more sequences as input. Input + type is any supported by Biopython (fasta, gbk, etc.) + pattern: "*" + - hmm: + type: file + description: Alternative HMM file(s) to use in HMMER format + pattern: "*.hmm" + - - model_dir: + type: directory + description: Path to an alternative CRF (Conditional Random Fields) module to + use output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genes: - type: file - description: TSV file containing detected/predicted genes with BGC probability scores. Will not be generated if no hits are found. - pattern: "*.genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.genes.tsv": + type: file + description: TSV file containing detected/predicted genes with BGC probability + scores. Will not be generated if no hits are found. + pattern: "*.genes.tsv" - features: - type: file - description: TSV file containing identified domains - pattern: "*.features.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.features.tsv": + type: file + description: TSV file containing identified domains + pattern: "*.features.tsv" - clusters: - type: file - description: TSV file containing coordinates of predicted clusters and BGC types. Will not be generated if no hits are found. - pattern: "*.clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clusters.tsv": + type: file + description: TSV file containing coordinates of predicted clusters and BGC types. Will + not be generated if no hits are found. + pattern: "*.clusters.tsv" - gbk: - type: file - description: Per cluster GenBank file (if found) containing sequence with annotations. Will not be generated if no hits are found. - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_cluster_*.gbk": + type: file + description: Per cluster GenBank file (if found) containing sequence with annotations. + Will not be generated if no hits are found. + pattern: "*.gbk" - json: - type: file - description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. Will not be generated if no hits are found. - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: AntiSMASH v6 sideload JSON file (if --antismash-sideload) supplied. + Will not be generated if no hits are found. + pattern: "*.gbk" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gem2/gem2bedmappability/meta.yml b/modules/nf-core/gem2/gem2bedmappability/meta.yml index a625c9e87ad9..6cc486a7c772 100644 --- a/modules/nf-core/gem2/gem2bedmappability/meta.yml +++ b/modules/nf-core/gem2/gem2bedmappability/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gem2bedmappability" description: Convert a mappability file to bedgraph format @@ -9,46 +8,57 @@ keywords: - gem tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." - homepage: "https://paoloribeca.science/gem" - # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise) + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." + homepage: + "https://paoloribeca.science/gem" + # This is not a valid link because all documentation is gone for this tool (it's here because the linter isn't happy otherwise) licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - map: - type: file - description: The mappability file created from the index - pattern: "*.mappability" - - meta2: - type: map - description: | - Groovy Map containing index information - - index: - type: file - description: The index of the reference FASTA - pattern: "*.gem" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: The mappability file created from the index + pattern: "*.mappability" + - - meta2: + type: map + description: | + Groovy Map containing index information + - index: + type: file + description: The index of the reference FASTA + pattern: "*.gem" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: The resulting bedgraph file - pattern: "*.bg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bg": + type: file + description: The resulting bedgraph file + pattern: "*.bg" - sizes: - type: file - description: The chromosome sizes - pattern: "*.sizes" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sizes": + type: file + description: The chromosome sizes + pattern: "*.sizes" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem2/gemindexer/meta.yml b/modules/nf-core/gem2/gemindexer/meta.yml index 00152b05649d..c0bb6a56f4b8 100644 --- a/modules/nf-core/gem2/gemindexer/meta.yml +++ b/modules/nf-core/gem2/gemindexer/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gemindexer" description: Create a GEM index from a FASTA file @@ -9,37 +8,47 @@ keywords: - mappability tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A reference FASTA file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A reference FASTA file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gem: - type: file - description: The created index - pattern: "*.gem" + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gem": + type: file + description: The GEM index file + pattern: "*.gem" - log: - type: file - description: The execution log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: The execution log + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem2/gemmappability/meta.yml b/modules/nf-core/gem2/gemmappability/meta.yml index 8157a85a6093..cf3885458637 100644 --- a/modules/nf-core/gem2/gemmappability/meta.yml +++ b/modules/nf-core/gem2/gemmappability/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem2_gemmappability" description: Define the mappability of a reference @@ -9,36 +8,40 @@ keywords: - reference tools: - "gem2": - description: "GEM2 is a high-performance mapping tool. It also provide a unique tool to evaluate mappability." + description: "GEM2 is a high-performance mapping tool. It also provide a unique + tool to evaluate mappability." homepage: "https://paoloribeca.science/gem" licence: ["Custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: The index created with gem-indexer from the reference FASTA - pattern: "*.gem" - - read_length: - type: integer - description: The read length to define the mappability of + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: The index created with gem-indexer from the reference FASTA + pattern: "*.gem" + - - read_length: + type: integer + description: The read length to define the mappability of output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - map: - type: file - description: The resulting mappability file - pattern: "*.mappability" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mappability": + type: file + description: The resulting mappability file + pattern: "*.mappability" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gem3/gem3indexer/meta.yml b/modules/nf-core/gem3/gem3indexer/meta.yml index b1c663502348..61ef661aa161 100644 --- a/modules/nf-core/gem3/gem3indexer/meta.yml +++ b/modules/nf-core/gem3/gem3indexer/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gem3_gem3indexer" description: Create a GEM index from a FASTA file @@ -11,34 +10,43 @@ tools: description: "The GEM indexer (v3)." homepage: "https://github.com/miqalvarez/gem3/tree/gem3-indexer" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information about the fasta file - e.g. [ id:'test' ] - - fasta: - type: file - description: A reference FASTA file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing information about the fasta file + e.g. [ id:'test' ] + - fasta: + type: file + description: A reference FASTA file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - gem: - type: file - description: The created index - pattern: "*.gem" + - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gem": + type: file + description: The GEM index file + pattern: "*.gem" - info: - type: file - description: The execution log - pattern: "*.info" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info": + type: file + description: The execution log + pattern: "*.info" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@miqalvarez" maintainers: diff --git a/modules/nf-core/gem3/gem3mapper/meta.yml b/modules/nf-core/gem3/gem3mapper/meta.yml index 8ef2f16dc98f..63e430bac9dd 100644 --- a/modules/nf-core/gem3/gem3mapper/meta.yml +++ b/modules/nf-core/gem3/gem3mapper/meta.yml @@ -9,42 +9,46 @@ tools: description: "The GEM indexer (v3)." homepage: "https://github.com/smarco/gem3-mapper" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference/index information - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fastq: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - - gem: - type: file - description: GEM3 genome index files - pattern: "*.{gem}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing reference/index information + e.g. [ id:'test' ] + - gem: + type: file + description: GEM3 genome index files + pattern: "*.{gem}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@miqalvarez" diff --git a/modules/nf-core/genescopefk/meta.yml b/modules/nf-core/genescopefk/meta.yml index b54cfbcd9765..7bba21a793e4 100644 --- a/modules/nf-core/genescopefk/meta.yml +++ b/modules/nf-core/genescopefk/meta.yml @@ -10,54 +10,94 @@ tools: homepage: "https://github.com/thegenemyers/GENESCOPE.FK" tool_dev_url: "https://github.com/thegenemyers/GENESCOPE.FK" licence: ["https://github.com/thegenemyers/GENESCOPE.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_histex_histogram: - type: file - description: A histogram formatted for GeneScope using the -G parameter from Fastk Histex - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_histex_histogram: + type: file + description: A histogram formatted for GeneScope using the -G parameter from + Fastk Histex + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - linear_plot: - type: file - description: A GeneScope linear plot in PNG format - pattern: "*_linear_plot.png" - - transformed_linear_plot: - type: file - description: A GeneScope transformed linear plot in PNG format - pattern: "*_transformed_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_linear_plot.png": + type: file + description: A GeneScope linear plot in PNG format + pattern: "*_linear_plot.png" - log_plot: - type: file - description: A GeneScope log plot in PNG format - pattern: "*_log_plot.png" - - transformed_log_plot: - type: file - description: A GeneScope transformed log plot in PNG format - pattern: "*_transformed_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_log_plot.png": + type: file + description: A GeneScope log plot in PNG format + pattern: "*_log_plot.png" - model: - type: file - description: GeneScope model fit summary - pattern: "*_model.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_model.txt": + type: file + description: GeneScope model fit summary + pattern: "*_model.txt" - summary: - type: file - description: GeneScope histogram summary - pattern: "*_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary.txt": + type: file + description: GeneScope histogram summary + pattern: "*_summary.txt" + - transformed_linear_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_transformed_linear_plot.png": + type: file + description: A GeneScope transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" + - transformed_log_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_transformed_log_plot.png": + type: file + description: A GeneScope transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" - kmer_cov: - type: float - description: Average kmer coverage value extracted from summary file - pattern: "[0-9.]+" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - KMERCOV: + type: float + description: Average kmer coverage value extracted from summary file + pattern: "[0-9.]+" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/genmap/index/meta.yml b/modules/nf-core/genmap/index/meta.yml index 8441333f3bfa..064a8a33dc15 100644 --- a/modules/nf-core/genmap/index/meta.yml +++ b/modules/nf-core/genmap/index/meta.yml @@ -12,29 +12,32 @@ tools: tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file to index - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file to index + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Genmap index directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Genmap index directory + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nvnieuwk" diff --git a/modules/nf-core/genmap/map/meta.yml b/modules/nf-core/genmap/map/meta.yml index 394fadb7d4d4..9026744905a1 100644 --- a/modules/nf-core/genmap/map/meta.yml +++ b/modules/nf-core/genmap/map/meta.yml @@ -15,50 +15,71 @@ tools: tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - index: - type: directory - description: index directory - - meta2: - type: map - description: | - Groovy Map containing regions information - e.g. [ id:'test', single_end:false ] - - regions: - type: file - description: optional - a bed file with regions to define the mappability off - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: directory + description: index directory + - - meta2: + type: map + description: | + Groovy Map containing regions information + e.g. [ id:'test', single_end:false ] + - regions: + type: file + description: optional - a bed file with regions to define the mappability off + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: genmap wig mappability file - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: genmap wig mappability file + pattern: "*.wig" - bedgraph: - type: file - description: genmap bedgraph mappability file - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedgraph": + type: file + description: genmap bedgraph mappability file + pattern: "*.bedgraph" - txt: - type: file - description: genmap text mappability file - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: genmap text mappability file + pattern: "*.txt" - csv: - type: file - description: genmap csv mappability file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: genmap csv mappability file + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nvnieuwk" diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml index 3c876ac588eb..bb4afb6b407b 100644 --- a/modules/nf-core/genmod/annotate/meta.yml +++ b/modules/nf-core/genmod/annotate/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_annotate.vcf": + type: file + description: Annotated VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml index aa5f7da52cd4..ebd6a110c8e9 100644 --- a/modules/nf-core/genmod/compound/meta.yml +++ b/modules/nf-core/genmod/compound/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] # + - "*_compound.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml index dd9001e04510..dca74095080a 100644 --- a/modules/nf-core/genmod/models/meta.yml +++ b/modules/nf-core/genmod/models/meta.yml @@ -11,38 +11,40 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: vcf file - pattern: "*.{vcf}" - - reduced_penetrance: - type: file - description: file with gene ids that have reduced penetrance - pattern: "*.{tsv}" - - family_file: - type: file - description: ped file - pattern: "*.{ped}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - - fam: + type: file + description: file with family information + - - reduced_penetrance: + type: file + description: file with gene ids that have reduced penetrance + pattern: "*.{tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_models.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml index 8998b00c9c65..32da6468d2c8 100644 --- a/modules/nf-core/genmod/score/meta.yml +++ b/modules/nf-core/genmod/score/meta.yml @@ -11,38 +11,40 @@ tools: documentation: "https://github.com/Clinical-Genomics/genmod" tool_dev_url: "https://github.com/moonso" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: vcf file - pattern: "*.{vcf}" - - family_file: - type: file - description: ped file - pattern: "*.{ped}" - - score_config: - type: file - description: rank model config file - pattern: "*.{ini}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_vcf: + type: file + description: vcf file + pattern: "*.{vcf}" + - - fam: + type: file + description: file with family information + - - score_config: + type: file + description: rank model config file + pattern: "*.{ini}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/genomad/download/meta.yml b/modules/nf-core/genomad/download/meta.yml index 5df21ee6a80f..7bb2f3bc55a5 100644 --- a/modules/nf-core/genomad/download/meta.yml +++ b/modules/nf-core/genomad/download/meta.yml @@ -16,15 +16,19 @@ tools: tool_dev_url: https://github.com/apcamargo/genomad/ doi: 10.1101/2023.03.05.531206 licence: ["Lawrence Berkeley National Labs BSD variant license"] + identifier: biotools:genomad output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - genomad_db: - type: directory - description: Directory containing downloaded data with directory being named "genomad_db" - pattern: "genomad_db" + - genomad_db/: + type: directory + description: Directory containing downloaded data with directory being named + "genomad_db" + pattern: "genomad_db" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/genomad/endtoend/meta.yml b/modules/nf-core/genomad/endtoend/meta.yml index 0b70dde77a87..085aeb9f489e 100644 --- a/modules/nf-core/genomad/endtoend/meta.yml +++ b/modules/nf-core/genomad/endtoend/meta.yml @@ -16,81 +16,159 @@ tools: tool_dev_url: https://github.com/apcamargo/genomad/ doi: 10.1101/2023.03.05.531206 licence: ["Lawrence Berkeley National Labs BSD variant license"] + identifier: biotools:genomad input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contigs/scaffolds/chromosomes - pattern: "*.{fasta,fna,fa}" - - genomad_db: - type: directory - description: Directory pointing to geNomad database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contigs/scaffolds/chromosomes + pattern: "*.{fasta,fna,fa}" + - - genomad_db: + type: directory + description: Directory pointing to geNomad database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - aggregated_classification: - type: file - description: Combined classification scores for each contig/scaffold/chromosome - pattern: "*_aggregated_classification.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_aggregated_classification/*_aggregated_classification.tsv": + type: file + description: Combined classification scores for each contig/scaffold/chromosome + pattern: "*_aggregated_classification.tsv" - taxonomy: - type: file - description: Detailed output of geNomad's marker gene taxonomy analysis - pattern: "*_taxonomy.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_annotate/*_taxonomy.tsv": + type: file + description: Detailed output of geNomad's marker gene taxonomy analysis + pattern: "*_taxonomy.tsv" - provirus: - type: file - description: Detailed output of each provirus identified by geNomad's find_proviruses module - pattern: "*_provirus.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_find_proviruses/*_provirus.tsv": + type: file + description: Detailed output of each provirus identified by geNomad's find_proviruses + module + pattern: "*_provirus.tsv" - compositions: - type: file - description: OPTIONAL - Predicted sample composition when `--enable-score-calibration` is used - pattern: "*_compositions.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score_calibration/*_compositions.tsv": + type: file + description: OPTIONAL - Predicted sample composition when `--enable-score-calibration` + is used + pattern: "*_compositions.tsv" - calibrated_classification: - type: file - description: OPTIONAL - Classification scores that have been adjusted based on sample composition when `--enable-score-calibration` is used` - pattern: "*_calibrated_aggregated_classification.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_score_calibration/*_calibrated_aggregated_classification.tsv": + type: file + description: OPTIONAL - Classification scores that have been adjusted based + on sample composition when `--enable-score-calibration` is used` + pattern: "*_calibrated_aggregated_classification.tsv" - plasmid_fasta: - type: file - description: FASTA file containing predicted plasmid sequences - pattern: "*_plasmid.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid.fna.gz": + type: file + description: FASTA file containing predicted plasmid sequences + pattern: "*_plasmid.fna" - plasmid_genes: - type: file - description: TSV file containing predicted plasmid genes and their annotations - pattern: "*_plasmid_genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_genes.tsv": + type: file + description: TSV file containing predicted plasmid genes and their annotations + pattern: "*_plasmid_genes.tsv" - plasmid_proteins: - type: file - description: FASTA file containing predicted plasmid protein sequences - pattern: "*_plasmid_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_proteins.faa.gz": + type: file + description: FASTA file containing predicted plasmid protein sequences + pattern: "*_plasmid_proteins.faa" - plasmid_summary: - type: file - description: TSV file containing a summary of geNomad's plasmid predictions - pattern: "*_plasmid_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_plasmid_summary.tsv": + type: file + description: TSV file containing a summary of geNomad's plasmid predictions + pattern: "*_plasmid_summary.tsv" - virus_fasta: - type: file - description: FASTA file containing predicted virus sequences - pattern: "*_virus.fna" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus.fna.gz": + type: file + description: FASTA file containing predicted virus sequences + pattern: "*_virus.fna" - virus_genes: - type: file - description: TSV file containing predicted virus genes and their annotations - pattern: "*_virus_genes.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_genes.tsv": + type: file + description: TSV file containing predicted virus genes and their annotations + pattern: "*_virus_genes.tsv" - virus_proteins: - type: file - description: FASTA file containing predicted virus protein sequences - pattern: "*_virus_proteins.faa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_proteins.faa.gz": + type: file + description: FASTA file containing predicted virus protein sequences + pattern: "*_virus_proteins.faa" - virus_summary: - type: file - description: TSV file containing a summary of geNomad's virus predictions - pattern: "*_virus_summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_summary/*_virus_summary.tsv": + type: file + description: TSV file containing a summary of geNomad's virus predictions + pattern: "*_virus_summary.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/genomescope2/meta.yml b/modules/nf-core/genomescope2/meta.yml index 928bb812d0c7..5076abf18384 100644 --- a/modules/nf-core/genomescope2/meta.yml +++ b/modules/nf-core/genomescope2/meta.yml @@ -1,5 +1,6 @@ name: "genomescope2" -description: Estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach +description: Estimate genome heterozygosity, repeat content, and size from sequencing + reads using a kmer-based statistical approach keywords: - "genome size" - "genome heterozygosity" @@ -12,62 +13,103 @@ tools: tool_dev_url: "https://github.com/tbenavi1/genomescope2.0" doi: "10.1038/s41467-020-14998-3" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - histogram: - type: file - description: A K-mer histogram file - pattern: "*.hist" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - histogram: + type: file + description: A K-mer histogram file + pattern: "*.hist" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - linear_plot_png: - type: file - description: A genomescope2 linear plot in PNG format - pattern: "*_linear_plot.png" - linear_plot_png: - type: file - description: A genomescope2 linear plot in PNG format - pattern: "*_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_linear_plot.png: + type: file + description: A genomescope2 linear plot in PNG format + pattern: "*_linear_plot.png" - transformed_linear_plot_png: - type: file - description: A genomescope2 transformed linear plot in PNG format - pattern: "*_transformed_linear_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_transformed_linear_plot.png: + type: file + description: A genomescope2 transformed linear plot in PNG format + pattern: "*_transformed_linear_plot.png" - log_plot_png: - type: file - description: A genomescope2 log plot in PNG format - pattern: "*_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_log_plot.png: + type: file + description: A genomescope2 log plot in PNG format + pattern: "*_log_plot.png" - transformed_log_plot_png: - type: file - description: A genomescope2 transformed log plot in PNG format - pattern: "*_transformed_log_plot.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_transformed_log_plot.png: + type: file + description: A genomescope2 transformed log plot in PNG format + pattern: "*_transformed_log_plot.png" - model: - type: file - description: Genomescope2 model fit summary - pattern: "*_model.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_model.txt: + type: file + description: Genomescope2 model fit summary + pattern: "*_model.txt" - summary: - type: file - description: Genomescope2 histogram summary - pattern: "*_summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_summary.txt: + type: file + description: Genomescope2 histogram summary + pattern: "*_summary.txt" - lookup_table: - type: file - description: Fitted histogram lookup table - pattern: "*_lookup_table.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_lookup_table.txt: + type: file + description: Fitted histogram lookup table + pattern: "*_lookup_table.txt" - fitted_histogram_png: - type: file - description: A genomescope2 fitted histogram plot in PNG format - pattern: "*_fitted_hist.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_fitted_hist.png: + type: file + description: A genomescope2 fitted histogram plot in PNG format + pattern: "*_fitted_hist.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/genotyphi/parse/meta.yml b/modules/nf-core/genotyphi/parse/meta.yml index 8648761e0fd3..4190b501d9ce 100644 --- a/modules/nf-core/genotyphi/parse/meta.yml +++ b/modules/nf-core/genotyphi/parse/meta.yml @@ -6,35 +6,39 @@ keywords: - Mykrobe tools: - "genotyphi": - description: "Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)" + description: "Assign genotypes to Salmonella Typhi genomes based on VCF files + (mapped to Typhi CT18 reference genome)" homepage: "https://github.com/katholt/genotyphi" documentation: "https://github.com/katholt/genotyphi" tool_dev_url: "https://github.com/katholt/genotyphi" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - json: - type: file - description: JSON formatted file of Mykrobe results - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - json: + type: file + description: JSON formatted file of Mykrobe results + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file of predicted genotypes - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited file of predicted genotypes + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/genrich/meta.yml b/modules/nf-core/genrich/meta.yml index 11c1466e4411..56f242f772b7 100644 --- a/modules/nf-core/genrich/meta.yml +++ b/modules/nf-core/genrich/meta.yml @@ -14,66 +14,91 @@ tools: documentation: https://github.com/jsh58/Genrich#readme tool_dev_url: https://github.com/jsh58/Genrich licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - treatment_bam: - type: file - description: Coordinate sorted BAM/SAM file from treatment sample or list of BAM/SAM files from biological replicates - pattern: "*.{bam,sam}" - - control_bam: - type: file - description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM files from control samples - pattern: "*.{bam,sam}" - - blacklist_bed: - type: file - description: Bed file containing genomic intervals to exclude from the analysis - pattern: "*.{bed}" - - save_pvalues: - type: boolean - description: Create bedgraph-ish file for p/q-values file - - save_pileup: - type: boolean - description: Create bedgraph-ish file for pileups and p-values - - save_bed: - type: boolean - description: Create BED file for reads/fragments/intervals - - save_duplicates: - type: boolean - description: Create PCR duplicates file (only works if -r option is set) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - treatment_bam: + type: file + description: Coordinate sorted BAM/SAM file from treatment sample or list of + BAM/SAM files from biological replicates + pattern: "*.{bam,sam}" + - control_bam: + type: file + description: Coordinate sorted BAM/SAM file from control sample or list of BAM/SAM + files from control samples + pattern: "*.{bam,sam}" + - - blacklist_bed: + type: file + description: Bed file containing genomic intervals to exclude from the analysis + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: Output file is in ENCODE narrowPeak format - pattern: "*.{narrowPeak}" + - peak: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.narrowPeak": + type: file + description: Narrow peak file containing genomic intervals of significant enrichment + pattern: "*.{narrowPeak}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bedgraph_pvalues: - type: file - description: bedGraph file containing p/q values - pattern: "*.{pvalues.bedGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvalues.bedGraph": + type: file + description: bedGraph file containing p/q values + pattern: "*.{pvalues.bedGraph}" + - ues: + type: file + description: bedGraph file containing p/q values + pattern: "*.{pvalues.bedGraph}" - bedgraph_pileup: - type: file - description: bedGraph file containing pileups and p-values - pattern: "*.{pileup.bedGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pileup.bedGraph": + type: file + description: bedGraph file containing pileups and p-values + pattern: "*.{pileup.bedGraph}" - bed_intervals: - type: file - description: Bed file containing annotated intervals - pattern: "*.{intervals.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.intervals.bed": + type: file + description: Bed file containing annotated intervals + pattern: "*.{intervals.bed}" + - s: + type: file + description: Bed file containing annotated intervals + pattern: "*.{intervals.bed}" - duplicates: - type: file - description: Text output file containing intervals corresponding to PCR duplicates - pattern: "*.{intervals.txt}" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.duplicates.txt": + type: file + description: Text output file containing intervals corresponding to PCR duplicates + pattern: "*.{intervals.txt}" authors: - "@JoseEspinosa" - "@samuelruizperez" diff --git a/modules/nf-core/geofetch/meta.yml b/modules/nf-core/geofetch/meta.yml index b7ef89e13ed2..a4377a4d224e 100644 --- a/modules/nf-core/geofetch/meta.yml +++ b/modules/nf-core/geofetch/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "geofetch" -description: geofetch is a command-line tool that downloads and organizes data and metadata from GEO and SRA +description: geofetch is a command-line tool that downloads and organizes data and + metadata from GEO and SRA keywords: - GEO - expression @@ -9,31 +9,34 @@ keywords: - sequencing tools: - "geofetch": - description: "Downloads data and metadata from GEO and SRA and creates standard PEPs." + description: "Downloads data and metadata from GEO and SRA and creates standard + PEPs." homepage: "http://geofetch.databio.org/" documentation: "http://geofetch.databio.org/" tool_dev_url: "https://github.com/pepkit/geofetch" licence: ["BSD-2-clause"] args_id: "$args" + identifier: "" input: - - geo_accession: - type: string - description: GEO accession ID - + - - geo_accession: + type: string + description: GEO accession ID output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - geo_accession: - type: string - description: String with the GEO accession - samples: - type: file - description: List of sample files fetched - pattern: "${geo_accession}/*.CEL.gz" - + - ${geo_accession}: + type: file + description: List of sample files fetched + pattern: "${geo_accession}/*.CEL.gz" + - ${geo_accession}/*.CEL.gz: + type: file + description: List of sample files fetched + pattern: "${geo_accession}/*.CEL.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mribeirodantas" maintainers: diff --git a/modules/nf-core/geoquery/getgeo/meta.yml b/modules/nf-core/geoquery/getgeo/meta.yml index b8000288415f..ceade89a64d2 100644 --- a/modules/nf-core/geoquery/getgeo/meta.yml +++ b/modules/nf-core/geoquery/getgeo/meta.yml @@ -12,32 +12,49 @@ tools: tool_dev_url: "https://github.com/seandavi/GEOquery" doi: "10.1093/bioinformatics/btm254" licence: ["MIT"] + identifier: biotools:geoquery input: - - meta: - type: map - description: | - Groovy Map containing metadata about the GEO dataset, minimally 'id'. - - querygse: - type: string - description: | - GSE identifier to pass to getGEO() + - - meta: + type: map + description: | + Groovy Map containing metadata about the GEO dataset, minimally 'id'. + - querygse: + type: string + description: | + GSE identifier to pass to getGEO() output: - rds: - type: file - description: R object containing GEO data - pattern: "*.rds" + - meta: + type: file + description: R object containing GEO data + pattern: "*.rds" + - "*.rds": + type: file + description: R object containing GEO data + pattern: "*.rds" - expression: - type: file - description: TSV-format expression matrix - pattern: "*matrix.tsv" + - meta: + type: file + description: TSV-format expression matrix + pattern: "*matrix.tsv" + - "*matrix.tsv": + type: file + description: TSV-format expression matrix + pattern: "*matrix.tsv" - annotation: - type: file - description: TSV-format annotation file - pattern: "*annotation.tsv" + - meta: + type: file + description: TSV-format annotation file + pattern: "*annotation.tsv" + - "*annotation.tsv": + type: file + description: TSV-format annotation file + pattern: "*annotation.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@azedinez" - "@pinin4fjords" diff --git a/modules/nf-core/getorganelle/config/meta.yml b/modules/nf-core/getorganelle/config/meta.yml index 832761d3bc57..5ca86baad75a 100644 --- a/modules/nf-core/getorganelle/config/meta.yml +++ b/modules/nf-core/getorganelle/config/meta.yml @@ -14,27 +14,26 @@ tools: tool_dev_url: "https://github.com/Kinggerm/GetOrganelle" doi: "10.1186/s13059-020-02154-5" licence: ["GPL v3"] + identifier: biotools:getorganelle input: - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - + - - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - - db: - type: directory - description: Downloaded database for GetOrganelle - + - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) + - getorganelle: + type: directory + description: Downloaded database for GetOrganelle + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erinyoung" diff --git a/modules/nf-core/getorganelle/fromreads/meta.yml b/modules/nf-core/getorganelle/fromreads/meta.yml index 193df60b2207..ba5b9176515f 100644 --- a/modules/nf-core/getorganelle/fromreads/meta.yml +++ b/modules/nf-core/getorganelle/fromreads/meta.yml @@ -13,48 +13,44 @@ tools: tool_dev_url: "https://github.com/Kinggerm/GetOrganelle" doi: "10.1186/s13059-020-02154-5" licence: ["GPL v3"] + identifier: biotools:getorganelle input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fastq: - type: file - description: Input fastq files - pattern: "*.{fastq.gz}" - - - organelle_type: - type: string - description: | - Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) - - - db: - type: directory - description: GetOrganelle database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: Input fastq files + pattern: "*.{fastq.gz}" + - - organelle_type: + type: string + description: | + Type of database, esp. embplant_pt (embryophyta plant plastome), other_pt (non-embryophyta plant plastome), embplant_mt (plant mitochondrion), embplant_nr (plant nuclear ribosomal RNA), animal_mt (animal mitochondrion), and fungus_mt (fungus mitochondrion), fungus_nr (fungus nuclear ribosomal RNA) + - db: + type: directory + description: GetOrganelle database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Complete or partial organelle sequences - pattern: "*.fasta.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - results/${prefix}.${organelle_type}.fasta.gz: + type: file + description: Complete or partial organelle sequences + pattern: "*.fasta.gz" - etc: - type: file - description: Other output files - + - results/*: + type: file + description: Other output files + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erinyoung" diff --git a/modules/nf-core/gfaffix/meta.yml b/modules/nf-core/gfaffix/meta.yml index 384696cf0b0c..f1f2966f2ac3 100644 --- a/modules/nf-core/gfaffix/meta.yml +++ b/modules/nf-core/gfaffix/meta.yml @@ -13,34 +13,43 @@ tools: homepage: https://github.com/marschall-lab/GFAffix documentation: https://github.com/marschall-lab/GFAffix licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Non-redundant variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: Non-redundant variation graph in GFA 1.0 format + pattern: "*.{gfa}" - affixes: - type: file - description: Shared affixes in tab-separated values (TSV) text format - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Shared affixes in tab-separated values (TSV) text format + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/gfastats/meta.yml b/modules/nf-core/gfastats/meta.yml index aaaf47caeb86..a621343388de 100644 --- a/modules/nf-core/gfastats/meta.yml +++ b/modules/nf-core/gfastats/meta.yml @@ -17,55 +17,66 @@ tools: tool_dev_url: "https://github.com/vgl-hub/gfastats" doi: "10.1093/bioinformatics/btac460" licence: ["MIT"] + identifier: biotools:gfastats input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly file - pattern: "*.{fasta,fastq,gfa}(.gz)?" - - out_fmt: - type: string - description: Output format (fasta, fastq, gfa) - - genome_size: - type: integer - description: estimated genome size (bp) for NG* statistics (optional). - - target: - type: string - description: target specific sequence by header, optionally with coordinates (optional). - - agpfile: - type: file - description: converts input agp to path and replaces existing paths. - - include_bed: - type: file - description: generates output on a subset list of headers or coordinates in 0-based bed format. - - exclude_bed: - type: file - description: opposite of --include-bed. They can be combined (no coordinates). - - instructions: - type: file - description: set of instructions provided as an ordered list. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly file + pattern: "*.{fasta,fastq,gfa}(.gz)?" + - - out_fmt: + type: string + description: Output format (fasta, fastq, gfa) + - - genome_size: + type: integer + description: estimated genome size (bp) for NG* statistics (optional). + - - target: + type: string + description: target specific sequence by header, optionally with coordinates + (optional). + - - agpfile: + type: file + description: converts input agp to path and replaces existing paths. + - - include_bed: + type: file + description: generates output on a subset list of headers or coordinates in + 0-based bed format. + - - exclude_bed: + type: file + description: opposite of --include-bed. They can be combined (no coordinates). + - - instructions: + type: file + description: set of instructions provided as an ordered list. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly_summary: - type: file - description: Assembly summary statistics file - pattern: "*.assembly_summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly_summary": + type: file + description: Assembly summary statistics file + pattern: "*.assembly_summary" - assembly: - type: file - description: The assembly as modified by gfastats - pattern: "*.{fasta,fastq,gfa}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${out_fmt}.gz": + type: file + description: The assembly as modified by gfastats + pattern: "*.{fasta,fastq,gfa}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gfatools/gfa2fa/meta.yml b/modules/nf-core/gfatools/gfa2fa/meta.yml index a22d50a0e392..1554218f0bca 100644 --- a/modules/nf-core/gfatools/gfa2fa/meta.yml +++ b/modules/nf-core/gfatools/gfa2fa/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gfatools_gfa2fa" description: Converts GFA or rGFA files to FASTA @@ -17,30 +16,33 @@ tools: tool_dev_url: "https://github.com/lh3/gfatools" doi: "no DOI available" licence: ["Unknown"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA or rGFA file - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA or rGFA file + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: FASTA file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta.gz": + type: file + description: FASTA file + pattern: "*.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gfatools/stat/meta.yml b/modules/nf-core/gfatools/stat/meta.yml index 58503165c471..29c53078cd31 100644 --- a/modules/nf-core/gfatools/stat/meta.yml +++ b/modules/nf-core/gfatools/stat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "gfatools_stat" description: Summary statistics for GFA files @@ -17,30 +16,33 @@ tools: tool_dev_url: "https://github.com/lh3/gfatools" doi: "no DOI available" licence: ["Unknown"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA or rGFA file - pattern: "*.gfa" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA or rGFA file + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Summary statistics of the GFA file - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.stats": + type: file + description: Summary statistics of the GFA file + pattern: "*.stats" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/gffcompare/meta.yml b/modules/nf-core/gffcompare/meta.yml index dd944f2f25b2..7c3a91e39d25 100644 --- a/modules/nf-core/gffcompare/meta.yml +++ b/modules/nf-core/gffcompare/meta.yml @@ -13,78 +13,127 @@ tools: tool_dev_url: "https://github.com/gpertea/gffcompare" doi: "10.12688/f1000research.23297.1" licence: ["MIT"] + identifier: biotools:gffcompare input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test', single_end:false ] - - gtfs: - type: file - description: | - GTF/GFF files - e.g. [ 'file_1.gtf', 'file_2.gtf' ] - pattern: "*.{gtf,gff}" - - fasta: - type: file - description: Genome reference fasta file (optional) - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Index for fasta file - pattern: "*.fai" - - reference_gtf: - type: file - description: Reference annotation in gtf/gff format (optional) - pattern: "*.{gtf,gff}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - gtfs: + type: file + description: | + GTF/GFF files + e.g. [ 'file_1.gtf', 'file_2.gtf' ] + pattern: "*.{gtf,gff}" + - - meta2: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome reference fasta file (optional) + pattern: "*.{fasta,fa}" + - fai: + type: file + description: Index for fasta file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - reference_gtf: + type: file + description: Reference annotation in gtf/gff format (optional) + pattern: "*.{gtf,gff}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test', single_end:false ] - annotated_gtf: - type: file - description: | - Annotated gtf file when reference gtf is provided (optional) - pattern: "*.annotated.gtf" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.annotated.gtf": + type: file + description: | + Annotated gtf file when reference gtf is provided (optional) + pattern: "*.annotated.gtf" - combined_gtf: - type: file - description: | - Combined gtf file when multiple input files are - provided (optional) - pattern: "*.annotated.gtf" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.combined.gtf": + type: file + description: | + Combined gtf file when multiple input files are + provided (optional) + pattern: "*.annotated.gtf" - tmap: - type: file - description: | - File listing the most closely matching reference transcript - for each query transcript (optional) - pattern: "*.tmap" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.tmap": + type: file + description: | + File listing the most closely matching reference transcript + for each query transcript (optional) + pattern: "*.tmap" - refmap: - type: file - description: | - File listing the reference transcripts with overlapping - query transcripts (optional) - pattern: "*.refmap" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.refmap": + type: file + description: | + File listing the reference transcripts with overlapping + query transcripts (optional) + pattern: "*.refmap" - loci: - type: file - description: File with loci - pattern: "*.loci" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.loci": + type: file + description: File with loci + pattern: "*.loci" - stats: - type: file - description: | - File with stats for input transcripts as compared to - reference alternatively stats for the combined gtf - pattern: "*.stats" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: | + File with stats for input transcripts as compared to + reference alternatively stats for the combined gtf + pattern: "*.stats" - tracking: - type: file - description: | - This file matches transcripts up between samples - pattern: "*.tracking" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test', single_end:false ] + - "*.tracking": + type: file + description: | + This file matches transcripts up between samples + pattern: "*.tracking" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" maintainers: diff --git a/modules/nf-core/gffread/meta.yml b/modules/nf-core/gffread/meta.yml index c060282084b5..bebe7f575c20 100644 --- a/modules/nf-core/gffread/meta.yml +++ b/modules/nf-core/gffread/meta.yml @@ -1,53 +1,73 @@ name: gffread -description: Validate, filter, convert and perform various other operations on GFF files +description: Validate, filter, convert and perform various other operations on GFF + files keywords: - gff - conversion - validation tools: - gffread: - description: GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more. + description: GFF/GTF utility providing format conversions, region filtering, FASTA + sequence extraction and more. homepage: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 licence: ["MIT"] + identifier: biotools:gffread input: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" - - fasta: - type: file - description: A multi-fasta file with the genomic sequences - pattern: "*.{fasta,fa,faa,fas,fsa}" + - - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - gff: + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" + - - fasta: + type: file + description: A multi-fasta file with the genomic sequences + pattern: "*.{fasta,fa,faa,fas,fsa}" output: - - meta: - type: map - description: | - Groovy Map containing meta data - e.g. [ id:'test' ] - gtf: - type: file - description: GTF file resulting from the conversion of the GFF input file if '-T' argument is present - pattern: "*.{gtf}" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gtf": + type: file + description: GTF file resulting from the conversion of the GFF input file if + '-T' argument is present + pattern: "*.{gtf}" - gffread_gff: - type: file - description: GFF3 file resulting from the conversion of the GFF input file if '-T' argument is absent - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.gff3": + type: file + description: GFF3 file resulting from the conversion of the GFF input file if + '-T' argument is absent + pattern: "*.gff3" - gffread_fasta: - type: file - description: Fasta file produced when either of '-w', '-x', '-y' parameters is present - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing meta data + e.g. [ id:'test' ] + - "*.fasta": + type: file + description: Fasta file produced when either of '-w', '-x', '-y' parameters + is present + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/gget/gget/meta.yml b/modules/nf-core/gget/gget/meta.yml index 103fd70653f2..6d0acec13a48 100644 --- a/modules/nf-core/gget/gget/meta.yml +++ b/modules/nf-core/gget/gget/meta.yml @@ -1,5 +1,8 @@ name: "gget_gget" -description: gget is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code. +description: gget is a free, open-source command-line tool and Python package that + enables efficient querying of genomic databases. gget consists of a collection of + separate but interoperable modules, each designed to facilitate one type of database + querying in a single line of code. keywords: - gget - reference @@ -14,34 +17,42 @@ tools: tool_dev_url: "https://github.com/pachterlab/gget" doi: "10.1093/bioinformatics/btac836" licence: ["BSD-2-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - files: - type: file - description: | - Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - files: + type: file + description: | + Optional input files which can be specified for certain tools. This is mostly used to supply a FASTA file for gget muscle. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!versions.yml][!${prefix}.${extension}]*": + type: file + description: File containing output of gget command. - output: - type: file - description: File containing output of gget command (-o for most gget tools). - pattern: "*.{json,csv}" - - file: - type: file - description: Path to any file downloaded by gget - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${extension}: + type: file + description: File containing output of gget command (-o for most gget tools). + pattern: "*.{json,csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/glimpse/chunk/meta.yml b/modules/nf-core/glimpse/chunk/meta.yml index e500d9e97151..e8ff401990a4 100644 --- a/modules/nf-core/glimpse/chunk/meta.yml +++ b/modules/nf-core/glimpse/chunk/meta.yml @@ -6,43 +6,50 @@ keywords: - low coverage tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file for the input VCF/BCF file. + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - chunk_chr: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab delimited output txt file containing buffer and imputation regions. + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: Tab delimited output txt file containing buffer and imputation regions. - pattern: "*.{txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/concordance/meta.yml b/modules/nf-core/glimpse/concordance/meta.yml index 2b2d7195df88..ea4c26087c54 100644 --- a/modules/nf-core/glimpse/concordance/meta.yml +++ b/modules/nf-core/glimpse/concordance/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_concordance" -description: Compute the r2 correlation between imputed dosages (in MAF bins) and highly-confident genotype calls from the high-coverage dataset. +description: Compute the r2 correlation between imputed dosages (in MAF bins) and + highly-confident genotype calls from the high-coverage dataset. keywords: - concordance - low-coverage @@ -7,78 +8,120 @@ keywords: - imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate: - type: file - description: Imputed data. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - min_prob: - type: float - description: Minimum posterior probability P(G|R) in validation data - - min_dp: - type: integer - description: | - Minimum coverage in validation data. - If FORMAT/DP is missing and --minDP > 0, the program exits with an error. - - bins: - type: string - description: | - Allele frequency bins used for rsquared computations. - By default they should as MAF bins [0-0.5], while - they should take the full range [0-1] if --use-ref-alt is used. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed data. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file for the imputed data. + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file for the allele frequencies file. + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file for the truth file. + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - min_prob: + type: float + description: Minimum posterior probability P(G|R) in validation data + - - min_dp: + type: integer + description: | + Minimum coverage in validation data. + If FORMAT/DP is missing and --minDP > 0, the program exits with an error. + - - bins: + type: string + description: | + Allele frequency bins used for rsquared computations. + By default they should as MAF bins [0-0.5], while + they should take the full range [0-1] if --use-ref-alt is used. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - errors_cal: - type: file - description: Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.cal.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.cal.txt.gz": + type: file + description: Calibration correlation errors between imputed dosages (in MAF + bins) and highly-confident genotype. + pattern: "*.errors.cal.txt.gz" - errors_grp: - type: file - description: Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.grp.txt.gz": + type: file + description: Groups correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.grp.txt.gz" - errors_spl: - type: file - description: Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.spl.txt.gz" - - rsquared_grp: - type: file - description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.grp.txt.gz" - - rsquared_spl: - type: file - description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.spl.txt.gz": + type: file + description: Samples correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.spl.txt.gz" + - rsquare_grp: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.grp.txt.gz": + type: file + description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. + pattern: "*.rsquare.grp.txt.gz" + - rsquare_spl: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.spl.txt.gz": + type: file + description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. + pattern: "*.rsquare.spl.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/ligate/meta.yml b/modules/nf-core/glimpse/ligate/meta.yml index c3b1485c436a..c1ed67ee67b5 100644 --- a/modules/nf-core/glimpse/ligate/meta.yml +++ b/modules/nf-core/glimpse/ligate/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_ligate" -description: Concatenates imputation chunks in a single VCF/BCF file ligating phased information. +description: Concatenates imputation chunks in a single VCF/BCF file ligating phased + information. keywords: - ligate - low-coverage @@ -7,42 +8,46 @@ keywords: - imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: VCF/BCF file containing genotype probabilities (GP field). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: VCF/BCF file containing genotype probabilities (GP field). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: | - Output VCF/BCF file for the merged regions. - Phased information (HS field) is updated accordingly for the full region. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file for the merged regions. + Phased information (HS field) is updated accordingly for the full region. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/phase/meta.yml b/modules/nf-core/glimpse/phase/meta.yml index 862033b7f831..e905b7581c87 100644 --- a/modules/nf-core/glimpse/phase/meta.yml +++ b/modules/nf-core/glimpse/phase/meta.yml @@ -1,5 +1,6 @@ name: "glimpse_phase" -description: main GLIMPSE algorithm, performs phasing and imputation refining genotype likelihoods +description: main GLIMPSE algorithm, performs phasing and imputation refining genotype + likelihoods keywords: - phase - imputation @@ -7,71 +8,76 @@ keywords: - glimpse tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - samples_file: - type: file - description: | - File with sample names and ploidy information. - One sample per line with a mandatory second column indicating ploidy (1 or 2). - Sample names that are not present are assumed to have ploidy 2 (diploids). - GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. - pattern: "*.{txt,tsv}" - - input_region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - samples_file: + type: file + description: | + File with sample names and ploidy information. + One sample per line with a mandatory second column indicating ploidy (1 or 2). + Sample names that are not present are assumed to have ploidy 2 (diploids). + GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. + pattern: "*.{txt,tsv}" + - input_region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phased_variants: - type: file - description: | - Output VCF/BCF file containing genotype probabilities (GP field), - imputed dosages (DS field), best guess genotypes (GT field), - sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file containing genotype probabilities (GP field), + imputed dosages (DS field), best guess genotypes (GT field), + sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse/sample/meta.yml b/modules/nf-core/glimpse/sample/meta.yml index 36937ec0c266..483f0c597770 100644 --- a/modules/nf-core/glimpse/sample/meta.yml +++ b/modules/nf-core/glimpse/sample/meta.yml @@ -6,36 +6,40 @@ keywords: - Imputation tools: - "glimpse": - description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: VCF/BCF file generated using GLIMPSE ligate - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: VCF/BCF file generated using GLIMPSE ligate + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - haplo_sampled: - type: file - description: Output VCF/BCF file containing phased genotypes. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Output VCF/BCF file containing phased genotypes. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/chunk/meta.yml b/modules/nf-core/glimpse2/chunk/meta.yml index 759ee0249bee..7757a7a445e4 100644 --- a/modules/nf-core/glimpse2/chunk/meta.yml +++ b/modules/nf-core/glimpse2/chunk/meta.yml @@ -7,66 +7,71 @@ keywords: - glimpse tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 requirements: - AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. [ map:'GRCh38' ] - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" - - model: - type: string - description: | - Algorithm model to use: - "recursive": Recursive algorithm - "sequential": Sequential algorithm (Recommended) - "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm - pattern: "{recursive,sequential,uniform-number-variants}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. [ map:'GRCh38' ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" + - - model: + type: string + description: | + Algorithm model to use: + "recursive": Recursive algorithm + "sequential": Sequential algorithm (Recommended) + "uniform-number-variants": Experimental. Uniform the number of variants in the sequential algorithm + pattern: "{recursive,sequential,uniform-number-variants}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - chunk_chr: - type: file - description: Tab delimited output txt file containing buffer and imputation regions. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab delimited output txt file containing buffer and imputation + regions. + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/concordance/meta.yml b/modules/nf-core/glimpse2/concordance/meta.yml index 7d145d2b4b13..f286f6e929d3 100644 --- a/modules/nf-core/glimpse2/concordance/meta.yml +++ b/modules/nf-core/glimpse2/concordance/meta.yml @@ -1,5 +1,6 @@ name: "glimpse2_concordance" -description: Program to compute the genotyping error rate at the sample or marker level. +description: Program to compute the genotyping error rate at the sample or marker + level. keywords: - concordance - low-coverage @@ -7,103 +8,160 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). Can also be a list of such regions. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate: - type: file - description: Imputed dataset file obtain after phasing. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - samples: - type: file - description: List of samples to process, one sample ID per line. - pattern: "*.{txt,tsv}" - - groups: - type: file - description: Alternative to frequency bins, group bins are user defined, provided in a file. - pattern: "*.{txt,tsv}" - - bins: - type: string - description: | - Allele frequency bins used for rsquared computations. - By default they should as MAF bins [0-0.5], while - they should take the full range [0-1] if --use-ref-alt is used. - pattern: "0 0.01 0.05 ... 0.5" - - ac_bins: - type: string - description: User-defined allele count bins used for rsquared computations. - pattern: "1 2 5 10 20 ... 100000" - - allele_counts: - type: string - description: | - Default allele count bins used for rsquared computations. - AN field must be defined in the frequency file. - - min_val_gl: - type: float - description: | - Minimum genotype likelihood probability P(G|R) in validation data. - Set to zero to have no filter of if using –gt-validation - - min_val_dp: - type: integer - description: | - Minimum coverage in validation data. - If FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error. - Set to zero to have no filter of if using –gt-validation + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed dataset file obtain after phasing. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file for the imputed dataset file. + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file for the truth file. + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file for the allele frequencies file. + - samples: + type: file + description: List of samples to process, one sample ID per line. + pattern: "*.{txt,tsv}" + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). Can also be a list of such regions. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - groups: + type: file + description: Alternative to frequency bins, group bins are user defined, provided + in a file. + pattern: "*.{txt,tsv}" + - bins: + type: string + description: | + Allele frequency bins used for rsquared computations. + By default they should as MAF bins [0-0.5], while + they should take the full range [0-1] if --use-ref-alt is used. + pattern: "0 0.01 0.05 ... 0.5" + - ac_bins: + type: string + description: User-defined allele count bins used for rsquared computations. + pattern: "1 2 5 10 20 ... 100000" + - allele_counts: + type: string + description: | + Default allele count bins used for rsquared computations. + AN field must be defined in the frequency file. + - - min_val_gl: + type: float + description: | + Minimum genotype likelihood probability P(G|R) in validation data. + Set to zero to have no filter of if using –gt-validation + - - min_val_dp: + type: integer + description: | + Minimum coverage in validation data. + If FORMAT/DP is missing and –min_val_dp > 0, the program exits with an error. + Set to zero to have no filter of if using –gt-validation output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - errors_cal: - type: file - description: Calibration correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.cal.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.cal.txt.gz": + type: file + description: Calibration correlation errors between imputed dosages (in MAF + bins) and highly-confident genotype. + pattern: "*.errors.cal.txt.gz" - errors_grp: - type: file - description: Groups correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.grp.txt.gz": + type: file + description: Groups correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.grp.txt.gz" - errors_spl: - type: file - description: Samples correlation errors between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.errors.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.error.spl.txt.gz": + type: file + description: Samples correlation errors between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.errors.spl.txt.gz" - rsquare_grp: - type: file - description: Groups r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.grp.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.grp.txt.gz": + type: file + description: Groups r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.rsquare.grp.txt.gz" - rsquare_spl: - type: file - description: Samples r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "*.rsquare.spl.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rsquare.spl.txt.gz": + type: file + description: Samples r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "*.rsquare.spl.txt.gz" - rsquare_per_site: - type: file - description: Variant r-squared correlation between imputed dosages (in MAF bins) and highly-confident genotype. - pattern: "_r2_sites.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_r2_sites.txt.gz": + type: file + description: Variant r-squared correlation between imputed dosages (in MAF bins) + and highly-confident genotype. + pattern: "_r2_sites.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/ligate/meta.yml b/modules/nf-core/glimpse2/ligate/meta.yml index 7c07973f75b8..14fc8dac578b 100644 --- a/modules/nf-core/glimpse2/ligate/meta.yml +++ b/modules/nf-core/glimpse2/ligate/meta.yml @@ -9,40 +9,44 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: VCF/BCF file containing genotype probabilities (GP field). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{csi,tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: VCF/BCF file containing genotype probabilities (GP field). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{csi,tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: Output ligated (phased) file in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Output ligated (phased) file in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/glimpse2/phase/meta.yml b/modules/nf-core/glimpse2/phase/meta.yml index 700b6204fe58..11d0860b7456 100644 --- a/modules/nf-core/glimpse2/phase/meta.yml +++ b/modules/nf-core/glimpse2/phase/meta.yml @@ -7,98 +7,109 @@ keywords: - glimpse tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input: - type: file - description: | - Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. - When using BAM/CRAM the name of the file is used as samples name. - pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" - - input_index: - type: file - description: Index file of the input BAM/CRAM/VCF/BCF file. - pattern: "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" - - samples_file: - type: file - description: | - File with sample names and ploidy information. - One sample per line with a mandatory second column indicating ploidy (1 or 2). - Sample names that are not present are assumed to have ploidy 2 (diploids). - GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. - pattern: "*.{txt,tsv}" - - input_region: - type: string - description: | - Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - Optional if reference panel is in bin format. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: | - Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - Optional if reference panel is in bin format. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. `[ map:'GRCh38' ]` - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: | - File containing the genetic map. - Optional if reference panel is in bin format. - pattern: "*.gmap" - - fasta_reference: - type: file - description: | - Faidx-indexed reference sequence file in the appropriate genome build. - Necessary for CRAM files. - pattern: "*.fasta" - - fasta_reference_index: - type: file - description: | - Faidx index of the reference sequence file in the appropriate genome build. - Necessary for CRAM files. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: | + Either one or multiple BAM/CRAM files in an array containing low-coverage sequencing reads or one VCF/BCF file containing the genotype likelihoods. + When using BAM/CRAM the name of the file is used as samples name. + pattern: "*.{bam,cram,vcf,vcf.gz,bcf,bcf.gz}" + - input_index: + type: file + description: Index file of the input BAM/CRAM/VCF/BCF file. + pattern: "*.{bam.bai,cram.crai,vcf.gz.csi,bcf.gz.csi}" + - samples_file: + type: file + description: | + File with sample names and ploidy information. + One sample per line with a mandatory second column indicating ploidy (1 or 2). + Sample names that are not present are assumed to have ploidy 2 (diploids). + GLIMPSE does NOT handle the use of sex (M/F) instead of ploidy. + pattern: "*.{txt,tsv}" + - input_region: + type: string + description: | + Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). + Optional if reference panel is in bin format. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: | + Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + Optional if reference panel is in bin format. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - map: + type: file + description: | + File containing the genetic map. + Optional if reference panel is in bin format. + pattern: "*.gmap" + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. `[ map:'GRCh38' ]` + - fasta_reference: + type: file + description: | + Faidx-indexed reference sequence file in the appropriate genome build. + Necessary for CRAM files. + pattern: "*.fasta" + - fasta_reference_index: + type: file + description: | + Faidx index of the reference sequence file in the appropriate genome build. + Necessary for CRAM files. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phased_variants: - type: file - description: | - Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{vcf,vcf.gz,bcf,bgen}": + type: file + description: | + Output VCF/BCF file containing genotype probabilities (GP field), imputed dosages (DS field), best guess genotypes (GT field), sampled haplotypes in the last (max 16) main iterations (HS field) and info-score. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - stats_coverage: - type: file - description: Optional coverage statistic file created when BAM/CRAM files are used as inputs. - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt.gz": + type: file + description: Optional coverage statistic file created when BAM/CRAM files are + used as inputs. + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/glimpse2/splitreference/meta.yml b/modules/nf-core/glimpse2/splitreference/meta.yml index c70ec024f766..192e6d659c4e 100644 --- a/modules/nf-core/glimpse2/splitreference/meta.yml +++ b/modules/nf-core/glimpse2/splitreference/meta.yml @@ -7,59 +7,64 @@ keywords: - imputation tools: - "glimpse2": - description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage sequencing studies." + description: "GLIMPSE2 is a phasing and imputation method for large-scale low-coverage + sequencing studies." homepage: "https://odelaneau.github.io/GLIMPSE" documentation: "https://odelaneau.github.io/GLIMPSE/commands.html" tool_dev_url: "https://github.com/odelaneau/GLIMPSE" doi: "10.1038/s41588-020-00756-0" licence: ["MIT"] + identifier: biotools:glimpse2 requirements: - AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - input_region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - output_region: - type: string - description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - meta2: - type: map - description: | - Groovy Map containing genomic map information - e.g. `[ map:'GRCh38' ]` - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - input_region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - output_region: + type: string + description: Target imputed region, excluding left and right buffers (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing genomic map information + e.g. `[ map:'GRCh38' ]` + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bin_ref: - type: file - description: binary reference panel - pattern: "*.bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bin": + type: file + description: binary reference panel + pattern: "*.bin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/glnexus/meta.yml b/modules/nf-core/glnexus/meta.yml index 416829cbf630..a79fc63cff3c 100644 --- a/modules/nf-core/glnexus/meta.yml +++ b/modules/nf-core/glnexus/meta.yml @@ -6,30 +6,38 @@ keywords: - joint-variant-calling tools: - glnexus: - description: scalable gVCF merging and joint variant calling for population sequencing projects. + description: scalable gVCF merging and joint variant calling for population sequencing + projects. homepage: https://github.com/dnanexus-rnd/GLnexus documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started doi: 10.1101/343970 licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - gvcfs: - type: list - description: Input genomic vcf files - pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - gvcfs: + type: list + description: Input genomic vcf files + pattern: "*.{gvcf,gvcf.gz,g.vcf,g.vcf.gz}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bcf: - type: file - description: merged BCF file - pattern: "*.bcf" + - meta: + type: file + description: merged BCF file + pattern: "*.bcf" + - "*.bcf": + type: file + description: merged BCF file + pattern: "*.bcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/gmmdemux/meta.yml b/modules/nf-core/gmmdemux/meta.yml index 5b53c9abf423..cca6932649f9 100644 --- a/modules/nf-core/gmmdemux/meta.yml +++ b/modules/nf-core/gmmdemux/meta.yml @@ -1,90 +1,125 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gmmdemux" -description: GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq). +description: GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample + barcoding data (cell hashing and MULTI-seq). keywords: - demultiplexing - hashing-based deconvolution - single-cell tools: - "gmmdemux": - description: "GMM-Demux is a Gaussian-Mixture-Model-based software for processing sample barcoding data (cell hashing and MULTI-seq)." + description: "GMM-Demux is a Gaussian-Mixture-Model-based software for processing + sample barcoding data (cell hashing and MULTI-seq)." homepage: "https://pypi.org/project/GMM-Demux/" documentation: "https://github.com/CHPGenetics/GMM-Demux" tool_dev_url: "https://github.com/CHPGenetics/GMM-demux" doi: "10.1186/s13059-020-02084-2" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - hto_matrix: - type: file - description: path to matrix from cell hashing data, the tool receives either CSV files or TSV, type must be specified using parameters - - hto_names: - type: string - description: | - Comma separated list of HTO names, without whitespace - - type_report: - type: boolean - description: | - If true, full classification report is generated, otherwise the simplified classification report. - - summary_report: - type: boolean - description: | - If true, summary report is generated. - - skip: - type: file - description: | - Load a full classification report and skip the mtx folder as input. Require a path argument. - - examine: - type: file - description: | - Provide the cell list. Requires a file argument. Only executes if -u is set. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - hto_matrix: + type: file + description: path to matrix from cell hashing data, the tool receives either + CSV files or TSV, type must be specified using parameters + - hto_names: + type: string + description: | + Comma separated list of HTO names, without whitespace + - - type_report: + type: boolean + description: | + If true, full classification report is generated, otherwise the simplified classification report. + - - summary_report: + type: boolean + description: | + If true, summary report is generated. + - - skip: + type: file + description: | + Load a full classification report and skip the mtx folder as input. Require a path argument. + - - examine: + type: file + description: | + Provide the cell list. Requires a file argument. Only executes if -u is set. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - barcodes: - type: file - description: | - barcodes tsv file with removed cell-hashing-identifiable multiplets - pattern: "barcodes.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'barcodes.tsv.gz" ': + type: file + description: | + barcodes tsv file with removed cell-hashing-identifiable multiplets + pattern: "barcodes.tsv.gz" - matrix: - type: file - description: | - matrix mtx.tsv file with removed cell-hashing-identifiable multiplets - pattern: "matrix.mtx.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'matrix.mtx.gz" ': + type: file + description: | + matrix mtx.tsv file with removed cell-hashing-identifiable multiplets + pattern: "matrix.mtx.gz" - features: - type: file - description: | - features tsv file with removed cell-hashing-identifiable multiplets - pattern: "features.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'features.tsv.gz" ': + type: file + description: | + features tsv file with removed cell-hashing-identifiable multiplets + pattern: "features.tsv.gz" - classification_report: - type: file - description: | - full or simplified classification report - pattern: "GMM_*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'GMM_*.csv" ': + type: file + description: | + full or simplified classification report + pattern: "GMM_*.csv" - config_report: - type: file - description: | - Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report. - pattern: "GMM_*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - 'GMM_*.config" ': + type: file + description: | + Configuration report mapping the results obtained by the tool to the respective names of the HTOs in the classification report. + pattern: "GMM_*.csv" - summary_report: - type: file - description: | - summary report, optional output - pattern: "test/summary_report_*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - summary_report_*.txt: + type: file + description: | + summary report, optional output + pattern: "test/summary_report_*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/gnu/sort/meta.yml b/modules/nf-core/gnu/sort/meta.yml index 9d961750c64d..c555dbb5c4b4 100644 --- a/modules/nf-core/gnu/sort/meta.yml +++ b/modules/nf-core/gnu/sort/meta.yml @@ -11,30 +11,29 @@ tools: homepage: "https://github.com/vgl-hub/gfastats" documentation: "https://www.gnu.org/software/coreutils/manual/html_node/sort-invocation.html" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Draft assembly file - pattern: "*.{txt,bed,interval,genome,bins}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Draft assembly file + pattern: "*.{txt,bed,interval,genome,bins}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sorted: - type: file - description: The sorted txt file generated by sort - pattern: "*.{txt,bed,interval,genome,bins}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/gnu/split/meta.yml b/modules/nf-core/gnu/split/meta.yml index da705b8f595c..da3bb3800143 100644 --- a/modules/nf-core/gnu/split/meta.yml +++ b/modules/nf-core/gnu/split/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gnu_split" description: Split a file into consecutive or interleaved sections @@ -9,35 +8,39 @@ keywords: - generic tools: - "gnu": - description: "The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system." + description: "The GNU Core Utilities are the basic file, shell and text manipulation + utilities of the GNU operating system. These are the core utilities which are + expected to exist on every operating system." homepage: "https://www.gnu.org/software/coreutils/" documentation: "https://www.gnu.org/software/coreutils/manual/html_node/index.html" tool_dev_url: "https://git.savannah.gnu.org/cgit/coreutils.git" doi: "10.5281/zenodo.581670" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - input: - type: file - description: Text file, possibly gzip file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Text file, possibly gzip file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - split: - type: file - description: Split files - pattern: "*split*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ' "*split*" ': + type: file + description: Split files + pattern: "*split*" - versions: - type: file - description: The split files - + - versions.yml: + type: file + description: The split files authors: - "@k1sauce" maintainers: diff --git a/modules/nf-core/goat/taxonsearch/meta.yml b/modules/nf-core/goat/taxonsearch/meta.yml index 1bb19e30d7b4..db8b8adc03e7 100644 --- a/modules/nf-core/goat/taxonsearch/meta.yml +++ b/modules/nf-core/goat/taxonsearch/meta.yml @@ -13,36 +13,39 @@ tools: documentation: https://github.com/genomehubs/goat-cli/wiki tool_dev_url: https://genomehubs.github.io/goat-cli/goat_cli/ licence: ["MIT"] + identifier: biotools:goat input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - taxon: - type: string - description: | - The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank. - - taxa_file: - type: file - description: | - A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line - should contain a single entry.File size is limited to 500 entries. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - taxon: + type: string + description: | + The taxon to search. An NCBI taxon ID, or the name of a taxon at any rank. + - taxa_file: + type: file + description: | + A file of NCBI taxonomy ID's (tips) and/or binomial names. Each line + should contain a single entry.File size is limited to 500 entries. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - taxonsearch: - type: file - description: TSV file containing search results. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing search results. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/goleft/indexcov/meta.yml b/modules/nf-core/goleft/indexcov/meta.yml index dd0cd655fbef..1619caf32d8f 100644 --- a/modules/nf-core/goleft/indexcov/meta.yml +++ b/modules/nf-core/goleft/indexcov/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "goleft_indexcov" -description: Quickly estimate coverage from a whole-genome bam or cram index. A bam index has 16KB resolution so that's what this gives, but it provides what appears to be a high-quality coverage estimate in seconds per genome. +description: Quickly estimate coverage from a whole-genome bam or cram index. A bam + index has 16KB resolution so that's what this gives, but it provides what appears + to be a high-quality coverage estimate in seconds per genome. keywords: - coverage - cnv @@ -9,43 +10,112 @@ keywords: - depth tools: - "goleft": - description: "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary" + description: "goleft is a collection of bioinformatics tools distributed under + MIT license in a single static binary" homepage: "https://github.com/brentp/goleft" documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false] - - bams: - type: file - description: Sorted BAM/CRAM/SAM files - pattern: "*.{bam,cram,sam}" - - indexes: - type: file - description: BAI/CRAI files - pattern: "*.{bai,crai}" - - fai: - type: file - description: FASTA index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - bams: + type: file + description: Sorted BAM/CRAM/SAM files + pattern: "*.{bam,cram,sam}" + - indexes: + type: file + description: BAI/CRAI files + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - fai: + type: file + description: FASTA index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Files generated by indexcov - - bams: - type: file - description: Sorted ans indexed BAM or CRAM index (.crai) files - pattern: "*.{bam,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*: + type: file + description: Files generated by indexcov + - ped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*ped: + type: file + description: ped files + pattern: "*ped" + - bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*bed.gz: + type: file + description: bed files + pattern: "*bed.gz" + - bed_index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*bed.gz.tbi: + type: file + description: bed index files + pattern: "*bed.gz.tbi" + - roc: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*roc: + type: file + description: roc files + pattern: "*roc" + - html: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*html: + type: file + description: html files + pattern: "*html" + - png: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*png: + type: file + description: png files + pattern: "*png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/goleft/indexsplit/meta.yml b/modules/nf-core/goleft/indexsplit/meta.yml index 49ee3b4f4ebd..e27840a2f485 100644 --- a/modules/nf-core/goleft/indexsplit/meta.yml +++ b/modules/nf-core/goleft/indexsplit/meta.yml @@ -1,5 +1,6 @@ name: "goleft_indexsplit" -description: Quickly generate evenly sized (by amount of data) regions across a number of bam/cram files +description: Quickly generate evenly sized (by amount of data) regions across a number + of bam/cram files keywords: - bam - bed @@ -8,45 +9,52 @@ keywords: - split tools: - "goleft": - description: "goleft is a collection of bioinformatics tools distributed under MIT license in a single static binary" + description: "goleft is a collection of bioinformatics tools distributed under + MIT license in a single static binary" homepage: "https://github.com/brentp/goleft" documentation: "https://github.com/brentp/goleft" tool_dev_url: "https://github.com/brentp/goleft" doi: "10.1093/gigascience/gix090" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bai: - type: file - description: BAI/CRAI file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bai: + type: file + description: BAI/CRAI file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - split: + type: boolean + description: Split the regions output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing split regions - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing split regions + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/gprofiler2/gost/meta.yml b/modules/nf-core/gprofiler2/gost/meta.yml index a2789f27ae45..33c9bff24b3e 100644 --- a/modules/nf-core/gprofiler2/gost/meta.yml +++ b/modules/nf-core/gprofiler2/gost/meta.yml @@ -8,95 +8,120 @@ keywords: - gene set tools: - "gprofiler2": - description: "An R interface corresponding to the 2019 update of g:Profiler web tool." + description: "An R interface corresponding to the 2019 update of g:Profiler web + tool." homepage: "https://biit.cs.ut.ee/gprofiler/page/r" documentation: "https://rdrr.io/cran/gprofiler2/" tool_dev_url: "https://gl.cs.ut.ee/biit/r-gprofiler2" doi: "10.1093/nar/gkad347" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - de_file: - type: file - pattern: "*.{csv,tsv}" - description: | - CSV or TSV-format tabular file with differential analysis outputs - - contrast_variable: - type: string - description: | - The contrast variable that is being investigated in DE analysis, e.g. "treatment". - - reference: - type: string - description: | - The contrast level of the reference samples, e.g. "control" - - target: - type: string - description: | - The contrast level of the target samples, e.g. "treated" - - background_file: - type: file - pattern: "*.{csv,tsv,txt}" - description: | - Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs. - - gmt_file: - type: file - pattern: "*.gmt" - description: | - Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases - + - - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - de_file: + type: file + pattern: "*.{csv,tsv}" + description: | + CSV or TSV-format tabular file with differential analysis outputs + - - gmt_file: + type: file + pattern: "*.gmt" + description: | + Path to a GMT file downloaded from g:profiler that should be queried instead of the online databases + - - background_file: + type: file + pattern: "*.{csv,tsv,txt}" + description: | + Path to a CSV/TSV/TXT file listing gene IDs that should be used as the background (will override count_file). This can be an expression matrix (see also background_column parameter); if so, will only consider those genes with an expression value > 0 in at least one sample. Alternatively, this can be a TXT file containing only a list of gene IDs. output: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - all_enrich: - type: file - description: | - TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found - pattern: "*gprofiler2.*all_enriched_pathways.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.all_enriched_pathways.tsv": + type: file + description: | + TSV file; table listing all enriched pathways that were found. This table will always be created (empty if no enrichment was found), the other output files are only created if enriched pathways were found + pattern: "*gprofiler2.*all_enriched_pathways.tsv" - rds: - type: file - description: | - RDS file; R object containing the results of the gost query - pattern: "*gprofiler2.*gost_results.rds" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gost_results.rds": + type: file + description: | + RDS file; R object containing the results of the gost query + pattern: "*gprofiler2.*gost_results.rds" - plot_png: - type: file - description: | - PNG file; Manhattan plot of all enriched pathways - pattern: "*gprofiler2.*gostplot.png" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gostplot.png": + type: file + description: | + PNG file; Manhattan plot of all enriched pathways + pattern: "*gprofiler2.*gostplot.png" - plot_html: - type: file - description: | - HTML file; interactive Manhattan plot of all enriched pathways - pattern: "*gprofiler2.*gostplot.html" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.gostplot.html": + type: file + description: | + HTML file; interactive Manhattan plot of all enriched pathways + pattern: "*gprofiler2.*gostplot.html" - sub_enrich: - type: file - description: | - TSV file; table listing enriched pathways that were found from one particular source - pattern: "*gprofiler2.*sub_enriched_pathways.tsv" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.*.sub_enriched_pathways.tsv": + type: file + description: | + TSV file; table listing enriched pathways that were found from one particular source + pattern: "*gprofiler2.*sub_enriched_pathways.tsv" - sub_plot: - type: file - description: | - PNG file; bar plot showing the fraction of genes that were found enriched in each pathway - pattern: "*gprofiler2.*sub_enriched_pathways.png" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*.gprofiler2.*.sub_enriched_pathways.png": + type: file + description: | + PNG file; bar plot showing the fraction of genes that were found enriched in each pathway + pattern: "*gprofiler2.*sub_enriched_pathways.png" - filtered_gmt: - type: file - description: | - GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources - pattern: "*ENSG_filtered.gmt" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*ENSG_filtered.gmt": + type: file + description: | + GMT file that was provided as input or that was downloaded from g:profiler if no input GMT file was given; filtered for the selected datasources + pattern: "*ENSG_filtered.gmt" - session_info: - type: file - description: | - Log file containing information about the R session that was run for this module - pattern: "*R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*R_sessionInfo.log": + type: file + description: | + Log file containing information about the R session that was run for this module + pattern: "*R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@WackerO" diff --git a/modules/nf-core/grabix/check/meta.yml b/modules/nf-core/grabix/check/meta.yml index 7997cdd6a122..cd65ea9525d9 100644 --- a/modules/nf-core/grabix/check/meta.yml +++ b/modules/nf-core/grabix/check/meta.yml @@ -1,4 +1,3 @@ ---- name: "grabix_check" description: Checks if the input file is bgzip compressed or not keywords: @@ -11,21 +10,27 @@ tools: homepage: "https://github.com/arq5x/grabix" documentation: "https://github.com/arq5x/grabix" + identifier: "" input: - - input: - type: file - pattern: "*.gz" - description: file to check compression - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + pattern: "*.gz" + description: file to check compression output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - compress_bgzip: - type: string - description: environmental variable with value "yes" or "no" - + - meta: + type: string + description: environmental variable with value "yes" or "no" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MartaSantanaSilva" maintainers: diff --git a/modules/nf-core/graphmap2/align/meta.yml b/modules/nf-core/graphmap2/align/meta.yml index b5e0f8ce4170..40087840a240 100644 --- a/modules/nf-core/graphmap2/align/meta.yml +++ b/modules/nf-core/graphmap2/align/meta.yml @@ -13,39 +13,40 @@ tools: homepage: https://github.com/lbcb-sci/graphmap2 documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads licence: ["MIT"] + identifier: biotools:Graphmap2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input FASTQ files - and paired-end data, respectively. - - fasta: - type: file - description: | - Reference database in FASTA format. - - index: - type: file - description: | - FASTA index in gmidx. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: file containing reads to be aligned. + - - fasta: + type: file + description: | + Reference database in FASTA format. + - - index: + type: file + description: | + FASTA index in gmidx. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: Alignment in SAM format - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Alignment in SAM format + pattern: "*.sam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/graphmap2/index/meta.yml b/modules/nf-core/graphmap2/index/meta.yml index 303f248945c4..6719574d3530 100644 --- a/modules/nf-core/graphmap2/index/meta.yml +++ b/modules/nf-core/graphmap2/index/meta.yml @@ -11,20 +11,23 @@ tools: homepage: https://github.com/lbcb-sci/graphmap2 documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads licence: ["MIT"] + identifier: biotools:Graphmap2 input: - - fasta: - type: file - description: | - Reference database in FASTA format. + - - fasta: + type: file + description: | + Reference database in FASTA format. output: - - gmidx: - type: file - description: Graphmap2 fasta index in gmidx format - pattern: "*.gmidx" + - index: + - "*.gmidx": + type: file + description: Index file in gmidx format + pattern: "*.gmidx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/graphtyper/genotype/meta.yml b/modules/nf-core/graphtyper/genotype/meta.yml index b440dce4928b..8e109be90a84 100644 --- a/modules/nf-core/graphtyper/genotype/meta.yml +++ b/modules/nf-core/graphtyper/genotype/meta.yml @@ -8,56 +8,80 @@ keywords: - pangenome tools: - "graphtyper": - description: A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants. + description: A graph-based variant caller capable of genotyping population-scale + short read data sets while incoperating previously discovered variants. homepage: "https://github.com/DecodeGenetics/graphtyper" documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" licence: ["MIT"] + identifier: biotools:Graphtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM index file. This is automatically found base on BAM input file name - pattern: "*.{bai}" - - ref: - type: file - description: Reference fasta file - pattern: "*.{fa, fasta, fas}" - - ref_fai: - type: file - description: Reference index file. This is automatically found based on referece input file name. - pattern: "*.{.fai}" - - region_file: - type: file - description: File with a list of chromosome/locations in reference genome to genotype. One region per line in the format :-. This or `--region` (in ext.args) must be specified. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM index file. This is automatically found base on BAM input file + name + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - ref: + type: file + description: Reference fasta file + pattern: "*.{fa, fasta, fas}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - ref_fai: + type: file + description: Reference index file. This is automatically found based on referece + input file name. + pattern: "*.{.fai}" + - - region_file: + type: file + description: File with a list of chromosome/locations in reference genome to + genotype. One region per line in the format :-. This or + `--region` (in ext.args) must be specified. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with genotyped variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/*/*.vcf.gz: + type: file + description: VCF file with genotyped variants + pattern: "*.{vcf.gz}" - tbi: - type: file - description: VCF index file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - results/*/*.vcf.gz.tbi: + type: file + description: VCF index file + pattern: "*.{vcf.gz.tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml index a34a83e83fc3..f2512a336167 100644 --- a/modules/nf-core/graphtyper/vcfconcatenate/meta.yml +++ b/modules/nf-core/graphtyper/vcfconcatenate/meta.yml @@ -7,40 +7,50 @@ keywords: - vcf tools: - "graphtyper": - description: A graph-based variant caller capable of genotyping population-scale short read data sets while incoperating previously discovered variants. + description: A graph-based variant caller capable of genotyping population-scale + short read data sets while incoperating previously discovered variants. homepage: "https://github.com/DecodeGenetics/graphtyper" documentation: "https://github.com/DecodeGenetics/graphtyper/wiki/User-guide" tool_dev_url: "https://github.com/DecodeGenetics/graphtyper" doi: "10.1038/ng.3964" licence: ["MIT"] + identifier: biotools:Graphtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: VCF files - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: VCF files + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Concatenated VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Concatenated VCF file + pattern: "*.{vcf.gz}" - tbi: - type: file - description: Concatenated VCF file index - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.tbi": + type: file + description: Concatenated VCF file index + pattern: "*.{tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/gridss/gridss/meta.yml b/modules/nf-core/gridss/gridss/meta.yml index a75bb46df9d0..7b26734b11e7 100644 --- a/modules/nf-core/gridss/gridss/meta.yml +++ b/modules/nf-core/gridss/gridss/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridss" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -13,41 +14,57 @@ tools: tool_dev_url: "https://github.com/PapenfussLab/gridss" doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - inputs: - type: file - description: One or more input BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - fasta: - type: file - description: The reference fasta - pattern: "*.{fa,fna,fasta}" - - fasta_fai: - type: file - description: The index of the reference fasta - pattern: "*.fai" - - bwa_index: - type: directory - description: OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - inputs: + type: file + description: One or more input BAM/CRAM file(s) + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + - fasta: + type: file + description: The reference fasta + pattern: "*.{fa,fna,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + - fasta_fai: + type: file + description: The index of the reference fasta + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + - bwa_index: + type: directory + description: OPTIONAL - The BWA index created from the reference fasta, will + be generated by Gridss in the setupreference step output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The called VCF file created by Gridss' call step - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: The called VCF file created by Gridss' call step + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml index 852e5ea402b5..fda9054e8208 100644 --- a/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml +++ b/modules/nf-core/gridss/gridssgenerateponbedpe/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridssgenerateponbedpe" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -15,69 +16,77 @@ tools: doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test'] - - meta3: - type: map - description: | - Groovy Map containing reference fai information - e.g. [ id:'test'] - - meta4: - type: map - description: | - Groovy Map containing bwa generated index information - e.g. [ id:'test'] - - vcf: - type: file - description: GRIDSS generated vcf file - pattern: "*.vcf" - - bedpe: - type: file - description: GRIDSS generated bedpe file - pattern: "*.bedpe" - - bed: - type: file - description: GRIDSS generated bed file - pattern: "*.bed" - - fasta: - type: file - description: The reference fasta - pattern: "*.{fa,fna,fasta}" - - fasta_fai: - type: file - description: The index of the reference fasta - pattern: "*.fai" - - bwa_index: - type: directory - description: OPTIONAL - The BWA index created from the reference fasta, will be generated by Gridss in the setupreference step - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: GRIDSS generated vcf file + pattern: "*.vcf" + - bedpe: + type: file + description: GRIDSS generated bedpe file + pattern: "*.bedpe" + - bed: + type: file + description: GRIDSS generated bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta + pattern: "*.{fa,fna,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference fai information + e.g. [ id:'test'] + - fai: + type: file + description: The index of the reference fasta + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bwa generated index information + e.g. [ id:'test'] + - bwa_index: + type: directory + description: OPTIONAL - The BWA index created from the reference fasta, will + be generated by Gridss in the setupreference step output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedpe: - type: file - description: GRIDSS generated breakpoint pon bedpe file - pattern: "*.bedpe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bedpe": + type: file + description: GRIDSS generated breakpoint pon bedpe file + pattern: "*.bedpe" - bed: - type: file - description: GRIDSS generated breakpoint pon bed file - pattern: "*.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bed": + type: file + description: GRIDSS generated breakpoint pon bed file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml index 3aea9b8cdd1d..cc54ea9ef4f3 100644 --- a/modules/nf-core/gridss/gridsssomaticfilter/meta.yml +++ b/modules/nf-core/gridss/gridsssomaticfilter/meta.yml @@ -1,5 +1,6 @@ name: "gridss_gridsssomaticfilter" -description: GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. +description: GRIDSS is a module software suite containing tools useful for the detection + of genomic rearrangements. keywords: - gridss - structural variants @@ -13,41 +14,51 @@ tools: doi: "10.1186/s13059-021-02423-x" licence: ["GPL v3"] + identifier: biotools:gridss input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing information for PONDIR - e.g. [ id:'test'] - - vcf: - type: file - description: Input VCF file, must be generated with GRIDSS - pattern: "*.{vcf,vcf.gz}" - - pondir: - type: directory - description: Directory containing Panel Of Normal bed/bedpe used to filter FP somatic events. Use gridss.GeneratePonBedpe to generate the PON. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: Input VCF file, must be generated with GRIDSS + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing information for PONDIR + e.g. [ id:'test'] + - pondir: + type: directory + description: Directory containing Panel Of Normal bed/bedpe used to filter FP + somatic events. Use gridss.GeneratePonBedpe to generate the PON. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - high_conf_sv: - type: file - description: VCF file including high confidence somatic SVs - pattern: "*.vcf.bgz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.high_confidence_somatic.vcf.bgz": + type: file + description: VCF file including high confidence somatic SVs + pattern: "*.vcf.bgz" - all_sv: - type: file - description: VCF file including all somatic SVs - pattern: "*.vcf.bgz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.all_somatic.vcf.bgz": + type: file + description: VCF file including all somatic SVs + pattern: "*.vcf.bgz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/gsea/gsea/meta.yml b/modules/nf-core/gsea/gsea/meta.yml index fe2d4c95692a..f3ce403fd04c 100644 --- a/modules/nf-core/gsea/gsea/meta.yml +++ b/modules/nf-core/gsea/gsea/meta.yml @@ -12,132 +12,245 @@ tools: documentation: "https://software.broadinstitute.org/cancer/software/gsea/wiki/index.php/Main_Page" doi: "10.1073/pnas.0506580102" licence: ["BSD-3-clause"] + identifier: biotools:gsea input: - - meta: - type: map - description: | - Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]. - - gct: - type: file - description: GCT file with expression values - pattern: "*.{gct}" - - cls: - type: file - description: CL file with the classes of the samples in the GCT file - pattern: "*.{gct}" - - gene_sets: - type: file - description: GMX or GMT file with gene sets - pattern: "*.{gmx,gmt}" - - reference: - type: string - description: | - String indicating which of the classes in the cls file should be used - as the reference level of the comparison. - - target: - type: string - description: | - String indicating which of the classes in the cls file should be used - as the target level of the comparison. - - chip: - type: file - description: | - optional Broad-style chip file mapping identifiers in gct to - those in gene_sets - pattern: "*.{chip}" + - - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ]. + - gct: + type: file + description: GCT file with expression values + pattern: "*.{gct}" + - cls: + type: file + description: CL file with the classes of the samples in the GCT file + pattern: "*.{gct}" + - gene_sets: + type: file + description: GMX or GMT file with gene sets + pattern: "*.{gmx,gmt}" + - - reference: + type: string + description: | + String indicating which of the classes in the cls file should be used + as the reference level of the comparison. + - target: + type: string + description: | + String indicating which of the classes in the cls file should be used + as the target level of the comparison. + - - chip: + type: file + description: | + optional Broad-style chip file mapping identifiers in gct to + those in gene_sets + pattern: "*.{chip}" output: - - meta: - type: map - description: | - Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] - rpt: - type: file - description: File containing parameter settings used - pattern: "*.rpt" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*.rpt": + type: file + description: File containing parameter settings used + pattern: "*.rpt" - index_html: - type: file - description: Top level report HTML file - pattern: "index.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*index.html": + type: file + description: Top level report HTML file + pattern: "index.html" - heat_map_corr_plot: - type: file - description: HTML file combining heatmap and rank correlation plot - pattern: "heat_map_corr_plot.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*heat_map_corr_plot.html": + type: file + description: HTML file combining heatmap and rank correlation plot + pattern: "heat_map_corr_plot.html" - report_tsvs_ref: - type: file - description: Main TSV results report file for the reference group. - pattern: "gsea_report_for_reference*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${reference}.tsv": + type: file + description: Main TSV results report file for the reference group. + pattern: "gsea_report_for_reference*.tsv" - report_htmls_ref: - type: file - description: Main HTML results report file for the reference group. sample groups - pattern: "gsea_report_for_reference*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${reference}.html": + type: file + description: Main HTML results report file for the reference group. sample groups + pattern: "gsea_report_for_reference*.html" - report_tsvs_target: - type: file - description: Main TSV results report file for the target group. - pattern: "gsea_report_for_target*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${target}.tsv": + type: file + description: Main TSV results report file for the target group. + pattern: "gsea_report_for_target*.tsv" - report_htmls_target: - type: file - description: Main HTML results report file for the target group. - pattern: "gsea_report_for_target*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gsea_report_for_${target}.html": + type: file + description: Main HTML results report file for the target group. + pattern: "gsea_report_for_target*.html" - ranked_gene_list: - type: file - description: TSV file with ranked gene list and scores - pattern: "ranked_gene_list*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*ranked_gene_list*.tsv": + type: file + description: TSV file with ranked gene list and scores + pattern: "ranked_gene_list*.tsv" - gene_set_sizes: - type: file - description: TSV file with gene set sizes - pattern: "gene_set_sizes.tsv" - - butterfly_plot: - type: file - description: Butterfly plot with gene rank plotted against score - pattern: "butterfly_plot.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gene_set_sizes.tsv": + type: file + description: TSV file with gene set sizes + pattern: "gene_set_sizes.tsv" - histogram: - type: file - description: Plot showing number of gene sets by enrichment score - pattern: "global_es_histogram.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*global_es_histogram.png": + type: file + description: Plot showing number of gene sets by enrichment score + pattern: "global_es_histogram.png" - heatmap: - type: file - description: Heat Map of the top 50 features for each phenotype in test - pattern: "heat_map_1.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*heat_map_1.png": + type: file + description: Heat Map of the top 50 features for each phenotype in test + pattern: "heat_map_1.png" - pvalues_vs_nes_plot: - type: file - description: Plot showing FDR q-value by normalised enrichment score - pattern: "pvalues_vs_nes_plot" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*pvalues_vs_nes_plot.png": + type: file + description: Plot showing FDR q-value by normalised enrichment score + pattern: "pvalues_vs_nes_plot" + - ues_vs_nes_plot: + type: file + description: Plot showing FDR q-value by normalised enrichment score + pattern: "pvalues_vs_nes_plot" - ranked_list_corr: - type: file - description: Ranked Gene List Correlation Profile - pattern: "ranked_list_corr_2.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*ranked_list_corr_2.png": + type: file + description: Ranked Gene List Correlation Profile + pattern: "ranked_list_corr_2.png" + - butterfly_plot: + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*butterfly_plot.png": + type: file + description: Butterfly plot with gene rank plotted against score + pattern: "butterfly_plot.png" - gene_set_tsv: - type: list - description: Where -make_sets is not set to false, TSV files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!gene_set_size|gsea_report|ranked_gene_list]*.tsv": + type: list + description: Where -make_sets is not set to false, TSV files, one file for each + gene set, with detail on enrichment for each gene + pattern: "[!gene_set_size|gsea_report|ranked_gene_list]*.tsv" - gene_set_html: - type: list - description: Where -make_sets is not set to false, HTML files, one file for each gene set, with detail on enrichment for each gene - pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html": + type: list + description: Where -make_sets is not set to false, HTML files, one file for + each gene set, with detail on enrichment for each gene + pattern: "[!gsea_report|heat_map_corr_plot|index|pos_snapshot|neg_snapshot]*.html" - gene_set_heatmap: - type: list - description: Where -make_sets is not set to false, PNG-format heatmaps, one file for each gene set, showing expression for each gene - pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png": + type: list + description: Where -make_sets is not set to false, PNG-format heatmaps, one + file for each gene set, showing expression for each gene + pattern: "[!butterfly|enplot|global_es_histogram|gset_rnd_es_dist|heat_map|pvalues_vs_nes_plot|ranked_list_corr]*.png" - snapshot: - type: list - description: HTML files, one each for positive and negative enrichment, collecting elements of gene_set_enplot - pattern: "*_snapshot*.html" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*_snapshot*.html": + type: list + description: HTML files, one each for positive and negative enrichment, collecting + elements of gene_set_enplot + pattern: "*_snapshot*.html" - gene_set_enplot: - type: list - description: Where -make_sets is not set to false, PNG-format enrichment (barcode) plots, one file for each gene set, showing how genes contribute to enrichment. - pattern: "enplot*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*enplot*.png": + type: list + description: Where -make_sets is not set to false, PNG-format enrichment (barcode) + plots, one file for each gene set, showing how genes contribute to enrichment. + pattern: "enplot*.png" - gene_set_dist: - type: list - description: Where -make_sets is not set to false, PNG-format enrichment score distributions plots, one file for each gene set. - pattern: "gset_rnd_es_dist*.png" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*gset_rnd_es_dist*.png": + type: list + description: Where -make_sets is not set to false, PNG-format enrichment score + distributions plots, one file for each gene set. + pattern: "gset_rnd_es_dist*.png" - archive: - type: file - description: Where -zip_report is set, a zip archive containing all outputs - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing metadata, at a minimum an id e.g. [ id:'test' ] + - "*.zip": + type: file + description: Where -zip_report is set, a zip archive containing all outputs + pattern: "*.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/gstama/collapse/meta.yml b/modules/nf-core/gstama/collapse/meta.yml index c9bca15bee43..0166dc24d6d4 100644 --- a/modules/nf-core/gstama/collapse/meta.yml +++ b/modules/nf-core/gstama/collapse/meta.yml @@ -16,66 +16,132 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: 10.1186/s12864-020-07123-7 licence: ["GNU GPL3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A sorted BAM or sam file of aligned reads - pattern: "*.{bam,sam}" - - fasta: - type: file - description: A fasta file of the genome used for the mapping - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: A sorted BAM or sam file of aligned reads + pattern: "*.{bam,sam}" + - - fasta: + type: file + description: A fasta file of the genome used for the mapping + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: a bed12 format file containing the final collapsed version of your transcriptome - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_collapsed.bed": + type: file + description: a bed12 format file containing the final collapsed version of your + transcriptome + pattern: "*.bed" - bed_trans_reads: - type: file - description: This file uses bed12 format to show the transcript model for each read based on the mapping prior to collapsing. This only contains the reads which were accepted according to the defined thresholds. You can use this file to see if there were any strange occurrences during collapsing. It also contains the relationships between reads and collapsed transcript models. The 1st subfield in the 4th column shows the final transcript ID and the 2nd subfield in the 4th column shows the read ID. If you used no_cap mode for collapsing there may be multiple lines for a single read. This happens when a 5' degraded read can match to multiple 5' longer transcript models. - pattern: "*_trans_read.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_read.bed": + type: file + description: This file uses bed12 format to show the transcript model for each + read based on the mapping prior to collapsing. This only contains the reads + which were accepted according to the defined thresholds. You can use this + file to see if there were any strange occurrences during collapsing. It also + contains the relationships between reads and collapsed transcript models. + The 1st subfield in the 4th column shows the final transcript ID and the 2nd + subfield in the 4th column shows the read ID. If you used no_cap mode for + collapsing there may be multiple lines for a single read. This happens when + a 5' degraded read can match to multiple 5' longer transcript models. + pattern: "*_trans_read.bed" - local_density_error: - type: file - description: This file contains the log of filtering for local density error around the splice junctions ("-lde") - pattern: "*_local_density_error.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_local_density_error.txt": + type: file + description: This file contains the log of filtering for local density error + around the splice junctions ("-lde") + pattern: "*_local_density_error.txt" - polya: - type: file - description: This file contains the reads with potential poly A truncation. - pattern: "*_polya.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_polya.txt": + type: file + description: This file contains the reads with potential poly A truncation. + pattern: "*_polya.txt" - read: - type: file - description: This file contains information for all mapped reads from the input SAM/BAM file. It shows both accepted and discarded reads and should match the number of mapped reads in your SAM/BAM file - pattern: "*_read.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_read.txt": + type: file + description: This file contains information for all mapped reads from the input + SAM/BAM file. It shows both accepted and discarded reads and should match + the number of mapped reads in your SAM/BAM file + pattern: "*_read.txt" - strand_check: - type: file - description: This file shows instances where the sam flag strand information contrasted the GMAP strand information. - pattern: "*_strand_check.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_strand_check.txt": + type: file + description: This file shows instances where the sam flag strand information + contrasted the GMAP strand information. + pattern: "*_strand_check.txt" - trans_report: - type: file - description: This file contains collapsing information for each transcript. - pattern: "*_trans_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This file contains collapsing information for each transcript. + pattern: "*_trans_report.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - varcov: - type: file - description: This file contains the coverage information for each variant detected. - pattern: "*_varcov.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_varcov.txt": + type: file + description: This file contains the coverage information for each variant detected. + pattern: "*_varcov.txt" - variants: - type: file - description: This file contains the variants called. Variants are only called if 5 or more reads show the variant at a specific locus. If you would like to change the threshold, please make an issue about this in the Github repo. - pattern: "*_variants.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_variants.txt": + type: file + description: This file contains the variants called. Variants are only called + if 5 or more reads show the variant at a specific locus. If you would like + to change the threshold, please make an issue about this in the Github repo. + pattern: "*_variants.txt" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/merge/meta.yml b/modules/nf-core/gstama/merge/meta.yml index adb2b32dd3d8..81cbc87b5afc 100644 --- a/modules/nf-core/gstama/merge/meta.yml +++ b/modules/nf-core/gstama/merge/meta.yml @@ -17,42 +17,79 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" licence: ["GPL v3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed12 file generated by TAMA collapse - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed12 file generated by TAMA collapse + pattern: "*.bed" + - - filelist: + type: file + description: list of files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - bed: - type: file - description: This is the main merged annotation file. Transcripts are coloured according to the source support for each model. Sources are numbered based on the order supplied in the input filelist file. For example the first file named in the filelist file would have its transcripts coloured in red. If a transcript has multiple sources the colour is shown as magenta. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bed": + type: file + description: This is the main merged annotation file. Transcripts are coloured + according to the source support for each model. Sources are numbered based + on the order supplied in the input filelist file. For example the first file + named in the filelist file would have its transcripts coloured in red. If + a transcript has multiple sources the colour is shown as magenta. + pattern: "*.bed" - gene_report: - type: file - description: This contains a report of the genes from the merged file. "num_clusters" refers to the number of source transcripts that were used to make this gene model. "num_final_trans" refers to the number of transcripts in the final gene model. - pattern: "*_gene_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_gene_report.txt": + type: file + description: This contains a report of the genes from the merged file. "num_clusters" + refers to the number of source transcripts that were used to make this gene + model. "num_final_trans" refers to the number of transcripts in the final + gene model. + pattern: "*_gene_report.txt" - merge: - type: file - description: This contains a bed12 format file which shows the coordinates of each input transcript matched to the merged transcript ID. I used the "txt" extension even though it is a bed file just to avoid confusion with the main bed file. You can use this file to map the final merged transcript models to their pre-merged supporting transcripts. The 1st subfield in the 4th column shows the final merged transcript ID while the 2nd subfield shows the pre-merged transcript ID with source prefix. - pattern: "*_merge.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_merge.txt": + type: file + description: This contains a bed12 format file which shows the coordinates of + each input transcript matched to the merged transcript ID. I used the "txt" + extension even though it is a bed file just to avoid confusion with the main + bed file. You can use this file to map the final merged transcript models + to their pre-merged supporting transcripts. The 1st subfield in the 4th column + shows the final merged transcript ID while the 2nd subfield shows the pre-merged + transcript ID with source prefix. + pattern: "*_merge.txt" - trans_report: - type: file - description: This contains the source information for each merged transcript. - pattern: "*_trans_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_trans_report.txt": + type: file + description: This contains the source information for each merged transcript. + pattern: "*_trans_report.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gstama/polyacleanup/meta.yml b/modules/nf-core/gstama/polyacleanup/meta.yml index d8d17543bb7b..7f7284a7c6e8 100644 --- a/modules/nf-core/gstama/polyacleanup/meta.yml +++ b/modules/nf-core/gstama/polyacleanup/meta.yml @@ -1,5 +1,6 @@ name: gstama_polyacleanup -description: Helper script, remove remaining polyA sequences from Full Length Non Chimeric reads (Pacbio isoseq3) +description: Helper script, remove remaining polyA sequences from Full Length Non + Chimeric reads (Pacbio isoseq3) keywords: - gstama - gstama/polyacleanup @@ -16,38 +17,55 @@ tools: tool_dev_url: https://github.com/sguizard/gs-tama doi: "10.1186/s12864-020-07123-7" licence: ["GPL v3 License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Full Length Non Chimeric reads in fasta format - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Full Length Non Chimeric reads in fasta format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: The Full Length Non Chimeric reads clened from remaining polyA tails. The sequences are in FASTA format compressed with gzip. - pattern: "*_tama.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama.fa.gz": + type: file + description: The Full Length Non Chimeric reads clened from remaining polyA + tails. The sequences are in FASTA format compressed with gzip. + pattern: "*_tama.fa.gz" - report: - type: file - description: A text file describing the number of polyA tails removed and their length. Compressed with gzip. - pattern: "*_tama_polya_flnc_report.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama_polya_flnc_report.txt.gz": + type: file + description: A text file describing the number of polyA tails removed and their + length. Compressed with gzip. + pattern: "*_tama_polya_flnc_report.txt.gz" - tails: - type: file - description: A gzip compressed FASTA file of trimmed polyA tails. - pattern: "*_tama_tails.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tama_tails.fa.gz": + type: file + description: A gzip compressed FASTA file of trimmed polyA tails. + pattern: "*_tama_tails.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/gt/gff3/meta.yml b/modules/nf-core/gt/gff3/meta.yml index 5cecd8d0f18f..62c4cbc6a010 100644 --- a/modules/nf-core/gt/gff3/meta.yml +++ b/modules/nf-core/gt/gff3/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3" -description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output GFF3 files" +description: "GenomeTools gt-gff3 utility to parse, possibly transform, and output + GFF3 files" keywords: - genome - gff3 @@ -14,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - gt_gff3: - type: file - description: Parsed gff3 file produced only if there is no parsing error - pattern: "*.gt.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.gt.gff3": + type: file + description: Parsed gff3 file produced only if there is no parsing error + pattern: "*.gt.gff3" - error_log: - type: file - description: Error log if gt-gff3 failed to parse the input gff3 file - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Error log if gt-gff3 failed to parse the input gff3 file + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@gallvp" maintainers: diff --git a/modules/nf-core/gt/gff3validator/meta.yml b/modules/nf-core/gt/gff3validator/meta.yml index 3322faf90cfc..98ff256d15a9 100644 --- a/modules/nf-core/gt/gff3validator/meta.yml +++ b/modules/nf-core/gt/gff3validator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_gff3validator" description: "GenomeTools gt-gff3validator utility to strictly validate a GFF3 file" @@ -15,34 +14,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - success_log: - type: file - description: Log file for successful validation - pattern: "*.success.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.success.log": + type: file + description: Log file for successful validation + pattern: "*.success.log" - error_log: - type: file - description: Log file for failed validation - pattern: "*.error.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.error.log": + type: file + description: Log file for failed validation + pattern: "*.error.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/ltrharvest/meta.yml b/modules/nf-core/gt/ltrharvest/meta.yml index a41813085226..a57501eaef1d 100644 --- a/modules/nf-core/gt/ltrharvest/meta.yml +++ b/modules/nf-core/gt/ltrharvest/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_ltrharvest" description: Predicts LTR retrotransposons using GenomeTools gt-ltrharvest utility @@ -17,42 +16,64 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - index: - type: directory - description: Folder containing the suffixerator index files - pattern: "suffixerator" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - index: + type: directory + description: Folder containing the suffixerator index files + pattern: "suffixerator" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - tabout: - type: file - description: Old tabular output by default or when `-tabout yes` argument is present - pattern: "*.tabout" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tabout": + type: file + description: Old tabular output by default or when `-tabout yes` argument is + present + pattern: "*.tabout" - gff3: - type: file - description: GFF3 output when `-tabout no` argument is present - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: GFF3 output when `-tabout no` argument is present + pattern: "*.gff3" - fasta: - type: file - description: FASTA output when `-out` argument is present - pattern: "*.{fa,fsa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $out_name: + type: file + description: FASTA output when `-out` argument is present + pattern: "*.{fa,fsa,fasta}" - inner_fasta: - type: file - description: FASTA output for inner regions when `-outinner` argument is present - pattern: "*.{fa,fsa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $outinner_name: + type: file + description: FASTA output for inner regions when `-outinner` argument is present + pattern: "*.{fa,fsa,fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/stat/meta.yml b/modules/nf-core/gt/stat/meta.yml index fa477f340a4a..3f62f8eba265 100644 --- a/modules/nf-core/gt/stat/meta.yml +++ b/modules/nf-core/gt/stat/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_stat" -description: "GenomeTools gt-stat utility to show statistics about features contained in GFF3 files" +description: "GenomeTools gt-stat utility to show statistics about features contained + in GFF3 files" keywords: - genome - gff3 @@ -16,30 +16,33 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - gff3: - type: file - description: Input gff3 file - pattern: "*.{gff,gff3}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - gff3: + type: file + description: Input gff3 file + pattern: "*.{gff,gff3}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - stats: - type: file - description: Stats file in yaml format - pattern: "*.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.yml: + type: file + description: Stats file in yaml format + pattern: "*.yml" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gt/suffixerator/meta.yml b/modules/nf-core/gt/suffixerator/meta.yml index 8fa39f1c8904..74e02f4ed0b2 100644 --- a/modules/nf-core/gt/suffixerator/meta.yml +++ b/modules/nf-core/gt/suffixerator/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "gt_suffixerator" description: Computes enhanced suffix array using GenomeTools gt-suffixerator utility @@ -15,33 +14,36 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input fasta file to index - pattern: "*.{fsa,fa,fasta}" - - mode: - type: string - description: Mode must be one of 'dna', or 'protein' + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input fasta file to index + pattern: "*.{fsa,fa,fasta}" + - - mode: + type: string + description: Mode must be one of 'dna', or 'protein' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - index: - type: directory - description: Folder containing the suffixerator index files - pattern: "suffixerator" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix: + type: directory + description: Folder containing the suffixerator index files + pattern: "suffixerator" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/gtdbtk/classifywf/meta.yml b/modules/nf-core/gtdbtk/classifywf/meta.yml index 0667dcd6d73f..fc081897d80c 100644 --- a/modules/nf-core/gtdbtk/classifywf/meta.yml +++ b/modules/nf-core/gtdbtk/classifywf/meta.yml @@ -1,5 +1,6 @@ name: gtdbtk_classifywf -description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. +description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications + to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. keywords: - GTDB taxonomy - taxonomic classification @@ -10,79 +11,135 @@ keywords: - archaea tools: - gtdbtk: - description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. + description: GTDB-Tk is a software toolkit for assigning objective taxonomic classifications + to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. homepage: https://ecogenomics.github.io/GTDBTk/ documentation: https://ecogenomics.github.io/GTDBTk/ tool_dev_url: https://github.com/Ecogenomics/GTDBTk doi: "10.1093/bioinformatics/btz848" licence: ["GNU General Public v3 (GPL v3)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, assembler:'spades' ] - - bins: - type: file - description: The binned fasta files from the assembler - pattern: "*.{fasta,fa}" - - database: - type: file - description: The local copy of the taxonomic database used by GTDB-tk (unzipped copy) - pattern: "*" - - use_pplacer_scratch_dir: - type: boolean - description: Set to true to reduce pplacer memory usage by writing to disk (slower) - - mash_db: - type: file - description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` mode is used (optional) - pattern: "*.msh" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, assembler:'spades' ] + - '"bins/*"': + type: file + description: bins + - - db_name: + type: string + description: The name of the GTDB database to use. + - '"database/*"': + type: file + description: GTDB database + - - use_pplacer_scratch_dir: + type: boolean + description: Set to true to reduce pplacer memory usage by writing to disk (slower) + - - mash_db: + type: file + description: The local copy of the Mash sketch database used by GTDB-tk if `ani_screen` + mode is used (optional) + pattern: "*.msh" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - summary: - type: file - description: A TSV summary file for the classification - pattern: "*.{summary.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.summary.tsv: + type: file + description: A TSV summary file for the classification + pattern: "*.{summary.tsv}" - tree: - type: file - description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment - pattern: "*.{classify.tree.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.classify.tree.gz: + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{classify.tree.gz}" - markers: - type: file - description: A TSV summary file lineage markers used for the classification. - pattern: "*.{markers_summary.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.markers_summary.tsv: + type: file + description: A TSV summary file lineage markers used for the classification. + pattern: "*.{markers_summary.tsv}" - msa: - type: file - description: Multiple sequence alignments file. - pattern: "*.{msa.fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.msa.fasta.gz: + type: file + description: Multiple sequence alignments file. + pattern: "*.{msa.fasta.gz}" - user_msa: - type: file - description: Multiple sequence alignments file for the user-provided files. - pattern: "*.{user_msa.fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.user_msa.fasta.gz: + type: file + description: Multiple sequence alignments file for the user-provided files. + pattern: "*.{user_msa.fasta.gz}" - filtered: - type: file - description: A list of genomes with an insufficient number of amino acids in MSA.. - pattern: "*.{filtered.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.*.filtered.tsv: + type: file + description: A list of genomes with an insufficient number of amino acids in + MSA.. + pattern: "*.{filtered.tsv}" + - failed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.failed_genomes.tsv: + type: file + description: A TSV summary of the genomes which GTDB-tk failed to classify. + pattern: "*.{failed_genomes.tsv}" - log: - type: file - description: GTDB-tk log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.log: + type: file + description: GTDB-tk log file + pattern: "*.{log}" - warnings: - type: file - description: GTDB-tk warnings log file - pattern: "*.{warnings.log}" - - failed: - type: file - description: A TSV summary of the genomes which GTDB-tk failed to classify. - pattern: "*.{failed_genomes.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtdbtk.${prefix}.warnings.log: + type: file + description: GTDB-tk warnings log file + pattern: "*.{warnings.log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@skrakau" - "@abhi18av" diff --git a/modules/nf-core/gtfsort/meta.yml b/modules/nf-core/gtfsort/meta.yml index 836b72e03d84..bc9842bab23b 100644 --- a/modules/nf-core/gtfsort/meta.yml +++ b/modules/nf-core/gtfsort/meta.yml @@ -1,4 +1,3 @@ ---- name: "gtfsort" description: Sort GTF files in chr/pos/feature order keywords: @@ -7,27 +6,30 @@ keywords: - genomics tools: - "gtfsort": - description: "A chr/pos/feature GTF sorter that uses a lexicographically-based index ordering algorithm." + description: "A chr/pos/feature GTF sorter that uses a lexicographically-based + index ordering algorithm." homepage: "https://github.com/alejandrogzi/gtfsort" documentation: "https://github.com/alejandrogzi/gtfsort" tool_dev_url: "https://github.com/alejandrogzi/gtfsort" licence: ["MIT"] + identifier: "" input: - - gtf: - type: file - description: Unsorted GTF/GFF file. - pattern: "*.gtf" - + - - gtf: + type: file + description: Unsorted GTF/GFF file. + pattern: "*.gtf" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gtf: - type: file - description: Sorted GTF file - pattern: "*.gtf" + - "*.sorted.gtf": + type: file + description: Sorted GTF file + pattern: "*.gtf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@georgiakes" maintainers: diff --git a/modules/nf-core/gubbins/meta.yml b/modules/nf-core/gubbins/meta.yml index 191660b82ae8..2bb4f24c7848 100644 --- a/modules/nf-core/gubbins/meta.yml +++ b/modules/nf-core/gubbins/meta.yml @@ -1,5 +1,8 @@ name: gubbins -description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. +description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) + is an algorithm that iteratively identifies loci containing elevated densities of + base substitutions while concurrently constructing a phylogeny based on the putative + point mutations outside of these regions. licence: ["GPL-2.0-only"] keywords: - recombination @@ -7,55 +10,67 @@ keywords: - phylogeny tools: - gubbins: - description: Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. + description: Rapid phylogenetic analysis of large samples of recombinant bacterial + whole genome sequences using Gubbins. homepage: https://sanger-pathogens.github.io/gubbins/ documentation: https://sanger-pathogens.github.io/gubbins/ + identifier: biotools:gubbins input: - - alignment: - type: file - description: fasta alignment file - pattern: "*.{fasta,fas,fa,aln}" + - - alignment: + type: file + description: fasta alignment file + pattern: "*.{fasta,fas,fa,aln}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Filtered variant alignment in fasta format - pattern: "*.{fasta}" - - embl_predicted: - type: file - description: Recombination predictions in embl format - pattern: "*.{recombination_predictions.embl}" + - "*.fasta": + type: file + description: Filtered variant alignment in fasta format + pattern: "*.{fasta}" - gff: - type: file - description: Recombination predictions in gff format - pattern: "*.{gff}" - - embl_branch: - type: file - description: Branch base reconstruction - pattern: "*.{branch_base_reconstruction.embl}" + - "*.gff": + type: file + description: Recombination predictions in gff format + pattern: "*.{gff}" - vcf: - type: file - description: SNP distribution - pattern: "*.{vcf}" + - "*.vcf": + type: file + description: SNP distribution + pattern: "*.{vcf}" - stats: - type: file - description: Per branch statistics - pattern: "*.{csv}" + - "*.csv": + type: file + description: Per branch statistics + pattern: "*.{csv}" - phylip: - type: file - description: Filtered variant alignment in phylip format - pattern: "*.{phylip}" + - "*.phylip": + type: file + description: Filtered variant alignment in phylip format + pattern: "*.{phylip}" + - embl_predicted: + - "*.recombination_predictions.embl": + type: file + description: Recombination predictions in embl format + pattern: "*.{recombination_predictions.embl}" + - embl_branch: + - "*.branch_base_reconstruction.embl": + type: file + description: Branch base reconstruction + pattern: "*.{branch_base_reconstruction.embl}" - tree: - type: file - description: Recombination removed RAxML phylogenetic tree - pattern: "*.{final_tree.tre}" + - "*.final_tree.tre": + type: file + description: Recombination removed RAxML phylogenetic tree + pattern: "*.{final_tree.tre}" - tree_labelled: - type: file - description: Recombination removed RAxML phylogenetic tree (nodes labelled) - pattern: "*.{node_labelled.final_tree.tre}" + - "*.node_labelled.final_tree.tre": + type: file + description: Recombination removed RAxML phylogenetic tree (nodes labelled) + pattern: "*.{node_labelled.final_tree.tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/gunc/downloaddb/meta.yml b/modules/nf-core/gunc/downloaddb/meta.yml index ac280236b392..41fa20e0f6c3 100644 --- a/modules/nf-core/gunc/downloaddb/meta.yml +++ b/modules/nf-core/gunc/downloaddb/meta.yml @@ -1,5 +1,6 @@ name: gunc_downloaddb -description: Download database for GUNC detection of Chimerism and Contamination in Prokaryotic Genomes +description: Download database for GUNC detection of Chimerism and Contamination in + Prokaryotic Genomes keywords: - download - prokaryote @@ -9,26 +10,30 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - db_name: - type: string - description: "Which database to download. Options: progenomes or gtdb" - pattern: "progenomes|gtdb" + - - db_name: + type: string + description: "Which database to download. Options: progenomes or gtdb" + pattern: "progenomes|gtdb" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: GUNC database file - pattern: "*.dmnd" + - "*.dmnd": + type: file + description: GUNC database file + pattern: "*.dmnd" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunc/mergecheckm/meta.yml b/modules/nf-core/gunc/mergecheckm/meta.yml index c7746b2eabb3..4a7a2c1ce1ae 100644 --- a/modules/nf-core/gunc/mergecheckm/meta.yml +++ b/modules/nf-core/gunc/mergecheckm/meta.yml @@ -11,40 +11,44 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gunc_file: - type: file - description: Path of a gunc_scores.tsv file (mandatory) - pattern: "*.{bam,cram,sam}" - - checkm_file: - type: file - description: Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory) - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gunc_file: + type: file + description: Path of a gunc_scores.tsv file (mandatory) + pattern: "*.{bam,cram,sam}" + - checkm_file: + type: file + description: Output TSV from CheckM qa (ideally with -o 2 extended format) (mandatory) + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Merged checkm/gunc results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Merged checkm/gunc results in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunc/run/meta.yml b/modules/nf-core/gunc/run/meta.yml index 7809b494fc5f..63f437f363b1 100644 --- a/modules/nf-core/gunc/run/meta.yml +++ b/modules/nf-core/gunc/run/meta.yml @@ -8,44 +8,54 @@ keywords: - chimeras tools: - gunc: - description: Python package for detection of chimerism and contamination in prokaryotic genomes. + description: Python package for detection of chimerism and contamination in prokaryotic + genomes. homepage: https://grp-bork.embl-community.io/gunc/ documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" licence: ["GNU General Public v3 or later (GPL v3+)"] + identifier: biotools:gunc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contig (bins) - pattern: "*.fa" - - db: - type: file - description: GUNC database file - pattern: "*.dmnd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contig (bins) + pattern: "*.fa" + - - db: + type: file + description: GUNC database file + pattern: "*.dmnd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - maxcss_levels_tsv: - type: file - description: Output file with scores for a taxonomic level with the highest CSS score - pattern: "*.tsv" + - maxcss_level_tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*maxCSS_level.tsv": + type: file + description: Output file with results for the maximum CSS level + pattern: "*.tsv" - all_levels_tsv: - type: file - description: Optional output file with results for each taxonomic level - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*all_levels.tsv": + type: file + description: Optional output file with results for each taxonomic level + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/gunzip/meta.yml b/modules/nf-core/gunzip/meta.yml index f32973a0a56a..9066c0353b19 100644 --- a/modules/nf-core/gunzip/meta.yml +++ b/modules/nf-core/gunzip/meta.yml @@ -10,25 +10,32 @@ tools: gzip is a file format and a software application used for file compression and decompression. documentation: https://www.gnu.org/software/gzip/manual/gzip.html licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" + - meta: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - $gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/gvcftools/extractvariants/meta.yml b/modules/nf-core/gvcftools/extractvariants/meta.yml index da2b7d884dd4..2075496cb5ee 100644 --- a/modules/nf-core/gvcftools/extractvariants/meta.yml +++ b/modules/nf-core/gvcftools/extractvariants/meta.yml @@ -1,5 +1,6 @@ name: "gvcftools_extractvariants" -description: Removes all non-variant blocks from a gVCF file to produce a smaller variant-only VCF file. +description: Removes all non-variant blocks from a gVCF file to produce a smaller + variant-only VCF file. keywords: - gvcftools - extract_variants @@ -8,35 +9,39 @@ keywords: - vcf tools: - "gvcftools": - description: "gvcftools is a package of small utilities for creating and analyzing gVCF files" + description: "gvcftools is a package of small utilities for creating and analyzing + gVCF files" homepage: "https://sites.google.com/site/gvcftools/home" documentation: "https://sites.google.com/site/gvcftools/home/configuration-and-analysis" tool_dev_url: "https://github.com/sequencing/gvcftools" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcf: - type: file - description: GVCF file - pattern: "*.{g.vcf,gvcf}.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcf: + type: file + description: GVCF file + pattern: "*.{g.vcf,gvcf}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Converted variant-only VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Converted variant-only VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/hamronization/abricate/meta.yml b/modules/nf-core/hamronization/abricate/meta.yml index 4a0867d6ce56..b1346892e591 100644 --- a/modules/nf-core/hamronization/abricate/meta.yml +++ b/modules/nf-core/hamronization/abricate/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_abricate" -description: Tool to convert and summarize ABRicate outputs using the hAMRonization specification +description: Tool to convert and summarize ABRicate outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -7,51 +8,61 @@ keywords: - abricate tools: - "hamronization": - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output TSV or CSV file from ABRicate - pattern: "*.{csv,tsv}" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of ABRicate used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of ABRicate used - pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output TSV or CSV file from ABRicate + pattern: "*.{csv,tsv}" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of ABRicate used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of ABRicate used + pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jasmezz" maintainers: diff --git a/modules/nf-core/hamronization/amrfinderplus/meta.yml b/modules/nf-core/hamronization/amrfinderplus/meta.yml index c09971505823..aba55b1f6526 100644 --- a/modules/nf-core/hamronization/amrfinderplus/meta.yml +++ b/modules/nf-core/hamronization/amrfinderplus/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_amrfinderplus" -description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization specification. +description: Tool to convert and summarize AMRfinderPlus outputs using the hAMRonization + specification. keywords: - amr - antimicrobial resistance @@ -9,51 +10,61 @@ keywords: - amrfinderplus tools: - "hamronization": - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .tsv file from AMRfinderPlus - pattern: "*.tsv" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of AMRfinder used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of ncbi_AMRfinder used - pattern: "[0-9]-[0-9]-[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .tsv file from AMRfinderPlus + pattern: "*.tsv" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of AMRfinder used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of ncbi_AMRfinder used + pattern: "[0-9]-[0-9]-[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/deeparg/meta.yml b/modules/nf-core/hamronization/deeparg/meta.yml index de01196e9d72..39149a346a0e 100644 --- a/modules/nf-core/hamronization/deeparg/meta.yml +++ b/modules/nf-core/hamronization/deeparg/meta.yml @@ -1,5 +1,6 @@ name: hamronization_deeparg -description: Tool to convert and summarize DeepARG outputs using the hAMRonization specification +description: Tool to convert and summarize DeepARG outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -7,51 +8,61 @@ keywords: - deeparg tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .mapping.ARG file from DeepARG - pattern: "*.mapping.ARG" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: integer - description: Database version of DeepARG used - pattern: "[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .mapping.ARG file from DeepARG + pattern: "*.mapping.ARG" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: integer + description: Database version of DeepARG used + pattern: "[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/fargene/meta.yml b/modules/nf-core/hamronization/fargene/meta.yml index 45a3811de7dd..efd3de36806d 100644 --- a/modules/nf-core/hamronization/fargene/meta.yml +++ b/modules/nf-core/hamronization/fargene/meta.yml @@ -1,5 +1,6 @@ name: "hamronization_fargene" -description: Tool to convert and summarize fARGene outputs using the hAMRonization specification +description: Tool to convert and summarize fARGene outputs using the hAMRonization + specification keywords: - amr - antimicrobial resistance @@ -9,51 +10,61 @@ keywords: - fARGene tools: - hamronization: - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .txt file from fARGene - pattern: "*.txt" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of fARGene used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of fARGene used - pattern: "[0-9].[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .txt file from fARGene + pattern: "*.txt" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of fARGene used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of fARGene used + pattern: "[0-9].[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hamronization/rgi/meta.yml b/modules/nf-core/hamronization/rgi/meta.yml index 0cca850261cb..525148e5bfd6 100644 --- a/modules/nf-core/hamronization/rgi/meta.yml +++ b/modules/nf-core/hamronization/rgi/meta.yml @@ -9,51 +9,61 @@ keywords: - rgi tools: - hamronization: - description: "Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification" + description: "Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification" homepage: "https://github.com/pha4ge/hAMRonization/" documentation: "https://github.com/pha4ge/hAMRonization/" tool_dev_url: "https://github.com/pha4ge/hAMRonization" licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Output .txt file from RGI - pattern: "*.txt" - - format: - type: string - description: Type of report file to be produced - pattern: "tsv|json" - - software_version: - type: string - description: Version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" - - reference_db_version: - type: string - description: Database version of DeepARG used - pattern: "[0-9].[0-9].[0-9]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Output .txt file from RGI + pattern: "*.txt" + - - format: + type: string + description: Type of report file to be produced + pattern: "tsv|json" + - - software_version: + type: string + description: Version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" + - - reference_db_version: + type: string + description: Database version of DeepARG used + pattern: "[0-9].[0-9].[0-9]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised report in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: hAMRonised report in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised report in TSV format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: hAMRonised report in TSV format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/hamronization/summarize/meta.yml b/modules/nf-core/hamronization/summarize/meta.yml index 7d4c7b688ba8..54ceeff36d95 100644 --- a/modules/nf-core/hamronization/summarize/meta.yml +++ b/modules/nf-core/hamronization/summarize/meta.yml @@ -1,42 +1,49 @@ name: hamronization_summarize -description: Tool to summarize and combine all hAMRonization reports into a single file +description: Tool to summarize and combine all hAMRonization reports into a single + file keywords: - amr - antimicrobial resistance - reporting tools: - hamronization: - description: Tool to convert and summarize AMR gene detection outputs using the hAMRonization specification + description: Tool to convert and summarize AMR gene detection outputs using the + hAMRonization specification homepage: https://github.com/pha4ge/hAMRonization/ documentation: https://github.com/pha4ge/hAMRonization/ tool_dev_url: https://github.com/pha4ge/hAMRonization licence: ["GNU Lesser General Public v3 (LGPL v3)"] + identifier: biotools:hamronization input: - - reports: - type: file - description: List of multiple hAMRonization reports in either JSON or TSV format - pattern: "*.{json,tsv}" - - format: - type: string - description: Type of final combined report file to be produced - pattern: "tsv|json|interactive" + - - reports: + type: file + description: List of multiple hAMRonization reports in either JSON or TSV format + pattern: "*.{json,tsv}" + - - format: + type: string + description: Type of final combined report file to be produced + pattern: "tsv|json|interactive" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: hAMRonised summary in JSON format - pattern: "*.json" + - hamronization_combined_report.json: + type: file + description: hAMRonised summary in JSON format + pattern: "*.json" - tsv: - type: file - description: hAMRonised summary in TSV format - pattern: "*.json" + - hamronization_combined_report.tsv: + type: file + description: hAMRonised summary in TSV format + pattern: "*.json" - html: - type: file - description: hAMRonised summary in HTML format - pattern: "*.html" + - hamronization_combined_report.html: + type: file + description: hAMRonised summary in HTML format + pattern: "*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/hapibd/meta.yml b/modules/nf-core/hapibd/meta.yml index 8def0c8d6625..6b27fc42a74b 100644 --- a/modules/nf-core/hapibd/meta.yml +++ b/modules/nf-core/hapibd/meta.yml @@ -1,56 +1,77 @@ name: "hapibd" -description: The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets with hundreds of thousands of samples. +description: The hap-ibd program detects identity-by-descent (IBD) segments and homozygosity-by-descent + (HBD) segments in phased genotype data. The hap-ibd program can analyze data sets + with hundreds of thousands of samples. keywords: - ibd - hbd - beagle tools: - "hapibd": - description: "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent (HBD) segments in phased genotype data." + description: "Hap-ibd Detects identity-by-descent (IBD) segments and homozygosity-by-descent + (HBD) segments in phased genotype data." homepage: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" documentation: "https://github.com/browning-lab/hap-ibd/blob/master/README.md" doi: "10.1016/j.ajhg.2020.02.010" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing cohort information - e.g. [ id:'test' ] - - vcf: - type: file - description: phased VCF file with a GT FORMAT subfield with no missing alleles - pattern: "*.{vcf,vcf.gz}" - - map: - type: file - description: genetic map with cM units in PLINK format - pattern: "*.{map,map.gz,map.zip}" - - exclude: - type: file - description: text file containing samples one sample per line to be excluded from the analysis - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - vcf: + type: file + description: phased VCF file with a GT FORMAT subfield with no missing alleles + pattern: "*.{vcf,vcf.gz}" + - - map: + type: file + description: genetic map with cM units in PLINK format + pattern: "*.{map,map.gz,map.zip}" + - - exclude: + type: file + description: text file containing samples one sample per line to be excluded + from the analysis + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing cohort information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hbd: - type: file - description: contains HBD segments within individuals - pattern: "*.hbd.gz" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.hbd.gz": + type: file + description: contains HBD segments within individuals + pattern: "*.hbd.gz" - ibd: - type: file - description: contains IBD segments shared between individuals - pattern: "*.ibd.gz" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.ibd.gz": + type: file + description: contains IBD segments shared between individuals + pattern: "*.ibd.gz" - log: - type: file - description: contains a summary of the analysis which includes the analysis parameters the number of markers the number of samples the number of output HBD and IBD segments and the mean number of HBD and IBD segments per sample - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing cohort information + e.g. [ id:'test' ] + - "*.log": + type: file + description: contains a summary of the analysis which includes the analysis + parameters the number of markers the number of samples the number of output + HBD and IBD segments and the mean number of HBD and IBD segments per sample + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" maintainers: diff --git a/modules/nf-core/haplocheck/meta.yml b/modules/nf-core/haplocheck/meta.yml index abf636f00f90..25e6127a7f42 100644 --- a/modules/nf-core/haplocheck/meta.yml +++ b/modules/nf-core/haplocheck/meta.yml @@ -10,40 +10,50 @@ keywords: - contamination tools: - "haplocheck": - description: "Detects in-sample contamination in mtDNA or WGS sequencing studies by analyzing the mitochondrial content." + description: "Detects in-sample contamination in mtDNA or WGS sequencing studies + by analyzing the mitochondrial content." homepage: "https://github.com/genepi/haplocheck" documentation: "https://github.com/genepi/haplocheck" tool_dev_url: "https://github.com/genepi/haplocheck" doi: 10.1101/gr.256545.119 licence: ["MIT"] + identifier: biotools:haplocheck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Raw report in txt format - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Raw report in txt format + pattern: "*.{txt}" - html: - type: file - description: Haplocheck HTML report - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Haplocheck HTML report + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lmtani" maintainers: diff --git a/modules/nf-core/haplogrep2/classify/meta.yml b/modules/nf-core/haplogrep2/classify/meta.yml index c5399f5c00dd..5f11335ba85e 100644 --- a/modules/nf-core/haplogrep2/classify/meta.yml +++ b/modules/nf-core/haplogrep2/classify/meta.yml @@ -11,33 +11,36 @@ tools: documentation: "https://github.com/seppinho/haplogrep-cmd" tool_dev_url: "https://github.com/seppinho/haplogrep-cmd" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputfile: - type: file - description: valid options are hsd, vcf, or fasta files - pattern: "*.{vcf,vcf.gz,fasta,hsd}" - - format: - type: string - description: either "vcf", "fasta" or "hsd" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputfile: + type: file + description: valid options are hsd, vcf, or fasta files + pattern: "*.{vcf,vcf.gz,fasta,hsd}" + - - format: + type: string + description: either "vcf", "fasta" or "hsd" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: text file with classification information - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: text file with classification information + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/happy/ftxpy/meta.yml b/modules/nf-core/happy/ftxpy/meta.yml index 266b6235fec2..15a673252661 100644 --- a/modules/nf-core/happy/ftxpy/meta.yml +++ b/modules/nf-core/happy/ftxpy/meta.yml @@ -12,61 +12,63 @@ tools: documentation: "https://github.com/Illumina/hap.py" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference fasta - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing sample information for reference fai - e.g. [ id:'test3' ] - - vcf: - type: file - description: VCF file to process - pattern: "*.{vcf,vcf.gz}" - - regions_bed: - type: file - description: BED file. Restrict analysis to given (sparse) regions. - pattern: "*.bed" - - targets_bed: - type: file - description: Restrict analysis to given (dense) regions. - pattern: "*.bed" - - bam: - type: file - description: Pass one or more BAM files for feature table extraction - pattern: "*.bam" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to process + pattern: "*.{vcf,vcf.gz}" + - regions_bed: + type: file + description: BED file. Restrict analysis to given (sparse) regions. + pattern: "*.bed" + - targets_bed: + type: file + description: Restrict analysis to given (dense) regions. + pattern: "*.bed" + - bam: + type: file + description: Pass one or more BAM files for feature table extraction + pattern: "*.bam" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference fasta + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for reference fai + e.g. [ id:'test3' ] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - features: - type: file - description: Fuature table - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Fuature table + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/happy/happy/meta.yml b/modules/nf-core/happy/happy/meta.yml index dc8ebf25a316..3582adef1f40 100644 --- a/modules/nf-core/happy/happy/meta.yml +++ b/modules/nf-core/happy/happy/meta.yml @@ -1,5 +1,8 @@ name: "happy_happy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather than comparing VCF records row by row, hap.py will generate and match alternate sequences in a superlocus. A superlocus is a small region of the genome (sized between 1 and around 1000 bp) that contains one or more variants. +description: Hap.py is a tool to compare diploid genotypes at haplotype level. Rather + than comparing VCF records row by row, hap.py will generate and match alternate + sequences in a superlocus. A superlocus is a small region of the genome (sized between + 1 and around 1000 bp) that contains one or more variants. keywords: - happy - benchmark @@ -12,127 +15,193 @@ tools: documentation: "https://github.com/Illumina/hap.py" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing fasta file information - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing fai file information - e.g. [ id:'test3'] - - meta4: - type: map - description: | - Groovy Map containing false_positives_bed file information - e.g. [ id:'test4'] - - meta5: - type: map - description: | - Groovy Map containing stratification_tsv file information - e.g. [ id:'test5'] - - meta6: - type: map - description: | - Groovy Map containing stratification_beds file information - e.g. [ id:'test6'] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Stratification file list in TSV format - pattern: "*.tsv" - - stratification_beds: - type: file - description: One or more BED files used for stratification (these should be referenced in the stratification TSV) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: VCF/GVCF file to query + pattern: "*.{gvcf,vcf}.gz" + - truth_vcf: + type: file + description: gold standard VCF file + pattern: "*.{gvcf,vcf}.gz" + - regions_bed: + type: file + description: Sparse regions to restrict the analysis to + pattern: "*.bed" + - targets_bed: + type: file + description: Dense regions to restrict the analysis to + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta file information + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fai file information + e.g. [ id:'test3'] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing false_positives_bed file information + e.g. [ id:'test4'] + - false_positives_bed: + type: file + description: False positive / confident call regions. Calls outside these regions + will be labelled as UNK. + pattern: "*.{bed,bed.gz}" + - - meta5: + type: map + description: | + Groovy Map containing stratification_tsv file information + e.g. [ id:'test5'] + - stratification_tsv: + type: file + description: Stratification file list in TSV format + pattern: "*.tsv" + - - meta6: + type: map + description: | + Groovy Map containing stratification_beds file information + e.g. [ id:'test6'] + - stratification_beds: + type: file + description: One or more BED files used for stratification (these should be + referenced in the stratification TSV) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary_csv: - type: file - description: A CSV file containing the summary of the benchmarking - pattern: "*.summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.csv": + type: file + description: A CSV file containing the summary of the benchmarking + pattern: "*.summary.csv" - roc_all_csv: - type: file - description: A CSV file containing ROC values for all variants - pattern: "*.roc.all.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.all.csv.gz": + type: file + description: A CSV file containing ROC values for all variants + pattern: "*.roc.all.csv.gz" - roc_indel_locations_csv: - type: file - description: A CSV file containing ROC values for all indels - pattern: "*.roc.Locations.INDEL.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.INDEL.csv.gz": + type: file + description: A CSV file containing ROC values for all indels + pattern: "*.roc.Locations.INDEL.csv.gz" - roc_indel_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all indels that passed all filters - pattern: "*.roc.Locations.INDEL.PASS.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.INDEL.PASS.csv.gz": + type: file + description: A CSV file containing ROC values for all indels that passed all + filters + pattern: "*.roc.Locations.INDEL.PASS.csv.gz" - roc_snp_locations_csv: - type: file - description: A CSV file containing ROC values for all SNPs - pattern: "*.roc.Locations.SNP.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.SNP.csv.gz": + type: file + description: A CSV file containing ROC values for all SNPs + pattern: "*.roc.Locations.SNP.csv.gz" - roc_snp_locations_pass_csv: - type: file - description: A CSV file containing ROC values for all SNPs that passed all filters - pattern: "*.roc.Locations.SNP.PASS.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.roc.Locations.SNP.PASS.csv.gz": + type: file + description: A CSV file containing ROC values for all SNPs that passed all filters + pattern: "*.roc.Locations.SNP.PASS.csv.gz" - extended_csv: - type: file - description: A CSV file containing extended info of the benchmarking - pattern: "*.extended.csv" - - metrics_json: - type: file - description: A JSON file containing the run info - pattern: "*.runinfo.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.extended.csv": + type: file + description: A CSV file containing extended info of the benchmarking + pattern: "*.extended.csv" - runinfo: - type: file - description: A JSON file containing the benchmarking metrics - pattern: "*.metrics.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.runinfo.json": + type: file + description: A JSON file containing the benchmarking metrics + pattern: "*.metrics.json.gz" + - metrics_json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json.gz": + type: file + description: A JSON file containing the run info + pattern: "*.runinfo.json" - vcf: - type: file - description: An annotated VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: An annotated VCF + pattern: "*.vcf.gz" - tbi: - type: file - description: The index of the annotated VCF - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: The index of the annotated VCF + pattern: "*.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/happy/prepy/meta.yml b/modules/nf-core/happy/prepy/meta.yml index 3e8898fcd682..f308cc889b16 100644 --- a/modules/nf-core/happy/prepy/meta.yml +++ b/modules/nf-core/happy/prepy/meta.yml @@ -11,52 +11,55 @@ tools: documentation: https://github.com/Illumina/hap.py tool_dev_url: https://github.com/Illumina/hap.py licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference fasta - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing sample information for reference fai - e.g. [ id:'test3' ] - - vcf: - type: file - description: VCF file to preprocess - pattern: "*.{vcf,vcf.gz}" - - bed: - type: file - description: BED file - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file to preprocess + pattern: "*.{vcf,vcf.gz}" + - bed: + type: file + description: BED file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference fasta + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for reference fai + e.g. [ id:'test3' ] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A preprocessed VCF file - pattern: "*.vcf.gz" + - preprocessed_vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Preprocessed VCF file + pattern: "*.vcf.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/happy/sompy/meta.yml b/modules/nf-core/happy/sompy/meta.yml index 8a04a6017392..f7847c4a2864 100644 --- a/modules/nf-core/happy/sompy/meta.yml +++ b/modules/nf-core/happy/sompy/meta.yml @@ -1,5 +1,6 @@ name: "happy_sompy" -description: Hap.py is a tool to compare diploid genotypes at haplotype level. som.py is a part of hap.py compares somatic variations. +description: Hap.py is a tool to compare diploid genotypes at haplotype level. som.py + is a part of hap.py compares somatic variations. keywords: - happy - sompy @@ -14,97 +15,113 @@ tools: documentation: "https://github.com/Illumina/hap.py/blob/master/doc/sompy.md" tool_dev_url: "https://github.com/Illumina/hap.py" licence: ["BSD-2-clause"] + identifier: biotools:happy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing fasta file information - e.g. [ id:'test2'] - - meta3: - type: map - description: | - Groovy Map containing fai file information - e.g. [ id:'test3'] - - meta4: - type: map - description: | - Groovy Map containing false_positives_bed file information - e.g. [ id:'test4'] - - meta5: - type: map - description: | - Groovy Map containing ambiguous_beds file information - e.g. [ id:'test5'] - - meta6: - type: map - description: | - Groovy Map containing bam file information - e.g. [ id:'test6'] - - query_vcf: - type: file - description: VCF/GVCF file to query - pattern: "*.{gvcf,vcf}.gz" - - truth_vcf: - type: file - description: gold standard VCF file - pattern: "*.{gvcf,vcf}.gz" - - regions_bed: - type: file - description: Sparse regions to restrict the analysis to - pattern: "*.bed" - - targets_bed: - type: file - description: Dense regions to restrict the analysis to - pattern: "*.bed" - - fasta: - type: file - description: FASTA file of the reference genome - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: The index of the reference FASTA - pattern: "*.fai" - - false_positives_bed: - type: file - description: False positive / confident call regions. Calls outside these regions will be labelled as UNK. - pattern: "*.{bed,bed.gz}" - - stratification_tsv: - type: file - description: Ambiguous region bed file(s) - pattern: "*.bed" - - bams: - type: file - description: one or more BAM files for feature table extraction - pattern: "*.bam" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: VCF/GVCF file to query + pattern: "*.{gvcf,vcf}.gz" + - truth_vcf: + type: file + description: gold standard VCF file + pattern: "*.{gvcf,vcf}.gz" + - regions_bed: + type: file + description: Sparse regions to restrict the analysis to + pattern: "*.bed" + - targets_bed: + type: file + description: Dense regions to restrict the analysis to + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta file information + e.g. [ id:'test2'] + - fasta: + type: file + description: FASTA file of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fai file information + e.g. [ id:'test3'] + - fasta_fai: + type: file + description: The index of the reference FASTA + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing false_positives_bed file information + e.g. [ id:'test4'] + - false_positives_bed: + type: file + description: False positive / confident call regions. Calls outside these regions + will be labelled as UNK. + pattern: "*.{bed,bed.gz}" + - - meta5: + type: map + description: | + Groovy Map containing ambiguous_beds file information + e.g. [ id:'test5'] + - ambiguous_beds: + type: file + description: Ambiguous regions + pattern: "*.{bed,bed.gz}" + - - meta6: + type: map + description: | + Groovy Map containing bam file information + e.g. [ id:'test6'] + - bams: + type: file + description: one or more BAM files for feature table extraction + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - features: - type: file - description: One or more than one (if AF count is on ) CSV file containing feature information - pattern: "*.features.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.features.csv": + type: file + description: One or more than one (if AF count is on ) CSV file containing feature + information + pattern: "*.features.csv" - metrics: - type: file - description: One or more than one (if AF count is on ) JSON file with metrics - pattern: "*.metrics.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json": + type: file + description: One or more than one (if AF count is on ) JSON file with metrics + pattern: "*.metrics.json" - stats: - type: file - description: One or more than one (if AF count is on ) CSV file with benchmark stats - pattern: "*.stats.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats.csv": + type: file + description: One or more than one (if AF count is on ) CSV file with benchmark + stats + pattern: "*.stats.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/hicap/meta.yml b/modules/nf-core/hicap/meta.yml index 6cc19b0f2d0b..2d4245fecc51 100644 --- a/modules/nf-core/hicap/meta.yml +++ b/modules/nf-core/hicap/meta.yml @@ -1,5 +1,6 @@ name: hicap -description: Identify cap locus serotype and structure in your Haemophilus influenzae assemblies +description: Identify cap locus serotype and structure in your Haemophilus influenzae + assemblies keywords: - fasta - serotype @@ -12,46 +13,61 @@ tools: tool_dev_url: https://github.com/scwatts/hicap doi: "10.1128/JCM.00190-19" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA formatted assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - database_dir: - type: directory - description: Optional - Directory containing locus database - pattern: "*/*" - - model_fp: - type: file - description: Optional - Prodigal model to use for gene prediction - pattern: "*.{bin}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA formatted assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - database_dir: + type: directory + description: Optional - Directory containing locus database + pattern: "*/*" + - - model_fp: + type: file + description: Optional - Prodigal model to use for gene prediction + pattern: "*.{bin}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gbk: - type: file - description: GenBank file and cap locus annotations - pattern: "*.gbk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gbk": + type: file + description: GenBank file and cap locus annotations + pattern: "*.gbk" - svg: - type: file - description: Visualization of annotated cap locus - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Visualization of annotated cap locus + pattern: "*.svg" - tsv: - type: file - description: Detailed summary of cap locus annotations - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Detailed summary of cap locus annotations + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/hicexplorer/hicpca/meta.yml b/modules/nf-core/hicexplorer/hicpca/meta.yml index 742b65148513..4fd39addc040 100644 --- a/modules/nf-core/hicexplorer/hicpca/meta.yml +++ b/modules/nf-core/hicexplorer/hicpca/meta.yml @@ -6,40 +6,56 @@ keywords: - hicPCA tools: - "hicexplorer": - description: "Set of programs to process, analyze and visualize Hi-C and capture Hi-C data" + description: "Set of programs to process, analyze and visualize Hi-C and capture + Hi-C data" homepage: "https://hicexplorer.readthedocs.io" documentation: "https://hicexplorer.readthedocs.io" tool_dev_url: "https://github.com/deeptools/HiCExplorer" doi: "10.1038/s41467-017-02525-w" licence: ["GPL v3"] + identifier: biotools:hicexplorer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', bin:50000 ] - - matrix: - type: file - description: HiCExplorer matrix in h5 format + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - matrix: + type: file + description: HiCExplorer matrix in h5 format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', bin:50000 ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: Outputs of hicPCA + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_*: + type: file + description: Outputs of hicPCA - pca1: - type: file - description: PCA1 file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_pca1.$format: + type: file + description: PCA1 file - pca2: - type: file - description: PCA2 file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', bin:50000 ] + - ${prefix}_pca2.$format: + type: file + description: PCA2 file + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/hifiasm/meta.yml b/modules/nf-core/hifiasm/meta.yml index d07c0828174f..5f948b798a93 100644 --- a/modules/nf-core/hifiasm/meta.yml +++ b/modules/nf-core/hifiasm/meta.yml @@ -15,81 +15,147 @@ tools: tool_dev_url: https://github.com/chhylp123/hifiasm doi: "10.1038/s41592-020-01056-5" licence: ["MIT"] + identifier: biotools:hifiasm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file with PacBio HiFi reads - pattern: "*.{fastq}" - - paternal_kmer_dump: - type: file - description: Yak kmer dump file for paternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - - maternal_kmer_dump: - type: file - description: Yak kmer dump file for maternal reads (can be used for haplotype resolution). It can have an arbitrary extension. - - use_parental_kmers: - type: boolean - description: A flag (true or false) signalling if the module should use the paternal and maternal kmer dumps. - - hic_read1: - type: file - description: Hi-C data Forward reads. - - hic_read2: - type: file - description: Hi-C data Reverse reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file with PacBio HiFi reads + pattern: "*.{fastq}" + - - paternal_kmer_dump: + type: file + description: Yak kmer dump file for paternal reads (can be used for haplotype + resolution). It can have an arbitrary extension. + - - maternal_kmer_dump: + type: file + description: Yak kmer dump file for maternal reads (can be used for haplotype + resolution). It can have an arbitrary extension. + - - hic_read1: + type: file + description: Hi-C data Forward reads. + - - hic_read2: + type: file + description: Hi-C data Reverse reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - raw_unitigs: - type: file - description: Raw unitigs - pattern: "*.r_utg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.r_utg.gfa": + type: file + description: Raw unitigs + pattern: "*.r_utg.gfa" + - corrected_reads: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ec.bin": + type: file + description: Corrected reads + pattern: "*.ec.bin" + - source_overlaps: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ovlp.source.bin": + type: file + description: Source overlaps + pattern: "*.ovlp.source.bin" + - reverse_overlaps: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ovlp.reverse.bin": + type: file + description: Reverse overlaps + pattern: "*.ovlp.reverse.bin" + - processed_contigs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bp.p_ctg.gfa": + type: file + description: Processed contigs + pattern: "*.bp.p_ctg.gfa" - processed_unitigs: - type: file - description: Processed unitigs - pattern: "*.p_utg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.p_utg.gfa": + type: file + description: Processed unitigs + pattern: "*.p_utg.gfa" - primary_contigs: - type: file - description: Primary contigs - pattern: "*.asm.p_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.asm.p_ctg.gfa": + type: file + description: Primary contigs + pattern: "*.asm.p_ctg.gfa" - alternate_contigs: - type: file - description: Alternative contigs - pattern: "*.asm.a_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.asm.a_ctg.gfa": + type: file + description: Alternative contigs + pattern: "*.asm.a_ctg.gfa" - paternal_contigs: - type: file - description: Paternal contigs - pattern: "*.hap1.p_ctg.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap1.p_ctg.gfa": + type: file + description: Paternal contigs + pattern: "*.hap1.p_ctg.gfa" - maternal_contigs: - type: file - description: Maternal contigs - pattern: "*.hap2.p_ctg.gfa" - - corrected_reads: - type: file - description: Corrected reads - pattern: "*.ec.bin" - - source_overlaps: - type: file - description: Source overlaps - pattern: "*.ovlp.source.bin" - - reverse_overlaps: - type: file - description: Reverse overlaps - pattern: "*.ovlp.reverse.bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap2.p_ctg.gfa": + type: file + description: Maternal contigs + pattern: "*.hap2.p_ctg.gfa" - log: - type: file - description: Stderr log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Stderr log + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" - "@scorreard" diff --git a/modules/nf-core/hisat2/align/meta.yml b/modules/nf-core/hisat2/align/meta.yml index b23eab75b98e..d869c5d567ba 100644 --- a/modules/nf-core/hisat2/align/meta.yml +++ b/modules/nf-core/hisat2/align/meta.yml @@ -7,58 +7,79 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - index: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - summary: - type: file - description: Aligment log - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Aligment log + pattern: "*.log" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*fastq.gz": + type: file + description: Output FastQ file + pattern: "*fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hisat2/build/meta.yml b/modules/nf-core/hisat2/build/meta.yml index 6c28eb21ca6b..3272f8e05c0e 100644 --- a/modules/nf-core/hisat2/build/meta.yml +++ b/modules/nf-core/hisat2/build/meta.yml @@ -8,53 +8,58 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fa,fasta,fna}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - splicesites: + type: file + description: Splices sites in gtf file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - index: - type: file - description: HISAT2 genome index file - pattern: "*.ht2" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - hisat2: + type: file + description: HISAT2 genome index file + pattern: "*.ht2" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/hisat2/extractsplicesites/meta.yml b/modules/nf-core/hisat2/extractsplicesites/meta.yml index 40d77ce00152..c1bdc9e65f8e 100644 --- a/modules/nf-core/hisat2/extractsplicesites/meta.yml +++ b/modules/nf-core/hisat2/extractsplicesites/meta.yml @@ -7,35 +7,40 @@ keywords: - reference tools: - hisat2: - description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. + description: HISAT2 is a fast and sensitive alignment program for mapping next-generation + sequencing reads (both DNA and RNA) to a population of human genomes as well + as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" licence: ["MIT"] + identifier: biotools:hisat2 input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - gtf: - type: file - description: Reference gtf annotation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - gtf: + type: file + description: Reference gtf annotation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] + - txt: + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - "*.splice_sites.txt": + type: file + description: Splice sites in txt file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - splicesites: - type: file - description: Splices sites in gtf file - pattern: "*.{splice_sites.txt}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" - "@ramprasadn" diff --git a/modules/nf-core/hlala/preparegraph/meta.yml b/modules/nf-core/hlala/preparegraph/meta.yml index a2a2fbf9dad9..6d3bdce9169e 100644 --- a/modules/nf-core/hlala/preparegraph/meta.yml +++ b/modules/nf-core/hlala/preparegraph/meta.yml @@ -13,18 +13,31 @@ tools: tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" licence: ["GPL"] + identifier: "" input: - - graph: - type: directory - description: PRG graph directory + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: directory + description: PRG graph directory output: + - graph: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${graph}: + type: directory + description: PRG graph directory - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - folder: - type: directory - description: Directory containing indexed graph + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9" maintainers: diff --git a/modules/nf-core/hlala/typing/meta.yml b/modules/nf-core/hlala/typing/meta.yml index 20c0844aa1d2..e2765acc4718 100644 --- a/modules/nf-core/hlala/typing/meta.yml +++ b/modules/nf-core/hlala/typing/meta.yml @@ -1,5 +1,6 @@ name: "hlala_typing" -description: Performs HLA typing based on a population reference graph and employs a new linear projection method to align reads to the graph. +description: Performs HLA typing based on a population reference graph and employs + a new linear projection method to align reads to the graph. keywords: - hla - hlala @@ -13,32 +14,108 @@ tools: tool_dev_url: "https://github.com/DiltheyLab/HLA-LA" doi: "10.1093/bioinformatics/btz235" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - graph: - type: directory - description: Path to prepared graph with hla-la --acton prepareGraph + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - graph: + type: directory + description: Path to prepared graph with hla-la --acton prepareGraph output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}: + type: file + description: results file + - extraction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction.bam*: + type: file + description: Extraction BAM file + pattern: "*.bam*" + - extraction_mapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction_mapped.bam: + type: file + description: Extraction mapped BAM file + pattern: "*.bam" + - extraction_unmpapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/extraction_unmapped.bam: + type: file + description: Extraction unmapped BAM file + pattern: "*.bam" + - hla: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/hla/*: + type: file + description: HLA results + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/*.fastq: + type: file + description: Fastq file + pattern: "*.fastq" + - reads_per_level: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/reads_per_level.txt: + type: file + description: Reads per level + pattern: "*.txt" + - remapped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}/remapped_with_a.bam*: + type: file + description: Remapped BAM file + pattern: "*.bam*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - folder: - type: directory - description: Folder containing the HLA typing output + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9" maintainers: diff --git a/modules/nf-core/hmmcopy/gccounter/meta.yml b/modules/nf-core/hmmcopy/gccounter/meta.yml index 7fb6990136c5..031a4127d1db 100644 --- a/modules/nf-core/hmmcopy/gccounter/meta.yml +++ b/modules/nf-core/hmmcopy/gccounter/meta.yml @@ -1,39 +1,44 @@ name: hmmcopy_gccounter -description: gcCounter function from HMMcopy utilities, used to generate GC content in non-overlapping windows from a fasta reference +description: gcCounter function from HMMcopy utilities, used to generate GC content + in non-overlapping windows from a fasta reference keywords: - hmmcopy - gccounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: wig file containing gc content of each window of the genome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: wig file containing gc content of each window of the genome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/hmmcopy/generatemap/meta.yml b/modules/nf-core/hmmcopy/generatemap/meta.yml index 89c773600767..cb648763d5e1 100644 --- a/modules/nf-core/hmmcopy/generatemap/meta.yml +++ b/modules/nf-core/hmmcopy/generatemap/meta.yml @@ -1,39 +1,45 @@ name: hmmcopy_generatemap -description: Perl script (generateMap.pl) generates the mappability of a genome given a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time on large genomes, is not parallelised at all. +description: Perl script (generateMap.pl) generates the mappability of a genome given + a certain size of reads, for input to hmmcopy mapcounter. Takes a very long time + on large genomes, is not parallelised at all. keywords: - hmmcopy - mapcounter - mappability tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigwig file containing the mappability of the genome - pattern: "*.bw" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bw": + type: file + description: bigwig file containing the mappability of the genome + pattern: "*.bw" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/hmmcopy/mapcounter/meta.yml b/modules/nf-core/hmmcopy/mapcounter/meta.yml index 4345d51fc60f..8a8132ee0ea6 100644 --- a/modules/nf-core/hmmcopy/mapcounter/meta.yml +++ b/modules/nf-core/hmmcopy/mapcounter/meta.yml @@ -1,40 +1,46 @@ name: hmmcopy_mapcounter -description: mapCounter function from HMMcopy utilities, used to generate mappability in non-overlapping windows from a bigwig file +description: mapCounter function from HMMcopy utilities, used to generate mappability + in non-overlapping windows from a bigwig file keywords: - hmmcopy - mapcounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bigwig: - type: file - description: BigWig file with the mappability score of the genome, for instance made with generateMap function. - pattern: "*.wig" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bigwig: + type: file + description: BigWig file with the mappability score of the genome, for instance + made with generateMap function. + pattern: "*.wig" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: wig file containing mappability of each window of the genome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: wig file containing mappability of each window of the genome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/hmmcopy/readcounter/meta.yml b/modules/nf-core/hmmcopy/readcounter/meta.yml index 511a0987f2db..a55f05edf414 100644 --- a/modules/nf-core/hmmcopy/readcounter/meta.yml +++ b/modules/nf-core/hmmcopy/readcounter/meta.yml @@ -1,40 +1,50 @@ name: hmmcopy_readcounter -description: readCounter function from HMMcopy utilities, used to generate read in windows +description: readCounter function from HMMcopy utilities, used to generate read in + windows keywords: - hmmcopy - readcounter - cnv tools: - hmmcopy: - description: C++ based programs for analyzing BAM files and preparing read counts -- used with bioconductor-hmmcopy + description: C++ based programs for analyzing BAM files and preparing read counts + -- used with bioconductor-hmmcopy homepage: https://github.com/shahcompbio/hmmcopy_utils documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils licence: ["GPL v3"] + identifier: biotools:hmmcopy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: A wig file with the number of reads lying within each window in each chromosome - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: A wig file with the number of reads lying within each window in + each chromosome + pattern: "*.wig" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/hmmer/eslalimask/meta.yml b/modules/nf-core/hmmer/eslalimask/meta.yml index 4a3d84e1bd73..4d16ca5de094 100644 --- a/modules/nf-core/hmmer/eslalimask/meta.yml +++ b/modules/nf-core/hmmer/eslalimask/meta.yml @@ -11,76 +11,87 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - unmaskedaln: - type: file - description: multiple sequence alignment, Stockholm or other formats - pattern: "*" - - fmask_rf: - type: boolean - description: Flag to output optional file with final mask of non-gap RF len - - fmask_all: - type: boolean - description: Flag to output optional file with final mask of full aln len - - gmask_rf: - type: boolean - description: Flag to output optional file gap-based 0/1 mask of non-gap RF len - - gmask_all: - type: boolean - description: Flag to output optional file gap-based 0/1 mask of full aln len - - pmask_rf: - type: boolean - description: Flag to output optional file with PP-based 0/1 mask of non-gap RF len - - pmask_all: - type: boolean - description: Flag to output optional file with PP-based 0/1 mask of full aln len - - maskfile: - type: file - description: mask file, see program documentation - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - unmaskedaln: + type: file + description: multiple sequence alignment, Stockholm or other formats + pattern: "*" + - fmask_rf: + type: boolean + description: Flag to output optional file with final mask of non-gap RF len + - fmask_all: + type: boolean + description: Flag to output optional file with final mask of full aln len + - gmask_rf: + type: boolean + description: Flag to output optional file gap-based 0/1 mask of non-gap RF len + - gmask_all: + type: boolean + description: Flag to output optional file gap-based 0/1 mask of full aln len + - pmask_rf: + type: boolean + description: Flag to output optional file with PP-based 0/1 mask of non-gap + RF len + - pmask_all: + type: boolean + description: Flag to output optional file with PP-based 0/1 mask of full aln + len + - - maskfile: + type: file + description: mask file, see program documentation + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maskedaln: - type: file - description: Masked alignment in gzipped Stockholm format - pattern: "*.sthlm.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.masked.sthlm.gz": + type: file + description: Masked alignment in gzipped Stockholm format + pattern: "*.sthlm.gz" - fmask_rf: - type: file - description: File with final mask of non-gap RF len - pattern: "*.fmask-rf.gz" + - "*.fmask-rf.gz": + type: file + description: File with final mask of non-gap RF len + pattern: "*.fmask-rf.gz" - fmask_all: - type: file - description: File with final mask of full aln len - pattern: "*.fmask-all.gz" + - "*.fmask-all.gz": + type: file + description: File with final mask of full aln len + pattern: "*.fmask-all.gz" - gmask_rf: - type: file - description: File with gap-based 0/1 mask of non-gap RF len - pattern: "*.gmask-rf.gz" + - "*.gmask-rf.gz": + type: file + description: File with gap-based 0/1 mask of non-gap RF len + pattern: "*.gmask-rf.gz" - gmask_all: - type: file - description: File with gap-based 0/1 mask of full aln len - pattern: "*.gmask-all.gz" + - "*.gmask-all.gz": + type: file + description: File with gap-based 0/1 mask of full aln len + pattern: "*.gmask-all.gz" - pmask_rf: - type: file - description: File with PP-based 0/1 mask of non-gap RF len - pattern: "*.pmask-rf.gz" + - "*.pmask-rf.gz": + type: file + description: File with PP-based 0/1 mask of non-gap RF len + pattern: "*.pmask-rf.gz" - pmask_all: - type: file - description: File with PP-based 0/1 mask of full aln len - pattern: "*.pmask-all.gz" + - "*.pmask-all.gz": + type: file + description: File with PP-based 0/1 mask of full aln len + pattern: "*.pmask-all.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/eslreformat/meta.yml b/modules/nf-core/hmmer/eslreformat/meta.yml index 009e35873a79..e21040349485 100644 --- a/modules/nf-core/hmmer/eslreformat/meta.yml +++ b/modules/nf-core/hmmer/eslreformat/meta.yml @@ -1,5 +1,7 @@ name: "hmmer_eslreformat" -description: reformats sequence files, see HMMER documentation for details. The module requires that the format is specified in ext.args in a config file, and that this comes last. See the tools help for possible values. +description: reformats sequence files, see HMMER documentation for details. The module + requires that the format is specified in ext.args in a config file, and that this + comes last. See the tools help for possible values. keywords: - sort - hmmer @@ -11,30 +13,33 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - seqfile: - type: file - description: Sequences, aligned or not, in any supported format - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - seqfile: + type: file + description: Sequences, aligned or not, in any supported format + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - seqreformated: - type: file - description: Reformated sequence file - pattern: "*.*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.*.gz": + type: file + description: Reformated sequence file + pattern: "*.*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmalign/meta.yml b/modules/nf-core/hmmer/hmmalign/meta.yml index df6a7b3c4fea..366cf4f5a580 100644 --- a/modules/nf-core/hmmer/hmmalign/meta.yml +++ b/modules/nf-core/hmmer/hmmalign/meta.yml @@ -1,5 +1,6 @@ name: hmmer_hmmalign -description: hmmalign from the HMMER suite aligns a number of sequences to an HMM profile +description: hmmalign from the HMMER suite aligns a number of sequences to an HMM + profile keywords: - alignment - HMMER @@ -13,34 +14,37 @@ tools: documentation: http://hmmer.org/documentation.html doi: "10.1371/journal.pcbi.1002195" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fasta: - type: file - description: Amino acid or nucleotide gzipped compressed fasta file - pattern: "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" - - hmm: - type: file - description: A gzipped HMM file - pattern: "*.hmm.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fasta: + type: file + description: Amino acid or nucleotide gzipped compressed fasta file + pattern: "*.{fna.gz,faa.gz,fasta.gz,fa.gz}" + - - hmm: + type: file + description: A gzipped HMM file + pattern: "*.hmm.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sthlm: - type: file - description: Multiple alignment in gzipped Stockholm format - pattern: "*.sthlm.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sthlm.gz": + type: file + description: Multiple alignment in gzipped Stockholm format + pattern: "*.sthlm.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" - "@jfy133" diff --git a/modules/nf-core/hmmer/hmmbuild/meta.yml b/modules/nf-core/hmmer/hmmbuild/meta.yml index fb9d50830016..9be14fe9a8a5 100644 --- a/modules/nf-core/hmmer/hmmbuild/meta.yml +++ b/modules/nf-core/hmmer/hmmbuild/meta.yml @@ -14,29 +14,42 @@ tools: tool_dev_url: "https://github.com/EddyRivasLab/hmmer" doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: multiple sequence alignment in fasta, clustal, stockholm or phylip format - pattern: "*" - - mxfile: - type: file - description: read substitution score matrix, for use when building profiles from single sequences (--singlemx option) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: multiple sequence alignment in fasta, clustal, stockholm or phylip + format + pattern: "*" + - - mxfile: + type: file + description: read substitution score matrix, for use when building profiles + from single sequences (--singlemx option) + pattern: "*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hmm: - type: file - description: Gzipped HMM file - pattern: "*.{hmm.gz}" + - meta: + type: file + description: Gzipped HMM file + pattern: "*.{hmm.gz}" + - "*.hmm.gz": + type: file + description: Gzipped HMM file + pattern: "*.{hmm.gz}" + - hmmbuildout: + - "*.hmmbuild.txt": + type: file + description: HMM build output + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmfetch/meta.yml b/modules/nf-core/hmmer/hmmfetch/meta.yml index 82668f68eb58..20616210dd4b 100644 --- a/modules/nf-core/hmmer/hmmfetch/meta.yml +++ b/modules/nf-core/hmmer/hmmfetch/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "hmmer_hmmfetch" description: extract hmm from hmm database file or create index for hmm database @@ -15,41 +14,55 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - hmm: - type: file - description: HMM file with multiple HMM models - pattern: "*.hmm" - - key: - type: string - description: Name of HMM to extract. Specify either this or keyfile. If none is specified, an index will be built. - - keyfile: - type: file - description: File containing list of HMM models to extract. Specify either this or key. If none is specified, an index will be built. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hmm: + type: file + description: HMM file with multiple HMM models + pattern: "*.hmm" + - - key: + type: string + description: Name of HMM to extract. Specify either this or keyfile. If none + is specified, an index will be built. + - - keyfile: + type: file + description: File containing list of HMM models to extract. Specify either this + or key. If none is specified, an index will be built. + pattern: "*.txt" + - - index: + type: file + description: Index file from another run. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hmm: - type: file - description: File with one or more HMM models - pattern: "selection.hmm" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hmm": + type: file + description: File with one or more HMM models + pattern: "selection.hmm" - index: - type: file - description: Index for HMM database. Created if neither key nor keyfile is specified. - pattern: "*.ssi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ssi": + type: file + description: Index for HMM database. Created if neither key nor keyfile is specified. + pattern: "*.ssi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmrank/environment.yml b/modules/nf-core/hmmer/hmmrank/environment.yml index 653e9ea1d517..fbce96e2508d 100644 --- a/modules/nf-core/hmmer/hmmrank/environment.yml +++ b/modules/nf-core/hmmer/hmmrank/environment.yml @@ -4,8 +4,8 @@ channels: dependencies: - conda-forge::r-base=4.2.3 - - conda-forge::r-stringi=1.8.4 - - conda-forge::r-stringr=1.5.1 - conda-forge::r-data.table=1.14.8 - conda-forge::r-dtplyr=1.3.1 + - conda-forge::r-stringi=1.8.4 + - conda-forge::r-stringr=1.5.1 - conda-forge::r-tidyverse=2.0.0 diff --git a/modules/nf-core/hmmer/hmmrank/meta.yml b/modules/nf-core/hmmer/hmmrank/meta.yml index 428b280b8cb3..96f9536187c5 100644 --- a/modules/nf-core/hmmer/hmmrank/meta.yml +++ b/modules/nf-core/hmmer/hmmrank/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "hmmer_hmmrank" description: R script that scores output from multiple runs of hmmer/hmmsearch @@ -14,11 +13,13 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" - "R": description: "A Language and Environment for Statistical Computing" homepage: https://www.r-project.org/ documentation: https://www.r-project.org/ licence: ["GPL v2"] + identifier: "" - "Tidyverse": description: "Tidyverse: R packages for data science" homepage: https://www.tidyverse.org/ @@ -26,37 +27,36 @@ tools: tool_dev_url: https://github.com/tidyverse doi: "10.21105/joss.01686" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - tblouts: - type: file - description: table outputs from hmmsearch - pattern: "*.tsv.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tblouts: + type: file + description: table outputs from hmmsearch + pattern: "*.tsv.gz" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - hmmrank: - type: file - description: TSV file with ranked hmmer results - pattern: "*.hmmrank.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.hmmrank.tsv.gz": + type: file + description: TSV file with ranked hmmer results + pattern: "*.hmmrank.tsv.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/hmmer/hmmsearch/meta.yml b/modules/nf-core/hmmer/hmmsearch/meta.yml index 39893c3bef4f..0e0786591d3d 100644 --- a/modules/nf-core/hmmer/hmmsearch/meta.yml +++ b/modules/nf-core/hmmer/hmmsearch/meta.yml @@ -13,55 +13,79 @@ tools: tool_dev_url: https://github.com/EddyRivasLab/hmmer doi: "10.1371/journal.pcbi.1002195" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - hmmfile: - type: file - description: One or more HMM profiles created with hmmbuild - pattern: "*.{hmm,hmm.gz}" - - seqdb: - type: file - description: Database of sequences in FASTA format - pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" - - write_align: - type: boolean - description: Flag to save optional alignment output. Specify with 'true' to save. - - write_target: - type: boolean - description: Flag to save optional per target summary. Specify with 'true' to save. - - write_domain: - type: boolean - description: Flag to save optional per domain summary. Specify with 'true' to save. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - hmmfile: + type: file + description: One or more HMM profiles created with hmmbuild + pattern: "*.{hmm,hmm.gz}" + - seqdb: + type: file + description: Database of sequences in FASTA format + pattern: "*.{fasta,fna,faa,fa,fasta.gz,fna.gz,faa.gz,fa.gz}" + - write_align: + type: boolean + description: Flag to save optional alignment output. Specify with 'true' to + save. + - write_target: + type: boolean + description: Flag to save optional per target summary. Specify with 'true' to + save. + - write_domain: + type: boolean + description: Flag to save optional per domain summary. Specify with 'true' to + save. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Human readable output summarizing hmmsearch results - pattern: "*.{txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Human readable output summarizing hmmsearch results + pattern: "*.{txt.gz}" - alignments: - type: file - description: Optional multiple sequence alignment (MSA) in Stockholm format - pattern: "*.{sto.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sto.gz": + type: file + description: Optional multiple sequence alignment (MSA) in Stockholm format + pattern: "*.{sto.gz}" - target_summary: - type: file - description: Optional tabular (space-delimited) summary of per-target output - pattern: "*.{tbl.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbl.gz": + type: file + description: Optional tabular (space-delimited) summary of per-target output + pattern: "*.{tbl.gz}" - domain_summary: - type: file - description: Optional tabular (space-delimited) summary of per-domain output - pattern: "*.{domtbl.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.domtbl.gz": + type: file + description: Optional tabular (space-delimited) summary of per-domain output + pattern: "*.{domtbl.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/hmtnote/annotate/meta.yml b/modules/nf-core/hmtnote/annotate/meta.yml index 4ab418313593..661d5cde0945 100644 --- a/modules/nf-core/hmtnote/annotate/meta.yml +++ b/modules/nf-core/hmtnote/annotate/meta.yml @@ -1,5 +1,6 @@ name: hmtnote_annotate -description: Human mitochondrial variants annotation using HmtVar. Contains .plk file with annotation, so can be run offline +description: Human mitochondrial variants annotation using HmtVar. Contains .plk file + with annotation, so can be run offline keywords: - hmtnote - mitochondria @@ -11,28 +12,31 @@ tools: documentation: https://hmtnote.readthedocs.io/en/latest/usage.html doi: "10.1101/600619" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - - vcf: - type: file - description: vcf file - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + - vcf: + type: file + description: vcf file + pattern: "*.vcf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: annotated vcf - pattern: "*_annotated.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + - "*_annotated.vcf": + type: file + description: annotated vcf + pattern: "*_annotated.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sysbiocoder" maintainers: diff --git a/modules/nf-core/homer/annotatepeaks/meta.yml b/modules/nf-core/homer/annotatepeaks/meta.yml index 0d76caba8d6f..37a8ea09597f 100644 --- a/modules/nf-core/homer/annotatepeaks/meta.yml +++ b/modules/nf-core/homer/annotatepeaks/meta.yml @@ -11,42 +11,50 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: The peak files in bed format - pattern: "*.bed" - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - gtf: - type: file - description: GTF file of reference genome - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peak: + type: file + description: Peak file to annotate + - - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - gtf: + type: file + description: GTF file of reference genome + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - annotated_peaks: - type: file - description: The annotated peaks - pattern: "*annotatePeaks.txt" - - annotation_stats: - type: file - description: the annStats file output from -annStats parameter - pattern: "*annStats.txt" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annotatePeaks.txt": + type: file + description: Annotated peaks in txt file + pattern: "*annotatePeaks.txt" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annStats.txt": + type: file + description: Annotation statistics in txt file + pattern: "*annStats.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/homer/findpeaks/meta.yml b/modules/nf-core/homer/findpeaks/meta.yml index 286032c30909..fdcc1055703d 100644 --- a/modules/nf-core/homer/findpeaks/meta.yml +++ b/modules/nf-core/homer/findpeaks/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "http://homer.ucsd.edu/homer/ngs/peaks.html" doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tagDir: + type: directory + description: "The 'Tag Directory'" + pattern: "tagDir" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: The found peaks - pattern: "*.peaks.txt" + - txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peaks.txt": + type: file + description: "Peaks in txt file" + pattern: "*.peaks.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/maketagdirectory/environment.yml b/modules/nf-core/homer/maketagdirectory/environment.yml index e1a60845799a..9864257f1029 100644 --- a/modules/nf-core/homer/maketagdirectory/environment.yml +++ b/modules/nf-core/homer/maketagdirectory/environment.yml @@ -1,10 +1,11 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::homer=4.11 - - bioconda::samtools=1.11 - - conda-forge::r-base=4.0.2 - bioconda::bioconductor-deseq2=1.30.0 - bioconda::bioconductor-edger=3.32.0 + - bioconda::homer=4.11 + - bioconda::samtools=1.11 - conda-forge::perl=5.26.2 + - conda-forge::r-base=4.0.2 diff --git a/modules/nf-core/homer/maketagdirectory/meta.yml b/modules/nf-core/homer/maketagdirectory/meta.yml index 8b240411b815..1e3b9c45bdb9 100644 --- a/modules/nf-core/homer/maketagdirectory/meta.yml +++ b/modules/nf-core/homer/maketagdirectory/meta.yml @@ -12,6 +12,7 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer - samtools: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -21,6 +22,7 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:homer - DESeq2: description: | Differential gene expression analysis based on the negative binomial distribution @@ -29,6 +31,7 @@ tools: tool_dev_url: "https://github.com/mikelove/DESeq2" doi: 10.18129/B9.bioc.DESeq2 licence: ["LGPL-3.0-or-later"] + identifier: biotools:homer - edgeR: description: | Empirical Analysis of Digital Gene Expression Data in R @@ -37,38 +40,47 @@ tools: tool_dev_url: "https://git.bioconductor.org/packages/edgeR" doi: 10.18129/B9.bioc.edgeR licence: ["GPL >=2"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/BED/SAM file - pattern: "*.{bam,bed,sam}" - - fasta: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/BED/SAM file + pattern: "*.{bam,bed,sam}" + - - fasta: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tagdir: - type: directory - description: The "Tag Directory" - pattern: "*_tagdir" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tagdir": + type: directory + description: The "Tag Directory" + pattern: "*_tagdir" - taginfo: - type: directory - description: The tagInfo.txt included to ensure there's proper output - pattern: "*_tagdir/tagInfo.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_tagdir/tagInfo.txt": + type: directory + description: The tagInfo.txt included to ensure there's proper output + pattern: "*_tagdir/tagInfo.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/makeucscfile/meta.yml b/modules/nf-core/homer/makeucscfile/meta.yml index 808c310f131b..6271f46618a7 100644 --- a/modules/nf-core/homer/makeucscfile/meta.yml +++ b/modules/nf-core/homer/makeucscfile/meta.yml @@ -11,30 +11,33 @@ tools: documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tagDir: + type: directory + description: "The 'Tag Directory'" + pattern: "tagDir" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedGraph: - type: file - description: The UCSC bed graph - pattern: "*.bedGraph.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph.gz": + type: file + description: The UCSC bed graph + pattern: "*.bedGraph.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/homer/pos2bed/meta.yml b/modules/nf-core/homer/pos2bed/meta.yml index f870fa7175ab..5fc5f9b1db46 100644 --- a/modules/nf-core/homer/pos2bed/meta.yml +++ b/modules/nf-core/homer/pos2bed/meta.yml @@ -13,30 +13,32 @@ tools: tool_dev_url: "http://homer.ucsd.edu/homer/ngs/miscellaneous.html" doi: 10.1016/j.molcel.2010.05.004. licence: ["GPL-3.0-or-later"] + identifier: biotools:homer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tagDir: - type: directory - description: "The 'Tag Directory'" - pattern: "tagDir" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peaks: + type: file + description: Peak file to convert to BED format output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/hpsuissero/meta.yml b/modules/nf-core/hpsuissero/meta.yml index a171da1477c8..28f919cb2e68 100644 --- a/modules/nf-core/hpsuissero/meta.yml +++ b/modules/nf-core/hpsuissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/jimmyliu1326/HpsuisSero tool_dev_url: https://github.com/jimmyliu1326/HpsuisSero licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited serotype prediction - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited serotype prediction + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/htseq/count/meta.yml b/modules/nf-core/htseq/count/meta.yml index 9373e680e022..7e30fe0063e1 100644 --- a/modules/nf-core/htseq/count/meta.yml +++ b/modules/nf-core/htseq/count/meta.yml @@ -1,4 +1,3 @@ ---- name: "htseq_count" description: count how many reads map to each feature keywords: @@ -8,44 +7,52 @@ keywords: - annotation tools: - "htseq/count": - description: "HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments." + description: "HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments." homepage: "https://htseq.readthedocs.io/en/latest/" documentation: "https://htseq.readthedocs.io/en/latest/index.html" doi: "10.1093/bioinformatics/btu638" licence: ["GPL v3"] + identifier: biotools:htseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - .gtf file information - e.g. `[ id:'test' ]` - - input: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: Contains indexed bam file - pattern: "*.bai" - - gtf: - type: file - description: Contains the features in the GTF format - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: Contains indexed bam file + pattern: "*.bai" + - - meta2: + type: map + description: | + .gtf file information + e.g. `[ id:'test' ]` + - gtf: + type: file + description: Contains the features in the GTF format + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - txt: - type: file - description: File containing feature counts output - pattern: ".txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: File containing feature counts output + pattern: ".txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zehrahazalsezer" maintainers: diff --git a/modules/nf-core/htsnimtools/vcfcheck/meta.yml b/modules/nf-core/htsnimtools/vcfcheck/meta.yml index 19304f7a1a2d..c34ecaa9057f 100644 --- a/modules/nf-core/htsnimtools/vcfcheck/meta.yml +++ b/modules/nf-core/htsnimtools/vcfcheck/meta.yml @@ -1,6 +1,7 @@ ---- name: "htsnimtools_vcfcheck" -description: This tools takes a background VCF, such as gnomad, that has full genome (though in some cases, users will instead want whole exome) coverage and uses that as an expectation of variants. +description: This tools takes a background VCF, such as gnomad, that has full genome + (though in some cases, users will instead want whole exome) coverage and uses that + as an expectation of variants. keywords: - validation - check @@ -12,50 +13,52 @@ tools: documentation: "https://github.com/brentp/hts-nim-tools" tool_dev_url: "https://github.com/brentp/hts-nim-tools" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: The query VCF file - pattern: "*.{vcf,vcf.gz,bcf}" - - tbi: - type: file - description: The index of the query VCF file - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy Map containing background VCF information - e.g. `[ id:'sample1', single_end:false ]` - - background_vcf: - type: file - description: The background VCF file - pattern: "*.{vcf,vcf.gz,bcf}" - - background_tbi: - type: file - description: The index of the background VCF file - pattern: "*.{tbi}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: The query VCF file + pattern: "*.{vcf,vcf.gz,bcf}" + - tbi: + type: file + description: The index of the query VCF file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing background VCF information + e.g. `[ id:'sample1', single_end:false ]` + - background_vcf: + type: file + description: The background VCF file + pattern: "*.{vcf,vcf.gz,bcf}" + - background_tbi: + type: file + description: The index of the background VCF file + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file comparing the variant count of each region in the query VCF and background VCF - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: A tab-delimited file comparing the variant count of each region + in the query VCF and background VCF + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/humid/meta.yml b/modules/nf-core/humid/meta.yml index c8548ea3a7ab..e5fa28df0b8b 100644 --- a/modules/nf-core/humid/meta.yml +++ b/modules/nf-core/humid/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "humid" -description: HUMID is a tool to quickly and easily remove duplicate reads from FastQ files, with or without UMIs. +description: HUMID is a tool to quickly and easily remove duplicate reads from FastQ + files, with or without UMIs. keywords: - umi - fastq @@ -15,59 +15,72 @@ tools: documentation: "https://humid.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/jfjlaros/HUMID" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: - type: file - description: Fastq file(s) to deduplicate - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - umis: - type: file - description: Fastq file(s) containing UMIs - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Fastq file(s) to deduplicate + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - umi_file: + type: file + description: UMI file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.log: + type: file + description: Log file of humid, containing progress and errors + pattern: "*.log" - dedup: - type: file - description: Deduplicated Fastq file(s) - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_dedup*.fastq.gz": + type: file + description: Deduplicated Fastq file(s) + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - annotated: - type: file - description: Annotated Fastq file(s) - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_annotated*.fastq.gz": + type: file + description: Annotated Fastq file(s) + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" - stats: - type: directory - description: Directory containg statistics file, use for multiqc. - pattern: "${prefix}/" - - - log: - type: file - description: Log file of humid, containing progress and errors - pattern: "*.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}: + type: directory + description: Directory containg statistics file, use for multiqc. + pattern: "${prefix}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/hypo/meta.yml b/modules/nf-core/hypo/meta.yml index 002b418f5c8c..f9887f08c433 100644 --- a/modules/nf-core/hypo/meta.yml +++ b/modules/nf-core/hypo/meta.yml @@ -13,47 +13,51 @@ tools: tool_dev_url: "https://github.com/kensung-lab/hypo" doi: "10.1101/2019.12.19.882506" licence: ["GPL v3"] + identifier: biotools:hypo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Short reads file(s). In fastq or fasta, compressed or uncompressed - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sr_bam: - type: file - description: Aligned short-read BAM/SAM file. Must have CIGAR information. - pattern: "*.{bam,sam}" - - draft: - type: file - description: Input (fasta) file containing draft contig assembly - - genome_size: - type: string - description: Estimated size of the genome. Number or nts or use suffixes k/m/g, e.g. 5m, 3.2g - - reads_coverage: - type: integer - description: Appprimate depth of coverage of short reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sr_bam: + type: file + description: Aligned short-read BAM/SAM file. Must have CIGAR information. + pattern: "*.{bam,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Short reads file(s). In fastq or fasta, compressed or uncompressed + - - draft: + type: file + description: Input (fasta) file containing draft contig assembly + - - genome_size: + type: string + description: Estimated size of the genome. Number or nts or use suffixes k/m/g, + e.g. 5m, 3.2g + - - reads_coverage: + type: integer + description: Appprimate depth of coverage of short reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Polished assembly fasta file - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Polished assembly fasta file + pattern: "*.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@remiolsen" maintainers: diff --git a/modules/nf-core/ichorcna/createpon/meta.yml b/modules/nf-core/ichorcna/createpon/meta.yml index d5fa233e39e8..9d0cb18c1877 100644 --- a/modules/nf-core/ichorcna/createpon/meta.yml +++ b/modules/nf-core/ichorcna/createpon/meta.yml @@ -1,5 +1,7 @@ name: ichorcna_createpon -description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals +description: ichorCNA is an R package for calculating copy number alteration from + (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This + module generates a panel of normals keywords: - ichorcna - cnv @@ -9,51 +11,61 @@ keywords: - panel_of_normals tools: - ichorcna: - description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole + genome sequencing. homepage: https://github.com/broadinstitute/ichorCNA documentation: https://github.com/broadinstitute/ichorCNA/wiki tool_dev_url: https://github.com/broadinstitute/ichorCNA doi: "10.1038/s41467-017-00965-y" licence: ["GPL v3"] + identifier: "" input: - - wigs: - type: file - description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals. - pattern: "*.{wig}" - - gc_wig: - type: file - description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window - pattern: "*.{wig}" - - map_wig: - type: file - description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window - pattern: "*.{wig}" - - centromere: - type: file - description: Text file giving centromere locations of each genome, to exclude these windows - pattern: "*.{txt}" - - rep_time_wig: - type: file - description: Replication/timing .wig file. - pattern: "*.{wig}" - - exons: - type: file - description: BED file for exon regions to annotate CNA regions. - pattern: "*.{bed}" - + - - wigs: + type: file + description: Any number of hmmcopy/readCounter processed .wig files giving the + number of reads in the sample, in each genomic window. These will be averaged + over to generate the panel of normals. + pattern: "*.{wig}" + - - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude + these windows + pattern: "*.{txt}" + - - rep_time_wig: + type: file + description: Replication/timing .wig file. + pattern: "*.{wig}" + - - exons: + type: file + description: BED file for exon regions to annotate CNA regions. + pattern: "*.{bed}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rds: - type: file - description: R data file (.rds) containing panel of normals data, medians of each bin. - pattern: "*.rds" + - ${prefix}*.rds: + type: file + description: R data file (.rds) containing panel of normals data, medians of + each bin. + pattern: "*.rds" - txt: - type: file - description: Text file containing panel of normals data, medians of each bin. - pattern: "*.txt" + - ${prefix}*.txt: + type: file + description: Text file containing panel of normals data, medians of each bin. + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ichorcna/run/meta.yml b/modules/nf-core/ichorcna/run/meta.yml index ef4a31c889be..aeca09df6cb2 100644 --- a/modules/nf-core/ichorcna/run/meta.yml +++ b/modules/nf-core/ichorcna/run/meta.yml @@ -1,5 +1,6 @@ name: ichorcna_run -description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA +description: ichorCNA is an R package for calculating copy number alteration from + (low-pass) whole genome sequencing, particularly for use in cell-free DNA keywords: - ichorcna - cnv @@ -8,111 +9,146 @@ keywords: - wgs tools: - ichorcna: - description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole + genome sequencing. homepage: https://github.com/broadinstitute/ichorCNA documentation: https://github.com/broadinstitute/ichorCNA/wiki tool_dev_url: https://github.com/broadinstitute/ichorCNA doi: "10.1038/s41467-017-00965-y" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - - wig: - type: file - description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window - pattern: "*.{wig}" - - - gc_wig: - type: file - description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window - pattern: "*.{wig}" - - - map_wig: - type: file - description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window - pattern: "*.{wig}" - - - normal_wig: - type: file - description: hmmcopy/readCounter processed .wig file giving the number of reads in the normal sample, in each genomic window - pattern: "*.{wig}" - - - normal_background: - type: file - description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc. - pattern: "*.{rds}" - - - centromere: - type: file - description: Text file giving centromere locations of each genome, to exclude these windows - pattern: "*.{txt}" - - - rep_time_wig: - type: file - description: Replication/timing .wig file. - pattern: "*.{wig}" - - - exons: - type: file - description: BED file for exon regions to annotate CNA regions. - pattern: "*.{bed}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - wig: + type: file + description: hmmcopy/readCounter processed .wig file giving the number of reads + in the sample, in each genomic window + pattern: "*.{wig}" + - - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in + the reference fasta, in each genomic window + pattern: "*.{wig}" + - - normal_wig: + type: file + description: hmmcopy/readCounter processed .wig file giving the number of reads + in the normal sample, in each genomic window + pattern: "*.{wig}" + - - normal_background: + type: file + description: Panel of normals data, generated by calling ichorCNA on a set of + normal samples with the same window size etc. + pattern: "*.{rds}" + - - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude + these windows + pattern: "*.{txt}" + - - rep_time_wig: + type: file + description: Replication/timing .wig file. + pattern: "*.{wig}" + - - exons: + type: file + description: BED file for exon regions to annotate CNA regions. + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - + - rdata: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.RData: + type: file + description: RData file containing all the intermediate R objects + pattern: "*.{cng.seg}" - seg: - type: file - description: Predicted copy number variation per segment - pattern: "*.{seg}" - - - seg_txt: - type: file - description: Predicted copy number variation per segment - pattern: "*.{seg.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.seg: + type: file + description: Predicted copy number variation per segment + pattern: "*.{seg}" - cna_seg: - type: file - description: Predicted copy number variation per segment - pattern: "*.{cng.seg}" - - - ichorcna_params: - type: file - description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc - pattern: "*.{params.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.cna.seg: + type: file + description: Predicted copy number variation per segment + pattern: "*.{cng.seg}" + - seg_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.seg.txt: + type: file + description: Predicted copy number variation per segment + pattern: "*.{seg.txt}" - corrected_depth: - type: file - description: A text file with corrected depth per bin - pattern: "*.{params.txt}" - - - genome_plot: - type: file - description: A plot with the best-fit genome-wide CNV data - pattern: "*.{genomeWide.pdf}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.correctedDepth.txt: + type: file + description: A text file with corrected depth per bin + pattern: "*.{params.txt}" + - ichorcna_params: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}.params.txt: + type: file + description: A text file showing the values that ichorCNA has estimated for + tumour fraction, ploidy etc + pattern: "*.{params.txt}" - plots: - type: file - description: Plots with e.g. individual chromosomes and different considered ploidy - pattern: "*.{pdf}" - - - rdata: - type: file - description: RData file containing all the intermediate R objects - pattern: "*.{cng.seg}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - ${prefix}/*.pdf: + type: file + description: Plots with e.g. individual chromosomes and different considered + ploidy + pattern: "*.{pdf}" + - genome_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "**/${prefix}_genomeWide.pdf": + type: file + description: A plot with the best-fit genome-wide CNV data + pattern: "*.{genomeWide.pdf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" - "@adamrtalbot" diff --git a/modules/nf-core/icountmini/metagene/meta.yml b/modules/nf-core/icountmini/metagene/meta.yml index 1ed324a8a216..78a833530c18 100644 --- a/modules/nf-core/icountmini/metagene/meta.yml +++ b/modules/nf-core/icountmini/metagene/meta.yml @@ -1,6 +1,6 @@ ---- name: icountmini_metagene -description: Plot a metagene of cross-link events/sites around various transcriptomic landmarks. +description: Plot a metagene of cross-link events/sites around various transcriptomic + landmarks. keywords: - iCLIP - gtf @@ -11,33 +11,36 @@ tools: homepage: https://icount.readthedocs.io/en/latest/ documentation: https://icount.readthedocs.io/en/latest/ licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: Metagene table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - metagene_*/*plot_data.tsv: + type: file + description: Metagene table + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/peaks/meta.yml b/modules/nf-core/icountmini/peaks/meta.yml index 2736ebfda90a..fceb24d70404 100644 --- a/modules/nf-core/icountmini/peaks/meta.yml +++ b/modules/nf-core/icountmini/peaks/meta.yml @@ -1,4 +1,3 @@ ---- name: "icountmini_peaks" description: Runs iCount peaks on a BED file of crosslinks keywords: @@ -13,34 +12,37 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bed}" - - sigxls: - type: file - description: TSV file of sigxls from iCount sigxls - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bed}" + - sigxls: + type: file + description: TSV file of sigxls from iCount sigxls + pattern: "*.{tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - peaks: - type: file - description: Crosslinks deemed significant by iCount - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peaks.bed.gz": + type: file + description: Crosslinks deemed significant by iCount + pattern: "*.{bed.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/segment/meta.yml b/modules/nf-core/icountmini/segment/meta.yml index f2b00839d9b6..2abf601f438d 100644 --- a/modules/nf-core/icountmini/segment/meta.yml +++ b/modules/nf-core/icountmini/segment/meta.yml @@ -1,4 +1,3 @@ ---- name: icountmini_segment description: Formats a GTF file for use with iCount sigxls keywords: @@ -13,29 +12,43 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gtf: - type: file - description: A GTF file to use for the segmentation - pattern: "*.{gtf}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtf: + type: file + description: A GTF file to use for the segmentation + pattern: "*.{gtf}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" output: - gtf: - type: file - description: Segmented GTF file for use with iCount sigxls - pattern: "*.{gtf}" + - meta: + type: map + description: Groovy Map containing sample information + - "*_seg.gtf": + type: file + description: Segmented GTF file for use with iCount sigxls + pattern: "*.{gtf}" + - regions: + - meta: + type: map + description: Groovy Map containing sample information + - "*_regions.gtf.gz": + type: file + description: Regions file for use with iCount sigxls + pattern: "*.{gtf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/sigxls/meta.yml b/modules/nf-core/icountmini/sigxls/meta.yml index 4a467707ab1f..c866404c5898 100644 --- a/modules/nf-core/icountmini/sigxls/meta.yml +++ b/modules/nf-core/icountmini/sigxls/meta.yml @@ -1,4 +1,3 @@ ---- name: "icountmini_sigxls" description: Runs iCount sigxls on a BED file of crosslinks keywords: @@ -14,38 +13,47 @@ tools: tool_dev_url: https://github.com/ulelab/iCount-Mini doi: "10.1038/nsmb.1838" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - pattern: "*.{bam,bam.gz}" - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + pattern: "*.{bam,bam.gz}" + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: Crosslinks deemed significant by iCount - pattern: "*.{bed.gz}" + - sigxls: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sigxls.bed.gz": + type: file + description: sigxls bed file + pattern: "*.{bed.gz}" - scores: - type: file - description: Crosslink scores calculated by iCount - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scores.tsv": + type: file + description: Crosslink scores calculated by iCount + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/icountmini/summary/meta.yml b/modules/nf-core/icountmini/summary/meta.yml index 37540429df4c..f4f9ef289f7c 100644 --- a/modules/nf-core/icountmini/summary/meta.yml +++ b/modules/nf-core/icountmini/summary/meta.yml @@ -1,4 +1,3 @@ ---- name: icountmini_summary description: Report proportion of cross-link events/sites on each region type. keywords: @@ -11,41 +10,56 @@ tools: homepage: https://icount.readthedocs.io/en/latest/ documentation: https://icount.readthedocs.io/en/latest/ licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file of crosslinks - - segmentation: - type: file - description: A iCount segmentation file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file of crosslinks + - - segmentation: + type: file + description: A iCount segmentation file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - summary_type: - type: file - description: Summary type output stats file - pattern: "*summary_type.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_type.tsv": + type: file + description: Summary type output stats file + pattern: "*summary_type.tsv" - summary_subtype: - type: file - description: Summary subtype output stats file - pattern: "*summary_subtype.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_subtype.tsv": + type: file + description: Summary subtype output stats file + pattern: "*summary_subtype.tsv" - summary_gene: - type: file - description: Summary gene output stats file - pattern: "*summary_gene.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*summary_gene.tsv": + type: file + description: Summary gene output stats file + pattern: "*summary_gene.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marc-jones" - "@chris-cheshire" diff --git a/modules/nf-core/idemux/meta.yml b/modules/nf-core/idemux/meta.yml index 085e8e9b25cf..97bd57bbbba0 100644 --- a/modules/nf-core/idemux/meta.yml +++ b/modules/nf-core/idemux/meta.yml @@ -12,38 +12,51 @@ tools: documentation: https://github.com/Lexogen-Tools/idemux tool_dev_url: https://github.com/Lexogen-Tools/idemux licence: ["LEXOGEN"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'NVQ', lane:1 ] - - reads: - type: file - description: | - List of input FastQ files - pattern: "Undetermined_S*.fastq.gz" - - samplesheet: - type: file - description: Input samplesheet - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'NVQ', lane:1 ] + - reads: + type: file + description: | + List of input FastQ files + pattern: "Undetermined_S*.fastq.gz" + - samplesheet: + type: file + description: Input samplesheet + pattern: "*.{csv}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "*.fastq.gz" + - meta: + type: file + description: Demultiplexed sample FASTQ files + pattern: "*.fastq.gz" + - "[!undetermined]*.fastq.gz": + type: file + description: Demultiplexed sample FASTQ files + pattern: "*.fastq.gz" - undetermined: - type: file - description: Optional undetermined sample FASTQ files - pattern: "Undetermined_R?.fastq.gz" + - meta: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_R?.fastq.gz" + - undetermined_R?.fastq.gz: + type: file + description: Optional undetermined sample FASTQ files + pattern: "Undetermined_R?.fastq.gz" - stats: - type: file - description: Demultiplexing Stats - pattern: "demultipexing_stats.tsv" + - demultipexing_stats.tsv: + type: file + description: Demultiplexing Stats + pattern: "demultipexing_stats.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jaanckae" maintainers: diff --git a/modules/nf-core/idr/meta.yml b/modules/nf-core/idr/meta.yml index 5f2ab1109e38..ef21bc208437 100644 --- a/modules/nf-core/idr/meta.yml +++ b/modules/nf-core/idr/meta.yml @@ -15,35 +15,40 @@ tools: experiments and provide highly stable thresholds based on reproducibility. tool_dev_url: https://github.com/kundajelab/idr licence: ["GPL v2"] + identifier: biotools:idr input: - - peaks: - type: list - description: BED, narrowPeak or broadPeak files of replicates - pattern: "*" - - peak_type: - type: string - description: Type of peak file - pattern: "{narrowPeak,broadPeak,bed}" - - prefix: - type: string - description: Prefix for output files + - - peaks: + type: list + description: BED, narrowPeak or broadPeak files of replicates + pattern: "*" + - - peak_type: + type: string + description: Type of peak file + pattern: "{narrowPeak,broadPeak,bed}" + - - prefix: + type: string + description: Prefix for output files output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idr: - type: file - description: Text file containing IDR values - pattern: "*.{txt}" + - "*idrValues.txt": + type: file + description: Text file containing IDR values + pattern: "*.{txt}" - log: - type: file - description: Log file - pattern: "*.{txt}" + - "*log.txt": + type: file + description: Log file + pattern: "*.{txt}" - png: - type: file - description: Plot generated by idr - pattern: "*{.png}" + - "*.png": + type: file + description: Plot generated by idr + pattern: "*{.png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/igv/js/meta.yml b/modules/nf-core/igv/js/meta.yml index 48fc3cc57f18..b7f01b44c7f5 100644 --- a/modules/nf-core/igv/js/meta.yml +++ b/modules/nf-core/igv/js/meta.yml @@ -18,42 +18,57 @@ tools: tool_dev_url: https://github.com/igvteam/igv.js doi: 10.1093/bioinformatics/btac830 licence: ["MIT"] + identifier: biotools:igv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: Index of sorted BAM/CRAM file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: Index of sorted BAM/CRAM file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - browser: - type: file - description: Genome browser HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genome-browser.html": + type: file + description: Genome browser HTML file + pattern: "*.{html}" - align_files: - type: file - description: Copy of the input sorted BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: Copy of the input sorted BAM/CRAM file + pattern: "*.{bam,cram}" - index_files: - type: file - description: Copy of the input index of sorted BAM/CRAM file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Copy of the input index of sorted BAM/CRAM file + pattern: "*.{bai,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/igvreports/meta.yml b/modules/nf-core/igvreports/meta.yml index d1170b247101..fc1a9f84eaf7 100644 --- a/modules/nf-core/igvreports/meta.yml +++ b/modules/nf-core/igvreports/meta.yml @@ -1,68 +1,73 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "igvreports" -description: A Python application to generate self-contained HTML reports for variant review and other genomic applications +description: A Python application to generate self-contained HTML reports for variant + review and other genomic applications keywords: - vcf - variant - genomics tools: - "igvreports": - description: "Creates self-contained html pages for visual variant review with IGV (igv.js)." + description: "Creates self-contained html pages for visual variant review with + IGV (igv.js)." homepage: "https://github.com/igvteam/igv-reports" documentation: "https://github.com/igvteam/igv-reports" tool_dev_url: "https://github.com/igvteam/igv-reports" doi: "10.1093/bioinformatics/btac830" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sites: - type: file - description: | - VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites - - tracks: - type: file - description: | - List of any set of files of the types that IGV can display, - eg BAM/CRAM, GTF/GFF, VCF, BED, etc - - tracks_indices: - type: file - description: | - Track index files, eg bai/crai files. This may not be required, - but for some file types, eg BAM/CRAM, they are. They are not used in the - igvreports cmds, but may need to exist in the working directory - - - meta2: - type: map - description: | - Groovy Map containing genome information - e.g. [ id:'genome_name' ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: Reference fasta file index - pattern: "*.{fai}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sites: + type: file + description: | + VCF, BED, MAF, BEDPE, or generic tab delimited file of genomic variant sites + - tracks: + type: file + description: | + List of any set of files of the types that IGV can display, + eg BAM/CRAM, GTF/GFF, VCF, BED, etc + - tracks_indicies: + type: file + description: | + List of indices for the tracks + - - meta2: + type: map + description: | + Groovy Map containing genome information + e.g. [ id:'genome_name' ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: Reference fasta file index + pattern: "*.{fai}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: | - html report with a table of genomic sites and an embedded - IGV genome browser for viewing data for each site - pattern: "*.{html}" - + - meta: + type: file + description: | + html report with a table of genomic sites and an embedded + IGV genome browser for viewing data for each site + pattern: "*.{html}" + - "*.html": + type: file + description: | + html report with a table of genomic sites and an embedded + IGV genome browser for viewing data for each site + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@souljamie" maintainers: diff --git a/modules/nf-core/ilastik/multicut/meta.yml b/modules/nf-core/ilastik/multicut/meta.yml index 36ac9e90b0ec..cab8ffa2acd7 100644 --- a/modules/nf-core/ilastik/multicut/meta.yml +++ b/modules/nf-core/ilastik/multicut/meta.yml @@ -1,58 +1,66 @@ name: "ilastik_multicut" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - multicut - segmentation - pixel classification tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" license: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - h5: - type: file - description: h5 file containing image stack to classify file - pattern: "*.{h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik .ilp project file - pattern: "*.{ilp}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - probs: - type: file - description: Probability map for boundary based segmentation - pattern: "*.{h5,,hdf5}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - h5: + type: file + description: h5 file containing image stack to classify file + pattern: "*.{h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik .ilp project file + pattern: "*.{ilp}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - probs: + type: file + description: Probability map for boundary based segmentation + pattern: "*.{h5,,hdf5}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out_tiff: - type: file - description: Multicut segmentation mask output. - pattern: "*.{tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tiff": + type: file + description: Multicut segmentation mask output. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/ilastik/pixelclassification/meta.yml b/modules/nf-core/ilastik/pixelclassification/meta.yml index ad100d9b827d..5d0403bbb3fa 100644 --- a/modules/nf-core/ilastik/pixelclassification/meta.yml +++ b/modules/nf-core/ilastik/pixelclassification/meta.yml @@ -1,47 +1,55 @@ name: "ilastik_pixelclassification" -description: Ilastik is a tool that utilizes machine learning algorithms to classify pixels, segment, track and count cells in images. Ilastik contains a graphical user interface to interactively label pixels. However, this nextflow module will implement the --headless mode, to apply pixel classification using a pre-trained .ilp file on an input image. +description: Ilastik is a tool that utilizes machine learning algorithms to classify + pixels, segment, track and count cells in images. Ilastik contains a graphical user + interface to interactively label pixels. However, this nextflow module will implement + the --headless mode, to apply pixel classification using a pre-trained .ilp file + on an input image. keywords: - pixel_classification - segmentation - probability_maps tools: - "ilastik": - description: "Ilastik is a user friendly tool that enables pixel classification, segmentation and analysis." + description: "Ilastik is a user friendly tool that enables pixel classification, + segmentation and analysis." homepage: "https://www.ilastik.org/" documentation: "https://www.ilastik.org/documentation/" tool_dev_url: "https://github.com/ilastik/ilastik" licence: ["GPL3"] + identifier: biotools:ilastik input: - - meta: - type: map - description: | - Groovy Map containing sample information for h5 file - e.g. [ id:'test', single_end:false ] - - input_img: - type: file - description: Input img file containing image stack to classify - - meta2: - type: map - description: | - Groovy Map containing sample information for ilp file - e.g. [ id:'test', single_end:false ] - - ilp: - type: file - description: Trained ilastik pixel classification .ilp project file - pattern: "*.{ilp}" + - - meta: + type: map + description: | + Groovy Map containing sample information for h5 file + e.g. [ id:'test', single_end:false ] + - input_img: + type: file + description: Input img file containing image stack to classify + - - meta2: + type: map + description: | + Groovy Map containing sample information for ilp file + e.g. [ id:'test', single_end:false ] + - ilp: + type: file + description: Trained ilastik pixel classification .ilp project file + pattern: "*.{ilp}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: Output file from ilastik pixel classification. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${suffix}": + type: file + description: Output file from ilastik pixel classification. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/instrain/compare/meta.yml b/modules/nf-core/instrain/compare/meta.yml index c7b072d5a988..52b5318bc8a1 100644 --- a/modules/nf-core/instrain/compare/meta.yml +++ b/modules/nf-core/instrain/compare/meta.yml @@ -14,54 +14,81 @@ tools: tool_dev_url: https://github.com/MrOlm/instrain doi: 10.1038/s41587-020-00797-0 licence: ["MIT"] + identifier: biotools:instrain input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - profiles: - type: directory - description: InStrain profile folders - pattern: "*.IS/" - - bams: - type: file - description: Path to .bam files that were profiled - pattern: "*.{bam,sam}" - - stb_file: - type: file - description: Path to .stb (scaffold to bin) file that was profiled - pattern: "*.stb" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bams: + type: file + description: Path to .bam files that were profiled + pattern: "*.{bam,sam}" + - profiles: + type: directory + description: InStrain profile folders + pattern: "*.IS/" + - - stb_file: + type: file + description: Path to .stb (scaffold to bin) file that was profiled + pattern: "*.stb" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - compare: - type: directory - description: inStrain compare folders - pattern: "*.IS_compare/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare": + type: directory + description: inStrain compare folders + pattern: "*.IS_compare/" - comparisons_table: - type: file - description: Comparisons table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_comparisonsTable.tsv": + type: file + description: Comparisons table + pattern: "*.tsv" - pooled_snv: - type: file - description: Pooled SNV - pattern: "*.tsv" - - snv_info: - type: file - description: SNV information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_data.tsv": + type: file + description: Pooled SNV + pattern: "*.tsv" - snv_keys: - type: file - description: SNV keys - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_data_keys.tsv": + type: file + description: SNV keys + pattern: "*.tsv" + - snv_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.IS_compare/output/*.IS_compare_pooled_SNV_info.tsv": + type: file + description: SNV information + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@margotl9" - "@CarsonJM" diff --git a/modules/nf-core/instrain/profile/meta.yml b/modules/nf-core/instrain/profile/meta.yml index 43462ca2f11c..04bda267854f 100644 --- a/modules/nf-core/instrain/profile/meta.yml +++ b/modules/nf-core/instrain/profile/meta.yml @@ -1,5 +1,8 @@ name: "instrain_profile" -description: inStrain is python program for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification +description: inStrain is python program for analysis of co-occurring genome populations + from metagenomes that allows highly accurate genome comparisons, analysis of coverage, + microdiversity, and linkage, and sensitive SNP detection with gene localization + and synonymous non-synonymous identification keywords: - instrain - metagenomics @@ -13,64 +16,104 @@ tools: tool_dev_url: https://github.com/MrOlm/instrain doi: 10.1038/s41587-020-00797-0 licence: ["MIT"] + identifier: biotools:instrain input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test'] - - bam: - type: file - description: Path to .bam file to be profiled - pattern: "*.{bam,sam}" - - genome_fasta: - type: file - description: Path to .fasta file to be profiled; MUST be the .fasta file that was mapped to to create the .bam file - pattern: "*.{fasta,fna,fa}" - - genes_fasta: - type: file - description: Path to .fna file of genes to be profiled (OPTIONAL) - pattern: "*.{fasta,fna,fa}" - - stb_file: - type: file - description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL) - pattern: "*.stb" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test'] + - bam: + type: file + description: Path to .bam file to be profiled + pattern: "*.{bam,sam}" + - - genome_fasta: + type: file + description: Path to .fasta file to be profiled; MUST be the .fasta file that + was mapped to to create the .bam file + pattern: "*.{fasta,fna,fa}" + - - genes_fasta: + type: file + description: Path to .fna file of genes to be profiled (OPTIONAL) + pattern: "*.{fasta,fna,fa}" + - - stb_file: + type: file + description: Path to .stb (scaffold to bin) file to be profiled (OPTIONAL) + pattern: "*.stb" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: directory - description: InStrain profile folder - pattern: "*.IS/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS": + type: directory + description: InStrain profile folder + pattern: "*.IS/" + - snvs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_SNVs.tsv": + type: file + description: SNVs + pattern: "*.tsv" - gene_info: - type: file - description: Gene information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_gene_info.tsv": + type: file + description: Gene information + pattern: "*.tsv" - genome_info: - type: file - description: Genome information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_genome_info.tsv": + type: file + description: Genome information + pattern: "*.tsv" - linkage: - type: file - description: Linkage information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_linkage.tsv": + type: file + description: Linkage information + pattern: "*.tsv" - mapping_info: - type: file - description: Mapping information - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_mapping_info.tsv": + type: file + description: Mapping information + pattern: "*.tsv" - scaffold_info: - type: file - description: Scaffold information - pattern: "*.tsv" - - snvs: - type: file - description: SNVs - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.IS/output/*.IS_scaffold_info.tsv": + type: file + description: Scaffold information + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mrolm" maintainers: diff --git a/modules/nf-core/interproscan/meta.yml b/modules/nf-core/interproscan/meta.yml index 44cce91b7ab5..0bb10f7daf90 100644 --- a/modules/nf-core/interproscan/meta.yml +++ b/modules/nf-core/interproscan/meta.yml @@ -1,5 +1,6 @@ name: "interproscan" -description: Produces protein annotations and predictions from an amino acids FASTA file +description: Produces protein annotations and predictions from an amino acids FASTA + file keywords: - annotation - fasta @@ -8,46 +9,70 @@ keywords: - interproscan tools: - "interproscan": - description: "InterPro integrates together predictive information about proteins function from a number of partner resources" + description: "InterPro integrates together predictive information about proteins + function from a number of partner resources" homepage: "https://www.ebi.ac.uk/interpro/search/sequence/" documentation: "https://interproscan-docs.readthedocs.io" tool_dev_url: "https://github.com/ebi-pf-team/interproscan" doi: "10.1093/bioinformatics/btu031" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing the amino acid or dna query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - interproscan_database: - type: directory - description: Path to the interproscan database (untarred http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing the amino acid or dna query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - interproscan_database: + type: directory + description: Path to the interproscan database (untarred + http://ftp.ebi.ac.uk/pub/software/unix/iprscan/5/${version_major}-${version_minor}/interproscan-${version_major}-${version_minor}-64-bit.tar.gz) output: - tsv: - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" + - meta: + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" - xml: - type: file - description: XML file containing with detailed hits - pattern: "*.{xml}" + - meta: + type: file + description: XML file containing with detailed hits + pattern: "*.{xml}" + - "*.xml": + type: file + description: XML file containing with detailed hits + pattern: "*.{xml}" - gff3: - type: file - description: GFF3 file containing with detailed hits - pattern: "*.{gff3}" + - meta: + type: file + description: GFF3 file containing with detailed hits + pattern: "*.{gff3}" + - "*.gff3": + type: file + description: GFF3 file containing with detailed hits + pattern: "*.{gff3}" - json: - type: file - description: JSON file containing with detailed hits - pattern: "*.{json}" + - meta: + type: file + description: JSON file containing with detailed hits + pattern: "*.{json}" + - "*.json": + type: file + description: JSON file containing with detailed hits + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" - "@mahesh-panchal" diff --git a/modules/nf-core/iphop/download/meta.yml b/modules/nf-core/iphop/download/meta.yml index b3a31992e7b2..f4b5939aebba 100644 --- a/modules/nf-core/iphop/download/meta.yml +++ b/modules/nf-core/iphop/download/meta.yml @@ -16,15 +16,18 @@ tools: tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" licence: ["Modified GPL v3"] + identifier: "" output: - iphop_db: - type: directory - description: Directory containing downloaded and md5 checked iPHoP database - pattern: "iphop_db/" + - iphop_db/: + type: directory + description: Directory containing downloaded and md5 checked iPHoP database + pattern: "iphop_db/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/iphop/predict/meta.yml b/modules/nf-core/iphop/predict/meta.yml index ce267dd13be6..d115364b8229 100644 --- a/modules/nf-core/iphop/predict/meta.yml +++ b/modules/nf-core/iphop/predict/meta.yml @@ -16,41 +16,58 @@ tools: tool_dev_url: https://bitbucket.org/srouxjgi/iphop/src/main/ doi: "10.1371/journal.pbio.3002083" licence: ["Modified GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing phage contigs/scaffolds/chromosomes - pattern: "*.{fasta,fna,fa}" - - iphop_db: - type: directory - description: Directory pointing to iPHoP database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing phage contigs/scaffolds/chromosomes + pattern: "*.{fasta,fna,fa}" + - - iphop_db: + type: directory + description: Directory pointing to iPHoP database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - iphop_genus: - type: file - description: File containing integrated host predictions at genus level, with a minimum score defined by the `--min_score` argument - pattern: "Host_prediction_to_genus_m*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Host_prediction_to_genus_m*.csv: + type: file + description: File containing integrated host predictions at genus level, with + a minimum score defined by the `--min_score` argument + pattern: "Host_prediction_to_genus_m*.csv" - iphop_genome: - type: file - description: File containing integrated host predictions at host genome level, with a minimum score defined by the `--min_score` argument - pattern: "Host_prediction_to_genome_m*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Host_prediction_to_genome_m*.csv: + type: file + description: File containing integrated host predictions at host genome level, + with a minimum score defined by the `--min_score` argument + pattern: "Host_prediction_to_genome_m*.csv" - iphop_detailed_output: - type: file - description: File containing each phage's top 5 hits via each method - pattern: "Detailed_output_by_tool.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - Detailed_output_by_tool.csv: + type: file + description: File containing each phage's top 5 hits via each method + pattern: "Detailed_output_by_tool.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/iqtree/meta.yml b/modules/nf-core/iqtree/meta.yml index 40b7601fc158..b20bdd88abf5 100644 --- a/modules/nf-core/iqtree/meta.yml +++ b/modules/nf-core/iqtree/meta.yml @@ -1,5 +1,6 @@ name: iqtree -description: Produces a Newick format phylogeny from a multiple sequence alignment using the maxium likelihood algorithm. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment + using the maxium likelihood algorithm. Capable of bacterial genome size alignments. keywords: - phylogeny - newick @@ -12,205 +13,343 @@ tools: tool_dev_url: https://github.com/iqtree/iqtree2 doi: 10.1093/molbev/msaa015 licence: ["GPL v2-or-later"] + identifier: biotools:iqtree input: - - meta: - type: map - description: | - Groovy map containing sample information for the - alignment/tree file, e.g. [ id: 'test' ] - - alignment: - type: file - description: Input alignment file in PHYLIP, - FASTA, NEXUS, CLUSTAL or MSF format (-s) - pattern: "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" - - tree: - type: file - description: "File containing one or multiple phylogenetic trees (-t): - - Single tree used e.g. as starting tree for tree search - - Set of trees used e.g. for distance computation, consensus tree construction" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - - tree_te: - type: file - description: "File containing single phylogenetic tree (-te) - Use cases: - - fixed user tree to skip tree search - - ancestral sequence reconstruction" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" - - lmclust: - type: file - description: NEXUS file containing taxon clusters - for quartet mapping analysis (-lmclust) - pattern: "*.nex{us}" - - mdef: - type: file - description: NEXUS model file defining new models (-mdef) - pattern: "*.nex{us}" - - partitions_equal: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-q) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - partitions_proportional: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-spp) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - partitions_unlinked: - type: file - description: Partition file for edge-equal partition - model, all partitions share same set of branch lengths (-sp) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - guide_tree: - type: file - description: File containing guide tree for inference of - site frequency profiles (-ft) - pattern: "*.{nex,nexus,tre,tree,treefile}" - - sitefreq_in: - type: file - description: Site frequency file (-fs) - pattern: "*.sitefreq" - - constraint_tree: - type: file - description: File containing opological constraint tree in - NEWICK format. The constraint tree can be a multifurcating - tree and need not to include all taxa. (-g) - pattern: "*.{nwk,newick}" - - trees_z: - type: file - description: File containing a set of trees for which - log-likelihoods should be computed (-z) - - suptree: - type: file - description: File containing input “target” tree, support - values are extracted from trees passed via -t, and mapped - onto the target tree (-sup) - - trees_rf: - type: file - description: "File containing a second tree set (-rf). Used - for computing the distance to the primary tree set (`tree`)" - pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - meta: + type: map + description: | + Groovy map containing sample information for the + alignment/tree file, e.g. [ id: 'test' ] + - alignment: + type: file + description: Input alignment file in PHYLIP, FASTA, NEXUS, CLUSTAL or MSF format + (-s) + pattern: "*.{fasta,fas,fa,mfa,phy,aln,nex,nexus,msf}" + - tree: + type: file + description: "File containing one or multiple phylogenetic trees (-t): - Single + tree used e.g. as starting tree for tree search - Set of trees used e.g. for + distance computation, consensus tree construction" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - tree_te: + type: file + description: "File containing single phylogenetic tree (-te) Use cases: - fixed + user tree to skip tree search - ancestral sequence reconstruction" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" + - - lmclust: + type: file + description: NEXUS file containing taxon clusters for quartet mapping analysis + (-lmclust) + pattern: "*.nex{us}" + - - mdef: + type: file + description: NEXUS model file defining new models (-mdef) + pattern: "*.nex{us}" + - - partitions_equal: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-q) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - partitions_proportional: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-spp) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - partitions_unlinked: + type: file + description: Partition file for edge-equal partition model, all partitions share + same set of branch lengths (-sp) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - guide_tree: + type: file + description: File containing guide tree for inference of site frequency profiles + (-ft) + pattern: "*.{nex,nexus,tre,tree,treefile}" + - - sitefreq_in: + type: file + description: Site frequency file (-fs) + pattern: "*.sitefreq" + - - constraint_tree: + type: file + description: File containing opological constraint tree in NEWICK format. The + constraint tree can be a multifurcating tree and need not to include all taxa. + (-g) + pattern: "*.{nwk,newick}" + - - trees_z: + type: file + description: File containing a set of trees for which log-likelihoods should + be computed (-z) + - - suptree: + type: file + description: File containing input “target” tree, support values are extracted + from trees passed via -t, and mapped onto the target tree (-sup) + - - trees_rf: + type: file + description: "File containing a second tree set (-rf). Used for computing the + distance to the primary tree set (`tree`)" + pattern: "*.{tre,tree,treefile,newick,nwk,nex,nexus}" output: - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{treefile}" + - meta: + type: file + description: A phylogeny in Newick format + pattern: "*.{treefile}" + - "*.treefile": + type: file + description: A phylogeny in Newick format + pattern: "*.{treefile}" - report: - type: file - description: | - Main report file containing computational - results as well as a textual visualization - of the final tree - pattern: "*.{iqtree}" + - meta: + type: file + description: | + Main report file containing computational + results as well as a textual visualization + of the final tree + pattern: "*.{iqtree}" + - "*.iqtree": + type: file + description: | + Main report file containing computational + results as well as a textual visualization + of the final tree + pattern: "*.{iqtree}" - mldist: - type: file - description: | - File containing the pairwise maximum - likelihood distances as a matrix - pattern: "*.{mldist}" + - meta: + type: file + description: | + File containing the pairwise maximum + likelihood distances as a matrix + pattern: "*.{mldist}" + - "*.mldist": + type: file + description: | + File containing the pairwise maximum + likelihood distances as a matrix + pattern: "*.{mldist}" - lmap_svg: - type: file - description: | - File containing likelihood mapping analysis - results in .svg format (-lmap/-lmclust) - pattern: "*.lmap.svg" + - meta: + type: file + description: | + File containing likelihood mapping analysis + results in .svg format (-lmap/-lmclust) + pattern: "*.lmap.svg" + - "*.lmap.svg": + type: file + description: | + File containing likelihood mapping analysis + results in .svg format (-lmap/-lmclust) + pattern: "*.lmap.svg" - lmap_eps: - type: file - description: | - File containing likelihood mapping analysis - results in .eps format (-lmap/-lmclust) - pattern: "*.lmap.eps" + - meta: + type: file + description: | + File containing likelihood mapping analysis + results in .eps format (-lmap/-lmclust) + pattern: "*.lmap.eps" + - "*.lmap.eps": + type: file + description: | + File containing likelihood mapping analysis + results in .eps format (-lmap/-lmclust) + pattern: "*.lmap.eps" - lmap_quartetlh: - type: file - description: | - File containing quartet log-likelihoods (-wql) - pattern: "*.lmap.quartetlh" + - meta: + type: file + description: | + File containing quartet log-likelihoods (-wql) + pattern: "*.lmap.quartetlh" + - "*.lmap.quartetlh": + type: file + description: | + File containing quartet log-likelihoods (-wql) + pattern: "*.lmap.quartetlh" - sitefreq_out: - type: file - description: | - File containing site frequency profiles (-ft) - pattern: "*.sitefreq" + - meta: + type: file + description: | + File containing site frequency profiles (-ft) + pattern: "*.sitefreq" + - "*.sitefreq": + type: file + description: | + File containing site frequency profiles (-ft) + pattern: "*.sitefreq" - bootstrap: - type: file - description: | - File containing all bootstrap trees (-wbt/-wbtl) - pattern: "*.ufboot" + - meta: + type: file + description: | + File containing all bootstrap trees (-wbt/-wbtl) + pattern: "*.ufboot" + - "*.ufboot": + type: file + description: | + File containing all bootstrap trees (-wbt/-wbtl) + pattern: "*.ufboot" - state: - type: file - description: | - File containing ancestral sequences for all - nodes of the tree by empirical Bayesian method (-asr) - pattern: "*.{state}" + - meta: + type: file + description: | + File containing ancestral sequences for all + nodes of the tree by empirical Bayesian method (-asr) + pattern: "*.{state}" + - "*.state": + type: file + description: | + File containing ancestral sequences for all + nodes of the tree by empirical Bayesian method (-asr) + pattern: "*.{state}" - contree: - type: file - description: | - File containing consensus tree (-con/-bb) - pattern: "*.{contree}" + - meta: + type: file + description: | + File containing consensus tree (-con/-bb) + pattern: "*.{contree}" + - "*.contree": + type: file + description: | + File containing consensus tree (-con/-bb) + pattern: "*.{contree}" - nex: - type: file - description: | - File containing consensus network (-net/-bb) - pattern: "*.{nex}" + - meta: + type: file + description: | + File containing consensus network (-net/-bb) + pattern: "*.{nex}" + - "*.nex": + type: file + description: | + File containing consensus network (-net/-bb) + pattern: "*.{nex}" - splits: - type: file - description: | - File containing consensus network in star-dot format (-wsplits) - pattern: "*.{splits}" + - meta: + type: file + description: | + File containing consensus network in star-dot format (-wsplits) + pattern: "*.{splits}" + - "*.splits": + type: file + description: | + File containing consensus network in star-dot format (-wsplits) + pattern: "*.{splits}" - suptree: - type: file - description: | - File containing tree with assigned support - values based on supplied "target" tree (-sup) - pattern: "*.{suptree}" + - meta: + type: file + description: | + File containing tree with assigned support + values based on supplied "target" tree (-sup) + pattern: "*.{suptree}" + - "*.suptree": + type: file + description: | + File containing tree with assigned support + values based on supplied "target" tree (-sup) + pattern: "*.{suptree}" - alninfo: - type: file - description: | - File containing alignment site statistics (-alninfo) - pattern: "*.{alninfo}" + - meta: + type: file + description: | + File containing alignment site statistics (-alninfo) + pattern: "*.{alninfo}" + - "*.alninfo": + type: file + description: | + File containing alignment site statistics (-alninfo) + pattern: "*.{alninfo}" - partlh: - type: file - description: | - File containing partition log-likelihoods (-wpl) - pattern: "*.{partlh}" + - meta: + type: file + description: | + File containing partition log-likelihoods (-wpl) + pattern: "*.{partlh}" + - "*.partlh": + type: file + description: | + File containing partition log-likelihoods (-wpl) + pattern: "*.{partlh}" - siteprob: - type: file - description: | - File containing site posterior probabilities (-wspr/-wspm/-wspmr) - pattern: "*.{siteprob}" + - meta: + type: file + description: | + File containing site posterior probabilities (-wspr/-wspm/-wspmr) + pattern: "*.{siteprob}" + - "*.siteprob": + type: file + description: | + File containing site posterior probabilities (-wspr/-wspm/-wspmr) + pattern: "*.{siteprob}" - sitelh: - type: file - description: | - File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) - pattern: "*.{sitelh}" + - meta: + type: file + description: | + File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) + pattern: "*.{sitelh}" + - "*.sitelh": + type: file + description: | + File containing site log-likelihoods (-wsl/-wslr/-wslm/-wslmr) + pattern: "*.{sitelh}" - treels: - type: file - description: | - File containing all locally optimal trees (-wt) - pattern: "*.{treels}" + - meta: + type: file + description: | + File containing all locally optimal trees (-wt) + pattern: "*.{treels}" + - "*.treels": + type: file + description: | + File containing all locally optimal trees (-wt) + pattern: "*.{treels}" - rate: - type: file - description: | - File containing inferred site-specific - evolutionary rates (-wsr) - pattern: "*.{rate}" + - meta: + type: file + description: | + File containing inferred site-specific + evolutionary rates (-wsr) + pattern: "*.{rate}" + - "*.rate ": + type: file + description: | + File containing inferred site-specific + evolutionary rates (-wsr) + pattern: "*.{rate}" - mlrate: - type: file - description: | - File containing site-specific subtitution - rates determined by maximum likelihood (--mlrate) - pattern: "*.{mlrate}" + - meta: + type: file + description: | + File containing site-specific subtitution + rates determined by maximum likelihood (--mlrate) + pattern: "*.{mlrate}" + - "*.mlrate": + type: file + description: | + File containing site-specific subtitution + rates determined by maximum likelihood (--mlrate) + pattern: "*.{mlrate}" - exch_matrix: - type: file - description: File containing the exchangeability - matrix obtained from the optimization (--link-exchange-rates) - pattern: "GTRPMIX.nex" + - meta: + type: file + description: File containing the exchangeability matrix obtained from the optimization + (--link-exchange-rates) + pattern: "GTRPMIX.nex" + - GTRPMIX.nex: + type: file + description: File containing the exchangeability matrix obtained from the optimization + (--link-exchange-rates) + pattern: "GTRPMIX.nex" - log: - type: file - description: Log file of entire run - pattern: "*.{log}" + - meta: + type: file + description: Log file of entire run + pattern: "*.{log}" + - "*.log": + type: file + description: Log file of entire run + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" - "@aunderwo" diff --git a/modules/nf-core/islandpath/meta.yml b/modules/nf-core/islandpath/meta.yml index 98d108e35950..b175aa24c71f 100644 --- a/modules/nf-core/islandpath/meta.yml +++ b/modules/nf-core/islandpath/meta.yml @@ -6,36 +6,47 @@ keywords: - prediction tools: - "islandpath": - description: "IslandPath-DIMOB is a standalone software to predict genomic islands (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) in bacterial and archaeal genomes based on the presence of dinucleotide biases and mobility genes." + description: "IslandPath-DIMOB is a standalone software to predict genomic islands + (GIs - clusters of genes in prokaryotic genomes of probable horizontal origin) + in bacterial and archaeal genomes based on the presence of dinucleotide biases + and mobility genes." homepage: https://github.com/brinkmanlab/islandpath documentation: https://github.com/brinkmanlab/islandpath#readme tool_dev_url: https://github.com/brinkmanlab/islandpath doi: "10.1093/bioinformatics/bty095" licence: ["GPL v3"] + identifier: biotools:islandpath input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genome: - type: file - description: | - Genome file in .gbk or .embl format. - pattern: "*.{gbk, embl, gbff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: | + Genome file in .gbk or .embl format. + pattern: "*.{gbk, embl, gbff}" output: - gff: - type: file - description: GFF file listing the predicted genomic islands and their coordinates - pattern: "*.gff" + - meta: + type: file + description: GFF file listing the predicted genomic islands and their coordinates + pattern: "*.gff" + - "*.gff": + type: file + description: GFF file listing the predicted genomic islands and their coordinates + pattern: "*.gff" - log: - type: file - description: Log file of the islandpath run - pattern: "*.log" + - Dimob.log: + type: file + description: Log file of the islandpath run + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/ismapper/meta.yml b/modules/nf-core/ismapper/meta.yml index f930901aa2c4..bb413e7a9f10 100644 --- a/modules/nf-core/ismapper/meta.yml +++ b/modules/nf-core/ismapper/meta.yml @@ -6,44 +6,48 @@ keywords: - bacteria tools: - ismapper: - description: A mapping-based tool for identification of the site and orientation of IS insertions in bacterial genomes. + description: A mapping-based tool for identification of the site and orientation + of IS insertions in bacterial genomes. homepage: https://github.com/jhawkey/IS_mapper documentation: https://github.com/jhawkey/IS_mapper tool_dev_url: https://github.com/jhawkey/IS_mapper doi: "10.1186/s12864-015-1860-2" licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A set of paired-end FASTQ files - pattern: "*.{fastq.gz,fq.gz}" - - reference: - type: file - description: Reference genome in GenBank format - pattern: "*.{gbk}" - - query: - type: file - description: Insertion sequences to query in FASTA format - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A set of paired-end FASTQ files + pattern: "*.{fastq.gz,fq.gz}" + - reference: + type: file + description: Reference genome in GenBank format + pattern: "*.{gbk}" + - query: + type: file + description: Insertion sequences to query in FASTA format + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing ISMapper result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing ISMapper result files + pattern: "*/*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/isoseq/cluster/meta.yml b/modules/nf-core/isoseq/cluster/meta.yml index a7879668dded..b3388abf261f 100644 --- a/modules/nf-core/isoseq/cluster/meta.yml +++ b/modules/nf-core/isoseq/cluster/meta.yml @@ -12,70 +12,134 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file generated by isoseq refine - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file generated by isoseq refine + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - bam: - type: file - description: BAM file of clustered consensus - pattern: "*.transcripts.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.bam": + type: file + description: BAM file of clustered consensus + pattern: "*.transcripts.bam" - pbi: - type: file - description: Pacbio Index of consensus reads generated by clustering - pattern: "*.transcripts.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.bam.pbi": + type: file + description: Pacbio Index of consensus reads generated by clustering + pattern: "*.transcripts.bam.pbi" - cluster: - type: file - description: A two columns (from, to) file describing original read name to new read name - pattern: "*.transcripts.cluster" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.cluster": + type: file + description: A two columns (from, to) file describing original read name to + new read name + pattern: "*.transcripts.cluster" - cluster_report: - type: file - description: A table files clusters (transcripts) members (read) - pattern: "*.transcripts.cluster_report.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.cluster_report.csv": + type: file + description: A table files clusters (transcripts) members (read) + pattern: "*.transcripts.cluster_report.csv" - transcriptset: - type: file - description: A metadata xml file which contains full paths to data files - pattern: "*.transcripts.transcriptset.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.transcriptset.xml": + type: file + description: A metadata xml file which contains full paths to data files + pattern: "*.transcripts.transcriptset.xml" - hq_bam: - type: file - description: High quality reads (when --use-qvs is set) - pattern: "*.transcripts.hq.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.hq.bam": + type: file + description: High quality reads (when --use-qvs is set) + pattern: "*.transcripts.hq.bam" - hq_pbi: - type: file - description: Pacbio index of high quality reads (when --use-qvs is set) - pattern: "*.transcripts.hq.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.hq.bam.pbi": + type: file + description: Pacbio index of high quality reads (when --use-qvs is set) + pattern: "*.transcripts.hq.bam.pbi" - lq_bam: - type: file - description: Low quality reads (when --use-qvs is set) - pattern: "*.transcripts.lq.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.lq.bam": + type: file + description: Low quality reads (when --use-qvs is set) + pattern: "*.transcripts.lq.bam" - lq_pbi: - type: file - description: Pacbio index of low quality reads (when --use-qvs is set) - pattern: "*.transcripts.lq.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.lq.bam.pbi": + type: file + description: Pacbio index of low quality reads (when --use-qvs is set) + pattern: "*.transcripts.lq.bam.pbi" - singletons_bam: - type: file - description: Unclustered reads (when --singletons is set) - pattern: "*.transcripts.singletons.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.singletons.bam": + type: file + description: Unclustered reads (when --singletons is set) + pattern: "*.transcripts.singletons.bam" - singletons_pbi: - type: file - description: Pacbio index of unclustered reads (when --singletons is set) - pattern: "*.transcripts.singletons.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.singletons.bam.pbi": + type: file + description: Pacbio index of unclustered reads (when --singletons is set) + pattern: "*.transcripts.singletons.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/isoseq/refine/meta.yml b/modules/nf-core/isoseq/refine/meta.yml index 40f6c4b0f0a8..f15b87d3968a 100644 --- a/modules/nf-core/isoseq/refine/meta.yml +++ b/modules/nf-core/isoseq/refine/meta.yml @@ -13,50 +13,80 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test ] - - bam: - type: file - description: BAM file, cleaned ccs generated by lima - pattern: "*.bam" - - primers: - type: file - description: fasta file of primers - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test ] + - bam: + type: file + description: BAM file, cleaned ccs generated by lima + pattern: "*.bam" + - - primers: + type: file + description: fasta file of primers + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - bam: - type: file - description: Set of complete reads (with polyA tail), where the polyA has been trimmed - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: Set of complete reads (with polyA tail), where the polyA has been + trimmed + pattern: "*.bam" - pbi: - type: file - description: Pacbio index file from polyA trimmed reads - pattern: "*.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file from polyA trimmed reads + pattern: "*.pbi" - consensusreadset: - type: file - description: Metadata about read library - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.consensusreadset.xml": + type: file + description: Metadata about read library + pattern: "*.xml" - summary: - type: file - description: json file describing number of full length reads, full length non chimeric reads and full length non chimeric polyA reads - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.filter_summary.report.json": + type: file + description: json file describing number of full length reads, full length non + chimeric reads and full length non chimeric polyA reads + pattern: "*.json" - report: - type: file - description: Metadata about primer and polyA detection (primers/polyA/insert length, strand, primer name) - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report.csv": + type: file + description: Metadata about primer and polyA detection (primers/polyA/insert + length, strand, primer name) + pattern: "*.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/isoseq3/tag/meta.yml b/modules/nf-core/isoseq3/tag/meta.yml index 55939a04c443..13468839802f 100644 --- a/modules/nf-core/isoseq3/tag/meta.yml +++ b/modules/nf-core/isoseq3/tag/meta.yml @@ -1,4 +1,3 @@ ---- name: "isoseq3_tag" description: Extract UMI and cell barcodes keywords: @@ -14,41 +13,50 @@ tools: documentation: "https://isoseq.how/" tool_dev_url: "https://github.com/PacificBiosciences/IsoSeq/tree/master" licence: ["BSD-3-clause-Clear"] + identifier: biotools:isoseq3 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - bam: - type: file - description: BAM file, one full-length CCS file generated by lima - pattern: "*.5p--3p.bam" - - design: - type: string - description: Barcoding design. Specifies which bases to use as cell/molecular barcodes. - pattern: "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\d{1,2}[UBGX])+$" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - bam: + type: file + description: BAM file, one full-length CCS file generated by lima + pattern: "*.5p--3p.bam" + - - design: + type: string + description: Barcoding design. Specifies which bases to use as cell/molecular + barcodes. + pattern: "^(?:\\d{1,2}[UBGX]-)+T$|^(?:\\d{1,2}[UBGX]-)+T(?:-\\d{1,2}[UBGX])+$|^T(?:-\\\ + d{1,2}[UBGX])+$" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with full-length tagged reads - pattern: "*.flt.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.flt.bam": + type: file + description: BAM file with full-length tagged reads + pattern: "*.flt.bam" - pbi: - type: file - description: Pacbio index file of full-length tagged reads - pattern: "*.flt.bam.pbi" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.flt.bam.pbi": + type: file + description: Pacbio index file of full-length tagged reads + pattern: "*.flt.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@skraettli" maintainers: diff --git a/modules/nf-core/ivar/consensus/meta.yml b/modules/nf-core/ivar/consensus/meta.yml index 99e11924bf85..afe8a3d6f2d5 100644 --- a/modules/nf-core/ivar/consensus/meta.yml +++ b/modules/nf-core/ivar/consensus/meta.yml @@ -11,46 +11,63 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar consensus - patter: "*.mpileup" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam + file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar consensus + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: iVar generated consensus sequence - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: iVar generated consensus sequence + pattern: "*.fa" - qual: - type: file - description: iVar generated quality file - pattern: "*.qual.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.qual.txt": + type: file + description: iVar generated quality file + pattern: "*.qual.txt" - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup": + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/ivar/trim/meta.yml b/modules/nf-core/ivar/trim/meta.yml index 3a99f6f3bf44..eaeec80cb4ec 100644 --- a/modules/nf-core/ivar/trim/meta.yml +++ b/modules/nf-core/ivar/trim/meta.yml @@ -11,42 +11,51 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Co-ordinate sorted BAM file - pattern: "*.bam" - - bai: - type: file - description: Index file for co-ordinate sorted BAM file - pattern: "*.bai" - - bed: - type: file - description: BED file with primer labels and positions - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Co-ordinate sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index file for co-ordinate sorted BAM file + pattern: "*.bai" + - - bed: + type: file + description: BED file with primer labels and positions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: iVar generated trimmed bam file (unsorted) - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: iVar generated trimmed bam file (unsorted) + pattern: "*.bam" - log: - type: file - description: Log file generated by iVar for use with MultiQC - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file generated by iVar for use with MultiQC + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/ivar/variants/meta.yml b/modules/nf-core/ivar/variants/meta.yml index 9dc9b05ca4ee..369032bef10b 100644 --- a/modules/nf-core/ivar/variants/meta.yml +++ b/modules/nf-core/ivar/variants/meta.yml @@ -11,50 +11,64 @@ tools: homepage: https://github.com/andersen-lab/ivar documentation: https://andersen-lab.github.io/ivar/html/manualpage.html licence: ["GPL-3.0-or-later"] + identifier: biotools:andersen-lab_ivar input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - fai: - type: file - description: The index for the reference sequence used for mapping and generating the BAM file - pattern: "*.fai" - - gff: - type: file - description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. - patter: "*.gff" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar variants - patter: "*.mpileup" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam + file + pattern: "*.bam" + - - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM + file + pattern: "*.fa" + - - fai: + type: file + description: The index for the reference sequence used for mapping and generating + the BAM file + pattern: "*.fai" + - - gff: + type: file + description: A GFF file in the GFF3 format can be supplied to specify coordinates + of open reading frames (ORFs). In absence of GFF file, amino acid translation + will not be done. + patter: "*.gff" + - - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar variants + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: iVar generated TSV file with the variants - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup": + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@andersgs" - "@drpatelh" diff --git a/modules/nf-core/jasminesv/environment.yml b/modules/nf-core/jasminesv/environment.yml index a0ef927ea416..7a0da03aa065 100644 --- a/modules/nf-core/jasminesv/environment.yml +++ b/modules/nf-core/jasminesv/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::jasminesv=1.1.5 - bioconda::htslib=1.15.1 + - bioconda::jasminesv=1.1.5 diff --git a/modules/nf-core/jasminesv/meta.yml b/modules/nf-core/jasminesv/meta.yml index 5d8b111cb8d0..404b32825546 100644 --- a/modules/nf-core/jasminesv/meta.yml +++ b/modules/nf-core/jasminesv/meta.yml @@ -13,61 +13,67 @@ tools: documentation: "https://github.com/mkirsche/Jasmine/wiki/Jasmine-User-Manual" tool_dev_url: "https://github.com/mkirsche/Jasmine" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - The VCF files that need to be merged - pattern: "*.{vcf,vcf.gz}" - - bams: - type: list - description: Optional - The BAM files from which the VCFs were created - pattern: "*.bam" - - sample_dists: - type: file - description: Optional - A txt file containing the distance thresholds for each sample - pattern: "*.txt" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Optional - The reference FASTA file used to create the VCFs - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: Optional - The index of the reference FASTA file used to create the VCFs - pattern: "*.fai" - - chr_norm: - type: file - description: Optional - A txt file containing the chromosomes and their aliases for normalization - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + The VCF files that need to be merged + pattern: "*.{vcf,vcf.gz}" + - bams: + type: list + description: Optional - The BAM files from which the VCFs were created + pattern: "*.bam" + - sample_dists: + type: file + description: Optional - A txt file containing the distance thresholds for each + sample + pattern: "*.txt" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Optional - The reference FASTA file used to create the VCFs + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: Optional - The index of the reference FASTA file used to create + the VCFs + pattern: "*.fai" + - - chr_norm: + type: file + description: Optional - A txt file containing the chromosomes and their aliases + for normalization + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The merged VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The merged VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/jupyternotebook/environment.yml b/modules/nf-core/jupyternotebook/environment.yml index d9ef11a3a9f2..a11d11b0c61e 100644 --- a/modules/nf-core/jupyternotebook/environment.yml +++ b/modules/nf-core/jupyternotebook/environment.yml @@ -1,9 +1,10 @@ channels: - conda-forge - bioconda + dependencies: - conda-forge::ipykernel=6.0.3 - conda-forge::jupytext=1.11.4 + - conda-forge::matplotlib=3.4.2 - conda-forge::nbconvert=6.1.0 - conda-forge::papermill=2.3.3 - - conda-forge::matplotlib=3.4.2 diff --git a/modules/nf-core/jupyternotebook/meta.yml b/modules/nf-core/jupyternotebook/meta.yml index 162171b62d4d..093217416e0a 100644 --- a/modules/nf-core/jupyternotebook/meta.yml +++ b/modules/nf-core/jupyternotebook/meta.yml @@ -16,51 +16,66 @@ tools: documentation: https://jupyter.org/documentation tool_dev_url: https://github.com/mwouts/jupytext/ license: ["MIT"] + identifier: "" - papermill: description: Parameterize, execute, and analyze notebooks homepage: https://github.com/nteract/papermill documentation: http://papermill.readthedocs.io/en/latest/ tool_dev_url: https://github.com/nteract/papermill license: ["BSD 3-clause"] + identifier: "" - nbconvert: description: Parameterize, execute, and analyze notebooks homepage: https://nbconvert.readthedocs.io/en/latest/ documentation: https://nbconvert.readthedocs.io/en/latest/ tool_dev_url: https://github.com/jupyter/nbconvert license: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - notebook: - type: file - description: Jupyter notebook or jupytext representation thereof - pattern: "*.{ipynb,py,md,Rmd,myst}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed - to papermill in order to create parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - notebook: + type: file + description: Jupyter notebook or jupytext representation thereof + pattern: "*.{ipynb,py,md,Rmd,myst}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed + to papermill in order to create parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: HTML report generated from Jupyter notebook - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML report generated from Jupyter notebook + pattern: "*.html" + - artifacts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - artifacts/: + type: directory + description: Directory containing all artifacts generated by the notebook + pattern: "artifacts/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/jvarkit/vcffilterjdk/meta.yml b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml index f4bce92102c3..09e2232e9b9b 100644 --- a/modules/nf-core/jvarkit/vcffilterjdk/meta.yml +++ b/modules/nf-core/jvarkit/vcffilterjdk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_vcffilterjdk" description: Filtering VCF with dynamically-compiled java expressions @@ -19,6 +18,7 @@ tools: licence: ["MIT License"] args_id: "$args2" + identifier: "" - "bcftools": description: | View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF @@ -27,91 +27,107 @@ tools: doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] args_id: ["$args1", "$args3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test_reference' ] - - vcf: - type: file - description: Input VCF/BCF file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - tbi: - type: file - description: Optional VCF/BCF index file - pattern: "*.{tbi,csi}" - - regions_file: - type: file - description: Optional. Restrict to regions listed in a file - pattern: "*.{bed,bed.gz,txt,tsv}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: Fasta reference file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing fasta.fai information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Fasta file index - pattern: "*.fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing fasta.dict information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - meta5: - type: map - description: | - Groovy Map containing code information - e.g. [ id:'test_reference' ] - - code: - type: file - description: File containing custom user code . May be empty if script if provided via `task.ext.args2`. - pattern: "*.{code,script,txt,tsv,java,js}" - - meta6: - type: map - description: | - Groovy Map containing pedigree information - e.g. [ id:'test_reference' ] - - pedigree: - type: file - description: Optional jvarkit pedigree. - pattern: "*.{tsv,ped,pedigree}" + - - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test_reference' ] + - vcf: + type: file + description: Input VCF/BCF file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - tbi: + type: file + description: Optional VCF/BCF index file + pattern: "*.{tbi,csi}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{bed,bed.gz,txt,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: Fasta reference file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Fasta file index + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta5: + type: map + description: | + Groovy Map containing code information + e.g. [ id:'test_reference' ] + - code: + type: file + description: File containing custom user code . May be empty if script if provided + via `task.ext.args2`. + pattern: "*.{code,script,txt,tsv,java,js}" + - - meta6: + type: map + description: | + Groovy Map containing pedigree information + e.g. [ id:'test_reference' ] + - pedigree: + type: file + description: Optional jvarkit pedigree. + pattern: "*.{tsv,ped,pedigree}" output: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/jvarkit/vcfpolyx/environment.yml b/modules/nf-core/jvarkit/vcfpolyx/environment.yml index c70f23523cb6..e71f3d436687 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/environment.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/environment.yml @@ -5,4 +5,3 @@ channels: - conda-forge dependencies: - "bioconda::jvarkit=2024.08.25" - - "bioconda:bcftools=1.20" diff --git a/modules/nf-core/jvarkit/vcfpolyx/meta.yml b/modules/nf-core/jvarkit/vcfpolyx/meta.yml index 0e9017047062..68b104887491 100644 --- a/modules/nf-core/jvarkit/vcfpolyx/meta.yml +++ b/modules/nf-core/jvarkit/vcfpolyx/meta.yml @@ -1,14 +1,11 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_vcfpolyx" description: annotate VCF files for poly repeats keywords: - vcf - bcf - - variant - annotation - repeats - - polyx tools: - "jvarkit": description: "Java utilities for Bioinformatics." @@ -17,7 +14,7 @@ tools: tool_dev_url: "https://github.com/lindenb/jvarkit" doi: "10.6084/m9.figshare.1425030" licence: ["MIT License"] - args_id: "$args2" + identifier: "" - "bcftools": description: | @@ -26,75 +23,79 @@ tools: documentation: "http://www.htslib.org/doc/bcftools.html" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] - args_id: ["$args1", "$args3"] + identifier: "" + input: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test_reference' ] - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test_reference' ] - - meta3: - type: map - description: | - Groovy Map containing fasta.fai information - e.g. [ id:'test_reference' ] - - meta4: - type: map - description: | - Groovy Map containing fasta.dict information - e.g. [ id:'test_reference' ] - - vcf: - type: file - description: Groovy Map containing reference genome information for vcf - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - tbi: - type: file - description: Optional VCF/BCF index file - pattern: "*.{tbi,csi}" - - regions_file: - type: file - description: Optional. Restrict to regions listed in a file - pattern: "*.{bed,bed.gz,txt,tsv}" - - fasta: - type: file - description: Groovy Map containing reference genome information for fai reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Groovy Map containing reference genome information for fai - pattern: "*.fasta.fai" - - dict: - type: file - description: Groovy Map containing reference genome information for GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing VCF information + - vcf: + type: file + description: Groovy Map containing reference genome information for vcf + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: Groovy Map containing reference genome information for fai reference + fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing fasta.fai information + - fai: + type: file + description: Groovy Map containing reference genome information for fai + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing fasta.dict information + - dict: + type: file + description: Groovy Map containing reference genome information for GATK sequence + dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing VCF information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - csi: - type: file - description: Default VCF file index - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: VCF filtered output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - tbi: - type: file - description: Alternative VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml index f087b0d89b33..aac166fc7a42 100644 --- a/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml +++ b/modules/nf-core/jvarkit/wgscoverageplotter/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "jvarkit_wgscoverageplotter" description: Plot whole genome coverage from BAM/CRAM file as SVG @@ -18,61 +17,64 @@ tools: tool_dev_url: "https://github.com/lindenb/jvarkit" doi: "10.6084/m9.figshare.1425030" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_reference' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference fai information - e.g. [ id:'test_reference' ] - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" - - meta4: - type: map - description: | - Groovy Map containing reference dict information - e.g. [ id:'test_reference' ] - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_reference' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference fai information + e.g. [ id:'test_reference' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference dict information + e.g. [ id:'test_reference' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing Sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output SVG file - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing Sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: Output SVG file + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lindenb" maintainers: diff --git a/modules/nf-core/kaiju/kaiju/meta.yml b/modules/nf-core/kaiju/kaiju/meta.yml index 33c85690757f..ac9c681ec912 100644 --- a/modules/nf-core/kaiju/kaiju/meta.yml +++ b/modules/nf-core/kaiju/kaiju/meta.yml @@ -1,5 +1,6 @@ name: kaiju_kaiju -description: Taxonomic classification of metagenomic sequence data using a protein reference database +description: Taxonomic classification of metagenomic sequence data using a protein + reference database keywords: - classify - metagenomics @@ -13,37 +14,40 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" - - db: - type: directory - description: | - List containing the database and nodes files for Kaiju - e.g. [ 'database.fmi', 'nodes.dmp' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}" + - - db: + type: directory + description: | + List containing the database and nodes files for Kaiju + e.g. [ 'database.fmi', 'nodes.dmp' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: Results with taxonomic classification of each read - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Results with taxonomic classification of each read + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@talnor" - "@sofstam" diff --git a/modules/nf-core/kaiju/kaiju2krona/meta.yml b/modules/nf-core/kaiju/kaiju2krona/meta.yml index 355416f84dde..965bf779a0fb 100644 --- a/modules/nf-core/kaiju/kaiju2krona/meta.yml +++ b/modules/nf-core/kaiju/kaiju2krona/meta.yml @@ -1,5 +1,6 @@ name: kaiju_kaiju2krona -description: Convert Kaiju's tab-separated output file into a tab-separated text file which can be imported into Krona. +description: Convert Kaiju's tab-separated output file into a tab-separated text file + which can be imported into Krona. keywords: - taxonomy - visualisation @@ -13,30 +14,36 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: Kaiju tab-separated output file - pattern: "*.{tsv,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tsv: + type: file + description: Kaiju tab-separated output file + pattern: "*.{tsv,txt}" + - - db: + type: file + description: Kaiju database file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Krona text-based input file converted from Kaiju report - pattern: "*.{txt,krona}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Krona text-based input file converted from Kaiju report + pattern: "*.{txt,krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/kaiju/kaiju2table/meta.yml b/modules/nf-core/kaiju/kaiju2table/meta.yml index 0f62374e8c5c..b212cf0e055f 100644 --- a/modules/nf-core/kaiju/kaiju2table/meta.yml +++ b/modules/nf-core/kaiju/kaiju2table/meta.yml @@ -12,36 +12,40 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - results: - type: file - description: File containing the kaiju classification results - pattern: "*.{txt}" - - taxon_rank: - type: string - description: | - Taxonomic rank to display in report - pattern: "phylum|class|order|family|genus|species" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Kaiju input file + - - db: + type: file + description: Kaiju database + - - taxon_rank: + type: string + description: | + Taxonomic rank to display in report + pattern: "phylum|class|order|family|genus|species" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - summary: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Kaiju output file + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - results: - type: file - description: | - Summary table for a given taxonomic rank - pattern: "*.{tsv}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@talnor" diff --git a/modules/nf-core/kaiju/mergeoutputs/meta.yml b/modules/nf-core/kaiju/mergeoutputs/meta.yml index 4ec5000344c7..b3b2deeef869 100644 --- a/modules/nf-core/kaiju/mergeoutputs/meta.yml +++ b/modules/nf-core/kaiju/mergeoutputs/meta.yml @@ -1,5 +1,6 @@ name: kaiju_mergeoutputs -description: Merge two tab-separated output files of Kaiju and Kraken in the column format +description: Merge two tab-separated output files of Kaiju and Kraken in the column + format keywords: - classify - metagenomics @@ -13,40 +14,44 @@ tools: tool_dev_url: https://github.com/bioinformatics-centre/kaiju doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kaiju: - type: file - description: | - Results with taxonomic classification of each read from Kaiju - - kraken: - type: file - description: | - Results with taxonomic classification of each read from Kraken - pattern: "*.{tsv}" - - db: - type: directory - description: | - List containing the database and nodes files for Kaiju - e.g. [ 'database.fmi', 'nodes.dmp' ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kaiju: + type: file + description: | + Results with taxonomic classification of each read from Kaiju + - kraken: + type: file + description: | + Results with taxonomic classification of each read from Kraken + pattern: "*.{tsv}" + - - db: + type: directory + description: | + List containing the database and nodes files for Kaiju + e.g. [ 'database.fmi', 'nodes.dmp' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - merged: - type: file - description: Results with merged taxonomic classification of each read based on the given strategy '1', '2', 'lca' [default] or 'lowest' - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Results with merged taxonomic classification of each read based + on the given strategy '1', '2', 'lca' [default] or 'lowest' + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/kaiju/mkfmi/meta.yml b/modules/nf-core/kaiju/mkfmi/meta.yml index fe06f3588f9a..165327037352 100644 --- a/modules/nf-core/kaiju/mkfmi/meta.yml +++ b/modules/nf-core/kaiju/mkfmi/meta.yml @@ -15,30 +15,32 @@ tools: tool_dev_url: "https://github.com/bioinformatics-centre/kaiju" doi: "10.1038/ncomms11257" licence: ["GNU GPL v3"] + identifier: biotools:kaiju input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Uncompressed Protein FASTA file (mandatory) - pattern: "*.{fa,faa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Uncompressed Protein FASTA file (mandatory) + pattern: "*.{fa,faa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fmi: - type: file - description: Kaiju FM-index file - pattern: "*.{fmi}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fmi": + type: file + description: Kaiju FM-index file + pattern: "*.{fmi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml index 187f6bc3fae4..8e9f5f137eed 100644 --- a/modules/nf-core/kalign/align/meta.yml +++ b/modules/nf-core/kalign/align/meta.yml @@ -12,33 +12,39 @@ tools: tool_dev_url: "https://github.com/TimoLassmann/kalign" doi: "10.1093/bioinformatics/btz795" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file. May be gzipped or uncompressed, depending on if `compress` is set to `true` or `false`. - pattern: "*.{aln}{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file. May be gzipped or uncompressed, depending on if + `compress` is set to `true` or `false`. + pattern: "*.{aln}{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/kallisto/index/meta.yml b/modules/nf-core/kallisto/index/meta.yml index d366aeb4553c..4541074ed429 100644 --- a/modules/nf-core/kallisto/index/meta.yml +++ b/modules/nf-core/kallisto/index/meta.yml @@ -6,35 +6,40 @@ keywords: - index tools: - kallisto: - description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. + description: Quantifying abundances of transcripts from bulk and single-cell RNA-Seq + data, or more generally of target sequences using high-throughput sequencing + reads. homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto licence: ["BSD-2-Clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: genome fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: genome fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - index: - type: directory - description: Kallisto genome index - pattern: "*.idx" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - kallisto: + type: directory + description: Kallisto genome index + pattern: "*.idx" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" maintainers: diff --git a/modules/nf-core/kallisto/quant/meta.yml b/modules/nf-core/kallisto/quant/meta.yml index d5100290ffbc..329268a170de 100644 --- a/modules/nf-core/kallisto/quant/meta.yml +++ b/modules/nf-core/kallisto/quant/meta.yml @@ -6,71 +6,85 @@ keywords: - pseudoalignment tools: - "kallisto": - description: "Quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads." + description: "Quantifying abundances of transcripts from RNA-Seq data, or more + generally of target sequences using high-throughput sequencing reads." homepage: https://pachterlab.github.io/kallisto/ documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "10.1038/nbt.3519" licence: ["BSD_2_clause"] + identifier: biotools:kallisto input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fastq,fastq.gz}" - - index: - type: file - description: Kallisto genome index. - pattern: "*.idx" - - gtf: - type: file - description: Optional gtf file for translation of transcripts into genomic coordinates. - pattern: "*.gtf" - - chromosomes: - type: file - description: Optional tab separated file with chromosome names and lengths. - pattern: "*.tsv" - - fragment_length: - type: integer - description: For single-end mode only, the estimated average fragment length. - - fragment_length_sd: - type: integer - description: For single-end mode only, the estimated standard deviation of the fragment length. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fastq,fastq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: Kallisto genome index. + pattern: "*.idx" + - - gtf: + type: file + description: Optional gtf file for translation of transcripts into genomic coordinates. + pattern: "*.gtf" + - - chromosomes: + type: file + description: Optional tab separated file with chromosome names and lengths. + pattern: "*.tsv" + - - fragment_length: + type: integer + description: For single-end mode only, the estimated average fragment length. + - - fragment_length_sd: + type: integer + description: For single-end mode only, the estimated standard deviation of the + fragment length. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Kallisto output file + - json_info: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.run_info.json": + type: file + description: JSON file containing information about the run + pattern: "*.run_info.json" - log: - type: file - description: File containing log information from running kallisto quant - pattern: "*.log.txt" - - abundance: - type: file - description: Plaintext file of the abundance estimates - pattern: "abundance.tsv" - - abundance_hdf5: - type: file - description: | - A HDF5 binary file containing run info, abundance estimates, bootstrap - estimates, and transcript length information - pattern: "abundance.h5" - - run_info: - type: file - description: A json file containing information about the run - pattern: "run_info.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File containing log information from running kallisto quant + pattern: "*.log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/kallistobustools/count/meta.yml b/modules/nf-core/kallistobustools/count/meta.yml index 55d5dc6cdc41..c8160d7ad512 100644 --- a/modules/nf-core/kallistobustools/count/meta.yml +++ b/modules/nf-core/kallistobustools/count/meta.yml @@ -8,60 +8,70 @@ keywords: - bustools tools: - kb: - description: kallisto and bustools are wrapped in an easy-to-use program called kb + description: kallisto and bustools are wrapped in an easy-to-use program called + kb homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: kb-ref index file (.idx) - pattern: "*.{idx}" - - t2g: - type: file - description: t2g file from kallisto - pattern: "*t2g.txt" - - t1c: - type: file - description: kb ref's c1 cdna_t2c file - pattern: "*.{cdna_t2c.txt}" - - t2c: - type: file - description: kb ref's c2 intron_t2c file - pattern: "*.{intron_t2c.txt}" - - workflow_mode: - type: string - description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) - pattern: "{standard,lamanno,nac}" - - technology: - type: string - description: String value defining the sequencing technology used. - pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - index: + type: file + description: kb-ref index file (.idx) + pattern: "*.{idx}" + - - t2g: + type: file + description: t2g file from kallisto + pattern: "*t2g.txt" + - - t1c: + type: file + description: kb ref's c1 cdna_t2c file + pattern: "*.{cdna_t2c.txt}" + - - t2c: + type: file + description: kb ref's c2 intron_t2c file + pattern: "*.{intron_t2c.txt}" + - - technology: + type: string + description: String value defining the sequencing technology used. + pattern: "{10XV1,10XV2,10XV3,CELSEQ,CELSEQ2,DROPSEQ,INDROPSV1,INDROPSV2,INDROPSV3,SCRUBSEQ,SURECELL,SMARTSEQ}" + - - workflow_mode: + type: string + description: String value defining workflow to use, can be one of "standard", + "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - count: - type: file - description: kb count output folder - pattern: "*.{count}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.count": + type: file + description: kb count output folder + pattern: "*.{count}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - matrix: + - "*.count/*/*.mtx": + type: file + description: file containing the count matrix + pattern: "*.mtx" authors: - "@flowuenne" maintainers: diff --git a/modules/nf-core/kallistobustools/ref/meta.yml b/modules/nf-core/kallistobustools/ref/meta.yml index 64deab9b53d9..6856c7fa5326 100644 --- a/modules/nf-core/kallistobustools/ref/meta.yml +++ b/modules/nf-core/kallistobustools/ref/meta.yml @@ -9,54 +9,64 @@ keywords: - index tools: - kb: - description: kallisto|bustools (kb) is a tool developed for fast and efficient processing of single-cell OMICS data. + description: kallisto|bustools (kb) is a tool developed for fast and efficient + processing of single-cell OMICS data. homepage: https://www.kallistobus.tools/ documentation: https://kb-python.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/pachterlab/kb_python doi: "10.22002/D1.1876" licence: ["MIT"] + identifier: "" input: - - fasta: - type: file - description: Genomic DNA fasta file - pattern: "*.{fasta,fasta.gz}" - - gtf: - type: file - description: Genomic gtf file - pattern: "*.{gtf,gtf.gz}" - - workflow_mode: - type: string - description: String value defining workflow to use, can be one of "standard", "nac", "lamanno" (obsolete) - pattern: "{standard,lamanno,nac}" + - - fasta: + type: file + description: Genomic DNA fasta file + pattern: "*.{fasta,fasta.gz}" + - - gtf: + type: file + description: Genomic gtf file + pattern: "*.{gtf,gtf.gz}" + - - workflow_mode: + type: string + description: String value defining workflow to use, can be one of "standard", + "nac", "lamanno" (obsolete) + pattern: "{standard,lamanno,nac}" output: - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - kb_ref_idx: - type: file - description: Index file from kb ref. - pattern: "*.{idx}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - index: + - kb_ref_out.idx: + type: file + description: kb ref index file + pattern: "*kb_ref_out.idx" - t2g: - type: file - description: Transcript to gene table - pattern: "*t2g.{txt}" + - t2g.txt: + type: file + description: Transcript to gene table + pattern: "*t2g.{txt}" - cdna: - type: file - description: cDNA fasta file - pattern: "*cdna.{fa}" + - cdna.fa: + type: file + description: cDNA fasta file + pattern: "*cdna.{fa}" - intron: - type: file - description: Intron fasta file - pattern: "*intron.{fa}" + - intron.fa: + type: file + description: Intron fasta file + pattern: "*intron.{fa}" - cdna_t2c: - type: file - description: cDNA transcript to capture file - pattern: "*cdna_t2c.{txt}" + - cdna_t2c.txt: + type: file + description: cDNA transcript to capture file + pattern: "*cdna_t2c.{txt}" - intron_t2c: - type: file - description: Intron transcript to capture file - pattern: "*intron_t2c.{txt}" + - intron_t2c.txt: + type: file + description: Intron transcript to capture file + pattern: "*intron_t2c.{txt}" authors: - "@flowuenne" maintainers: diff --git a/modules/nf-core/kat/hist/meta.yml b/modules/nf-core/kat/hist/meta.yml index c933c9582c3d..02743621bdd4 100644 --- a/modules/nf-core/kat/hist/meta.yml +++ b/modules/nf-core/kat/hist/meta.yml @@ -6,57 +6,91 @@ keywords: - count tools: - "kat": - description: "KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts" + description: "KAT is a suite of tools that analyse jellyfish hashes or sequence + files (fasta or fastq) using kmer counts" homepage: https://www.earlham.ac.uk/kat-tools documentation: https://kat.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/TGAC/KAT doi: 10.1093/bioinformatics/btw663 licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: KAT histogram of k-mer counts - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: KAT histogram of k-mer counts + pattern: "*.hist" - json: - type: file - description: KAT histogram summary of distance analysis - pattern: "*.hist.dist_analysis.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.dist_analysis.json": + type: file + description: KAT histogram summary of distance analysis + pattern: "*.hist.dist_analysis.json" - png: - type: file - description: KAT plot of k-mer histogram in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: KAT plot of k-mer histogram in PNG format + pattern: "*.png" - ps: - type: file - description: KAT plot of k-mer histogram in PS format - pattern: "*.ps" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ps": + type: file + description: KAT plot of k-mer histogram in PS format + pattern: "*.ps" - pdf: - type: file - description: KAT plot of k-mer histogram in PDF format - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: KAT plot of k-mer histogram in PDF format + pattern: "*.pdf" - jellyfish_hash: - type: file - description: Jellyfish hash file - pattern: "*-hist.jf*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-hash.jf*": + type: file + description: Jellyfish hash file + pattern: "*-hist.jf*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/khmer/normalizebymedian/meta.yml b/modules/nf-core/khmer/normalizebymedian/meta.yml index 847d2b84d4d3..757c1ae96ec5 100644 --- a/modules/nf-core/khmer/normalizebymedian/meta.yml +++ b/modules/nf-core/khmer/normalizebymedian/meta.yml @@ -1,5 +1,7 @@ name: khmer_normalizebymedian -description: Module that calls normalize-by-median.py from khmer. The module can take a mix of paired end (interleaved) and single end reads. If both types are provided, only a single file with single ends is possible. +description: Module that calls normalize-by-median.py from khmer. The module can take + a mix of paired end (interleaved) and single end reads. If both types are provided, + only a single file with single ends is possible. keywords: - digital normalization - khmer @@ -12,27 +14,30 @@ tools: tool_dev_url: https://github.com/dib-lab/khmer doi: "10.12688/f1000research.6924.1" licence: ["BSD License"] + identifier: biotools:khmer input: - - pe_reads: - type: file - description: Paired-end interleaved fastq files - pattern: "*.{fq,fastq}.gz" - - se_reads: - type: file - description: Single-end fastq files - pattern: "*.{fq,fastq}.gz" - - name: - type: string - description: filename for output file(s); ".fastq.gz" will be appended + - - pe_reads: + type: file + description: Paired-end interleaved fastq files + pattern: "*.{fq,fastq}.gz" + - - se_reads: + type: file + description: Single-end fastq files + pattern: "*.{fq,fastq}.gz" + - - name: + type: string + description: filename for output file(s); ".fastq.gz" will be appended output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Interleaved fastq files - pattern: "*.{fq,fastq}.gz" + - ${name}.fastq.gz: + type: file + description: Interleaved fastq files + pattern: "*.{fq,fastq}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@erikrikarddaniel" maintainers: diff --git a/modules/nf-core/khmer/uniquekmers/meta.yml b/modules/nf-core/khmer/uniquekmers/meta.yml index f875bb7177d0..a90294a880e5 100644 --- a/modules/nf-core/khmer/uniquekmers/meta.yml +++ b/modules/nf-core/khmer/uniquekmers/meta.yml @@ -1,5 +1,6 @@ name: "khmer_uniquekmers" -description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more +description: In-memory nucleotide sequence k-mer counting, filtering, graph traversal + and more keywords: - khmer - k-mer @@ -12,27 +13,31 @@ tools: tool_dev_url: https://github.com/dib-lab/khmer doi: "10.12688/f1000research.6924.1" licence: ["BSD License"] + identifier: biotools:khmer input: - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fasta}" - - kmer_size: - type: integer - description: k-mer size to use + - - fasta: + type: file + description: fasta file + pattern: "*.{fa,fasta}" + - - kmer_size: + type: integer + description: k-mer size to use output: - report: - type: file - description: Text file containing unique-kmers.py execution report - pattern: "report.txt" + - report.txt: + type: file + description: Text file containing unique-kmers.py execution report + pattern: "report.txt" - kmers: - type: file - description: Text file containing number of kmers - pattern: "kmers.txt" + - kmers.txt: + type: file + description: Text file containing number of kmers + pattern: "kmers.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/kleborate/meta.yml b/modules/nf-core/kleborate/meta.yml index 543375270718..3fe9453a1f3a 100644 --- a/modules/nf-core/kleborate/meta.yml +++ b/modules/nf-core/kleborate/meta.yml @@ -1,5 +1,6 @@ name: kleborate -description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC). +description: Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae + and the Klebsiella pneumoniae species complex (KpSC). keywords: - screen - assembly @@ -7,36 +8,40 @@ keywords: - pneumoniae tools: - kleborate: - description: Screening Klebsiella genome assemblies for MLST, sub-species, and other Klebsiella related genes of interest + description: Screening Klebsiella genome assemblies for MLST, sub-species, and + other Klebsiella related genes of interest homepage: https://github.com/katholt/Kleborate documentation: https://github.com/katholt/Kleborate/wiki tool_dev_url: https://github.com/katholt/Kleborate doi: 10.1038/s41467-021-24448-3 licence: ["GPL v3 or later (GPL v3+)"] + identifier: biotools:kleborate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastas: - type: list - description: Klebsiella genome assemblies to be screened - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastas: + type: list + description: Klebsiella genome assemblies to be screened + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Result file generated after screening - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Result file generated after screening + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@rpetit3" diff --git a/modules/nf-core/kmcp/compute/meta.yml b/modules/nf-core/kmcp/compute/meta.yml index 20cfe4a2c04d..b10494230fcb 100644 --- a/modules/nf-core/kmcp/compute/meta.yml +++ b/modules/nf-core/kmcp/compute/meta.yml @@ -9,40 +9,52 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: fasta file, or a directory containing FASTA files - pattern: "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: fasta file, or a directory containing FASTA files + pattern: "**/*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - outdir: - type: directory - description: Output directory containing all .unik files and a summary file in .txt format. Every .unik file contains the sequence/reference ID,chunk index, number of chunks, and genome size of reference. - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Output directory containing all .unik files and a summary file + in .txt format. Every .unik file contains the sequence/reference ID,chunk + index, number of chunks, and genome size of reference. + pattern: "*/" - info: - type: file - description: Summary file that is generated for later use - pattern: "*_info.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/_info.txt: + type: file + description: Summary file that is generated for later use + pattern: "*_info.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/index/meta.yml b/modules/nf-core/kmcp/index/meta.yml index 6942dc0fdf29..e3e4a91e3521 100644 --- a/modules/nf-core/kmcp/index/meta.yml +++ b/modules/nf-core/kmcp/index/meta.yml @@ -10,40 +10,50 @@ keywords: - index tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - compute_dir: - type: directory - description: Output directory generated by "kmcp compute" - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - compute_dir: + type: directory + description: Output directory generated by "kmcp compute" + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - kmcp: - type: directory - description: Output directory containing the database from k-mer files. - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Output directory containing the database from k-mer files. + pattern: "*/" - log: - type: file - description: A log of kmcp/index output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: A log of kmcp/index output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/merge/meta.yml b/modules/nf-core/kmcp/merge/meta.yml index 3a367fa42e99..99650fb806ba 100644 --- a/modules/nf-core/kmcp/merge/meta.yml +++ b/modules/nf-core/kmcp/merge/meta.yml @@ -9,36 +9,40 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - search_out: - type: file - description: The output file created by kmcp search - pattern: "*.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - search_out: + type: file + description: The output file created by kmcp search + pattern: "*.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - result: - type: file - description: Output file in gzipped format - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Output file in gzipped format + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/profile/meta.yml b/modules/nf-core/kmcp/profile/meta.yml index ba1ca2a27ed9..be5fe9cd1247 100644 --- a/modules/nf-core/kmcp/profile/meta.yml +++ b/modules/nf-core/kmcp/profile/meta.yml @@ -10,40 +10,43 @@ keywords: - index tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://bioinf.shenwei.me/kmcp/usage/#profile" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - search_results: - type: file - description: Gzipped file output from kmcp search module - pattern: "*.gz" - - db: - type: directory - description: Database directory containing taxdump files and taxid file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - search_results: + type: file + description: Gzipped file output from kmcp search module + pattern: "*.gz" + - - db: + type: directory + description: Database directory containing taxdump files and taxid file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-delimited format file with 17 columns. - pattern: "*.profile" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.profile": + type: file + description: Tab-delimited format file with 17 columns. + pattern: "*.profile" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kmcp/search/meta.yml b/modules/nf-core/kmcp/search/meta.yml index 6d003b04f699..11baf5bda013 100644 --- a/modules/nf-core/kmcp/search/meta.yml +++ b/modules/nf-core/kmcp/search/meta.yml @@ -9,40 +9,44 @@ keywords: - kmers tools: - "kmcp": - description: "Accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping" + description: "Accurate metagenomic profiling of both prokaryotic and viral populations + by pseudo-mapping" homepage: "https://github.com/shenwei356/kmcp" documentation: "https://github.com/shenwei356/kmcp#documents" tool_dev_url: "https://github.com/shenwei356/kmcp" doi: "10.1093/bioinformatics/btac845" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: gzipped fasta or fastq files - pattern: "*.{fq.gz,fastq.gz,fa.gz}" - - db: - type: directory - description: Database directory created by "kmcp index" - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: gzipped fasta or fastq files + pattern: "*.{fq.gz,fastq.gz,fa.gz}" + - - db: + type: directory + description: Database directory created by "kmcp index" + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - result: - type: file - description: Output file in tab-delimited format with 15 columns - pattern: "*.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Output file in tab-delimited format with 15 columns + pattern: "*.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" maintainers: diff --git a/modules/nf-core/kofamscan/meta.yml b/modules/nf-core/kofamscan/meta.yml index 06f2872a4e8d..d7cc333db736 100644 --- a/modules/nf-core/kofamscan/meta.yml +++ b/modules/nf-core/kofamscan/meta.yml @@ -1,48 +1,62 @@ name: "kofamscan" -description: Produces annotation using kofamscan against a Profile database and a KO list +description: Produces annotation using kofamscan against a Profile database and a + KO list keywords: - fasta - kegg - kofamscan tools: - "kofamscan": - description: "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH against KOfam" + description: "KofamKOALA assigns K numbers to the user's sequence data by HMMER/HMMSEARCH + against KOfam" homepage: "https://www.genome.jp/tools/kofamkoala/" documentation: "https://github.com/takaram/kofam_scan" tool_dev_url: "https://github.com/takaram/kofam_scan" doi: "10.1093/bioinformatics/btz859" licence: ["MIT License"] + identifier: biotools:kofamscan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta}" - - profiles: - type: directory - description: Directory containing the Profiles database - pattern: "*" - - ko_list: - type: file - description: File containing list of KO entries with their data - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta}" + - - profiles: + type: directory + description: Directory containing the Profiles database + pattern: "*" + - - ko_list: + type: file + description: File containing list of KO entries with their data + pattern: "*.{fa,fasta}" output: - txt: - type: file - description: Application-specific text file with hits information - pattern: "*.{txt}" + - meta: + type: file + description: Application-specific text file with hits information + pattern: "*.{txt}" + - "*.txt": + type: file + description: Application-specific text file with hits information + pattern: "*.{txt}" - tsv: - type: file - description: Tab separated file containing with detailed hits - pattern: "*.{tsv}" + - meta: + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Tab separated file containing with detailed hits + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@toniher" maintainers: diff --git a/modules/nf-core/kraken2/add/meta.yml b/modules/nf-core/kraken2/add/meta.yml index e5bc2d79c4f1..e1ad7d93aadf 100644 --- a/modules/nf-core/kraken2/add/meta.yml +++ b/modules/nf-core/kraken2/add/meta.yml @@ -9,48 +9,52 @@ keywords: - add tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fasta: - type: file - description: fasta file that will be added to the database - pattern: "*.{fa,fasta,fna,ffn}" - - taxonomy_names: - type: file - description: used for associating sequences with taxonomy IDs - pattern: "*.dmp" - - taxonomy_nodes: - type: file - description: tree nodes using NCBI taxonomy nomenclature - pattern: "*.dmp" - - accession2taxid: - type: file - description: associates sequence accession IDs to taxonomy IDs - pattern: "*.accession2taxid" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: fasta file that will be added to the database + pattern: "*.{fa,fasta,fna,ffn}" + - - taxonomy_names: + type: file + description: used for associating sequences with taxonomy IDs + pattern: "*.dmp" + - - taxonomy_nodes: + type: file + description: tree nodes using NCBI taxonomy nomenclature + pattern: "*.dmp" + - - accession2taxid: + type: file + description: associates sequence accession IDs to taxonomy IDs + pattern: "*.accession2taxid" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - db: - type: directory - description: contains required files to build the database - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: directory + description: contains required files to build the database + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/kraken2/build/meta.yml b/modules/nf-core/kraken2/build/meta.yml index 50f6d19379cb..6d7da1d14b66 100644 --- a/modules/nf-core/kraken2/build/meta.yml +++ b/modules/nf-core/kraken2/build/meta.yml @@ -8,40 +8,45 @@ keywords: - kraken2 tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] args_id: "$args" + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - db: - type: directory - description: contains required files to build the database - pattern: "*/" - - cleaning: - type: boolean - description: activate or deactivate (true or false) cleaning of intermediate files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - db: + type: directory + description: contains required files to build the database + pattern: "*/" + - - cleaning: + type: boolean + description: activate or deactivate (true or false) cleaning of intermediate + files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - db: - type: directory - description: contains the database that can be used to perform taxonomic classification - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: directory + description: contains the database that can be used to perform taxonomic classification + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/kraken2/buildstandard/meta.yml b/modules/nf-core/kraken2/buildstandard/meta.yml index d09ac3d239fc..566b10b5a4ef 100644 --- a/modules/nf-core/kraken2/buildstandard/meta.yml +++ b/modules/nf-core/kraken2/buildstandard/meta.yml @@ -10,26 +10,32 @@ keywords: - download tools: - kraken2: - description: "Kraken2 is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies." + description: "Kraken2 is a system for assigning taxonomic labels to short DNA + sequences, usually obtained through metagenomic studies." homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual tool_dev_url: "https://github.com/DerrickWood/kraken2" doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] args_id: "$args" + identifier: biotools:kraken2 input: - - cleaning: - type: boolean - description: activate or deactivate (true or false) cleaning of intermediate files + - - cleaning: + type: boolean + description: activate or deactivate (true or false) cleaning of intermediate + files output: - db: - type: directory - description: Directory containing the Kraken2 'standard' database that can be used to perform taxonomic classification - pattern: "*/" + - $prefix: + type: directory + description: Directory containing the Kraken2 'standard' database that can be + used to perform taxonomic classification + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@egreenberg7" maintainers: diff --git a/modules/nf-core/kraken2/kraken2/meta.yml b/modules/nf-core/kraken2/kraken2/meta.yml index 7909ffe7e179..8693764679c5 100644 --- a/modules/nf-core/kraken2/kraken2/meta.yml +++ b/modules/nf-core/kraken2/kraken2/meta.yml @@ -13,63 +13,84 @@ tools: documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 licence: ["MIT"] + identifier: biotools:kraken2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - db: - type: directory - description: Kraken2 database - - save_output_fastqs: - type: string - description: | - If true, optional commands are added to save classified and unclassified reads - as fastq files - - save_reads_assignment: - type: string - description: | - If true, an optional command is added to save a file reporting the taxonomic - classification of each input read + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - db: + type: directory + description: Kraken2 database + - - save_output_fastqs: + type: string + description: | + If true, optional commands are added to save classified and unclassified reads + as fastq files + - - save_reads_assignment: + type: string + description: | + If true, an optional command is added to save a file reporting the taxonomic + classification of each input read output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads_fastq: - type: file - description: | - Reads classified as belonging to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified{.,_}*": + type: file + description: | + Reads classified as belonging to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - unclassified_reads_fastq: - type: file - description: | - Reads not classified to any of the taxa - on the Kraken2 database. - pattern: "*{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified{.,_}*": + type: file + description: | + Reads not classified to any of the taxa + on the Kraken2 database. + pattern: "*{fastq.gz}" - classified_reads_assignment: - type: file - description: | - Kraken2 output file indicating the taxonomic assignment of - each input read + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classifiedreads.txt": + type: file + description: | + Kraken2 output file indicating the taxonomic assignment of + each input read - report: - type: file - description: | - Kraken2 report containing stats about classified - and not classifed reads. - pattern: "*.{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: | + Kraken2 report containing stats about classified + and not classifed reads. + pattern: "*.{report.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/krakentools/combinekreports/meta.yml b/modules/nf-core/krakentools/combinekreports/meta.yml index b35d12147e67..bb69d34a6945 100644 --- a/modules/nf-core/krakentools/combinekreports/meta.yml +++ b/modules/nf-core/krakentools/combinekreports/meta.yml @@ -1,5 +1,6 @@ name: krakentools_combinekreports -description: Takes multiple kraken-style reports and combines them into a single report file +description: Takes multiple kraken-style reports and combines them into a single report + file keywords: - kraken - krakentools @@ -9,33 +10,38 @@ keywords: - merging tools: - krakentools: - description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs. + description: KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs. homepage: https://github.com/jenniferlu717/KrakenTools licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kreports: - type: file - description: List of kraken-style report files - pattern: "*.{txt,kreport}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kreports: + type: file + description: List of kraken-style report files + pattern: "*.{txt,kreport}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined kreport file of all input files - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Combined kreport file of all input files + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakentools/extractkrakenreads/meta.yml b/modules/nf-core/krakentools/extractkrakenreads/meta.yml index ee8b125d938f..b772ba0f5be3 100644 --- a/modules/nf-core/krakentools/extractkrakenreads/meta.yml +++ b/modules/nf-core/krakentools/extractkrakenreads/meta.yml @@ -6,49 +6,64 @@ keywords: - metagenomics tools: - "krakentools": - description: "KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs." + description: "KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs." homepage: https://github.com/jenniferlu717/KrakenTools documentation: https://github.com/jenniferlu717/KrakenTools?tab=readme-ov-file#extract_kraken_readspy tool_dev_url: https://github.com/jenniferlu717/KrakenTools doi: 10.1038/s41596-022-00738-y licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - taxid: - type: string - description: A list of taxid separated by spaces - - classified_reads_assignment: - type: file - description: A file contains the taxonomic classification of each input read. - pattern: "*.{classifiedreads.txt}" - - classified_reads_fastq: - type: file - description: Classified reads as belonging to any of the taxa on the kraken2 database. - pattern: "*.{fastq.gz}" - - report: - type: file - description: Optional Kraken2 report containing stats about classified and not classifed reads. - pattern: "*.{report.txt}" - + - - taxid: + type: string + description: A list of taxid separated by spaces + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - classified_reads_assignment: + type: file + description: A file contains the taxonomic classification of each input read. + pattern: "*.{classifiedreads.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - classified_reads_fastq: + type: file + description: Classified reads as belonging to any of the taxa on the kraken2 + database. + pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - report: + type: file + description: Optional Kraken2 report containing stats about classified and not + classifed reads. + pattern: "*.{report.txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - extracted_kraken2_reads: - type: file - description: Reads assigned to a taxid list. - pattern: "*.{fastq,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{fastq,fasta}": + type: file + description: Reads assigned to a taxid list. + pattern: "*.{fastq,fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/krakentools/kreport2krona/meta.yml b/modules/nf-core/krakentools/kreport2krona/meta.yml index ae5bf2f15b82..d0f0a57e3b4a 100644 --- a/modules/nf-core/krakentools/kreport2krona/meta.yml +++ b/modules/nf-core/krakentools/kreport2krona/meta.yml @@ -7,33 +7,38 @@ keywords: - visualization tools: - krakentools: - description: KrakenTools is a suite of scripts to be used for post-analysis of Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if using KrakenTools with any of the listed programs. + description: KrakenTools is a suite of scripts to be used for post-analysis of + Kraken/KrakenUniq/Kraken2/Bracken results. Please cite the relevant paper if + using KrakenTools with any of the listed programs. homepage: https://github.com/jenniferlu717/KrakenTools licence: ["GPL v3"] + identifier: biotools:krakentools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - kreport: - type: file - description: Kraken report - pattern: "*.{txt,kreport}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - kreport: + type: file + description: Kraken report + pattern: "*.{txt,kreport}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Krona text-based input file converted from Kraken report - pattern: "*.{txt,krona}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Krona text-based input file converted from Kraken report + pattern: "*.{txt,krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/krakenuniq/build/meta.yml b/modules/nf-core/krakenuniq/build/meta.yml index f63b3250d257..bafc3cfa04e0 100644 --- a/modules/nf-core/krakenuniq/build/meta.yml +++ b/modules/nf-core/krakenuniq/build/meta.yml @@ -8,40 +8,48 @@ keywords: - ncbi tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - custom_library_dir: - type: directory - description: Optional directory containing custom fasta files for database build - pattern: "*" - - custom_taxonomy_dir: - type: directory - description: Optional directory containing custom taxonomy files for database build - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - custom_library_dir: + type: directory + description: Optional directory containing custom fasta files for database build + pattern: "*" + - custom_taxonomy_dir: + type: directory + description: Optional directory containing custom taxonomy files for database + build + pattern: "*" + - custom_seqid2taxid: + type: file + description: custom seqid2taxid output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing KrakenUniq database - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix/: + type: directory + description: Directory containing KrakenUniq database + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/download/meta.yml b/modules/nf-core/krakenuniq/download/meta.yml index ace0f6bec46b..fdbac474744b 100644 --- a/modules/nf-core/krakenuniq/download/meta.yml +++ b/modules/nf-core/krakenuniq/download/meta.yml @@ -8,34 +8,30 @@ keywords: - ncbi tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq tool_dev_url: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pattern: - type: string - description: Pattern indicating what type of NCBI data to download. See KrakenUniq documnation for possibilities. + - - pattern: + type: string + description: Pattern indicating what type of NCBI data to download. See KrakenUniq + documnation for possibilities. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: directory - description: Directory containing downloaded data with directory naming being the user provided pattern. + - ${pattern}/: + type: directory + description: Directory containing downloaded data with directory naming being + the user provided pattern. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml index bb6409a62897..1af2350d69bc 100644 --- a/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml +++ b/modules/nf-core/krakenuniq/preloadedkrakenuniq/meta.yml @@ -8,77 +8,103 @@ keywords: - db tools: - "krakenuniq": - description: "Metagenomics classifier with unique k-mer counting for more specific results" + description: "Metagenomics classifier with unique k-mer counting for more specific + results" homepage: https://github.com/fbreitwieser/krakenuniq documentation: https://github.com/fbreitwieser/krakenuniq doi: 10.1186/s13059-018-1568-0 licence: ["MIT"] + identifier: biotools:KrakenUniq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequences: - type: file - description: List of input files containing sequences. All of them must be either in FASTA or FASTQ format. - - sequence_type: - type: string - description: Format of all given sequencing files as literal string, either 'fasta' or 'fastq'. - pattern: "{fasta,fastq}" - - db: - type: directory - description: KrakenUniq database - - ram_chunk_size: - type: string - description: Amount of maximum amount of RAM each chunk of database that should be loaded at any one time - pattern: "*GB" - - save_output_reads: - type: boolean - description: | - Optionally, commands are added to save classified and unclassified reads - as FASTQ or FASTA files depending on the input format. When the input - is paired-end, the single output FASTQ contains merged reads. - - report_file: - type: boolean - description: Whether to generate a report of relative abundances. - - save_output: - type: boolean - description: Whether to save a file reporting the taxonomic classification of each input read. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences: + type: file + description: List of input files containing sequences. All of them must be either + in FASTA or FASTQ format. + - - sequence_type: + type: string + description: Format of all given sequencing files as literal string, either + 'fasta' or 'fastq'. + pattern: "{fasta,fastq}" + - - db: + type: directory + description: KrakenUniq database + - - ram_chunk_size: + type: string + description: Amount of maximum amount of RAM each chunk of database that should + be loaded at any one time + pattern: "*GB" + - - save_output_reads: + type: boolean + description: | + Optionally, commands are added to save classified and unclassified reads + as FASTQ or FASTA files depending on the input format. When the input + is paired-end, the single output FASTQ contains merged reads. + - - report_file: + type: boolean + description: Whether to generate a report of relative abundances. + - - save_output: + type: boolean + description: Whether to save a file reporting the taxonomic classification of + each input read. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classified_reads: - type: file - description: | - Reads classified as belonging to any of the taxa - in the KrakenUniq reference database. - pattern: "*.classified.{fastq,fasta}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.classified.${sequence_type}.gz": + type: file + description: | + Reads classified as belonging to any of the taxa + in the KrakenUniq reference database. + pattern: "*.classified.{fastq,fasta}.gz" - unclassified_reads: - type: file - description: | - Reads not classified to any of the taxa - in the KrakenUniq reference database. - pattern: "*.unclassified.{fastq,fasta}.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unclassified.${sequence_type}.gz": + type: file + description: | + Reads not classified to any of the taxa + in the KrakenUniq reference database. + pattern: "*.unclassified.{fastq,fasta}.gz" - classified_assignment: - type: file - description: | - KrakenUniq output file indicating the taxonomic assignment of - each input read ## DOUBLE CHECK!! - pattern: "*.krakenuniq.classified.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.krakenuniq.classified.txt": + type: file + description: | + KrakenUniq output file indicating the taxonomic assignment of + each input read ## DOUBLE CHECK!! + pattern: "*.krakenuniq.classified.txt" - report: - type: file - description: | - KrakenUniq report containing statistics about classified - and unclassified reads. - pattern: "*.krakenuniq.report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.krakenuniq.report.txt": + type: file + description: | + KrakenUniq report containing statistics about classified + and unclassified reads. + pattern: "*.krakenuniq.report.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjamy" - "@Midnighter" diff --git a/modules/nf-core/krona/kronadb/meta.yml b/modules/nf-core/krona/kronadb/meta.yml index 0d42bb10fc26..2eaf3f880978 100644 --- a/modules/nf-core/krona/kronadb/meta.yml +++ b/modules/nf-core/krona/kronadb/meta.yml @@ -6,20 +6,25 @@ keywords: - krona tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: https://github.com/marbl/Krona/wiki/Installing - doi: 10.1186/1471-2105-12-385 -# There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + doi: + 10.1186/1471-2105-12-385 + # There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + identifier: biotools:krona output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: A TAB separated file that contains a taxonomy database. - pattern: "*.{tab}" + - taxonomy/taxonomy.tab: + type: file + description: A TAB separated file that contains a taxonomy database. + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/krona/ktimporttaxonomy/meta.yml b/modules/nf-core/krona/ktimporttaxonomy/meta.yml index 3504b13e57b6..87f84787c1fc 100644 --- a/modules/nf-core/krona/ktimporttaxonomy/meta.yml +++ b/modules/nf-core/krona/ktimporttaxonomy/meta.yml @@ -1,5 +1,6 @@ name: krona_ktimporttaxonomy -description: KronaTools Import Taxonomy imports taxonomy classifications and produces an interactive Krona plot. +description: KronaTools Import Taxonomy imports taxonomy classifications and produces + an interactive Krona plot. keywords: - plot - taxonomy @@ -9,36 +10,47 @@ keywords: - krona chart tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html doi: 10.1186/1471-2105-12-385 + identifier: biotools:krona input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - taxonomy: - type: file - description: | - Path to a Krona taxonomy .tab file normally downloaded and generated by - krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but - must end in `.tab`. - pattern: "*tab" - - report: - type: file - description: "A tab-delimited file with taxonomy IDs and (optionally) query IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy IDs from column 2, and scores from column 3. Lines beginning with # will be ignored." - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - report: + type: file + description: "A tab-delimited file with taxonomy IDs and (optionally) query + IDs, magnitudes, and scores. Query IDs are taken from column 1, taxonomy + IDs from column 2, and scores from column 3. Lines beginning with # will + be ignored." + pattern: "*.{tsv}" + - - taxonomy: + type: file + description: | + Path to a Krona taxonomy .tab file normally downloaded and generated by + krona/ktUpdateTaxonomy. Custom taxonomy files can have any name, but + must end in `.tab`. + pattern: "*tab" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: A html file containing an interactive krona plot. - pattern: "*.{html}" + - meta: + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - "*.html": + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/krona/ktimporttext/meta.yml b/modules/nf-core/krona/ktimporttext/meta.yml index 5288ea0b47ef..56b150965547 100644 --- a/modules/nf-core/krona/ktimporttext/meta.yml +++ b/modules/nf-core/krona/ktimporttext/meta.yml @@ -10,36 +10,45 @@ keywords: - metagenomics tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: http://manpages.ubuntu.com/manpages/impish/man1/ktImportTaxonomy.1.html tool_dev_url: https://github.com/marbl/Krona doi: 10.1186/1471-2105-12-385 licence: ["https://raw.githubusercontent.com/marbl/Krona/master/KronaTools/LICENSE.txt"] + identifier: biotools:krona input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - report: - type: file - description: "Tab-delimited text file. Each line should be a number followed by a list of wedges to contribute to (starting from the highest level). If no wedges are listed (and just a quantity is given), it will contribute to the top level. If the same lineage is listed more than once, the values will be added. Quantities can be omitted if -q is specified. Lines beginning with '#' will be ignored." - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - report: + type: file + description: "Tab-delimited text file. Each line should be a number followed + by a list of wedges to contribute to (starting from the highest level). If + no wedges are listed (and just a quantity is given), it will contribute to + the top level. If the same lineage is listed more than once, the values will + be added. Quantities can be omitted if -q is specified. Lines beginning with + '#' will be ignored." + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: A html file containing an interactive krona plot. - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.html": + type: file + description: A html file containing an interactive krona plot. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/krona/ktupdatetaxonomy/meta.yml b/modules/nf-core/krona/ktupdatetaxonomy/meta.yml index 40540cce3ba1..d7b5e80d08dd 100644 --- a/modules/nf-core/krona/ktupdatetaxonomy/meta.yml +++ b/modules/nf-core/krona/ktupdatetaxonomy/meta.yml @@ -7,20 +7,25 @@ keywords: - visualisation tools: - krona: - description: Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. + description: Krona Tools is a set of scripts to create Krona charts from several + Bioinformatics tools as well as from text and XML files. homepage: https://github.com/marbl/Krona/wiki/KronaTools documentation: https://github.com/marbl/Krona/wiki/Installing - doi: 10.1186/1471-2105-12-385 -# There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + doi: + 10.1186/1471-2105-12-385 + # There is no input. This module downloads a pre-built taxonomy database for use with Krona Tools. + identifier: biotools:krona output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: A TAB separated file that contains a taxonomy database. - pattern: "*.{tab}" + - taxonomy/taxonomy.tab: + type: file + description: A TAB separated file that contains a taxonomy database. + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjakobs" maintainers: diff --git a/modules/nf-core/last/dotplot/meta.yml b/modules/nf-core/last/dotplot/meta.yml index 5243743a5f95..1bb1460cd69b 100644 --- a/modules/nf-core/last/dotplot/meta.yml +++ b/modules/nf-core/last/dotplot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_dotplot" description: Makes a dotplot (Oxford Grid) of pair-wise sequence alignments @@ -15,45 +14,61 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" - - format: - type: string - description: Output format (PNG or GIF). - - annot_a: - type: file - description: Annotation file in BED, Repeamasker, genePred or AGP format for the first (horizontal) sequence - pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" - - annot_b: - type: file - description: Annotation file in BED, Repeamasker, genePred or AGP format for the second (vertical) sequence - pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - annot_b: + type: file + description: Annotation file in BED, Repeamasker, genePred or AGP format for + the second (vertical) sequence + pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample2', single_end:false ]` + - annot_a: + type: file + description: Annotation file in BED, Repeamasker, genePred or AGP format for + the first (horizontal) sequence + pattern: "*.{bed,bed.gz,out,out.gz,rmsk.txt,rmsk.txt.gz,genePred,genePred.gz,gff,gff.gz,gtf,gtf.gz,gap.txt,gap.txt.gz}" + - - format: + type: string + description: Output format (PNG or GIF). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - png: - type: file - description: Pairwise alignment dot plot image, in PNG format. - pattern: "*.png" - gif: - type: file - description: Pairwise alignment dot plot image, in GIF format. - pattern: "*.gif" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gif": + type: file + description: Pairwise alignment dot plot image, in GIF format. + pattern: "*.gif" + - png: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.png": + type: file + description: Pairwise alignment dot plot image, in PNG format. + pattern: "*.png" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastal/meta.yml b/modules/nf-core/last/lastal/meta.yml index c14fa27989d3..ed6610f7ba71 100644 --- a/modules/nf-core/last/lastal/meta.yml +++ b/modules/nf-core/last/lastal/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastal" description: Aligns query sequences to target sequences indexed with lastdb @@ -14,42 +13,51 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: FASTA/FASTQ file - pattern: "*.{fasta,fastq}" - - param_file: - type: file - description: Trained parameter file - pattern: "*.train" - - index: - type: directory - description: Directory containing the files of the LAST index - pattern: "lastdb/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: FASTA/FASTQ file + pattern: "*.{fasta,fastq}" + - param_file: + type: file + description: Trained parameter file + pattern: "*.train" + - - index: + type: directory + description: Directory containing the files of the LAST index + pattern: "lastdb/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Gzipped MAF (Multiple Alignment Format) file - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Gzipped MAF (Multiple Alignment Format) file + pattern: "*.{maf.gz}" - multiqc: - type: file - description: Alignment summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/lastdb/meta.yml b/modules/nf-core/last/lastdb/meta.yml index c3b499e73223..5c7be3786020 100644 --- a/modules/nf-core/last/lastdb/meta.yml +++ b/modules/nf-core/last/lastdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_lastdb" description: Prepare sequences for subsequent alignment with lastal. @@ -14,31 +13,34 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: > - Sequence file in FASTA or FASTQ format. May be compressed with gzip. - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: > + Sequence file in FASTA or FASTQ format. May be compressed with gzip. + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: directory containing the files of the LAST index - pattern: "lastdb/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - lastdb: + type: directory + description: directory containing the files of the LAST index + pattern: "lastdb/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/mafconvert/meta.yml b/modules/nf-core/last/mafconvert/meta.yml index e9ee29a3a70a..0bc690aa7661 100644 --- a/modules/nf-core/last/mafconvert/meta.yml +++ b/modules/nf-core/last/mafconvert/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_mafconvert" description: Converts MAF alignments in another format. @@ -14,65 +13,118 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" - - format: - type: string - description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, sam, or tab) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" + - - format: + type: string + description: Output format (one of axt, blast, blasttab, chain, gff, html, psl, + sam, or tab) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - axt_gz: - type: file - description: Gzipped pairwise alignment in Axt (Blastz) format (optional) - pattern: "*.axt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.axt.gz": + type: file + description: Gzipped pairwise alignment in Axt (Blastz) format (optional) + pattern: "*.axt.gz" - blast_gz: - type: file - description: Gzipped pairwise alignment in blast format (optional) - pattern: "*.blast.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.blast.gz": + type: file + description: Gzipped pairwise alignment in blast format (optional) + pattern: "*.blast.gz" - blasttab_gz: - type: file - description: Gzipped pairwise alignment in blasttab format (optional) - pattern: "*.blasttab.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.blasttab.gz": + type: file + description: Gzipped pairwise alignment in blasttab format (optional) + pattern: "*.blasttab.gz" - chain_gz: - type: file - description: Gzipped pairwise alignment in UCSC chain format (optional) - pattern: "*.chain.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.chain.gz": + type: file + description: Gzipped pairwise alignment in UCSC chain format (optional) + pattern: "*.chain.gz" - gff_gz: - type: file - description: Gzipped pairwise alignment in GFF format (optional) - pattern: "*.gff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gff.gz": + type: file + description: Gzipped pairwise alignment in GFF format (optional) + pattern: "*.gff.gz" - html_gz: - type: file - description: Gzipped pairwise alignment in HTML format (optional) - pattern: "*.html.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html.gz": + type: file + description: Gzipped pairwise alignment in HTML format (optional) + pattern: "*.html.gz" - psl_gz: - type: file - description: Gzipped pairwise alignment in PSL (BLAT) format (optional) - pattern: "*.psl.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psl.gz": + type: file + description: Gzipped pairwise alignment in PSL (BLAT) format (optional) + pattern: "*.psl.gz" - sam_gz: - type: file - description: Gzipped pairwise alignment in SAM format (optional) - pattern: "*.sam.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.sam.gz": + type: file + description: Gzipped pairwise alignment in SAM format (optional) + pattern: "*.sam.gz" - tab_gz: - type: file - description: Gzipped pairwise alignment in TAB format (optional) - pattern: "*.tab.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tab.gz": + type: file + description: Gzipped pairwise alignment in TAB format (optional) + pattern: "*.tab.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/last/mafswap/meta.yml b/modules/nf-core/last/mafswap/meta.yml index aa0fc09d443e..4b9642a648a1 100644 --- a/modules/nf-core/last/mafswap/meta.yml +++ b/modules/nf-core/last/mafswap/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_mafswap" description: Reorder alignments in a MAF file @@ -14,30 +13,34 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/postmask/meta.yml b/modules/nf-core/last/postmask/meta.yml index 7be957ffe650..925e07561d23 100644 --- a/modules/nf-core/last/postmask/meta.yml +++ b/modules/nf-core/last/postmask/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_postmask" description: Post-alignment masking @@ -15,30 +14,34 @@ tools: tool_dev_url: "https://gitlab.com/mcfrith/last" doi: "10.1371/journal.pone.0028819" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, optionally compressed with gzip - pattern: "*.{maf.gz,maf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, optionally compressed with + gzip + pattern: "*.{maf.gz,maf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charles-plessy" maintainers: diff --git a/modules/nf-core/last/split/meta.yml b/modules/nf-core/last/split/meta.yml index 2e23f8b4c6a3..7864d0fff322 100644 --- a/modules/nf-core/last/split/meta.yml +++ b/modules/nf-core/last/split/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_split" description: Find split or spliced alignments in a MAF file @@ -15,35 +14,43 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - maf: + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - maf: - type: file - description: Multiple Aligment Format (MAF) file, compressed with gzip - pattern: "*.{maf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.maf.gz": + type: file + description: Multiple Aligment Format (MAF) file, compressed with gzip + pattern: "*.{maf.gz}" - multiqc: - type: file - description: Alignment summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/last/train/meta.yml b/modules/nf-core/last/train/meta.yml index d55e82734b36..d91cecaf7967 100644 --- a/modules/nf-core/last/train/meta.yml +++ b/modules/nf-core/last/train/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "last_train" description: Find suitable score parameters for sequence alignment @@ -14,38 +13,47 @@ tools: documentation: "https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst" tool_dev_url: "https://gitlab.com/mcfrith/last" licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: FASTA/FASTQ file - pattern: "*.{fasta,fastq}" - - index: - type: directory - description: Directory containing the files of the LAST index - pattern: "lastdb/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastx: + type: file + description: FASTA/FASTQ file + pattern: "*.{fasta,fastq}" + - - index: + type: directory + description: Directory containing the files of the LAST index + pattern: "lastdb/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - param_file: - type: file - description: Trained parameter file - pattern: "*.train" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.train": + type: file + description: Trained parameter file + pattern: "*.train" - multiqc: - type: file - description: Alignment parameter summary for MultiQC - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Alignment parameter summary for MultiQC + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aleksandrabliznina" - "@charles-plessy" diff --git a/modules/nf-core/learnmsa/align/meta.yml b/modules/nf-core/learnmsa/align/meta.yml index 66a9f7d12c94..b3e549fea7b8 100644 --- a/modules/nf-core/learnmsa/align/meta.yml +++ b/modules/nf-core/learnmsa/align/meta.yml @@ -12,33 +12,38 @@ tools: tool_dev_url: "https://github.com/Gaius-Augustus/learnMSA" doi: "10.1093/gigascience/giac104" licence: ["MIT"] + identifier: biotools:learnMSA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format. May be gz-compressed or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format. May be gz-compressed or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed. + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/leehom/meta.yml b/modules/nf-core/leehom/meta.yml index 38f5407b3348..fb466319fb80 100644 --- a/modules/nf-core/leehom/meta.yml +++ b/modules/nf-core/leehom/meta.yml @@ -17,58 +17,103 @@ tools: tool_dev_url: "https://github.com/grenaud/leeHom" doi: "10.1093/nar/gku699" licence: ["GPL v3"] + identifier: biotools:leehom input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Unaligned BAM or one or two gzipped FASTQ file(s) - pattern: "*.{bam,fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Unaligned BAM or one or two gzipped FASTQ file(s) + pattern: "*.{bam,fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file + pattern: "*.bam" - fq_pass: - type: file - description: Trimmed and merged FASTQ - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fq.gz: + type: file + description: Trimmed and merged FASTQ + pattern: "*.fq.gz" - fq_fail: - type: file - description: Failed trimmed and merged FASTQs - pattern: "*.fail.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fail.fq.gz: + type: file + description: Failed trimmed and merged FASTQs + pattern: "*.fail.fq.gz" - unmerged_r1_fq_pass: - type: file - description: Passed unmerged R1 FASTQs - pattern: "*.r1.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r1.fq.gz: + type: file + description: Passed unmerged R1 FASTQs + pattern: "*.r1.fq.gz" - unmerged_r1_fq_fail: - type: file - description: Failed unmerged R1 FASTQs - pattern: "*.r1.fail.fq.gz" - - unmerged_r2_fq_pass: - type: file - description: Passed unmerged R2 FASTQs - pattern: "*.r2.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r1.fail.fq.gz: + type: file + description: Failed unmerged R1 FASTQs + pattern: "*.r1.fail.fq.gz" - unmerged_r2_fq_pass: - type: file - description: Failed unmerged R2 FASTQs - pattern: "*.r2.fail.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r2.fq.gz: + type: file + description: Passed unmerged R2 FASTQs + pattern: "*.r2.fq.gz" + - unmerged_r2_fq_fail: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_r2.fail.fq.gz: + type: file + description: Failed unmerged R2 FASTQs + pattern: "*.r2.fail.fq.gz" - log: - type: file - description: Log file of command - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file of command + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/legsta/meta.yml b/modules/nf-core/legsta/meta.yml index 734498e06126..bccb2e9e8b30 100644 --- a/modules/nf-core/legsta/meta.yml +++ b/modules/nf-core/legsta/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/tseemann/legsta tool_dev_url: https://github.com/tseemann/legsta licence: ["GPL v3"] + identifier: biotools:legsta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA, GenBank or EMBL formatted files - pattern: "*.{fasta,gbk,embl}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA, GenBank or EMBL formatted files + pattern: "*.{fasta,gbk,embl}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited summary of the results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited summary of the results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/leviosam2/index/meta.yml b/modules/nf-core/leviosam2/index/meta.yml index ab5a3a279b2e..780cf2301551 100644 --- a/modules/nf-core/leviosam2/index/meta.yml +++ b/modules/nf-core/leviosam2/index/meta.yml @@ -1,4 +1,3 @@ ---- name: "leviosam2_index" description: Index chain files for lift over keywords: @@ -11,34 +10,37 @@ tools: homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - - fai: - type: file - description: FAI (FASTA index) file of the target reference - pattern: "*.{fai}" - - chain: - type: file - description: Chain file to index. - pattern: "*.{chain}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - fai: + type: file + description: FAI (FASTA index) file of the target reference + pattern: "*.{fai}" + - - chain: + type: file + description: Chain file to index. + pattern: "*.{chain}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - clft: - type: file - description: Clft file of indexed chain - pattern: "*.{clft}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - "*.clft": + type: file + description: Clft file of indexed chain + pattern: "*.{clft}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lgrochowalski" maintainers: diff --git a/modules/nf-core/leviosam2/lift/meta.yml b/modules/nf-core/leviosam2/lift/meta.yml index 043e5286b3df..f56b8d33b54c 100644 --- a/modules/nf-core/leviosam2/lift/meta.yml +++ b/modules/nf-core/leviosam2/lift/meta.yml @@ -1,6 +1,6 @@ ---- name: "leviosam2_lift" -description: Converting aligned short and long reads records from one reference to another +description: Converting aligned short and long reads records from one reference to + another keywords: - leviosam2 - index @@ -11,39 +11,42 @@ tools: homepage: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" documentation: "https://github.com/milkschen/leviosam2/blob/main/workflow/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - input: - type: file - description: SAM/BAM/CRAM file to be lifted - pattern: "*.{bam}" - - meta_ref: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'reference' ]` - - clft: - type: file - description: Clft file of indexed ChainMap. - pattern: "*.{clft}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - input: + type: file + description: SAM/BAM/CRAM file to be lifted + pattern: "*.{bam}" + - - meta_ref: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'reference' ]` + - clft: + type: file + description: Clft file of indexed ChainMap. + pattern: "*.{clft}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'reference' ]` - bam: - type: file - description: Lifted bam file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'reference' ]` + - "*.bam": + type: file + description: Lifted bam file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lgrochowalski" maintainers: diff --git a/modules/nf-core/liftoff/meta.yml b/modules/nf-core/liftoff/meta.yml index 10e502c150b3..a8ed079fbd53 100644 --- a/modules/nf-core/liftoff/meta.yml +++ b/modules/nf-core/liftoff/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "liftoff" description: | @@ -20,51 +19,66 @@ tools: tool_dev_url: "https://github.com/agshumate/Liftoff" doi: "10.1093/bioinformatics/bty191" licence: ["GPL v3 License"] + identifier: biotools:liftoff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - target_fa: - type: file - description: Target assembly in fasta format - pattern: "*.{fsa,fa,fasta}" - - ref_fa: - type: file - description: Reference assembly in fasta format - pattern: "*.{fsa,fa,fasta}" - - ref_annotation: - type: file - description: Reference assembly annotations in gtf or gff3 format - pattern: "*.{gtf,gff3}" - - ref_db: - type: file - description: | - Name of feature database; if not specified, the -g argument must - be provided and a database will be built automatically + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - target_fa: + type: file + description: Target assembly in fasta format + pattern: "*.{fsa,fa,fasta}" + - - ref_fa: + type: file + description: Reference assembly in fasta format + pattern: "*.{fsa,fa,fasta}" + - - ref_annotation: + type: file + description: Reference assembly annotations in gtf or gff3 format + pattern: "*.{gtf,gff3}" + - - ref_db: + type: file + description: | + Name of feature database; if not specified, the -g argument must + be provided and a database will be built automatically output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - gff3: - type: file - description: Lifted annotations for the target assembly in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.gff3: + type: file + description: Lifted annotations for the target assembly in gff3 format + pattern: "*.gff3" - polished_gff3: - type: file - description: Polished lifted annotations for the target assembly in gff3 format - pattern: "*.polished.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.polished.gff3": + type: file + description: Polished lifted annotations for the target assembly in gff3 format + pattern: "*.polished.gff3" - unmapped_txt: - type: file - description: List of unmapped reference annotations - pattern: "*.unmapped.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.unmapped.txt": + type: file + description: List of unmapped reference annotations + pattern: "*.unmapped.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/lima/meta.yml b/modules/nf-core/lima/meta.yml index ad4ebbfa0c5d..f22973f0fca3 100644 --- a/modules/nf-core/lima/meta.yml +++ b/modules/nf-core/lima/meta.yml @@ -13,82 +13,161 @@ tools: documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - ccs: - type: file - description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads or ccs - pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" - - primers: - type: file - description: Fasta file, sequences of primers - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - ccs: + type: file + description: A BAM or fasta or fasta.gz or fastq or fastq.gz file of subreads + or ccs + pattern: "*.{bam,fasta,fasta.gz,fastq,fastq.gz}" + - - primers: + type: file + description: Fasta file, sequences of primers + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: A bam file of ccs purged of primers - pattern: "*.bam" - - pbi: - type: file - description: Pacbio index file of ccs purged of primers - pattern: "*.bam" - - xml: - type: file - description: An XML file representing a set of a particular sequence data type such as subreads, references or aligned subreads. - pattern: "*.xml" - - json: - type: file - description: A metadata json file - pattern: "*.json" - - clips: - type: file - description: A fasta file of clipped primers - pattern: "*.clips" - counts: - type: file - description: A tabulated file of describing pairs of primers - pattern: "*.counts" - - guess: - type: file - description: A second tabulated file of describing pairs of primers (no doc available) - pattern: "*.guess" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.counts": + type: file + description: A tabulated file of describing pairs of primers + pattern: "*.counts" - report: - type: file - description: A tab-separated file about each ZMW, unfiltered - pattern: "*.report" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.report": + type: file + description: A tab-separated file about each ZMW, unfiltered + pattern: "*.report" - summary: - type: file - description: This file shows how many ZMWs have been filtered, how ZMWs many are same/different, and how many reads have been filtered. - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.summary": + type: file + description: This file shows how many ZMWs have been filtered, how ZMWs many + are same/different, and how many reads have been filtered. + pattern: "*.summary" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: A bam file of ccs purged of primers + pattern: "*.bam" + - pbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam.pbi": + type: file + description: Pacbio index file of ccs purged of primers + pattern: "*.bam" - fasta: - type: file - description: A fasta file of ccs purged of primers. - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa, fasta}": + type: file + description: A fasta file of ccs purged of primers. + pattern: "*.fa" - fastagz: - type: file - description: A fasta.gz file of ccs purged of primers. - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.{fa.gz, fasta.gz}": + type: file + description: A fasta.gz file of ccs purged of primers. + pattern: "*.fasta.gz" - fastq: - type: file - description: A fastq file of ccs purged of primers. - pattern: "*.fastq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq": + type: file + description: A fastq file of ccs purged of primers. + pattern: "*.fastq" - fastqgz: - type: file - description: A fastq.gz file of ccs purged of primers. - pattern: "*.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.fastq.gz": + type: file + description: A fastq.gz file of ccs purged of primers. + pattern: "*.fastq.gz" + - xml: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.xml": + type: file + description: An XML file representing a set of a particular sequence data type + such as subreads, references or aligned subreads. + pattern: "*.xml" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: A metadata json file + pattern: "*.json" + - clips: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.clips": + type: file + description: A fasta file of clipped primers + pattern: "*.clips" + - guess: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.guess": + type: file + description: A second tabulated file of describing pairs of primers (no doc + available) + pattern: "*.guess" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/limma/differential/meta.yml b/modules/nf-core/limma/differential/meta.yml index 132573db2cb1..f76c57a42b30 100644 --- a/modules/nf-core/limma/differential/meta.yml +++ b/modules/nf-core/limma/differential/meta.yml @@ -13,68 +13,96 @@ tools: tool_dev_url: https://github.com/cran/limma"" doi: "10.18129/B9.bioc.limma" licence: ["LGPL >=3"] + identifier: biotools:limma input: - - meta: - type: map - description: | - Groovy Map containing contrast information. This can be used at the - workflow level to pass optional parameters to the module, e.g. - [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: - '--blocking_variable $meta.blocking'. - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for - comparison - - reference: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the reference samples - - target: - type: string - description: | - The value within the contrast_variable column of the sample sheet that - should be used to derive the target samples - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet - and matrix - - samplesheeet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata - - intensities: - type: file - description: | - Raw TSV or CSV format expression matrix with probes by row and samples - by column + - - meta: + type: map + description: | + Groovy Map containing contrast information. This can be used at the + workflow level to pass optional parameters to the module, e.g. + [ id:'contrast1', blocking:'patient' ] passed in as ext.args like: + '--blocking_variable $meta.blocking'. + - contrast_variable: + type: string + description: | + The column in the sample sheet that should be used to define groups for + comparison + - reference: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the reference samples + - target: + type: string + description: | + The value within the contrast_variable column of the sample sheet that + should be used to derive the target samples + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet + and matrix + - samplesheet: + type: file + description: Sample sheet file + - intensities: + type: file + description: | + Raw TSV or CSV format expression matrix with probes by row and samples + by column output: - results: - type: file - description: TSV-format table of differential expression information as output by Limma - pattern: "*.limma.results.tsv" + - meta: + type: file + description: TSV-format table of differential expression information as output + by Limma + pattern: "*.limma.results.tsv" + - "*.limma.results.tsv": + type: file + description: TSV-format table of differential expression information as output + by Limma + pattern: "*.limma.results.tsv" - md_plot: - type: file - description: Limma mean difference plot - pattern: "*.mean_difference.png" + - meta: + type: file + description: Limma mean difference plot + pattern: "*.mean_difference.png" + - "*.limma.mean_difference.png": + type: file + description: Limma mean difference plot + pattern: "*.mean_difference.png" - rdata: - type: file - description: Serialised MArrayLM object - pattern: "*.MArrayLM.limma.rds" + - meta: + type: file + description: Serialised MArrayLM object + pattern: "*.MArrayLM.limma.rds" + - "*.MArrayLM.limma.rds": + type: file + description: Serialised MArrayLM object + pattern: "*.MArrayLM.limma.rds" - model: - type: file - description: TXT-format limma model - pattern: "*.limma.model.tsv" + - meta: + type: file + description: TXT-format limma model + pattern: "*.limma.model.tsv" + - "*.limma.model.txt": + type: file + description: TXT-format limma model + pattern: "*.limma.model.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: file + description: dump of R SessionInfo + pattern: "*.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/lissero/meta.yml b/modules/nf-core/lissero/meta.yml index 92a7eee7d650..cf74f9d34b38 100644 --- a/modules/nf-core/lissero/meta.yml +++ b/modules/nf-core/lissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/MDU-PHL/LisSero/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/lissero licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/lofreq/alnqual/meta.yml b/modules/nf-core/lofreq/alnqual/meta.yml index b80a73ce39ef..22ddc74db857 100644 --- a/modules/nf-core/lofreq/alnqual/meta.yml +++ b/modules/nf-core/lofreq/alnqual/meta.yml @@ -7,39 +7,43 @@ keywords: - bam tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM/CRAM/SAM file with base and indel alignment qualities - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: BAM/CRAM/SAM file with base and indel alignment qualities + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/lofreq/call/meta.yml b/modules/nf-core/lofreq/call/meta.yml index 523790d5932e..d2895b8d90a3 100644 --- a/modules/nf-core/lofreq/call/meta.yml +++ b/modules/nf-core/lofreq/call/meta.yml @@ -7,42 +7,46 @@ keywords: - lofreq/call tools: - lofreq: - description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data + description: A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM input file - pattern: "*.{bam}" - - intervals: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - fasta: - type: file - description: The reference fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM input file + pattern: "*.{bam}" + - intervals: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - fasta: + type: file + description: The reference fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF output file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF output file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/lofreq/callparallel/meta.yml b/modules/nf-core/lofreq/callparallel/meta.yml index 2884773231e3..25a33e85c486 100644 --- a/modules/nf-core/lofreq/callparallel/meta.yml +++ b/modules/nf-core/lofreq/callparallel/meta.yml @@ -7,65 +7,76 @@ keywords: - variants tools: - lofreq: - description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's call-parallel programme predicts variants using multiple processors + description: Lofreq is a fast and sensitive variant-caller for inferring SNVs + and indels from next-generation sequencing data. It's call-parallel programme + predicts variants using multiple processors homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - bam: - type: file - description: Tumor sample sorted BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bam.bai}" - - intervals: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing sample information about the reference fasta fai - e.g. [ id:'reference' ] - - fai: - type: file - description: Reference genome FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: Tumor sample sorted BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bam.bai}" + - intervals: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information about the reference fasta fai + e.g. [ id:'reference' ] + - fai: + type: file + description: Reference genome FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Predicted variants file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Predicted variants file + pattern: "*.{vcf}" - tbi: - type: file - description: Index of vcf file - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of vcf file + pattern: "*.{vcf.gz.tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" - "@bjohnnyd" diff --git a/modules/nf-core/lofreq/filter/meta.yml b/modules/nf-core/lofreq/filter/meta.yml index debc303e7bba..f73d440e387f 100644 --- a/modules/nf-core/lofreq/filter/meta.yml +++ b/modules/nf-core/lofreq/filter/meta.yml @@ -1,5 +1,6 @@ name: lofreq_filter -description: Lofreq subcommand to remove variants with low coverage or strand bias potential +description: Lofreq subcommand to remove variants with low coverage or strand bias + potential keywords: - variant calling - low frequency variant calling @@ -8,35 +9,39 @@ keywords: - lofreq/filter tools: - lofreq: - description: A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data + description: A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: VCF filtered output file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/lofreq/indelqual/meta.yml b/modules/nf-core/lofreq/indelqual/meta.yml index ac82792f7e53..00788b114fec 100644 --- a/modules/nf-core/lofreq/indelqual/meta.yml +++ b/modules/nf-core/lofreq/indelqual/meta.yml @@ -8,43 +8,48 @@ keywords: - qualities tools: - lofreq: - description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file + description: Lofreq is a fast and sensitive variant-caller for inferring SNVs + and indels from next-generation sequencing data. It's indelqual programme inserts + indel qualities in a BAM file homepage: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with indel qualities inserted into it - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with indel qualities inserted into it + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/lofreq/somatic/meta.yml b/modules/nf-core/lofreq/somatic/meta.yml index f29b538481d2..face259e5304 100644 --- a/modules/nf-core/lofreq/somatic/meta.yml +++ b/modules/nf-core/lofreq/somatic/meta.yml @@ -1,5 +1,6 @@ name: "lofreq_somatic" -description: Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available +description: Lofreq subcommand to call low frequency variants from alignments when + tumor-normal paired samples are available keywords: - variant calling - low frequency variant calling @@ -8,63 +9,68 @@ keywords: - vcf tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: Groovy Map containing reference information - - meta3: - type: map - description: Groovy Map containing reference information - - tumor: - type: file - description: tumor sample input BAM file - pattern: "*.{bam}" - - tumor_index: - type: file - description: tumor sample BAM index file - pattern: "*.{bam.bai}" - - normal: - type: file - description: normal sample input BAM file - pattern: "*.{bam}" - - normal_index: - type: file - description: normal sample BAM index file - pattern: "*.{bam.bai}" - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" - - fai: - type: file - description: Reference genome FASTA index file - pattern: "*.{fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - tumor: + type: file + description: tumor sample input BAM file + pattern: "*.{bam}" + - tumor_index: + type: file + description: tumor sample BAM index file + pattern: "*.{bam.bai}" + - normal: + type: file + description: normal sample input BAM file + pattern: "*.{bam}" + - normal_index: + type: file + description: normal sample BAM index file + pattern: "*.{bam.bai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - - meta2: + type: map + description: Groovy Map containing reference information + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" + - - meta3: + type: map + description: Groovy Map containing reference information + - fai: + type: file + description: Reference genome FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nevinwu" maintainers: diff --git a/modules/nf-core/lofreq/viterbi/meta.yml b/modules/nf-core/lofreq/viterbi/meta.yml index 197e91585646..f05d2b778d72 100644 --- a/modules/nf-core/lofreq/viterbi/meta.yml +++ b/modules/nf-core/lofreq/viterbi/meta.yml @@ -1,5 +1,6 @@ name: "lofreq_viterbi" -description: Lofreq subcommand to call low frequency variants from alignments when tumor-normal paired samples are available +description: Lofreq subcommand to call low frequency variants from alignments when + tumor-normal paired samples are available keywords: - variant calling - low frequency variant calling @@ -8,47 +9,49 @@ keywords: - probabilistic realignment tools: - "lofreq": - description: "A fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data" + description: "A fast and sensitive variant-caller for inferring SNVs and indels + from next-generation sequencing data" homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: 10.1093/nar/gks918 licence: ["MIT"] + identifier: biotools:lofreq input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing sample information about the reference fasta - e.g. [ id:'reference' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the reference fasta + e.g. [ id:'reference' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Realignment and sorted BAM file - pattern: "*.{bam}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Realignment and sorted BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MarieLataretu" maintainers: diff --git a/modules/nf-core/longphase/haplotag/meta.yml b/modules/nf-core/longphase/haplotag/meta.yml index 2fe7c5693b1b..d2f2ec8d5832 100644 --- a/modules/nf-core/longphase/haplotag/meta.yml +++ b/modules/nf-core/longphase/haplotag/meta.yml @@ -1,88 +1,93 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "longphase_haplotag" -description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. +description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, + small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. keywords: - haplotag - long-read - genomics tools: - "longphase": - description: "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms." + description: "LongPhase is an ultra-fast program for simultaneously co-phasing + SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio + platforms." homepage: "https://github.com/twolinin/longphase" documentation: "https://github.com/twolinin/longphase" tool_dev_url: "https://github.com/twolinin/longphase" doi: "10.1093/bioinformatics/btac058" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of sorted BAM/CRAM file - pattern: "*.{bai,crai,csi}" - - snps: - type: file - description: VCF file with SNPs (and INDELs) - pattern: "*.{vcf,vcf.gz}" - - svs: - type: file - description: VCF file with SVs - pattern: "*.{vcf,vcf.gz}" - - mods: - type: file - description: modcall-generated VCF with modifications - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fai: - type: file - description: Reference fai index - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of sorted BAM/CRAM file + pattern: "*.{bai,crai,csi}" + - snps: + type: file + description: VCF file with SNPs (and INDELs) + pattern: "*.{vcf,vcf.gz}" + - svs: + type: file + description: VCF file with SVs + pattern: "*.{vcf,vcf.gz}" + - mods: + type: file + description: modcall-generated VCF with modifications + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fai: + type: file + description: Reference fai index + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with haplotagged reads - pattern: "*.bam" - - cram: - type: file - description: CRAM file with haplotagged reads - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{bam,cram}": + type: file + description: BAM file with haplotagged reads + pattern: "*.bam" - log: - type: file - description: Log file - pattern: "*.log" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/longphase/phase/environment.yml b/modules/nf-core/longphase/phase/environment.yml index 96e04eb61b97..bb2d0eeebd1e 100644 --- a/modules/nf-core/longphase/phase/environment.yml +++ b/modules/nf-core/longphase/phase/environment.yml @@ -1,8 +1,7 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - - "bioconda::longphase=1.7.3" - - "bioconda::htslib=1.20" + - bioconda::htslib=1.20 + - bioconda::longphase=1.7.3 diff --git a/modules/nf-core/longphase/phase/meta.yml b/modules/nf-core/longphase/phase/meta.yml index 42899177603d..823645d441ed 100644 --- a/modules/nf-core/longphase/phase/meta.yml +++ b/modules/nf-core/longphase/phase/meta.yml @@ -1,80 +1,83 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "longphase_phase" -description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. +description: LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, + small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms. keywords: - phase - long-read - genomics tools: - "longphase": - description: "LongPhase is an ultra-fast program for simultaneously co-phasing SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio platforms." + description: "LongPhase is an ultra-fast program for simultaneously co-phasing + SNPs, small indels, large SVs, and (5mC) modifications for Nanopore and PacBio + platforms." homepage: "https://github.com/twolinin/longphase" documentation: "https://github.com/twolinin/longphase" tool_dev_url: "https://github.com/twolinin/longphase" doi: "10.1093/bioinformatics/btac058" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file(s) - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index of sorted BAM/CRAM file(s) - pattern: "*.{bai,crai,csi}" - - snps: - type: file - description: VCF file with SNPs (and INDELs) - pattern: "*.{vcf,vcf.gz}" - - svs: - type: file - description: VCF file with SVs - pattern: "*.{vcf,vcf.gz}" - - mods: - type: file - description: modcall-generated VCF with modifications - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fai: - type: file - description: Reference fai index - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file(s) + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index of sorted BAM/CRAM file(s) + pattern: "*.{bai,crai,csi}" + - snps: + type: file + description: VCF file with SNPs (and INDELs) + pattern: "*.{vcf,vcf.gz}" + - svs: + type: file + description: VCF file with SVs + pattern: "*.{vcf,vcf.gz}" + - mods: + type: file + description: modcall-generated VCF with modifications + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fai: + type: file + description: Reference fai index + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file with phased variants - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Compressed VCF file with phased variants + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/ltrfinder/meta.yml b/modules/nf-core/ltrfinder/meta.yml index e3c672b9cd35..547fb67d0f88 100644 --- a/modules/nf-core/ltrfinder/meta.yml +++ b/modules/nf-core/ltrfinder/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrfinder" description: | @@ -19,41 +18,52 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_FINDER_parallel" doi: "10.1186/s13100-019-0193-0" licence: ["MIT"] + identifier: "" - "LTR_Finder": - description: An efficient program for finding full-length LTR retrotranspsons in genome sequences + description: An efficient program for finding full-length LTR retrotranspsons + in genome sequences homepage: "https://github.com/xzhub/LTR_Finder" documentation: "https://github.com/xzhub/LTR_Finder" tool_dev_url: "https://github.com/xzhub/LTR_Finder" doi: "10.1093/nar/gkm286" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Genome sequences in fasta format - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Genome sequences in fasta format + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - scn: - type: file - description: Annotation in LTRharvest or LTR_FINDER format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Annotation in LTRharvest or LTR_FINDER format + pattern: "*.scn" - gff: - type: file - description: Annotation in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Annotation in gff3 format + pattern: "*.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrharvest/meta.yml b/modules/nf-core/ltrharvest/meta.yml index 256b3ce52f2c..18064183d7a4 100644 --- a/modules/nf-core/ltrharvest/meta.yml +++ b/modules/nf-core/ltrharvest/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrharvest" description: | @@ -18,6 +17,7 @@ tools: documentation: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" tool_dev_url: "https://github.com/oushujun/EDTA/tree/v2.2.0/bin/LTR_HARVEST_parallel" licence: ["MIT"] + identifier: "" - "gt": description: "The GenomeTools genome analysis system" homepage: "https://genometools.org/index.html" @@ -25,34 +25,43 @@ tools: tool_dev_url: "https://github.com/genometools/genometools" doi: "10.1109/TCBB.2013.68" licence: ["ISC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Input genome fasta - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Input genome fasta + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff3: - type: file - description: Predicted LTR candidates in gff3 format - pattern: "*.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gff3": + type: file + description: Predicted LTR candidates in gff3 format + pattern: "*.gff3" - scn: - type: file - description: Predicted LTR candidates in scn format - pattern: "*.scn" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.scn": + type: file + description: Predicted LTR candidates in scn format + pattern: "*.scn" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrretriever/lai/meta.yml b/modules/nf-core/ltrretriever/lai/meta.yml index f84cf6ca3293..56efcccc05ef 100644 --- a/modules/nf-core/ltrretriever/lai/meta.yml +++ b/modules/nf-core/ltrretriever/lai/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_lai" description: | @@ -20,50 +19,59 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1093/nar/gky730" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The genome file that is used to generate everything - pattern: "*.{fsa,fa,fasta}" - - pass_list: - type: file - description: A list of intact LTR-RTs generated by LTR_retriever - pattern: "*.pass.list" - - annotation_out: - type: file - description: RepeatMasker annotation of all LTR sequences in the genome - pattern: "*.out" - - monoploid_seqs: - type: file - description: | - This parameter is mainly for ployploid genomes. User provides a list of - sequence names that represent a monoploid (1x). LAI will be calculated only - on these sequences if provided. - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The genome file that is used to generate everything + pattern: "*.{fsa,fa,fasta}" + - - pass_list: + type: file + description: A list of intact LTR-RTs generated by LTR_retriever + pattern: "*.pass.list" + - - annotation_out: + type: file + description: RepeatMasker annotation of all LTR sequences in the genome + pattern: "*.out" + - - monoploid_seqs: + type: file + description: | + This parameter is mainly for ployploid genomes. User provides a list of + sequence names that represent a monoploid (1x). LAI will be calculated only + on these sequences if provided. + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - log: - type: file - description: Log from LAI - pattern: "*.LAI.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.log": + type: file + description: Log from LAI + pattern: "*.LAI.log" - lai_out: - type: file - description: | - Output file from LAI if LAI is able to estimate the index from the inputs - pattern: "*.LAI.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.LAI.out": + type: file + description: | + Output file from LAI if LAI is able to estimate the index from the inputs + pattern: "*.LAI.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/ltrretriever/ltrretriever/meta.yml b/modules/nf-core/ltrretriever/ltrretriever/meta.yml index a310b04af812..9645de2d9573 100644 --- a/modules/nf-core/ltrretriever/ltrretriever/meta.yml +++ b/modules/nf-core/ltrretriever/ltrretriever/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ltrretriever_ltrretriever" description: Identifies LTR retrotransposons using LTR_retriever @@ -16,67 +15,104 @@ tools: tool_dev_url: "https://github.com/oushujun/LTR_retriever" doi: "10.1104/pp.17.01310" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - genome: - type: file - description: Genomic sequences in fasta format - pattern: "*.{fsa,fa,fasta}" - - harvest: - type: file - description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" - - finder: - type: file - description: LTR-RT candidates from LTR_FINDER - pattern: "*.scn" - - mgescan: - type: file - description: LTR-RT candidates from MGEScan_LTR - pattern: "*.out" - - non_tgca: - type: file - description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in the old tabular format - pattern: "*.tabout" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - genome: + type: file + description: Genomic sequences in fasta format + pattern: "*.{fsa,fa,fasta}" + - - harvest: + type: file + description: LTR-RT candidates from GenomeTools ltrharvest in the old tabular + format + pattern: "*.tabout" + - - finder: + type: file + description: LTR-RT candidates from LTR_FINDER + pattern: "*.scn" + - - mgescan: + type: file + description: LTR-RT candidates from MGEScan_LTR + pattern: "*.out" + - - non_tgca: + type: file + description: Non-canonical LTR-RT candidates from GenomeTools ltrharvest in + the old tabular format + pattern: "*.tabout" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - log: - type: file - description: Output log from LTR_retriever - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Output log from LTR_retriever + pattern: "*.log" - pass_list: - type: file - description: Intact LTR-RTs with coordinate and structural information in summary table format - pattern: "*.pass.list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.pass.list: + type: file + description: Intact LTR-RTs with coordinate and structural information in summary + table format + pattern: "*.pass.list" - pass_list_gff: - type: file - description: Intact LTR-RTs with coordinate and structural information in gff3 format - pattern: "*.pass.list.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.pass.list.gff3": + type: file + description: Intact LTR-RTs with coordinate and structural information in gff3 + format + pattern: "*.pass.list.gff3" - ltrlib: - type: file - description: All non-redundant LTR-RTs - pattern: "*.LTRlib.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.LTRlib.fa": + type: file + description: All non-redundant LTR-RTs + pattern: "*.LTRlib.fa" - annotation_out: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.out: + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library + pattern: "*.out" - annotation_gff: - type: file - description: Whole-genome LTR-RT annotation by the non-redundant library in gff3 format - pattern: "*.out.gff3" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.out.gff3": + type: file + description: Whole-genome LTR-RT annotation by the non-redundant library in + gff3 format + pattern: "*.out.gff3" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/macrel/contigs/meta.yml b/modules/nf-core/macrel/contigs/meta.yml index ba0b0e6f5d5b..c1c03f42526c 100644 --- a/modules/nf-core/macrel/contigs/meta.yml +++ b/modules/nf-core/macrel/contigs/meta.yml @@ -1,5 +1,7 @@ name: macrel_contigs -description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by predicting peptides from genomes (provided as contigs) and outputs all the predicted anti-microbial peptides found. +description: A tool that mines antimicrobial peptides (AMPs) from (meta)genomes by + predicting peptides from genomes (provided as contigs) and outputs all the predicted + anti-microbial peptides found. keywords: - AMP - antimicrobial peptides @@ -14,46 +16,76 @@ tools: tool_dev_url: https://github.com/BigDataBiology/macrel doi: "10.7717/peerj.10555" licence: ["MIT"] + identifier: biotools:macrel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A fasta file with nucleotide sequences. - pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A fasta file with nucleotide sequences. + pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - amp_prediction: - type: file - description: A zipped file, with all predicted amps in a table format. - pattern: "*.prediction.gz" - smorfs: - type: file - description: A zipped fasta file containing aminoacid sequences showing the general gene prediction information in the contigs. - pattern: "*.smorfs.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.smorfs.faa.gz": + type: file + description: A zipped fasta file containing aminoacid sequences showing the + general gene prediction information in the contigs. + pattern: "*.smorfs.faa.gz" - all_orfs: - type: file - description: A zipped fasta file containing amino acid sequences showing the general gene prediction information in the contigs. - pattern: "*.all_orfs.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.all_orfs.faa.gz": + type: file + description: A zipped fasta file containing amino acid sequences showing the + general gene prediction information in the contigs. + pattern: "*.all_orfs.faa.gz" + - amp_prediction: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.prediction.gz": + type: file + description: A zipped file, with all predicted amps in a table format. + pattern: "*.prediction.gz" - readme_file: - type: file - description: A readme file containing tool specific information (e.g. citations, details about the output, etc.). - pattern: "*.md" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.md": + type: file + description: A readme file containing tool specific information (e.g. citations, + details about the output, etc.). + pattern: "*.md" - log_file: - type: file - description: A log file containing the information pertaining to the run. - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*_log.txt": + type: file + description: A log file containing the information pertaining to the run. + pattern: "*_log.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/macs2/callpeak/meta.yml b/modules/nf-core/macs2/callpeak/meta.yml index 68ecd4ef372c..149f04df3cdd 100644 --- a/modules/nf-core/macs2/callpeak/meta.yml +++ b/modules/nf-core/macs2/callpeak/meta.yml @@ -12,46 +12,75 @@ tools: tool_dev_url: https://github.com/macs3-project/MACS doi: "10.1101/496521" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ipbam: - type: file - description: The ChIP-seq treatment file - - controlbam: - type: file - description: The control file - - macs2_gsize: - type: string - description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ipbam: + type: file + description: The ChIP-seq treatment file + - controlbam: + type: file + description: The control file + - - macs2_gsize: + type: string + description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' + for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and + 'dm' for fruitfly (1.2e8) output: - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - peak: - type: file - description: BED file containing annotated peaks - pattern: "*.gappedPeak,*.narrowPeak}" + - meta: + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" + - "*.{narrowPeak,broadPeak}": + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" - xls: - type: file - description: xls file containing annotated peaks - pattern: "*.xls" + - meta: + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - "*.xls": + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" - gapped: - type: file - description: Optional BED file containing gapped peak - pattern: "*.gappedPeak" + - meta: + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" + - "*.gappedPeak": + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" - bed: - type: file - description: Optional BED file containing peak summits locations for every peak - pattern: "*.bed" + - meta: + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" + - "*.bed": + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" - bdg: - type: file - description: Optional bedGraph files for input and treatment input samples - pattern: "*.bdg" + - meta: + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" + - "*.bdg": + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" authors: - "@ntoda03" - "@JoseEspinosa" diff --git a/modules/nf-core/macs3/callpeak/meta.yml b/modules/nf-core/macs3/callpeak/meta.yml index 1603b8e2e923..5d97a036ca83 100644 --- a/modules/nf-core/macs3/callpeak/meta.yml +++ b/modules/nf-core/macs3/callpeak/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "macs3_callpeak" description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments @@ -15,58 +14,83 @@ tools: tool_dev_url: "https://github.com/macs3-project/MACS/" doi: "10.1101/496521" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample_1', single_end:false ]` - - ipbam: - type: file - description: The ChIP-seq treatment file - - controlbam: - type: file - description: The control file - - macs3_gsize: - type: string - description: | - Effective genome size. It can be 1.0e+9 or 1000000000, - or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse - (2,652,783,500), 'ce' for C. elegans (100,286,401) - and 'dm' for fruitfly (142,573,017), Default:hs. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample_1', single_end:false ]` + - ipbam: + type: file + description: The ChIP-seq treatment file + - controlbam: + type: file + description: The control file + - - macs3_gsize: + type: string + description: | + Effective genome size. It can be 1.0e+9 or 1000000000, + or shortcuts:'hs' for human (2,913,022,398), 'mm' for mouse + (2,652,783,500), 'ce' for C. elegans (100,286,401) + and 'dm' for fruitfly (142,573,017), Default:hs. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - peak: - type: file - description: BED file containing annotated peaks - pattern: "*.gappedPeak,*.narrowPeak}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{narrowPeak,broadPeak}": + type: file + description: BED file containing annotated peaks + pattern: "*.gappedPeak,*.narrowPeak}" - xls: - type: file - description: xls file containing annotated peaks - pattern: "*.xls" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.xls": + type: file + description: xls file containing annotated peaks + pattern: "*.xls" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" - gapped: - type: file - description: Optional BED file containing gapped peak - pattern: "*.gappedPeak" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gappedPeak": + type: file + description: Optional BED file containing gapped peak + pattern: "*.gappedPeak" - bed: - type: file - description: Optional BED file containing peak summits locations for every peak - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bed": + type: file + description: Optional BED file containing peak summits locations for every peak + pattern: "*.bed" - bdg: - type: file - description: Optional bedGraph files for input and treatment input samples - pattern: "*.bdg" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bdg": + type: file + description: Optional bedGraph files for input and treatment input samples + pattern: "*.bdg" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mafft/meta.yml b/modules/nf-core/mafft/meta.yml index 90b9ed39c327..ed5e1ea31a4a 100644 --- a/modules/nf-core/mafft/meta.yml +++ b/modules/nf-core/mafft/meta.yml @@ -6,88 +6,101 @@ keywords: - multiple sequence alignment tools: - "mafft": - description: Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform + description: Multiple alignment program for amino acid or nucleotide sequences + based on fast Fourier transform homepage: https://mafft.cbrc.jp/alignment/software/ documentation: https://mafft.cbrc.jp/alignment/software/manual/manual.html tool_dev_url: https://mafft.cbrc.jp/alignment/software/source.html doi: "10.1093/nar/gkf436" licence: ["BSD"] + identifier: biotools:MAFFT - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: biotools:MAFFT input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing the sequences to align. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - add: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--add`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfragments: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfragments`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addfull: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addfull`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addprofile: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addprofile`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - meta6: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - addlong: - type: file - description: FASTA file containing sequences to align to the sequences in `fasta` using `--addlong`. May be gzipped or uncompressed. - pattern: "*.{fa,fasta}{.gz,}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing the sequences to align. May be gzipped or + uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - add: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--add`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addfragments: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addfragments`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addfull: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addfull`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addprofile: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addprofile`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - addlong: + type: file + description: FASTA file containing sequences to align to the sequences in `fasta` + using `--addlong`. May be gzipped or uncompressed. + pattern: "*.{fa,fasta}{.gz,}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fas: - type: file - description: Aligned sequences in FASTA format. May be gzipped or uncompressed. - pattern: "*.fas{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fas{.gz,}": + type: file + description: Aligned sequences in FASTA format. May be gzipped or uncompressed. + pattern: "*.fas{.gz,}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MillironX" maintainers: diff --git a/modules/nf-core/mageck/count/meta.yml b/modules/nf-core/mageck/count/meta.yml index 6450de0a6b29..4b5e425a03e1 100644 --- a/modules/nf-core/mageck/count/meta.yml +++ b/modules/nf-core/mageck/count/meta.yml @@ -1,5 +1,6 @@ name: "mageck_count" -description: mageck count for functional genomics, reads are usually mapped to a specific sgRNA +description: mageck count for functional genomics, reads are usually mapped to a specific + sgRNA keywords: - sort - functional genomics @@ -7,43 +8,54 @@ keywords: - CRISPR-Cas9 tools: - mageck: - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/" documentation: "https://sourceforge.net/p/mageck/wiki/demo/#step-4-run-the-mageck-count-command" doi: "10.1186/s13059-014-0554-4" licence: ["BSD License"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - library: - type: file - description: library file containing the sgRNA and gene name - pattern: "*.{csv,txt,tsv}" - - inputfile: - type: file - description: library fastq file containing the sgRNA and gene name or count table containing the sgRNA and number of reads to per sample - pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputfile: + type: file + description: library fastq file containing the sgRNA and gene name or count + table containing the sgRNA and number of reads to per sample + pattern: "*.{fq,fastq,fastq.gz,fq.gz,csv,txt,tsv}" + - - library: + type: file + description: library file containing the sgRNA and gene name + pattern: "*.{csv,txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - norm: - type: file - description: File containing normalized read counts - pattern: "*.count_normalized.txt" - count: - type: file - description: File containing read counts - pattern: "*.countsummary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*count.txt": + type: file + description: File containing read counts + pattern: "*.countsummary.txt" + - norm: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.count_normalized.txt": + type: file + description: File containing normalized read counts + pattern: "*.count_normalized.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/mle/meta.yml b/modules/nf-core/mageck/mle/meta.yml index 0b944aafa867..8c577fbd51b3 100644 --- a/modules/nf-core/mageck/mle/meta.yml +++ b/modules/nf-core/mageck/mle/meta.yml @@ -6,52 +6,62 @@ keywords: - CRISPR tools: - "mageck": - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/#mle" documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" licence: ["BSD"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_table: - type: file - description: | - Count table file. - Each line in the table should include - sgRNA name (1st column), target gene (2nd column) - and read counts in each sample. - pattern: "*.{txt,tsv}" - - design_matrix: - type: file - description: Design matrix describing the samples and conditions - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_table: + type: file + description: | + Count table file. + Each line in the table should include + sgRNA name (1st column), target gene (2nd column) + and read counts in each sample. + pattern: "*.{txt,tsv}" + - - design_matrix: + type: file + description: Design matrix describing the samples and conditions + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gene_summary: - type: file - description: | - Gene summary file describing the fitness score - and associated p-values. - pattern: "*.{gene_summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gene_summary.txt": + type: file + description: | + Gene summary file describing the fitness score + and associated p-values. + pattern: "*.{gene_summary}" - sgrna_summary: - type: file - description: | - sgRNA summary file describing the sgRNA and - associated gene - pattern: "*.{gene_summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sgrna_summary.txt": + type: file + description: | + sgRNA summary file describing the sgRNA and + associated gene + pattern: "*.{gene_summary}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/mageck/test/meta.yml b/modules/nf-core/mageck/test/meta.yml index d0d93f33f9de..790367774aa3 100644 --- a/modules/nf-core/mageck/test/meta.yml +++ b/modules/nf-core/mageck/test/meta.yml @@ -1,59 +1,76 @@ name: "mageck_test" -description: Mageck test performs a robust ranking aggregation (RRA) to identify positively or negatively selected genes in functional genomics screens. +description: Mageck test performs a robust ranking aggregation (RRA) to identify positively + or negatively selected genes in functional genomics screens. keywords: - sort - rra - CRISPR tools: - mageck: - description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), an algorithm to process, QC, analyze and visualize CRISPR screening data." + description: "MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout), + an algorithm to process, QC, analyze and visualize CRISPR screening data." homepage: "https://sourceforge.net/p/mageck/wiki/Home/#mle" documentation: "https://sourceforge.net/p/mageck/wiki/Home/" tool_dev_url: "https://bitbucket.org/liulab/mageck/src" doi: "10.1186/s13059-015-0843-6" licence: ["BSD License"] + identifier: biotools:mageck input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - count_table: - type: file - description: | - Count table file. - Each line in the table should include - sgRNA name (1st column), target gene (2nd column) - and read counts in each sample. - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - count_table: + type: file + description: | + Count table file. + Each line in the table should include + sgRNA name (1st column), target gene (2nd column) + and read counts in each sample. + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gene_summary: - type: file - description: | - Gene summary file describing the fitness score - and associated p-values. - pattern: "*.{gene_summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gene_summary.txt": + type: file + description: | + Gene summary file describing the fitness score + and associated p-values. + pattern: "*.{gene_summary.txt}" - sgrna_summary: - type: file - description: | - sgRNA summary file describing the sgRNA and - associated gene - pattern: "*.{sgrna_summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sgrna_summary.txt": + type: file + description: | + sgRNA summary file describing the sgRNA and + associated gene + pattern: "*.{sgrna_summary.txt}" - r_script: - type: file - description: | - R script allowing to output plots - from main hit genes - pattern: "*.R" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.R": + type: file + description: | + R script allowing to output plots + from main hit genes + pattern: "*.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LaurenceKuhl" maintainers: diff --git a/modules/nf-core/magus/align/meta.yml b/modules/nf-core/magus/align/meta.yml index f9ada96a23d2..e5d7cdb0c469 100644 --- a/modules/nf-core/magus/align/meta.yml +++ b/modules/nf-core/magus/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "magus_align" description: Multiple Sequence Alignment using Graph Clustering @@ -15,53 +14,53 @@ tools: tool_dev_url: "https://github.com/vlasmirnov/MAGUS" doi: "10.1093/bioinformatics/btaa992" licence: ["MIT"] + identifier: biotools:magus input: - - meta: - type: map - description: | - Groovy Map containing the fasta meta information - e.g. `[ id:'test', single_end:false ]` - - - meta2: - type: map - description: | - Groovy Map containing sample information for the specified guide tree (if supplied) - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: file - description: Input sequences in FASTA format. - pattern: "*.{fa,fna,fasta}" - - - tree: - type: file - description: Optional path to a file containing a guide tree in newick format to use as input. - If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, MAGUS will construct its own guide tree. If empty, `fasttree` is used as a default. - pattern: "*.{dnd,tree}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing the fasta meta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input sequences in FASTA format. + pattern: "*.{fa,fna,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for the specified guide tree (if supplied) + e.g. `[ id:'test', single_end:false ]` + - tree: + type: file + description: Optional path to a file containing a guide tree in newick format + to use as input. If empty, or overwritten by passing `-t [fasttree|fasttree-noml|clustal|parttree]`, + MAGUS will construct its own guide tree. If empty, `fasttree` is used as a + default. + pattern: "*.{dnd,tree}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample meta information. - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - alignment: - type: file - description: File containing the output alignment, in FASTA format containing gaps. - The sequences may be in a different order than in the input FASTA. - The output file may or may not be gzipped, depending on the value supplied to `compress`. - pattern: "*.aln{.gz,}" - + - meta: + type: map + description: | + Groovy Map containing sample meta information. + e.g. `[ id:'test', single_end:false ]` + - "*.aln{.gz,}": + type: file + description: File containing the output alignment, in FASTA format containing + gaps. The sequences may be in a different order than in the input FASTA. The + output file may or may not be gzipped, depending on the value supplied to + `compress`. + pattern: "*.aln{.gz,}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/magus/guidetree/meta.yml b/modules/nf-core/magus/guidetree/meta.yml index 7d21391ad859..2cc3020d9595 100644 --- a/modules/nf-core/magus/guidetree/meta.yml +++ b/modules/nf-core/magus/guidetree/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "magus_guidetree" description: Multiple Sequence Alignment using Graph Clustering @@ -15,35 +14,33 @@ tools: tool_dev_url: "https://github.com/vlasmirnov/MAGUS" doi: "10.1093/bioinformatics/btaa992" licence: ["MIT"] + identifier: biotools:magus input: - - meta: - type: map - description: | - Groovy Map containing fasta meta information - e.g. `[ id:'test', single_end:false ]` - - - fasta: - type: file - description: Input sequences in FASTA format. - pattern: "*.{fa,fna,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing fasta meta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Input sequences in FASTA format. + pattern: "*.{fa,fna,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tree: - type: file - description: File containing the output guidetree, in newick format. - pattern: "*.tree" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tree": + type: file + description: File containing the output guidetree, in newick format. + pattern: "*.tree" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/malt/build/meta.yml b/modules/nf-core/malt/build/meta.yml index b95fc527007c..da1fc6c260d3 100644 --- a/modules/nf-core/malt/build/meta.yml +++ b/modules/nf-core/malt/build/meta.yml @@ -1,5 +1,7 @@ name: malt_build -description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. +description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and + analysis tool designed for processing high-throughput sequencing data, especially + in the context of metagenomics. keywords: - malt - alignment @@ -17,32 +19,36 @@ tools: documentation: https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf doi: "10.1038/s41559-017-0446-6" licence: ["GPL v3"] + identifier: "" input: - - fastas: - type: file - description: Directory of, or list of FASTA reference files for indexing - pattern: "*/|*.fasta" - - gff: - type: file - description: Directory of, or GFF3 files of input FASTA files - pattern: "*/|*.gff|*.gff3" - - mapping_db: - type: file - description: MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html - pattern: "*.db" + - - fastas: + type: file + description: Directory of, or list of FASTA reference files for indexing + pattern: "*/|*.fasta" + - - gff: + type: file + description: Directory of, or GFF3 files of input FASTA files + pattern: "*/|*.gff|*.gff3" + - - mapping_db: + type: file + description: MEGAN .db file from https://software-ab.cs.uni-tuebingen.de/download/megan6/welcome.html + pattern: "*.db" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Directory containing MALT database index directory - pattern: "malt_index/" + - malt_index/: + type: directory + description: Directory containing MALT database index directory + pattern: "malt_index/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log: - type: file - description: Log file from STD out of malt-build - pattern: "malt-build.log" + - malt-build.log: + type: file + description: Log file from STD out of malt-build + pattern: "malt-build.log" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/malt/run/meta.yml b/modules/nf-core/malt/run/meta.yml index 5bb7d9b3f329..ed92805a1d09 100644 --- a/modules/nf-core/malt/run/meta.yml +++ b/modules/nf-core/malt/run/meta.yml @@ -1,5 +1,7 @@ name: malt_run -description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and analysis tool designed for processing high-throughput sequencing data, especially in the context of metagenomics. +description: MALT, an acronym for MEGAN alignment tool, is a sequence alignment and + analysis tool designed for processing high-throughput sequencing data, especially + in the context of metagenomics. keywords: - malt - alignment @@ -16,37 +18,54 @@ tools: documentation: https://software-ab.cs.uni-tuebingen.de/download/malt/manual.pdf doi: "10.1038/s41559-017-0446-6" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastqs: - type: file - description: Input FASTQ files - pattern: "*.{fastq.gz,fq.gz}" - - index: - type: directory - description: Index/database directory from malt-build - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastqs: + type: file + description: Input FASTQ files + pattern: "*.{fastq.gz,fq.gz}" + - - index: + type: directory + description: Index/database directory from malt-build + pattern: "*/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rma6: - type: file - description: MEGAN6 RMA6 file - pattern: "*.rma6" + - meta: + type: file + description: MEGAN6 RMA6 file + pattern: "*.rma6" + - "*.rma6": + type: file + description: MEGAN6 RMA6 file + pattern: "*.rma6" - alignments: - type: file - description: Alignment files in Tab, Text or MEGAN-compatible SAM format - pattern: "*.{tab,txt,sam}" + - meta: + type: file + description: Alignment files in Tab, Text or MEGAN-compatible SAM format + pattern: "*.{tab,txt,sam}" + - "*.{tab,text,sam,tab.gz,text.gz,sam.gz}": + type: file + description: Alignment files in Tab, Text or MEGAN-compatible SAM format + pattern: "*.{tab,txt,sam}" - log: - type: file - description: Log of verbose MALT stdout - pattern: "*-malt-run.log" + - meta: + type: file + description: Log of verbose MALT stdout + pattern: "*-malt-run.log" + - "*.log": + type: file + description: Log of verbose MALT stdout + pattern: "*-malt-run.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/maltextract/meta.yml b/modules/nf-core/maltextract/meta.yml index f7648d807c1e..129315a61c94 100644 --- a/modules/nf-core/maltextract/meta.yml +++ b/modules/nf-core/maltextract/meta.yml @@ -1,5 +1,6 @@ name: maltextract -description: Tool for evaluation of MALT results for true positives of ancient metagenomic taxonomic screening +description: Tool for evaluation of MALT results for true positives of ancient metagenomic + taxonomic screening keywords: - malt - MaltExtract @@ -22,33 +23,40 @@ tools: tool_dev_url: https://github.com/rhuebler/hops doi: "10.1186/s13059-019-1903-0" licence: ["GPL 3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rma6: - type: file - description: RMA6 files from MALT - pattern: "*.rma6" - - taxon_list: - type: file - description: List of target taxa to evaluate - pattern: "*.txt" - - ncbi_dir: - type: directory - description: Directory containing NCBI taxonomy map and tre files - pattern: "${ncbi_dir}/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rma6: + type: file + description: RMA6 files from MALT + pattern: "*.rma6" + - - taxon_list: + type: file + description: List of target taxa to evaluate + pattern: "*.txt" + - - ncbi_dir: + type: directory + description: Directory containing NCBI taxonomy map and tre files + pattern: "${ncbi_dir}/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing MaltExtract text results files - pattern: "results/" + - meta: + type: directory + description: Directory containing MaltExtract text results files + pattern: "results/" + - results: + type: directory + description: Directory containing MaltExtract text results files + pattern: "results/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/manta/convertinversion/meta.yml b/modules/nf-core/manta/convertinversion/meta.yml index 865ef87c513d..3a70814d7f73 100644 --- a/modules/nf-core/manta/convertinversion/meta.yml +++ b/modules/nf-core/manta/convertinversion/meta.yml @@ -1,5 +1,7 @@ name: "manta_convertinversion" -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. This script reformats inversions into single inverted sequence junctions which was the format used in Manta versions <= 1.4.0. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. This script reformats inversions into single inverted sequence + junctions which was the format used in Manta versions <= 1.4.0. keywords: - structural variants - conversion @@ -12,43 +14,52 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file produces by Manta - pattern: "*.vcf.gz" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file produces by Manta + pattern: "*.vcf.gz" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with reformatted inversions - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with reformatted inversions + pattern: "*.vcf.gz" - tbi: - type: file - description: TBI file produces by Manta - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: TBI file produces by Manta + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/manta/germline/meta.yml b/modules/nf-core/manta/germline/meta.yml index 72ed15f8bc29..4072ab8e564d 100644 --- a/modules/nf-core/manta/germline/meta.yml +++ b/modules/nf-core/manta/germline/meta.yml @@ -1,5 +1,7 @@ name: manta_germline -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,84 +18,117 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file. For joint calling use a list of files. - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM/CRAM/SAM index file. For joint calling use a list of files. - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file. For joint calling use a list of files. + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM/CRAM/SAM index file. For joint calling use a list of files. + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - diploid_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*diploid_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - diploid_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*diploid_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@ramprasadn" diff --git a/modules/nf-core/manta/somatic/meta.yml b/modules/nf-core/manta/somatic/meta.yml index e658edaaa4cb..11f1fc1ca0ae 100644 --- a/modules/nf-core/manta/somatic/meta.yml +++ b/modules/nf-core/manta/somatic/meta.yml @@ -1,5 +1,7 @@ name: manta_somatic -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,100 +18,145 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_normal: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - input_tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_tumor: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_normal: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - input_tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_tumor: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - diploid_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diploid_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - diploid_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diploid_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - somatic_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - somatic_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@nvnieuwk" diff --git a/modules/nf-core/manta/tumoronly/meta.yml b/modules/nf-core/manta/tumoronly/meta.yml index 63556c59b4e5..6f629b24dc48 100644 --- a/modules/nf-core/manta/tumoronly/meta.yml +++ b/modules/nf-core/manta/tumoronly/meta.yml @@ -1,5 +1,7 @@ name: manta_tumoronly -description: Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. +description: Manta calls structural variants (SVs) and indels from mapped paired-end + sequencing reads. It is optimized for analysis of germline variation in small sets + of individuals and somatic variation in tumor/normal sample pairs. keywords: - somatic - wgs @@ -16,84 +18,117 @@ tools: tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" licence: ["GPL v3"] + identifier: biotools:manta_sv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_tbi: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - config: - type: file - description: Manta configuration file - pattern: "*.{ini,conf,config}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_tbi: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" + - - config: + type: file + description: Manta configuration file + pattern: "*.{ini,conf,config}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - candidate_small_indels_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_small_indels_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_small_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - candidate_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - candidate_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*candidate_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - tumor_sv_vcf: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*tumor_sv.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - tumor_sv_vcf_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*tumor_sv.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@nvnieuwk" diff --git a/modules/nf-core/mapad/index/meta.yml b/modules/nf-core/mapad/index/meta.yml index 2c94d9fc6a90..3b7d0addc8b9 100644 --- a/modules/nf-core/mapad/index/meta.yml +++ b/modules/nf-core/mapad/index/meta.yml @@ -12,30 +12,33 @@ tools: documentation: "https://github.com/mpieva/mapAD" tool_dev_url: "https://github.com/mpieva/mapAD" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: mapAD genome index files - pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mapad/: + type: directory + description: mapAD genome index files + pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jch-13" maintainers: diff --git a/modules/nf-core/mapad/map/meta.yml b/modules/nf-core/mapad/map/meta.yml index 1ca5e9d2cd22..c83c28202f78 100644 --- a/modules/nf-core/mapad/map/meta.yml +++ b/modules/nf-core/mapad/map/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mapad_map" description: Map short-reads to an indexed reference genome @@ -33,62 +32,66 @@ tools: documentation: "https://github.com/mpieva/mapAD" tool_dev_url: "https://github.com/mpieva/mapAD" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory) - pattern: "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: mapAD genome index files (mandatory) - pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" - - mismatch_parameter: - type: float - description: | - Minimum probability of the number of mismatches under `-D` base error rate - - double_stranded_library: - type: boolean - description: Library preparation method - specify if double stranded else it's assumed single stranded - - five_prime_overhang: - type: float - description: 5'-overhang length parameter - - three_prime_overhang: - type: float - description: 3'-overhang length parameter - - deam_rate_double_stranded: - type: float - description: Deamination rate in double-stranded stem of a read - - deam_rate_single_stranded: - type: float - description: Deamination rate in single-stranded ends of a read - - indel_rate: - type: float - description: Expected rate of indels between reads and reference + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Sequencing reads in FASTQ or BAM (unmapped/mapped) related formats. Supports only single-end or merged paired-end data (mandatory) + pattern: "*.{bam,cram,fastq,fastq.gz,fq,fq.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: mapAD genome index files (mandatory) + pattern: "*.{tbw,tle,toc,tos,tpi,trt,tsa}" + - - mismatch_parameter: + type: float + description: | + Minimum probability of the number of mismatches under `-D` base error rate + - - double_stranded_library: + type: boolean + description: Library preparation method - specify if double stranded else it's + assumed single stranded + - - five_prime_overhang: + type: float + description: 5'-overhang length parameter + - - three_prime_overhang: + type: float + description: 3'-overhang length parameter + - - deam_rate_double_stranded: + type: float + description: Deamination rate in double-stranded stem of a read + - - deam_rate_single_stranded: + type: float + description: Deamination rate in single-stranded ends of a read + - - indel_rate: + type: float + description: Expected rate of indels between reads and reference output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM/SAM file containing read alignments - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM/SAM file containing read alignments + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jch-13" maintainers: diff --git a/modules/nf-core/mapdamage2/meta.yml b/modules/nf-core/mapdamage2/meta.yml index 884e520aff89..f27fc17f131a 100644 --- a/modules/nf-core/mapdamage2/meta.yml +++ b/modules/nf-core/mapdamage2/meta.yml @@ -1,5 +1,6 @@ name: mapdamage2 -description: Computational framework for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. +description: Computational framework for tracking and quantifying DNA damage patterns + among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. keywords: - ancient DNA - DNA damage @@ -14,98 +15,202 @@ tools: tool_dev_url: https://github.com/ginolhac/mapDamage doi: "10.1093/bioinformatics/btt193" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Fasta file, the reference the input BAM was mapped against - pattern: "*.{fasta}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - fasta: + type: file + description: Fasta file, the reference the input BAM was mapped against + pattern: "*.{fasta}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - runtime_log: - type: file - description: Log file with a summary of command lines used and timestamps. - pattern: "Runtime_log.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Runtime_log.txt: + type: file + description: Log file with a summary of command lines used and timestamps. + pattern: "Runtime_log.txt" - fragmisincorporation_plot: - type: file - description: A pdf file that displays both fragmentation and misincorporation patterns. - pattern: "Fragmisincorporation_plot.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Fragmisincorporation_plot.pdf: + type: file + description: A pdf file that displays both fragmentation and misincorporation + patterns. + pattern: "Fragmisincorporation_plot.pdf" - length_plot: - type: file - description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. - pattern: "Length_plot.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Length_plot.pdf: + type: file + description: A pdf file that displays length distribution of singleton reads + per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end + are also displayed per strand. + pattern: "Length_plot.pdf" - misincorporation: - type: file - description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. - pattern: "misincorporation.txt" - - pctot_freq: - type: file - description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. - pattern: "5pCtoT_freq.txt" - - pgtoa_freq: - type: file - description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. - pattern: "3pGtoA_freq.txt" - - dnacomp: - type: file - description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. - pattern: "dnacomp.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/misincorporation.txt: + type: file + description: Contains a table with occurrences for each type of mutations and + relative positions from the reads ends. + pattern: "misincorporation.txt" - lgdistribution: - type: file - description: Contains a table with read length distributions per strand. - pattern: "lgdistribution.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/lgdistribution.txt: + type: file + description: Contains a table with read length distributions per strand. + pattern: "lgdistribution.txt" + - dnacomp: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/dnacomp.txt: + type: file + description: Contains a table of the reference genome base composition per position, + inside reads and adjacent regions. + pattern: "dnacomp.txt" - stats_out_mcmc_hist: - type: file - description: A MCMC histogram for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_hist.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_hist.pdf: + type: file + description: A MCMC histogram for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_hist.pdf" - stats_out_mcmc_iter: - type: file - description: Values for the damage parameters and log likelihood in each MCMC iteration. - pattern: "Stats_out_MCMC_iter.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_iter.csv: + type: file + description: Values for the damage parameters and log likelihood in each MCMC + iteration. + pattern: "Stats_out_MCMC_iter.csv" - stats_out_mcmc_trace: - type: file - description: A MCMC trace plot for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_trace.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_trace.pdf: + type: file + description: A MCMC trace plot for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_trace.pdf" - stats_out_mcmc_iter_summ_stat: - type: file - description: Summary statistics for the damage parameters estimated posterior distributions. - pattern: "Stats_out_MCMC_iter_summ_stat.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_iter_summ_stat.csv: + type: file + description: Summary statistics for the damage parameters estimated posterior + distributions. + pattern: "Stats_out_MCMC_iter_summ_stat.csv" - stats_out_mcmc_post_pred: - type: file - description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. - pattern: "Stats_out_MCMC_post_pred.pdf" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_post_pred.pdf: + type: file + description: Empirical misincorporation frequency and posterior predictive intervals + from the fitted model. + pattern: "Stats_out_MCMC_post_pred.pdf" - stats_out_mcmc_correct_prob: - type: file - description: Position specific probability of a C->T and G->A misincorporation is due to damage. - pattern: "Stats_out_MCMC_correct_prob.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/Stats_out_MCMC_correct_prob.csv: + type: file + description: Position specific probability of a C->T and G->A misincorporation + is due to damage. + pattern: "Stats_out_MCMC_correct_prob.csv" - dnacomp_genome: - type: file - description: Contains the global reference genome base composition (computed by seqtk). - pattern: "dnacomp_genome.csv" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/dnacomp_genome.csv: + type: file + description: Contains the global reference genome base composition (computed + by seqtk). + pattern: "dnacomp_genome.csv" - rescaled: - type: file - description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. - pattern: "*.{bam}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/*rescaled.bam: + type: file + description: Rescaled BAM file, where likely post-mortem damaged bases have + downscaled quality scores. + pattern: "*.{bam}" + - pctot_freq: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/5pCtoT_freq.txt: + type: file + description: Contains frequencies of Cytosine to Thymine mutations per position + from the 5'-ends. + pattern: "5pCtoT_freq.txt" + - pgtoa_freq: + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/3pGtoA_freq.txt: + type: file + description: Contains frequencies of Guanine to Adenine mutations per position + from the 3'-ends. + pattern: "3pGtoA_freq.txt" - fasta: - type: file - description: Allignments in a FASTA file, only if flagged by -d. - pattern: "*.{fasta}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - results_*/*.fasta: + type: file + description: Allignments in a FASTA file, only if flagged by -d. + pattern: "*.{fasta}" - folder: - type: directory - description: Folder created when --plot-only, --rescale and --stats-only flags are passed. - pattern: "*/" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*/": + type: directory + description: Folder created when --plot-only, --rescale and --stats-only flags + are passed. + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/mash/dist/meta.yml b/modules/nf-core/mash/dist/meta.yml index e0827c1be6d8..3b7ce0ad6c73 100644 --- a/modules/nf-core/mash/dist/meta.yml +++ b/modules/nf-core/mash/dist/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: FASTA, FASTQ or Mash sketch - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" - - query: - type: file - description: FASTA, FASTQ or Mash sketch - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: FASTA, FASTQ or Mash sketch + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" + - - reference: + type: file + description: FASTA, FASTQ or Mash sketch + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz,msh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - dist: - type: file - description: The results from mash dist - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The results from mash dist + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mash/screen/meta.yml b/modules/nf-core/mash/screen/meta.yml index 9b482bef1587..751cfd06cd89 100644 --- a/modules/nf-core/mash/screen/meta.yml +++ b/modules/nf-core/mash/screen/meta.yml @@ -13,34 +13,41 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query: - type: file - description: Query sequences - pattern: "*.fastq.gz" - - sequence_sketch: - type: file - description: Sequence files to match against - pattern: "*.msh" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query: + type: file + description: Query sequences + pattern: "*.fastq.gz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequences_sketch: + type: file + description: sketch file of sequences output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - screen: - type: file - description: List of sequences from fastx_db similar to query sequences - pattern: "*.screen" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.screen": + type: file + description: List of sequences from fastx_db similar to query sequences + pattern: "*.screen" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/mash/sketch/meta.yml b/modules/nf-core/mash/sketch/meta.yml index ac23657258c1..f253717dc138 100644 --- a/modules/nf-core/mash/sketch/meta.yml +++ b/modules/nf-core/mash/sketch/meta.yml @@ -16,33 +16,42 @@ tools: tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] + identifier: biotools:mash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mash: - type: file - description: Sketch output - pattern: "*.{mash}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.msh": + type: file + description: Sketch output + pattern: "*.{mash}" - stats: - type: file - description: Sketch statistics - pattern: "*.{mash_stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mash_stats": + type: file + description: Sketch statistics + pattern: "*.{mash_stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@thanhleviet" maintainers: diff --git a/modules/nf-core/mashmap/meta.yml b/modules/nf-core/mashmap/meta.yml index f9a608c8affb..f53cd79130af 100644 --- a/modules/nf-core/mashmap/meta.yml +++ b/modules/nf-core/mashmap/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mashmap" -description: Mashmap is an approximate long read or contig mapper based on Jaccard similarity +description: Mashmap is an approximate long read or contig mapper based on Jaccard + similarity keywords: - mapper - aligner @@ -15,41 +15,43 @@ tools: tool_dev_url: "https://github.com/marbl/MashMap" doi: "10.1007/978-3-319-56970-3_5" licence: ["Public Domain"] + identifier: biotools:mashmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - - reference: - type: file - description: Input fasta file containing reference sequences - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reference: + type: file + description: Input fasta file containing reference sequences + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mberacochea" diff --git a/modules/nf-core/mashtree/meta.yml b/modules/nf-core/mashtree/meta.yml index e110fc45d1e7..56d1e422587e 100644 --- a/modules/nf-core/mashtree/meta.yml +++ b/modules/nf-core/mashtree/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: https://github.com/lskatz/mashtree doi: "10.21105/joss.01762" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTA, FASTQ, GenBank, or Mash sketch files - pattern: "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTA, FASTQ, GenBank, or Mash sketch files + pattern: "*.{fna,fna.gz,fasta,fasta.gz,fa,fa.gz,gbk,gbk.gz,fastq.gz,msh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tree: - type: file - description: A Newick formatted tree file - pattern: "*.{dnd}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dnd": + type: file + description: A Newick formatted tree file + pattern: "*.{dnd}" - matrix: - type: file - description: A TSV matrix of pair-wise Mash distances - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV matrix of pair-wise Mash distances + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/maxbin2/meta.yml b/modules/nf-core/maxbin2/meta.yml index 65535c387658..6b5a98c766d8 100644 --- a/modules/nf-core/maxbin2/meta.yml +++ b/modules/nf-core/maxbin2/meta.yml @@ -11,67 +11,118 @@ keywords: - contigs tools: - maxbin2: - description: MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. + description: MaxBin is software for binning assembled metagenomic sequences based + on an Expectation-Maximization algorithm. homepage: https://sourceforge.net/projects/maxbin/ documentation: https://sourceforge.net/projects/maxbin/ tool_dev_url: https://sourceforge.net/projects/maxbin/ doi: "10.1093/bioinformatics/btv638" licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - contigs: - type: file - description: Multi FASTA file containing assembled contigs of a given sample - pattern: "*.fasta" - - reads: - type: file - description: Reads used to assemble contigs in FASTA or FASTQ format. Do not supply at the same time as abundance files. - pattern: "*.fasta" - - abund: - type: file - description: Contig abundance files, i.e. reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs: + type: file + description: Multi FASTA file containing assembled contigs of a given sample + pattern: "*.fasta" + - reads: + type: file + description: Reads used to assemble contigs in FASTA or FASTQ format. Do not + supply at the same time as abundance files. + pattern: "*.fasta" + - abund: + type: file + description: Contig abundance files, i.e. reads against each contig. See MaxBin2 + README for details. Do not supply at the same time as read files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - binned_fastas: - type: file - description: Binned contigs, one per bin designated with numeric IDs - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Binned contigs, one per bin designated with numeric IDs + pattern: "*.fasta.gz" - summary: - type: file - description: Summary file describing which contigs are being classified into which bin - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary": + type: file + description: Summary file describing which contigs are being classified into + which bin + pattern: "*.summary" - log: - type: file - description: Log file recording the core steps of MaxBin algorithm - pattern: "*.log.gz" - - marker: - type: file - description: Marker gene presence numbers for each bin - pattern: "*.marker.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log.gz": + type: file + description: Log file recording the core steps of MaxBin algorithm + pattern: "*.log.gz" + - marker_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.marker.gz": + type: file + description: Marker counts + pattern: "*.marker.gz" - unbinned_fasta: - type: file - description: All sequences that pass the minimum length threshold but are not classified successfully. - pattern: "*.noclass.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.noclass.gz": + type: file + description: All sequences that pass the minimum length threshold but are not + classified successfully. + pattern: "*.noclass.gz" - tooshort_fasta: - type: file - description: All sequences that do not meet the minimum length threshold. - pattern: "*.tooshort.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tooshort.gz": + type: file + description: All sequences that do not meet the minimum length threshold. + pattern: "*.tooshort.gz" + - marker_bins: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bin.tar.gz": - marker_genes: - type: file - description: All sequences that do not meet the minimum length threshold. - pattern: "*.marker_of_each_gene.tar.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_gene.tar.gz": + type: file + description: Marker genes + pattern: "*_gene.tar.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/maxquant/lfq/meta.yml b/modules/nf-core/maxquant/lfq/meta.yml index 634f70eafd65..ad60199f120b 100644 --- a/modules/nf-core/maxquant/lfq/meta.yml +++ b/modules/nf-core/maxquant/lfq/meta.yml @@ -1,47 +1,51 @@ name: maxquant_lfq -description: Run standard proteomics data analysis with MaxQuant, mostly dedicated to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" +description: Run standard proteomics data analysis with MaxQuant, mostly dedicated + to label-free. Paths to fasta and raw files needs to be marked by "PLACEHOLDER" keywords: - sort - proteomics - mass-spectroscopy tools: - maxquant: - description: MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. License restricted. + description: MaxQuant is a quantitative proteomics software package designed for + analyzing large mass-spectrometric data sets. License restricted. homepage: https://www.maxquant.org/ documentation: http://coxdocs.org/doku.php?id=maxquant:start licence: ["http://www.coxdocs.org/lib/exe/fetch.php?media=license_agreement.pdf"] + identifier: biotools:maxquant input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - raw: - type: file - description: raw files with mass spectra - pattern: "*.{raw,RAW,Raw}" - - fasta: - type: file - description: fasta file with protein sequences - pattern: "*.{fasta}" - - parfile: - type: file - description: MaxQuant parameter file (XML) - pattern: "*.{xml}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file with protein sequences + pattern: "*.{fasta}" + - paramfile: + type: file + description: MaxQuant parameter file + - - raw: + type: file + description: raw files with mass spectra + pattern: "*.{raw,RAW,Raw}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - maxquant_txt: - type: file - description: tables with peptides and protein information - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: tables with peptides and protein information + pattern: "*.{txt}" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@veitveit" maintainers: diff --git a/modules/nf-core/mcquant/meta.yml b/modules/nf-core/mcquant/meta.yml index 1423074bddbe..76ef8ac3396f 100644 --- a/modules/nf-core/mcquant/meta.yml +++ b/modules/nf-core/mcquant/meta.yml @@ -1,5 +1,6 @@ name: "mcquant" -description: Mcquant extracts single-cell data given a multi-channel image and a segmentation mask. +description: Mcquant extracts single-cell data given a multi-channel image and a segmentation + mask. keywords: - quantification - image_analysis @@ -7,54 +8,58 @@ keywords: - highly_multiplexed_imaging tools: - "mcquant": - description: "Module for single-cell data extraction given a segmentation mask and multi-channel image. The CSV structure is aligned with histoCAT output." + description: "Module for single-cell data extraction given a segmentation mask + and multi-channel image. The CSV structure is aligned with histoCAT output." homepage: "https://github.com/labsyspharm/quantification" documentation: "https://github.com/labsyspharm/quantification/blob/master/README.md" tool_dev_url: "https://github.com/labsyspharm/quantification" doi: 10.1038/s41592-021-01308-y licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - image: - type: file - description: Multi-channel image file - pattern: "*.{tiff,tif,h5,hdf5}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mask: - type: file - description: Labeled segmentation mask for image - pattern: "*.{tiff,tif,h5,hdf5}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - markerfile: - type: file - description: Marker file with channel names for image to quantify - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - image: + type: file + description: Multi-channel image file + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mask: + type: file + description: Labeled segmentation mask for image + pattern: "*.{tiff,tif,h5,hdf5}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - markerfile: + type: file + description: Marker file with channel names for image to quantify + pattern: "*.{csv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Quantified regionprops_table - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Quantified regionprops_table + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mcroni/meta.yml b/modules/nf-core/mcroni/meta.yml index 570a9cca160d..0a1f3fc4d040 100644 --- a/modules/nf-core/mcroni/meta.yml +++ b/modules/nf-core/mcroni/meta.yml @@ -6,39 +6,49 @@ keywords: - mcr-1 tools: - "mcroni": - description: "Scripts for finding and processing promoter variants upstream of mcr-1" + description: "Scripts for finding and processing promoter variants upstream of + mcr-1" homepage: "https://github.com/liampshaw/mcroni" documentation: "https://github.com/liampshaw/mcroni" tool_dev_url: "https://github.com/liampshaw/mcroni" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A fasta file. - pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A fasta file. + pattern: "*.{fasta.gz,fasta,fa.gz,fa,fna.gz,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: mcroni results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: mcroni results in TSV format + pattern: "*.tsv" - fa: - type: file - description: mcr-1 matching sequences - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa": + type: file + description: mcr-1 matching sequences + pattern: "*.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mcstaging/imc2mc/meta.yml b/modules/nf-core/mcstaging/imc2mc/meta.yml index 6dbbc29f73f0..ee596f61f5eb 100644 --- a/modules/nf-core/mcstaging/imc2mc/meta.yml +++ b/modules/nf-core/mcstaging/imc2mc/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mcstaging_imc2mc" -description: Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files to .tif files with OME-XML metadata. Includes optional hot pixel removal. +description: Staging module for MCMICRO transforming Imaging Mass Cytometry .txt files + to .tif files with OME-XML metadata. Includes optional hot pixel removal. keywords: - imaging - ome-tif @@ -14,38 +14,36 @@ tools: documentation: "https://github.com/SchapiroLabor/imc2mc/README.md" tool_dev_url: "https://github.com/SchapiroLabor/imc2mc" licence: ["GPL-3.0 license"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - txtfile: - type: file - description: Acquisition .txt file - pattern: "*.{txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - txtfile: + type: file + description: Acquisition .txt file + pattern: "*.{txt}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tif: - type: file - description: One output .tif file containing acquisition and metadata - pattern: "*.{tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tif": + type: file + description: One output .tif file containing acquisition and metadata + pattern: "*.{tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MargotCh" maintainers: diff --git a/modules/nf-core/mcstaging/phenoimager2mc/meta.yml b/modules/nf-core/mcstaging/phenoimager2mc/meta.yml index 2e387a896219..8c3fab20a96a 100644 --- a/modules/nf-core/mcstaging/phenoimager2mc/meta.yml +++ b/modules/nf-core/mcstaging/phenoimager2mc/meta.yml @@ -1,6 +1,7 @@ # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mcstaging_phenoimager2mc" -description: Staging module for MCMICRO transforming PhenoImager .tif files into stacked and normalized ome-tif files per cycle, compatible as ASHLAR input. +description: Staging module for MCMICRO transforming PhenoImager .tif files into stacked + and normalized ome-tif files per cycle, compatible as ASHLAR input. keywords: - imaging - registration @@ -14,36 +15,34 @@ tools: documentation: "https://github.com/SchapiroLabor/phenoimager2mc/README.md" tool_dev_url: "https://github.com/SchapiroLabor/phenoimager2mc" licence: ["GPL-2.0 license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - tiles: - type: list - description: Folder or list with .tif files of one cycle from PhenoImager - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tiles: + type: list + description: Folder or list with .tif files of one cycle from PhenoImager output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - tif: - type: file - description: One output .tif file containing concatenated tiles of the cycle. - pattern: "*.{tif,tiff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tif": + type: file + description: One output .tif file containing concatenated tiles of the cycle. + pattern: "*.{tif,tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chiarasch" maintainers: diff --git a/modules/nf-core/md5sum/meta.yml b/modules/nf-core/md5sum/meta.yml index 1659ae7007a5..363d763faf2e 100644 --- a/modules/nf-core/md5sum/meta.yml +++ b/modules/nf-core/md5sum/meta.yml @@ -10,30 +10,38 @@ tools: homepage: "https://www.gnu.org" documentation: "https://man7.org/linux/man-pages/man1/md5sum.1.html" licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files: - type: file - description: Any number of files. One md5sum file will be generated for each. - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files: + type: file + description: Any number of files. One md5sum file will be generated for each. + pattern: "*.*" + - - as_separate_files: + type: boolean + description: | + If true, each file will have its own md5sum file. If false, all files will be + checksummed into a single md5sum file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checksum: - type: file - description: File containing checksum - pattern: "*.md5" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.md5": + type: file + description: File containing checksum + pattern: "*.md5" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/medaka/meta.yml b/modules/nf-core/medaka/meta.yml index 9ed3589dd5e0..d267488c9b11 100644 --- a/modules/nf-core/medaka/meta.yml +++ b/modules/nf-core/medaka/meta.yml @@ -1,5 +1,6 @@ name: medaka -description: A tool to create consensus sequences and variant calls from nanopore sequencing data +description: A tool to create consensus sequences and variant calls from nanopore + sequencing data keywords: - assembly - polishing @@ -11,34 +12,37 @@ tools: documentation: https://nanoporetech.github.io/medaka/index.html tool_dev_url: https://github.com/nanoporetech/medaka licence: ["Mozilla Public License 2.0"] + identifier: biotools:medaka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input nanopore fasta/FastQ files - pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" - - assembly: - type: file - description: Genome assembly - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input nanopore fasta/FastQ files + pattern: "*.{fasta,fa,fastq,fastq.gz,fq,fq.gz}" + - assembly: + type: file + description: Genome assembly + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly: - type: file - description: Polished genome assembly - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: Polished genome assembly + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/megahit/meta.yml b/modules/nf-core/megahit/meta.yml index 656f4f8ac172..04dab4c22f61 100644 --- a/modules/nf-core/megahit/meta.yml +++ b/modules/nf-core/megahit/meta.yml @@ -8,69 +8,106 @@ keywords: - metagenomics tools: - megahit: - description: "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph" + description: "An ultra-fast single-node solution for large and complex metagenomics + assembly via succinct de Bruijn graph" homepage: https://github.com/voutcn/megahit documentation: https://github.com/voutcn/megahit tool_dev_url: https://github.com/voutcn/megahit doi: "10.1093/bioinformatics/btv033" licence: ["GPL v3"] args_id: "$args" + identifier: biotools:megahit - pigz: description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" args_id: "$args2" + identifier: biotools:megahit input: - - meta: - type: map - description: | - Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) - e.g. [ id:'test', single_end:false ] - - reads1: - type: file - description: | - A single or list of input FastQ files for single-end or R1 of paired-end library(s), - respectively in gzipped or uncompressed FASTQ or FASTA format. - - reads2: - type: file - description: | - A single or list of input FastQ files for R2 of paired-end library(s), - respectively in gzipped or uncompressed FASTQ or FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information and input single, or paired-end FASTA/FASTQ files (optionally decompressed) + e.g. [ id:'test', single_end:false ] + - reads1: + type: file + description: | + A single or list of input FastQ files for single-end or R1 of paired-end library(s), + respectively in gzipped or uncompressed FASTQ or FASTA format. + - reads2: + type: file + description: | + A single or list of input FastQ files for R2 of paired-end library(s), + respectively in gzipped or uncompressed FASTQ or FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: Final final contigs result of the assembly in FASTA format. - pattern: "*.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fa.gz": + type: file + description: Final final contigs result of the assembly in FASTA format. + pattern: "*.contigs.fa.gz" - k_contigs: - type: file - description: Contigs assembled from the de Bruijn graph of order-K - pattern: "k*.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.contigs.fa.gz: + type: file + description: Contigs assembled from the de Bruijn graph of order-K + pattern: "k*.contigs.fa.gz" - addi_contigs: - type: file - description: Contigs assembled after iteratively removing local low coverage unitigs in the de Bruijn graph of order-K - pattern: "k*.addi.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.addi.fa.gz: + type: file + description: Contigs assembled after iteratively removing local low coverage + unitigs in the de Bruijn graph of order-K + pattern: "k*.addi.fa.gz" - local_contigs: - type: file - description: Contigs of the locally assembled contigs for k=K - pattern: "k*.local.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.local.fa.gz: + type: file + description: Contigs of the locally assembled contigs for k=K + pattern: "k*.local.fa.gz" - kfinal_contigs: - type: file - description: Stand-alone contigs for k=K; if local assembly is turned on, the file will be empty - pattern: "k*.final.contigs.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intermediate_contigs/k*.final.contigs.fa.gz: + type: file + description: Stand-alone contigs for k=K; if local assembly is turned on, the + file will be empty + pattern: "k*.final.contigs.fa.gz" - log: - type: file - description: Log file containing statistics of the assembly output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing statistics of the assembly output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/megan/daa2info/meta.yml b/modules/nf-core/megan/daa2info/meta.yml index 5b1c7e366389..a38bb0986b48 100644 --- a/modules/nf-core/megan/daa2info/meta.yml +++ b/modules/nf-core/megan/daa2info/meta.yml @@ -14,37 +14,46 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: ["GPL >=3"] + identifier: biotools:megan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - daa: - type: file - description: DAA file from DIAMOND - pattern: "*.daa" - - megan_summary: - type: boolean - description: Specify whether to generate a MEGAN summary file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - daa: + type: file + description: DAA file from DIAMOND + pattern: "*.daa" + - - megan_summary: + type: boolean + description: Specify whether to generate a MEGAN summary file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt_gz: - type: file - description: Compressed text file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Compressed text file + pattern: "*.txt.gz" - megan: - type: file - description: Optionally generated MEGAN summary file - pattern: "*.megan" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.megan": + type: file + description: Optionally generated MEGAN summary file + pattern: "*.megan" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/megan/rma2info/meta.yml b/modules/nf-core/megan/rma2info/meta.yml index 158c86742fac..3cd0facc3fee 100644 --- a/modules/nf-core/megan/rma2info/meta.yml +++ b/modules/nf-core/megan/rma2info/meta.yml @@ -13,37 +13,46 @@ tools: tool_dev_url: "https://github.com/husonlab/megan-ce" doi: "10.1371/journal.pcbi.1004957" licence: ["GPL >=3"] + identifier: biotools:megan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rma6: - type: file - description: RMA6 file from MEGAN or MALT - pattern: "*.rma6" - - megan_summary: - type: boolean - description: Specify whether to generate an MEGAN summary file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rma6: + type: file + description: RMA6 file from MEGAN or MALT + pattern: "*.rma6" + - - megan_summary: + type: boolean + description: Specify whether to generate an MEGAN summary file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Compressed text file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Compressed text file + pattern: "*.txt.gz" - megan_summary: - type: file - description: Optionally generated MEGAN summary file - pattern: "*.megan" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.megan": + type: file + description: Optionally generated MEGAN summary file + pattern: "*.megan" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/meningotype/meta.yml b/modules/nf-core/meningotype/meta.yml index 9bb624a9ea97..7fe755ab6907 100644 --- a/modules/nf-core/meningotype/meta.yml +++ b/modules/nf-core/meningotype/meta.yml @@ -6,35 +6,39 @@ keywords: - serotype tools: - meningotype: - description: In silico serotyping and finetyping (porA and fetA) of Neisseria meningitidis + description: In silico serotyping and finetyping (porA and fetA) of Neisseria + meningitidis homepage: https://github.com/MDU-PHL/meningotype documentation: https://github.com/MDU-PHL/meningotype tool_dev_url: https://github.com/MDU-PHL/meningotype licence: ["GPL v3"] + identifier: biotools:meningotype input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/merfin/hist/meta.yml b/modules/nf-core/merfin/hist/meta.yml index a2c80d06a9ce..f9064cc106da 100644 --- a/modules/nf-core/merfin/hist/meta.yml +++ b/modules/nf-core/merfin/hist/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "merfin_hist" -description: Compare k-mer frequency in reads and assembly to devise the metrics K* and QV* +description: Compare k-mer frequency in reads and assembly to devise the metrics K* + and QV* keywords: - assembly - evaluation @@ -9,71 +9,76 @@ keywords: - completeness tools: - "merfin": - description: "Merfin (k-mer based finishing tool) is a suite of subtools to variant filtering, assembly evaluation and polishing via k-mer validation. The subtool -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) for each scaffold/contig and genome-wide averages. In addition, Merfin produces a QV* estimate, which accounts also for kmers that are seen in excess with respect to their expected multiplicity predicted from the reads." + description: "Merfin (k-mer based finishing tool) is a suite of subtools to variant + filtering, assembly evaluation and polishing via k-mer validation. The subtool + -hist estimates the QV (quality value of [Merqury](https://github.com/marbl/merqury)) + for each scaffold/contig and genome-wide averages. In addition, Merfin produces + a QV* estimate, which accounts also for kmers that are seen in excess with respect + to their expected multiplicity predicted from the reads." homepage: "https://github.com/arangrhie/merfin" documentation: "https://github.com/arangrhie/merfin/wiki/Best-practices-for-Merfin" doi: "10.1038/s41592-022-01445-y" licence: ["Apache-2.0"] + identifier: biotools:merfin input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fasta_assembly: - type: file - description: Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED] - pattern: "*.{fasta, fasta.gz}" - - - meta1: - type: map - description: | - Groovy Map containing sample read information - e.g. `[ id:'sample1', single_end:false ]` - - - meryl_db_reads: - type: file - description: K-mer database produced from raw reads using Meryl [REQUIRED] - pattern: "*.{meryl_db}" - - - lookup_table: - type: file - description: Input vector of k-mer probabilities (obtained by genomescope2 with parameter --fitted_hist) [OPTIONAL] - pattern: "lookup_table.txt" - - - seqmers: - type: file - description: Input for pre-built sequence meryl db. By default, the sequence meryl db will be generated from the input genome assembly [OPTIONAL] - pattern: "*.{meryl_db}" - - - peak: - type: float - description: Input to hard set copy 1 and infer multiplicity to copy number. Can be calculated using genomescope2 [REQUIRED] - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta_assembly: + type: file + description: Genome assembly in FASTA; uncompressed, gz compressed [REQUIRED] + pattern: "*.{fasta, fasta.gz}" + - - meta1: + type: map + description: | + Groovy Map containing sample read information + e.g. `[ id:'sample1', single_end:false ]` + - meryl_db_reads: + type: file + description: K-mer database produced from raw reads using Meryl [REQUIRED] + pattern: "*.{meryl_db}" + - - lookup_table: + type: file + description: Input vector of k-mer probabilities (obtained by genomescope2 with + parameter --fitted_hist) [OPTIONAL] + pattern: "lookup_table.txt" + - - seqmers: + type: file + description: Input for pre-built sequence meryl db. By default, the sequence + meryl db will be generated from the input genome assembly [OPTIONAL] + pattern: "*.{meryl_db}" + - - peak: + type: float + description: Input to hard set copy 1 and infer multiplicity to copy number. + Can be calculated using genomescope2 [REQUIRED] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - hist: - type: file - description: The generated 0-centered k* histogram for sequences in . Positive k* values are expected collapsed copies. Negative k* values are expected expanded copies. Closer to 0 means the expected and found k-mers are well balenced, 1:1. - pattern: "*.{hist}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.hist": + type: file + description: The generated 0-centered k* histogram for sequences in . + Positive k* values are expected collapsed copies. Negative k* values are expected + expanded copies. Closer to 0 means the expected and found k-mers are well + balenced, 1:1. + pattern: "*.{hist}" - log_stderr: - type: file - description: Log (stderr) of hist tool execution. The QV and QV* metrics are reported at the end. - pattern: "*.{hist.stderr.log}" - + - "*.hist.stderr.log": + type: file + description: Log (stderr) of hist tool execution. The QV and QV* metrics are + reported at the end. + pattern: "*.{hist.stderr.log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rodtheo" maintainers: diff --git a/modules/nf-core/merqury/hapmers/meta.yml b/modules/nf-core/merqury/hapmers/meta.yml index 6693f540e7f0..2c37d3acf761 100644 --- a/modules/nf-core/merqury/hapmers/meta.yml +++ b/modules/nf-core/merqury/hapmers/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "merqury_hapmers" description: A script to generate hap-mer dbs for trios @@ -13,57 +12,85 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["United States Government Work"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - child_meryl: - type: directory - description: Childs' k-mers (all, from WGS reads) - pattern: "*.meryl" - - maternal_meryl: - type: directory - description: Haplotype1 k-mers (all, ex. maternal) - pattern: "*.meryl" - - paternal_meryl: - type: directory - description: Haplotype2 k-mers (all, ex. paternal) - pattern: "*.meryl" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - child_meryl: + type: directory + description: Childs' k-mers (all, from WGS reads) + pattern: "*.meryl" + - - maternal_meryl: + type: directory + description: Haplotype1 k-mers (all, ex. maternal) + pattern: "*.meryl" + - - paternal_meryl: + type: directory + description: Haplotype2 k-mers (all, ex. paternal) + pattern: "*.meryl" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mat_hapmer_meryl: - type: directory - description: Inherited maternal hap-mer dbs - pattern: "*_mat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_mat.hapmer.meryl": + type: directory + description: Inherited maternal hap-mer dbs + pattern: "*_mat.hapmer.meryl" - pat_hapmer_meryl: - type: directory - description: Inherited paternal hap-mer dbs - pattern: "*_pat.hapmer.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_pat.hapmer.meryl": + type: directory + description: Inherited paternal hap-mer dbs + pattern: "*_pat.hapmer.meryl" - inherited_hapmers_fl_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.fl.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.fl.png" - inherited_hapmers_ln_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.ln.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.ln.png" - inherited_hapmers_st_png: - type: file - description: k-mer distribution of the inherited dbs and cutoffs used to generate hap-mer dbs - pattern: "*_inherited_hapmers.st.png" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_inherited_hapmers.st.png": + type: file + description: k-mer distribution of the inherited dbs and cutoffs used to generate + hap-mer dbs + pattern: "*_inherited_hapmers.st.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/merqury/merqury/meta.yml b/modules/nf-core/merqury/merqury/meta.yml index 19cb11b38f4a..7e8d875a66d2 100644 --- a/modules/nf-core/merqury/merqury/meta.yml +++ b/modules/nf-core/merqury/merqury/meta.yml @@ -10,92 +10,187 @@ tools: tool_dev_url: "https://github.com/marbl/merqury" doi: "10.1186/s13059-020-02134-9" licence: ["PUBLIC DOMAIN"] + identifier: biotools:merqury input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_db: - type: file - description: "Meryl read database" - - assembly: - type: file - description: FASTA assembly file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_db: + type: file + description: "Meryl read database" + - assembly: + type: file + description: FASTA assembly file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly_only_kmers_bed: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .bed" - pattern: "*_only.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.bed": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .bed" + pattern: "*_only.bed" - assembly_only_kmers_wig: - type: file - description: "The positions of the k-mers found only in an assembly for further investigation in .wig" - pattern: "*_only.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_only.wig": + type: file + description: "The positions of the k-mers found only in an assembly for further + investigation in .wig" + pattern: "*_only.wig" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.completeness.stats": + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - dist_hist: - type: file - description: Histogram - pattern: "*.dist_only.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dist_only.hist": + type: file + description: Histogram + pattern: "*.dist_only.hist" - spectra_cn_fl_png: - type: file - description: "Unstacked copy number spectra filled plot in PNG format" - pattern: "*.spectra-cn.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.fl.png": + type: file + description: "Unstacked copy number spectra filled plot in PNG format" + pattern: "*.spectra-cn.fl.png" + - spectra_cn_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.hist": + type: file + description: "Copy number spectra histogram" + pattern: "*.spectra-cn.hist" - spectra_cn_ln_png: - type: file - description: "Unstacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.ln.png": + type: file + description: "Unstacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.ln.png" - spectra_cn_st_png: - type: file - description: "Stacked copy number spectra line plot in PNG format" - pattern: "*.spectra-cn.st.png" - - spectra_cn_hist: - type: file - description: "Copy number spectra histogram" - pattern: "*.spectra-cn.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-cn.st.png": + type: file + description: "Stacked copy number spectra line plot in PNG format" + pattern: "*.spectra-cn.st.png" - spectra_asm_fl_png: - type: file - description: "Unstacked assembly spectra filled plot in PNG format" - pattern: "*.spectra-asm.fl.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.fl.png": + type: file + description: "Unstacked assembly spectra filled plot in PNG format" + pattern: "*.spectra-asm.fl.png" + - spectra_asm_hist: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.hist": + type: file + description: "Assembly spectra histogram" + pattern: "*.spectra-asm.hist" - spectra_asm_ln_png: - type: file - description: "Unstacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.ln.png": + type: file + description: "Unstacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.ln.png" - spectra_asm_st_png: - type: file - description: "Stacked assembly spectra line plot in PNG format" - pattern: "*.spectra-asm.st.png" - - spectra_asm_hist: - type: file - description: "Assembly spectra histogram" - pattern: "*.spectra-asm.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spectra-asm.st.png": + type: file + description: "Stacked assembly spectra line plot in PNG format" + pattern: "*.spectra-asm.st.png" - assembly_qv: - type: file - description: "Assembly consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "Assembly consensus quality estimation" + pattern: "*.qv" - scaffold_qv: - type: file - description: "Scaffold consensus quality estimation" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "Scaffold consensus quality estimation" + pattern: "*.qv" - read_ploidy: - type: file - description: "Ploidy estimate from read k-mer database" - pattern: "*.hist.ploidy" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist.ploidy": + type: file + description: "Ploidy estimate from read k-mer database" + pattern: "*.hist.ploidy" - hapmers_blob_png: - type: file - description: "Hap-mer blob plot" - pattern: "*.hapmers.blob.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hapmers.blob.png": + type: file + description: "Hap-mer blob plot" + pattern: "*.hapmers.blob.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/katcomp/meta.yml b/modules/nf-core/merquryfk/katcomp/meta.yml index 15de42949747..f629c2a0f689 100644 --- a/modules/nf-core/merquryfk/katcomp/meta.yml +++ b/modules/nf-core/merquryfk/katcomp/meta.yml @@ -10,62 +10,95 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk1_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk1_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - fastk2_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk2_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk1_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk1_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" + - fastk2_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk2_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in filled PNG format. - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in filled PNG format. + pattern: "*.fi.png" - line_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in line PNG format. - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in line PNG format. + pattern: "*.ln.png" - stacked_png: - type: file - description: Comparison of Kmers between sample 1 and 2 in stacked PNG format. - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: Comparison of Kmers between sample 1 and 2 in stacked PNG format. + pattern: "*.st.png" - filled_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in filled PDF format. - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in filled PDF format. + pattern: "*.fi.pdf" - line_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in line PDF format. - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in line PDF format. + pattern: "*.ln.pdf" - stacked_pdf: - type: file - description: Comparison of Kmers between sample 1 and 2 in stacked PDF format. - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: Comparison of Kmers between sample 1 and 2 in stacked PDF format. + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/katgc/meta.yml b/modules/nf-core/merquryfk/katgc/meta.yml index f3689b0370c9..0d553d5c2c0e 100644 --- a/modules/nf-core/merquryfk/katgc/meta.yml +++ b/modules/nf-core/merquryfk/katgc/meta.yml @@ -11,54 +11,87 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" license: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: ktab files from the program FastK - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: ktab files from the program FastK + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_gc_plot_png: - type: file - description: A filled GC content plot in PNG format - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: A filled GC content plot in PNG format + pattern: "*.fi.png" - filled_gc_plot_pdf: - type: file - description: A filled GC content plot in PDF format - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: A filled GC content plot in PDF format + pattern: "*.fi.pdf" - line_gc_plot_png: - type: file - description: A line GC content plot in PNG format - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: A line GC content plot in PNG format + pattern: "*.ln.png" - line_gc_plot_pdf: - type: file - description: A line GC content plot in PDF format - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: A line GC content plot in PDF format + pattern: "*.ln.pdf" - stacked_gc_plot_png: - type: file - description: A stacked GC content plot in PNG format - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: A stacked GC content plot in PNG format + pattern: "*.st.png" - stacked_gc_plot_pdf: - type: file - description: A stacked GC content plot in PDF format - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: A stacked GC content plot in PDF format + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/merquryfk/merquryfk/meta.yml b/modules/nf-core/merquryfk/merquryfk/meta.yml index bba26d12411a..82bfbec46534 100644 --- a/modules/nf-core/merquryfk/merquryfk/meta.yml +++ b/modules/nf-core/merquryfk/merquryfk/meta.yml @@ -10,110 +10,205 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: Histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - matktab: - type: file - description: trio maternal histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - patktab: - type: file - description: trio paternal histogram ktab files from the program FastK (option -t) - pattern: "*.ktab*" - - assembly: - type: file - description: Genome (primary) assembly files (fasta format) - pattern: ".fasta" - - haplotigs: - type: file - description: Assembly haplotigs (fasta format) - pattern: ".fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: Histogram ktab files from the program FastK (option -t) + pattern: "*.ktab*" + - assembly: + type: file + description: Genome (primary) assembly files (fasta format) + pattern: ".fasta" + - haplotigs: + type: file + description: Assembly haplotigs (fasta format) + pattern: ".fasta" + - - matktab: + type: file + description: trio maternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" + - - patktab: + type: file + description: trio paternal histogram ktab files from the program FastK (option + -t) + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Assembly statistics file - pattern: "*.completeness.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.completeness.stats: + type: file + description: Assembly statistics file + pattern: "*.completeness.stats" - bed: - type: file - description: Assembly only kmer positions not supported by reads in bed format - pattern: "*_only.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*_only.bed: + type: file + description: Assembly only kmer positions not supported by reads in bed format + pattern: "*_only.bed" + - assembly_qv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.qv: + type: file + description: "error and qv table for each scaffold of the assembly" + pattern: "*.qv" - spectra_cn_fl: - type: file - description: "Unstacked copy number spectra filled plot in PNG or PDF format" - pattern: "*.spectra-cn.fl.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.fl.{png,pdf}: + type: file + description: "Unstacked copy number spectra filled plot in PNG or PDF format" + pattern: "*.spectra-cn.fl.{png,pdf}" - spectra_cn_ln: - type: file - description: "Unstacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.ln.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.ln.{png,pdf}: + type: file + description: "Unstacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.ln.{png,pdf}" - spectra_cn_st: - type: file - description: "Stacked copy number spectra line plot in PNG or PDF format" - pattern: "*.spectra-cn.st.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.*.spectra-cn.st.{png,pdf}: + type: file + description: "Stacked copy number spectra line plot in PNG or PDF format" + pattern: "*.spectra-cn.st.{png,pdf}" + - qv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.qv: + type: file + description: "error and qv of each assembly as a whole" + pattern: "*.qv" - spectra_asm_fl: - type: file - description: "Unstacked assembly spectra filled plot in PNG or PDF format" - pattern: "*.spectra-asm.fl.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.fl.{png,pdf}: + type: file + description: "Unstacked assembly spectra filled plot in PNG or PDF format" + pattern: "*.spectra-asm.fl.{png,pdf}" - spectra_asm_ln: - type: file - description: "Unstacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.ln.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.ln.{png,pdf}: + type: file + description: "Unstacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.ln.{png,pdf}" - spectra_asm_st: - type: file - description: "Stacked assembly spectra line plot in PNG or PDF format" - pattern: "*.spectra-asm.st.{png,pdf}" - - assembly_qv: - type: file - description: "error and qv table for each scaffold of the assembly" - pattern: "*.qv" - - qv: - type: file - description: "error and qv of each assembly as a whole" - pattern: "*.qv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.spectra-asm.st.{png,pdf}: + type: file + description: "Stacked assembly spectra line plot in PNG or PDF format" + pattern: "*.spectra-asm.st.{png,pdf}" - phased_block_bed: - type: file - description: Assembly kmer positions seperated by block in bed format - pattern: "*.phased.block.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.bed: + type: file + description: Assembly kmer positions seperated by block in bed format + pattern: "*.phased.block.bed" - phased_block_stats: - type: file - description: phased assembly statistics file - pattern: "*.phased.block.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.phased_block.stats: + type: file + description: phased assembly statistics file + pattern: "*.phased.block.stats" - continuity_N: - type: file - description: "Stacked assembly N continuity plot in PNG or PDF format" - pattern: "*.continuity.N.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.continuity.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity plot in PNG or PDF format" + pattern: "*.continuity.N.{png,pdf}" - block_N: - type: file - description: "Stacked assembly N continuity by block plot in PNG or PDF format" - pattern: "*.block.N.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.N.{pdf,png}: + type: file + description: "Stacked assembly N continuity by block plot in PNG or PDF format" + pattern: "*.block.N.{png,pdf}" - block_blob: - type: file - description: "Stacked assembly block plot in PNG or PDF format" - pattern: "*.block.blob.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.block.blob.{pdf,png}: + type: file + description: "Stacked assembly block plot in PNG or PDF format" + pattern: "*.block.blob.{png,pdf}" - hapmers_blob: - type: file - description: "Stacked assembly hapmers block plot in PNG or PDF format" - pattern: "*.hapmers.blob.{png,pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.hapmers.blob.{pdf,png}: + type: file + description: "Stacked assembly hapmers block plot in PNG or PDF format" + pattern: "*.hapmers.blob.{png,pdf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" - "@yumisims" diff --git a/modules/nf-core/merquryfk/ploidyplot/meta.yml b/modules/nf-core/merquryfk/ploidyplot/meta.yml index 62fa9857b18d..ab3756efad5e 100644 --- a/modules/nf-core/merquryfk/ploidyplot/meta.yml +++ b/modules/nf-core/merquryfk/ploidyplot/meta.yml @@ -10,54 +10,87 @@ tools: homepage: "https://github.com/thegenemyers/MERQURY.FK" tool_dev_url: "https://github.com/thegenemyers/MERQURY.FK" licence: ["https://github.com/thegenemyers/MERQURY.FK/blob/main/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastk_hist: - type: file - description: A histogram files from the program FastK - pattern: "*.hist" - - fastk_ktab: - type: file - description: ktab files from the program FastK - pattern: "*.ktab*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastk_hist: + type: file + description: A histogram files from the program FastK + pattern: "*.hist" + - fastk_ktab: + type: file + description: ktab files from the program FastK + pattern: "*.ktab*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filled_ploidy_plot_png: - type: file - description: A filled ploidy plot in PNG format - pattern: "*.fi.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.png": + type: file + description: A filled ploidy plot in PNG format + pattern: "*.fi.png" - filled_ploidy_plot_pdf: - type: file - description: A filled ploidy plot in PDF format - pattern: "*.fi.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fi.pdf": + type: file + description: A filled ploidy plot in PDF format + pattern: "*.fi.pdf" - line_ploidy_plot_png: - type: file - description: A line ploidy plot in PNG format - pattern: "*.ln.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.png": + type: file + description: A line ploidy plot in PNG format + pattern: "*.ln.png" - line_ploidy_plot_pdf: - type: file - description: A lin4 ploidy plot in PDF format - pattern: "*.ln.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ln.pdf": + type: file + description: A lin4 ploidy plot in PDF format + pattern: "*.ln.pdf" - stacked_ploidy_plot_png: - type: file - description: A stacked ploidy plot in PNG format - pattern: "*.st.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.png": + type: file + description: A stacked ploidy plot in PNG format + pattern: "*.st.png" - stacked_ploidy_plot_pdf: - type: file - description: A stacked ploidy plot in PDF format - pattern: "*.st.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.st.pdf": + type: file + description: A stacked ploidy plot in PDF format + pattern: "*.st.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/count/meta.yml b/modules/nf-core/meryl/count/meta.yml index 809a32fec410..a110a6101601 100644 --- a/modules/nf-core/meryl/count/meta.yml +++ b/modules/nf-core/meryl/count/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meryl_db: - type: directory - description: A Meryl k-mer database - pattern: "*.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.meryl": + type: directory + description: A Meryl k-mer database + pattern: "*.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/histogram/meta.yml b/modules/nf-core/meryl/histogram/meta.yml index c974558c8a79..dce558ed26a4 100644 --- a/modules/nf-core/meryl/histogram/meta.yml +++ b/modules/nf-core/meryl/histogram/meta.yml @@ -11,32 +11,35 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_db: - type: directory - description: Meryl k-mer database - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_db: + type: directory + description: Meryl k-mer database + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hist: - type: file - description: Histogram of k-mers - pattern: "*.hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hist": + type: file + description: Histogram of k-mers + pattern: "*.hist" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml index 77d0784c5303..e9e1305126c5 100644 --- a/modules/nf-core/meryl/unionsum/meta.yml +++ b/modules/nf-core/meryl/unionsum/meta.yml @@ -11,32 +11,35 @@ tools: documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html" tool_dev_url: "https://github.com/marbl/meryl" licence: ["GPL"] + identifier: biotools:meryl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meryl_dbs: - type: directory - description: Meryl k-mer databases - - kvalue: - type: integer - description: An integer value of k to use as the k-mer value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - meryl_dbs: + type: directory + description: Meryl k-mer databases + - - kvalue: + type: integer + description: An integer value of k to use as the k-mer value. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meryl_db: - type: directory - description: A Meryl k-mer database that is the union sum of the input databases - pattern: "*.unionsum.meryl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unionsum.meryl": + type: directory + description: A Meryl k-mer database that is the union sum of the input databases + pattern: "*.unionsum.meryl" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml index 97aa50356bb2..0f851e554f68 100644 --- a/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml +++ b/modules/nf-core/metabat2/jgisummarizebamcontigdepths/meta.yml @@ -15,34 +15,37 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" licence: ["BSD-3-clause-LBNL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM file of reads aligned on the assembled contigs - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bam.bai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM file of reads aligned on the assembled contigs + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bam.bai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth: - type: file - description: Text file listing the coverage per contig - pattern: ".txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Text file listing the coverage per contig + pattern: ".txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/metabat2/metabat2/meta.yml b/modules/nf-core/metabat2/metabat2/meta.yml index 09306c8e7010..5d720867b49a 100644 --- a/modules/nf-core/metabat2/metabat2/meta.yml +++ b/modules/nf-core/metabat2/metabat2/meta.yml @@ -15,52 +15,79 @@ tools: tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" licence: ["BSD-3-clause-LBNL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the assembled contigs - pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}" - - depth: - type: file - description: | - Optional text file listing the coverage per contig pre-generated - by metabat2_jgisummarizebamcontigdepths - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the assembled contigs + pattern: "*.{fa,fas,fasta,fna,fa.gz,fas.gz,fasta.gz,fna.gz}" + - depth: + type: file + description: | + Optional text file listing the coverage per contig pre-generated + by metabat2_jgisummarizebamcontigdepths + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fasta: - type: file - description: Bins created from assembled contigs in fasta file - pattern: "*.fa.gz" - tooshort: - type: file - description: Contigs that did not pass length filtering - pattern: "*.tooShort.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tooShort.fa.gz": + type: file + description: Contigs that did not pass length filtering + pattern: "*.tooShort.fa.gz" - lowdepth: - type: file - description: Contigs that did not have sufficient depth for binning - pattern: "*.lowDepth.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lowDepth.fa.gz": + type: file + description: Contigs that did not have sufficient depth for binning + pattern: "*.lowDepth.fa.gz" - unbinned: - type: file - description: Contigs that pass length and depth filtering but could not be binned - pattern: "*.unbinned.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unbinned.fa.gz": + type: file + description: Contigs that pass length and depth filtering but could not be binned + pattern: "*.unbinned.fa.gz" - membership: - type: file - description: cluster memberships as a matrix format. - pattern: "*.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv.gz": + type: file + description: cluster memberships as a matrix format. + pattern: "*.tsv.gz" + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!lowDepth|tooShort|unbinned].fa.gz": + type: file + description: Bins created from assembled contigs in fasta file + pattern: "*.fa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" - "@jfy133" diff --git a/modules/nf-core/metaeuk/easypredict/meta.yml b/modules/nf-core/metaeuk/easypredict/meta.yml index 3943926ca3de..5f5012cd5160 100644 --- a/modules/nf-core/metaeuk/easypredict/meta.yml +++ b/modules/nf-core/metaeuk/easypredict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "metaeuk_easypredict" description: Annotation of eukaryotic metagenomes using MetaEuk @@ -8,51 +7,75 @@ keywords: - fasta tools: - "metaeuk": - description: "MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics" + description: "MetaEuk - sensitive, high-throughput gene discovery and annotation + for large-scale eukaryotic metagenomics" homepage: https://github.com/soedinglab/metaeuk documentation: https://github.com/soedinglab/metaeuk tool_dev_url: https://github.com/soedinglab/metaeuk doi: "10.1186/s40168-020-00808-x" licence: ["GPL v3"] + identifier: biotools:MetaEuk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide FASTA file for annotation - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - database: - type: file - description: Either a fasta file containing protein sequences, or a directory containing an mmseqs2-formatted protein database + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide FASTA file for annotation + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - database: + type: file + description: Either a fasta file containing protein sequences, or a directory + containing an mmseqs2-formatted protein database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - faa: - type: file - description: Protein FASTA file containing the exons from the input FASTA file - pattern: "*.{fas}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fas: + type: file + description: Protein FASTA file containing the exons from the input FASTA file + pattern: "*.{fas}" - codon: - type: file - description: Nucleotide FASTA file of protein-coding sequences - pattern: "*.{codon.fas}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.codon.fas: + type: file + description: Nucleotide FASTA file of protein-coding sequences + pattern: "*.{codon.fas}" - tsv: - type: file - description: TSV file containing locations of each protein coding sequence in the input fasta - pattern: "*.headersMap.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV file containing locations of each protein coding sequence in + the input fasta + pattern: "*.headersMap.{tsv}" - gff: - type: file - description: Annotation file in GFF format - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: Annotation file in GFF format + pattern: "*.{gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/metamaps/classify/meta.yml b/modules/nf-core/metamaps/classify/meta.yml index 32c3dd49a754..844adc8adef9 100644 --- a/modules/nf-core/metamaps/classify/meta.yml +++ b/modules/nf-core/metamaps/classify/meta.yml @@ -13,73 +13,110 @@ tools: tool_dev_url: https://github.com/DiltheyLab/MetaMaps doi: "10.1038/s41467-019-10934-2" licence: ["Public Domain"] + identifier: biotools:metamaps input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - classification_res: - type: file - description: Coordinates where reads map - pattern: "*.{classification_res}" - - meta_file: - type: file - description: Statistics for mapping result - pattern: "*.{classification_res.meta}" - - meta_unmappedreadsLengths: - type: file - description: Statistics for length of unmapped reads - pattern: "*.{classification_res.meta.unmappedReadsLengths}" - - para_file: - type: file - description: Log with parameters - pattern: "*.{classification_res.parameters}" - - database_folder: - type: directory - description: Path to MetaMaps database - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - classification_res: + type: file + description: Coordinates where reads map + pattern: "*.{classification_res}" + - meta_file: + type: file + description: Statistics for mapping result + pattern: "*.{classification_res.meta}" + - meta_unmappedreadsLengths: + type: file + description: Statistics for length of unmapped reads + pattern: "*.{classification_res.meta.unmappedReadsLengths}" + - para_file: + type: file + description: Log with parameters + pattern: "*.{classification_res.parameters}" + - - database_folder: + type: directory + description: Path to MetaMaps database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wimp: - type: file - description: Sample composition at different taxonomic levels - pattern: "*.{classification_res.EM.WIMP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.WIMP": + type: file + description: Sample composition at different taxonomic levels + pattern: "*.{classification_res.EM.WIMP}" - evidence_unknown_species: - type: file - description: Statistics on read identities and zero-coverage regions - pattern: "*.{classification_res.EM.evidenceUnknownSpecies}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.evidenceUnknownSpecies": + type: file + description: Statistics on read identities and zero-coverage regions + pattern: "*.{classification_res.EM.evidenceUnknownSpecies}" - reads2taxon: - type: file - description: Taxon ID assignement of reads - pattern: "*.{classification_res.EM.reads2Taxon}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.reads2Taxon": + type: file + description: Taxon ID assignement of reads + pattern: "*.{classification_res.EM.reads2Taxon}" - em: - type: file - description: The final and complete set of approximate read mappings - pattern: "*.{classification_res.EM}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM": + type: file + description: The final and complete set of approximate read mappings + pattern: "*.{classification_res.EM}" - contig_coverage: - type: file - description: Read coverage for contigs - pattern: "*.{classification_res.EM.contigCoverage}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.contigCoverage": + type: file + description: Read coverage for contigs + pattern: "*.{classification_res.EM.contigCoverage}" - length_and_id: - type: file - description: Read length and estimated identity for all reads - pattern: "*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.lengthAndIdentitiesPerMappingUnit": + type: file + description: Read length and estimated identity for all reads + pattern: "*.{classification_res.EM.lengthAndIdentitiesPerMappingUnit}" - krona: - type: file - description: Taxon ID assignement of reads in Krona format - pattern: "*.{classification_res.EM.reads2Taxon.krona}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.EM.reads2Taxon.krona": + type: file + description: Taxon ID assignement of reads in Krona format + pattern: "*.{classification_res.EM.reads2Taxon.krona}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@henningonsbring" - "@sofstam" diff --git a/modules/nf-core/metamaps/mapdirectly/meta.yml b/modules/nf-core/metamaps/mapdirectly/meta.yml index 4ac8e9403735..d3d49b1d4f3a 100644 --- a/modules/nf-core/metamaps/mapdirectly/meta.yml +++ b/modules/nf-core/metamaps/mapdirectly/meta.yml @@ -13,49 +13,68 @@ tools: tool_dev_url: https://github.com/DiltheyLab/MetaMaps doi: "10.1038/s41467-019-10934-2" licence: ["Public Domain"] + identifier: biotools:metamaps input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input fastq file containing query sequences - pattern: "*.{fq,fastq,fastq.gz,fq.gz}" - - database: - type: file - description: Database file in fasta format - pattern: "*.{fa,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input fastq file containing query sequences + pattern: "*.{fq,fastq,fastq.gz,fq.gz}" + - - database: + type: file + description: Database file in fasta format + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - classification_res: - type: file - description: Coordinates where reads map - pattern: "*.{classification_res}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res": + type: file + description: Coordinates where reads map + pattern: "*.{classification_res}" - meta_file: - type: file - description: Statistics for mapping result - pattern: "*.{classification_res.meta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.meta": + type: file + description: Statistics for mapping result + pattern: "*.{classification_res.meta}" - meta_unmappedreadsLengths: - type: file - description: Statistics for length of unmapped reads - pattern: "*.{classification_res.meta.unmappedReadsLengths}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.meta.unmappedReadsLengths": + type: file + description: Statistics for length of unmapped reads + pattern: "*.{classification_res.meta.unmappedReadsLengths}" - para_file: - type: file - description: Log with parameters - pattern: "*.{classification_res.parameters}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*classification_res.parameters": + type: file + description: Log with parameters + pattern: "*.{classification_res.parameters}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@henningonsbring" - "@sofstam" diff --git a/modules/nf-core/metaphlan/makedb/meta.yml b/modules/nf-core/metaphlan/makedb/meta.yml index d19ba30758da..d371ca64a0a2 100644 --- a/modules/nf-core/metaphlan/makedb/meta.yml +++ b/modules/nf-core/metaphlan/makedb/meta.yml @@ -7,20 +7,24 @@ keywords: - metagenomics tools: - metaphlan: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: biotools:metaphlan output: - db: - type: directory - description: Output directory containing the indexed METAPHLAN database - pattern: "*/" + - metaphlan_db_latest: + type: directory + description: Output directory containing the indexed METAPHLAN database + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml b/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml index 03aaae06f7af..7272add26e41 100644 --- a/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml +++ b/modules/nf-core/metaphlan/mergemetaphlantables/meta.yml @@ -8,35 +8,39 @@ keywords: - profiles tools: - metaphlan4: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.1038/s41587-023-01688-w" licence: ["MIT License"] + identifier: biotools:metaphlan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: List of per-sample MetaPhlAn4 taxonomic abundance tables - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: List of per-sample MetaPhlAn4 taxonomic abundance tables + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined MetaPhlAn4 table - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Combined MetaPhlAn4 table + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@LilyAnderssonLee" diff --git a/modules/nf-core/metaphlan/metaphlan/meta.yml b/modules/nf-core/metaphlan/metaphlan/meta.yml index d9be48e406e9..e1dab779117b 100644 --- a/modules/nf-core/metaphlan/metaphlan/meta.yml +++ b/modules/nf-core/metaphlan/metaphlan/meta.yml @@ -1,5 +1,6 @@ name: metaphlan_metaphlan -description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. +description: MetaPhlAn is a tool for profiling the composition of microbial communities + from metagenomic shotgun sequencing data. keywords: - metagenomics - classification @@ -8,49 +9,71 @@ keywords: - sam tools: - metaphlan: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.1038/s41587-023-01688-w" licence: ["MIT License"] + identifier: biotools:metaphlan input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Metaphlan can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out) - pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - - metaphlan_db_latest: - type: file - description: | - Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/. - Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN! - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Metaphlan can classify the metagenome from a variety of input data + types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced + SAM files (produced from alignments to the MetaPHlAn marker database) and + intermediate bowtie2 alignment files (bowtie2out) + pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" + - - metaphlan_db_latest: + type: file + description: | + Directory containing pre-downloaded and uncompressed MetaPhlAn database downloaded from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/. + Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_vJan21_TOY_CHOCOPhlAnSGB_202103') in your module.conf ext.args for METAPHLAN_METAPHLAN! + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-separated output file of the predicted taxon relative abundances - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_profile.txt": + type: file + description: Tab-separated output file of the predicted taxon relative abundances + pattern: "*.{txt}" - biom: - type: file - description: General-use format for representing biological sample by observation contingency tables - pattern: "*.{biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.biom": + type: file + description: General-use format for representing biological sample by observation + contingency tables + pattern: "*.{biom}" - bt2out: - type: file - description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 ) - pattern: "*.{bowtie2out.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bowtie2out.txt": + type: file + description: Intermediate Bowtie2 output produced from mapping the metagenome + against the MetaPHlAn marker database ( not compatible with `bowtie2out` files + generated with MetaPhlAn versions below 3 ) + pattern: "*.{bowtie2out.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" - "@LilyAnderssonLee" diff --git a/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml b/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml index ff87b4e696b4..95ae8c083a4b 100644 --- a/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml +++ b/modules/nf-core/metaphlan3/mergemetaphlantables/meta.yml @@ -8,35 +8,39 @@ keywords: - profiles tools: - metaphlan3: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: List of per-sample MetaPhlAn3 taxonomic abundance tables - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: List of per-sample MetaPhlAn3 taxonomic abundance tables + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: Combined MetaPhlAn3 table - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Combined MetaPhlAn3 table + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/metaphlan3/metaphlan3/meta.yml b/modules/nf-core/metaphlan3/metaphlan3/meta.yml index 1e64797f6121..cc521e9c42c1 100644 --- a/modules/nf-core/metaphlan3/metaphlan3/meta.yml +++ b/modules/nf-core/metaphlan3/metaphlan3/meta.yml @@ -1,5 +1,6 @@ name: metaphlan3_metaphlan3 -description: MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. +description: MetaPhlAn is a tool for profiling the composition of microbial communities + from metagenomic shotgun sequencing data. keywords: - metagenomics - classification @@ -8,49 +9,69 @@ keywords: - fasta tools: - metaphlan3: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained + from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" licence: ["MIT License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Metaphlan 3.0 can classify the metagenome from a variety of input data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced SAM files (produced from alignments to the MetaPHlAn marker database) and intermediate bowtie2 alignment files (bowtie2out) - pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" - - metaphlan_db: - type: file - description: | - Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/. - Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3! - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Metaphlan 3.0 can classify the metagenome from a variety of input + data types, including FASTQ files (single-end and paired-end), FASTA, bowtie2-produced + SAM files (produced from alignments to the MetaPHlAn marker database) and + intermediate bowtie2 alignment files (bowtie2out) + pattern: "*.{fastq.gz, fasta, fasta.gz, sam, bowtie2out.txt}" + - - metaphlan_db: + type: file + description: | + Directory containing pre-downloaded and uncompressed MetaPhlAn3 database downloaded from: http://cmprod1.cibio.unitn.it/biobakery3/metaphlan_databases/. + Note that you will also need to specify `--index` and the database version name (e.g. 'mpa_v31_CHOCOPhlAn_201901') in your module.conf ext.args for METAPHLAN3_METAPHLAN3! + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - profile: - type: file - description: Tab-separated output file of the predicted taxon relative abundances - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_profile.txt": + type: file + description: Tab-separated output file of the predicted taxon relative abundances + pattern: "*.{txt}" - biom: - type: file - description: General-use format for representing biological sample by observation contingency tables - pattern: "*.{biom}" - - bowtie2out: - type: file - description: Intermediate Bowtie2 output produced from mapping the metagenome against the MetaPHlAn marker database ( not compatible with `bowtie2out` files generated with MetaPhlAn versions below 3 ) - pattern: "*.{bowtie2out.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.biom": + type: file + description: General-use format for representing biological sample by observation + contingency tables + pattern: "*.{biom}" + - bt2out: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bowtie2out.txt": + type: file + description: Bowtie2 output file + pattern: "*.{bowtie2out.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon09" maintainers: diff --git a/modules/nf-core/methyldackel/extract/meta.yml b/modules/nf-core/methyldackel/extract/meta.yml index 7ce950c7fc04..2f17738f8311 100644 --- a/modules/nf-core/methyldackel/extract/meta.yml +++ b/modules/nf-core/methyldackel/extract/meta.yml @@ -18,46 +18,55 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bedgraph: - type: file - description: bedGraph file, containing per-base methylation metrics - pattern: "*.bedGraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file, containing per-base methylation metrics + pattern: "*.bedGraph" - methylkit: - type: file - description: methylKit file, containing per-base methylation metrics - pattern: "*.methylKit" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.methylKit": + type: file + description: methylKit file, containing per-base methylation metrics + pattern: "*.methylKit" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/methyldackel/mbias/meta.yml b/modules/nf-core/methyldackel/mbias/meta.yml index e3b55f972713..10b3dcad9033 100644 --- a/modules/nf-core/methyldackel/mbias/meta.yml +++ b/modules/nf-core/methyldackel/mbias/meta.yml @@ -19,42 +19,45 @@ tools: homepage: https://github.com/dpryan79/MethylDackel documentation: https://github.com/dpryan79/MethylDackel/blob/master/README.md licence: ["MIT"] + identifier: biotools:methyldackel input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Text file containing methylation bias - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mbias.txt": + type: file + description: Text file containing methylation bias + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/midas/run/meta.yml b/modules/nf-core/midas/run/meta.yml index e41505ebd1c0..6a7a5866015f 100644 --- a/modules/nf-core/midas/run/meta.yml +++ b/modules/nf-core/midas/run/meta.yml @@ -6,44 +6,48 @@ keywords: - abundance tools: - "midas": - description: "An integrated pipeline for estimating strain-level genomic variation from metagenomic data" + description: "An integrated pipeline for estimating strain-level genomic variation + from metagenomic data" homepage: "https://github.com/snayfach/MIDAS" documentation: "https://github.com/snayfach/MIDAS" tool_dev_url: "https://github.com/snayfach/MIDAS" doi: "10.1101/gr.201863.115" licence: ["GPL v3"] + identifier: biotools:midashla input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Reads in FASTQ format - pattern: "*.{fastq.gz}" - - db: - type: file - description: A database formatted for MIDAS - pattern: "*.{db}" - - mode: - type: string - description: The mode to run MIDAS is - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Reads in FASTQ format + pattern: "*.{fastq.gz}" + - - db: + type: file + description: A database formatted for MIDAS + pattern: "*.{db}" + - - mode: + type: string + description: The mode to run MIDAS is + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: file - description: A directory of results from MIDAS run - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: file + description: A directory of results from MIDAS run + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/mindagap/duplicatefinder/meta.yml b/modules/nf-core/mindagap/duplicatefinder/meta.yml index b92d419c7bd2..437bdcba424a 100644 --- a/modules/nf-core/mindagap/duplicatefinder/meta.yml +++ b/modules/nf-core/mindagap/duplicatefinder/meta.yml @@ -6,38 +6,42 @@ keywords: - spatial_transcriptomics tools: - "mindagap": - description: "Takes a single panorama image and fills the empty grid lines with neighbour-weighted values." + description: "Takes a single panorama image and fills the empty grid lines with + neighbour-weighted values." homepage: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" tool_dev_url: "https://github.com/ViriatoII/MindaGap" licence: ["BSD 3-clause License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - spot_table: - type: file - description: tsv file containing one spot per row with order x,y,z,gene without column header. - pattern: "*.{tsv,txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - spot_table: + type: file + description: tsv file containing one spot per row with order x,y,z,gene without + column header. + pattern: "*.{tsv,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - marked_dups_spots: - type: file - description: tsv file containing one spot per row, with duplicated spots labeled with "Duplicated" in their gene column. - pattern: "*.{markedDups.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*markedDups.txt": + type: file + description: tsv file containing one spot per row, with duplicated spots labeled + with "Duplicated" in their gene column. + pattern: "*.{markedDups.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FloWuenne" maintainers: diff --git a/modules/nf-core/mindagap/mindagap/meta.yml b/modules/nf-core/mindagap/mindagap/meta.yml index efd00004739e..ef617400b8bf 100644 --- a/modules/nf-core/mindagap/mindagap/meta.yml +++ b/modules/nf-core/mindagap/mindagap/meta.yml @@ -1,40 +1,47 @@ name: "mindagap_mindagap" -description: Takes a single panorama image and fills the empty grid lines with neighbour-weighted values. +description: Takes a single panorama image and fills the empty grid lines with neighbour-weighted + values. keywords: - imaging - resolve_bioscience - spatial_transcriptomics tools: - "mindagap": - description: "Mindagap is a collection of tools to process multiplexed FISH data, such as produced by Resolve Biosciences Molecular Cartography." + description: "Mindagap is a collection of tools to process multiplexed FISH data, + such as produced by Resolve Biosciences Molecular Cartography." homepage: "https://github.com/ViriatoII/MindaGap" documentation: "https://github.com/ViriatoII/MindaGap/blob/main/README.md" tool_dev_url: "https://github.com/ViriatoII/MindaGap" licence: ["BSD-3-Clause license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - panorama: - type: file - description: A tiff file containing gridlines as produced by Molecular Cartography imaging. - pattern: "*.{tif,tiff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - panorama: + type: file + description: A tiff file containing gridlines as produced by Molecular Cartography + imaging. + pattern: "*.{tif,tiff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tiff: - type: file - description: A tiff file with gridlines filled based on consecutive gaussian blurring. - pattern: "*.{tiff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tif,tiff}": + type: file + description: A tiff file with gridlines filled based on consecutive gaussian + blurring. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ViriatoII" - "@flowuenne" diff --git a/modules/nf-core/minia/meta.yml b/modules/nf-core/minia/meta.yml index 04fd8f88c854..b1751e07168a 100644 --- a/modules/nf-core/minia/meta.yml +++ b/modules/nf-core/minia/meta.yml @@ -12,38 +12,53 @@ tools: homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia licence: ["AGPL-3.0-or-later"] + identifier: biotools:minia input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads in FastQ format - pattern: "*.{fastq.gz, fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads in FastQ format + pattern: "*.{fastq.gz, fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - contigs: - type: file - description: The assembled contigs - pattern: "*.contigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.contigs.fa": + type: file + description: The assembled contigs + pattern: "*.contigs.fa" - unitigs: - type: file - description: The assembled unitigs - pattern: "*.unitigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unitigs.fa": + type: file + description: The assembled unitigs + pattern: "*.unitigs.fa" - h5: - type: file - description: Minia output h5 file - pattern: "*{.h5}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5": + type: file + description: Minia output h5 file + pattern: "*{.h5}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/miniasm/meta.yml b/modules/nf-core/miniasm/meta.yml index 9387eea6b56c..84fd414ab062 100644 --- a/modules/nf-core/miniasm/meta.yml +++ b/modules/nf-core/miniasm/meta.yml @@ -6,44 +6,54 @@ keywords: - nanopore tools: - miniasm: - description: Ultrafast de novo assembly for long noisy reads (though having no consensus step) + description: Ultrafast de novo assembly for long noisy reads (though having no + consensus step) homepage: https://github.com/lh3/miniasm documentation: https://github.com/lh3/miniasm tool_dev_url: https://github.com/lh3/miniasm doi: "10.1093/bioinformatics/btw152" licence: ["MIT"] + identifier: biotools:miniasm input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input PacBio/ONT FastQ files. - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" - - paf: - type: file - description: Alignment in PAF format - pattern: "*{.paf,.paf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input PacBio/ONT FastQ files. + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - paf: + type: file + description: Alignment in PAF format + pattern: "*{.paf,.paf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gfa: - type: file - description: Assembly graph - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa.gz": + type: file + description: Assembly graph + pattern: "*.gfa.gz" - assembly: - type: file - description: Genome assembly - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Genome assembly + pattern: "*.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/minimap2/align/meta.yml b/modules/nf-core/minimap2/align/meta.yml index 8996f881a215..a4cfc891a530 100644 --- a/modules/nf-core/minimap2/align/meta.yml +++ b/modules/nf-core/minimap2/align/meta.yml @@ -14,62 +14,77 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test_ref'] - - reference: - type: file - description: | - Reference database in FASTA format. - - bam_format: - type: boolean - description: Specify that output should be in BAM format - - bam_index_extension: - type: string - description: BAM alignment index extension (e.g. "bai") - - cigar_paf_format: - type: boolean - description: Specify that output CIGAR should be in PAF format - - cigar_bam: - type: boolean - description: | - Write CIGAR with >65535 ops at the CG tag. This is recommended when - doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test_ref'] + - reference: + type: file + description: | + Reference database in FASTA format. + - - bam_format: + type: boolean + description: Specify that output should be in BAM format + - - bam_index_extension: + type: string + description: BAM alignment index extension (e.g. "bai") + - - cigar_paf_format: + type: boolean + description: Specify that output CIGAR should be in PAF format + - - cigar_bam: + type: boolean + description: | + Write CIGAR with >65535 ops at the CG tag. This is recommended when + doing XYZ (https://github.com/lh3/minimap2#working-with-65535-cigar-operations) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - bam: - type: file - description: Alignment in BAM format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Alignment in BAM format + pattern: "*.bam" - index: - type: file - description: BAM alignment index - pattern: "*.bam.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam.${bam_index_extension}": + type: file + description: BAM alignment index + pattern: "*.bam.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" - "@sofstam" diff --git a/modules/nf-core/minimap2/index/meta.yml b/modules/nf-core/minimap2/index/meta.yml index 1d29e3f2d68d..57c80e29fca5 100644 --- a/modules/nf-core/minimap2/index/meta.yml +++ b/modules/nf-core/minimap2/index/meta.yml @@ -11,30 +11,33 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2#uguide licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: Minimap2 fasta index. - pattern: "*.mmi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mmi": + type: file + description: Minimap2 fasta index. + pattern: "*.mmi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/miniprot/align/meta.yml b/modules/nf-core/miniprot/align/meta.yml index 8b4ffe9edaac..aadd6fdfdd19 100644 --- a/modules/nf-core/miniprot/align/meta.yml +++ b/modules/nf-core/miniprot/align/meta.yml @@ -14,40 +14,49 @@ tools: homepage: https://github.com/lh3/miniprot documentation: https://github.com/lh3/miniprot licence: ["MIT"] + identifier: biotools:miniprot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pep: - type: file - description: a fasta file contains one or multiple protein sequences - - meta2: - type: map - description: | - Groovy Map containing reference information - - ref: - type: file - description: Reference database in FASTA format or miniprot index format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pep: + type: file + description: a fasta file contains one or multiple protein sequences + - - meta2: + type: map + description: | + Groovy Map containing reference information + - ref: + type: file + description: Reference database in FASTA format or miniprot index format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignment in PAF format + pattern: "*.paf" - gff: - type: file - description: Alignment in gff format - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gff": + type: file + description: Alignment in gff format + pattern: "*.gff" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@muffato" diff --git a/modules/nf-core/miniprot/index/meta.yml b/modules/nf-core/miniprot/index/meta.yml index 779a636dded8..bd076ada1cba 100644 --- a/modules/nf-core/miniprot/index/meta.yml +++ b/modules/nf-core/miniprot/index/meta.yml @@ -12,30 +12,33 @@ tools: homepage: https://github.com/lh3/miniprot documentation: https://github.com/lh3/miniprot licence: ["MIT"] + identifier: biotools:miniprot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - Reference database in FASTA format. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: file - description: miniprot fasta index. - pattern: "*.mpi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpi": + type: file + description: miniprot fasta index. + pattern: "*.mpi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" - "@muffato" diff --git a/modules/nf-core/miranda/meta.yml b/modules/nf-core/miranda/meta.yml index 2f551da0def8..ecfd2e59bc1b 100644 --- a/modules/nf-core/miranda/meta.yml +++ b/modules/nf-core/miranda/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://cbio.mskcc.org/miRNA2003/miranda.html" doi: "10.1186/gb-2003-5-1-r1" licence: ["GNU Public License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - query: - type: file - description: FASTA file containing the microRNA query sequences - pattern: "*.{fa,fasta}" - - mirbase: - type: file - description: FASTA file containing the sequence(s) to be scanned - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - query: + type: file + description: FASTA file containing the microRNA query sequences + pattern: "*.{fa,fasta}" + - - mirbase: + type: file + description: FASTA file containing the sequence(s) to be scanned + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - txt: - type: file - description: Reformatted TXT file containing microRNA targets - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.txt": + type: file + description: Reformatted TXT file containing microRNA targets + pattern: "*.{txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/mirtop/counts/meta.yml b/modules/nf-core/mirtop/counts/meta.yml index 904dbd3102f7..679df7b0abf8 100644 --- a/modules/nf-core/mirtop/counts/meta.yml +++ b/modules/nf-core/mirtop/counts/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_counts" -description: mirtop counts generates a file with the minimal information about each sequence and the count data in columns for each samples. +description: mirtop counts generates a file with the minimal information about each + sequence and the count data in columns for each samples. keywords: - mirna - isomir @@ -13,44 +13,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - counts/*.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/export/meta.yml b/modules/nf-core/mirtop/export/meta.yml index d797f78373d5..25f66c3b6e4f 100644 --- a/modules/nf-core/mirtop/export/meta.yml +++ b/modules/nf-core/mirtop/export/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_export" -description: mirtop export generates files such as fasta, vcf or compatible with isomiRs bioconductor package +description: mirtop export generates files such as fasta, vcf or compatible with isomiRs + bioconductor package keywords: - mirna - isomir @@ -13,52 +13,75 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: GFF file - pattern: "*.{gff}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: GFF file + pattern: "*.{gff}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*_rawData.tsv: + type: file + description: TSV file + pattern: "*.{tsv}" - fasta: - type: file - description: FASTA file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa}" - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - export/*.vcf*: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/gff/meta.yml b/modules/nf-core/mirtop/gff/meta.yml index 454d5edfe1db..8e23f054e269 100644 --- a/modules/nf-core/mirtop/gff/meta.yml +++ b/modules/nf-core/mirtop/gff/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_gff" description: mirtop gff generates the GFF3 adapter format to capture miRNA variations @@ -13,44 +12,55 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - hairpin: - type: file - description: Hairpin file - pattern: "*.{fa,fasta}" - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" - - species: - type: string - description: Species name of the GTF file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - hairpin: + type: file + description: Hairpin file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" + - species: + type: string + description: Species name of the GTF file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: GFF file - pattern: "*.{gff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop/*mirtop.gff: + type: file + description: GFF file + pattern: "*.{gff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtop/stats/meta.yml b/modules/nf-core/mirtop/stats/meta.yml index 1bcd224832d8..ebce7d99fe2b 100644 --- a/modules/nf-core/mirtop/stats/meta.yml +++ b/modules/nf-core/mirtop/stats/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtop_stats" -description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF file by isomiR category. +description: mirtop gff gets the number of isomiRs and miRNAs annotated in the GFF + file by isomiR category. keywords: - mirna - isomir @@ -13,37 +13,44 @@ tools: documentation: "https://mirtop.readthedocs.io/en/latest/" tool_dev_url: "https://github.com/miRTop/mirtop" licence: ["MIT License"] + identifier: biotools:miRTop input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mirtop_gff: - type: file - description: Mirtop GFF file obtained with mirtop_gff - pattern: "*.{gff}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mirtop_gff: + type: file + description: Mirtop GFF file obtained with mirtop_gff + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: TXT file with stats - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*.txt: + type: file + description: TXT file with stats + pattern: "*.{txt}" - log: - type: file - description: log file with stats - pattern: "*.{log}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - stats/*_stats.log: + type: file + description: log file with stats + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mirtrace/qc/meta.yml b/modules/nf-core/mirtrace/qc/meta.yml index 9870437d98d6..e83ab3897816 100644 --- a/modules/nf-core/mirtrace/qc/meta.yml +++ b/modules/nf-core/mirtrace/qc/meta.yml @@ -1,68 +1,108 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mirtrace_qc" -description: "A tool for quality control and tracing taxonomic origins of microRNA sequencing data" +description: "A tool for quality control and tracing taxonomic origins of microRNA + sequencing data" keywords: - microRNA - smrnaseq - QC tools: - "mirtrace": - description: "miRTrace is a new quality control and taxonomic tracing tool developed specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized by profiling sequencing quality, read length, sequencing depth and miRNA complexity and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, rRNAs and sequencing artifacts). In addition to these routine quality control (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins of small RNA-Seq data based on the composition of clade-specific miRNAs. This feature can be used to detect cross-clade contaminations in typical lab settings. It can also be applied for more specific applications in forensics, food quality control and clinical diagnosis, for instance tracing the origins of meat products or detecting parasitic microRNAs in host serum." + description: "miRTrace is a new quality control and taxonomic tracing tool developed + specifically for small RNA sequencing data (sRNA-Seq). Each sample is characterized + by profiling sequencing quality, read length, sequencing depth and miRNA complexity + and also the amounts of miRNAs versus undesirable sequences (derived from tRNAs, + rRNAs and sequencing artifacts). In addition to these routine quality control + (QC) analyses, miRTrace can accurately and sensitively resolve taxonomic origins + of small RNA-Seq data based on the composition of clade-specific miRNAs. This + feature can be used to detect cross-clade contaminations in typical lab settings. + It can also be applied for more specific applications in forensics, food quality + control and clinical diagnosis, for instance tracing the origins of meat products + or detecting parasitic microRNAs in host serum." homepage: "https://github.com/friedlanderlab/mirtrace/tree/master" documentation: "https://github.com/friedlanderlab/mirtrace/blob/master/release-bundle-includes/doc/manual/mirtrace_manual.pdf" tool_dev_url: "https://github.com/friedlanderlab/mirtrace/tree/master" doi: "10.1186/s13059-018-1588-9" licence: ["GPL v2"] + identifier: biotools:miRTrace input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - reads: - type: file - description: microRNA sequencing data - pattern: "*.{fastq,fastq.gz}" - - mirtrace_config: - type: file - description: (Optional) CSV with list of FASTQ files to process with one entry per row. No headers. Each row consists of the following columns "FASTQ file path, id, adapter, PHRED-ASCII-offset". - - mirtrace_species: - type: string - description: Target species in microRNA sequencing data (miRbase encoding, e.g. “hsa” for Homo sapiens) - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: microRNA sequencing data + pattern: "*.{fastq,fastq.gz}" + - mirtrace_config: + type: file + description: (Optional) CSV with list of FASTQ files to process with one entry + per row. No headers. Each row consists of the following columns "FASTQ file + path, id, adapter, PHRED-ASCII-offset". + - - mirtrace_species: + type: string + description: Target species in microRNA sequencing data (miRbase encoding, e.g. + “hsa” for Homo sapiens) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html": + type: file + description: HTML file + pattern: "*.{html}" - json: - type: file - description: JSON file - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: JSON file + pattern: "*.{json}" - tsv: - type: file - description: TSV file - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file + pattern: "*.{tsv}" - all_fa: - type: file - description: QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - qc_passed_reads.all.collapsed/*.{fa,fasta}: + type: file + description: QC-passed reads in FASTA file. Identical reads are collapsed. Entries + are sorted by abundance. + pattern: "*.{fa,fasta}" - rnatype_unknown_fa: - type: file - description: Unknown RNA type QC-passed reads in FASTA file. Identical reads are collapsed. Entries are sorted by abundance. - pattern: "*.{fa,fasta}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - qc_passed_reads.rnatype_unknown.collapsed/*.{fa,fasta}: + type: file + description: Unknown RNA type QC-passed reads in FASTA file. Identical reads + are collapsed. Entries are sorted by abundance. + pattern: "*.{fa,fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/mitohifi/findmitoreference/meta.yml b/modules/nf-core/mitohifi/findmitoreference/meta.yml index 462da521c663..bb3d9e09f5fe 100644 --- a/modules/nf-core/mitohifi/findmitoreference/meta.yml +++ b/modules/nf-core/mitohifi/findmitoreference/meta.yml @@ -12,24 +12,42 @@ tools: tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" licence: ["MIT"] + identifier: biotools:mitohifi input: - - species: - type: string - description: Latin name of the species for which a mitochondrial genome should be fetched - pattern: "[A-Z]?[a-z]* [a-z]*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - species: + type: string + description: Latin name of the species for which a mitochondrial genome should + be fetched + pattern: "[A-Z]?[a-z]* [a-z]*" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Downloaded mitochondrial genome in Fasta format - pattern: "*.{fasta,fa}" + - meta: + type: file + description: Downloaded mitochondrial genome in Fasta format + pattern: "*.{fasta,fa}" + - "*.fasta": + type: file + description: Downloaded mitochondrial genome in Fasta format + pattern: "*.{fasta,fa}" - gb: - type: file - description: Downloaded mitochondrial genome in Genbank format - pattern: "*.gb" + - meta: + type: file + description: Downloaded mitochondrial genome in Genbank format + pattern: "*.gb" + - "*.gb": + type: file + description: Downloaded mitochondrial genome in Genbank format + pattern: "*.gb" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@verku" maintainers: diff --git a/modules/nf-core/mitohifi/mitohifi/meta.yml b/modules/nf-core/mitohifi/mitohifi/meta.yml index bd80dc27234a..2924dbe8f348 100644 --- a/modules/nf-core/mitohifi/mitohifi/meta.yml +++ b/modules/nf-core/mitohifi/mitohifi/meta.yml @@ -12,96 +12,188 @@ tools: tool_dev_url: https://github.com/marcelauliano/MitoHiFi doi: "10.1101/2022.12.23.521667" licence: ["MIT"] + identifier: biotools:mitohifi input: - - input: - type: file - description: Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified in ext.args2 - pattern: "*.{fa,fa.gz,fasta,fasta.gz}" - - ref_fa: - type: file - description: Reference sequence - pattern: "*.{fa,fasta}" - - ref_gb: - type: file - description: Reference annotation - pattern: "*.{gb}" - - input_mode: - type: string - description: Specifies type of input - reads or contigs - pattern: "{r,c}" - - code: - type: integer - description: Mitochndrial code for annotation - pattern: "[0-9]*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Path to PacBio HiFi reads or contigs. Type (-r/-c) is specified + in ext.args2 + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + - - ref_fa: + type: file + description: Reference sequence + pattern: "*.{fa,fasta}" + - - ref_gb: + type: file + description: Reference annotation + pattern: "*.{gb}" + - - input_mode: + type: string + description: Specifies type of input - reads or contigs + pattern: "{r,c}" + - - mito_code: + type: string + description: Mitochondrial genetic code output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Mitochondrial sequence - pattern: "*.{fasta,fa}" + - meta: + type: file + description: Mitochondrial sequence + pattern: "*.{fasta,fa}" + - "*fasta": + type: file + description: Mitochondrial sequence + pattern: "*.{fasta,fa}" + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*contigs_stats.tsv": + type: file + description: Contigs statistics + pattern: "*contigs_stats.tsv" - gb: - type: file - description: Genome annotation in case mitofinder was used - pattern: "*.gb" + - meta: + type: file + description: Genome annotation in case mitofinder was used + pattern: "*.gb" + - "*gb": + type: file + description: Genome annotation in case mitofinder was used + pattern: "*.gb" - gff: - type: file - description: Genome annotation in case mitos was used - pattern: "*.gff" + - meta: + type: file + description: Genome annotation in case mitos was used + pattern: "*.gff" + - "*gff": + type: file + description: Genome annotation in case mitos was used + pattern: "*.gff" - all_potential_contigs: - type: file - description: Contains sequences of all potential contigs - pattern: "*all_potential_contigs.fa" + - meta: + type: file + description: Contains sequences of all potential contigs + pattern: "*all_potential_contigs.fa" + - "*all_potential_contigs.fa": + type: file + description: Contains sequences of all potential contigs + pattern: "*all_potential_contigs.fa" - contigs_annotations: - type: file - description: Graphical representation of annotated genes and tRNAs - pattern: "*contigs_annotations.png" + - meta: + type: file + description: Graphical representation of annotated genes and tRNAs + pattern: "*contigs_annotations.png" + - "*contigs_annotations.png": + type: file + description: Graphical representation of annotated genes and tRNAs + pattern: "*contigs_annotations.png" - contigs_circularization: - type: directory - description: Contains circularization reports - pattern: "*contigs_circularization" + - meta: + type: directory + description: Contains circularization reports + pattern: "*contigs_circularization" + - "*contigs_circularization": + type: directory + description: Contains circularization reports + pattern: "*contigs_circularization" - contigs_filtering: - type: directory - description: Contains files with initial blast matches - pattern: "*contigs_filtering" + - meta: + type: directory + description: Contains files with initial blast matches + pattern: "*contigs_filtering" + - "*contigs_filtering": + type: directory + description: Contains files with initial blast matches + pattern: "*contigs_filtering" - coverage_mapping: - type: directory - description: Contains statistics on coverage mapping - pattern: "*coverage_mapping" + - meta: + type: directory + description: Contains statistics on coverage mapping + pattern: "*coverage_mapping" + - "*coverage_mapping": + type: directory + description: Contains statistics on coverage mapping + pattern: "*coverage_mapping" - coverage_plot: - type: file - description: Read coverage plot for mitochondrial contigs - pattern: "*coverage_plot.png" + - meta: + type: file + description: Read coverage plot for mitochondrial contigs + pattern: "*coverage_plot.png" + - "*coverage_plot.png": + type: file + description: Read coverage plot for mitochondrial contigs + pattern: "*coverage_plot.png" - final_mitogenome_annotation: - type: file - description: Graphical representation of annotated genes for the final mito contig - pattern: "*final_mitogenome.annotation.png" + - meta: + type: file + description: Graphical representation of annotated genes for the final mito + contig + pattern: "*final_mitogenome.annotation.png" + - "*final_mitogenome.annotation.png": + type: file + description: Graphical representation of annotated genes for the final mito + contig + pattern: "*final_mitogenome.annotation.png" - final_mitogenome_choice: - type: directory - description: Files with potential contigs clusterings and alignments - pattern: "*final_mitogenome_choice" + - meta: + type: directory + description: Files with potential contigs clusterings and alignments + pattern: "*final_mitogenome_choice" + - "*final_mitogenome_choice": + type: directory + description: Files with potential contigs clusterings and alignments + pattern: "*final_mitogenome_choice" - final_mitogenome_coverage: - type: file - description: Graphical representation of reads coverage plot for the final mito contig - pattern: "*final_mitogenome.coverage.png" + - meta: + type: file + description: Graphical representation of reads coverage plot for the final mito + contig + pattern: "*final_mitogenome.coverage.png" + - "*final_mitogenome.coverage.png": + type: file + description: Graphical representation of reads coverage plot for the final mito + contig + pattern: "*final_mitogenome.coverage.png" - potential_contigs: - type: directory - description: Files with sequences and annotations of the potential contigs - pattern: "*potential_contigs" + - meta: + type: directory + description: Files with sequences and annotations of the potential contigs + pattern: "*potential_contigs" + - "*potential_contigs": + type: directory + description: Files with sequences and annotations of the potential contigs + pattern: "*potential_contigs" - reads_mapping_and_assembly: - type: directory - description: Read mapping files for run from the raw reads - pattern: "*reads_mapping_and_assembly" + - meta: + type: directory + description: Read mapping files for run from the raw reads + pattern: "*reads_mapping_and_assembly" + - "*reads_mapping_and_assembly": + type: directory + description: Read mapping files for run from the raw reads + pattern: "*reads_mapping_and_assembly" - shared_genes: - type: directory - description: Report on genes shared with the reference genome - pattern: "*shared_genes.tsv" + - meta: + type: directory + description: Report on genes shared with the reference genome + pattern: "*shared_genes.tsv" + - "*shared_genes.tsv": + type: directory + description: Report on genes shared with the reference genome + pattern: "*shared_genes.tsv" - versions: - type: file - description: Software versions used in the run - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" maintainers: diff --git a/modules/nf-core/mlst/meta.yml b/modules/nf-core/mlst/meta.yml index 5a4ec8871a44..90663c0ac26e 100644 --- a/modules/nf-core/mlst/meta.yml +++ b/modules/nf-core/mlst/meta.yml @@ -10,30 +10,33 @@ tools: description: Scan contig files against PubMLST typing schemes homepage: https://github.com/tseemann/mlst licence: ["GPL v2"] + identifier: biotools:mlst input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly fasta file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly fasta file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: MLST calls in tsv format - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: MLST calls in tsv format + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lskatz" - "@tseemann" diff --git a/modules/nf-core/mmseqs/cluster/meta.yml b/modules/nf-core/mmseqs/cluster/meta.yml index 0c1cfb3c362c..ec974854282f 100644 --- a/modules/nf-core/mmseqs/cluster/meta.yml +++ b/modules/nf-core/mmseqs/cluster/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_cluster" description: Cluster sequences using MMSeqs2 cluster. @@ -11,34 +10,38 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input_db: - type: directory - description: a MMseqs2 database used for clustering + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_input: + type: file + description: Input database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_cluster: - type: file - description: a clustered MMseqs2 database used for clustering + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: file + description: a clustered MMseqs2 database used for clustering - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/createdb/meta.yml b/modules/nf-core/mmseqs/createdb/meta.yml index a011020b9b62..c392a360f807 100644 --- a/modules/nf-core/mmseqs/createdb/meta.yml +++ b/modules/nf-core/mmseqs/createdb/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_createdb" description: Create an MMseqs database from an existing FASTA/Q file @@ -11,35 +10,40 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sequence: - type: file - description: Input sequences in FASTA/Q (zipped or unzipped) format to parse into an mmseqs database - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sequence: + type: file + description: Input sequences in FASTA/Q (zipped or unzipped) format to parse + into an mmseqs database + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db: - type: directory - description: The created MMseqs2 database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: directory + description: The created MMseqs2 database - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/createindex/meta.yml b/modules/nf-core/mmseqs/createindex/meta.yml index 0e34e5bb5103..c118ea3fdbc5 100644 --- a/modules/nf-core/mmseqs/createindex/meta.yml +++ b/modules/nf-core/mmseqs/createindex/meta.yml @@ -8,34 +8,43 @@ keywords: - indexing tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db: - type: directory - description: | - Directory containing the DB to be indexed - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db: + type: directory + description: | + Directory containing the DB to be indexed + pattern: "*" output: - - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" - db_indexed: - type: directory - description: | - Directory containing the DB and the generated indexes - pattern: "*" + - meta: + type: directory + description: | + Directory containing the DB and the generated indexes + pattern: "*" + - db: + type: directory + description: | + Directory containing the DB and the generated indexes + pattern: "*" + - versions: + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mmseqs/createtsv/meta.yml b/modules/nf-core/mmseqs/createtsv/meta.yml index e85b066f8902..5a50ff349c03 100644 --- a/modules/nf-core/mmseqs/createtsv/meta.yml +++ b/modules/nf-core/mmseqs/createtsv/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_createtsv" -description: Create a tsv file from a query and a target database as well as the result database +description: Create a tsv file from a query and a target database as well as the result + database keywords: - protein sequence - databases @@ -12,53 +12,58 @@ keywords: - tsv tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_result: - type: directory - description: an MMseqs2 database with result data - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_query: - type: directory - description: an MMseqs2 database with query data - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_target: - type: directory - description: an MMseqs2 database with target data + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_result: + type: directory + description: an MMseqs2 database with result data + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: directory + description: an MMseqs2 database with query data + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_target: + type: directory + description: an MMseqs2 database with target data output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - tsv: - type: file - description: The resulting tsv file created using the query, target and result MMseqs databases - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tsv": + type: file + description: The resulting tsv file created using the query, target and result + MMseqs databases + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/databases/meta.yml b/modules/nf-core/mmseqs/databases/meta.yml index 803a87f6243c..be9380fb197f 100644 --- a/modules/nf-core/mmseqs/databases/meta.yml +++ b/modules/nf-core/mmseqs/databases/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_databases" description: Download an mmseqs-formatted database @@ -9,24 +8,29 @@ keywords: - searching tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - database: - type: string - description: Database available through the mmseqs2 databases interface - see https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details + - - database: + type: string + description: Database available through the mmseqs2 databases interface - see + https://github.com/soedinglab/MMseqs2/wiki#downloading-databases for details output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - database: - type: directory - description: Directory containing processed mmseqs database + - ${prefix}/: + type: directory + description: Directory containing processed mmseqs database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/mmseqs/easysearch/meta.yml b/modules/nf-core/mmseqs/easysearch/meta.yml index 5c7b0971d39b..acf1b20d4dc7 100644 --- a/modules/nf-core/mmseqs/easysearch/meta.yml +++ b/modules/nf-core/mmseqs/easysearch/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_easysearch" description: Searches for the sequences of a fasta file in a databse using MMseqs2 @@ -9,44 +8,48 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing input fasta file information - e.g. `[ id:'test' ]` - - fasta: - type: file - description: Fasta file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing database information - e.g. `[ id:'test' ]` - - db_target: - type: directory - description: an MMseqs2 database with target data, e.g. uniref90 + - - meta: + type: map + description: | + Groovy Map containing input fasta file information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing database information + e.g. `[ id:'test' ]` + - db_target: + type: directory + description: an MMseqs2 database with target data, e.g. uniref90 output: - - meta: - type: map - description: | - Groovy Map containing input fasta file information - e.g. `[ id:'test']` - tsv: - type: file - description: tsv file with the results of the search - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing input fasta file information + e.g. `[ id:'test']` + - ${prefix}.tsv: + type: file + description: tsv file with the results of the search + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/mmseqs/linclust/meta.yml b/modules/nf-core/mmseqs/linclust/meta.yml index 8513b3ebdd08..986e2d83d0a9 100644 --- a/modules/nf-core/mmseqs/linclust/meta.yml +++ b/modules/nf-core/mmseqs/linclust/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_linclust" description: Cluster sequences in linear time using MMSeqs2 linclust. @@ -11,34 +10,38 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - input_db: - type: directory - description: a MMseqs2 database used for clustering + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_input: + type: file + description: Input database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_cluster: - type: directory - description: a clustered MMseqs2 database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}/: + type: directory + description: a clustered MMseqs2 database - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vagkaratzas" maintainers: diff --git a/modules/nf-core/mmseqs/search/meta.yml b/modules/nf-core/mmseqs/search/meta.yml index 5376bdbd0eb5..e722862ad753 100644 --- a/modules/nf-core/mmseqs/search/meta.yml +++ b/modules/nf-core/mmseqs/search/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mmseqs_search" -description: Search and calculate a score for similar sequences in a query and a target database. +description: Search and calculate a score for similar sequences in a query and a target + database. keywords: - protein sequence - databases @@ -11,42 +11,46 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - query_db: - type: directory - description: an MMseqs2 database with query data - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - target_db: - type: directory - description: an MMseqs2 database with target data, e.g. uniref90 + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: file + description: Query database + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_target: + type: file + description: Target database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db_search: - type: directory - description: an MMseqs2 database with search results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}: + type: directory + description: an MMseqs2 database with search results + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/mmseqs/taxonomy/meta.yml b/modules/nf-core/mmseqs/taxonomy/meta.yml index d836029cf9a0..15756feb8c52 100644 --- a/modules/nf-core/mmseqs/taxonomy/meta.yml +++ b/modules/nf-core/mmseqs/taxonomy/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "mmseqs_taxonomy" -description: Computes the lowest common ancestor by identifying the query sequence homologs against the target database. +description: Computes the lowest common ancestor by identifying the query sequence + homologs against the target database. keywords: - protein sequence - nucleotide sequence @@ -11,37 +11,41 @@ keywords: - mmseqs2 tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - db_query: - type: directory - description: An MMseqs2 database with query data - - db_target: - type: directory - description: an MMseqs2 database with target data including the taxonomy classification + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - db_query: + type: directory + description: An MMseqs2 database with query data + - - db_target: + type: directory + description: an MMseqs2 database with target data including the taxonomy classification output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - db_taxonomy: - type: directory - description: An MMseqs2 database with target data including the taxonomy classification + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}_taxonomy: + type: directory + description: An MMseqs2 database with target data including the taxonomy classification - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@darcy220606" maintainers: diff --git a/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml b/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml index 37c7554fca65..4e8890addfa8 100644 --- a/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml +++ b/modules/nf-core/mmseqs/tsv2exprofiledb/meta.yml @@ -1,5 +1,6 @@ name: "mmseqs_tsv2exprofiledb" -description: Conversion of expandable profile to databases to the MMseqs2 databases format +description: Conversion of expandable profile to databases to the MMseqs2 databases + format keywords: - protein sequence - databases @@ -8,29 +9,33 @@ keywords: - indexing tools: - "mmseqs": - description: "MMseqs2: ultra fast and sensitive sequence search and clustering suite" + description: "MMseqs2: ultra fast and sensitive sequence search and clustering + suite" homepage: "https://github.com/soedinglab/MMseqs2" documentation: "https://mmseqs.com/latest/userguide.pdf" tool_dev_url: "https://github.com/soedinglab/MMseqs2" doi: "10.1093/bioinformatics/btw006" licence: ["GPL v3"] + identifier: biotools:mmseqs input: - - db: - type: directory - description: | - Directory containing the DB to be indexed - pattern: "*" + - - db: + type: directory + description: | + Directory containing the DB to be indexed + pattern: "*" output: - - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" - db_exprofile: - type: directory - description: | - Directory containing the expandable profile DB - pattern: "*" + - db: + type: directory + description: | + Directory containing the expandable profile DB + pattern: "*" + - versions: + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" maintainers: diff --git a/modules/nf-core/mobsuite/recon/meta.yml b/modules/nf-core/mobsuite/recon/meta.yml index 65d67ff09126..f60522c3f2c3 100644 --- a/modules/nf-core/mobsuite/recon/meta.yml +++ b/modules/nf-core/mobsuite/recon/meta.yml @@ -6,48 +6,71 @@ keywords: - cluster tools: - mobsuite: - description: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies. + description: Software tools for clustering, reconstruction and typing of plasmids + from draft assemblies. homepage: https://github.com/phac-nml/mob-suite documentation: https://github.com/phac-nml/mob-suite tool_dev_url: https://github.com/phac-nml/mob-suite doi: "10.1099/mgen.0.000435" licence: ["Apache License, Version 2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A bacterial genome assembly in FASTA format - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A bacterial genome assembly in FASTA format + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - chromosome: - type: file - description: FASTA file of all contigs found to belong to the chromosome - pattern: "chromosome.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/chromosome.fasta: + type: file + description: FASTA file of all contigs found to belong to the chromosome + pattern: "chromosome.fasta" - contig_report: - type: file - description: Assignment of the contig to chromosome or a particular plasmid grouping - pattern: "contig_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/contig_report.txt: + type: file + description: Assignment of the contig to chromosome or a particular plasmid + grouping + pattern: "contig_report.txt" - plasmids: - type: file - description: Each plasmid group is written to an individual FASTA - pattern: "plasmid_*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/plasmid_*.fasta: + type: file + description: Each plasmid group is written to an individual FASTA + pattern: "plasmid_*.fasta" - mobtyper_results: - type: file - description: Aggregate MOB-typer report files for all identified plasmid - pattern: "mobtyper_results.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/mobtyper_results.txt: + type: file + description: Aggregate MOB-typer report files for all identified plasmid + pattern: "mobtyper_results.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/modkit/pileup/meta.yml b/modules/nf-core/modkit/pileup/meta.yml index eb2875f439ba..2f274d0c8cdd 100644 --- a/modules/nf-core/modkit/pileup/meta.yml +++ b/modules/nf-core/modkit/pileup/meta.yml @@ -6,67 +6,83 @@ keywords: - long-read tools: - "modkit": - description: A bioinformatics tool for working with modified bases in Oxford Nanopore sequencing data + description: A bioinformatics tool for working with modified bases in Oxford Nanopore + sequencing data homepage: https://github.com/nanoporetech/modkit documentation: https://github.com/nanoporetech/modkit tool_dev_url: https://github.com/nanoporetech/modkit licence: ["Oxford Nanopore Technologies PLC. Public License Version 1.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Associated index file for BAM - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'hg38' ]` - - fasta: - type: file - description: Reference sequence in FASTA format. Required for motif (e.g. CpG) filtering - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing BED file information - e.g. `[ id:'regions' ]` - - bed: - type: file - description: - BED file that will restrict threshold estimation and pileup results to positions overlapping intervals in the - file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Associated index file for BAM + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'hg38' ]` + - fasta: + type: file + description: Reference sequence in FASTA format. Required for motif (e.g. CpG) + filtering + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing BED file information + e.g. `[ id:'regions' ]` + - bed: + type: file + description: BED file that will restrict threshold estimation and pileup results + to positions overlapping intervals in the file + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: bedMethyl output file(s) - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: bedMethyl output file(s) + pattern: "*.bed" - bedgraph: - type: file - description: bedgraph output files - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bedgraph": + type: file + description: bedgraph output files + pattern: "*.bedgraph" - log: - type: file - description: File for debug logs to be written to - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.log": + type: file + description: File for debug logs to be written to + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Michal-Babins" - "@fellen31" diff --git a/modules/nf-core/molkartgarage/clahe/meta.yml b/modules/nf-core/molkartgarage/clahe/meta.yml index 9ca71304aa33..6952813af3ef 100644 --- a/modules/nf-core/molkartgarage/clahe/meta.yml +++ b/modules/nf-core/molkartgarage/clahe/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "molkartgarage_clahe" -description: Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images. +description: Contrast-limited adjusted histogram equalization (CLAHE) on single-channel + tif images. keywords: - clahe - image_processing @@ -9,43 +9,42 @@ keywords: - correction tools: - "molkartgarage": - description: "One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines." + description: "One-stop-shop for scripts and tools for processing data for molkart + and spatial omics pipelines." homepage: https://github.com/SchapiroLabor/molkart-local/tree/main documentation: https://github.com/SchapiroLabor/molkart-local/tree/main tool_dev_url: https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - image: - type: file - description: Single-channel tiff file to be corrected. - pattern: "*.{tif,tiff}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - image: + type: file + description: Single-channel tiff file to be corrected. + pattern: "*.{tif,tiff}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - img_clahe: - type: file - description: CLAHE corrected tiff file. - pattern: "*.{tiff}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.tiff": + type: file + description: CLAHE corrected tiff file. + pattern: "*.{tiff}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kbestak" maintainers: diff --git a/modules/nf-core/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 9caaf2cdbc7e..dc783c9006a4 100644 --- a/modules/nf-core/mosdepth/meta.yml +++ b/modules/nf-core/mosdepth/meta.yml @@ -12,91 +12,161 @@ tools: documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 licence: ["MIT"] + identifier: biotools:mosdepth input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: Index for BAM/CRAM file - pattern: "*.{bai,crai}" - - bed: - type: file - description: BED file with intersected intervals - pattern: "*.{bed}" - - meta2: - type: map - description: | - Groovy Map containing bed information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: Index for BAM/CRAM file + pattern: "*.{bai,crai}" + - bed: + type: file + description: BED file with intersected intervals + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - global_txt: - type: file - description: Text file with global cumulative coverage distribution - pattern: "*.{global.dist.txt}" - - regions_txt: - type: file - description: Text file with region cumulative coverage distribution - pattern: "*.{region.dist.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.global.dist.txt": + type: file + description: Text file with global cumulative coverage distribution + pattern: "*.{global.dist.txt}" - summary_txt: - type: file - description: Text file with summary mean depths per chromosome and regions - pattern: "*.{summary.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: Text file with summary mean depths per chromosome and regions + pattern: "*.{summary.txt}" + - regions_txt: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.region.dist.txt": + type: file + description: Text file with region cumulative coverage distribution + pattern: "*.{region.dist.txt}" + - per_base_d4: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.d4": + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" - per_base_bed: - type: file - description: BED file with per-base coverage - pattern: "*.{per-base.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz": + type: file + description: BED file with per-base coverage + pattern: "*.{per-base.bed.gz}" - per_base_csi: - type: file - description: Index file for BED file with per-base coverage - pattern: "*.{per-base.bed.gz.csi}" - - per_base_d4: - type: file - description: D4 file with per-base coverage - pattern: "*.{per-base.d4}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.per-base.bed.gz.csi": + type: file + description: Index file for BED file with per-base coverage + pattern: "*.{per-base.bed.gz.csi}" - regions_bed: - type: file - description: BED file with per-region coverage - pattern: "*.{regions.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz": + type: file + description: BED file with per-region coverage + pattern: "*.{regions.bed.gz}" - regions_csi: - type: file - description: Index file for BED file with per-region coverage - pattern: "*.{regions.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.regions.bed.gz.csi": + type: file + description: Index file for BED file with per-region coverage + pattern: "*.{regions.bed.gz.csi}" - quantized_bed: - type: file - description: BED file with binned coverage - pattern: "*.{quantized.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz": + type: file + description: BED file with binned coverage + pattern: "*.{quantized.bed.gz}" - quantized_csi: - type: file - description: Index file for BED file with binned coverage - pattern: "*.{quantized.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.quantized.bed.gz.csi": + type: file + description: Index file for BED file with binned coverage + pattern: "*.{quantized.bed.gz.csi}" - thresholds_bed: - type: file - description: BED file with the number of bases in each region that are covered at or above each threshold - pattern: "*.{thresholds.bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz": + type: file + description: BED file with the number of bases in each region that are covered + at or above each threshold + pattern: "*.{thresholds.bed.gz}" - thresholds_csi: - type: file - description: Index file for BED file with threshold coverage - pattern: "*.{thresholds.bed.gz.csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.thresholds.bed.gz.csi": + type: file + description: Index file for BED file with threshold coverage + pattern: "*.{thresholds.bed.gz.csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/motus/downloaddb/meta.yml b/modules/nf-core/motus/downloaddb/meta.yml index 6cf509e97eec..38f9afbe0059 100644 --- a/modules/nf-core/motus/downloaddb/meta.yml +++ b/modules/nf-core/motus/downloaddb/meta.yml @@ -9,28 +9,29 @@ keywords: - download tools: - "motus": - description: "The mOTU profiler is a computational tool that estimates relative taxonomic abundance of known and currently unknown microbial community members using metagenomic shotgun sequencing data." + description: "The mOTU profiler is a computational tool that estimates relative + taxonomic abundance of known and currently unknown microbial community members + using metagenomic shotgun sequencing data." documentation: "https://github.com/motu-tool/mOTUs/wiki" tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - motus_downloaddb: - type: directory - description: | - The mOTUs downloadDB script source file. - It is the source file installed or - remote source in github such as https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py - pattern: "downloadDB.py" + - - motus_downloaddb_script: + type: file + description: The script to download the mOTUs database output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: The mOTUs database directory - pattern: "db_mOTU" + - db_mOTU/: + type: directory + description: The mOTUs database directory + pattern: "db_mOTU" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/motus/merge/meta.yml b/modules/nf-core/motus/merge/meta.yml index 0d7af231a9b3..57c95a547ff9 100644 --- a/modules/nf-core/motus/merge/meta.yml +++ b/modules/nf-core/motus/merge/meta.yml @@ -16,37 +16,54 @@ tools: tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - input: - type: file - description: | - List of output files (more than one) from motus profile, - or a single directory containing motus output files. - - db: - type: directory - description: | - mOTUs database downloaded by `motus downloadDB` - pattern: "db_mOTU/" - - profile_version_yml: - type: file - description: | - A single versions.yml file output from motus/profile. motus/merge cannot reconstruct - this itself without having the motus database present and configured with the tool - so here we take it from what is already reported by the upstream module. - pattern: "versions.yml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - input: + type: file + description: | + List of output files (more than one) from motus profile, + or a single directory containing motus output files. + - - db: + type: directory + description: | + mOTUs database downloaded by `motus downloadDB` + pattern: "db_mOTU/" + - - profile_version_yml: + type: file + description: | + A single versions.yml file output from motus/profile. motus/merge cannot reconstruct + this itself without having the motus database present and configured with the tool + so here we take it from what is already reported by the upstream module. + pattern: "versions.yml" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: OTU table in txt format, if BIOM format not requested - pattern: "*.txt" + - meta: + type: file + description: OTU table in txt format, if BIOM format not requested + pattern: "*.txt" + - "*.txt": + type: file + description: OTU table in txt format, if BIOM format not requested + pattern: "*.txt" - biom: - type: file - description: OTU table in biom format, if BIOM format requested - pattern: "*.biom" + - meta: + type: file + description: OTU table in biom format, if BIOM format requested + pattern: "*.biom" + - "*.biom": + type: file + description: OTU table in biom format, if BIOM format requested + pattern: "*.biom" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/motus/profile/meta.yml b/modules/nf-core/motus/profile/meta.yml index d6fffebcc5bd..8ce98f569c3d 100644 --- a/modules/nf-core/motus/profile/meta.yml +++ b/modules/nf-core/motus/profile/meta.yml @@ -13,51 +13,72 @@ tools: tool_dev_url: "https://github.com/motu-tool/mOTUs" doi: "10.1186/s40168-022-01410-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, - respectively. - Or the intermediate bam file mapped by bwa to the mOTUs database or - the output bam file from motus profile. - Or the intermediate mgc read counts table. - pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" - - db: - type: directory - description: | - mOTUs database downloaded by `motus downloadDB` + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fastq/fasta files of size 1 and 2 for single-end and paired-end data, + respectively. + Or the intermediate bam file mapped by bwa to the mOTUs database or + the output bam file from motus profile. + Or the intermediate mgc read counts table. + pattern: "*.{fastq,fq,fasta,fa,fastq.gz,fq.gz,fasta.gz,fa.gz,.bam,.mgc}" + - - db: + type: directory + description: | + mOTUs database downloaded by `motus downloadDB` output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out: - type: file - description: Results with taxonomic classification of each read - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out": + type: file + description: Results with taxonomic classification of each read + pattern: "*.out" - bam: - type: file - description: Optional intermediate sorted BAM file from BWA - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Optional intermediate sorted BAM file from BWA + pattern: "*.{bam}" - mgc: - type: file - description: Optional intermediate mgc read count table file saved with `-M`. - pattern: "*.{mgc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mgc": + type: file + description: Optional intermediate mgc read count table file saved with `-M`. + pattern: "*.{mgc}" - log: - type: file - description: Standard error logging file containing summary statistics - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Standard error logging file containing summary statistics + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/msisensor/msi/meta.yml b/modules/nf-core/msisensor/msi/meta.yml index 3d4620b4c2f6..29d0ed33a8e3 100644 --- a/modules/nf-core/msisensor/msi/meta.yml +++ b/modules/nf-core/msisensor/msi/meta.yml @@ -1,5 +1,6 @@ name: msisensor_msi -description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing data +description: Evaluate microsattelite instability (MSI) using paired tumor-normal sequencing + data keywords: - homoploymer - microsatellite @@ -7,62 +8,83 @@ keywords: - instability tools: - msisensor: - description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. + description: MSIsensor is a C++ program to detect replication slippage variants + at microsatellite regions, and differentiate them as somatic or germline. homepage: https://github.com/ding-lab/msisensor doi: "10.1093/bioinformatics/btt755" licence: ["MIT"] + identifier: biotools:msisensor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_bam: - type: file - description: Coordinate sorted BAM/CRAM/SAM file from normal tissue - pattern: "*.{bam,cram,sam}" - - normal_bai: - type: file - description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue - pattern: "*.{bam,cram,sam}" - - tumor_bam: - type: file - description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue - pattern: "*.{bam,cram,sam}" - - tumor_bai: - type: file - description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue - pattern: "*.{bam,cram,sam}" - - homopolymers: - type: file - description: Output file from MSIsensor scan module - pattern: "*.msisensor_scan.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_bam: + type: file + description: Coordinate sorted BAM/CRAM/SAM file from normal tissue + pattern: "*.{bam,cram,sam}" + - normal_bai: + type: file + description: Index for coordinate sorted BAM/CRAM/SAM file from normal tissue + pattern: "*.{bam,cram,sam}" + - tumor_bam: + type: file + description: Coordinate sorted BAM/CRAM/SAM file from tumor tissue + pattern: "*.{bam,cram,sam}" + - tumor_bai: + type: file + description: Index for coordinate sorted BAM/CRAM/SAM file from tumor tissue + pattern: "*.{bam,cram,sam}" + - metascan: + type: file + description: metascan file + - homopolymers: + type: file + description: Output file from MSIsensor scan module + pattern: "*.msisensor_scan.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: Output file from MSIsensor msi module + - output_dis: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: Output file from MSIsensor module + - output_germline: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_germline: + type: file + description: Output file from MSIsensor module + - output_somatic: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: Output file from MSIsensor module - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: MSIsensor MSI final report file - pattern: "*.output" - - txt: - type: file - description: MSIsensor MSI DIS report file - pattern: "*.output_dis" - - txt: - type: file - description: MSIsensor MSI germline report file - pattern: "*.output_germline" - - txt: - type: file - description: MSIsensor MSI somatic report file - pattern: "*.output_somatic" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" maintainers: diff --git a/modules/nf-core/msisensor/scan/meta.yml b/modules/nf-core/msisensor/scan/meta.yml index 2b786cecd850..ae2cc7b9f709 100644 --- a/modules/nf-core/msisensor/scan/meta.yml +++ b/modules/nf-core/msisensor/scan/meta.yml @@ -6,34 +6,38 @@ keywords: - MSI tools: - msisensor: - description: MSIsensor is a C++ program to detect replication slippage variants at microsatellite regions, and differentiate them as somatic or germline. + description: MSIsensor is a C++ program to detect replication slippage variants + at microsatellite regions, and differentiate them as somatic or germline. homepage: https://github.com/ding-lab/msisensor doi: "10.1093/bioinformatics/btt755" licence: ["MIT"] + identifier: biotools:msisensor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - txt: - type: file - description: MSIsensor scan output file of homopolymers & minisatellites - pattern: "*.msisensor_scan.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: MSIsensor scan output file of homopolymers & minisatellites + pattern: "*.msisensor_scan.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevbrick" maintainers: diff --git a/modules/nf-core/msisensor2/msi/meta.yml b/modules/nf-core/msisensor2/msi/meta.yml index 497225168892..123dcd8e7ae1 100644 --- a/modules/nf-core/msisensor2/msi/meta.yml +++ b/modules/nf-core/msisensor2/msi/meta.yml @@ -8,52 +8,83 @@ keywords: - cfDNA tools: - "msisensor2": - description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data." + description: "MSIsensor2 is a novel algorithm based machine learning, featuring + a large upgrade in the microsatellite instability (MSI) detection for tumor + only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) + and other sample types. The original MSIsensor is specially designed for tumor/normal + paired sequencing data." homepage: "https://github.com/niu-lab/msisensor2" documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md" tool_dev_url: "https://github.com/niu-lab/msisensor2" license: ["GPL-3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tumor_bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - normal_bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - intervals: - type: file - description: BED - pattern: "*.bed" - - models: - type: file - description: Folder of MSISensor2 models (available from Github or as a product of msisensor2/scan) - pattern: "*/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tumor_bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - tumor_bam_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - normal_bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - normal_bam_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai}" + - intervals: + type: file + description: BED + pattern: "*.bed" + - - scan: + type: file + description: Input scan file from MSIsensor2 scan module + - - models: + type: file + description: Folder of MSISensor2 models (available from Github or as a product + of msisensor2/scan) + pattern: "*/*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - msi: - type: file - description: MSI classifications as a text file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: MSI classifications as a text file - distribution: - type: file - description: Read count distributions of MSI regions + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: Read count distributions of MSI regions - somatic: - type: file - description: Somatic MSI regions detected. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: Somatic MSI regions detected. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/msisensor2/scan/meta.yml b/modules/nf-core/msisensor2/scan/meta.yml index 6baeb6b3ed14..3d993f1b2fdf 100644 --- a/modules/nf-core/msisensor2/scan/meta.yml +++ b/modules/nf-core/msisensor2/scan/meta.yml @@ -7,28 +7,34 @@ keywords: - tumor tools: - "msisensor2": - description: "MSIsensor2 is a novel algorithm based machine learning, featuring a large upgrade in the microsatellite instability (MSI) detection for tumor only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) and other sample types. The original MSIsensor is specially designed for tumor/normal paired sequencing data." + description: "MSIsensor2 is a novel algorithm based machine learning, featuring + a large upgrade in the microsatellite instability (MSI) detection for tumor + only sequencing data, including Cell-Free DNA (cfDNA), Formalin-Fixed Paraffin-Embedded(FFPE) + and other sample types. The original MSIsensor is specially designed for tumor/normal + paired sequencing data." homepage: "https://github.com/niu-lab/msisensor2" documentation: "https://github.com/niu-lab/msisensor2/blob/master/README.md" tool_dev_url: "https://github.com/niu-lab/msisensor2" licence: ["GPL-3.0"] + identifier: "" input: - - fasta: - type: file - description: Path to reference genome. - pattern: "*.fasta" - - output: - type: string - description: Name of output MSI scan to write. + - - fasta: + type: file + description: Path to reference genome. + pattern: "*.fasta" + - - output: + type: string + description: Name of output MSI scan to write. output: + - scan: + - output_path: + type: file + description: Path to output MSI scan file. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Output scan of MSI regions in FASTA file. - pattern: "*" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/msisensorpro/msisomatic/meta.yml b/modules/nf-core/msisensorpro/msisomatic/meta.yml index 7f7f4281e3d4..48daa6cc6452 100644 --- a/modules/nf-core/msisensorpro/msisomatic/meta.yml +++ b/modules/nf-core/msisensorpro/msisomatic/meta.yml @@ -1,5 +1,7 @@ name: msisensorpro_msisomatic -description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients + with next generation sequencing data. It accepts the whole genome sequencing, whole + exome sequencing and target region (panel) sequencing data as input keywords: - micro-satellite-scan - msisensor-pro @@ -7,68 +9,91 @@ keywords: - somatic tools: - msisensorpro: - description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + description: Microsatellite Instability (MSI) detection using high-throughput + sequencing data. homepage: https://github.com/xjtu-omics/msisensor-pro documentation: https://github.com/xjtu-omics/msisensor-pro/wiki tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - normal_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - tumor_index: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - intervals: - type: file - description: bed file containing interval information, optional - pattern: "*.{bed}" - - fasta: - type: file - description: Reference genome - pattern: "*.{fasta}" - - msisensor_scan: - type: file - description: Output from msisensor-pro/scan, containing list of msi regions - pattern: "*.list" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - normal_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - tumor_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - intervals: + type: file + description: bed file containing interval information, optional + pattern: "*.{bed}" + - - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" + - - msisensor_scan: + type: file + description: Output from msisensor-pro/scan, containing list of msi regions + pattern: "*.list" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output_report: - type: file - description: File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: File containing final report with all detected microsatellites, + unstable somatic microsatellites, msi score - output_dis: - type: file - description: File containing distribution results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_dis: + type: file + description: File containing distribution results - output_germline: - type: file - description: File containing germline results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_germline: + type: file + description: File containing germline results - output_somatic: - type: file - description: File containing somatic results + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_somatic: + type: file + description: File containing somatic results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/msisensorpro/scan/meta.yml b/modules/nf-core/msisensorpro/scan/meta.yml index aec743ede567..ac9674b8385e 100644 --- a/modules/nf-core/msisensorpro/scan/meta.yml +++ b/modules/nf-core/msisensorpro/scan/meta.yml @@ -1,41 +1,47 @@ name: msisensorpro_scan -description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients + with next generation sequencing data. It accepts the whole genome sequencing, whole + exome sequencing and target region (panel) sequencing data as input keywords: - micro-satellite-scan - msisensor-pro - scan tools: - msisensorpro: - description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + description: Microsatellite Instability (MSI) detection using high-throughput + sequencing data. homepage: https://github.com/xjtu-omics/msisensor-pro documentation: https://github.com/xjtu-omics/msisensor-pro/wiki tool_dev_url: https://github.com/xjtu-omics/msisensor-pro doi: "10.1016/j.gpb.2020.02.001" licence: ["Custom Licence"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference genome - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - list: - type: file - description: File containing microsatellite list - pattern: "*.{list}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list": + type: file + description: File containing microsatellite list + pattern: "*.{list}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/mtmalign/align/meta.yml b/modules/nf-core/mtmalign/align/meta.yml index 1e444e1c6baa..281434da0ad2 100644 --- a/modules/nf-core/mtmalign/align/meta.yml +++ b/modules/nf-core/mtmalign/align/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mtmalign_align" description: Aligns protein structures using mTM-align @@ -15,42 +14,54 @@ tools: tool_dev_url: "http://yanglab.nankai.edu.cn/mTM-align/" doi: "10.1093/bioinformatics/btx828" licence: ["None"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - pdbs: - type: file - description: Input protein structures in PDB format. Files may be gzipped or uncompressed. - They should contain exactly one chain! - pattern: "*.{pdb}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - pdbs: + type: file + description: Input protein structures in PDB format. Files may be gzipped or + uncompressed. They should contain exactly one chain! + pattern: "*.{pdb}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment in FASTA format. May be gzipped or uncompressed. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "${prefix}.aln${compress ? '.gz' : ''}": + type: file + description: Alignment in FASTA format. May be gzipped or uncompressed. + pattern: "*.aln{.gz,}" - structure: - type: file - description: Overlaid structures in PDB format. May be gzipped or uncompressed. - pattern: "${prefix}.pdb{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "${prefix}.pdb${compress ? '.gz' : ''}": + type: file + description: Overlaid structures in PDB format. May be gzipped or uncompressed. + pattern: "${prefix}.pdb{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" maintainers: diff --git a/modules/nf-core/mtnucratio/meta.yml b/modules/nf-core/mtnucratio/meta.yml index 6c289720dd44..fc4075022ab6 100644 --- a/modules/nf-core/mtnucratio/meta.yml +++ b/modules/nf-core/mtnucratio/meta.yml @@ -1,5 +1,6 @@ name: mtnucratio -description: A small Java tool to calculate ratios between MT and nuclear sequencing reads in a given BAM file. +description: A small Java tool to calculate ratios between MT and nuclear sequencing + reads in a given BAM file. keywords: - mtnucratio - ratio @@ -16,37 +17,50 @@ tools: tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator doi: "10.1186/s13059-016-0918-z" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: (coordinate) sorted BAM/SAM file - pattern: "*.{bam,sam}" - - mt_id: - type: string - description: Identifier of the contig/chromosome of interest (e.g. chromosome, contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for mitochondria + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: (coordinate) sorted BAM/SAM file + pattern: "*.{bam,sam}" + - - mt_id: + type: string + description: Identifier of the contig/chromosome of interest (e.g. chromosome, + contig) as in the aligned against reference FASTA file, e.g. mt or chrMT for + mitochondria output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mtnucratio: - type: file - description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, mt_nuc_ratio) - pattern: "*.mtnucratio" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mtnucratio": + type: file + description: Text file containing metrics (mtreads, mt_cov_avg, nucreads, nuc_cov_avg, + mt_nuc_ratio) + pattern: "*.mtnucratio" - json: - type: file - description: JSON file, containing metadata map with sample name, tool name and version, and metrics as in txt file - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file, containing metadata map with sample name, tool name + and version, and metrics as in txt file + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/mudskipper/bulk/meta.yml b/modules/nf-core/mudskipper/bulk/meta.yml index 1edfb4df7aeb..93a4758ad9f9 100644 --- a/modules/nf-core/mudskipper/bulk/meta.yml +++ b/modules/nf-core/mudskipper/bulk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mudskipper_bulk" description: Convert genomic BAM/SAM files to transcriptomic BAM/RAD files. @@ -11,50 +10,59 @@ keywords: - rad tools: - "mudskipper": - description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files." + description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic + BAM/RAD files." homepage: "https://github.com/OceanGenomics/mudskipper" documentation: "https://github.com/OceanGenomics/mudskipper" tool_dev_url: "https://github.com/OceanGenomics/mudskipper" licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Name-Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - gtf: - type: file - description: Annotation file - pattern: "*.{gtf,gff,gff3}" - - index: - type: directory - description: Annotation index created by mudskipper/index - - rad: - type: string - description: File type - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Name-Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - index: + type: directory + description: Annotation index created by mudskipper/index + - - gtf: + type: file + description: Annotation file + pattern: "*.{gtf,gff,gff3}" + - - rad: + type: string + description: File type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.bam: + type: file + description: Sorted BAM file + pattern: "*.bam" - rad: - type: file - description: RAD file - pattern: "*.rad" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${prefix}.rad: + type: file + description: RAD file + pattern: "*.rad" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" diff --git a/modules/nf-core/mudskipper/index/meta.yml b/modules/nf-core/mudskipper/index/meta.yml index 3421f6727295..1df41388f29e 100644 --- a/modules/nf-core/mudskipper/index/meta.yml +++ b/modules/nf-core/mudskipper/index/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "mudskipper_index" -description: Build and store a gtf index, which is useful for converting genomic BAM/SAM files to transcriptomic BAM/SAM files. +description: Build and store a gtf index, which is useful for converting genomic BAM/SAM + files to transcriptomic BAM/SAM files. keywords: - bam - transcriptome @@ -11,27 +11,29 @@ keywords: - sam tools: - "mudskipper": - description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic BAM/RAD files." + description: "mudskipper is a tool for converting genomic BAM/SAM files to transcriptomic + BAM/RAD files." homepage: "https://github.com/OceanGenomics/mudskipper" documentation: "https://github.com/OceanGenomics/mudskipper" tool_dev_url: "https://github.com/OceanGenomics/mudskipper" licence: ["BSD 3-clause"] + identifier: "" input: - - gtf: - type: file - description: Transcript annotation file. - pattern: "*.{gtf,gff,gff3}" - + - - gtf: + type: file + description: Transcript annotation file. + pattern: "*.{gtf,gff,gff3}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: directory - description: Mudskipper index for running mudskipper conversion tools - pattern: "*/" - + - index/: + type: directory + description: Mudskipper index for running mudskipper conversion tools + pattern: "*/" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index 0fe1264441d4..f1cd99b07923 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.25 + - bioconda::multiqc=1.24.1 diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 382c08cbc257..b16c1879238d 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,6 @@ name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report +description: Aggregate results from bioinformatics analyses across many samples into + a single report keywords: - QC - bioinformatics tools @@ -12,53 +13,59 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] + identifier: biotools:multiqc input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" - - replace_names: - type: file - description: | - Optional two-column sample renaming file. First column a set of - patterns, second column a set of corresponding replacements. Passed via - MultiQC's `--replace-names` option. - pattern: "*.{tsv}" - - sample_names: - type: file - description: | - Optional TSV file with headers, passed to the MultiQC --sample_names - argument. - pattern: "*.{tsv}" + - - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - - multiqc_config: + type: file + description: Optional config yml for MultiQC + pattern: "*.{yml,yaml}" + - - extra_multiqc_config: + type: file + description: Second optional config yml for MultiQC. Will override common sections + in multiqc_config. + pattern: "*.{yml,yaml}" + - - multiqc_logo: + type: file + description: Optional logo file for MultiQC + pattern: "*.{png}" + - - replace_names: + type: file + description: | + Optional two-column sample renaming file. First column a set of + patterns, second column a set of corresponding replacements. Passed via + MultiQC's `--replace-names` option. + pattern: "*.{tsv}" + - - sample_names: + type: file + description: | + Optional TSV file with headers, passed to the MultiQC --sample_names + argument. + pattern: "*.{tsv}" output: - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" + - "*multiqc_report.html": + type: file + description: MultiQC report file + pattern: "multiqc_report.html" - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" + - "*_data": + type: directory + description: MultiQC data dir + pattern: "multiqc_data" - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" + - "*_plots": + type: file + description: Plots created by MultiQC + pattern: "*_data" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@bunop" diff --git a/modules/nf-core/multivcfanalyzer/meta.yml b/modules/nf-core/multivcfanalyzer/meta.yml index 01663745253b..6c1a8b6f0d5d 100644 --- a/modules/nf-core/multivcfanalyzer/meta.yml +++ b/modules/nf-core/multivcfanalyzer/meta.yml @@ -1,5 +1,6 @@ name: "multivcfanalyzer" -description: SNP table generator from GATK UnifiedGenotyper with functionality geared for aDNA +description: SNP table generator from GATK UnifiedGenotyper with functionality geared + for aDNA keywords: - vcf - ancient DNA @@ -9,111 +10,194 @@ keywords: - SNP table tools: - "multivcfanalyzer": - description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for aDNA. License on Github repository." + description: "MultiVCFAnalyzer is a VCF file post-processing tool tailored for + aDNA. License on Github repository." homepage: "https://github.com/alexherbig/MultiVCFAnalyzer" documentation: "https://github.com/alexherbig/MultiVCFAnalyzer" tool_dev_url: "https://github.com/alexherbig/MultiVCFAnalyzer" doi: "10.1038/nature13591" licence: ["GPL >=3"] + identifier: "" input: - - vcfs: - type: file - description: One or a list of uncompressed VCF file - pattern: "*.vcf" - - fasta: - type: file - description: Reference genome VCF was generated against - pattern: "*.{fasta,fna,fa}" - - snpeff_results: - type: file - description: Results from snpEff in txt format (Optional) - pattern: "*.txt" - - gff: - type: file - description: GFF file corresponding to reference genome fasta (Optional) - pattern: "*.gff" - - allele_freqs: - type: boolean - description: | - Whether to include the percentage of reads a given allele is - present in in the SNP table. - - genotype_quality: - type: integer - description: | - Minimum GATK genotyping threshold threshold of which a SNP call - falling under is 'discarded' - - coverage: - type: integer - description: | - Minimum number of a reads that a position must be covered by to be - reported - - homozygous_freq: - type: integer - description: Fraction of reads a base must have to be called 'homozygous' - - heterozygous_freq: - type: integer - description: | - Fraction of which whereby if a call falls above this value, and lower - than the homozygous threshold, a base will be called 'heterozygous'. - - gff_exclude: - type: file - description: | - file listing positions that will be 'filtered' (i.e. ignored) - (Optional) - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcfs: + type: file + description: One or a list of uncompressed VCF file + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome VCF was generated against + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - snpeff_results: + type: file + description: Results from snpEff in txt format (Optional) + pattern: "*.txt" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff: + type: file + description: GFF file corresponding to reference genome fasta (Optional) + pattern: "*.gff" + - - allele_freqs: + type: boolean + description: | + Whether to include the percentage of reads a given allele is + present in in the SNP table. + - - genotype_quality: + type: integer + description: | + Minimum GATK genotyping threshold threshold of which a SNP call + falling under is 'discarded' + - - coverage: + type: integer + description: | + Minimum number of a reads that a position must be covered by to be + reported + - - homozygous_freq: + type: integer + description: Fraction of reads a base must have to be called 'homozygous' + - - heterozygous_freq: + type: integer + description: | + Fraction of which whereby if a call falls above this value, and lower + than the homozygous threshold, a base will be called 'heterozygous'. + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - gff_exclude: + type: file + description: | + file listing positions that will be 'filtered' (i.e. ignored) + (Optional) + pattern: "*.vcf" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - full_alignment: - type: file - description: Fasta a fasta file of all positions contained in the VCF files i.e. including ref calls - pattern: ".fasta.gz" + - meta: + type: file + description: Fasta a fasta file of all positions contained in the VCF files + i.e. including ref calls + pattern: ".fasta.gz" + - fullAlignment.fasta.gz: + type: file + description: Fasta a fasta file of all positions contained in the VCF files + i.e. including ref calls + pattern: ".fasta.gz" - info_txt: - type: file - description: Information about the run - pattern: ".txt" + - meta: + type: file + description: Information about the run + pattern: ".txt" + - info.txt: + type: file + description: Information about the run + pattern: ".txt" - snp_alignment: - type: file - description: A fasta file of just SNP positions with samples only - pattern: ".fasta.gz" + - meta: + type: file + description: A fasta file of just SNP positions with samples only + pattern: ".fasta.gz" + - snpAlignment.fasta.gz: + type: file + description: A fasta file of just SNP positions with samples only + pattern: ".fasta.gz" - snp_genome_alignment: - type: file - description: A fasta file of just SNP positions with reference genome - pattern: ".fasta.gz" + - meta: + type: file + description: A fasta file of just SNP positions with reference genome + pattern: ".fasta.gz" + - snpAlignmentIncludingRefGenome.fasta.gz: + type: file + description: A fasta file of just SNP positions with reference genome + pattern: ".fasta.gz" - snpstatistics: - type: file - description: Some basic statistics about the SNP calls of each sample - pattern: ".tsv" + - meta: + type: file + description: Some basic statistics about the SNP calls of each sample + pattern: ".tsv" + - snpStatistics.tsv: + type: file + description: Some basic statistics about the SNP calls of each sample + pattern: ".tsv" - snptable: - type: file - description: Basic SNP table of combined positions taken from each VCF file - pattern: ".tsv" + - meta: + type: file + description: Basic SNP table of combined positions taken from each VCF file + pattern: ".tsv" + - snpTable.tsv: + type: file + description: Basic SNP table of combined positions taken from each VCF file + pattern: ".tsv" - snptable_snpeff: - type: file - description: Input file for SnpEff - pattern: ".tsv" + - meta: + type: file + description: Input file for SnpEff + pattern: ".tsv" + - snpTableForSnpEff.tsv: + type: file + description: Input file for SnpEff + pattern: ".tsv" - snptable_uncertainty: - type: file - description: Same as above, but with lower case characters indicating uncertain calls - pattern: ".tsv" + - meta: + type: file + description: Same as above, but with lower case characters indicating uncertain + calls + pattern: ".tsv" + - snpTableWithUncertaintyCalls.tsv: + type: file + description: Same as above, but with lower case characters indicating uncertain + calls + pattern: ".tsv" - structure_genotypes: - type: file - description: Input file for STRUCTURE - pattern: ".tsv" + - meta: + type: file + description: Input file for STRUCTURE + pattern: ".tsv" + - structureGenotypes.tsv: + type: file + description: Input file for STRUCTURE + pattern: ".tsv" - structure_genotypes_nomissing: - type: file - description: Alternate input file for STRUCTURE - pattern: ".tsv" + - meta: + type: file + description: Alternate input file for STRUCTURE + pattern: ".tsv" + - structureGenotypes_noMissingData-Columns.tsv: + type: file + description: Alternate input file for STRUCTURE + pattern: ".tsv" - json: - type: file - description: Summary statistics in MultiQC JSON format - pattern: ".json" + - meta: + type: file + description: Summary statistics in MultiQC JSON format + pattern: ".json" + - MultiVCFAnalyzer.json: + type: file + description: Summary statistics in MultiQC JSON format + pattern: ".json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/mummer/meta.yml b/modules/nf-core/mummer/meta.yml index 9e100f44bd48..3a4be42f0d62 100644 --- a/modules/nf-core/mummer/meta.yml +++ b/modules/nf-core/mummer/meta.yml @@ -12,34 +12,38 @@ tools: tool_dev_url: http://mummer.sourceforge.net/ doi: 10.1186/gb-2004-5-2-r12 licence: ["The Artistic License"] + identifier: biotools:mummer input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: FASTA file of the reference sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - query: - type: file - description: FASTA file of the query sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: FASTA file of the reference sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - query: + type: file + description: FASTA file of the query sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - coords: - type: file - description: File containing coordinates of matches between reference and query sequence - pattern: "*.coords" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coords": + type: file + description: File containing coordinates of matches between reference and query + sequence + pattern: "*.coords" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" - "@sateeshperi" diff --git a/modules/nf-core/muscle/meta.yml b/modules/nf-core/muscle/meta.yml index c03941bd0504..be60ba21bdc1 100644 --- a/modules/nf-core/muscle/meta.yml +++ b/modules/nf-core/muscle/meta.yml @@ -1,58 +1,108 @@ name: muscle -description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two +description: MUSCLE is a program for creating multiple alignments of amino acid or + nucleotide sequences. A range of options are provided that give you the choice of + optimizing accuracy, speed, or some compromise between the two keywords: - msa - multiple sequence alignment - phylogeny tools: - muscle: - description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput + description: MUSCLE is a multiple sequence alignment tool with high accuracy and + throughput homepage: https://www.drive5.com/muscle documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840 doi: "10.1093/nar/gkh340" licence: ["http://www.drive5.com/muscle/manual/license.html"] + identifier: biotools:muscle input: - - fasta: - type: file - description: Input sequences for alignment must be in FASTA format - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Input sequences for alignment must be in FASTA format + pattern: "*.{fasta,fa,fna}" output: - aligned_fasta: - type: file - description: Multiple sequence alignment produced in FASTA format - pattern: "*.{afa}" - - msf: - type: file - description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) - pattern: "*.{msf}" - - clustalw: - type: file - description: Multiple sequence alignment produced in ClustalW format without base/residue numbering - pattern: "*.{clw}" + - meta: + type: file + description: Multiple sequence alignment produced in FASTA format + pattern: "*.{afa}" + - "*.afa": + type: file + description: Multiple sequence alignment produced in FASTA format + pattern: "*.{afa}" - phyi: - type: file - description: Multiple sequence alignment produced in PHYLIP interleaved format - pattern: "*.{phyi}" + - meta: + type: file + description: Multiple sequence alignment produced in PHYLIP interleaved format + pattern: "*.{phyi}" + - "*.phyi": + type: file + description: Multiple sequence alignment produced in PHYLIP interleaved format + pattern: "*.{phyi}" - phys: - type: file - description: Multiple sequence alignment produced in PHYLIP sequential format - pattern: "*.{phys}" + - meta: + type: file + description: Multiple sequence alignment produced in PHYLIP sequential format + pattern: "*.{phys}" + - "*.phys": + type: file + description: Multiple sequence alignment produced in PHYLIP sequential format + pattern: "*.{phys}" + - clustalw: + - meta: + type: file + description: Multiple sequence alignment produced in ClustalW format without + base/residue numbering + pattern: "*.{clw}" + - "*.clw": + type: file + description: Multiple sequence alignment produced in ClustalW format without + base/residue numbering + pattern: "*.{clw}" - html: - type: file - description: Multiple sequence alignment produced in HTML format - pattern: "*.{html}" + - meta: + type: file + description: Multiple sequence alignment produced in HTML format + pattern: "*.{html}" + - "*.html": + type: file + description: Multiple sequence alignment produced in HTML format + pattern: "*.{html}" + - msf: + - meta: + type: file + description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) + pattern: "*.{msf}" + - "*.msf": + type: file + description: GCG Multiple Sequence File (MSF) alignment format (similar to CLUSTALW) + pattern: "*.{msf}" - tree: - type: file - description: NJ or UPGMA tree in Newick format produced from a multiple sequence alignment - pattern: "*.{tree}" + - meta: + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{tree}" + - "*.tree": + type: file + description: NJ or UPGMA tree in Newick format produced from a multiple sequence + alignment + pattern: "*.{tree}" - log: - type: file - description: Log file of MUSCLE run - pattern: "*{.log}" + - "*.log": + type: file + description: Log file of MUSCLE run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@MGordon" maintainers: diff --git a/modules/nf-core/muscle5/super5/meta.yml b/modules/nf-core/muscle5/super5/meta.yml index 057128dc8559..0959c565fe55 100644 --- a/modules/nf-core/muscle5/super5/meta.yml +++ b/modules/nf-core/muscle5/super5/meta.yml @@ -1,5 +1,7 @@ name: "muscle5_super5" -description: Muscle is a program for creating multiple alignments of amino acid or nucleotide sequences. This particular module uses the super5 algorithm for very big alignments. It can permutate the guide tree according to a set of flags. +description: Muscle is a program for creating multiple alignments of amino acid or + nucleotide sequences. This particular module uses the super5 algorithm for very + big alignments. It can permutate the guide tree according to a set of flags. keywords: - align - msa @@ -11,37 +13,44 @@ tools: documentation: "https://drive5.com/muscle5/manual/" doi: "10.1101/2021.06.20.449169" licence: ["Public Domain"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input sequences for alignment must be in FASTA format - pattern: "*.{fasta,fa,fna}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input sequences for alignment must be in FASTA format + pattern: "*.{fasta,fa,fna}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - alignment: - type: file - description: Multiple sequence alignment produced in gzipped FASTA format. If '-perm all' is passed in ext.args, this will be multiple files per input! - pattern: "*.{aln.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.aln{.gz,}": + type: file + description: Multiple sequence alignment produced in gzipped FASTA format. If + '-perm all' is passed in ext.args, this will be multiple files per input! + pattern: "*.{aln.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alessiovignoli" - "@JoseEspinosa" diff --git a/modules/nf-core/mygene/meta.yml b/modules/nf-core/mygene/meta.yml index f7aaa455613e..c83f22f79b7d 100644 --- a/modules/nf-core/mygene/meta.yml +++ b/modules/nf-core/mygene/meta.yml @@ -12,42 +12,49 @@ tools: tool_dev_url: "https://github.com/biothings/mygene.py" doi: "10.1093/nar/gks1114" licence: ["Apache-2.0"] + identifier: biotools:mygene input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gene_list: - type: file - description: A tsv/csv file that contains a list of gene ids in one of the columns. - By default, the column name should be "gene_id", but this can be changed - by using "--columname gene_id" in ext.args. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gene_list: + type: file + description: A tsv/csv file that contains a list of gene ids in one of the columns. + By default, the column name should be "gene_id", but this can be changed by + using "--columname gene_id" in ext.args. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - gmt: - type: file - description: | - Each row contains the GO id, a description, and a list of gene ids. - pattern: "*.gmt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gmt": + type: file + description: | + Each row contains the GO id, a description, and a list of gene ids. + pattern: "*.gmt" - tsv: - type: file - description: | - (optional) A tsv file with the following columns: - query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: | + (optional) A tsv file with the following columns: + query, mygene_id, go_id, go_term, go_evidence, go_category, symbol, name, taxid + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" maintainers: diff --git a/modules/nf-core/mykrobe/predict/meta.yml b/modules/nf-core/mykrobe/predict/meta.yml index ad5652ada184..57a3a440838c 100644 --- a/modules/nf-core/mykrobe/predict/meta.yml +++ b/modules/nf-core/mykrobe/predict/meta.yml @@ -12,38 +12,47 @@ tools: tool_dev_url: "https://github.com/Mykrobe-tools/mykrobe" doi: "10.1038/ncomms10063" licence: ["MIT"] + identifier: biotools:Mykrobe input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: BAM or FASTQ file - pattern: "*.{bam,fastq.gz,fq.gz}" - - species: - type: string - description: Species to make AMR prediction against - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: BAM or FASTQ file + pattern: "*.{bam,fastq.gz,fq.gz}" + - - species: + type: string + description: Species to make AMR prediction against + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: AMR predictions in CSV format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.csv: + type: file + description: AMR predictions in CSV format + pattern: "*.csv" - json: - type: file - description: AMR predictions in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.json: + type: file + description: AMR predictions in JSON format + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/nanocomp/meta.yml b/modules/nf-core/nanocomp/meta.yml index 85ddf0cd28fa..3b482d3c9c2d 100644 --- a/modules/nf-core/nanocomp/meta.yml +++ b/modules/nf-core/nanocomp/meta.yml @@ -12,94 +12,190 @@ tools: homepage: "https://github.com/wdecoster/nanocomp" documentation: "https://github.com/wdecoster/nanocomp" licence: ["MIT License"] + identifier: biotools:nanocomp input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - filelist: - type: file - description: List of all the files you want to compare, they have to be all the same filetype (either fastq, fasta, bam or Nanopore sequencing summary) - pattern: "*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - filelist: + type: file + description: List of all the files you want to compare, they have to be all + the same filetype (either fastq, fasta, bam or Nanopore sequencing summary) + pattern: "*.{fastq,fq,fna,ffn,faa,frn,fa,fasta,txt,bam}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - report_html: - type: file - description: Summary of all collected statistics - pattern: "*NanoComp-report.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp-report.html": + type: file + description: Summary of all collected statistics + pattern: "*NanoComp-report.html" - lengths_violin_html: - type: file - description: Violin plot of the sequence lengths - pattern: "*NanoComp_lengths_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_lengths_violin.html": + type: file + description: Violin plot of the sequence lengths + pattern: "*NanoComp_lengths_violin.html" - log_length_violin_html: - type: file - description: Violin plot of the sequence lengths, log function applied - pattern: "*NanoComp_log_length_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_log_length_violin.html": + type: file + description: Violin plot of the sequence lengths, log function applied + pattern: "*NanoComp_log_length_violin.html" - n50_html: - type: file - description: Bar plot of N50 sequence length per sample - pattern: "*NanoComp_N50.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_N50.html": + type: file + description: Bar plot of N50 sequence length per sample + pattern: "*NanoComp_N50.html" - number_of_reads_html: - type: file - description: Bar plot of number of reads per sample - pattern: "*NanoComp_number_of_reads.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_number_of_reads.html": + type: file + description: Bar plot of number of reads per sample + pattern: "*NanoComp_number_of_reads.html" - overlay_histogram_html: - type: file - description: Histogram of all read lengths per sample - pattern: "*NanoComp_OverlayHistogram.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram.html": + type: file + description: Histogram of all read lengths per sample + pattern: "*NanoComp_OverlayHistogram.html" - overlay_histogram_normalized_html: - type: file - description: Normalized histogram of all read lengths per sample - pattern: "*NanoComp_OverlayHistogram_Normalized.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_Normalized.html": + type: file + description: Normalized histogram of all read lengths per sample + pattern: "*NanoComp_OverlayHistogram_Normalized.html" - overlay_log_histogram_html: - type: file - description: Histogram of all read lengths per sample, log function applied - pattern: "*NanoComp_OverlayLogHistogram.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayLogHistogram.html": + type: file + description: Histogram of all read lengths per sample, log function applied + pattern: "*NanoComp_OverlayLogHistogram.html" - overlay_log_histogram_normalized_html: - type: file - description: Normalized histogram of all read lengths per sample, log function applied - pattern: "*NanoComp_OverlayLogHistogram_Normalized.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayLogHistogram_Normalized.html": + type: file + description: Normalized histogram of all read lengths per sample, log function + applied + pattern: "*NanoComp_OverlayLogHistogram_Normalized.html" - total_throughput_html: - type: file - description: Barplot comparing throughput in bases - pattern: "*NanoComp_total_throughput.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_total_throughput.html": + type: file + description: Barplot comparing throughput in bases + pattern: "*NanoComp_total_throughput.html" - quals_violin_html: - type: file - description: Violin plot of base qualities, only for bam, fastq and sequencing summary input - pattern: "*NanoComp_quals_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_quals_violin.html": + type: file + description: Violin plot of base qualities, only for bam, fastq and sequencing + summary input + pattern: "*NanoComp_quals_violin.html" - overlay_histogram_identity_html: - type: file - description: Histogram of perfect reference identity, only for bam input - pattern: "*NanoComp_OverlayHistogram_Identity.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_Identity.html": + type: file + description: Histogram of perfect reference identity, only for bam input + pattern: "*NanoComp_OverlayHistogram_Identity.html" - overlay_histogram_phredscore_html: - type: file - description: Histogram of phred scores, only for bam input - pattern: "*NanoComp_OverlayHistogram_PhredScore.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_OverlayHistogram_PhredScore.html": + type: file + description: Histogram of phred scores, only for bam input + pattern: "*NanoComp_OverlayHistogram_PhredScore.html" - percent_identity_violin_html: - type: file - description: Violin plot comparing perfect reference identity, only for bam input - pattern: "*NanoComp_percentIdentity_violin.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_percentIdentity_violin.html": + type: file + description: Violin plot comparing perfect reference identity, only for bam + input + pattern: "*NanoComp_percentIdentity_violin.html" - active_pores_over_time_html: - type: file - description: Scatter plot of active pores over time, only for sequencing summary input - pattern: "*NanoComp_ActivePoresOverTime.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_ActivePoresOverTime.html": + type: file + description: Scatter plot of active pores over time, only for sequencing summary + input + pattern: "*NanoComp_ActivePoresOverTime.html" - cumulative_yield_plot_gigabases_html: - type: file - description: Scatter plot of cumulative yield, only for sequencing summary input - pattern: "*NanoComp_CumulativeYieldPlot_Gigabases.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_CumulativeYieldPlot_Gigabases.html": + type: file + description: Scatter plot of cumulative yield, only for sequencing summary input + pattern: "*NanoComp_CumulativeYieldPlot_Gigabases.html" - sequencing_speed_over_time_html: - type: file - description: Scatter plot of sequencing speed over time, only for sequencing summary input - pattern: "*NanoComp_sequencing_speed_over_time.html" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoComp_sequencing_speed_over_time.html": + type: file + description: Scatter plot of sequencing speed over time, only for sequencing + summary input + pattern: "*NanoComp_sequencing_speed_over_time.html" - stats_txt: - type: file - description: txt file with basic statistics - pattern: "*NanoStats.txt" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*NanoStats.txt": + type: file + description: txt file with basic statistics + pattern: "*NanoStats.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@paulwolk" maintainers: diff --git a/modules/nf-core/nanofilt/meta.yml b/modules/nf-core/nanofilt/meta.yml index af15136ce1a3..ed495e3a2b7e 100644 --- a/modules/nf-core/nanofilt/meta.yml +++ b/modules/nf-core/nanofilt/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nanofilt" description: Filtering and trimming of Oxford Nanopore Sequencing data @@ -14,45 +13,43 @@ tools: tool_dev_url: "https://github.com/wdecoster/nanofilt" doi: "10.1093/bioinformatics/bty149" licence: ["GLP-3.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Gunziped fastq files from Oxford Nanopore sequencing. - pattern: "*.fastq.gz" - - - summary_file: - type: file - description: Optional - Albacore or guppy summary file for quality scores - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Gunziped fastq files from Oxford Nanopore sequencing. + pattern: "*.fastq.gz" + - - summary_file: + type: file + description: Optional - Albacore or guppy summary file for quality scores output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - filtreads: - type: file - description: Gunziped fastq files after filtering. - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: Gunziped fastq files after filtering. + pattern: "*.fastq.gz" - log_file: - type: file - description: Log file generated by --logfile option in NanoFilt, the file must end with .log extension. - pattern: "*.log" - + - "*.log": + type: file + description: Log file generated by --logfile option in NanoFilt, the file must + end with .log extension. + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lfreitasl" maintainers: diff --git a/modules/nf-core/nanolyse/meta.yml b/modules/nf-core/nanolyse/meta.yml index 20a1b289cc14..b0db2b7f8fda 100644 --- a/modules/nf-core/nanolyse/meta.yml +++ b/modules/nf-core/nanolyse/meta.yml @@ -11,40 +11,44 @@ tools: homepage: https://github.com/wdecoster/nanolyse documentation: https://github.com/wdecoster/nanolyse#nanolyse licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - Basecalled reads in FASTQ.GZ format - pattern: "*.fastq.gz" - - fasta: - type: file - description: | - A reference fasta file against which to filter. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + Basecalled reads in FASTQ.GZ format + pattern: "*.fastq.gz" + - - fasta: + type: file + description: | + A reference fasta file against which to filter. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Reads with contaminants removed in FASTQ format - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Reads with contaminants removed in FASTQ format + pattern: "*.fastq.gz" - log: - type: file - description: Log of the Nanolyse run. - pattern: "*.log" + - "*.log": + type: file + description: Log of the Nanolyse run. + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" maintainers: diff --git a/modules/nf-core/nanomonsv/parse/meta.yml b/modules/nf-core/nanomonsv/parse/meta.yml index db42b42adbd3..5b92be94ba9b 100644 --- a/modules/nf-core/nanomonsv/parse/meta.yml +++ b/modules/nf-core/nanomonsv/parse/meta.yml @@ -21,62 +21,107 @@ tools: tool_dev_url: https://github.com/friend1ws/nanomonsv doi: "10.1101/2020.07.22.214262 " licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - insertions: - type: file - description: Gzipped BED file containing reads supporting insertions - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertion.sorted.bed.gz: + type: file + description: Gzipped BED file containing reads supporting insertions + pattern: "*.{bed.gz}" - insertions_index: - type: file - description: Index for gzipped BED file containing reads supporting insertions - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertion.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting insertions + pattern: "*.{bed.gz.tbi}" - deletions: - type: file - description: Gzipped BED file containing reads supporting deletions - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.deletion.sorted.bed.gz: + type: file + description: Gzipped BED file containing reads supporting deletions + pattern: "*.{bed.gz}" - deletions_index: - type: file - description: Index for gzipped BED file containing reads supporting deletions - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.deletion.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting deletions + pattern: "*.{bed.gz.tbi}" - rearrangements: - type: file - description: Gzipped BED file containing reads supporting rearrangements - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.rearrangement.sorted.bedpe.gz: + type: file + description: Gzipped BED file containing reads supporting rearrangements + pattern: "*.{bed.gz}" - rearrangements_index: - type: file - description: Index for gzipped BED file containing reads supporting rearrangements - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.rearrangement.sorted.bedpe.gz.tbi: + type: file + description: Index for gzipped BED file containing reads supporting rearrangements + pattern: "*.{bed.gz.tbi}" - bp_info: - type: file - description: Gzipped BED file containing breakpoint info - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bp_info.sorted.bed.gz: + type: file + description: Gzipped BED file containing breakpoint info + pattern: "*.{bed.gz}" - bp_info_index: - type: file - description: Index for gzipped BED file containing breakpoint info - pattern: "*.{bed.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bp_info.sorted.bed.gz.tbi: + type: file + description: Index for gzipped BED file containing breakpoint info + pattern: "*.{bed.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@awgymer" maintainers: diff --git a/modules/nf-core/nanoplot/meta.yml b/modules/nf-core/nanoplot/meta.yml index 46fbd562bc70..8af83355ecd8 100644 --- a/modules/nf-core/nanoplot/meta.yml +++ b/modules/nf-core/nanoplot/meta.yml @@ -14,46 +14,62 @@ tools: homepage: http://nanoplot.bioinf.be documentation: https://github.com/wdecoster/NanoPlot licence: ["GPL-3.0-or-later"] + identifier: biotools:nanoplot input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input basecalled-FastQ files. - - summary_txt: - type: file - description: | - List of sequencing_summary.txt files from running basecalling. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ontfile: + type: file + description: ONT file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: NanoPlot report - pattern: "*{.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: NanoPlot report + pattern: "*{.html}" - png: - type: file - description: Plots generated by NanoPlot - pattern: "*{.png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: Plots generated by NanoPlot + pattern: "*{.png}" - txt: - type: file - description: Stats from NanoPlot - pattern: "*{.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Stats from NanoPlot + pattern: "*{.txt}" - log: - type: file - description: log file of NanoPlot run - pattern: "*{.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: log file of NanoPlot run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa" diff --git a/modules/nf-core/nanoq/meta.yml b/modules/nf-core/nanoq/meta.yml index 85c0c9789a15..0ff2b9b4efee 100644 --- a/modules/nf-core/nanoq/meta.yml +++ b/modules/nf-core/nanoq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nanoq" -description: Nanoq implements ultra-fast read filters and summary reports for high-throughput nanopore reads. +description: Nanoq implements ultra-fast read filters and summary reports for high-throughput + nanopore reads. keywords: - nanoq - Read filters @@ -15,45 +15,48 @@ tools: tool_dev_url: "https://github.com/esteinig/nanoq" doi: "10.21105/joss.02991" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - ontreads: - type: file - description: Compressed or uncompressed nanopore reads in fasta or fastq formats. - pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" - - - output_format: - type: string - description: "Specifies the output format. One of these formats: fasta, fastq; fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ontreads: + type: file + description: Compressed or uncompressed nanopore reads in fasta or fastq formats. + pattern: "*.{fa,fna,faa,fasta,fq,fastq}{,.gz,.bz2,.xz}" + - - output_format: + type: string + description: "Specifies the output format. One of these formats: fasta, fastq; + fasta.gz, fastq.gz; fasta.bz2, fastq.bz2; fasta.lzma, fastq.lzma." output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - stats: - type: file - description: Summary report of reads statistics. - pattern: "*.{stats,json}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{stats,json}": + type: file + description: Summary report of reads statistics. + pattern: "*.{stats,json}" - reads: - type: file - description: Filtered reads. - pattern: "*.{fasta,fastq}{,.gz,.bz2,.lzma}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_filtered.${output_format}": + type: file + description: Filtered reads. + pattern: "*.{fasta,fastq}{,.gz,.bz2,.lzma}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/narfmap/align/environment.yml b/modules/nf-core/narfmap/align/environment.yml index 57ce13586f1f..9a0831a3d28f 100644 --- a/modules/nf-core/narfmap/align/environment.yml +++ b/modules/nf-core/narfmap/align/environment.yml @@ -1,9 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - # renovate: datasource=conda depName=bioconda/narfmap - narfmap=1.4.2 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.18 - pigz=2.8 + - samtools=1.18 diff --git a/modules/nf-core/narfmap/align/meta.yml b/modules/nf-core/narfmap/align/meta.yml index 0924a0b08054..557507c9abd9 100644 --- a/modules/nf-core/narfmap/align/meta.yml +++ b/modules/nf-core/narfmap/align/meta.yml @@ -13,35 +13,64 @@ tools: documentation: https://github.com/edmundmiller/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage tool_dev_url: https://github.com/edmundmiller/narfmap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - hashmap: - type: file - description: NARFMAP hash table - pattern: "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - hashmap: + type: file + description: NARFMAP hash table + pattern: "Directory containing NARFMAP hash table *.{cmp,.bin,.txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fa,fna}" + - - sort_bam: + type: boolean + description: Sort the BAM file after alignment output: - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: Log file of NARFMAP run + pattern: "*{.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/narfmap/hashtable/meta.yml b/modules/nf-core/narfmap/hashtable/meta.yml index 9b6715af8bf6..7fc344ce836e 100644 --- a/modules/nf-core/narfmap/hashtable/meta.yml +++ b/modules/nf-core/narfmap/hashtable/meta.yml @@ -12,29 +12,32 @@ tools: documentation: https://github.com/edmundmiller/NARFMAP/blob/main/doc/usage.md#basic-command-line-usage tool_dev_url: https://github.com/edmundmiller/narfmap licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - hashmap: - type: file - description: NARFMAP hash table - pattern: "*.{cmp,.bin,.txt}" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - narfmap: + type: file + description: NARFMAP hash table + pattern: "*.{cmp,.bin,.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/ncbigenomedownload/meta.yml b/modules/nf-core/ncbigenomedownload/meta.yml index e7d372010736..794d931038a8 100644 --- a/modules/nf-core/ncbigenomedownload/meta.yml +++ b/modules/nf-core/ncbigenomedownload/meta.yml @@ -11,85 +11,169 @@ tools: documentation: https://github.com/kblin/ncbi-genome-download tool_dev_url: https://github.com/kblin/ncbi-genome-download licence: ["Apache Software License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - accessions: - type: file - description: List of accessions (one per line) to download - pattern: "*.txt" - - taxids: - type: file - description: List of taxids (one per line) to download - pattern: "*.txt" - - groups: - type: string - description: NCBI taxonomic groups to download. Can be a comma-separated list. Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral'] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - - accessions: + type: file + description: List of accessions (one per line) to download + pattern: "*.txt" + - - taxids: + type: file + description: List of taxids (one per line) to download + pattern: "*.txt" + - - groups: + type: string + description: NCBI taxonomic groups to download. Can be a comma-separated list. + Options are ['all', 'archaea', 'bacteria', 'fungi', 'invertebrate', 'metagenomes', + 'plant', 'protozoa', 'vertebrate_mammalian', 'vertebrate_other', 'viral'] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gbk: - type: file - description: GenBank format of the genomic sequence(s) in the assembly - pattern: "*_genomic.gbff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.gbff.gz": + type: file + description: GenBank format of the genomic sequence(s) in the assembly + pattern: "*_genomic.gbff.gz" - fna: - type: file - description: FASTA format of the genomic sequence(s) in the assembly. - pattern: "*_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.fna.gz": + type: file + description: FASTA format of the genomic sequence(s) in the assembly. + pattern: "*_genomic.fna.gz" - rm: - type: file - description: RepeatMasker output for eukaryotes. - pattern: "*_rm.out.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rm.out.gz": + type: file + description: RepeatMasker output for eukaryotes. + pattern: "*_rm.out.gz" - features: - type: file - description: Tab-delimited text file reporting locations and attributes for a subset of annotated features - pattern: "*_feature_table.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_feature_table.txt.gz": + type: file + description: Tab-delimited text file reporting locations and attributes for + a subset of annotated features + pattern: "*_feature_table.txt.gz" - gff: - type: file - description: Annotation of the genomic sequence(s) in GFF3 format - pattern: "*_genomic.gff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_genomic.gff.gz": + type: file + description: Annotation of the genomic sequence(s) in GFF3 format + pattern: "*_genomic.gff.gz" - faa: - type: file - description: FASTA format of the accessioned protein products annotated on the genome assembly. - pattern: "*_protein.faa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_protein.faa.gz": + type: file + description: FASTA format of the accessioned protein products annotated on the + genome assembly. + pattern: "*_protein.faa.gz" - gpff: - type: file - description: GenPept format of the accessioned protein products annotated on the genome assembly. - pattern: "*_protein.gpff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_protein.gpff.gz": + type: file + description: GenPept format of the accessioned protein products annotated on + the genome assembly. + pattern: "*_protein.gpff.gz" - wgs_gbk: - type: file - description: GenBank flat file format of the WGS master for the assembly - pattern: "*_wgsmaster.gbff.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_wgsmaster.gbff.gz": + type: file + description: GenBank flat file format of the WGS master for the assembly + pattern: "*_wgsmaster.gbff.gz" - cds: - type: file - description: FASTA format of the nucleotide sequences corresponding to all CDS features annotated on the assembly - pattern: "*_cds_from_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_cds_from_genomic.fna.gz": + type: file + description: FASTA format of the nucleotide sequences corresponding to all CDS + features annotated on the assembly + pattern: "*_cds_from_genomic.fna.gz" - rna: - type: file - description: FASTA format of accessioned RNA products annotated on the genome assembly - pattern: "*_rna.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rna.fna.gz": + type: file + description: FASTA format of accessioned RNA products annotated on the genome + assembly + pattern: "*_rna.fna.gz" - rna_fna: - type: file - description: FASTA format of the nucleotide sequences corresponding to all RNA features annotated on the assembly - pattern: "*_rna_from_genomic.fna.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rna_from_genomic.fna.gz": + type: file + description: FASTA format of the nucleotide sequences corresponding to all RNA + features annotated on the assembly + pattern: "*_rna_from_genomic.fna.gz" - report: - type: file - description: Tab-delimited text file reporting the name, role and sequence accession.version for objects in the assembly - pattern: "*_assembly_report.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_report.txt": + type: file + description: Tab-delimited text file reporting the name, role and sequence accession.version + for objects in the assembly + pattern: "*_assembly_report.txt" - stats: - type: file - description: Tab-delimited text file reporting statistics for the assembly - pattern: "*_assembly_stats.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_stats.txt": + type: file + description: Tab-delimited text file reporting statistics for the assembly + pattern: "*_assembly_stats.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ncbitools/vecscreen/meta.yml b/modules/nf-core/ncbitools/vecscreen/meta.yml index 45f0f7e27807..54f28f6c3b6d 100644 --- a/modules/nf-core/ncbitools/vecscreen/meta.yml +++ b/modules/nf-core/ncbitools/vecscreen/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "NCBITOOLS_VECSCREEN" -description: NCBI tool for detecting vector contamination in nucleic acid sequences. This tool is older than NCBI's FCS-adaptor, which is for the same purpose +description: NCBI tool for detecting vector contamination in nucleic acid sequences. + This tool is older than NCBI's FCS-adaptor, which is for the same purpose keywords: - assembly - genomics @@ -17,34 +17,43 @@ tools: documentation: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/interpretation/" tool_dev_url: "https://www.ncbi.nlm.nih.gov/tools/vecscreen/" licence: ["The Open Database License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'6973' ] - - fasta_file: - type: file - description: FASTA file that will be screened for contaminants - - adapters_database_file: - type: file - description: Path to a nucleotide BLAST database file with vector sequences - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'6973' ] + - fasta_file: + type: file + description: FASTA file that will be screened for contaminants + - - adapters_database_meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - adapters_database_directory: + type: directory + description: Directory containing the adapters database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', taxid:'9606' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vecscreen_output: - type: file - description: VecScreen report file. This can be in different formats depending on the value of the optional -f parameter. 0 = HTML format, with alignments. 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, no alignments. default = 0 - pattern: "*.vecscreen.out" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', taxid:'9606' ] + - ${meta.id}.vecscreen.out: + type: file + description: VecScreen report file. This can be in different formats depending + on the value of the optional -f parameter. 0 = HTML format, with alignments. + 1 = HTML format, no alignments. 2 = Text list, with alignments. 3 = Text list, + no alignments. default = 0 + pattern: "*.vecscreen.out" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@eeaunin" diff --git a/modules/nf-core/nextclade/datasetget/meta.yml b/modules/nf-core/nextclade/datasetget/meta.yml index 290ed0cd9263..c60721da6944 100644 --- a/modules/nf-core/nextclade/datasetget/meta.yml +++ b/modules/nf-core/nextclade/datasetget/meta.yml @@ -1,34 +1,40 @@ name: nextclade_datasetget -description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) +description: Get dataset for SARS-CoV-2 genome clade assignment, mutation calling, + and sequence quality checks (C++ implementation) keywords: - nextclade - variant - consensus tools: - nextclade: - description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks + description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence + quality checks homepage: https://github.com/nextstrain/nextclade documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade licence: ["MIT"] + identifier: biotools:nextclade input: - - dataset: - type: string - description: Name of dataset to retrieve. A list of available datasets can be obtained using the nextclade dataset list command. - pattern: ".+" - - tag: - type: string - description: Version tag of the dataset to download. A list of available datasets can be obtained using the nextclade dataset list command. - pattern: ".+" + - - dataset: + type: string + description: Name of dataset to retrieve. A list of available datasets can be + obtained using the nextclade dataset list command. + pattern: ".+" + - - tag: + type: string + description: Version tag of the dataset to download. A list of available datasets + can be obtained using the nextclade dataset list command. + pattern: ".+" output: + - dataset: + - $prefix: + type: directory + description: Directory containing the dataset - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - prefix: - type: directory - description: A directory containing the dataset files needed for nextclade run - pattern: "prefix" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@antunderwood" - "@drpatelh" diff --git a/modules/nf-core/nextclade/run/meta.yml b/modules/nf-core/nextclade/run/meta.yml index bb7bf6c2d0ef..4062b3f4d572 100644 --- a/modules/nf-core/nextclade/run/meta.yml +++ b/modules/nf-core/nextclade/run/meta.yml @@ -1,81 +1,140 @@ name: nextclade_run -description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks (C++ implementation) +description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality + checks (C++ implementation) keywords: - nextclade - variant - consensus tools: - nextclade: - description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence quality checks + description: SARS-CoV-2 genome clade assignment, mutation calling, and sequence + quality checks homepage: https://github.com/nextstrain/nextclade documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade licence: ["MIT"] + identifier: biotools:nextclade input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - dataset: - type: directory - description: Path containing the dataset files obtained by running nextclade dataset get - pattern: "*" - - fasta: - type: file - description: FASTA file containing one or more consensus sequences - pattern: "*.{fasta,fa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing one or more consensus sequences + pattern: "*.{fasta,fa}" + - - dataset: + type: directory + description: Path containing the dataset files obtained by running nextclade + dataset get + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: CSV file containing nextclade results - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.csv: + type: file + description: CSV file containing nextclade results + pattern: "*.{csv}" - csv_errors: - type: file - description: CSV file containing errors from nextclade results - pattern: "*.{errors.csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.errors.csv: + type: file + description: CSV file containing errors from nextclade results + pattern: "*.{errors.csv}" - csv_insertions: - type: file - description: CSV file containing insertions from nextclade results - pattern: "*.{insertions.csv}" - - fasta_aligned: - type: file - description: FASTA file containing aligned sequences from nextclade results - pattern: "*.{aligned.fasta}" - - fasta_translation: - type: file - description: FASTA file containing aligned peptides from nextclade results - pattern: "*.{_translation.}*.{fasta}" - - ndjson: - type: file - description: newline-delimited JSON file containing nextclade results - pattern: "*.{ndjson}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.insertions.csv: + type: file + description: CSV file containing insertions from nextclade results + pattern: "*.{insertions.csv}" + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: TSV file containing nextclade results + pattern: "*.{tsv}" - json: - type: file - description: JSON file containing nextclade results - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.json: + type: file + description: JSON file containing nextclade results + pattern: "*.{json}" - json_auspice: - type: file - description: Auspice JSON V2 containing nextclade results - pattern: "*.{tree.json}" - - tsv: - type: file - description: TSV file containing nextclade results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.auspice.json: + type: file + description: Auspice JSON V2 containing nextclade results + pattern: "*.{tree.json}" + - ndjson: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.ndjson: + type: file + description: newline-delimited JSON file containing nextclade results + pattern: "*.{ndjson}" + - fasta_aligned: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.aligned.fasta: + type: file + description: FASTA file containing aligned sequences from nextclade results + pattern: "*.{aligned.fasta}" + - fasta_translation: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_translation.*.fasta": + type: file + description: FASTA file containing aligned peptides from nextclade results + pattern: "*.{_translation.}*.{fasta}" - nwk: - type: file - description: NWK file containing nextclade results - pattern: "*.{nwk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.nwk: + type: file + description: NWK file containing nextclade results + pattern: "*.{nwk}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@antunderwood" - "@drpatelh" diff --git a/modules/nf-core/nextgenmap/meta.yml b/modules/nf-core/nextgenmap/meta.yml index 3b05d8eb8932..dd8cb2a6c08b 100644 --- a/modules/nf-core/nextgenmap/meta.yml +++ b/modules/nf-core/nextgenmap/meta.yml @@ -18,39 +18,42 @@ tools: documentation: https://github.com/Cibiv/NextGenMap/wiki doi: 10.1093/bioinformatics/btt468 licence: ["MIT"] + identifier: biotools:nextgenmap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1, if meta.single_end is true, and 2 - if meta.single_end is false. - - fasta: - type: file - description: | - Genomic reference fasta file - pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1, if meta.single_end is true, and 2 + if meta.single_end is false. + - - fasta: + type: file + description: | + Genomic reference fasta file + pattern: "*.{fa,fa.gz,fas,fas.gz,fna,fna.gz,fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. First item of tuple with - bam, below. - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: | - Output BAM file containing read alignments. Second item of tuple with - meta, above - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information. First item of tuple with + bam, below. + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: | + Output BAM file containing read alignments. Second item of tuple with + meta, above + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@cmatkhan" maintainers: diff --git a/modules/nf-core/ngmaster/meta.yml b/modules/nf-core/ngmaster/meta.yml index b4a3677ef310..7f6eaefd600d 100644 --- a/modules/nf-core/ngmaster/meta.yml +++ b/modules/nf-core/ngmaster/meta.yml @@ -6,36 +6,40 @@ keywords: - serotype tools: - ngmaster: - description: In silico multi-antigen sequence typing for Neisseria gonorrhoeae (NG-MAST) + description: In silico multi-antigen sequence typing for Neisseria gonorrhoeae + (NG-MAST) homepage: https://github.com/MDU-PHL/ngmaster/blob/master/README.md documentation: https://github.com/MDU-PHL/ngmaster/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/ngmaster doi: "10.1099/mgen.0.000076" licence: ["GPL v3 only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited result file - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited result file + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/ngmerge/meta.yml b/modules/nf-core/ngmerge/meta.yml index 7e83a14a0af8..0d2305728cd9 100644 --- a/modules/nf-core/ngmerge/meta.yml +++ b/modules/nf-core/ngmerge/meta.yml @@ -1,4 +1,3 @@ ---- name: "ngmerge" description: Merging paired-end reads and removing sequencing adapters. keywords: @@ -13,39 +12,54 @@ tools: tool_dev_url: "https://github.com/jsh58/NGmerge" doi: "10.1186/s12859-018-2579-2" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: | - List of input FastQ files of size 2; i.e., paired-end data. - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: | + List of input FastQ files of size 2; i.e., paired-end data. + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_reads: - type: file - description: fastq file merged reads - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.merged.fq.gz": + type: file + description: fastq file merged reads + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - unstitched_read1: - type: file - description: fastq file unstitched read 1 - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_1.fastq.gz": + type: file + description: fastq file unstitched read 1 + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" - unstitched_read2: - type: file - description: fastq file unstitched read 2 - pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_2.fastq.gz": + type: file + description: fastq file unstitched read 2 + pattern: "*.{fa,fasta,fastq,fq,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charlotteanne" - "@jsh58" diff --git a/modules/nf-core/ngsbits/samplegender/meta.yml b/modules/nf-core/ngsbits/samplegender/meta.yml index 961462b3f7df..54a611812dfa 100644 --- a/modules/nf-core/ngsbits/samplegender/meta.yml +++ b/modules/nf-core/ngsbits/samplegender/meta.yml @@ -1,4 +1,3 @@ ---- name: "ngsbits_samplegender" description: Determines the gender of a sample from the BAM/CRAM file. keywords: @@ -13,56 +12,60 @@ tools: documentation: "https://github.com/imgag/ngs-bits" tool_dev_url: "https://github.com/imgag/ngs-bits" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: One or more BAM/CRAM files to determine the gender of - pattern: "*.{bam,cram}" - - bai: - type: file - description: The index file(s) from the input BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference fasta information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA to use (mandatory when CRAM files are used) - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index information - e.g. [ id:'test' ] - - fasta: - type: file - description: The index of the reference FASTA to use (mandatory when CRAM files are used) - pattern: "*.fai" - - method: - type: string - description: The method to use to define the gender (posibilities are 'xy', 'hetx' and 'sry') - pattern: "(xy|hetx|sry)" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: One or more BAM/CRAM files to determine the gender of + pattern: "*.{bam,cram}" + - bai: + type: file + description: The index file(s) from the input BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA to use (mandatory when CRAM files are used) + pattern: "*.{fasta,fa,fna}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta information + e.g. [ id:'test' ] + - fai: + type: file + description: The index file from the reference FASTA + pattern: "*.fai" + - - method: + type: string + description: The method to use to define the gender (posibilities are 'xy', + 'hetx' and 'sry') + pattern: "(xy|hetx|sry)" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: An output TSV file containing the results of the gender prediction - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: An output TSV file containing the results of the gender prediction + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/ngscheckmate/fastq/meta.yml b/modules/nf-core/ngscheckmate/fastq/meta.yml index 3553deaca6d7..47a6aaf7541e 100644 --- a/modules/nf-core/ngscheckmate/fastq/meta.yml +++ b/modules/nf-core/ngscheckmate/fastq/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_fastq" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates vaf files for individual fastq file(s), ready for the vafncm module. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates vaf files for individual fastq file(s), + ready for the vafncm module. keywords: - ngscheckmate - matching @@ -9,45 +10,52 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the fastq files - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: Raw fastq files for one sample, single or paired end. - pattern: "*.{fastq.gz}" - - meta2: - type: file - description: | - Groovy Map containing sample information about the NGSCheckMate SNP pt file - e.g. `[ id:'test', single_end:false ]` - - snp_pt: - type: file - description: PT file containing SNP data, generated by ngscheckmate/patterngenerator. For human data, use the files from NGSCheckMate's github repository. - pattern: "*.{pt}" + - - meta: + type: map + description: | + Groovy Map containing sample information about the fastq files + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: Raw fastq files for one sample, single or paired end. + pattern: "*.{fastq.gz}" + - - meta2: + type: file + description: | + Groovy Map containing sample information about the NGSCheckMate SNP pt file + e.g. `[ id:'test', single_end:false ]` + - snp_pt: + type: file + description: PT file containing SNP data, generated by ngscheckmate/patterngenerator. + For human data, use the files from NGSCheckMate's github repository. + pattern: "*.{pt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - vaf: - type: file - description: Text file containing reference/alt allele depth for each SNP position contained in the PT file. - pattern: "*.{vaf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vaf": + type: file + description: Text file containing reference/alt allele depth for each SNP position + contained in the PT file. + pattern: "*.{vaf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/ncm/meta.yml b/modules/nf-core/ngscheckmate/ncm/meta.yml index 0defad00644f..06c131d6b076 100644 --- a/modules/nf-core/ngscheckmate/ncm/meta.yml +++ b/modules/nf-core/ngscheckmate/ncm/meta.yml @@ -1,70 +1,105 @@ name: ngscheckmate_ncm -description: Determining whether sequencing data comes from the same individual by using SNP matching. Designed for humans on vcf or bam files. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. Designed for humans on vcf or bam files. keywords: - ngscheckmate - matching - snp tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - files: - type: file - description: VCF or BAM files for each sample, in a merged channel (possibly gzipped). BAM files require an index too. - pattern: "*.{vcf,vcf.gz,bam,bai}" - - meta2: - type: map - description: | - Groovy Map containing SNP information - e.g. [ id:'test' ] - - snp_bed: - type: file - description: BED file containing the SNPs to analyse - pattern: "*.{bed}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index information - e.g. [ id:'test' ] - - fasta: - type: file - description: fasta file for the genome, only used in the bam mode - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - files: + type: file + description: VCF or BAM files for each sample, in a merged channel (possibly + gzipped). BAM files require an index too. + pattern: "*.{vcf,vcf.gz,bam,bai}" + - - meta2: + type: map + description: | + Groovy Map containing SNP information + e.g. [ id:'test' ] + - snp_bed: + type: file + description: BED file containing the SNPs to analyse + pattern: "*.{bed}" + - - meta3: + type: map + description: | + Groovy Map containing reference fasta index information + e.g. [ id:'test' ] + - fasta: + type: file + description: fasta file for the genome, only used in the bam mode + pattern: "*.{bed}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pdf: - type: file - description: A pdf containing a dendrogram showing how the samples match up - pattern: "*.{pdf}" - corr_matrix: - type: file - description: A text file containing the correlation matrix between each sample - pattern: "*corr_matrix.txt" + - meta: + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" + - "*_corr_matrix.txt": + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" - matched: - type: file - description: A txt file containing only the samples that match with each other - pattern: "*matched.txt" + - meta: + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" + - "*_matched.txt": + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" - all: - type: file - description: A txt file containing all the sample comparisons, whether they match or not - pattern: "*all.txt" + - meta: + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - "*_all.txt": + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - pdf: + - meta: + type: file + description: A pdf containing a dendrogram showing how the samples match up + pattern: "*.{pdf}" + - "*.pdf": + type: file + description: A pdf containing a dendrogram showing how the samples match up + pattern: "*.{pdf}" - vcf: - type: file - description: If ran in bam mode, vcf files for each sample giving the SNP calls used - pattern: "*.vcf" + - meta: + type: file + description: If ran in bam mode, vcf files for each sample giving the SNP calls + used + pattern: "*.vcf" + - "*.vcf": + type: file + description: If ran in bam mode, vcf files for each sample giving the SNP calls + used + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml index 92c9ec1da419..370060bcf1b1 100644 --- a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml +++ b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_patterngenerator" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates PT files from a bed file containing individual + positions. keywords: - ngscheckmate - matching @@ -9,48 +10,59 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the bed file - e.g. `[ id:'test', single_end:false ]` - - bed: - type: file - description: BED file containing population-level SNPs to use - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing sample information about the fasta genome - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Genome fasta file - pattern: "*.fasta" - - bowtie_index: - type: directory - description: Folder of Bowtie genome index files + - - meta: + type: map + description: | + Groovy Map containing sample information about the bed file + e.g. `[ id:'test', single_end:false ]` + - bed: + type: file + description: BED file containing population-level SNPs to use + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information about the fasta genome + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bowtie_index: + type: directory + description: Folder of Bowtie genome index files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pt: - type: file - description: Generated binary pattern file, containing FASTQ strings to match from within raw data - pattern: "*.pt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.pt": + type: file + description: Generated binary pattern file, containing FASTQ strings to match + from within raw data + pattern: "*.pt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/ngscheckmate/vafncm/meta.yml b/modules/nf-core/ngscheckmate/vafncm/meta.yml index 3877a88bff53..e96f65a371bf 100644 --- a/modules/nf-core/ngscheckmate/vafncm/meta.yml +++ b/modules/nf-core/ngscheckmate/vafncm/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "ngscheckmate_vafncm" -description: Determining whether sequencing data comes from the same individual by using SNP matching. This module generates PT files from a bed file containing individual positions. +description: Determining whether sequencing data comes from the same individual by + using SNP matching. This module generates PT files from a bed file containing individual + positions. keywords: - ngscheckmate - matching @@ -9,48 +10,75 @@ keywords: - qc tools: - ngscheckmate: - description: NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual, including matching between DNA and RNA. + description: NGSCheckMate is a software package for identifying next generation + sequencing (NGS) data files from the same individual, including matching between + DNA and RNA. homepage: https://github.com/parklab/NGSCheckMate documentation: https://github.com/parklab/NGSCheckMate tool_dev_url: https://github.com/parklab/NGSCheckMate doi: "10.1093/nar/gkx193" licence: ["MIT"] + identifier: biotools:ngscheckmate input: - - meta: - type: map - description: | - Groovy Map containing sample information about the combined set of files - e.g. `[ id:'combined' ]` - - vafs: - type: file - description: Text files containing information about reference/alternate allele depths for the SNP positions, generated by ngscheckmate/fastq - pattern: "*.{vaf}" + - - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - vafs: + type: file + description: Text files containing information about reference/alternate allele + depths for the SNP positions, generated by ngscheckmate/fastq + pattern: "*.{vaf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information about the combined set of files - e.g. `[ id:'combined' ]` - pdf: - type: file - description: A pdf containing a dendrogram showing how the samples match up. | Note due to a bug in the R script used by the tool this is not produced when only two samples are given. - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*.pdf": + type: file + description: A pdf containing a dendrogram showing how the samples match up. + | Note due to a bug in the R script used by the tool this is not produced + when only two samples are given. + pattern: "*.{pdf}" - corr_matrix: - type: file - description: A text file containing the correlation matrix between each sample - pattern: "*corr_matrix.txt" - - matched: - type: file - description: A txt file containing only the samples that match with each other - pattern: "*matched.txt" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_corr_matrix.txt": + type: file + description: A text file containing the correlation matrix between each sample + pattern: "*corr_matrix.txt" - all: - type: file - description: A txt file containing all the sample comparisons, whether they match or not - pattern: "*all.txt" + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_all.txt": + type: file + description: A txt file containing all the sample comparisons, whether they + match or not + pattern: "*all.txt" + - matched: + - meta: + type: map + description: | + Groovy Map containing sample information about the combined set of files + e.g. `[ id:'combined' ]` + - "*_matched.txt": + type: file + description: A txt file containing only the samples that match with each other + pattern: "*matched.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/nonpareil/curve/meta.yml b/modules/nf-core/nonpareil/curve/meta.yml index 87aaa363e829..cd80f16fe960 100644 --- a/modules/nf-core/nonpareil/curve/meta.yml +++ b/modules/nf-core/nonpareil/curve/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_curve" -description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil npo file +description: Visualise metagenome redundancy curve in PNG format from a single Nonpareil + npo file keywords: - metagenomics - statistics @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - npo: - type: file - description: Single npo redundancy summary file from nonpareil itself - pattern: "*.npo" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - npo: + type: file + description: Single npo redundancy summary file from nonpareil itself + pattern: "*.npo" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: PNG file of the Nonpareil curve - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: PNG file of the Nonpareil curve + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/nonpareil/meta.yml b/modules/nf-core/nonpareil/nonpareil/meta.yml index 59f8bc05610a..9890166dd13e 100644 --- a/modules/nf-core/nonpareil/nonpareil/meta.yml +++ b/modules/nf-core/nonpareil/nonpareil/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_nonpareil" description: Calculate metagenome redundancy curve from FASTQ files @@ -17,50 +16,71 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: FASTQ or FASTA file (ideally uncompressed, but not required) - pattern: "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" - - format: - type: string - description: File format of input file - pattern: "fasta|fastq" - - mode: - type: string - description: Mode of redundancy estimation - pattern: "kmer|alignment" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: FASTQ or FASTA file (ideally uncompressed, but not required) + pattern: "*.{fasta,fna,fas,fa,fastq,fq,fasta.gz,fna.gz,fas.gz,fa.gz,fastq.gz,fq.gz}" + - - format: + type: string + description: File format of input file + pattern: "fasta|fastq" + - - mode: + type: string + description: Mode of redundancy estimation + pattern: "kmer|alignment" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npa: - type: file - description: Raw redundancy values - pattern: "*.npa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npa": + type: file + description: Raw redundancy values + pattern: "*.npa" - npc: - type: file - description: Mates distribution file - pattern: "*.npc" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npc": + type: file + description: Mates distribution file + pattern: "*.npc" - npl: - type: file - description: Log file - pattern: "*.npl" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npl": + type: file + description: Log file + pattern: "*.npl" - npo: - type: file - description: Redundancy summary file - pattern: "*.npo" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.npo": + type: file + description: Redundancy summary file + pattern: "*.npo" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml b/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml index a4aeeb63d344..1649b990a427 100644 --- a/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml +++ b/modules/nf-core/nonpareil/nonpareilcurvesr/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "nonpareil_nonpareilcurvesr" -description: Generate summary reports with raw data for Nonpareil NPO curves, including MultiQC compatible JSON/TSV files +description: Generate summary reports with raw data for Nonpareil NPO curves, including + MultiQC compatible JSON/TSV files keywords: - metagenomics - statistics @@ -18,45 +18,67 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - npos: - type: file - description: One or a list of Nonpareil NPO files (From nonpareil/nonpareil) - pattern: "*.{npo}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - npos: + type: file + description: One or a list of Nonpareil NPO files (From nonpareil/nonpareil) + pattern: "*.{npo}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.json" - tsv: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.tsv" ': + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.tsv" - csv: - type: file - description: Raw nonpareil data used for generating and plotting curves in JSON format - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.csv" ': + type: file + description: Raw nonpareil data used for generating and plotting curves in JSON + format + pattern: "*.csv" - pdf: - type: file - description: Plotted nonpareil curves in PDF format - pattern: "*.pdf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - '*.pdf" ': + type: file + description: Plotted nonpareil curves in PDF format + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nonpareil/set/meta.yml b/modules/nf-core/nonpareil/set/meta.yml index 74a26122eab6..511eeb4fd6a2 100644 --- a/modules/nf-core/nonpareil/set/meta.yml +++ b/modules/nf-core/nonpareil/set/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "nonpareil_set" -description: Visualise metagenome redundancy curves in PNG format from multiple Nonpareil npo files in a single image +description: Visualise metagenome redundancy curves in PNG format from multiple Nonpareil + npo files in a single image keywords: - metagenomics - statistics @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/lmrodriguezr/nonpareil" doi: "10.1128/msystems.00039-" licence: ["Artistic License 2.0"] + identifier: biotools:nonpareil input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - npos: - type: file - description: A list of npo redundancy summary files from nonpareil itself - pattern: "*.npo" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - npos: + type: file + description: A list of npo redundancy summary files from nonpareil itself + pattern: "*.npo" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: PNG file of all the Nonpareil curves of the input npo files - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: PNG file of all the Nonpareil curves of the input npo files + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/nucmer/meta.yml b/modules/nf-core/nucmer/meta.yml index 8cc8f1639f05..1c93f6b43cf4 100644 --- a/modules/nf-core/nucmer/meta.yml +++ b/modules/nf-core/nucmer/meta.yml @@ -1,48 +1,59 @@ name: nucmer -description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. +description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide + sequences. keywords: - align - nucleotide - sequence tools: - nucmer: - description: NUCmer is a pipeline for the alignment of multiple closely related nucleotide sequences. + description: NUCmer is a pipeline for the alignment of multiple closely related + nucleotide sequences. homepage: http://mummer.sourceforge.net/ documentation: http://mummer.sourceforge.net/ tool_dev_url: http://mummer.sourceforge.net/ doi: "10.1186/gb-2004-5-2-r12" licence: ["The Artistic License"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: FASTA file of the reference sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - query: - type: file - description: FASTA file of the query sequence - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: FASTA file of the reference sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - query: + type: file + description: FASTA file of the query sequence + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - delta: - type: file - description: File containing coordinates of matches between reference and query + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.delta": + type: file + description: File containing coordinates of matches between reference and query - coords: - type: file - description: NUCmer1.1 coords output file - pattern: "*.{coords}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coords": + type: file + description: NUCmer1.1 coords output file + pattern: "*.{coords}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/oatk/meta.yml b/modules/nf-core/oatk/meta.yml index 022482078cc6..95196adc3e2f 100644 --- a/modules/nf-core/oatk/meta.yml +++ b/modules/nf-core/oatk/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "oatk" description: An nf-core module for the OATK @@ -17,147 +16,195 @@ tools: tool_dev_url: "https://github.com/c-zhou/oatk" doi: "10.5281/zenodo.10400173" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'Cladonia_norvegica' ] - - - reads: - type: file - description: HiFi reads in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz}" - - - mito_hmm: - type: file - description: mitochondria gene annotation HMM profile database - pattern: "*.{fa,fam}" - - - mito_hmm_h3f: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3f}" - - - mito_hmm_h3i: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3i}" - - - mito_hmm_h3m: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3m}" - - - mito_hmm_h3p: - type: file - description: mitochondria gene annotation HMM profile binary auxfile - pattern: "*.{h3p}" - - - pltd_hmm: - type: file - description: plastid gene annotation HMM profile database - pattern: "*.{fa,fam}" - - - pltd_hmm_h3f: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3f}" - - - pltd_hmm_h3i: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3i}" - - - pltd_hmm_h3m: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3m}" - - - pltd_hmm_h3p: - type: file - description: plastid gene annotation HMM profile binary auxfile - pattern: "*.{h3p}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'Cladonia_norvegica' ] + - reads: + type: file + description: HiFi reads in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz}" + - - mito_hmm: + type: file + description: mitochondria gene annotation HMM profile database + pattern: "*.{fa,fam}" + - mito_hmm_h3f: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3f}" + - mito_hmm_h3i: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3i}" + - mito_hmm_h3m: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3m}" + - mito_hmm_h3p: + type: file + description: mitochondria gene annotation HMM profile binary auxfile + pattern: "*.{h3p}" + - - pltd_hmm: + type: file + description: plastid gene annotation HMM profile database + pattern: "*.{fa,fam}" + - pltd_hmm_h3f: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3f}" + - pltd_hmm_h3i: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3i}" + - pltd_hmm_h3m: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3m}" + - pltd_hmm_h3p: + type: file + description: plastid gene annotation HMM profile binary auxfile + pattern: "*.{h3p}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - mito_fasta: - type: file - description: the structure-solved MT contigs - pattern: "*mito.ctg.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.ctg.fasta": + type: file + description: the structure-solved MT contigs + pattern: "*mito.ctg.fasta" - pltd_fasta: - type: file - description: the structure-solved PT contigs - pattern: "*pltd.ctg.fasta" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.ctg.fasta": + type: file + description: the structure-solved PT contigs + pattern: "*pltd.ctg.fasta" - mito_bed: - type: file - description: the gene annotation for the MT sequences - pattern: "*mito.ctg.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.ctg.bed": + type: file + description: the gene annotation for the MT sequences + pattern: "*mito.ctg.bed" - pltd_bed: - type: file - description: the gene annotation for the PT sequences - pattern: "*pltd.ctg.bed" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.ctg.bed": + type: file + description: the gene annotation for the PT sequences + pattern: "*pltd.ctg.bed" - mito_gfa: - type: file - description: the subgraph for the MT genome - pattern: "*mito.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*mito.gfa": + type: file + description: the subgraph for the MT genome + pattern: "*mito.gfa" - pltd_gfa: - type: file - description: the subgraph for the PT genome - pattern: "*pltd.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pltd.gfa": + type: file + description: the subgraph for the PT genome + pattern: "*pltd.gfa" - annot_mito_txt: - type: file - description: the MT gene annotation file over all assembled sequences - pattern: "*annot_mito.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annot_mito.txt": + type: file + description: the MT gene annotation file over all assembled sequences + pattern: "*annot_mito.txt" - annot_pltd_txt: - type: file - description: the PT gene annotation file over all assembled sequences - pattern: "*annot_pltd.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*annot_pltd.txt": + type: file + description: the PT gene annotation file over all assembled sequences + pattern: "*annot_pltd.txt" - clean_gfa: - type: file - description: the GFA file for the clean genome assembly - pattern: "*utg.clean.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.clean.gfa": + type: file + description: the GFA file for the clean genome assembly + pattern: "*utg.clean.gfa" - final_gfa: - type: file - description: the GFA file for the final genome assembly - pattern: "*utg.final.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.final.gfa": + type: file + description: the GFA file for the final genome assembly + pattern: "*utg.final.gfa" - initial_gfa: - type: file - description: the GFA file for the initial genome assembly - pattern: "*utg.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.gfa": + type: file + description: the GFA file for the initial genome assembly + pattern: "*utg.gfa" - multiplex_gfa: - type: file - description: the mutliplexed GFA file - pattern: "*utg.multiplex.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.multiplex.gfa": + type: file + description: the mutliplexed GFA file + pattern: "*utg.multiplex.gfa" - unzip_gfa: - type: file - description: the unzipped GFA file - pattern: "*utg.unzip.gfa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*utg.unzip.gfa": + type: file + description: the unzipped GFA file + pattern: "*utg.unzip.gfa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" diff --git a/modules/nf-core/odgi/build/meta.yml b/modules/nf-core/odgi/build/meta.yml index 8ec550746596..f9028ae39257 100644 --- a/modules/nf-core/odgi/build/meta.yml +++ b/modules/nf-core/odgi/build/meta.yml @@ -13,30 +13,34 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - og: - type: file - description: File containing a pangenome graph in ODGI binary format. Usually ends with '.og' - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: File containing a pangenome graph in ODGI binary format. Usually + ends with '.og' + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/draw/meta.yml b/modules/nf-core/odgi/draw/meta.yml index 807463ac29c9..063071c6a0d6 100644 --- a/modules/nf-core/odgi/draw/meta.yml +++ b/modules/nf-core/odgi/draw/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or ODGI binary format - pattern: "*.{gfa,og}" - - lay: - type: file - description: 2D layout from 'odgi layout' in LAY binary format - pattern: "*.{lay}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or ODGI binary format + pattern: "*.{gfa,og}" + - lay: + type: file + description: 2D layout from 'odgi layout' in LAY binary format + pattern: "*.{lay}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: File in PNG format containing a 2D drawing of a pangenome graph - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: File in PNG format containing a 2D drawing of a pangenome graph + pattern: "*.{png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/layout/meta.yml b/modules/nf-core/odgi/layout/meta.yml index 5d7694a3c8ee..83c1483f12c1 100644 --- a/modules/nf-core/odgi/layout/meta.yml +++ b/modules/nf-core/odgi/layout/meta.yml @@ -1,5 +1,6 @@ name: "odgi_layout" -description: Establish 2D layouts of the graph using path-guided stochastic gradient descent. The graph must be sorted and id-compacted. +description: Establish 2D layouts of the graph using path-guided stochastic gradient + descent. The graph must be sorted and id-compacted. keywords: - variation graph - pangenome graph @@ -13,34 +14,47 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lay: - type: file - description: File containing a 2D layout of a pangenome graph in a binary format. Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. Either this or the TSV layout output must be specified. - pattern: "*.{lay}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lay": + type: file + description: File containing a 2D layout of a pangenome graph in a binary format. + Usually ends with '.lay'. Optional output specified by the `--out FILE` argument. + Either this or the TSV layout output must be specified. + pattern: "*.{lay}" - tsv: - type: file - description: File containing a 2D layout of a pangenome graph in TSV format. Optional output specified by the `--tsv FILE` argument. Either this or the binary layout output must be specified. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: File containing a 2D layout of a pangenome graph in TSV format. + Optional output specified by the `--tsv FILE` argument. Either this or the + binary layout output must be specified. + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/sort/meta.yml b/modules/nf-core/odgi/sort/meta.yml index 792dc381c595..6ce0493162b4 100644 --- a/modules/nf-core/odgi/sort/meta.yml +++ b/modules/nf-core/odgi/sort/meta.yml @@ -1,5 +1,6 @@ name: "odgi_sort" -description: Apply different kind of sorting algorithms to a graph. The most prominent one is the PG-SGD sorting algorithm. +description: Apply different kind of sorting algorithms to a graph. The most prominent + one is the PG-SGD sorting algorithm. keywords: - variation graph - pangenome graph @@ -13,30 +14,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sorted_graph: - type: file - description: 1D sorted pangenome graph in ODGI binary format - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: 1D sorted pangenome graph in ODGI binary format + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/squeeze/meta.yml b/modules/nf-core/odgi/squeeze/meta.yml index 5ffaa618d106..3e016908049b 100644 --- a/modules/nf-core/odgi/squeeze/meta.yml +++ b/modules/nf-core/odgi/squeeze/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graphs: - type: file - description: Pangenome graph files in ODGI format. - pattern: "*.{og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graphs: + type: file + description: Pangenome graph files in ODGI format. + pattern: "*.{og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - graph: - type: file - description: Squeezed pangenome graph in ODGI format. - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: Squeezed pangenome graph in ODGI format. + pattern: "*.{og}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/stats/meta.yml b/modules/nf-core/odgi/stats/meta.yml index e8e26e02839e..c679e1362d4e 100644 --- a/modules/nf-core/odgi/stats/meta.yml +++ b/modules/nf-core/odgi/stats/meta.yml @@ -13,34 +13,43 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in binary ODGI or in GFA v1.0 format - pattern: "*.{og,gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in binary ODGI or in GFA v1.0 format + pattern: "*.{og,gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Optional output file that contains graph statistics in TSV format. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og.stats.tsv": + type: file + description: Optional output file that contains graph statistics in TSV format. + pattern: "*.{tsv}" - yaml: - type: file - description: Optional output file that contains graph statistics in YAML format. - pattern: "*.{yaml}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og.stats.yaml": + type: file + description: Optional output file that contains graph statistics in YAML format. + pattern: "*.{yaml}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/unchop/meta.yml b/modules/nf-core/odgi/unchop/meta.yml index 5dc31f0697ea..e7a510f8830c 100644 --- a/modules/nf-core/odgi/unchop/meta.yml +++ b/modules/nf-core/odgi/unchop/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - unchopped_graph: - type: file - description: Unchopped pangenome graph in ODGI binary format - pattern: "*.{og}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.og": + type: file + description: Unchopped pangenome graph in ODGI binary format + pattern: "*.{og}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/view/meta.yml b/modules/nf-core/odgi/view/meta.yml index 2b8b0d4d5292..e67a4bd7f9c6 100644 --- a/modules/nf-core/odgi/view/meta.yml +++ b/modules/nf-core/odgi/view/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in GFA v1.0 format or in ODGI binary format - pattern: "*.{gfa,og}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in GFA v1.0 format or in ODGI binary format + pattern: "*.{gfa,og}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gfa: - type: file - description: File containing a pangenome graph in GFA v1.0 format. - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: File containing a pangenome graph in GFA v1.0 format. + pattern: "*.{gfa}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/odgi/viz/meta.yml b/modules/nf-core/odgi/viz/meta.yml index 8f8a0370653b..9c021edc5e6d 100644 --- a/modules/nf-core/odgi/viz/meta.yml +++ b/modules/nf-core/odgi/viz/meta.yml @@ -13,30 +13,33 @@ tools: tool_dev_url: "https://github.com/pangenome/odgi" doi: "10.1093/bioinformatics/btac308" licence: ["MIT"] + identifier: biotools:odgi input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - graph: - type: file - description: Pangenome graph in binary ODGI or in GFA v1.0 format - pattern: "*.{og,gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - graph: + type: file + description: Pangenome graph in binary ODGI or in GFA v1.0 format + pattern: "*.{og,gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: A 1D visualization of a pangenome graph. - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: A 1D visualization of a pangenome graph. + pattern: "*.{png}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/oncocnv/meta.yml b/modules/nf-core/oncocnv/meta.yml index 4f1bde83f6f3..049029a0ad54 100644 --- a/modules/nf-core/oncocnv/meta.yml +++ b/modules/nf-core/oncocnv/meta.yml @@ -12,53 +12,70 @@ tools: tool_dev_url: "https://github.com/BoevaLab/ONCOCNV/" doi: "10.1093/bioinformatics/btu436" license: ["GPL-3.0-or-later"] + identifier: biotools:oncocnv input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal: - type: file - description: BAM files - pattern: "*.bam" - - normal_index: - type: file - description: BAM file indices - pattern: "*.bam.bai" - - tumor: - type: file - description: BAM files - pattern: "*.bam" - - tumor_index: - type: file - description: BAM file indices - pattern: "*.bam.bai" - - bed: - type: file - description: annotated BED file containing target regions - pattern: "*.bed" - - fasta: - type: file - description: genome FASTA file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal: + type: file + description: BAM files + pattern: "*.bam" + - normal_index: + type: file + description: BAM file indices + pattern: "*.bam.bai" + - tumor: + type: file + description: BAM files + pattern: "*.bam" + - tumor_index: + type: file + description: BAM file indices + pattern: "*.bam.bai" + - - bed: + type: file + description: annotated BED file containing target regions + pattern: "*.bed" + - - fasta: + type: file + description: genome FASTA file + pattern: "*.fasta" output: - png: - type: file - description: PNG file containing profile plot - pattern: "*.profile.png" + - meta: + type: file + description: PNG file containing profile plot + pattern: "*.profile.png" + - "*.profile.png": + type: file + description: PNG file containing profile plot + pattern: "*.profile.png" - profile: - type: file - description: TXT file containing profile data - pattern: "*.profile.txt" + - meta: + type: file + description: TXT file containing profile data + pattern: "*.profile.txt" + - "*.profile.txt": + type: file + description: TXT file containing profile data + pattern: "*.profile.txt" - summary: - type: file - description: TXT file containing summarized data - pattern: "*.summary.txt" + - meta: + type: file + description: TXT file containing summarized data + pattern: "*.summary.txt" + - "*.summary.txt": + type: file + description: TXT file containing summarized data + pattern: "*.summary.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/openms/decoydatabase/meta.yml b/modules/nf-core/openms/decoydatabase/meta.yml index 4979b8475ac0..ce9399d27c45 100644 --- a/modules/nf-core/openms/decoydatabase/meta.yml +++ b/modules/nf-core/openms/decoydatabase/meta.yml @@ -8,36 +8,40 @@ keywords: - fasta tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Fasta file containing protein sequences - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Fasta file containing protein sequences + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - decoy_fasta: - type: file - description: Fasta file containing proteins and decoy proteins - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: Fasta file containing proteins and decoy proteins + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idfilter/meta.yml b/modules/nf-core/openms/idfilter/meta.yml index 02667aa066b3..d333e4b3b11b 100644 --- a/modules/nf-core/openms/idfilter/meta.yml +++ b/modules/nf-core/openms/idfilter/meta.yml @@ -7,43 +7,45 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - id_file: - type: file - description: Peptide-spectrum matches. - pattern: "*.{idXML,consensusXML}" - - filter_file: - type: file - description: Optional idXML file to filter on/out peptides or proteins - patter: "*.{idXML,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - id_file: + type: file + description: Peptide-spectrum matches. + pattern: "*.{idXML,consensusXML}" + - filter_file: + type: file + description: Optional idXML file to filter on/out peptides or proteins + patter: "*.{idXML,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filtered: - type: file - description: Filtered peptide-spectrum matches. - pattern: "*.{idXML,consensusXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{idXML,consensusXML}": + type: file + description: Filtered peptide-spectrum matches. + pattern: "*.{idXML,consensusXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idmassaccuracy/meta.yml b/modules/nf-core/openms/idmassaccuracy/meta.yml index e14a2eb09bb3..5e8b1f2fdbdf 100644 --- a/modules/nf-core/openms/idmassaccuracy/meta.yml +++ b/modules/nf-core/openms/idmassaccuracy/meta.yml @@ -1,55 +1,64 @@ name: "openms_idmassaccuracy" -description: Calculates a distribution of the mass error from given mass spectra and IDs. +description: Calculates a distribution of the mass error from given mass spectra and + IDs. keywords: - mass_error - openms - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - mzmls: - type: file - description: | - List containing one or more mzML files - e.g. `[ 'file1.mzML', 'file2.mzML' ]` - pattern: "*.{mzML}" - - idxmls: - type: file - description: | - List containing one or more idXML files - e.g. `[ 'file1.idXML', 'file2.idXML' ]` - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - mzmls: + type: file + description: | + List containing one or more mzML files + e.g. `[ 'file1.mzML', 'file2.mzML' ]` + pattern: "*.{mzML}" + - idxmls: + type: file + description: | + List containing one or more idXML files + e.g. `[ 'file1.idXML', 'file2.idXML' ]` + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - frag_err: - type: file - description: TSV file containing the fragment mass errors - pattern: "*frag_mass_err.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*frag_mass_err.tsv": + type: file + description: TSV file containing the fragment mass errors + pattern: "*frag_mass_err.{tsv}" - prec_err: - type: file - description: Optional TSV file containing the precursor mass errors - pattern: "*prec_mass_err.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*prec_mass_err.tsv": + type: file + description: Optional TSV file containing the precursor mass errors + pattern: "*prec_mass_err.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" diff --git a/modules/nf-core/openms/idmerger/meta.yml b/modules/nf-core/openms/idmerger/meta.yml index 19df33fb0f57..bf87a645e0ba 100644 --- a/modules/nf-core/openms/idmerger/meta.yml +++ b/modules/nf-core/openms/idmerger/meta.yml @@ -7,40 +7,42 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - idxmls: - type: file - description: | - List containing 2 or more idXML files - e.g. `[ 'file1.idXML', 'file2.idXML' ]` - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - idxmls: + type: file + description: | + List containing 2 or more idXML files + e.g. `[ 'file1.idXML', 'file2.idXML' ]` + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: Merged idXML output file - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.idXML": + type: file + description: Merged idXML output file + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" diff --git a/modules/nf-core/openms/idripper/meta.yml b/modules/nf-core/openms/idripper/meta.yml index 8170e796535f..ac35b7bc732b 100644 --- a/modules/nf-core/openms/idripper/meta.yml +++ b/modules/nf-core/openms/idripper/meta.yml @@ -1,5 +1,6 @@ name: openms_idripper -description: Split a merged identification file into their originating identification files +description: Split a merged identification file into their originating identification + files keywords: - split - idXML @@ -7,39 +8,41 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - merged_idxml: - type: file - description: Merged idXML file - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - merged_idxml: + type: file + description: Merged idXML file + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxmls: - type: file - description: Multiple idXML files - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: Multiple idXML files + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/idscoreswitcher/meta.yml b/modules/nf-core/openms/idscoreswitcher/meta.yml index d37fcd8b9fe3..ac4c50703137 100644 --- a/modules/nf-core/openms/idscoreswitcher/meta.yml +++ b/modules/nf-core/openms/idscoreswitcher/meta.yml @@ -1,5 +1,6 @@ name: "openms_idscoreswitcher" -description: Switches between different scores of peptide or protein hits in identification data +description: Switches between different scores of peptide or protein hits in identification + data keywords: - switch - score @@ -8,41 +9,43 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - idxml: - type: file - description: Identification file containing a primary PSM score - pattern: "*.{idXML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - idxml: + type: file + description: Identification file containing a primary PSM score + pattern: "*.{idXML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: | - Identification file containing a new primary PSM score - obtained from a specified meta value - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: | + Identification file containing a new primary PSM score + obtained from a specified meta value + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/peakpickerhires/meta.yml b/modules/nf-core/openms/peakpickerhires/meta.yml index 479d8192281c..b10460b9422b 100644 --- a/modules/nf-core/openms/peakpickerhires/meta.yml +++ b/modules/nf-core/openms/peakpickerhires/meta.yml @@ -1,5 +1,6 @@ name: "openms_peakpickerhires" -description: A tool for peak detection in high-resolution profile data (Orbitrap or FTICR) +description: A tool for peak detection in high-resolution profile data (Orbitrap or + FTICR) keywords: - peak picking - mzml @@ -7,39 +8,41 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - mzml: - type: file - description: Mass spectrometer output file in mzML format - pattern: "*.{mzML}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - mzml: + type: file + description: Mass spectrometer output file in mzML format + pattern: "*.{mzML}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mzml: - type: file - description: Peak-picked mass spectrometer output file in mzML format - pattern: "*.{mzML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.mzML": + type: file + description: Peak-picked mass spectrometer output file in mzML format + pattern: "*.{mzML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openms/peptideindexer/meta.yml b/modules/nf-core/openms/peptideindexer/meta.yml index 94759d352c5d..10f808d23851 100644 --- a/modules/nf-core/openms/peptideindexer/meta.yml +++ b/modules/nf-core/openms/peptideindexer/meta.yml @@ -1,4 +1,3 @@ ---- name: "openms_peptideindexer" description: Refreshes the protein references for all peptide hits. keywords: @@ -8,42 +7,49 @@ keywords: - proteomics tools: - "openms": - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - id_file: - type: file - description: idXML identification file - pattern: "*.{idXML}" - - id_fasta: - type: file - description: Input sequence database in FASTA format - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - id_file: + type: file + description: idXML identification file + pattern: "*.{idXML}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - id_fasta: + type: file + description: Input sequence database in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - id_file_pi: - type: file - description: Refreshed idXML identification file - pattern: "*.{idXML}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: Refreshed idXML identification file + pattern: "*.{idXML}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml index e37f6af8264c..fc7e688102d4 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml +++ b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml @@ -8,47 +8,55 @@ keywords: - proteomics tools: - openms: - description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses" + description: "OpenMS is an open-source software C++ library for LC-MS data management + and analyses" homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" doi: "10.1038/nmeth.3959" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - mzml: - type: file - description: File containing mass spectra in mzML format - pattern: "*.{mzML}" - - fasta: - type: file - description: Protein sequence database containing targets and decoys - pattern: "*.{fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - mzml: + type: file + description: File containing mass spectra in mzML format + pattern: "*.{mzML}" + - fasta: + type: file + description: Protein sequence database containing targets and decoys + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - idxml: - type: file - description: File containing target and decoy hits in idXML format - pattern: "*.{idXML}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.idXML": + type: file + description: File containing target and decoy hits in idXML format + pattern: "*.{idXML}" - pin: - type: file - description: TSV file tailored as Percolator input (pin) file - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file tailored as Percolator input (pin) file + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/optitype/meta.yml b/modules/nf-core/optitype/meta.yml index 980596ab77ec..eb5bfef86825 100644 --- a/modules/nf-core/optitype/meta.yml +++ b/modules/nf-core/optitype/meta.yml @@ -11,38 +11,47 @@ tools: documentation: https://github.com/FRED-2/OptiType doi: "10.1093/bioinformatics/btu548" licence: ["BSD-3-Clause"] + identifier: biotools:optitype input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', seq_type:'DNA' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hla_type: - type: file - description: HLA type - pattern: "${prefix}/*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', seq_type:'DNA' ] + - ${prefix}/*.tsv: + type: file + description: HLA type + pattern: "${prefix}/*.tsv" - coverage_plot: - type: file - description: OptiType coverage plot - pattern: "${prefix}/*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', seq_type:'DNA' ] + - ${prefix}/*.pdf: + type: file + description: OptiType coverage plot + pattern: "${prefix}/*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/orthofinder/meta.yml b/modules/nf-core/orthofinder/meta.yml index 8c7689b3e86d..4aeb46b3b4d3 100644 --- a/modules/nf-core/orthofinder/meta.yml +++ b/modules/nf-core/orthofinder/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "orthofinder" -description: OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. +description: OrthoFinder is a fast, accurate and comprehensive platform for comparative + genomics. keywords: - genomics - orthogroup @@ -12,50 +12,59 @@ keywords: - phylogeny tools: - "orthofinder": - description: "Accurate inference of orthogroups, orthologues, gene trees and rooted species tree made easy!" + description: "Accurate inference of orthogroups, orthologues, gene trees and rooted + species tree made easy!" homepage: "https://github.com/davidemms/OrthoFinder" documentation: "https://github.com/davidemms/OrthoFinder" tool_dev_url: "https://github.com/davidemms/OrthoFinder" doi: "10.1186/s13059-019-1832-y" licence: ["GPL v3"] + identifier: biotools:OrthoFinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastas: - type: list - description: Input fasta files - pattern: "*.{fa,faa,fasta,fas,pep}" - - meta2: - type: map - description: | - Groovy Map containing a name - e.g. `[ id:'folder1' ]` - - prior_run: - type: directory - description: | - A folder container containing a previous WorkingDirectory from Orthofinder. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastas: + type: list + description: Input fasta files + pattern: "*.{fa,faa,fasta,fas,pep}" + - - meta2: + type: map + description: | + Groovy Map containing a name + e.g. `[ id:'folder1' ]` + - prior_run: + type: directory + description: | + A folder container containing a previous WorkingDirectory from Orthofinder. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - orthofinder: - type: directory - description: Orthofinder output directory + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix: + type: directory + description: Orthofinder output directory - working: - type: directory - description: Orthofinder output WorkingDirectory (used for the orthofinder resume function) - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - $prefix/WorkingDirectory: + type: directory + description: Orthofinder output WorkingDirectory (used for the orthofinder resume + function) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/paftools/sam2paf/meta.yml b/modules/nf-core/paftools/sam2paf/meta.yml index 438ab2dd4bb7..e58297401ef1 100644 --- a/modules/nf-core/paftools/sam2paf/meta.yml +++ b/modules/nf-core/paftools/sam2paf/meta.yml @@ -11,30 +11,28 @@ tools: homepage: https://github.com/lh3/minimap2 documentation: https://github.com/lh3/minimap2/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An input bam file to be converted into paf. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: An input bam file to be converted into paf. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: | - An output paf containing detailed data about the sample - pattern: "${prefix}.paf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/pairix/meta.yml b/modules/nf-core/pairix/meta.yml index f52771825144..e94f2d328441 100644 --- a/modules/nf-core/pairix/meta.yml +++ b/modules/nf-core/pairix/meta.yml @@ -13,29 +13,36 @@ tools: documentation: "https://github.com/4dn-dcic/pairix" tool_dev_url: "https://github.com/4dn-dcic/pairix" licence: ["MIT"] + identifier: biotools:pairix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pair: - type: file - description: pair file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pair: + type: file + description: pair file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: pair index file - pattern: "*.px2" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pair: + type: file + description: pair index file + pattern: "*.px2" + - "*.px2": + type: file + description: pair index file + pattern: "*.px2" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/dedup/meta.yml b/modules/nf-core/pairtools/dedup/meta.yml index 3c67e3fbe262..0f2860e005d7 100644 --- a/modules/nf-core/pairtools/dedup/meta.yml +++ b/modules/nf-core/pairtools/dedup/meta.yml @@ -12,33 +12,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: pair file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: pair file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Duplicates removed pairs - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Duplicates removed pairs + pattern: "*.{pairs.gz}" - stat: - type: file - description: stats of the pairs - pattern: "*.{pairs.stat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.stat": + type: file + description: stats of the pairs + pattern: "*.{pairs.stat}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/flip/meta.yml b/modules/nf-core/pairtools/flip/meta.yml index 58739acb3ca0..c2122019d93f 100644 --- a/modules/nf-core/pairtools/flip/meta.yml +++ b/modules/nf-core/pairtools/flip/meta.yml @@ -11,32 +11,35 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sam: - type: file - description: pair file - - chromsizes: - type: file - description: chromosome size file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sam: + type: file + description: pair file + - - chromsizes: + type: file + description: chromosome size file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - flip: - type: file - description: output file of flip - pattern: "*.{flip.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flip.gz": + type: file + description: output file of flip + pattern: "*.{flip.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/merge/meta.yml b/modules/nf-core/pairtools/merge/meta.yml index b7bccc3c1ee5..790c5bbcd7d5 100644 --- a/modules/nf-core/pairtools/merge/meta.yml +++ b/modules/nf-core/pairtools/merge/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - allpairs: - type: file - description: All pair files to merge + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - allpairs: + type: file + description: All pair files to merge output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Merged pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*pairs.gz": + type: file + description: Merged pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" maintainers: diff --git a/modules/nf-core/pairtools/parse/meta.yml b/modules/nf-core/pairtools/parse/meta.yml index e7e448efd746..27411d021643 100644 --- a/modules/nf-core/pairtools/parse/meta.yml +++ b/modules/nf-core/pairtools/parse/meta.yml @@ -11,37 +11,46 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - chromsizes: - type: file - description: chromosome size file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - chromsizes: + type: file + description: chromosome size file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairsam: - type: file - description: parsed pair file - pattern: "*.{pairsam.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairsam.gz": + type: file + description: parsed pair file + pattern: "*.{pairsam.gz}" - stat: - type: file - description: stats of the pairs - pattern: "*.{pairsam.stat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairsam.stat": + type: file + description: stats of the pairs + pattern: "*.{pairsam.stat}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/restrict/meta.yml b/modules/nf-core/pairtools/restrict/meta.yml index 12f6b9863c5d..c43a35bb183d 100644 --- a/modules/nf-core/pairtools/restrict/meta.yml +++ b/modules/nf-core/pairtools/restrict/meta.yml @@ -11,35 +11,38 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairs file - - frag: - type: file - description: | - a tab-separated BED file with the positions of restriction fragments - (chrom, start, end). - Can be generated using cooler digest. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairs file + - - frag: + type: file + description: | + a tab-separated BED file with the positions of restriction fragments + (chrom, start, end). + Can be generated using cooler digest. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - restrict: - type: file - description: Filtered pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Filtered pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/select/meta.yml b/modules/nf-core/pairtools/select/meta.yml index e9aef9a22d7b..47ef25e14428 100644 --- a/modules/nf-core/pairtools/select/meta.yml +++ b/modules/nf-core/pairtools/select/meta.yml @@ -11,33 +11,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - selected: - type: file - description: Selected pairs file - pattern: "*.{selected.pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selected.pairs.gz": + type: file + description: Selected pairs file + pattern: "*.{selected.pairs.gz}" - unselected: - type: file - description: Rest pairs file. - pattern: "*.{unselected.pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unselected.pairs.gz": + type: file + description: Rest pairs file. + pattern: "*.{unselected.pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/pairtools/sort/meta.yml b/modules/nf-core/pairtools/sort/meta.yml index 987aebb0f51b..b1650e8ff7a9 100644 --- a/modules/nf-core/pairtools/sort/meta.yml +++ b/modules/nf-core/pairtools/sort/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: A pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: A pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sorted: - type: file - description: Sorted pairs file - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.gz": + type: file + description: Sorted pairs file + pattern: "*.{pairs.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@nservant" diff --git a/modules/nf-core/pairtools/split/meta.yml b/modules/nf-core/pairtools/split/meta.yml index e659f93a8ae1..7ff8fe132ca1 100644 --- a/modules/nf-core/pairtools/split/meta.yml +++ b/modules/nf-core/pairtools/split/meta.yml @@ -11,35 +11,42 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairsam file - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairsam file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pairs: - type: file - description: Duplicates removed pairs - pattern: "*.{pairs.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.split.pairs.gz": + type: file + description: Duplicates removed pairs + pattern: "*.{pairs.gz}" - bam: - type: file - description: Output BAM file - pattern: "*.bam" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" diff --git a/modules/nf-core/pairtools/stats/meta.yml b/modules/nf-core/pairtools/stats/meta.yml index da2a1fa3f1c5..f3ab7a3d9f82 100644 --- a/modules/nf-core/pairtools/stats/meta.yml +++ b/modules/nf-core/pairtools/stats/meta.yml @@ -11,29 +11,32 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pairs: - type: file - description: pairs file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pairs: + type: file + description: pairs file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pairs.stat": + type: file + description: Pairs statistics + pattern: "*{.pairs.stat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - stat: - type: file - description: stats of the pairs - pattern: "*.{pairs.stat}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nservant" maintainers: diff --git a/modules/nf-core/panacus/histgrowth/meta.yml b/modules/nf-core/panacus/histgrowth/meta.yml index 800170c182bd..a9b94020a2b1 100644 --- a/modules/nf-core/panacus/histgrowth/meta.yml +++ b/modules/nf-core/panacus/histgrowth/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "panacus_histgrowth" -description: Calculates a coverage histogram from a GFA file and constructs a growth table from this as either a TSV or HTML file +description: Calculates a coverage histogram from a GFA file and constructs a growth + table from this as either a TSV or HTML file keywords: - statistics - pangenome @@ -14,49 +14,50 @@ tools: homepage: "https://github.com/marschall-lab/panacus" documentation: "https://github.com/marschall-lab/panacus" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - gfa: - type: file - description: GFA file containing a graph without overlapping nodes - pattern: "*.gfa" - - bed_subset: - type: file - description: Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for getting counts by subsetting the graph - pattern: "*.{txt, bed}" - - bed_exclude: - type: file - description: Optional 1-column TXT-list of paths or 3-/12-column BED file of path coordinates for excluding bp/nodes/edges that intersect these paths - pattern: "*.{txt, bed}" - - tsv_groupby: - type: file - description: Optional 2-column TSV file containing path to group mapping according to which counts from different paths get merged - pattern: "*.{txt, bed}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - gfa: + type: file + description: GFA file containing a graph without overlapping nodes + pattern: "*.gfa" + - - bed_subset: + type: file + description: Optional 1-column TXT-list of paths or 3-/12-column BED file of + path coordinates for getting counts by subsetting the graph + pattern: "*.{txt, bed}" + - - bed_exclude: + type: file + description: Optional 1-column TXT-list of paths or 3-/12-column BED file of + path coordinates for excluding bp/nodes/edges that intersect these paths + pattern: "*.{txt, bed}" + - - tsv_groupby: + type: file + description: Optional 2-column TSV file containing path to group mapping according + to which counts from different paths get merged + pattern: "*.{txt, bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file containing the statistics. Alternatively, the HTML file can be the output - pattern: "*.tsv" - - html: - type: file - description: HTML file containing a report with the statistics. Alternatively, the TSV file can be the output - pattern: "*.html" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{tsv, html}": + type: file + description: TSV file containing the statistics. Alternatively, the HTML file + can be the output + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heringerp" maintainers: diff --git a/modules/nf-core/panacus/visualize/meta.yml b/modules/nf-core/panacus/visualize/meta.yml index 3b2fd6df8b38..59aaa8a4e349 100644 --- a/modules/nf-core/panacus/visualize/meta.yml +++ b/modules/nf-core/panacus/visualize/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "panacus_visualize" description: Create visualizations from a tsv coverage histogram created with panacus. @@ -15,33 +14,34 @@ tools: homepage: "https://github.com/marschall-lab/panacus" documentation: "https://github.com/marschall-lab/panacus" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - tsv: - type: file - description: TSV coverage histogram created with panacus histgrowth - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - tsv: + type: file + description: TSV coverage histogram created with panacus histgrowth + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - image: - type: file - description: Visualizations created from the coverage histogram - pattern: "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}": + type: file + description: Visualizations created from the coverage histogram + pattern: "*.{eps,jpg,jpeg,pdf,pgf,png,ps,raw,rgba,svg,svgz,tif,tiff,webp}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heringerp" maintainers: diff --git a/modules/nf-core/panaroo/run/meta.yml b/modules/nf-core/panaroo/run/meta.yml index 47655d218a96..d69339e72e4d 100644 --- a/modules/nf-core/panaroo/run/meta.yml +++ b/modules/nf-core/panaroo/run/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/gtonkinhill/panaroo" doi: "10.1186/s13059-020-02090-4" licence: ["MIT"] + identifier: biotools:panaroo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing Panaroo result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing Panaroo result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by Panaroo (Optional) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/core_gene_alignment.aln: + type: file + description: Core-genome alignment produced by Panaroo (Optional) + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pangolin/meta.yml b/modules/nf-core/pangolin/meta.yml index 6493f2c82904..9220aefc1453 100644 --- a/modules/nf-core/pangolin/meta.yml +++ b/modules/nf-core/pangolin/meta.yml @@ -11,24 +11,31 @@ tools: homepage: https://github.com/cov-lineages/pangolin#pangolearn-description manual: https://github.com/cov-lineages/pangolin#pangolearn-description licence: ["GPL-3.0-or-later"] + identifier: biotools:pangolin_cov-lineages input: - - meta: - type: map - description: | - Groovy Map containing sample information - - fasta: - type: file - description: | - The genome assembly to be evaluated + - - meta: + type: map + description: | + Groovy Map containing sample information + - fasta: + type: file + description: | + The genome assembly to be evaluated output: - report: - type: file - description: Pangolin lineage report - pattern: "*.{csv}" + - meta: + type: file + description: Pangolin lineage report + pattern: "*.{csv}" + - "*.csv": + type: file + description: Pangolin lineage report + pattern: "*.{csv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/parabricks/applybqsr/meta.yml b/modules/nf-core/parabricks/applybqsr/meta.yml index d76ee61a066d..09fdbacab1b5 100644 --- a/modules/nf-core/parabricks/applybqsr/meta.yml +++ b/modules/nf-core/parabricks/applybqsr/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_applybqsr" -description: NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration (BQSR). +description: NVIDIA Clara Parabricks GPU-accelerated apply Base Quality Score Recalibration + (BQSR). keywords: - bqsr - bam @@ -11,50 +12,63 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/" licence: ["https://docs.nvidia.com/clara/parabricks/3.8.0/gettingstarted.html#licensing"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: bai index corresponding to input bam file. Only necessary if intervals are provided. - pattern: "*.bai" - - bqsr_table: - type: file - description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator. - pattern: "*.table" - - interval_file: - type: file - description: File or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: Reference fasta - must be unzipped. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bam_index: + type: file + description: BAM index file + pattern: "*.bai" + - bqsr_table: + type: file + description: Table from calculating BQSR. Output from parabricks/fq2bam or gatk4/baserecalibrator. + pattern: "*.table" + - intervals: + type: file + description: intervals + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - bam: - type: file - description: BAM file after applying BQSR. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.bam": + type: file + description: BAM file after applying BQSR. + pattern: "*.bam" - bai: - type: file - description: bai index corresponding to output bam file. - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.bai": + type: file + description: bai index corresponding to output bam file. + pattern: "*.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" maintainers: diff --git a/modules/nf-core/parabricks/dbsnp/meta.yml b/modules/nf-core/parabricks/dbsnp/meta.yml index 0ee3fbc38b31..095110cf45e8 100644 --- a/modules/nf-core/parabricks/dbsnp/meta.yml +++ b/modules/nf-core/parabricks/dbsnp/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_dbsnp" -description: NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based on dbSNP database +description: NVIDIA Clara Parabricks GPU-accelerated variant calls annotation based + on dbSNP database keywords: - annotation - dbsnp @@ -11,40 +12,41 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - vcf_file: - type: file - description: VCF file undergoing annotation. - pattern: "*.vcf" - - dbsnp_file: - type: file - description: dbSNP file required for annotation. - pattern: "*.vcf.gz" - - tabix_file: - type: file - description: dbSNP file index. - pattern: "*.vcf.gz.tbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - vcf_file: + type: file + description: VCF file undergoing annotation. + pattern: "*.vcf" + - dbsnp_file: + type: file + description: dbSNP file required for annotation. + pattern: "*.vcf.gz" + - tabix_file: + type: file + description: dbSNP file index. + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: VCF file. + pattern: "*{.vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - ann_vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" diff --git a/modules/nf-core/parabricks/deepvariant/meta.yml b/modules/nf-core/parabricks/deepvariant/meta.yml index b68e96e5c298..55998ea65e97 100644 --- a/modules/nf-core/parabricks/deepvariant/meta.yml +++ b/modules/nf-core/parabricks/deepvariant/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_deepvariant" -description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating deepvariant. +description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating + deepvariant. keywords: - variant - deep variant @@ -12,49 +13,52 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.0.1/documentation/ licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing tumor sample information - id must match read groups for this sample. - [ id:'test'] - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: bai index corresponding to input bam file. Only necessary if intervals are provided. - pattern: "*.bai" - - interval_file: - type: file - description: file or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing tumor sample information - id must match read groups for this sample. + [ id:'test'] + - input: + type: file + description: bam file for sample to be variant called. + pattern: "*.bam" + - input_index: + type: file + description: bai index corresponding to input bam file. Only necessary if intervals + are provided. + pattern: "*.bai" + - interval_file: + type: file + description: file or files containing genomic intervals for use in base quality + score recalibration. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - vcf: - type: file - description: Variant file. - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Variant file. + pattern: "*.vcf" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/parabricks/fq2bam/meta.yml b/modules/nf-core/parabricks/fq2bam/meta.yml index d8f60f3b4ba1..c86ff19aade9 100644 --- a/modules/nf-core/parabricks/fq2bam/meta.yml +++ b/modules/nf-core/parabricks/fq2bam/meta.yml @@ -1,5 +1,7 @@ name: "parabricks_fq2bam" -description: NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, and duplicate marking. Note this nf-core module requires files to be copied into the working directory and not symlinked. +description: NVIDIA Clara Parabricks GPU-accelerated alignment, sorting, BQSR calculation, + and duplicate marking. Note this nf-core module requires files to be copied into + the working directory and not symlinked. keywords: - align - sort @@ -11,70 +13,86 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/4.0.1/Documentation/" licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq.gz files - pattern: "*.fastq.gz" - - interval_file: - type: file - description: (optional) file(s) containing genomic intervals for use in base quality score recalibration (BQSR) - pattern: "*.{bed,interval_list,picard,list,intervals}" - - meta2: - type: map - description: | - Groovy Map containing fasta information - - fasta: - type: file - description: reference fasta file - must be unzipped - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing index information - - index: - type: file - description: reference BWA index - pattern: "*.{amb,ann,bwt,pac,sa}" - - known_sites: - type: file - description: (optional) known sites file(s) for calculating BQSR. markdups must be true to perform BQSR. - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq.gz files + pattern: "*.fastq.gz" + - interval_file: + type: file + description: (optional) file(s) containing genomic intervals for use in base + quality score recalibration (BQSR) + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + - fasta: + type: file + description: reference fasta file - must be unzipped + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing index information + - index: + type: file + description: reference BWA index + pattern: "*.{amb,ann,bwt,pac,sa}" + - - known_sites: + type: file + description: (optional) known sites file(s) for calculating BQSR. markdups must + be true to perform BQSR. + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.bam" - bai: - type: file - description: index corresponding to sorted BAM file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: index corresponding to sorted BAM file + pattern: "*.bai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - qc_metrics: - type: directory - description: (optional) optional directory of qc metrics - pattern: "qc_metrics" + - qc_metrics: + type: directory + description: (optional) optional directory of qc metrics + pattern: "qc_metrics" - bqsr_table: - type: file - description: (optional) table from base quality score recalibration calculation, to be used with parabricks/applybqsr - pattern: "*.table" + - "*.table": + type: file + description: (optional) table from base quality score recalibration calculation, + to be used with parabricks/applybqsr + pattern: "*.table" - duplicate_metrics: - type: file - description: (optional) metrics calculated from marking duplcates in the bam file - pattern: "*-duplicate-metrics.txt" + - duplicate-metrics.txt: + type: file + description: (optional) metrics calculated from marking duplcates in the bam + file + pattern: "*-duplicate-metrics.txt" authors: - "@bsiranosian" - "@adamrtalbot" diff --git a/modules/nf-core/parabricks/genotypegvcf/meta.yml b/modules/nf-core/parabricks/genotypegvcf/meta.yml index 21ccf18860b1..a876011edd0e 100644 --- a/modules/nf-core/parabricks/genotypegvcf/meta.yml +++ b/modules/nf-core/parabricks/genotypegvcf/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_genotypegvcf" -description: NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating GATK GenotypeGVCFs +description: NVIDIA Clara Parabricks GPU-accelerated joint genotyping, replicating + GATK GenotypeGVCFs keywords: - joint-genotyping - gvcf @@ -12,42 +13,43 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: gvcf file for samples to be jointly genotyped. - pattern: "*.{g.vcf,g.vcf.gz}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - input: + type: file + description: gvcf file for samples to be jointly genotyped. + pattern: "*.{g.vcf,g.vcf.gz}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file after gvcf conversion. - pattern: "*.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.vcf": + type: file + description: vcf file after gvcf conversion. + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" - "@bsiranosian" diff --git a/modules/nf-core/parabricks/haplotypecaller/meta.yml b/modules/nf-core/parabricks/haplotypecaller/meta.yml index 1b8ca3dd48c1..be0c83283905 100644 --- a/modules/nf-core/parabricks/haplotypecaller/meta.yml +++ b/modules/nf-core/parabricks/haplotypecaller/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_haplotypecaller" -description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating GATK haplotypecaller. +description: NVIDIA Clara Parabricks GPU-accelerated germline variant calling, replicating + GATK haplotypecaller. keywords: - variant - vcf @@ -11,49 +12,51 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.2.0/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - [ id:'test'] - - ref_meta: - type: map - description: | - Groovy Map containing reference information. - [ id:'test'] - - input: - type: file - description: bam file for sample to be variant called. - pattern: "*.bam" - - input_index: - type: file - description: (Optional) bai index corresponding to input bam file. Only necessary when using intervals. - pattern: "*.bai" - - interval_file: - type: file - description: file or files containing genomic intervals. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - + - - meta: + type: map + description: | + Groovy Map containing sample information. + [ id:'test'] + - input: + type: file + description: bam file for sample to be variant called. + pattern: "*.bam" + - input_index: + type: file + description: (Optional) bai index corresponding to input bam file. Only necessary + when using intervals. + pattern: "*.bai" + - interval_file: + type: file + description: file or files containing genomic intervals. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information. + [ id:'test'] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - vcf: - type: file - description: variant file. - pattern: "*.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: variant file. + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/parabricks/indexgvcf/meta.yml b/modules/nf-core/parabricks/indexgvcf/meta.yml index 50097d90a2f7..be57547075a2 100644 --- a/modules/nf-core/parabricks/indexgvcf/meta.yml +++ b/modules/nf-core/parabricks/indexgvcf/meta.yml @@ -13,31 +13,32 @@ tools: homepage: "https://www.nvidia.com/en-us/clara/genomics/" documentation: "https://docs.nvidia.com/clara/parabricks/" licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing gvcf information - - gvcf: - type: file - description: gvcf file to be indexed - pattern: "*.{vcf,vcf.gz}" - + - - meta: + type: map + description: | + Groovy Map containing gvcf information + - gvcf: + type: file + description: gvcf file to be indexed + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing output information - gvcf_index: - type: file - description: Indexed gvcf file - pattern: "*.g.vcf" + - meta: + type: map + description: | + Groovy Map containing output information + - "*.g.vcf*": + type: file + description: Indexed gvcf file + pattern: "*.g.vcf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Furentsu" - "@bsiranosian" diff --git a/modules/nf-core/parabricks/mutectcaller/meta.yml b/modules/nf-core/parabricks/mutectcaller/meta.yml index ce50cd3d14ca..e3c2a37e0fff 100644 --- a/modules/nf-core/parabricks/mutectcaller/meta.yml +++ b/modules/nf-core/parabricks/mutectcaller/meta.yml @@ -1,5 +1,6 @@ name: "parabricks_mutectcaller" -description: NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating GATK Mutect2. +description: NVIDIA Clara Parabricks GPU-accelerated somatic variant calling, replicating + GATK Mutect2. keywords: - variant - vcf @@ -12,69 +13,80 @@ tools: homepage: https://www.nvidia.com/en-us/clara/genomics/ documentation: https://docs.nvidia.com/clara/parabricks/4.0.1/index.html licence: ["custom"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. - [ id:'test', tumor_id:'tumor', normal_id:'normal' ] - - tumor_bam: - type: file - description: bam file for tumor sample. - pattern: "*.bam" - - tumor_bam_index: - type: file - description: (Optional) bai index corresponding to tumor bam file. Only required if intervals are provided. - pattern: "*.bam" - - normal_bam: - type: file - description: (Optional) bam file for normal sample in tumor-vs-normal calling. - pattern: "*.bam" - - normal_bam_index: - type: file - description: (Optional) bai index corresponding to normal bam file. Only required if intervals are provided. - pattern: "*.bam" - - interval_file: - type: file - description: (Optional) file or files containing genomic intervals for use in base quality score recalibration. - pattern: "*.{bed,interval_list,picard,list,intervals}" - - ref_meta: - type: map - description: | - Groovy Map containing reference information - [ id:'homo_sapiens' ] - - fasta: - type: file - description: reference fasta - must be unzipped. - pattern: "*.fasta" - - panel_of_normals: - type: file - description: (Optional) pannel of normals file. - pattern: "*.vcf.gz" - - panel_of_normals_index: - type: file - description: (Optional) tbi index corresponding to pannel of normals file. - pattern: "*.tbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information - tumor_id and normal_id must match read groups for the respective samples. + [ id:'test', tumor_id:'tumor', normal_id:'normal' ] + - tumor_bam: + type: file + description: bam file for tumor sample. + pattern: "*.bam" + - tumor_bam_index: + type: file + description: (Optional) bai index corresponding to tumor bam file. Only required + if intervals are provided. + pattern: "*.bam" + - normal_bam: + type: file + description: (Optional) bam file for normal sample in tumor-vs-normal calling. + pattern: "*.bam" + - normal_bam_index: + type: file + description: (Optional) bai index corresponding to normal bam file. Only required + if intervals are provided. + pattern: "*.bam" + - interval_file: + type: file + description: (Optional) file or files containing genomic intervals for use in + base quality score recalibration. + pattern: "*.{bed,interval_list,picard,list,intervals}" + - - ref_meta: + type: map + description: | + Groovy Map containing reference information + [ id:'homo_sapiens' ] + - fasta: + type: file + description: reference fasta - must be unzipped. + pattern: "*.fasta" + - - panel_of_normals: + type: file + description: (Optional) pannel of normals file. + pattern: "*.vcf.gz" + - - panel_of_normals_index: + type: file + description: (Optional) tbi index corresponding to pannel of normals file. + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Compressed variants file. Will include an annoted vcf file if pannel of normals is used. - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Compressed variants file. Will include an annoted vcf file if pannel + of normals is used. + pattern: "*.vcf.gz" - stats: - type: file - description: Variant statistics. - pattern: "*.vcf.gz.stats" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz.stats": + type: file + description: Variant statistics. + pattern: "*.vcf.gz.stats" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@bsiranosian" diff --git a/modules/nf-core/paraclu/meta.yml b/modules/nf-core/paraclu/meta.yml index fc61d788dbb8..96d1bb9dea12 100644 --- a/modules/nf-core/paraclu/meta.yml +++ b/modules/nf-core/paraclu/meta.yml @@ -11,34 +11,37 @@ tools: documentation: https://gitlab.com/mcfrith/paraclu tool_dev_url: https://gitlab.com/mcfrith/paraclu licence: ["GPL v3-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: BED file - pattern: "*.bed" - - min_cluster: - type: integer - description: Minimum size of cluster - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file + pattern: "*.bed" + - - min_cluster: + type: integer + description: Minimum size of cluster + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: clustered BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: clustered BED file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mashehu" maintainers: diff --git a/modules/nf-core/paragraph/idxdepth/meta.yml b/modules/nf-core/paragraph/idxdepth/meta.yml index 19e90df24b8e..9af96b918b56 100644 --- a/modules/nf-core/paragraph/idxdepth/meta.yml +++ b/modules/nf-core/paragraph/idxdepth/meta.yml @@ -13,56 +13,67 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing information for the fasta - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing information for the fasta_fai - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference genome FASTA - pattern: "*.{fasta,fna,fa}" - - fasta_fai: - type: file - description: Index of the reference genome FASTA - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing information for the fasta + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome FASTA + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing information for the fasta_fai + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: Index of the reference genome FASTA + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - depth: - type: file - description: A JSON file containing depth, depth variance, read length and other parameters - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: A JSON file containing depth, depth variance, read length and other + parameters + pattern: "*.json" - binned_depth: - type: file - description: A TSV file containing the binned normalized depth. Can only be calculated for CRAM files - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV file containing the binned normalized depth. Can only be + calculated for CRAM files + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paragraph/multigrmpy/meta.yml b/modules/nf-core/paragraph/multigrmpy/meta.yml index 56075bbf1da7..34138d5e5972 100644 --- a/modules/nf-core/paragraph/multigrmpy/meta.yml +++ b/modules/nf-core/paragraph/multigrmpy/meta.yml @@ -14,70 +14,81 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variants: - type: file - description: A VCF or JSON file containing called structural variants - pattern: "*.{vcf,json}" - - variants_index: - type: file - description: The index for the VCF file - pattern: "*.tbi" - - reads: - type: file - description: BAM or CRAM file(s) to genotype against. These should be specified inside the `manifest` - pattern: "*.{bam,cram}" - - reads_index: - type: file - description: The index/indices for the BAM/CRAM file(s) - pattern: "*.{bai,crai}" - - manifest: - type: file - description: | - A tab separated file containing information on the BAM/CRAM files. - This information can be generated using paragraph/idxdepth. - More information can be found here: https://github.com/Illumina/paragraph#sample-manifest - - meta2: - type: map - description: | - Groovy Map containing sample information for the FASTA file - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference FASTA file used to generate the VCF and BAM/CRAM files - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing sample information for the FASTA index file - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variants: + type: file + description: A VCF or JSON file containing called structural variants + pattern: "*.{vcf,json}" + - variants_index: + type: file + description: The index for the VCF file + pattern: "*.tbi" + - reads: + type: file + description: BAM or CRAM file(s) to genotype against. These should be specified + inside the `manifest` + pattern: "*.{bam,cram}" + - reads_index: + type: file + description: The index/indices for the BAM/CRAM file(s) + pattern: "*.{bai,crai}" + - manifest: + type: file + description: | + A tab separated file containing information on the BAM/CRAM files. + This information can be generated using paragraph/idxdepth. + More information can be found here: https://github.com/Illumina/paragraph#sample-manifest + - - meta2: + type: map + description: | + Groovy Map containing sample information for the FASTA file + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference FASTA file used to generate the VCF and BAM/CRAM + files + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing sample information for the FASTA index file + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The genotyped VCF file in BGZIP format - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The genotyped VCF file in BGZIP format + pattern: "*.vcf.gz" - json: - type: file - description: The genotyped JSON file in GZIP format - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json.gz": + type: file + description: The genotyped JSON file in GZIP format + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paragraph/vcf2paragraph/meta.yml b/modules/nf-core/paragraph/vcf2paragraph/meta.yml index c60991218c98..6ae3b93b759a 100644 --- a/modules/nf-core/paragraph/vcf2paragraph/meta.yml +++ b/modules/nf-core/paragraph/vcf2paragraph/meta.yml @@ -12,30 +12,42 @@ tools: tool_dev_url: "https://github.com/Illumina/paragraph" doi: "10.1101/635011" licence: ["Apache License 2.0"] + identifier: biotools:Paragraph input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF/BCF file - pattern: "*.{vcf,bcf}(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF/BCF file + pattern: "*.{vcf,bcf}(.gz)?" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: Reference genome VCF was generated against + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - graph: - type: file - description: The created graph in BGZIP format - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json.gz": + type: file + description: The created graph in BGZIP format + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/paraphase/meta.yml b/modules/nf-core/paraphase/meta.yml index e6cc6d635780..50c3c9e04aa5 100644 --- a/modules/nf-core/paraphase/meta.yml +++ b/modules/nf-core/paraphase/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "paraphase" description: "HiFi-based caller for highly homologous genes" @@ -14,73 +13,96 @@ tools: tool_dev_url: "https://github.com/PacificBiosciences/paraphase" doi: "10.1016/j.ajhg.2023.01.001" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - - bam: - type: file - description: Sorted BAM file - pattern: "*.bam" - - - bai: - type: file - description: Index of BAM file - pattern: "*.bai" - - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing config information - e.g. [ id:'config' ] - - config: - type: file - description: Config file - pattern: "*.yaml" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index of BAM file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing config information + e.g. [ id:'config' ] + - config: + type: file + description: Config file + pattern: "*.yaml" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.json": + type: file + description: Summary of haplotype and variant calls + pattern: "*.paraphase.json" - bam: - type: file - description: (re)aligned BAM file - pattern: "*.paraphase.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam": + type: file + description: (re)aligned BAM file + pattern: "*.paraphase.bam" - bai: - type: file - description: Index of (re)aligned BAM file - pattern: "*.paraphase.bam.bai" - - json: - type: file - description: Summary of haplotype and variant calls - pattern: "*.paraphase.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - "*.paraphase.bam.bai": + type: file + description: Index of (re)aligned BAM file + pattern: "*.paraphase.bam.bai" - vcf: - type: file - description: compressed VCF file(s) per gene - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz: + type: file + description: compressed VCF file(s) per gene + pattern: "*.vcf.gz" - vcf_index: - type: file - description: compressed VCF file index - pattern: "*.vcf.gz.{tbi,csi}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - ${prefix}_paraphase_vcfs/*.vcf.gz.{csi,tbi}: + type: file + description: compressed VCF file index + pattern: "*.vcf.gz.{tbi,csi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/pasty/meta.yml b/modules/nf-core/pasty/meta.yml index 8f7de15f4298..6705a4a636e8 100644 --- a/modules/nf-core/pasty/meta.yml +++ b/modules/nf-core/pasty/meta.yml @@ -12,38 +12,53 @@ tools: documentation: "https://github.com/rpetit3/pasty" tool_dev_url: "https://github.com/rpetit3/pasty" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: An assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: An assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file with the predicted serogroup - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A tab-delimited file with the predicted serogroup + pattern: "*.tsv" - blast: - type: file - description: A tab-delimited file of all blast hits - pattern: "*.blastn.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.blastn.tsv: + type: file + description: A tab-delimited file of all blast hits + pattern: "*.blastn.tsv" - details: - type: file - description: A tab-delimited file with details for each serogroup - pattern: "*.details.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.details.tsv: + type: file + description: A tab-delimited file with details for each serogroup + pattern: "*.details.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pbbam/pbmerge/meta.yml b/modules/nf-core/pbbam/pbmerge/meta.yml index 83c664d6d152..5debcce908bb 100644 --- a/modules/nf-core/pbbam/pbmerge/meta.yml +++ b/modules/nf-core/pbbam/pbmerge/meta.yml @@ -1,5 +1,7 @@ name: pbbam_pbmerge -description: The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities. +description: The pbbam software package provides components to create, query, & edit + PacBio BAM files and associated indices. These components include a core C++ library, + bindings for additional languages, and command-line utilities. keywords: - pbbam - pbmerge @@ -11,34 +13,43 @@ tools: documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html tool_dev_url: https://github.com/pacificbiosciences/pbbam/ licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM files to merge - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM files to merge + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: The merged bam file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: The merged bam file + pattern: "*.bam" - pbi: - type: file - description: BAM Pacbio index file - pattern: "*.bam.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pbi": + type: file + description: BAM Pacbio index file + pattern: "*.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/pbccs/meta.yml b/modules/nf-core/pbccs/meta.yml index ded53e06ac2a..28c53ac0a1d9 100644 --- a/modules/nf-core/pbccs/meta.yml +++ b/modules/nf-core/pbccs/meta.yml @@ -7,61 +7,89 @@ keywords: - subreads tools: - pbccs: - description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads (HiFi Reads) + description: pbccs - Generate Highly Accurate Single-Molecule Consensus Reads + (HiFi Reads) homepage: https://github.com/PacificBiosciences/pbbioconda documentation: https://ccs.how/ tool_dev_url: https://github.com/PacificBiosciences/ccs licence: ["BSD-3-Clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: id of the split file - - bam: - type: file - description: Raw subreads bam - pattern: "*.subreads.bam" - - pbi: - type: file - description: Pacbio BAM Index - pattern: "*.pbi" - - chunk_num: - type: integer - description: BAM part to process - - chunk_on: - type: integer - description: Total number of bam parts to process + - - meta: + type: map + description: | + Groovy Map containing sample information + id: id of the split file + - bam: + type: file + description: Raw subreads bam + pattern: "*.subreads.bam" + - pbi: + type: file + description: Pacbio BAM Index + pattern: "*.pbi" + - - chunk_num: + type: integer + description: BAM part to process + - - chunk_on: + type: integer + description: Total number of bam parts to process output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: CCS sequences in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam": + type: file + description: CCS sequences in bam format + pattern: "*.bam" - pbi: - type: file - description: PacBio Index of CCS sequences - pattern: "*.pbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chunk*.bam.pbi": + type: file + description: PacBio Index of CCS sequences + pattern: "*.pbi" - report_txt: - type: file - description: Summary of CCS in txt format - pattern: ".txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.report.txt" ': + type: file + description: Summary of CCS in txt format + pattern: ".txt" - report_json: - type: file - description: Summary of CCS in txt json - pattern: ".json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '*.report.json" ': + type: file + description: Summary of CCS in txt json + pattern: ".json" - metrics: - type: file - description: Metrics about zmws - pattern: "*.json.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.json.gz": + type: file + description: Metrics about zmws + pattern: "*.json.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/pbptyper/meta.yml b/modules/nf-core/pbptyper/meta.yml index c12086adbd27..97cec8479cf9 100644 --- a/modules/nf-core/pbptyper/meta.yml +++ b/modules/nf-core/pbptyper/meta.yml @@ -7,43 +7,53 @@ keywords: - assembly tools: - "pbptyper": - description: "In silico Penicillin Binding Protein (PBP) typer for Streptococcus pneumoniae assemblies" + description: "In silico Penicillin Binding Protein (PBP) typer for Streptococcus + pneumoniae assemblies" homepage: "https://github.com/rpetit3/pbptyper" documentation: "https://github.com/rpetit3/pbptyper" tool_dev_url: "https://github.com/rpetit3/pbptyper" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: An assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" - - db: - type: file - description: A reference PBP database (optional) - pattern: "*.{fasta,fna,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: An assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fna,fna.gz,fa,fa.gz}" + - - db: + type: file + description: A reference PBP database (optional) + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited file with the predicted PBP type - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A tab-delimited file with the predicted PBP type + pattern: "*.tsv" - blast: - type: file - description: A tab-delimited file of all blast hits - pattern: "*.tblastn.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tblastn.tsv": + type: file + description: A tab-delimited file of all blast hits + pattern: "*.tblastn.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/pbtk/bam2fastq/meta.yml b/modules/nf-core/pbtk/bam2fastq/meta.yml index 1ba2d7511f4d..fbc16a3bf1ec 100644 --- a/modules/nf-core/pbtk/bam2fastq/meta.yml +++ b/modules/nf-core/pbtk/bam2fastq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pbtk_bam2fastq" description: converts pacbio bam files to fastq.gz using PacBioToolKit (pbtk) bam2fastq @@ -15,41 +14,38 @@ tools: tool_dev_url: "https://github.com/PacificBiosciences/pbtk" doi: "no DOI available" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - bam: - type: file - description: PacBio BAM file - pattern: "*.bam" - - - pbi: - type: file - description: PacBio BAM file index (.pbi) - pattern: "*.pbi" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - bam: + type: file + description: PacBio BAM file + pattern: "*.bam" + - pbi: + type: file + description: PacBio BAM file index (.pbi) + pattern: "*.pbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: Gzipped FASTQ file - pattern: "*.fastq.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.$extension": + type: file + description: Gzipped FASTQ file + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mbeavitt" - "@gallvp" diff --git a/modules/nf-core/pbtk/pbindex/meta.yml b/modules/nf-core/pbtk/pbindex/meta.yml index 1bf319653890..012ca995365e 100644 --- a/modules/nf-core/pbtk/pbindex/meta.yml +++ b/modules/nf-core/pbtk/pbindex/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pbtk_pbindex" -description: Minimalistic tool which creates an index file that enables random access into PacBio BAM files +description: Minimalistic tool which creates an index file that enables random access + into PacBio BAM files keywords: - genomics - bam @@ -14,34 +14,34 @@ tools: documentation: "https://github.com/PacificBiosciences/pbtk" tool_dev_url: "https://github.com/PacificBiosciences/pbtk" licence: ["BSD-3-clause-Clear"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - bam: - type: file - description: Input BAM file - pattern: "*.bam" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Input BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pbi: - type: file - description: Index file - pattern: "*.bam.pbi" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pbi": + type: file + description: Index file + pattern: "*.bam.pbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/pear/meta.yml b/modules/nf-core/pear/meta.yml index 8f100600364b..a09b2901dcd7 100644 --- a/modules/nf-core/pear/meta.yml +++ b/modules/nf-core/pear/meta.yml @@ -1,5 +1,6 @@ name: "pear" -description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. +description: PEAR is an ultrafast, memory-efficient and highly accurate pair-end read + merger. keywords: - pair-end - read @@ -10,38 +11,57 @@ tools: homepage: "https://cme.h-its.org/exelixis/web/software/pear/" documentation: "https://cme.h-its.org/exelixis/web/software/pear/doc.html" licence: ["Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported"] + identifier: biotools:pear input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - reads: - type: file - description: | - List of input FastQ files with paired-end reads forward and reverse. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - reads: + type: file + description: | + List of input FastQ files with paired-end reads forward and reverse. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembled: - type: file - description: FastQ file containing Assembled reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.assembled.fastq.gz": + type: file + description: FastQ file containing Assembled reads. + pattern: "*.{fastq.gz}" - unassembled: - type: file - description: FastQ files containing Unassembled forward and reverse reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.unassembled.forward.fastq.gz": + type: file + description: FastQ files containing Unassembled forward and reverse reads. + pattern: "*.{fastq.gz}" + - "*.unassembled.reverse.fastq.gz": + type: file + description: FastQ files containing Unassembled forward and reverse reads. + pattern: "*.{fastq.gz}" - discarded: - type: file - description: FastQ file containing discarded reads. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.discarded.fastq.gz": + type: file + description: FastQ file containing discarded reads. + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/peddy/meta.yml b/modules/nf-core/peddy/meta.yml index 24a82e190fe4..6b6b7347d03c 100644 --- a/modules/nf-core/peddy/meta.yml +++ b/modules/nf-core/peddy/meta.yml @@ -6,56 +6,78 @@ keywords: - family tools: - peddy: - description: genotype, ped correspondence check, ancestry check, sex check. directly, quickly on VCF + description: genotype, ped correspondence check, ancestry check, sex check. directly, + quickly on VCF homepage: https://github.com/brentp/peddy documentation: https://peddy.readthedocs.io/en/latest/ tool_dev_url: https://github.com/brentp/peddy doi: "10.1016/j.ajhg.2017.01.017" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" - - ped: - type: file - description: PED/FAM file - pattern: "*.{ped,fam}" - - vcf_tbi: - type: file - description: TBI file - pattern: "*.{vcf.gz.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf.gz}" + - vcf_tbi: + type: file + description: TBI file + pattern: "*.{vcf.gz.tbi}" + - - ped: + type: file + description: PED/FAM file + pattern: "*.{ped,fam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ped: - type: file - description: PED/FAM file - pattern: "*.peddy.{ped}" - html: - type: file - description: HTML file - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML file + pattern: "*.{html}" - csv: - type: file - description: CSV file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: CSV file + pattern: "*.{csv}" + - ped: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.peddy.ped": + type: file + description: PED/FAM file + pattern: "*.peddy.{ped}" - png: - type: file - description: PNG file - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: PNG file + pattern: "*.{png}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/peka/meta.yml b/modules/nf-core/peka/meta.yml index 6c1adf1db1f0..8ec588131faf 100644 --- a/modules/nf-core/peka/meta.yml +++ b/modules/nf-core/peka/meta.yml @@ -1,4 +1,3 @@ ---- name: "peka" description: Runs PEKA CLIP peak k-mer analysis keywords: @@ -9,55 +8,124 @@ keywords: - k-mer tools: - "peka": - description: "Positionally-enriched k-mer analysis (PEKA) is a software package for identifying enriched protein-RNA binding motifs from CLIP datasets" + description: "Positionally-enriched k-mer analysis (PEKA) is a software package + for identifying enriched protein-RNA binding motifs from CLIP datasets" homepage: "https://github.com/ulelab/peka" documentation: "https://github.com/ulelab/peka" tool_dev_url: "https://github.com/ulelab/peka" doi: "10.1186/s13059-022-02755-2" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - peaks: - type: file - description: BED file of peak regions - pattern: "*.{bed,bed.gz}" - - crosslinks: - type: file - description: BED file of crosslinks - pattern: "*.{bed,bed.gz}" - - fasta: - type: file - description: Genome reference sequence used - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FAI file corresponding to the reference sequence - pattern: "*.{fai}" - - gtf: - type: file - description: A segmented GTF used to annotate peaks - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peaks: + type: file + description: BED file of peak regions + pattern: "*.{bed,bed.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - crosslinks: + type: file + description: BED file of crosslinks + pattern: "*.{bed,bed.gz}" + - - fasta: + type: file + description: Genome reference sequence used + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: FAI file corresponding to the reference sequence + pattern: "*.{fai}" + - - gtf: + type: file + description: A segmented GTF used to annotate peaks + pattern: "*.{gtf}" output: - cluster: - type: file - description: TSV file of summed occurrence distributions of k-mers within defined clusters - pattern: "*.tsv" + - meta: + type: file + description: TSV file of summed occurrence distributions of k-mers within defined + clusters + pattern: "*.tsv" + - "*mer_cluster_distribution*": + type: file + description: TSV file of summed occurrence distributions of k-mers within defined + clusters + pattern: "*.tsv" - distribution: - type: file - description: TSV file with calculated PEKA score and occurrence distribution for all possible k-mers - pattern: "*.tsv" + - meta: + type: file + description: TSV file with calculated PEKA score and occurrence distribution + for all possible k-mers + pattern: "*.tsv" + - "*mer_distribution*": + type: file + description: TSV file with calculated PEKA score and occurrence distribution + for all possible k-mers + pattern: "*.tsv" + - rtxn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*rtxn*": + type: file + description: rtxn file + pattern: "*rtxn*" - pdf: - type: file - description: PDF file with graphs showing k-mer occurrence distributions around thresholded crosslink sites - pattern: "*.pdf" + - meta: + type: file + description: PDF file with graphs showing k-mer occurrence distributions around + thresholded crosslink sites + pattern: "*.pdf" + - "*.pdf": + type: file + description: PDF file with graphs showing k-mer occurrence distributions around + thresholded crosslink sites + pattern: "*.pdf" + - tsites: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*thresholded_sites*.bed.gz": + type: file + description: BED file of thresholded sites + pattern: "*thresholded_sites*.bed.gz" + - oxn: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*oxn*.bed.gz": + type: file + description: BED file of oxn sites + pattern: "*oxn*.bed.gz" + - clust: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_clusters.csv": + type: file + description: CSV file of clusters + pattern: "*_clusters.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kkuret" - "@codeprimate123" diff --git a/modules/nf-core/phantompeakqualtools/meta.yml b/modules/nf-core/phantompeakqualtools/meta.yml index 276f6fddf6f8..d9c7cdac832c 100644 --- a/modules/nf-core/phantompeakqualtools/meta.yml +++ b/modules/nf-core/phantompeakqualtools/meta.yml @@ -19,40 +19,55 @@ tools: tool_dev_url: "https://github.com/kundajelab/phantompeakqualtools" doi: "10.1101/gr.136184.111" licence: ["BSD-3-clause"] + identifier: biotools:phantompeakqualtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spp: - type: file - description: | - A ChIP-Seq Processing Pipeline file containing - peakshift/phantomPeak results - pattern: "*.{out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out": + type: file + description: | + A ChIP-Seq Processing Pipeline file containing + peakshift/phantomPeak results + pattern: "*.{out}" - pdf: - type: file - description: A pdf containing save cross-correlation plots - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: A pdf containing save cross-correlation plots + pattern: "*.{pdf}" - rdata: - type: file - description: Rdata file containing the R session - pattern: "*.{Rdata}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Rdata": + type: file + description: Rdata file containing the R session + pattern: "*.{Rdata}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/pharokka/installdatabases/meta.yml b/modules/nf-core/pharokka/installdatabases/meta.yml index a4d0f63d6d5a..e70d8f7edbae 100644 --- a/modules/nf-core/pharokka/installdatabases/meta.yml +++ b/modules/nf-core/pharokka/installdatabases/meta.yml @@ -17,17 +17,19 @@ tools: tool_dev_url: "https://github.com/gbouras13/pharokka" doi: "10.1093/bioinformatics/btac776" licence: ["MIT"] + identifier: biotools:pharokka output: - pharokka_db: - type: directory - description: Directory pointing to Pharokka's database - pattern: "${prefix}/" + - ${prefix}/: + type: directory + description: Directory pointing to Pharokka's database + pattern: "${prefix}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/pharokka/pharokka/meta.yml b/modules/nf-core/pharokka/pharokka/meta.yml index fbba281b6331..c73eb479b583 100644 --- a/modules/nf-core/pharokka/pharokka/meta.yml +++ b/modules/nf-core/pharokka/pharokka/meta.yml @@ -15,56 +15,100 @@ tools: tool_dev_url: "https://github.com/gbouras13/pharokka" doi: "10.1093/bioinformatics/btac776" licence: ["MIT"] + identifier: biotools:pharokka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - phage_fasta: - type: file - description: A FASTA file containing phage sequence(s) - pattern: "*.{fasta,fna,fa}" - - pharokka_db: - type: file - description: Directory containing Pharokka's database - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - phage_fasta: + type: file + description: A FASTA file containing phage sequence(s) + pattern: "*.{fasta,fna,fa}" + - - pharokka_db: + type: file + description: Directory containing Pharokka's database output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - log: - type: file - description: Log file containing all logging output - pattern: "*.log" + - cds_final_merged_output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_cds_final_merged_output.tsv: + type: file + description: A file containing the final merged output of CDSs + pattern: "*_cds_final_merged_output.tsv" - cds_functions: - type: file - description: A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and PHROG functions assigned to CDSs - pattern: "*_cds_functions.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_cds_functions.tsv: + type: file + description: A file that includes count of CDSs, tRNAs, CRISPRs, tmRNAs, and + PHROG functions assigned to CDSs + pattern: "*_cds_functions.tsv" + - length_gc_cds_density: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_length_gc_cds_density.tsv: + type: file + description: A file containing the length, GC content, and CDS density of + the phage genome + pattern: "*_length_gc_cds_density.tsv" - card: - type: file - description: OPTIONAL - A file containing any CARD database hits - pattern: "*top_hits_card.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_card.tsv: + type: file + description: OPTIONAL - A file containing any CARD database hits + pattern: "*top_hits_card.tsv" - vfdb: - type: file - description: OPTIONAL - A file containing any VFDB database hits - pattern: "*top_hits_vfdb.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_vfdb.tsv: + type: file + description: OPTIONAL - A file containing any VFDB database hits + pattern: "*top_hits_vfdb.tsv" - mash: - type: file - description: OPTIONAL - File containing top hits to INPHARED database - pattern: "*_top_hits_mash_inphared.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_top_hits_mash_inphared.tsv: + type: file + description: OPTIONAL - File containing top hits to INPHARED database + pattern: "*_top_hits_mash_inphared.tsv" - reoriented: - type: file - description: OPTIONAL - FASTA file reoriented to start with the large terminase subunit - pattern: "*_genome_terminase_reoriented.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}_pharokka/${prefix}_genome_terminase_reoriented.fasta: + type: file + description: OPTIONAL - FASTA file reoriented to start with the large terminase + subunit + pattern: "*_genome_terminase_reoriented.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/phispy/meta.yml b/modules/nf-core/phispy/meta.yml index e9c65aeaf300..fd47eb4f561f 100644 --- a/modules/nf-core/phispy/meta.yml +++ b/modules/nf-core/phispy/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "phispy" description: Predict prophages in bacterial genomes @@ -17,80 +16,143 @@ tools: tool_dev_url: "https://github.com/linsalrob/PhiSpy/" doi: "10.1093/nar/gks406" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gbk: - type: file - description: Genome file in .gbk or .gbff format. - pattern: "*.{gbk,gbff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gbk: + type: file + description: Genome file in .gbk or .gbff format. + pattern: "*.{gbk,gbff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - coordinates: - type: file - description: | - Coordinates of each prophage identified in the genome, - and their att sites (if found). - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: | + Coordinates of each prophage identified in the genome, + and their att sites (if found). + pattern: "*.{tsv}" - gbk: - type: file - description: | - A duplicate GenBank record that is the same as the input record, - but we have inserted the prophage information, including att - sites into the record. - pattern: "*.{gbk,gbff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.gb*: + type: file + description: | + A duplicate GenBank record that is the same as the input record, + but we have inserted the prophage information, including att + sites into the record. + pattern: "*.{gbk,gbff}" - log: - type: file - description: File containing the PhiSpy execution log - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.log: + type: file + description: File containing the PhiSpy execution log + pattern: "*.{log}" - information: - type: file - description: | - File containing all the genes of the genome, one per line. - The tenth column describes how likely the gene is a phage gene. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage_information.tsv: + type: file + description: | + File containing all the genes of the genome, one per line. + The tenth column describes how likely the gene is a phage gene. + pattern: "*.{tsv}" - bacteria_fasta: - type: file - description: Genome with prophage regions masked with N. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_bacteria.fasta: + type: file + description: Genome with prophage regions masked with N. + pattern: "*.{fasta}" - bacteria_gbk: - type: file - description: Genome sequences identified as bacterial. - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_bacteria.gbk: + type: file + description: Genome sequences identified as bacterial. + pattern: "*.{gbk}" - phage_fasta: - type: file - description: Phage sequences extracted from the genome. - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_phage.fasta: + type: file + description: Phage sequences extracted from the genome. + pattern: "*.{fasta}" - phage_gbk: - type: file - description: Phage sequences extracted from the genome. - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_phage.gbk: + type: file + description: Phage sequences extracted from the genome. + pattern: "*.{gbk}" - prophage_gff: - type: file - description: Prophage information in GFF3 format. - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.gff3: + type: file + description: Prophage information in GFF3 format. + pattern: "*.{gff3}" - prophage_tbl: - type: file - description: | - File containing prophage number and its location in the genome. - pattern: "*.{tbl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.tbl: + type: file + description: | + File containing prophage number and its location in the genome. + pattern: "*.{tbl}" - prophage_tsv: - type: file - description: | - A file containing simpler version of the coordinates file, - with only prophage number, contig, start and stop. - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_prophage.tsv: + type: file + description: | + A file containing simpler version of the coordinates file, + with only prophage number, contig, start and stop. + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvfe" maintainers: diff --git a/modules/nf-core/phyloflash/meta.yml b/modules/nf-core/phyloflash/meta.yml index 1b7ab8bec44a..5d0c9ad906c5 100644 --- a/modules/nf-core/phyloflash/meta.yml +++ b/modules/nf-core/phyloflash/meta.yml @@ -1,49 +1,53 @@ name: phyloflash -description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. +description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore + phylogenetic composition of an illumina (meta)genomic dataset. keywords: - metagenomics - illumina datasets - phylogenetic composition tools: - phyloflash: - description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset. + description: phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and + explore phylogenetic composition of an illumina (meta)genomic dataset. homepage: https://hrgv.github.io/phyloFlash/ documentation: https://hrgv.github.io/phyloFlash/usage.html tool_dev_url: https://github.com/HRGV/phyloFlash doi: "10.1128/mSystems.00920-20" licence: ["GPL v3"] + identifier: biotools:phyloflash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Channel containing single or paired-end reads - pattern: "*.{fastq.gz,fq.gz}" - - sliva_db: - type: directory - description: Folder containing the SILVA database - pattern: "ref" - - univec_db: - type: directory - description: Folder containing UniVec database - pattern: "UniVec" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Channel containing single or paired-end reads + pattern: "*.{fastq.gz,fq.gz}" + - - silva_db: + type: directory + description: Folder containing SILVA database + - - univec_db: + type: directory + description: Folder containing UniVec database + pattern: "UniVec" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Folder containing the results of phyloFlash analysis - pattern: "${prefix}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${meta.id}*/*: + type: directory + description: Folder containing the results of phyloFlash analysis + pattern: "${prefix}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/picard/addorreplacereadgroups/meta.yml b/modules/nf-core/picard/addorreplacereadgroups/meta.yml index efd5b86dc059..77ce85035f07 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/meta.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/meta.yml @@ -14,56 +14,71 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037226472-AddOrReplaceReadGroups-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Sequence reads file, can be SAM/BAM/CRAM format - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_index: + type: file + description: Reference genome index file + pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Output BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Output BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/bedtointervallist/meta.yml b/modules/nf-core/picard/bedtointervallist/meta.yml index 862736d39675..e9e35a29bb16 100644 --- a/modules/nf-core/picard/bedtointervallist/meta.yml +++ b/modules/nf-core/picard/bedtointervallist/meta.yml @@ -15,38 +15,45 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - bed: - type: file - description: Input bed file - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - dict: - type: file - description: Sequence dictionary - pattern: "*.dict" - - arguments_file: - type: file - description: File containing command line arguments (optional) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bed: + type: file + description: Input bed file + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - dict: + type: file + description: Sequence dictionary + pattern: "*.dict" output: - interval_list: - type: file - description: gatk interval list file - pattern: "*.interval_list" + - meta: + type: file + description: gatk interval list file + pattern: "*.interval_list" + - "*.interval_list": + type: file + description: gatk interval list file + pattern: "*.interval_list" + - _list: + type: file + description: gatk interval list file + pattern: "*.interval_list" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@matthdsm" diff --git a/modules/nf-core/picard/cleansam/meta.yml b/modules/nf-core/picard/cleansam/meta.yml index a74fe2e100d6..ae981700c618 100644 --- a/modules/nf-core/picard/cleansam/meta.yml +++ b/modules/nf-core/picard/cleansam/meta.yml @@ -1,5 +1,6 @@ name: picard_cleansam -description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments and setting MAPQ to 0 for unmapped reads +description: Cleans the provided BAM, soft-clipping beyond-end-of-reference alignments + and setting MAPQ to 0 for unmapped reads keywords: - clean - bam @@ -15,30 +16,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036491452-CleanSam-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Cleaned BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Cleaned BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/collecthsmetrics/meta.yml b/modules/nf-core/picard/collecthsmetrics/meta.yml index 4b6d53b807d2..ea6deda3e56a 100644 --- a/modules/nf-core/picard/collecthsmetrics/meta.yml +++ b/modules/nf-core/picard/collecthsmetrics/meta.yml @@ -17,71 +17,75 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: An aligned BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Optional aligned BAM/CRAM/SAM file index - pattern: "*.{bai,crai,sai}" - - bait_intervals: - type: file - description: An interval file that contains the locations of the baits used. - pattern: "*.{interval_list,bed,bed.gz}" - - target_intervals: - type: file - description: An interval file that contains the locations of the targets. - pattern: "*.{interval_list,bed,bed.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: | - A reference file to calculate dropout metrics measuring reduced representation of reads. - Optional input. - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Sequence dictionary of FASTA file. Only needed when bed interval lists are supplied. - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: An aligned BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Optional aligned BAM/CRAM/SAM file index + pattern: "*.{bai,crai,sai}" + - bait_intervals: + type: file + description: An interval file that contains the locations of the baits used. + pattern: "*.{interval_list,bed,bed.gz}" + - target_intervals: + type: file + description: An interval file that contains the locations of the targets. + pattern: "*.{interval_list,bed,bed.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: | + A reference file to calculate dropout metrics measuring reduced representation of reads. + Optional input. + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of FASTA file. Only needed when fasta is supplied. + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Sequence dictionary of FASTA file. Only needed when bed interval + lists are supplied. + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml index e2749cb62175..0947048dc672 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/meta.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/meta.yml @@ -13,34 +13,43 @@ tools: documentation: "https://broadinstitute.github.io/picard/" tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pdf: - type: file - description: Histogram plots of the insert size metrics computed by Picard - pattern: "*.pdf" - metrics: - type: file - description: Values used by Picard to generate the insert size histograms - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Values used by Picard to generate the insert size histograms + pattern: "*.txt" + - histogram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Insert size histogram in PDF format + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FerriolCalvet" maintainers: diff --git a/modules/nf-core/picard/collectmultiplemetrics/meta.yml b/modules/nf-core/picard/collectmultiplemetrics/meta.yml index 67bba57b21dc..2b7981ac6b3a 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/meta.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/meta.yml @@ -15,55 +15,64 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: SAM/BAM/CRAM file - pattern: "*.{sam,bam,cram}" - - bai: - type: file - description: Optional SAM/BAM/CRAM file index - pattern: "*.{sai,bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fasta: - type: file - description: Genome fasta file - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome'] - - fai: - type: file - description: Index of FASTA file. Only needed when fasta is supplied. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: SAM/BAM/CRAM file + pattern: "*.{sam,bam,cram}" + - bai: + type: file + description: Optional SAM/BAM/CRAM file index + pattern: "*.{sai,bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fasta: + type: file + description: Genome fasta file + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome'] + - fai: + type: file + description: Index of FASTA file. Only needed when fasta is supplied. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" - pdf: - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: PDF plots of metrics + pattern: "*.{pdf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml index 8a7bd2346ae6..15d146baac0e 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/meta.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/meta.yml @@ -16,45 +16,52 @@ tools: documentation: "https://broadinstitute.github.io/picard/" tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, strandedness:true ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - ref_flat: - type: file - description: Genome ref_flat file - - gene_pred: - type: file - description: genome gene_pred file as an alternative to the ref_flat file - - fasta: - type: file - description: Genome fasta file - - rrna_intervals: - type: file - description: Interval file of ribosomal RNA regions + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, strandedness:true ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - - ref_flat: + type: file + description: Genome ref_flat file + - - fasta: + type: file + description: Genome fasta file + - - rrna_intervals: + type: file + description: Interval file of ribosomal RNA regions output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: RNA alignment metrics files generated by picard - pattern: "*.rna_metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rna_metrics": + type: file + description: RNA alignment metrics files generated by picard + pattern: "*.rna_metrics" - pdf: - type: file - description: Plot normalized position vs. coverage in a pdf file generated by picard + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: Plot normalized position vs. coverage in a pdf file generated by + picard - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@anoronh4" maintainers: diff --git a/modules/nf-core/picard/collectwgsmetrics/meta.yml b/modules/nf-core/picard/collectwgsmetrics/meta.yml index 5576ef9287b0..bb748080983f 100644 --- a/modules/nf-core/picard/collectwgsmetrics/meta.yml +++ b/modules/nf-core/picard/collectwgsmetrics/meta.yml @@ -1,5 +1,6 @@ name: picard_collectwgsmetrics -description: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. +description: Collect metrics about coverage and performance of whole genome sequencing + (WGS) experiments. keywords: - alignment - metrics @@ -14,55 +15,59 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Aligned reads file - pattern: "*.{bam, cram}" - - bai: - type: file - description: (Optional) Aligned reads file index - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Genome fasta file index - pattern: "*.{fai}" - - intervallist: - type: file - description: Picard Interval List. Defines which contigs to include. Can be generated from a BED file with GATK BedToIntervalList. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Aligned reads file + pattern: "*.{bam, cram}" + - bai: + type: file + description: (Optional) Aligned reads file index + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Genome fasta file index + pattern: "*.{fai}" + - - intervallist: + type: file + description: Picard Interval List. Defines which contigs to include. Can be + generated from a BED file with GATK BedToIntervalList. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_metrics": + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@flowuenne" diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml index 0cb79cfe5c46..67616703118a 100644 --- a/modules/nf-core/picard/createsequencedictionary/meta.yml +++ b/modules/nf-core/picard/createsequencedictionary/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reference_dict: - type: file - description: picard dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dict": + type: file + description: picard dictionary file + pattern: "*.{dict}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/crosscheckfingerprints/meta.yml b/modules/nf-core/picard/crosscheckfingerprints/meta.yml index 1db3b866f21d..898a11a8004e 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/meta.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/meta.yml @@ -1,5 +1,6 @@ name: "picard_crosscheckfingerprints" -description: Checks that all data in the set of input files appear to come from the same individual +description: Checks that all data in the set of input files appear to come from the + same individual keywords: - alignment - metrics @@ -15,60 +16,59 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input1: - type: file - description: List containing 1 or more bam/vcf files or a file containing filepaths - pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" - - input1_index: - type: file - description: List containing 1 or more bam/vcf files indexes - pattern: "*.{bai,csi,crai,tbi}" - - input2: - type: file - description: Optional list containing 1 or more bam/vcf files or a file containing filepaths - pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" - - input2_index: - type: file - description: List containing 1 or more bam/vcf files indexes - pattern: "*.{bai,csi,crai,tbi}" - - haplotype_map: - type: file - description: Haplotype map file - pattern: "*.{txt,vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - fasta_index: - type: file - description: Reference genome index file - pattern: "*.{fai,fasta.fai,fa.fai,fasta.gz.fai,fa.gz.fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input1: + type: file + description: List containing 1 or more bam/vcf files or a file containing filepaths + pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" + - input1_index: + type: file + description: List containing 1 or more bam/vcf files indexes + pattern: "*.{bai,csi,crai,tbi}" + - input2: + type: file + description: Optional list containing 1 or more bam/vcf files or a file containing + filepaths + pattern: "*.{bam,vcf,vcf.gz,txt,fofn}" + - input2_index: + type: file + description: List containing 1 or more bam/vcf files indexes + pattern: "*.{bai,csi,crai,tbi}" + - haplotype_map: + type: file + description: Haplotype map file + pattern: "*.{txt,vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - crosscheck_metrics: - type: file - description: Metrics created by crosscheckfingerprints - pattern: "*.{crosscheck_metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crosscheck_metrics.txt": + type: file + description: Metrics created by crosscheckfingerprints + pattern: "*.{crosscheck_metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/picard/extractfingerprint/meta.yml b/modules/nf-core/picard/extractfingerprint/meta.yml index 5c6ccb42cccc..d8f6144f54fb 100644 --- a/modules/nf-core/picard/extractfingerprint/meta.yml +++ b/modules/nf-core/picard/extractfingerprint/meta.yml @@ -1,5 +1,6 @@ name: "picard_extractfingerprint" -description: Computes/Extracts the fingerprint genotype likelihoods from the supplied file. It is given as a list of PLs at the fingerprinting sites. +description: Computes/Extracts the fingerprint genotype likelihoods from the supplied + file. It is given as a list of PLs at the fingerprinting sites. keywords: - picard - extract @@ -14,30 +15,63 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: file - description: | - Input SAM/BAM/CRAM file - - reference: - type: file - description: | - Reference sequence file - - haplotype_map: - type: file - description: | - A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. - See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details. - pattern: "*.{txt,vcf,vcf.gz}" + - - meta: + type: file + description: | + Input SAM/BAM/CRAM file + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - - haplotype_map: + type: file + description: | + A file of haplotype information. The file lists a set of SNPs, optionally arranged in high-LD blocks, to be used for fingerprinting. + See https://software.broadinstitute.org/gatk/documentation/article?id=9526 for details. + pattern: "*.{txt,vcf,vcf.gz}" + - - fasta: + type: file + description: Reference sequence file + pattern: "*.{fasta,fna,fa}" + - - fasta_fai: + type: file + description: Reference sequence index file + pattern: "*.{fai}" + - - sequence_dictionary: + type: file + description: Reference sequence dictionary file output: - - fingerprint: - type: file - description: | - Output fingerprint file (VCF) + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Tabix index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" - "@mauro-saporita" diff --git a/modules/nf-core/picard/fastqtosam/meta.yml b/modules/nf-core/picard/fastqtosam/meta.yml index 673914386070..4cf42d855bd2 100644 --- a/modules/nf-core/picard/fastqtosam/meta.yml +++ b/modules/nf-core/picard/fastqtosam/meta.yml @@ -13,32 +13,34 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036510672-FastqToSam-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Unaligned bam file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Unaligned bam file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/picard/filtersamreads/meta.yml b/modules/nf-core/picard/filtersamreads/meta.yml index 0be39002ee94..9fe52dec14c7 100644 --- a/modules/nf-core/picard/filtersamreads/meta.yml +++ b/modules/nf-core/picard/filtersamreads/meta.yml @@ -1,5 +1,6 @@ name: picard_filtersamreads -description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads or based on a read list +description: Filters SAM/BAM files to include/exclude either aligned/unaligned reads + or based on a read list keywords: - bam - filter @@ -14,37 +15,41 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam - pattern: "*.{bam}" - - filter: - type: string - description: Picard filter type - pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" - - readlist: - type: file - description: Optional text file containing reads IDs to include or exclude + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM files. If filtering without read list must be sorted + by queryname with picard sortsam + pattern: "*.{bam}" + - readlist: + type: file + description: Optional text file containing reads IDs to include or exclude + - - filter: + type: string + description: Picard filter type + pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Filtered BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered BAM file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/picard/fixmateinformation/meta.yml b/modules/nf-core/picard/fixmateinformation/meta.yml index 35849993c299..ec562e97e1d7 100644 --- a/modules/nf-core/picard/fixmateinformation/meta.yml +++ b/modules/nf-core/picard/fixmateinformation/meta.yml @@ -14,30 +14,33 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036713471-FixMateInformation-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: mate-pair verified BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: mate-pair verified BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/picard/liftovervcf/meta.yml b/modules/nf-core/picard/liftovervcf/meta.yml index 9ccba6d24ad2..10fbfc837851 100644 --- a/modules/nf-core/picard/liftovervcf/meta.yml +++ b/modules/nf-core/picard/liftovervcf/meta.yml @@ -11,56 +11,66 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037060932-LiftoverVcf-Picard tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - input_vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: dictionary for fasta file - pattern: "*.{dict}" - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - chain: - type: file - description: The liftover chain file + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - input_vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: dictionary for fasta file + pattern: "*.{dict}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: fasta file + pattern: "*.fasta" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - chain: + type: file + description: The liftover chain file output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf_lifted: - type: file - description: VCF file containing successfully lifted variants - pattern: "*.{lifted.vcf.gz}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.lifted.vcf.gz": + type: file + description: VCF file containing successfully lifted variants + pattern: "*.{lifted.vcf.gz}" - vcf_unlifted: - type: file - description: VCF file containing unsuccessfully lifted variants - pattern: "*.{unlifted.vcf.gz}" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.unlifted.vcf.gz": + type: file + description: VCF file containing unsuccessfully lifted variants + pattern: "*.{unlifted.vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" - "@ramprasadn" diff --git a/modules/nf-core/picard/markduplicates/meta.yml b/modules/nf-core/picard/markduplicates/meta.yml index 1f0ffe16c2fc..bcaf916055a3 100644 --- a/modules/nf-core/picard/markduplicates/meta.yml +++ b/modules/nf-core/picard/markduplicates/meta.yml @@ -15,60 +15,82 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Sequence reads file, can be SAM/BAM/CRAM format - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file, required for CRAM input - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Reference genome fasta index - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Sequence reads file, can be SAM/BAM/CRAM format + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file, required for CRAM input + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Reference genome fasta index + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with duplicate reads marked/removed - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" - cram: - type: file - description: Output CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Output CRAM file + pattern: "*.{cram}" - metrics: - type: file - description: Duplicate metrics file generated by picard - pattern: "*.{metrics.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics.txt": + type: file + description: Duplicate metrics file generated by picard + pattern: "*.{metrics.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@projectoriented" diff --git a/modules/nf-core/picard/mergesamfiles/meta.yml b/modules/nf-core/picard/mergesamfiles/meta.yml index c1ca98cf7416..df356b0d41d6 100644 --- a/modules/nf-core/picard/mergesamfiles/meta.yml +++ b/modules/nf-core/picard/mergesamfiles/meta.yml @@ -13,30 +13,33 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: list + description: List of input BAM files to be merged + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Merged BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Merged BAM file + pattern: "*.{bam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml b/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml index 7b5dd29fe371..3b19eed3f47a 100644 --- a/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml +++ b/modules/nf-core/picard/positionbaseddownsamplesam/meta.yml @@ -1,5 +1,6 @@ name: picard_positionbaseddownsamplesam -description: Samples a SAM/BAM/CRAM file using flowcell position information for the best approximation of having sequenced fewer reads +description: Samples a SAM/BAM/CRAM file using flowcell position information for the + best approximation of having sequenced fewer reads keywords: - sample - bam @@ -13,39 +14,55 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam,cram,sam}" - - fraction: - type: float - description: Fraction of reads to downsample to + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam,cram,sam}" + - fraction: + type: float + description: Fraction of reads to downsample to output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: A downsampled BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ds*.bam": + type: file + description: A downsampled BAM file + pattern: "*.{bam}" - bai: - type: file - description: An optional BAM index file. If desired, --CREATE_INDEX must be passed as a flag - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ds*.bai": + type: file + description: An optional BAM index file. If desired, --CREATE_INDEX must be + passed as a flag + pattern: "*.{bai}" - num_reads: - type: integer - description: The actual number of downsampled reads + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ACTUAL_NUM_READS: + type: integer + description: The actual number of downsampled reads - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bwlang" diff --git a/modules/nf-core/picard/renamesampleinvcf/meta.yml b/modules/nf-core/picard/renamesampleinvcf/meta.yml index 528002d07bb8..7c279fe1eff0 100644 --- a/modules/nf-core/picard/renamesampleinvcf/meta.yml +++ b/modules/nf-core/picard/renamesampleinvcf/meta.yml @@ -13,30 +13,33 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Lucpen" maintainers: diff --git a/modules/nf-core/picard/scatterintervalsbyns/meta.yml b/modules/nf-core/picard/scatterintervalsbyns/meta.yml index c81ed7bf59a3..f18bf6a5e1a4 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/meta.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "picard_scatterintervalsbyns" -description: Writes an interval list created by splitting a reference at Ns.A Program for breaking up a reference into intervals of alternating regions of N and ACGT bases +description: Writes an interval list created by splitting a reference at Ns.A Program + for breaking up a reference into intervals of alternating regions of N and ACGT + bases keywords: - interval_list - scatter @@ -15,48 +16,55 @@ tools: documentation: https://broadinstitute.github.io/picard/ tool_dev_url: "https://github.com/broadinstitute/picard" licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file to derive the intervals from - pattern: "*.{fasta,fa,fna}" - - meta2: - type: map - description: | - Groovy Map containing fai information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index of the fasta file - pattern: "*.fai" - - meta3: - type: map - description: | - Groovy Map containing dictionary information - e.g. [ id:'test', single_end:false ] - - dict: - type: file - description: Sequence dictionary of the fasta file - pattern: "*.dict" + - - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file to derive the intervals from + pattern: "*.{fasta,fa,fna}" + - - meta2: + type: map + description: | + Groovy Map containing fai information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of the fasta file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing dictionary information + e.g. [ id:'test', single_end:false ] + - dict: + type: file + description: Sequence dictionary of the fasta file + pattern: "*.dict" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - intervals: - type: file - description: The scattered intervals - pattern: "*.interval_list" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interval_list": + type: file + description: The scattered intervals + pattern: "*.interval_list" + - s: + type: file + description: The scattered intervals + pattern: "*.interval_list" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/picard/sortsam/meta.yml b/modules/nf-core/picard/sortsam/meta.yml index 509942f994d3..24ea9d37dfee 100644 --- a/modules/nf-core/picard/sortsam/meta.yml +++ b/modules/nf-core/picard/sortsam/meta.yml @@ -13,34 +13,37 @@ tools: homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,sam}" - - sort_order: - type: string - description: Picard sort order type - pattern: "unsorted|queryname|coordinate|duplicate|unknown" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,sam}" + - - sort_order: + type: string + description: Picard sort order type + pattern: "unsorted|queryname|coordinate|duplicate|unknown" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/picard/sortvcf/meta.yml b/modules/nf-core/picard/sortvcf/meta.yml index 62507a085dd6..6dc28e03fecb 100644 --- a/modules/nf-core/picard/sortvcf/meta.yml +++ b/modules/nf-core/picard/sortvcf/meta.yml @@ -6,52 +6,56 @@ keywords: - sortvcf tools: - picard: - description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF format + description: Java tools for working with NGS data in the BAM/CRAM/SAM and VCF + format homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/command-line-overview.html#SortVcf licence: ["MIT"] + identifier: biotools:picard_tools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - dict: - type: file - description: Reference genome dictionary file - pattern: "*.{dict}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - dict: + type: file + description: Reference genome dictionary file + pattern: "*.{dict}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Sorted VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_sorted.vcf.gz": + type: file + description: Sorted VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/pigz/compress/meta.yml b/modules/nf-core/pigz/compress/meta.yml index 42efd7351c6e..0966e651178e 100644 --- a/modules/nf-core/pigz/compress/meta.yml +++ b/modules/nf-core/pigz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "pigz_compress" description: Compresses files with pigz. @@ -12,35 +11,33 @@ tools: homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - raw_file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw_file: + type: file + description: File to be compressed + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - archive: - type: file - description: The compressed file - pattern: "*.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $archive: + type: file + description: The compressed file + pattern: "*.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/pigz/uncompress/meta.yml b/modules/nf-core/pigz/uncompress/meta.yml index c2d16cd4e4ea..3f583b22698c 100644 --- a/modules/nf-core/pigz/uncompress/meta.yml +++ b/modules/nf-core/pigz/uncompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pigz_uncompress" description: write your description here @@ -12,31 +11,32 @@ tools: homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - zip: - type: file - description: Gzipped file - pattern: "*.{gzip}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - zip: + type: file + description: Gzipped file + pattern: "*.{gzip}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - file: - type: file - description: File to compress - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - ${uncompressed_filename}: + type: file + description: File to compress + pattern: "*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lrauschning" diff --git a/modules/nf-core/pilon/meta.yml b/modules/nf-core/pilon/meta.yml index 7a11c4dde1a5..38d9006db671 100644 --- a/modules/nf-core/pilon/meta.yml +++ b/modules/nf-core/pilon/meta.yml @@ -1,74 +1,111 @@ name: "pilon" -description: Automatically improve draft assemblies and find variation among strains, including large event detection +description: Automatically improve draft assemblies and find variation among strains, + including large event detection keywords: - polishing - assembly - variant calling tools: - "pilon": - description: "Pilon is an automated genome assembly improvement and variant detection tool." + description: "Pilon is an automated genome assembly improvement and variant detection + tool." homepage: "https://github.com/broadinstitute/pilon/wiki" documentation: "https://github.com/broadinstitute/pilon/wiki/Requirements-&-Usage" tool_dev_url: "https://github.com/broadinstitute/pilon" doi: "10.1371/journal.pone.0112963" licence: ["GPL-2.0-or-later"] + identifier: biotools:pilon input: - - meta: - type: map - description: | - Groovy Map containing sample information for the fasta - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA of the input genome - pattern: "*.{fasta}" - - meta2: - type: map - description: | - Groovy Map containing sample information for the bam file - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file of reads aligned to the input genome - pattern: "*.{bam}" - - bai: - type: file - description: BAI file (BAM index) of BAM reads aligned to the input genome - pattern: "*.{bai}" - - pilon_mode: - type: string - description: Indicates the type of bam file used (frags for paired-end sequencing of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, jumps for paired sequencing data of larger insert size, such as Illumina mate pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing reads, bam will automatically classify the BAM as one of the three types above (version 1.17 and higher). - enum: ["frags", "jumps", "unpaired", "bam"] + - - meta: + type: map + description: | + Groovy Map containing sample information for the fasta + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA of the input genome + pattern: "*.{fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for the bam file + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file of reads aligned to the input genome + pattern: "*.{bam}" + - bai: + type: file + description: BAI file (BAM index) of BAM reads aligned to the input genome + pattern: "*.{bai}" + - - pilon_mode: + type: string + description: Indicates the type of bam file used (frags for paired-end sequencing + of DNA fragments, such as Illumina paired-end reads of fragment size <1000bp, + jumps for paired sequencing data of larger insert size, such as Illumina mate + pair libraries, typically of insert size >1000bp, unpaired for unpaired sequencing + reads, bam will automatically classify the BAM as one of the three types above + (version 1.17 and higher). + enum: ["frags", "jumps", "unpaired", "bam"] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - improved_assembly: - type: file - description: fasta file, improved assembly - pattern: "*.{fasta}" - - change_record: - type: file - description: file containing a space-delimited record of every change made in the assembly as instructed by the --fix option - pattern: "*.{change}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: fasta file, improved assembly + pattern: "*.{fasta}" - vcf: - type: file - description: Pilon variant output - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Pilon variant output + pattern: "*.{vcf}" + - change_record: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.change": + type: file + description: file containing a space-delimited record of every change made in + the assembly as instructed by the --fix option + pattern: "*.{change}" - tracks_bed: - type: file - description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: files that may be viewed in genome browsers such as IGV, GenomeView, + and other applications that support these formats + pattern: "*.{bed}" - tracks_wig: - type: file - description: files that may be viewed in genome browsers such as IGV, GenomeView, and other applications that support these formats - pattern: "*.{wig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: files that may be viewed in genome browsers such as IGV, GenomeView, + and other applications that support these formats + pattern: "*.{wig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/pindel/pindel/meta.yml b/modules/nf-core/pindel/pindel/meta.yml index 6b44f78e1500..a4983337d1e2 100644 --- a/modules/nf-core/pindel/pindel/meta.yml +++ b/modules/nf-core/pindel/pindel/meta.yml @@ -1,89 +1,150 @@ name: "pindel_pindel" -description: Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data +description: Pindel can detect breakpoints of large deletions, medium sized insertions, + inversions, tandem duplications and other structural variants at single-based resolution + from next-gen sequence data keywords: - deletions - insertions - tandem duplications tools: - "pindel": - description: "Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data" + description: "Pindel can detect breakpoints of large deletions, medium sized insertions, + inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data" homepage: "https://gmt.genome.wustl.edu/packages/pindel/" documentation: https://gmt.genome.wustl.edu/packages/pindel/user-manual.html licence: ["GPL v3"] + identifier: biotools:pindel input: - - meta: - type: map - description: | - Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics - or a sensible default - setting ext.args2 to either in modules.conf - e.g. [ id:'test', single_end:false, insert_size:500 ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - bed: - type: file - description: BED file containing regions of interest - - fasta: - type: file - description: Input reference genome fasta file - - fai: - type: file - description: Input reference genome fasta index file + - - meta: + type: map + description: | + Groovy Map containing sample information, insert_size is either determined using Picard/CollectInsertSizeMetrics + or a sensible default - setting ext.args2 to either in modules.conf + e.g. [ id:'test', single_end:false, insert_size:500 ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - fasta: + type: file + description: Input reference genome fasta file + - - fai: + type: file + description: Input reference genome fasta index file + - - bed: + type: file + description: BED file containing regions of interest output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bp: - type: file - description: File containing breakpoints - pattern: "*_{BP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_BP": + type: file + description: File containing breakpoints + pattern: "*_{BP}" - cem: - type: file - description: File containing close end reads - pattern: "*_{CloseEndMapped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_CloseEndMapped": + type: file + description: File containing close end reads + pattern: "*_{CloseEndMapped}" - del: - type: file - description: File containing deletions - pattern: "*_{D}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_D": + type: file + description: File containing deletions + pattern: "*_{D}" - dd: - type: file - description: File containing dispersed duplications - pattern: "*_{DD}" - - int_{final: - type: file - description: File containing interchromosomal events - pattern: "*_{INT_final}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_DD": + type: file + description: File containing dispersed duplications + pattern: "*_{DD}" + - int_final: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_INT_final": + type: file + description: int file + pattern: "*_INT_final" - inv: - type: file - description: File containing inversions - pattern: "*_{INV}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_INV": + type: file + description: File containing inversions + pattern: "*_{INV}" - li: - type: file - description: File containing long insertions - pattern: "*_{LI}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_LI": + type: file + description: File containing long insertions + pattern: "*_{LI}" - rp: - type: file - description: File containing read-pair evidence - pattern: "*_{RP}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_RP": + type: file + description: File containing read-pair evidence + pattern: "*_{RP}" - si: - type: file - description: File containing short insertions - pattern: "*_{SI}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_SI": + type: file + description: File containing short insertions + pattern: "*_{SI}" - td: - type: file - description: File containing tandem duplications - pattern: "*_{TD}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_TD": + type: file + description: File containing tandem duplications + pattern: "*_{TD}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/pints/caller/meta.yml b/modules/nf-core/pints/caller/meta.yml index ec749b0515d0..851ead841ba1 100644 --- a/modules/nf-core/pints/caller/meta.yml +++ b/modules/nf-core/pints/caller/meta.yml @@ -20,52 +20,73 @@ tools: tool_dev_url: "https://github.com/hyulab/PINTS" doi: "10.1038/s41587-022-01211-7" licence: ["GPL v3"] + identifier: biotools:pyPINTS input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or more BAM files - pattern: "*.{bam}" - - bais: - type: file - description: Corresponding BAM file indexes - pattern: "*.bam.bai" - - assay: - type: string - description: Assay name + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or more BAM files + pattern: "*.{bam}" + - bais: + type: file + description: Corresponding BAM file indexes + pattern: "*.bam.bai" + - - assay_type: + type: string + description: Assay type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - divergent_TREs: - type: file - description: Divergent TREs - pattern: "*_divergent_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_divergent_peaks.bed": + type: file + description: Divergent TREs + pattern: "*_divergent_peaks.bed" + optional: true - bidirectional_TREs: - type: file - description: Divergent TREs and convergent TREs - pattern: "*_bidirectional_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bidirectional_peaks.bed": + type: file + description: Divergent TREs and convergent TREs + pattern: "*_bidirectional_peaks.bed" + optional: true - unidirectional_TREs: - type: file - description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs) - pattern: "*_unidirectional_peaks.bed" - optional: true + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unidirectional_peaks.bed": + type: file + description: Unidirectional TREs, maybe lncRNAs transcribed from enhancers (e-lncRNAs) + pattern: "*_unidirectional_peaks.bed" + optional: true - peakcalling_log: - type: file - description: Peakcalling log for debugging purposes - pattern: "peakcalling_*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - peakcalling_*.log: + type: file + description: Peakcalling log for debugging purposes + pattern: "peakcalling_*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@edmundmiller" maintainers: diff --git a/modules/nf-core/pirate/meta.yml b/modules/nf-core/pirate/meta.yml index 657dc8285e0f..b53ca30db299 100644 --- a/modules/nf-core/pirate/meta.yml +++ b/modules/nf-core/pirate/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: https://github.com/SionBayliss/PIRATE doi: "10.1093/gigascience/giz119" licence: ["GPL v3"] + identifier: biotools:PIRATE input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing PIRATE result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing PIRATE result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by PIRATE (Optional) - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/core_alignment.fasta: + type: file + description: Core-genome alignment produced by PIRATE (Optional) + pattern: "*.{fasta}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/plasmidfinder/meta.yml b/modules/nf-core/plasmidfinder/meta.yml index 946d29f07411..6d3a554d4cb3 100644 --- a/modules/nf-core/plasmidfinder/meta.yml +++ b/modules/nf-core/plasmidfinder/meta.yml @@ -6,52 +6,80 @@ keywords: - plasmid tools: - "plasmidfinder": - description: "PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria." + description: "PlasmidFinder allows identification of plasmids in total or partial + sequenced isolates of bacteria." homepage: "https://cge.cbs.dtu.dk/services/PlasmidFinder/" documentation: "https://bitbucket.org/genomicepidemiology/plasmidfinder" tool_dev_url: "https://bitbucket.org/genomicepidemiology/plasmidfinder" doi: "10.1128/AAC.02412-14" licence: ["Apache-2.0"] + identifier: biotools:PlasmidFinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Input FASTA or FASTQ formatted genome sequences - pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Input FASTA or FASTQ formatted genome sequences + pattern: "*.{fastq.gz,fq.gz,fastq.gz,fna.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: The results from analysis in JSON format - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: The results from analysis in JSON format + pattern: "*.json" - txt: - type: file - description: The summary of results from analysis - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: The summary of results from analysis + pattern: "*.txt" - tsv: - type: file - description: The results from analysis in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The results from analysis in TSV format + pattern: "*.tsv" - genome_seq: - type: file - description: FASTA of sequences in the input with a hit - pattern: "*-hit_in_genome_seq.fsa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-hit_in_genome_seq.fsa": + type: file + description: FASTA of sequences in the input with a hit + pattern: "*-hit_in_genome_seq.fsa" - plasmid_seq: - type: file - description: FASTA of plasmid sequences with a hit against the input - pattern: "*-plasmid_seqs.fsa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-plasmid_seqs.fsa": + type: file + description: FASTA of plasmid sequences with a hit against the input + pattern: "*-plasmid_seqs.fsa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/plasmidid/meta.yml b/modules/nf-core/plasmidid/meta.yml index 664793598ee4..5fc9b722aa1f 100644 --- a/modules/nf-core/plasmidid/meta.yml +++ b/modules/nf-core/plasmidid/meta.yml @@ -11,62 +11,107 @@ tools: documentation: https://github.com/BU-ISCIII/plasmidID#readme tool_dev_url: https://github.com/BU-ISCIII/plasmidID licence: ["GPL v3"] + identifier: biotools:plasmidid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - scaffold: - type: file - description: | - Fasta file containing scaffold - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: | + Fasta file containing scaffold + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: html file with results rendered - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*final_results.html: + type: file + description: html file with results rendered + pattern: "*.{html}" - tab: - type: file - description: Results in a tabular file - pattern: "*.{tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*final_results.tab: + type: file + description: Results in a tabular file + pattern: "*.{tab}" - images: - type: directory - description: Directory containing the images produced by plasmidid - pattern: "images" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/images/: + type: directory + description: Directory containing the images produced by plasmidid + pattern: "images" - logs: - type: directory - description: Directory containing the logs produced by plasmidid - pattern: "logs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/logs/: + type: directory + description: Directory containing the logs produced by plasmidid + pattern: "logs" - data: - type: directory - description: Directory containing the data produced by plasmidid - pattern: "data" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/data/: + type: directory + description: Directory containing the data produced by plasmidid + pattern: "data" - database: - type: directory - description: Directory containing the database produced by plasmidid - pattern: "database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/database/: + type: directory + description: Directory containing the database produced by plasmidid + pattern: "database" - fasta_files: - type: directory - description: Directory containing the fasta files produced by plasmidid - pattern: "fasta_files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/fasta_files/: + type: directory + description: Directory containing the fasta files produced by plasmidid + pattern: "fasta_files" - kmer: - type: directory - description: Directory containing the kmer files produced by plasmidid - pattern: "database" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/kmer/: + type: directory + description: Directory containing the kmer files produced by plasmidid + pattern: "database" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/platypus/meta.yml b/modules/nf-core/platypus/meta.yml index ade5de56ba25..5ffeaa2f0db7 100644 --- a/modules/nf-core/platypus/meta.yml +++ b/modules/nf-core/platypus/meta.yml @@ -1,5 +1,6 @@ name: platypus -description: Platypus is a tool that efficiently and accurately calling genetic variants from next-generation DNA sequencing data +description: Platypus is a tool that efficiently and accurately calling genetic variants + from next-generation DNA sequencing data keywords: - variant - call @@ -7,68 +8,86 @@ keywords: - genetic tools: - platypus: - description: Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. + description: Platypus is a tool designed for efficient and accurate variant-detection + in high-throughput sequencing data. homepage: https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-a-haplotype-based-variant-caller-for-next-generation-sequence-data documentation: https://www.well.ox.ac.uk/research/research-groups/lunter-group/lunter-group/platypus-documentation tool_dev_url: https://github.com/andyrimmer/Platypus doi: "10.1038/ng.3036" licence: ["BSD-3-clause"] + identifier: biotools:platypus input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - tumor_file: - type: file - description: Tumor or metastatic sample, BAM or CRAM file - pattern: "*.{bam,cram}" - - tummor_file_bai: - type: file - description: Index of BAMfile - pattern: "*.{bai,crai}" - - control_file: - type: file - description: Control (or blood) of matching tumor/metastatic sample, BAM or CRAM file - pattern: "*.{bam,cram}" - - control_file_bai: - type: file - description: Index of BAMfile - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fa" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" - - skipregions_file: - type: file - description: File with regions to skip, region as comma-separated list of chr:start-end, or just list of chr, or nothing - pattern: "*.bed|*.txt|*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - tumor_file: + type: file + description: Tumor or metastatic sample, BAM or CRAM file + pattern: "*.{bam,cram}" + - tumor_file_bai: + type: file + description: Index of BAM file + pattern: "*.{bai,crai}" + - control_file: + type: file + description: Control (or blood) of matching tumor/metastatic sample, BAM or + CRAM file + pattern: "*.{bam,cram}" + - control_file_bai: + type: file + description: Index of BAMfile + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fa" + - - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" + - - skipregions_file: + type: file + description: File with regions to skip, region as comma-separated list of chr:start-end, + or just list of chr, or nothing + pattern: "*.bed|*.txt|*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: Output VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz": + type: file + description: Output VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.log": + type: file + description: Log file + pattern: "*.log" - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - versions.yml: + type: file + description: File containing software version + pattern: "*.{version.txt}" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/plink/bcf/meta.yml b/modules/nf-core/plink/bcf/meta.yml index c86b66826764..d31239f2f9fc 100644 --- a/modules/nf-core/plink/bcf/meta.yml +++ b/modules/nf-core/plink/bcf/meta.yml @@ -8,43 +8,59 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bcf: - type: file - description: Binary variant call format file (bcf) - pattern: "*.{bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bcf: + type: file + description: Binary variant call format file (bcf) + pattern: "*.{bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/epistasis/meta.yml b/modules/nf-core/plink/epistasis/meta.yml index 47581bc64d2c..eda5dd0bc395 100644 --- a/modules/nf-core/plink/epistasis/meta.yml +++ b/modules/nf-core/plink/epistasis/meta.yml @@ -1,96 +1,118 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_epistasis" -description: Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. +description: Epistasis in PLINK, analyzing how the effects of one gene depend on the + presence of others. keywords: - interactions - variants - regression tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option. - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option. + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - epi: - type: file - description: PLINK epistasis file - pattern: "*.{epi.cc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc": + type: file + description: PLINK epistasis file + pattern: "*.{epi.cc}" - episummary: - type: file - description: PLINK epistasis summary file - pattern: "*.{epi.cc.summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc.summary": + type: file + description: PLINK epistasis summary file + pattern: "*.{epi.cc.summary}" - log: - type: file - description: PLINK epistasis log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: PLINK epistasis log file + pattern: "*.{log}" - nosex: - type: file - description: Ambiguous sex ID file - pattern: "*.{nosex}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: Ambiguous sex ID file + pattern: "*.{nosex}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/exclude/meta.yml b/modules/nf-core/plink/exclude/meta.yml index 5f861ce3b0b3..462d2f6b9b92 100644 --- a/modules/nf-core/plink/exclude/meta.yml +++ b/modules/nf-core/plink/exclude/meta.yml @@ -6,53 +6,69 @@ keywords: - variant identifiers tools: - plink: - description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + description: Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner. homepage: https://www.cog-genomics.org/plink licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - variants: - type: file - description: A text file containing variant identifiers to remove (one per line) - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - variants: + type: file + description: A text file containing variant identifiers to remove (one per line) + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/extract/meta.yml b/modules/nf-core/plink/extract/meta.yml index 859ea49e52c1..2007cf0e3ead 100644 --- a/modules/nf-core/plink/extract/meta.yml +++ b/modules/nf-core/plink/extract/meta.yml @@ -7,53 +7,69 @@ keywords: - bfiles tools: - plink: - description: Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. + description: Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner. homepage: https://www.cog-genomics.org/plink licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - variants: - type: file - description: A text file containing variant identifiers to keep (one per line) - pattern: "*.{keep}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - variants: + type: file + description: A text file containing variant identifiers to keep (one per line) + pattern: "*.{keep}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink/fastepistasis/meta.yml b/modules/nf-core/plink/fastepistasis/meta.yml index 0545c66dd619..2d61f21a02ac 100644 --- a/modules/nf-core/plink/fastepistasis/meta.yml +++ b/modules/nf-core/plink/fastepistasis/meta.yml @@ -1,96 +1,118 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_fastepistasis" -description: Fast Epistasis in PLINK, analyzing how the effects of one gene depend on the presence of others. +description: Fast Epistasis in PLINK, analyzing how the effects of one gene depend + on the presence of others. keywords: - interactions - variants - regression tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option. - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option. + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fepi: - type: file - description: PLINK fast-epistasis file - pattern: "*.{epi.cc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc": + type: file + description: PLINK fast-epistasis file + pattern: "*.{epi.cc}" - fepisummary: - type: file - description: PLINK fast-epistasis summary file - pattern: "*.{epi.cc.summary}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.epi.cc.summary": + type: file + description: PLINK fast-epistasis summary file + pattern: "*.{epi.cc.summary}" - flog: - type: file - description: PLINK fast-epistasis log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: PLINK fast-epistasis log file + pattern: "*.{log}" - fnosex: - type: file - description: Ambiguous sex ID file - pattern: "*.{nosex}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: Ambiguous sex ID file + pattern: "*.{nosex}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/gwas/meta.yml b/modules/nf-core/plink/gwas/meta.yml index 4bdb0ed0f0ca..67a62720b45c 100644 --- a/modules/nf-core/plink/gwas/meta.yml +++ b/modules/nf-core/plink/gwas/meta.yml @@ -6,85 +6,102 @@ keywords: - case/control tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to the PLINK native file input - - meta2: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF file input - - meta3: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta3 is associated to BCF file input - - meta4: - type: map - description: | - Groovy Map containing sample information, - e.g. [ id:'test', single_end:false ] - meta4 is associated to phenotype file input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - bcf: - type: file - description: PLINK variant information + sample ID + genotype call binary file - pattern: "*.{bcf}" - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" - - phe: - type: file - description: PLINK file containing phenotype information. This phenotype information can be read from the third column with the --pheno option or from a specific column with the --pheno-name option - pattern: "*.{phe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to the PLINK native file input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF file input + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" + - - meta3: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta3 is associated to BCF file input + - bcf: + type: file + description: PLINK variant information + sample ID + genotype call binary file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information, + e.g. [ id:'test', single_end:false ] + meta4 is associated to phenotype file input + - phe: + type: file + description: PLINK file containing phenotype information. This phenotype information + can be read from the third column with the --pheno option or from a specific + column with the --pheno-name option + pattern: "*.{phe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - assoc: - type: file - description: PLINK GWAS association file - pattern: "*.{assoc}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assoc": + type: file + description: PLINK GWAS association file + pattern: "*.{assoc}" - log: - type: file - description: PLINK GWAS association log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: PLINK GWAS association log file + pattern: "*.{log}" - nosex: - type: file - description: PLINK GWAS association file that retains phenotypes for samples with ambiguous sex. Produced with the option --allow-no-sex - pattern: "*.{nosex}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.nosex": + type: file + description: PLINK GWAS association file that retains phenotypes for samples + with ambiguous sex. Produced with the option --allow-no-sex + pattern: "*.{nosex}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LorenzoS96" maintainers: diff --git a/modules/nf-core/plink/hwe/meta.yml b/modules/nf-core/plink/hwe/meta.yml index 5624e24c8884..6d9cf2726d7a 100644 --- a/modules/nf-core/plink/hwe/meta.yml +++ b/modules/nf-core/plink/hwe/meta.yml @@ -6,65 +6,69 @@ keywords: - hwe equilibrium tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to PLINK native files input - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF files input - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to BCF files input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - vcf: - type: file - description: VCF format input file - pattern: "*.{vcf} | *{vcf.gz}" - - bcf: - type: file - description: BCF format input file - pattern: "*.{bcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to PLINK native files input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF files input + - vcf: + type: file + description: VCF format input file + pattern: "*.{vcf} | *{vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to BCF files input + - bcf: + type: file + description: BCF format input file + pattern: "*.{bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - hwe: - type: file - description: | - Summary file containing observed vs expected heterozygous frequencies and the - p-value of the hardy-weinberg statistics + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hwe": + type: file + description: | + Summary file containing observed vs expected heterozygous frequencies and the + p-value of the hardy-weinberg statistics + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/plink/indep/meta.yml b/modules/nf-core/plink/indep/meta.yml index 9d6b7500ec93..d0c6a02e49c6 100644 --- a/modules/nf-core/plink/indep/meta.yml +++ b/modules/nf-core/plink/indep/meta.yml @@ -1,5 +1,6 @@ name: plink_indep -description: Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. +description: Produce a pruned subset of markers that are in approximate linkage equilibrium + with each other. keywords: - plink - indep @@ -8,56 +9,70 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - window_size: - type: string - description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - - variant_count: - type: string - description: Variant count to shift the window at the end of each step. - - variance_inflation_factor: - type: string - description: Variance inflation factor (VIF) threshold. At each step, all variants in the current window with VIF exceeding the threshold are removed. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - window_size: + type: string + description: Window size in variant count or kilobase (if the 'kb' modifier + is present) units, a variant count to shift the window at the end of each + step, and a variance inflation factor (VIF) threshold. + - - variant_count: + type: string + description: Variant count to shift the window at the end of each step. + - - variance_inflation_factor: + type: string + description: Variance inflation factor (VIF) threshold. At each step, all variants + in the current window with VIF exceeding the threshold are removed. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - prunein: - type: file - description: File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other - pattern: "*.{prune.in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.in": + type: file + description: File with IDs of pruned subset of markers that are in approximate + linkage equilibrium with each other + pattern: "*.{prune.in}" - pruneout: - type: file - description: File with IDs of excluded variants - pattern: "*.{prune.out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.out": + type: file + description: File with IDs of excluded variants + pattern: "*.{prune.out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/indeppairwise/meta.yml b/modules/nf-core/plink/indeppairwise/meta.yml index 470ce24880ee..5ef9d3cd8ee9 100644 --- a/modules/nf-core/plink/indeppairwise/meta.yml +++ b/modules/nf-core/plink/indeppairwise/meta.yml @@ -1,5 +1,8 @@ name: plink_indeppairwise -description: Produce a pruned subset of markers that are in approximate linkage equilibrium with each other. Pairs of variants in the current window with squared correlation greater than the threshold are noted and variants are greedily pruned from the window until no such pairs remain. +description: Produce a pruned subset of markers that are in approximate linkage equilibrium + with each other. Pairs of variants in the current window with squared correlation + greater than the threshold are noted and variants are greedily pruned from the window + until no such pairs remain. keywords: - plink - indep pairwise @@ -8,56 +11,71 @@ keywords: - fam tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - window_size: - type: string - description: Window size in variant count or kilobase (if the 'kb' modifier is present) units, a variant count to shift the window at the end of each step, and a variance inflation factor (VIF) threshold. - - variant_count: - type: string - description: Variant count to shift the window at the end of each step. - - r2_threshold: - type: string - description: Pairwise r2 threshold. At each step, pairs of variants in the current window with squared correlation greater than the threshold are noted, and variants are greedily pruned from the window until no such pairs remain + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - window_size: + type: string + description: Window size in variant count or kilobase (if the 'kb' modifier + is present) units, a variant count to shift the window at the end of each + step, and a variance inflation factor (VIF) threshold. + - - variant_count: + type: string + description: Variant count to shift the window at the end of each step. + - - r2_threshold: + type: string + description: Pairwise r2 threshold. At each step, pairs of variants in the current + window with squared correlation greater than the threshold are noted, and + variants are greedily pruned from the window until no such pairs remain output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - prunein: - type: file - description: File with IDs of pruned subset of markers that are in approximate linkage equilibrium with each other - pattern: "*.{prune.in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.in": + type: file + description: File with IDs of pruned subset of markers that are in approximate + linkage equilibrium with each other + pattern: "*.{prune.in}" - pruneout: - type: file - description: File with IDs of excluded variants - pattern: "*.{prune.out}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.prune.out": + type: file + description: File with IDs of excluded variants + pattern: "*.{prune.out}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/ld/meta.yml b/modules/nf-core/plink/ld/meta.yml index 3e16ab4b6bc6..804feed8494e 100644 --- a/modules/nf-core/plink/ld/meta.yml +++ b/modules/nf-core/plink/ld/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "plink_ld" description: LD analysis in PLINK examines genetic variant associations within populations @@ -8,86 +7,100 @@ keywords: - variants tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to PLINK native files input - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta2 is associated to VCF files input - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to BCF files input - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - meta is associated to randomly selected snp files input - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" - - vcf: - type: file - description: VCF format input file - pattern: "*.{vcf} | *{vcf.gz}" - - bcf: - type: file - description: BCF format input file - pattern: "*.{bcf}" - - snpfile: - type: file - description: randomly selected snp identifiers, used to calculate linkage disequilibrium - pattern: "*.{txt}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to PLINK native files input + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta2 is associated to VCF files input + - vcf: + type: file + description: VCF format input file + pattern: "*.{vcf} | *{vcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to BCF files input + - bcf: + type: file + description: BCF format input file + pattern: "*.{bcf}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + meta is associated to randomly selected snp files input + - snpfile: + type: file + description: randomly selected snp identifiers, used to calculate linkage disequilibrium + pattern: "*.{txt}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ld: - type: file - description: | - The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R². + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.ld": + type: file + description: | + The output of a linkage disequilibrium analysis in PLINK typically includes a table showing variant pairs and their associated LD values, often expressed as R². - log: - type: file - description: | - Log file of the ld process + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: | + Log file of the ld process - nosex: - type: file - description: | - Ambiguous sex ID file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.nosex": + type: file + description: | + Ambiguous sex ID file + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@davidebag" maintainers: diff --git a/modules/nf-core/plink/recode/meta.yml b/modules/nf-core/plink/recode/meta.yml index 7f2bd053f52b..4316bd193d4a 100644 --- a/modules/nf-core/plink/recode/meta.yml +++ b/modules/nf-core/plink/recode/meta.yml @@ -7,135 +7,282 @@ keywords: - whole genome association tools: - "plink": - description: "Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner." + description: "Whole genome association analysis toolset, designed to perform a + range of basic, large-scale analyses in a computationally efficient manner." homepage: "https://www.cog-genomics.org/plink" documentation: "https://www.cog-genomics.org/plink/1.9/data#recode" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: PLINK binary biallelic genotype table file - pattern: "*.{bed}" - - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" - - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: PLINK binary biallelic genotype table file + pattern: "*.{bed}" + - bim: + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" + - fam: + type: file + description: PLINK sample information file + pattern: "*.{fam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - ped: - type: file - description: PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced by the default "--recode" or by "--recode 12". - pattern: "*.{ped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ped": + type: file + description: PLINK/MERLIN/Haploview text pedigree + genotype table file. Produced + by the default "--recode" or by "--recode 12". + pattern: "*.{ped}" - map: - type: file - description: PLINK text fileset variant information file. Produced by the default "--recode" or by "--recode 12". - pattern: "*.{map}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.map": + type: file + description: PLINK text fileset variant information file. Produced by the default + "--recode" or by "--recode 12". + pattern: "*.{map}" - txt: - type: file - description: Text file. Produced by "--recode 23". Can only be used in a file with only one sample. - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Text file. Produced by "--recode 23". Can only be used in a file + with only one sample. + pattern: "*.{txt}" - raw: - type: file - description: Additive + dominant component file. Produced by "--recode AD" or "--recode A". - pattern: "*.{raw}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.raw": + type: file + description: Additive + dominant component file. Produced by "--recode AD" or + "--recode A". + pattern: "*.{raw}" - traw: - type: file - description: Variant-major additive component file. Produced by "--recode A-transpose". - pattern: "*.{traw}" - - beagle-dat: - type: file - description: Single BEAGLE unphased genotype file. Produced by "--recode beagle" in 'beagle-nomap' mode. - pattern: "*.{beagle.dat}" - - chr-dat: - type: file - description: BEAGLE unphased genotype and variant information files. Produced by "--recode beagle". - pattern: "*.{*.chr-*.dat}" - - chr-map: - type: file - description: BEAGLE variant information files. Produced by "--recode beagle". - pattern: "*.{*chr-*.map}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.traw": + type: file + description: Variant-major additive component file. Produced by "--recode A-transpose". + pattern: "*.{traw}" + - beagledat: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.beagle.dat": + type: file + description: BEAGLE file + pattern: "*.{beagle.dat}" + - chrdat: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.chr-*.dat": + type: file + description: chr file + pattern: "*.{chr-*.dat}" + - chrmap: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - .*chr-*.map: + type: file + description: chr map file + pattern: "*.{chr-*.map}" - geno: - type: file - description: BIMBAM genotype file. Produced by "--recode bimbam". - pattern: "*.{recode.geno.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.geno.txt": + type: file + description: BIMBAM genotype file. Produced by "--recode bimbam". + pattern: "*.{recode.geno.txt}" - pheno: - type: file - description: BIMBAM phenotype file. Produced by "--recode bimbam". - pattern: "*.{recode.pheno.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.pheno.txt": + type: file + description: BIMBAM phenotype file. Produced by "--recode bimbam". + pattern: "*.{recode.pheno.txt}" - pos: - type: file - description: BIMBAM variant position file. Produced by "--recode bimbam". - pattern: "*.{recode.pos.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.pos.txt": + type: file + description: BIMBAM variant position file. Produced by "--recode bimbam". + pattern: "*.{recode.pos.txt}" - phase: - type: file - description: fastPHASE format. Produced by "--recode fastphase". - pattern: "*.{recode.phase.inp}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.recode.phase.inp": + type: file + description: fastPHASE format. Produced by "--recode fastphase". + pattern: "*.{recode.phase.inp}" - info: - type: file - description: Haploview map file. Produced by "--recode HV". - pattern: "*.{info}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.info": + type: file + description: Haploview map file. Produced by "--recode HV". + pattern: "*.{info}" - lgen: - type: file - description: PLINK long-format genotype file. Produced by "--recode lgen". - pattern: "*.{lgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lgen": + type: file + description: PLINK long-format genotype file. Produced by "--recode lgen". + pattern: "*.{lgen}" - list: - type: file - description: Genotype list file. Produced by "--recode list". - pattern: "*.{list}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list": + type: file + description: Genotype list file. Produced by "--recode list". + pattern: "*.{list}" - gen: - type: file - description: Oxford genotype file format. Produced by "--recode oxford". - pattern: "*.{gen}" - - genz: - type: file - description: Compressed Oxford genotype file format. Produced by "--recode oxford gen-gz". - pattern: "*.{genz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gen": + type: file + description: Oxford genotype file format. Produced by "--recode oxford". + pattern: "*.{gen}" + - gengz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gen.gz": + type: file + description: Compressed Oxford genotype file format + pattern: "*.{gen.gz}" - sample: - type: file - description: Oxford sample information file. Produced by "--recode oxford". - pattern: "*.{sample}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sample": + type: file + description: Oxford sample information file. Produced by "--recode oxford". + pattern: "*.{sample}" - rlist: - type: file - description: Rare genotype list file. Produced by "--recode rlist". - pattern: "*.{rlist}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.rlist": + type: file + description: Rare genotype list file. Produced by "--recode rlist". + pattern: "*.{rlist}" - strctin: - type: file - description: Structure-format file. Produced by "--recode structure". - pattern: "*.{strct_in}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.strct_in": + type: file + description: Structure-format file. Produced by "--recode structure". + pattern: "*.{strct_in}" - tped: - type: file - description: Transposed text PED file. Produced by "--recode transpose". - pattern: "*.{tped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tped": + type: file + description: Transposed text PED file. Produced by "--recode transpose". + pattern: "*.{tped}" - tfam: - type: file - description: Transposed text FAM file. Produced by "--recode transpose". - pattern: "*.{tfam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tfam": + type: file + description: Transposed text FAM file. Produced by "--recode transpose". + pattern: "*.{tfam}" - vcf: - type: file - description: Variant calling file (VCF). Produced by "--recode vcf". - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant calling file (VCF). Produced by "--recode vcf". + pattern: "*.{vcf}" - vcfgz: - type: file - description: Compressed variant calling file (VCF). Produced by "--recode vcf bgz". - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed variant calling file (VCF). Produced by "--recode vcf + bgz". + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/plink/vcf/meta.yml b/modules/nf-core/plink/vcf/meta.yml index 2a3ee4b11be4..d6eefd9a4cb8 100644 --- a/modules/nf-core/plink/vcf/meta.yml +++ b/modules/nf-core/plink/vcf/meta.yml @@ -13,38 +13,53 @@ tools: homepage: "https://www.cog-genomics.org/plink" tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" licence: ["GPL"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: PLINK binary biallelic genotype table - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: PLINK binary biallelic genotype table + pattern: "*.{bed}" - bim: - type: file - description: PLINK extended MAP file - pattern: "*.{bim}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bim": + type: file + description: PLINK extended MAP file + pattern: "*.{bim}" - fam: - type: file - description: PLINK sample information file - pattern: "*.{fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fam": + type: file + description: PLINK sample information file + pattern: "*.{fam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Mxrcon" - "@abhi18av" diff --git a/modules/nf-core/plink2/extract/meta.yml b/modules/nf-core/plink2/extract/meta.yml index aeda84cda9f8..0d758817c825 100644 --- a/modules/nf-core/plink2/extract/meta.yml +++ b/modules/nf-core/plink2/extract/meta.yml @@ -13,50 +13,65 @@ tools: documentation: http://www.cog-genomics.org/plink/2.0/general_usage doi: "10.1186/s13742-015-0047-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" - - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" - - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar}" - - variants: - type: file - description: A text file containing variant identifiers to keep (one per line) - pattern: "*.{keep}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pgen: + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" + - psam: + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" + - pvar: + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar}" + - variants: + type: file + description: A text file containing variant identifiers to keep (one per line) + pattern: "*.{keep}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - extract_pgen: - type: file - description: PLINK 2 binary genotype table, containing extracted variants - pattern: "*.{pgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pgen": + type: file + description: PLINK 2 binary genotype table, containing extracted variants + pattern: "*.{pgen}" - extract_psam: - type: file - description: PLINK 2 sample information file associated with the extracted data - pattern: "*.{psam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psam": + type: file + description: PLINK 2 sample information file associated with the extracted data + pattern: "*.{psam}" - extract_pvar: - type: file - description: PLINK 2 variant information file, containing extracted variants - pattern: "*.{pvar.zst}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar.zst": + type: file + description: PLINK 2 variant information file, containing extracted variants + pattern: "*.{pvar.zst}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink2/score/meta.yml b/modules/nf-core/plink2/score/meta.yml index 9fc7f436161e..ea20bb355ee1 100644 --- a/modules/nf-core/plink2/score/meta.yml +++ b/modules/nf-core/plink2/score/meta.yml @@ -13,42 +13,45 @@ tools: documentation: http://www.cog-genomics.org/plink/2.0/general_usage doi: "10.1186/s13742-015-0047-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" - - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" - - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar}" - - scorefile: - type: file - description: A text file containing variant identifiers and weights - pattern: "*.{scores,txt,scorefile}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pgen: + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" + - psam: + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" + - pvar: + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar}" + - - scorefile: + type: file + description: A text file containing variant identifiers and weights + pattern: "*.{scores,txt,scorefile}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - score: - type: file - description: A text file containing sample scores, in plink 2 .sscore format - pattern: "*.{sscore}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sscore": + type: file + description: A text file containing sample scores, in plink 2 .sscore format + pattern: "*.{sscore}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/plink2/vcf/meta.yml b/modules/nf-core/plink2/vcf/meta.yml index 7ea8a8976a2a..c745532c7473 100644 --- a/modules/nf-core/plink2/vcf/meta.yml +++ b/modules/nf-core/plink2/vcf/meta.yml @@ -12,42 +12,63 @@ tools: homepage: http://www.cog-genomics.org/plink/2.0/ documentation: http://www.cog-genomics.org/plink/2.0/general_usage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Variant calling file (vcf) - pattern: "*.{vcf}, *.{vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Variant calling file (vcf) + pattern: "*.{vcf}, *.{vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pgen: - type: file - description: PLINK 2 binary genotype table - pattern: "*.{pgen}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pgen": + type: file + description: PLINK 2 binary genotype table + pattern: "*.{pgen}" - psam: - type: file - description: PLINK 2 sample information file - pattern: "*.{psam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.psam": + type: file + description: PLINK 2 sample information file + pattern: "*.{psam}" - pvar: - type: file - description: PLINK 2 variant information file - pattern: "*.{pvar.zst}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar": + type: file + description: PLINK 2 variant information file + pattern: "*.{pvar.zst}" - pvar_zst: - type: file - description: PLINK 2 variant information zst file - pattern: "*.pvar.zst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pvar.zst": + type: file + description: PLINK 2 variant information zst file + pattern: "*.pvar.zst" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/pmdtools/filter/meta.yml b/modules/nf-core/pmdtools/filter/meta.yml index 6161b1ffbe60..0a55262789ca 100644 --- a/modules/nf-core/pmdtools/filter/meta.yml +++ b/modules/nf-core/pmdtools/filter/meta.yml @@ -13,41 +13,44 @@ tools: tool_dev_url: https://github.com/pontussk/PMDtools doi: "10.1073/pnas.1318934111" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - threshold: - type: float - description: Post-mortem damage score threshold - - reference: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - threshold: + type: float + description: Post-mortem damage score threshold + - - reference: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Filtered BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alexandregilardet" maintainers: diff --git a/modules/nf-core/pneumocat/meta.yml b/modules/nf-core/pneumocat/meta.yml index 8015826add92..e7f885171dd6 100644 --- a/modules/nf-core/pneumocat/meta.yml +++ b/modules/nf-core/pneumocat/meta.yml @@ -1,47 +1,57 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "pneumocat" -description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads +description: Determine Streptococcus pneumoniae serotype from Illumina paired-end + reads keywords: - fastq - serotype - Streptococcus pneumoniae tools: - "pneumocat": - description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)" + description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach + to assign capsular type to S.pneumoniae genomic data (Illumina)" homepage: "https://github.com/ukhsa-collaboration/PneumoCaT" documentation: "https://github.com/ukhsa-collaboration/PneumoCaT" tool_dev_url: "https://github.com/ukhsa-collaboration/PneumoCaT" doi: "10.7717/peerj.2477" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input Illunina paired-end FASTQ files - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input Illunina paired-end FASTQ files + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xml: - type: file - description: The predicted serotype in XML format - pattern: "*.xml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.xml": + type: file + description: The predicted serotype in XML format + pattern: "*.xml" - txt: - type: file - description: A detailed description of the predicted serotype - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: A detailed description of the predicted serotype + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/poolsnp/meta.yml b/modules/nf-core/poolsnp/meta.yml index 8de67751c65b..36054b58aca6 100644 --- a/modules/nf-core/poolsnp/meta.yml +++ b/modules/nf-core/poolsnp/meta.yml @@ -1,97 +1,110 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "poolsnp" -description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs. +description: PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference + genome in FASTA format as inputs. keywords: - poolseq - mpileup - variant-calling tools: - "poolsnp": - description: "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and a reference genome in FASTA format as inputs." + description: "PoolSNP is a heuristic SNP caller, which uses an MPILEUP file and + a reference genome in FASTA format as inputs." homepage: "https://github.com/capoony/PoolSNP" documentation: "https://github.com/capoony/PoolSNP/blob/master/README.md" licence: ["Apache-2.0"] args_id: "$args" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. `[ id:'sample1', single_end:false ]` - - - mpileup: - type: file - description: | - MPILEUP file. This file contains the base calls and alignment information - for each position in the reference genome. - It is used as input for variant calling and other downstream analyses. - pattern: "*.mpileup" - - - meta2: - type: map - description: | - Groovy Map containing sample information. - e.g. `[ id:'sample1' ]` - - - reference: - type: file - description: | - Reference genome in FASTA format. - May NOT contain any special characters such as "/|,:" - pattern: "*.{fasta,fa}" - - - max_cov: - type: float - description: | - Maximum coverage is calculated for every library and chromosomal arm - as the percentile of a coverage distribution, - e.g. max-cov=0.98 will only consider positions within the 98% coverage percentile - for a given sample and chromosomal arm. - Note: Provide `max_cov` or `max_cov_file` but not both. - Read more: https://github.com/capoony/PoolSNP - - - max_cov_file: - type: file - description: | - File containing the maximum coverage thresholds for all chromosomal arms and libraries. - This file needs to be tab-delimited with two columns: - 1. Chromosomal name - 2. Comma-separated list of coverage thresholds for each sample in the mpileup file. - e.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples - and 200 for the last two samples on chromosomal arm 2L. - Note: Provide `max_cov` or `max_cov_file` but not both. - Read more: https://github.com/capoony/PoolSNP - + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1', single_end:false ]` + - mpileup: + type: file + description: | + MPILEUP file. This file contains the base calls and alignment information + for each position in the reference genome. + It is used as input for variant calling and other downstream analyses. + pattern: "*.mpileup" + - - meta2: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1' ]` + - reference: + type: file + description: | + Reference genome in FASTA format. + May NOT contain any special characters such as "/|,:" + pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. `[ id:'sample1', single_end:false ]` + - max_cov: + type: float + description: | + Maximum coverage is calculated for every library and chromosomal arm + as the percentile of a coverage distribution, + e.g. max-cov=0.98 will only consider positions within the 98% coverage percentile + for a given sample and chromosomal arm. + Note: Provide `max_cov` or `max_cov_file` but not both. + Read more: https://github.com/capoony/PoolSNP + - max_cov_file: + type: file + description: | + File containing the maximum coverage thresholds for all chromosomal arms and libraries. + This file needs to be tab-delimited with two columns: + 1. Chromosomal name + 2. Comma-separated list of coverage thresholds for each sample in the mpileup file. + e.g. `2L 100,100,100,200,200` would mean a threshold of 100 for the first three samples + and 200 for the last two samples on chromosomal arm 2L. + Note: Provide `max_cov` or `max_cov_file` but not both. + Read more: https://github.com/capoony/PoolSNP output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: Gzipped VCF file containing allele counts and frequencies for every position and library - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Gzipped VCF file containing allele counts and frequencies for every + position and library + pattern: "*.vcf.gz" - max_cov: - type: file - description: File containing the maximum coverage thresholds for all chromosomal arms and libraries - pattern: "*cov-*.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*cov-*.txt": + type: file + description: File containing the maximum coverage thresholds for all chromosomal + arms and libraries + pattern: "*cov-*.txt" - bad_sites: - type: file - description: File containing a list of sites (variable and invariable) that did not pass the SNP calling criteria - pattern: "*BS.txt.gz" - optional: true - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*BS.txt.gz": + type: file + description: File containing a list of sites (variable and invariable) that + did not pass the SNP calling criteria + pattern: "*BS.txt.gz" + optional: true - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhilesh" maintainers: diff --git a/modules/nf-core/popscle/demuxlet/meta.yml b/modules/nf-core/popscle/demuxlet/meta.yml index 56224512d5ff..3ffb07b9f6ef 100644 --- a/modules/nf-core/popscle/demuxlet/meta.yml +++ b/modules/nf-core/popscle/demuxlet/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_demuxlet" -description: Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is available. +description: Software to deconvolute sample identity and identify multiplets when + multiple samples are pooled by barcoded single cell sequencing and external genotyping + data for each sample is available. keywords: - popscle - demultiplexing @@ -9,51 +10,53 @@ keywords: - single cell tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - plp_prefix: - type: string - description: Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. - - - bam: - type: file - description: Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must be sorted by coordinates and indexed. - pattern: "*.{bam,cram,sam}" - - - donor_genotype: - type: file - description: Input VCF/BCF file, containing the individual genotypes (GT), posterior probability (GP), or genotype likelihood (PL) to assign each barcode to a specific sample (or a pair of samples) in the VCF file. - pattern: "*.{vcf,bcf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - plp_prefix: + type: string + description: Prefix of pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. + - bam: + type: file + description: Input SAM/BAM/CRAM file without running popscle/dsc_pileup, must + be sorted by coordinates and indexed. + pattern: "*.{bam,cram,sam}" + - donor_genotype: + type: file + description: Input VCF/BCF file, containing the individual genotypes (GT), posterior + probability (GP), or genotype likelihood (PL) to assign each barcode to a + specific sample (or a pair of samples) in the VCF file. + pattern: "*.{vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - demuxlet_result: - type: file - description: Result of demuxlet containing the best guess of the sample identity, with detailed statistics to reach to the best guess. - pattern: "*.best" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.best": + type: file + description: Result of demuxlet containing the best guess of the sample identity, + with detailed statistics to reach to the best guess. + pattern: "*.best" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/popscle/dscpileup/meta.yml b/modules/nf-core/popscle/dscpileup/meta.yml index 234a18307595..70442d830f07 100644 --- a/modules/nf-core/popscle/dscpileup/meta.yml +++ b/modules/nf-core/popscle/dscpileup/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_dscpileup" -description: Software to pileup reads and corresponding base quality for each overlapping SNPs and each barcode. +description: Software to pileup reads and corresponding base quality for each overlapping + SNPs and each barcode. keywords: - popscle - demultiplexing @@ -10,62 +10,81 @@ keywords: - pile up tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - bam: - type: file - description: Input SAM/BAM/CRAM file produced by the standard 10x sequencing platform, or any other barcoded single cell RNA-seq. - pattern: "*.{bam,cram,sam}" - - - vcf: - type: file - description: Input VCF/BCF file files containing (AC) and (AN) from referenced population (e.g. 1000g). - pattern: "*.{vcf,bcf}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - bam: + type: file + description: Input SAM/BAM/CRAM file produced by the standard 10x sequencing + platform, or any other barcoded single cell RNA-seq. + pattern: "*.{bam,cram,sam}" + - vcf: + type: file + description: Input VCF/BCF file files containing (AC) and (AN) from referenced + population (e.g. 1000g). + pattern: "*.{vcf,bcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - cel: - type: file - description: Contains the relation between numerated barcode ID and barcode and the number of SNP and number of UMI for each barcoded droplet. - pattern: "*.cel.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.cel.gz": + type: file + description: Contains the relation between numerated barcode ID and barcode + and the number of SNP and number of UMI for each barcoded droplet. + pattern: "*.cel.gz" - plp: - type: file - description: Contains the overlapping SNP and the corresponding read and base quality for each barcode ID. - pattern: "*.plp.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.plp.gz": + type: file + description: Contains the overlapping SNP and the corresponding read and base + quality for each barcode ID. + pattern: "*.plp.gz" - var: - type: file - description: Contains the position, reference allele and allele frequency for each SNP. - pattern: "*.var.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.var.gz": + type: file + description: Contains the position, reference allele and allele frequency for + each SNP. + pattern: "*.var.gz" - umi: - type: file - description: Contains the position covered by each umi. - pattern: "*.umi.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - "*.umi.gz": + type: file + description: Contains the position covered by each umi. + pattern: "*.umi.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/popscle/freemuxlet/meta.yml b/modules/nf-core/popscle/freemuxlet/meta.yml index 34eaaa59dc97..dffcd3431dc9 100644 --- a/modules/nf-core/popscle/freemuxlet/meta.yml +++ b/modules/nf-core/popscle/freemuxlet/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "popscle_freemuxlet" -description: Software to deconvolute sample identity and identify multiplets when multiple samples are pooled by barcoded single cell sequencing and external genotyping data for each sample is not available. +description: Software to deconvolute sample identity and identify multiplets when + multiple samples are pooled by barcoded single cell sequencing and external genotyping + data for each sample is not available. keywords: - popscle - demultiplexing @@ -9,64 +10,88 @@ keywords: - single cell tools: - "popscle": - description: "A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools" + description: "A suite of population scale analysis tools for single-cell genomics + data including implementation of Demuxlet / Freemuxlet methods and auxilary + tools" homepage: "https://github.com/statgen/popscle" documentation: "https://github.com/statgen/popscle" tool_dev_url: "https://github.com/statgen/popscle" doi: "10.1038/nbt.4042" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - plp: - type: directory - description: Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. - - n_sample: - type: integer - description: Number of samples multiplexed together. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - plp: + type: directory + description: Directory contains pileup files (CEL,VAR and PLP) produced by popscle/dsc_pileup. + - n_sample: + type: integer + description: Number of samples multiplexed together. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - result: - type: file - description: Output file contains the best guess of the sample identity, with detailed statistics to reach to the best guess. - pattern: "*.clust1.samples.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust1.samples.gz": + type: file + description: Output file contains the best guess of the sample identity, with + detailed statistics to reach to the best guess. + pattern: "*.clust1.samples.gz" - vcf: - type: file - description: Output vcf file for each sample inferred and clustered from freemuxlet. - pattern: "*.clust1.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust1.vcf.gz": + type: file + description: Output vcf file for each sample inferred and clustered from freemuxlet. + pattern: "*.clust1.vcf.gz" - lmix: - type: file - description: Output file contains basic statistics for each barcode. - pattern: "*.lmix" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.lmix": + type: file + description: Output file contains basic statistics for each barcode. + pattern: "*.lmix" - singlet_result: - type: file - description: Optional output file contains the best sample identity assuming all droplets are singlets when writing auxiliary output files is turned on. - pattern: "*.clust0.samples.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust0.samples.gz": + type: file + description: Optional output file contains the best sample identity assuming + all droplets are singlets when writing auxiliary output files is turned on. + pattern: "*.clust0.samples.gz" - singlet_vcf: - type: file - description: Optional output vcf file for each sample inferred and clustered from freemuxlet assuming all droplets are singlets when writing auxiliary output files is turned on. - pattern: "*.clust0.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.clust0.vcf.gz": + type: file + description: Optional output vcf file for each sample inferred and clustered + from freemuxlet assuming all droplets are singlets when writing auxiliary + output files is turned on. + pattern: "*.clust0.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@wxicu" maintainers: diff --git a/modules/nf-core/porechop/abi/meta.yml b/modules/nf-core/porechop/abi/meta.yml index a856ffbe65c9..6016da7560f5 100644 --- a/modules/nf-core/porechop/abi/meta.yml +++ b/modules/nf-core/porechop/abi/meta.yml @@ -1,45 +1,56 @@ name: "porechop_abi" -description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads. +description: Extension of Porechop whose purpose is to process adapter sequences in + ONT reads. keywords: - porechop_abi - adapter - nanopore tools: - "porechop_abi": - description: Extension of Porechop whose purpose is to process adapter sequences in ONT reads. + description: Extension of Porechop whose purpose is to process adapter sequences + in ONT reads. homepage: "https://github.com/bonsai-team/Porechop_ABI" documentation: "https://github.com/bonsai-team/Porechop_ABI" tool_dev_url: "https://github.com/bonsai-team/Porechop_ABI" doi: "10.1101/2022.07.07.499093" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq/fastq.gz file - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq/fastq.gz file + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Adapter-trimmed fastq.gz file - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Adapter-trimmed fastq.gz file + pattern: "*.fastq.gz" - log: - type: file - description: Log file containing stdout information - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "LilyAnderssonLee" diff --git a/modules/nf-core/porechop/porechop/meta.yml b/modules/nf-core/porechop/porechop/meta.yml index 13be76f26bbc..9e61c05421bd 100644 --- a/modules/nf-core/porechop/porechop/meta.yml +++ b/modules/nf-core/porechop/porechop/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/rrwick/Porechop" doi: "10.1099/mgen.0.000132" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: fastq/fastq.gz file - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: fastq/fastq.gz file + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Demultiplexed and/or adapter-trimmed fastq.gz file - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Demultiplexed and/or adapter-trimmed fastq.gz file + pattern: "*.{fastq.gz}" - log: - type: file - description: Log file containing stdout information - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stdout information + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ggabernet" - "@jasmezz" diff --git a/modules/nf-core/preseq/ccurve/meta.yml b/modules/nf-core/preseq/ccurve/meta.yml index f804b0669b93..39fb249128f8 100644 --- a/modules/nf-core/preseq/ccurve/meta.yml +++ b/modules/nf-core/preseq/ccurve/meta.yml @@ -1,44 +1,55 @@ name: preseq_ccurve -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - ccurve: - type: file - description: File containing output of Preseq c curve - pattern: "*.{c_curve.txt}" + - c_curve: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.c_curve.txt": + type: file + description: Preseq c_curve output file + pattern: "*.{c_curve.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/preseq/lcextrap/meta.yml b/modules/nf-core/preseq/lcextrap/meta.yml index c00fa8eef311..28fb449ca923 100644 --- a/modules/nf-core/preseq/lcextrap/meta.yml +++ b/modules/nf-core/preseq/lcextrap/meta.yml @@ -1,44 +1,55 @@ name: preseq_lcextrap -description: Software for predicting library complexity and genome coverage in high-throughput sequencing +description: Software for predicting library complexity and genome coverage in high-throughput + sequencing keywords: - preseq - library - complexity tools: - preseq: - description: Software for predicting library complexity and genome coverage in high-throughput sequencing + description: Software for predicting library complexity and genome coverage in + high-throughput sequencing homepage: http://smithlabresearch.org/software/preseq/ documentation: http://smithlabresearch.org/wp-content/uploads/manual.pdf tool_dev_url: https://github.com/smithlabcode/preseq licence: ["GPL"] + identifier: biotools:preseq input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - lc_extrap: - type: file - description: File containing output of Preseq lcextrap - pattern: "*.{lc_extrap.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lc_extrap.txt": + type: file + description: File containing output of Preseq lcextrap + pattern: "*.{lc_extrap.txt}" - log: - type: file - description: Log file containing stderr produced by Preseq - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file containing stderr produced by Preseq + pattern: "*.{log}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@edmundmiller" diff --git a/modules/nf-core/president/meta.yml b/modules/nf-core/president/meta.yml index 7d6d3c9bcb91..0162ab531230 100644 --- a/modules/nf-core/president/meta.yml +++ b/modules/nf-core/president/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "president" description: "Calculate pairwise nucleotide identity with respect to a reference sequence" @@ -9,53 +8,92 @@ keywords: - nucleotides tools: - "president": - description: "Calculate pairwise nucleotide identity with respect to a reference sequence" + description: "Calculate pairwise nucleotide identity with respect to a reference + sequence" homepage: "https://github.com/rki-mf1/president" documentation: "https://github.com/rki-mf1/president" tool_dev_url: "https://github.com/rki-mf1/president" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: Groovy Map containing information, e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: One fasta file or a list of multiple fasta files to perform president on. Has to be uncompressed! - pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - - meta2: - type: map - description: Groovy Map containing information about the reference genome - - reference: - type: file - description: Fasta of a reference genome. Has to be uncompressed! - pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" - - compress: - type: boolean - description: Set to "true" if fasta output should be compressed - + - - meta: + type: map + description: Groovy Map containing information, e.g. [ id:'test', single_end:false + ] + - fasta: + type: file + description: One fasta file or a list of multiple fasta files to perform president + on. Has to be uncompressed! + pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + - - meta2: + type: map + description: Groovy Map containing information about the reference genome + - reference: + type: file + description: Fasta of a reference genome. Has to be uncompressed! + pattern: "*.{fasta,fas,fa,fna,ffn,faa,mpfa,frn}" + - - compress: + type: boolean + description: Set to "true" if fasta output should be compressed output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - valid_fasta: - type: file - description: Fasta file containing sequences which passed the qc ("valid.fasta"). If true is set on the "compress" input value, the file is gz-compressed. - pattern: "*.{fasta.gz, fasta}" + - meta: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" + - ${prefix}_valid.fasta*: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" + - id_fasta: + type: file + description: Fasta file containing sequences which passed the qc ("valid.fasta"). + If true is set on the "compress" input value, the file is gz-compressed. + pattern: "*.{fasta.gz, fasta}" - invalid_fasta: - type: file - description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). If true is set on the "compress" input value, the files are gz-compressed. - pattern: "*_invalid.{fasta.gz, fasta}" + - meta: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" + - ${prefix}_invalid.fasta*: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" + - id_fasta: + type: file + description: Fasta file containing sequences which didn't pass the qc ("invalid.fasta"). + If true is set on the "compress" input value, the files are gz-compressed. + pattern: "*_invalid.{fasta.gz, fasta}" - report: - type: file - description: Report with some information for every sample, like statistic values. See docs for details - pattern: "*.tsv" + - meta: + type: file + description: Report with some information for every sample, like statistic values. + See docs for details + pattern: "*.tsv" + - "*.tsv": + type: file + description: Report with some information for every sample, like statistic values. + See docs for details + pattern: "*.tsv" - log: - type: file - description: Log file of president - pattern: "*.log" - + - meta: + type: file + description: Log file of president + pattern: "*.log" + - "*.log": + type: file + description: Log file of president + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@paulwolk" maintainers: diff --git a/modules/nf-core/presto/filterseq/meta.yml b/modules/nf-core/presto/filterseq/meta.yml index 6b0b6c85e5ca..32e13e03aa10 100644 --- a/modules/nf-core/presto/filterseq/meta.yml +++ b/modules/nf-core/presto/filterseq/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "presto_filterseq" description: Filter reads by quality score. @@ -9,46 +8,50 @@ keywords: - immunoinformatics tools: - "presto": - description: "A bioinformatics toolkit for processing high-throughput lymphocyte receptor sequencing data." + description: "A bioinformatics toolkit for processing high-throughput lymphocyte + receptor sequencing data." homepage: "https://immcantation.readthedocs.io" documentation: "https://presto.readthedocs.io" tool_dev_url: "https://bitbucket.org/kleinstein/presto" doi: "10.1093/bioinformatics/btu138" licence: ["AGPL v3"] + identifier: biotools:presto-measure input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq file - pattern: "*.{fastq}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: fastq file + pattern: "*.{fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: filtered fastq file - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*_quality-pass.fastq": + type: file + description: filtered fastq file + pattern: "*.{fastq}" - logs: - type: file - description: command logs - pattern: "*.txt" + - "*_command_log.txt": + type: file + description: command logs + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - log_tab: - type: file - description: parsed log table - pattern: "*.tab" - + - "*.tab": + type: file + description: parsed log table + pattern: "*.tab" authors: - "@ggabernet" diff --git a/modules/nf-core/pretextmap/meta.yml b/modules/nf-core/pretextmap/meta.yml index 97158cda0d5c..d79295cd723b 100644 --- a/modules/nf-core/pretextmap/meta.yml +++ b/modules/nf-core/pretextmap/meta.yml @@ -6,47 +6,51 @@ keywords: - map tools: - "pretextmap": - description: "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into genome contact maps." + description: "Paired REad TEXTure Mapper. Converts SAM formatted read pairs into + genome contact maps." homepage: "https://github.com/wtsi-hpag/PretextMap" documentation: "https://github.com/wtsi-hpag/PretextMap/blob/master/README.md" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file or pairs formatted reads file - pattern: "*.{bam,cram,sam,pairs.gz}" - - input: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test2', single_end:false ] - - input: - type: file - description: FASTA file - pattern: "*.{fasta,fa,fna}" - - input: - type: file - description: Fasta index - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file or pairs formatted reads file + pattern: "*.{bam,cram,sam,pairs.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference sequence file + pattern: "*.{fasta,fna,fa}" + - fai: + type: file + description: Reference sequence index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pretext: - type: file - description: pretext map - pattern: "*.pretext" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pretext": + type: file + description: pretext map + pattern: "*.pretext" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" - "@getrudeln" diff --git a/modules/nf-core/pretextsnapshot/meta.yml b/modules/nf-core/pretextsnapshot/meta.yml index 59e3862be244..434da68e4208 100644 --- a/modules/nf-core/pretextsnapshot/meta.yml +++ b/modules/nf-core/pretextsnapshot/meta.yml @@ -14,30 +14,33 @@ tools: homepage: "https://github.com/wtsi-hpag/PretextSnapshot" tool_dev_url: "https://github.com/wtsi-hpag/PretextSnapshot" licence: ["https://github.com/wtsi-hpag/PretextSnapshot/blob/master/LICENSE"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - pretext_map: - type: file - description: pretext hic map - pattern: "*.pretext" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pretext_map: + type: file + description: pretext hic map + pattern: "*.pretext" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - image: - type: file - description: image of a hic contact map - pattern: "*.{png,jpg,bmp}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{jpeg,png,bmp}": + type: file + description: image of a hic contact map + pattern: "*.{png,jpg,bmp}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@epaule" maintainers: diff --git a/modules/nf-core/prinseqplusplus/meta.yml b/modules/nf-core/prinseqplusplus/meta.yml index a978be4a5cd5..5e09ba4546c7 100644 --- a/modules/nf-core/prinseqplusplus/meta.yml +++ b/modules/nf-core/prinseqplusplus/meta.yml @@ -1,5 +1,6 @@ name: "prinseqplusplus" -description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It can be used to filter, reformat or trim genomic and metagenomic sequence data +description: PRINSEQ++ is a C++ implementation of the prinseq-lite.pl program. It + can be used to filter, reformat or trim genomic and metagenomic sequence data keywords: - fastq - fasta @@ -13,46 +14,67 @@ tools: tool_dev_url: "https://github.com/Adrian-Cantu/PRINSEQ-plus-plus" doi: "10.7287/peerj.preprints.27553v1" licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end - data, respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - good_reads: - type: file - description: Reads passing filter(s) in gzipped FASTQ format - pattern: "*_good_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_good_out*.fastq.gz": + type: file + description: Reads passing filter(s) in gzipped FASTQ format + pattern: "*_good_out_{R1,R2}.fastq.gz" - single_reads: - type: file - description: | - Single reads without the pair passing filter(s) in gzipped FASTQ format - pattern: "*_single_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_single_out*.fastq.gz": + type: file + description: | + Single reads without the pair passing filter(s) in gzipped FASTQ format + pattern: "*_single_out_{R1,R2}.fastq.gz" - bad_reads: - type: file - description: | - Reads without not passing filter(s) in gzipped FASTQ format - pattern: "*_bad_out_{R1,R2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bad_out*.fastq.gz": + type: file + description: | + Reads without not passing filter(s) in gzipped FASTQ format + pattern: "*_bad_out_{R1,R2}.fastq.gz" - log: - type: file - description: | - Verbose level 2 STDOUT information in a log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: | + Verbose level 2 STDOUT information in a log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/prodigal/meta.yml b/modules/nf-core/prodigal/meta.yml index a5d15d58e5ef..7d3d459ee697 100644 --- a/modules/nf-core/prodigal/meta.yml +++ b/modules/nf-core/prodigal/meta.yml @@ -1,55 +1,78 @@ name: prodigal -description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program +description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a + microbial (bacterial and archaeal) gene finding program keywords: - prokaryotes - gene finding - microbial tools: - prodigal: - description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program + description: Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program homepage: https://github.com/hyattpd/Prodigal documentation: https://github.com/hyattpd/prodigal/wiki tool_dev_url: https://github.com/hyattpd/Prodigal doi: "10.1186/1471-2105-11-119" licence: ["GPL v3"] + identifier: biotools:prodigal input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genome: - type: file - description: fasta/fasta.gz file - - output_format: - type: string - description: Output format ("gbk"/"gff"/"sqn"/"sco") + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: fasta/fasta.gz file + - - output_format: + type: string + description: Output format ("gbk"/"gff"/"sqn"/"sco") output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - gene_annotations: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${output_format}.gz: + type: file + description: gene annotations in output_format given as input + pattern: "*.{output_format}" - nucleotide_fasta: - type: file - description: nucleotide sequences file - pattern: "*.{fna}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.fna.gz: + type: file + description: nucleotide sequences file + pattern: "*.{fna}" - amino_acid_fasta: - type: file - description: protein translations file - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.faa.gz: + type: file + description: protein translations file + pattern: "*.{faa}" - all_gene_annotations: - type: file - description: complete starts file - pattern: "*.{_all.txt}" - - gene_annotations: - type: file - description: gene annotations in output_format given as input - pattern: "*.{output_format}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}_all.txt.gz: + type: file + description: complete starts file + pattern: "*.{_all.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/prokka/meta.yml b/modules/nf-core/prokka/meta.yml index 9d82ffac7203..907457355e56 100644 --- a/modules/nf-core/prokka/meta.yml +++ b/modules/nf-core/prokka/meta.yml @@ -10,80 +10,151 @@ tools: homepage: https://github.com/tseemann/prokka doi: "10.1093/bioinformatics/btu153" licence: ["GPL v2"] + identifier: biotools:prokka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: | - FASTA file to be annotated. Has to contain at least a non-empty string dummy value. - - proteins: - type: file - description: FASTA file of trusted proteins to first annotate from (optional) - - prodigal_tf: - type: file - description: Training file to use for Prodigal (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + FASTA file to be annotated. Has to contain at least a non-empty string dummy value. + - - proteins: + type: file + description: FASTA file of trusted proteins to first annotate from (optional) + - - prodigal_tf: + type: file + description: Training file to use for Prodigal (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gff: - type: file - description: annotation in GFF3 format, containing both sequences and annotations - pattern: "*.{gff}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gff: + type: file + description: annotation in GFF3 format, containing both sequences and annotations + pattern: "*.{gff}" - gbk: - type: file - description: annotation in GenBank format, containing both sequences and annotations - pattern: "*.{gbk}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.gbk: + type: file + description: annotation in GenBank format, containing both sequences and annotations + pattern: "*.{gbk}" - fna: - type: file - description: nucleotide FASTA file of the input contig sequences - pattern: "*.{fna}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fna: + type: file + description: nucleotide FASTA file of the input contig sequences + pattern: "*.{fna}" - faa: - type: file - description: protein FASTA file of the translated CDS sequences - pattern: "*.{faa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.faa: + type: file + description: protein FASTA file of the translated CDS sequences + pattern: "*.{faa}" - ffn: - type: file - description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) - pattern: "*.{ffn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.ffn: + type: file + description: nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, + tRNA, tmRNA, misc_RNA) + pattern: "*.{ffn}" - sqn: - type: file - description: an ASN1 format "Sequin" file for submission to Genbank - pattern: "*.{sqn}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.sqn: + type: file + description: an ASN1 format "Sequin" file for submission to Genbank + pattern: "*.{sqn}" - fsa: - type: file - description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" to create the .sqn file - pattern: "*.{fsa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.fsa: + type: file + description: nucleotide FASTA file of the input contig sequences, used by "tbl2asn" + to create the .sqn file + pattern: "*.{fsa}" - tbl: - type: file - description: feature Table file, used by "tbl2asn" to create the .sqn file - pattern: "*.{tbl}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.tbl: + type: file + description: feature Table file, used by "tbl2asn" to create the .sqn file + pattern: "*.{tbl}" - err: - type: file - description: unacceptable annotations - the NCBI discrepancy report. - pattern: "*.{err}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.err: + type: file + description: unacceptable annotations - the NCBI discrepancy report. + pattern: "*.{err}" - log: - type: file - description: contains all the output that Prokka produced during its run - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.log: + type: file + description: contains all the output that Prokka produced during its run + pattern: "*.{log}" - txt: - type: file - description: statistics relating to the annotated features found - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.txt: + type: file + description: statistics relating to the annotated features found + pattern: "*.{txt}" - tsv: - type: file - description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/*.tsv: + type: file + description: tab-separated file of all features (locus_tag,ftype,len_bp,gene,EC_number,COG,product) + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/propr/grea/meta.yml b/modules/nf-core/propr/grea/meta.yml index d78d7c8b33f2..58f73fc4d861 100644 --- a/modules/nf-core/propr/grea/meta.yml +++ b/modules/nf-core/propr/grea/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "propr_grea" description: Perform Gene Ratio Enrichment Analysis @@ -17,44 +16,49 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.2202/1544-6115.1175" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the knowledge database - - adj: - type: file - description: adjacency matrix for gene ratio proportionality/differential proportionality - pattern: "*.{csv,tsv}" - - gmt: - type: file - description: relational database containing genes and GO terms (generated by mygene module) - pattern: "*.{gmt}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - adj: + type: file + description: adjacency matrix for gene ratio proportionality/differential proportionality + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the knowledge database + - gmt: + type: file + description: relational database containing genes and GO terms (generated by + mygene module) + pattern: "*.{gmt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - enrichedGO: - type: file - description: File containing GO terms and their enrichment values - pattern: "*.{csv}" - - session_info: - type: file - description: R session log - pattern: "*.R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.go.tsv": + type: file + description: File containing GO terms and their enrichment values + pattern: "*.{csv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - session_info: + - "*.R_sessionInfo.log": + type: file + description: R session log + pattern: "*.R_sessionInfo.log" authors: - "@caraiz2001" maintainers: diff --git a/modules/nf-core/propr/logratio/meta.yml b/modules/nf-core/propr/logratio/meta.yml index 77d6438254e6..30f8ac887ffb 100644 --- a/modules/nf-core/propr/logratio/meta.yml +++ b/modules/nf-core/propr/logratio/meta.yml @@ -1,5 +1,6 @@ name: "propr_logratio" -description: Transform the data matrix using centered logratio transformation (CLR) or additive logratio transformation (ALR) +description: Transform the data matrix using centered logratio transformation (CLR) + or additive logratio transformation (ALR) keywords: - alr - clr @@ -15,39 +16,44 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing additional information. - meta.id can be used to name the output files. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value. - You may want to handle the zeros with a different method beforehand. - pattern: "*.{csv,tsv}" + - - meta: + type: map + description: | + Groovy Map containing additional information. + meta.id can be used to name the output files. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. Otherwise, they will be first replaced by the minimun value. + You may want to handle the zeros with a different method beforehand. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing additional information. - meta.id can be used to name the output files. - [id: 'test', ...] - logratio: - type: file - description: ALR/CLR transformed data matrix. With rows = variables or genes, columns = samples or cells. - pattern: "*.logratio.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + meta.id can be used to name the output files. + [id: 'test', ...] + - "*.logratio.tsv": + type: file + description: ALR/CLR transformed data matrix. With rows = variables or genes, + columns = samples or cells. + pattern: "*.logratio.tsv" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" - "@oprana22" diff --git a/modules/nf-core/propr/propd/meta.yml b/modules/nf-core/propr/propd/meta.yml index 7dcb46259bf4..261e80ed216e 100644 --- a/modules/nf-core/propr/propd/meta.yml +++ b/modules/nf-core/propr/propd/meta.yml @@ -14,62 +14,88 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing additional information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. One should plug this module after another one that handles the zeros. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy map containing study-wide metadata related to the sample sheet and matrix - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata + - - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. One should plug this module after another one that handles the zeros. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy map containing study-wide metadata related to the sample sheet and matrix + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata output: - - meta: - type: map - description: | - Groovy Map containing additional information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - propd: - type: file - description: R propd object - pattern: "*.propd.rds" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propd.rds": + type: file + description: R propd object + pattern: "*.propd.rds" - results: - type: file - description: Results table - pattern: "*.propd.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propd.tsv": + type: file + description: Results table + pattern: "*.propd.tsv" - fdr: - type: file - description: (optional) propd fdr table - pattern: "*.fdr.tsv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.fdr.tsv": + type: file + description: (optional) propd fdr table + pattern: "*.fdr.tsv" - adj: - type: file - description: (optional) propd adj table - pattern: "*.adj.csv" + - meta: + type: map + description: | + Groovy Map containing additional information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.adj.csv": + type: file + description: (optional) propd adj table + pattern: "*.adj.csv" - warnings: - type: file - description: propd warnings - pattern: "*.warnings.txt" + - "*.warnings.log": + type: file + description: propd warnings + pattern: "*.warnings.txt" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" maintainers: diff --git a/modules/nf-core/propr/propr/meta.yml b/modules/nf-core/propr/propr/meta.yml index 206565168ccb..cdfc5982b729 100644 --- a/modules/nf-core/propr/propr/meta.yml +++ b/modules/nf-core/propr/propr/meta.yml @@ -18,63 +18,88 @@ tools: tool_dev_url: "https://github.com/tpq/propr" doi: "10.1038/s41598-017-16520-0" licence: ["GPL-2"] + identifier: biotools:propr - "corpcor": description: "Efficient Estimation of Covariance and (Partial) Correlation" homepage: "https://cran.r-project.org/web/packages/corpcor/index.html" documentation: "https://cran.r-project.org/web/packages/corpcor/corpcor.pdf" doi: "10.2202/1544-6115.1175" licence: ["GPL >=3"] + identifier: biotools:propr input: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - - count: - type: file - description: | - Count matrix, where rows = variables or genes, columns = samples or cells. - This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. - It is recommended to handle the zeros beforehand with the method of preference. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - count: + type: file + description: | + Count matrix, where rows = variables or genes, columns = samples or cells. + This matrix should not contain zeros. Otherwise, they will be replaced by the minimun number. + It is recommended to handle the zeros beforehand with the method of preference. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - This can be used at the workflow level to pass optional parameters to the module. - [id: 'test', ...] - propr: - type: file - description: R propr object - pattern: "*.propr.rds" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propr.rds": + type: file + description: R propr object + pattern: "*.propr.rds" - matrix: - type: file - description: Coefficient matrix - pattern: "*.propr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.propr.tsv": + type: file + description: Coefficient matrix + pattern: "*.propr.tsv" - fdr: - type: file - description: (optional) propr fdr table - pattern: "*.fdr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.fdr.tsv": + type: file + description: (optional) propr fdr table + pattern: "*.fdr.tsv" - adj: - type: file - description: (optional) propr adjacency table - pattern: "*.adj.csv" - - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.R_sessionInfo.log" + - meta: + type: map + description: | + Groovy Map containing sample information. + This can be used at the workflow level to pass optional parameters to the module. + [id: 'test', ...] + - "*.adj.csv": + type: file + description: (optional) propr adjacency table + pattern: "*.adj.csv" - warnings: - type: file - description: Warnings - pattern: "*.warnings.log" + - "*.warnings.log": + type: file + description: Warnings + pattern: "*.warnings.log" + - session_info: + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.R_sessionInfo.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" diff --git a/modules/nf-core/proteinortho/meta.yml b/modules/nf-core/proteinortho/meta.yml index 58e8eefd4c9b..b54e84f2600d 100644 --- a/modules/nf-core/proteinortho/meta.yml +++ b/modules/nf-core/proteinortho/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "proteinortho" description: Proteinortho is a tool to detect orthologous genes within different species. @@ -12,42 +11,59 @@ keywords: - genomics tools: - "proteinortho": - description: "Proteinortho is a tool to detect orthologous genes within different species." + description: "Proteinortho is a tool to detect orthologous genes within different + species." homepage: "https://gitlab.com/paulklemm_PHD/proteinortho" documentation: "https://gitlab.com/paulklemm_PHD/proteinortho#proteinortho" tool_dev_url: "https://gitlab.com/paulklemm_PHD/proteinortho" doi: "10.3389/fbinf.2023.1322477" licence: ["GPL v3"] + identifier: biotools:proteinortho input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - fasta_files: - type: file - description: Input fasta files (proteomes or transcriptomes), at least 2 are needed - pattern: "*.{fa,fasta,faa,fna,fn}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - fasta_files: + type: file + description: Input fasta files (proteomes or transcriptomes), at least 2 are + needed + pattern: "*.{fa,fasta,faa,fna,fn}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - orthologgroups: - type: file - description: Orthology table - pattern: "*.proteinortho.tsv" + - meta: + type: file + description: Orthology table + pattern: "*.proteinortho.tsv" + - ${meta.id}.proteinortho.tsv: + type: file + description: Orthology table + pattern: "*.proteinortho.tsv" - orthologgraph: - type: file - description: Orthology graph - pattern: "*.proteinortho-graph" + - meta: + type: file + description: Orthology graph + pattern: "*.proteinortho-graph" + - ${meta.id}.proteinortho-graph: + type: file + description: Orthology graph + pattern: "*.proteinortho-graph" - blastgraph: - type: file - description: BLAST graph - pattern: "*.blast-graph" - + - meta: + type: file + description: BLAST graph + pattern: "*.blast-graph" + - ${meta.id}.blast-graph: + type: file + description: BLAST graph + pattern: "*.blast-graph" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pmjklemm" maintainers: diff --git a/modules/nf-core/proteus/readproteingroups/environment.yml b/modules/nf-core/proteus/readproteingroups/environment.yml index 47fc6415956e..986db59603a1 100644 --- a/modules/nf-core/proteus/readproteingroups/environment.yml +++ b/modules/nf-core/proteus/readproteingroups/environment.yml @@ -1,9 +1,10 @@ channels: - conda-forge - bioconda + dependencies: - - conda-forge::r-base=4.2.1 - - bioconda::r-proteus-bartongroup=0.2.16 - - conda-forge::r-plotly=4.10.2 - bioconda::bioconductor-limma=3.54.0 + - bioconda::r-proteus-bartongroup=0.2.16 + - conda-forge::r-base=4.2.1 - conda-forge::r-ggplot2=3.4.4 + - conda-forge::r-plotly=4.10.2 diff --git a/modules/nf-core/proteus/readproteingroups/meta.yml b/modules/nf-core/proteus/readproteingroups/meta.yml index 4e67cf0c289d..d1d7e8c9f5e5 100644 --- a/modules/nf-core/proteus/readproteingroups/meta.yml +++ b/modules/nf-core/proteus/readproteingroups/meta.yml @@ -12,68 +12,107 @@ tools: tool_dev_url: "https://github.com/bartongroup/Proteus" doi: "10.1101/416511" licence: ["GPL v2"] + identifier: biotools:proteus-engineering input: - - meta: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - samplesheet: - type: file - description: | - CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html - - intensities: - type: file - description: | - proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html - - meta2: - type: map - description: | - Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - contrast_variable: - type: string - description: | - The column in the sample sheet that should be used to define groups for comparison + - - meta: + type: map + description: | + Groovy Map containing contrast information, e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - samplesheet: + type: file + description: | + CSV or TSV format sample sheet with sample metadata; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html + - intensities: + type: file + description: | + proteinGroups TXT file with protein intensities information from maxQuant; check here for specifications: https://rdrr.io/github/bartongroup/Proteus/man/readProteinGroups.html output: - dendro_plot: - type: file - description: | - PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities + - meta: + type: file + description: | + PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities + - "*dendrogram.png": + type: file + description: | + PNG file; dendrogram of the normalized samples hierarchically clustered by their intensities - mean_var_plot: - type: file - description: | - PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples + - meta: + type: file + description: | + PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples + - "*mean_variance_relationship.png": + type: file + description: | + PNG file; plot of the log-intensity variance vs log-intensity mean of each condition in the normalized samples - raw_dist_plot: - type: file - description: | - PNG file; plot of the intensity/ratio distributions of the raw samples + - meta: + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the raw samples + - "*raw_distributions.png": + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the raw samples - norm_dist_plot: - type: file - description: | - PNG file; plot of the intensity/ratio distributions of the normalized samples + - meta: + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the normalized samples + - "*normalized_distributions.png": + type: file + description: | + PNG file; plot of the intensity/ratio distributions of the normalized samples - raw_rdata: - type: file - description: | - RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info + - meta: + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info + - "*raw_proteingroups.rds": + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains raw protein intensities and additional info - norm_rdata: - type: file - description: | - RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info + - meta: + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info + - "*normalized_proteingroups.rds": + type: file + description: | + RDS file of a proteinGroups object from Proteus, contains normalized protein intensities and additional info - raw_tab: - type: file - description: | - TSV-format intensities table from Proteus, contains raw protein intensities + - meta: + type: file + description: | + TSV-format intensities table from Proteus, contains raw protein intensities + - "*raw_proteingroups_tab.tsv": + type: file + description: | + TSV-format intensities table from Proteus, contains raw protein intensities - norm_tab: - type: file - description: | - TSV-format intensities table from Proteus, contains normalized protein intensities + - meta: + type: file + description: | + TSV-format intensities table from Proteus, contains normalized protein intensities + - "*normalized_proteingroups_tab.tsv": + type: file + description: | + TSV-format intensities table from Proteus, contains normalized protein intensities - session_info: - type: file - description: | - LOG file of the R sessionInfo from the module run + - meta: + type: file + description: | + LOG file of the R sessionInfo from the module run + - "*R_sessionInfo.log": + type: file + description: | + LOG file of the R sessionInfo from the module run - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@WackerO" maintainers: diff --git a/modules/nf-core/pureclip/meta.yml b/modules/nf-core/pureclip/meta.yml index 48308ce6344b..ceec2106718c 100644 --- a/modules/nf-core/pureclip/meta.yml +++ b/modules/nf-core/pureclip/meta.yml @@ -1,70 +1,85 @@ ---- name: "pureclip" -description: PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. +description: PureCLIP is a tool to detect protein-RNA interaction footprints from + single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. keywords: - iCLIP - eCLIP - CLIP tools: - "pureclip": - description: "PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP." + description: "PureCLIP is a tool to detect protein-RNA interaction footprints + from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP." homepage: "https://github.com/skrakau/PureCLIP" documentation: "https://pureclip.readthedocs.io/en/latest/GettingStarted/index.html" tool_dev_url: "https://github.com/skrakau/PureCLIP" doi: "10.1186/s13059-017-1364-2" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - ipbam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - controlbam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - ipbai: - type: file - description: BAM index - pattern: "*.{bai}" - - controlbai: - type: file - description: BAM index - pattern: "*.{bai}" - - input_control: - type: boolean - description: Whether to run PureCLIP with an input control - - genome_fasta: - type: file - description: FASTA file of reference genome - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ipbam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - controlbam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ipbai: + type: file + description: BAM index + pattern: "*.{bai}" + - controlbai: + type: file + description: BAM index + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - genome_fasta: + type: file + description: FASTA file of reference genome + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - input_control: + type: boolean + description: Whether to run PureCLIP with an input control output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - crosslinks: - type: file - description: Bed file of crosslinks - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${crosslinks_output_name}: + type: file + description: Bed file of crosslinks + pattern: "*.{bed}" - peaks: - type: file - description: Bed file of peaks - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${peaks_output_name}: + type: file + description: Bed file of peaks + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@charlotteanne" - "@marcjones" diff --git a/modules/nf-core/purecn/coverage/environment.yml b/modules/nf-core/purecn/coverage/environment.yml index cbd210aa4960..ffb69fe35cc3 100644 --- a/modules/nf-core/purecn/coverage/environment.yml +++ b/modules/nf-core/purecn/coverage/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: + - bioconda::bioconductor-org.hs.eg.db=3.16.0 - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 - - bioconda::bioconductor-org.hs.eg.db=3.16.0 diff --git a/modules/nf-core/purecn/coverage/meta.yml b/modules/nf-core/purecn/coverage/meta.yml index e88bb21a1480..aba8770dbc24 100644 --- a/modules/nf-core/purecn/coverage/meta.yml +++ b/modules/nf-core/purecn/coverage/meta.yml @@ -1,5 +1,6 @@ name: "purecn_coverage" -description: Calculate intervals coverage for each sample. N.B. the tool can not handle staging files with symlinks, stageInMode should be set to 'link'. +description: Calculate intervals coverage for each sample. N.B. the tool can not handle + staging files with symlinks, stageInMode should be set to 'link'. keywords: - copy number alteration calling - intervals coverage @@ -8,63 +9,85 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" license: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM index file - pattern: "*.{bai}" - - intervals: - type: file - description: Annotated targets optimized for copy number calling - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - - intervals: + type: file + description: Annotated targets optimized for copy number calling + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - description: Intervals coverage file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Intervals coverage file + pattern: "*.txt.gz" - png: - type: file - description: | - GC-normalized intervals coverage plot. - Generated only when GC-normalization is enabled. - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: | + GC-normalized intervals coverage plot. + Generated only when GC-normalization is enabled. + pattern: "*.png" - loess_qc_txt: - type: file - description: | - GC-normalized intervals coverage metrics. - Generated only when GC-normalization is enabled. - pattern: "*_loess_qc.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_loess_qc.txt": + type: file + description: | + GC-normalized intervals coverage metrics. + Generated only when GC-normalization is enabled. + pattern: "*_loess_qc.txt" - loess_txt: - type: file - description: | - GC-normalized intervals coverage file. - Generated only when GC-normalization is enabled. - pattern: "*_loess.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_loess.txt.gz": + type: file + description: | + GC-normalized intervals coverage file. + Generated only when GC-normalization is enabled. + pattern: "*_loess.txt.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/intervalfile/meta.yml b/modules/nf-core/purecn/intervalfile/meta.yml index 489fed1cd073..0965574e2212 100644 --- a/modules/nf-core/purecn/intervalfile/meta.yml +++ b/modules/nf-core/purecn/intervalfile/meta.yml @@ -8,56 +8,66 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z." licence: ["Artistic-2.0"] + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - target_bed: - type: file - description: BED file of target intervals - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: FASTA reference sequence of the genome being used - pattern: "*.fasta" - - genome: - type: string - description: Genome used for the BED file (e.g., "hg38", "mm10"...) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - target_bed: + type: file + description: BED file of target intervals + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: FASTA reference sequence of the genome being used + pattern: "*.fasta" + - - genome: + type: string + description: Genome used for the BED file (e.g., "hg38", "mm10"...) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - txt: - type: file - pattern: "*.txt" - description: | - Annotated targets optimized for copy number calling + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + pattern: "*.txt" + description: | + Annotated targets optimized for copy number calling - bed: - type: file - pattern: "*.bed" - description: | - Modified and optimized targets exported as a BED file. - Generate the file using the --export command-line switch - IntervalFile.R. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + pattern: "*.bed" + description: | + Modified and optimized targets exported as a BED file. + Generate the file using the --export command-line switch + IntervalFile.R. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/normaldb/meta.yml b/modules/nf-core/purecn/normaldb/meta.yml index cddabe9f0e1b..4fbe29d643ca 100644 --- a/modules/nf-core/purecn/normaldb/meta.yml +++ b/modules/nf-core/purecn/normaldb/meta.yml @@ -1,5 +1,9 @@ name: "purecn_normaldb" -description: Build a normal database for coverage normalization from all the (GC-normalized) normal coverage files. N.B. as reported in https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, it is advised to provide a normal panel (VCF format) to precompute mapping bias for faster runtimes. +description: Build a normal database for coverage normalization from all the (GC-normalized) + normal coverage files. N.B. as reported in + https://www.bioconductor.org/packages/devel/bioc/vignettes/PureCN/inst/doc/Quick.html, + it is advised to provide a normal panel (VCF format) to precompute mapping bias + for faster runtimes. keywords: - copy number alteration calling - normal database @@ -9,62 +13,96 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" licence: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - coverage_files: - type: file - description: Coverage files from normal samples - pattern: "*.txt.gz" - - normal_vcf: - type: file - description: | - Normal panel in VCF format, used to precompute mapping bias - for faster runtimes. Optional. - pattern: "*.vcf.gz" - - genome: - type: string - description: Genome build - - assay: - type: string - description: Assay name + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - coverage_files: + type: file + description: Coverage files from normal samples + pattern: "*.txt.gz" + - normal_vcf: + type: file + description: | + Normal panel in VCF format, used to precompute mapping bias + for faster runtimes. Optional. + pattern: "*.vcf.gz" + - normal_vcf_tbi: + type: file + description: Normal panel in VCF format + pattern: "*.vcf.gz.tbi" + - - genome: + type: string + description: Genome build + - - assay: + type: string + description: Assay name output: - rds: - type: file - description: File containing the generated panel of normals - pattern: "normalDB*.rds" + - meta: + type: file + description: File containing the generated panel of normals + pattern: "normalDB*.rds" + - normalDB*.rds: + type: file + description: File containing the generated panel of normals + pattern: "normalDB*.rds" - png: - type: file - description: Plot of interval weights calculated from the panel of normals - pattern: "interval_weights*.png" + - meta: + type: file + description: Plot of interval weights calculated from the panel of normals + pattern: "interval_weights*.png" + - interval_weights*.png: + type: file + description: Plot of interval weights calculated from the panel of normals + pattern: "interval_weights*.png" - bias_rds: - type: file - description: Calculated mapping bias from the normal files - pattern: "mapping_bias*.rds" + - meta: + type: file + description: Calculated mapping bias from the normal files + pattern: "mapping_bias*.rds" + - mapping_bias*.rds: + type: file + description: Calculated mapping bias from the normal files + pattern: "mapping_bias*.rds" - bias_bed: - type: file - description: Calculated mapping bias sites from the normal files - pattern: "mapping_bias_hq_sites*.bed" + - meta: + type: file + description: Calculated mapping bias sites from the normal files + pattern: "mapping_bias_hq_sites*.bed" + - mapping_bias_hq_sites*.bed: + type: file + description: Calculated mapping bias sites from the normal files + pattern: "mapping_bias_hq_sites*.bed" - low_cov_bed: - type: file - description: | - BED with possibly low coverage targets identified, only - generated if there are low coverage targets - pattern: "low_coverage_targets*.bed" + - meta: + type: file + description: | + BED with possibly low coverage targets identified, only + generated if there are low coverage targets + pattern: "low_coverage_targets*.bed" + - low_coverage_targets*.bed: + type: file + description: | + BED with possibly low coverage targets identified, only + generated if there are low coverage targets + pattern: "low_coverage_targets*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purecn/run/environment.yml b/modules/nf-core/purecn/run/environment.yml index cbd210aa4960..ffb69fe35cc3 100644 --- a/modules/nf-core/purecn/run/environment.yml +++ b/modules/nf-core/purecn/run/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: + - bioconda::bioconductor-org.hs.eg.db=3.16.0 - bioconda::bioconductor-purecn=2.4.0 - bioconda::bioconductor-txdb.hsapiens.ucsc.hg38.knowngene=3.16.0 - bioconductor-txdb.hsapiens.ucsc.hg19.knowngene=3.2.2 - - bioconda::bioconductor-org.hs.eg.db=3.16.0 diff --git a/modules/nf-core/purecn/run/meta.yml b/modules/nf-core/purecn/run/meta.yml index f70f780e8694..6817837fbb5a 100644 --- a/modules/nf-core/purecn/run/meta.yml +++ b/modules/nf-core/purecn/run/meta.yml @@ -7,96 +7,167 @@ keywords: - DNA sequencing tools: - "purecn": - description: "Copy number calling and SNV classification using targeted short read sequencing" + description: "Copy number calling and SNV classification using targeted short + read sequencing" homepage: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" documentation: "https://bioconductor.org/packages/release/bioc/html/PureCN.html" tool_dev_url: "https://github.com/lima1/PureCN" doi: "10.1186/s13029-016-0060-z" license: ["Artistic-2.0"] args_id: "$args" + identifier: biotools:purecn input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - intervals: - type: file - description: | - BED file of target intervals, generated from IntervalFile.R - pattern: "{*.bed,*.txt}" - - coverage: - type: file - description: Coverage file generated from Coverage.R - pattern: "*.txt" - - normaldb: - type: file - description: | - Normal panel in RDS format, generated from NormalDB.R - pattern: "*.rds" - - genome: - type: string - description: Genome build + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: | + BED file of target intervals, generated from IntervalFile.R + pattern: "{*.bed,*.txt}" + - coverage: + type: file + description: Coverage file generated from Coverage.R + pattern: "*.txt" + - - normal_db: + type: file + description: normal pannel database + - - genome: + type: string + description: Genome build output: - pdf: - type: file - description: | - PDF file containing copy number plots - pattern: "*.pdf" + - meta: + type: file + description: | + PDF file containing copy number plots + pattern: "*.pdf" + - "*.pdf": + type: file + description: | + PDF file containing copy number plots + pattern: "*.pdf" - local_optima_pdf: - type: file - description: | - PDF file containing local optima plots - pattern: "*_local_optima.pdf" + - meta: + type: file + description: | + PDF file containing local optima plots + pattern: "*_local_optima.pdf" + - "*_local_optima.pdf": + type: file + description: | + PDF file containing local optima plots + pattern: "*_local_optima.pdf" - seg: - type: file - description: | - Tab-delimited file containing segmentation results - pattern: "*_dnacopy.seg" + - meta: + type: file + description: | + Tab-delimited file containing segmentation results + pattern: "*_dnacopy.seg" + - "*_dnacopy.seg": + type: file + description: | + Tab-delimited file containing segmentation results + pattern: "*_dnacopy.seg" - genes_csv: - type: file - description: | - CSV file containing gene copy number calls. Optional - pattern: "*_genes.csv" + - meta: + type: file + description: | + CSV file containing gene copy number calls. Optional + pattern: "*_genes.csv" + - "*_genes.csv": + type: file + description: | + CSV file containing gene copy number calls. Optional + pattern: "*_genes.csv" - amplification_pvalues_csv: - type: file - description: | - CSV file containing amplification p-values. Optional - pattern: "*_amplification_pvalues.csv" + - meta: + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" + - "*_amplification_pvalues.csv": + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" + - ues_csv: + type: file + description: | + CSV file containing amplification p-values. Optional + pattern: "*_amplification_pvalues.csv" - vcf_gz: - type: file - description: | - GZipped VCF file containing SNV calls. Optional - pattern: "*.vcf.gz" + - meta: + type: file + description: | + GZipped VCF file containing SNV calls. Optional + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: | + GZipped VCF file containing SNV calls. Optional + pattern: "*.vcf.gz" - variants_csv: - type: file - description: | - CSV file containing SNV calls. Optional - pattern: "*_variants.csv" + - meta: + type: file + description: | + CSV file containing SNV calls. Optional + pattern: "*_variants.csv" + - "*_variants.csv": + type: file + description: | + CSV file containing SNV calls. Optional + pattern: "*_variants.csv" - loh_csv: - type: file - description: | - CSV file containing LOH calls. Optional - pattern: "*_loh.csv" + - meta: + type: file + description: | + CSV file containing LOH calls. Optional + pattern: "*_loh.csv" + - "*_loh.csv": + type: file + description: | + CSV file containing LOH calls. Optional + pattern: "*_loh.csv" - chr_pdf: - type: file - description: | - PDF file containing chromosome plots. Optional - pattern: "*_chromosomes.pdf" + - meta: + type: file + description: | + PDF file containing chromosome plots. Optional + pattern: "*_chromosomes.pdf" + - "*_chromosomes.pdf": + type: file + description: | + PDF file containing chromosome plots. Optional + pattern: "*_chromosomes.pdf" - segmentation_pdf: - type: file - description: | - PDF file containing segmentation plots. Optional - pattern: "*_segmentation.pdf" - - multisample.seg: - type: file - description: | - Tab-delimited file containing segmentation data from multiple samples. Optional - pattern: "*_multisample.seg" + - meta: + type: file + description: | + PDF file containing segmentation plots. Optional + pattern: "*_segmentation.pdf" + - "*_segmentation.pdf": + type: file + description: | + PDF file containing segmentation plots. Optional + pattern: "*_segmentation.pdf" + - multisample_seg: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_multisample.seg": + type: file + description: multisample segmentation results + pattern: "*_multisample.seg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aldosr" - "@lbeltrame" diff --git a/modules/nf-core/purgedups/calcuts/meta.yml b/modules/nf-core/purgedups/calcuts/meta.yml index 94fcec79502f..4c236d652270 100644 --- a/modules/nf-core/purgedups/calcuts/meta.yml +++ b/modules/nf-core/purgedups/calcuts/meta.yml @@ -6,40 +6,50 @@ keywords: - purge duplications tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stat: - type: file - description: Histogram of coverage - pattern: "*.stat" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stat: + type: file + description: Histogram of coverage + pattern: "*.stat" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cutoff: - type: file - description: Cutoff file - pattern: "*.cutoffs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cutoffs": + type: file + description: Cutoff file + pattern: "*.cutoffs" - log: - type: file - description: Log file - pattern: ".calcuts.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.calcuts.log": + type: file + description: Log file + pattern: ".calcuts.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/getseqs/meta.yml b/modules/nf-core/purgedups/getseqs/meta.yml index 2b759ce4f022..41d85b649701 100644 --- a/modules/nf-core/purgedups/getseqs/meta.yml +++ b/modules/nf-core/purgedups/getseqs/meta.yml @@ -7,44 +7,54 @@ keywords: - assembly curation tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly in fasta format - pattern: "*.fasta" - - bed: - type: file - description: Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly in fasta format + pattern: "*.fasta" + - bed: + type: file + description: Bed file listing duplicated sequences, produced by PURGEDUPS_PURGEDUPS + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - haplotigs: - type: file - description: Fasta file containing purged haplotigs - pattern: "*.hap.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.fa": + type: file + description: Fasta file containing purged haplotigs + pattern: "*.hap.fa" - purged: - type: file - description: Fasta file purged of duplicated haplotigs - pattern: "*.purged.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.purged.fa": + type: file + description: Fasta file purged of duplicated haplotigs + pattern: "*.purged.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/histplot/meta.yml b/modules/nf-core/purgedups/histplot/meta.yml index 47596104f217..f4215c497695 100644 --- a/modules/nf-core/purgedups/histplot/meta.yml +++ b/modules/nf-core/purgedups/histplot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "purgedups_histplot" description: Plots the read coverage from a purge dups statistics file and cutoffs. @@ -8,40 +7,44 @@ keywords: - Read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - statfile: - type: file - description: A Purge dups statistic file - pattern: "*.stat" - - cutoff: - type: file - description: A Purge dups cutoff file - pattern: "*.cutoffs" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - statfile: + type: file + description: A Purge dups statistic file + pattern: "*.stat" + - cutoff: + type: file + description: A Purge dups cutoff file + pattern: "*.cutoffs" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: A png file of the read depth coverage. - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.png": + type: file + description: A png file of the read depth coverage. + pattern: "*.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/pbcstat/meta.yml b/modules/nf-core/purgedups/pbcstat/meta.yml index 875de168cf89..db635a23fe30 100644 --- a/modules/nf-core/purgedups/pbcstat/meta.yml +++ b/modules/nf-core/purgedups/pbcstat/meta.yml @@ -1,5 +1,6 @@ name: "purgedups_pbcstat" -description: Create read depth histogram and base-level read depth for an assembly based on pacbio data +description: Create read depth histogram and base-level read depth for an assembly + based on pacbio data keywords: - sort - genome assembly @@ -7,40 +8,50 @@ keywords: - read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf_alignment: - type: file - description: PAF alignment file - pattern: "*.paf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf_alignment: + type: file + description: PAF alignment file + pattern: "*.paf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stat: - type: file - description: PacBio Statistic file - pattern: "*.PB.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.PB.stat": + type: file + description: PacBio Statistic file + pattern: "*.PB.stat" - basecov: - type: file - description: PacBio Base coverage file - pattern: "*.PB.base.cov" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.PB.base.cov": + type: file + description: PacBio Base coverage file + pattern: "*.PB.base.cov" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/purgedups/meta.yml b/modules/nf-core/purgedups/purgedups/meta.yml index d79ab58ed937..ecee7b805489 100644 --- a/modules/nf-core/purgedups/purgedups/meta.yml +++ b/modules/nf-core/purgedups/purgedups/meta.yml @@ -8,48 +8,58 @@ keywords: - Read depth tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - basecov: - type: file - description: A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT - pattern: "*.PB.base.cov" - - cutoff: - type: file - description: A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS - pattern: "*.cutoffs" - - paf: - type: file - description: A file of assembly alignments to itself - pattern: "*.paf(.gz)?" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - basecov: + type: file + description: A file containing a histogram of base coverage. Obtained from PURGEDUPS_PBCSTAT + pattern: "*.PB.base.cov" + - cutoff: + type: file + description: A file containing duplication cutoff points. Obtained from PURGEDUPS_CALCUTS + pattern: "*.cutoffs" + - paf: + type: file + description: A file of assembly alignments to itself + pattern: "*.paf(.gz)?" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: A bed file of sequences purged of false duplications - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dups.bed": + type: file + description: A bed file of sequences purged of false duplications + pattern: "*.bed" - log: - type: file - description: A log of the tool output - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.purge_dups.log": + type: file + description: A log of the tool output + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/purgedups/splitfa/meta.yml b/modules/nf-core/purgedups/splitfa/meta.yml index 938cc225f0cb..a3a9eeaa4b7a 100644 --- a/modules/nf-core/purgedups/splitfa/meta.yml +++ b/modules/nf-core/purgedups/splitfa/meta.yml @@ -7,36 +7,40 @@ keywords: - purging tools: - "purgedups": - description: "Purge_dups is a package used to purge haplotigs and overlaps in an assembly based on read depth" + description: "Purge_dups is a package used to purge haplotigs and overlaps in + an assembly based on read depth" homepage: "https://github.com/dfguan/purge_dups" documentation: "https://github.com/dfguan/purge_dups" tool_dev_url: "https://github.com/dfguan/purge_dups" doi: "10.1093/bioinformatics/btaa025" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - assembly: - type: file - description: Draft assembly file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - assembly: + type: file + description: Draft assembly file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - split_fasta: - type: file - description: Fasta split by N's - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.split.fasta.gz": + type: file + description: Fasta split by N's + pattern: "*.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/pycoqc/meta.yml b/modules/nf-core/pycoqc/meta.yml index cfbd85163373..c535c56469e3 100644 --- a/modules/nf-core/pycoqc/meta.yml +++ b/modules/nf-core/pycoqc/meta.yml @@ -7,39 +7,49 @@ keywords: - nanopore tools: - pycoqc: - description: PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data + description: PycoQC computes metrics and generates interactive QC plots for Oxford + Nanopore technologies sequencing data homepage: https://github.com/tleonardi/pycoQC documentation: https://tleonardi.github.io/pycoQC/ tool_dev_url: https://github.com/tleonardi/pycoQC doi: "10.21105/joss.01236" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:pycoqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - summary: - type: file - description: sequencing summary file - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - summary: + type: file + description: sequencing summary file + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - html: - type: file - description: Results in HTML format + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: Results in HTML format - json: - type: file - description: Results in JSON format - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: Results in JSON format + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/pydamage/analyze/meta.yml b/modules/nf-core/pydamage/analyze/meta.yml index fd6aa513e6ce..d862fd3d42d9 100644 --- a/modules/nf-core/pydamage/analyze/meta.yml +++ b/modules/nf-core/pydamage/analyze/meta.yml @@ -20,34 +20,37 @@ tools: documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: PyDamage results as csv files - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pydamage_results/pydamage_results.csv: + type: file + description: PyDamage results as csv files + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/pydamage/filter/meta.yml b/modules/nf-core/pydamage/filter/meta.yml index 6b1b0bb87534..eb20375440f1 100644 --- a/modules/nf-core/pydamage/filter/meta.yml +++ b/modules/nf-core/pydamage/filter/meta.yml @@ -20,30 +20,33 @@ tools: documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - csv: - type: file - description: csv file from pydamage analyze - pattern: "*.csv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - csv: + type: file + description: csv file from pydamage analyze + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: PyDamage filtered results as csv file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pydamage_results/pydamage_filtered_results.csv: + type: file + description: PyDamage filtered results as csv file + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/pyrodigal/meta.yml b/modules/nf-core/pyrodigal/meta.yml index 0967606f34d3..d8394d070694 100644 --- a/modules/nf-core/pyrodigal/meta.yml +++ b/modules/nf-core/pyrodigal/meta.yml @@ -1,5 +1,6 @@ name: "pyrodigal" -description: Pyrodigal is a Python module that provides bindings to Prodigal, a fast, reliable protein-coding gene prediction for prokaryotic genomes. +description: Pyrodigal is a Python module that provides bindings to Prodigal, a fast, + reliable protein-coding gene prediction for prokaryotic genomes. keywords: - sort - annotation @@ -7,52 +8,75 @@ keywords: - prokaryote tools: - "pyrodigal": - description: "Pyrodigal is a Python module that provides bindings to Prodigal (ORF finder for microbial sequences) using Cython." + description: "Pyrodigal is a Python module that provides bindings to Prodigal + (ORF finder for microbial sequences) using Cython." homepage: "https://pyrodigal.readthedocs.org/" documentation: "https://pyrodigal.readthedocs.org/" tool_dev_url: "https://github.com/althonos/pyrodigal/" doi: "10.21105/joss.04296" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta.gz,fa.gz,fna.gz}" - - output_format: - type: string - description: Output format - pattern: "{gbk,gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta.gz,fa.gz,fna.gz}" + - - output_format: + type: string + description: Output format + pattern: "{gbk,gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - annotations: - type: file - description: Gene annotations. The file format is specified via input channel "output_format". - pattern: "*.{gbk,gff}.gz" - - faa: - type: file - description: protein translations file - pattern: "*.{faa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.${output_format}.gz": + type: file + description: Gene annotations. The file format is specified via input channel + "output_format". + pattern: "*.{gbk,gff}.gz" - fna: - type: file - description: nucleotide sequences file - pattern: "*.{fna.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fna.gz": + type: file + description: nucleotide sequences file + pattern: "*.{fna.gz}" + - faa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.faa.gz": + type: file + description: protein translations file + pattern: "*.{faa.gz}" - score: - type: file - description: all potential genes (with scores) - pattern: "*.{score.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.score.gz": + type: file + description: all potential genes (with scores) + pattern: "*.{score.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" maintainers: diff --git a/modules/nf-core/qcat/meta.yml b/modules/nf-core/qcat/meta.yml index c00a21eef450..81bf47b8bfd3 100644 --- a/modules/nf-core/qcat/meta.yml +++ b/modules/nf-core/qcat/meta.yml @@ -11,30 +11,36 @@ tools: homepage: https://github.com/nanoporetech/qcat documentation: https://github.com/nanoporetech/qcat#qcat licence: ["MPL-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Non-demultiplexed fastq files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Non-demultiplexed fastq files + - - barcode_kit: + type: string + description: Barcode kit used for demultiplexing output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Demultiplexed fastq samples - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq/*.fastq.gz: + type: file + description: Demultiplexed fastq samples + pattern: "*.fastq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" - "@drpatelh" diff --git a/modules/nf-core/qualimap/bamqc/meta.yml b/modules/nf-core/qualimap/bamqc/meta.yml index 7756d4975b61..8be33c00a587 100644 --- a/modules/nf-core/qualimap/bamqc/meta.yml +++ b/modules/nf-core/qualimap/bamqc/meta.yml @@ -15,34 +15,37 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@phue" maintainers: diff --git a/modules/nf-core/qualimap/bamqccram/meta.yml b/modules/nf-core/qualimap/bamqccram/meta.yml index ec388b309ae3..4b7225a595b2 100644 --- a/modules/nf-core/qualimap/bamqccram/meta.yml +++ b/modules/nf-core/qualimap/bamqccram/meta.yml @@ -15,38 +15,49 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bacramm: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" - - fasta: - type: file - description: Reference file of cram file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: Input cram file + pattern: "*.{cram}" + - crai: + type: file + description: Index file for cram file + pattern: "*.{crai}" + - - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" + - - fasta: + type: file + description: Reference file of cram file + pattern: "*.{fasta,fa,fna}" + - - fasta_fai: + type: file + description: Index file for reference file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/qualimap/rnaseq/meta.yml b/modules/nf-core/qualimap/rnaseq/meta.yml index 6f766e4f5039..a730261b5965 100644 --- a/modules/nf-core/qualimap/rnaseq/meta.yml +++ b/modules/nf-core/qualimap/rnaseq/meta.yml @@ -15,39 +15,42 @@ tools: documentation: http://qualimap.conesalab.org/doc_html/index.html doi: 10.1093/bioinformatics/bts503 licence: ["GPL-2.0-only"] + identifier: biotools:qualimap input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - results: - type: directory - description: Qualimap results dir - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Qualimap results dir + pattern: "*/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/quartonotebook/meta.yml b/modules/nf-core/quartonotebook/meta.yml index 5d95e8b66302..e3c3c1cfedd2 100644 --- a/modules/nf-core/quartonotebook/meta.yml +++ b/modules/nf-core/quartonotebook/meta.yml @@ -13,70 +13,96 @@ tools: documentation: https://quarto.org/docs/reference/ tool_dev_url: https://github.com/quarto-dev/quarto-cli licence: ["MIT"] + identifier: "" - papermill: description: Parameterize, execute, and analyze notebooks homepage: https://github.com/nteract/papermill documentation: http://papermill.readthedocs.io/en/latest/ tool_dev_url: https://github.com/nteract/papermill licence: ["BSD 3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]`. - - notebook: - type: file - description: The Quarto notebook to be rendered. - pattern: "*.{qmd}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed to Quarto to - generate parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" - - extensions: - type: file - description: | - A quarto `_extensions` directory with custom template(s) to be - available for rendering. - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - notebook: + type: file + description: The Quarto notebook to be rendered. + pattern: "*.{qmd}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed to Quarto to + generate parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" + - - extensions: + type: file + description: | + A quarto `_extensions` directory with custom template(s) to be + available for rendering. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]`. - html: - type: file - description: HTML report generated by Quarto. - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - "*.html": + type: file + description: HTML report generated by Quarto. + pattern: "*.html" - notebook: - type: file - description: The original, un-rendered notebook. - pattern: "*.[qmd,ipynb,rmd]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - ${notebook}: + type: file + description: The original, un-rendered notebook. + pattern: "*.[qmd,ipynb,rmd]" - artifacts: - type: file - description: Artifacts generated during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - artifacts/*: + type: file + description: Artifacts generated during report rendering. + pattern: "*" - params_yaml: - type: file - description: Parameters used during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - params.yml: + type: file + description: Parameters used during report rendering. + pattern: "*" - extensions: - type: file - description: Quarto extensions used during report rendering. - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]`. + - _extensions: + type: file + description: Quarto extensions used during report rendering. + pattern: "*" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@fasterius" maintainers: diff --git a/modules/nf-core/quast/meta.yml b/modules/nf-core/quast/meta.yml index 5850ff98c867..ea4924bdfc64 100644 --- a/modules/nf-core/quast/meta.yml +++ b/modules/nf-core/quast/meta.yml @@ -13,46 +13,94 @@ tools: homepage: http://bioinf.spbau.ru/quast doi: 10.1093/bioinformatics/btt086 licence: ["GPL-2.0-only"] + identifier: biotools:quast input: - - consensus: - type: file - description: | - Fasta file containing the assembly of interest - - fasta: - type: file - description: | - The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. - - gff: - type: file - description: The genome GFF file. Has to contain at least a non-empty string dummy value. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - consensus: + type: file + description: | + Fasta file containing the assembly of interest + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + The genome assembly to be evaluated. Has to contain at least a non-empty string dummy value. + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: The genome GFF file. Has to contain at least a non-empty string + dummy value. output: - - quast: - type: directory - description: Directory containing complete quast report - pattern: "{prefix}/" - - report: - type: file - description: tab-separated version of the summary, suitable for spreadsheets and mqc - pattern: "${prefix}.tsv" - - misassemblies: - type: file - description: | - Report containing misassemblies, only when a reference fasta is provided - pattern: "${prefix}_misassemblies.tsv" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: | + Directory containing the results of the QUAST analysis + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: TSV file + pattern: "${prefix}.tsv" - transcriptome: - type: file - description: | - Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided - pattern: "${prefix}_transcriptome.tsv" + - meta: + type: file + description: | + Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided + pattern: "${prefix}_transcriptome.tsv" + - ${prefix}_transcriptome.tsv: + type: file + description: | + Report containing all the alignments of transcriptome to the assembly, only when a reference fasta is provided + pattern: "${prefix}_transcriptome.tsv" + - misassemblies: + - meta: + type: file + description: | + Report containing misassemblies, only when a reference fasta is provided + pattern: "${prefix}_misassemblies.tsv" + - ${prefix}_misassemblies.tsv: + type: file + description: | + Report containing misassemblies, only when a reference fasta is provided + pattern: "${prefix}_misassemblies.tsv" - unaligned: - type: file - description: | - Report containing unaligned contigs, only when a reference fasta is provided - pattern: "${prefix}_unaligned.tsv" + - meta: + type: file + description: | + Report containing unaligned contigs, only when a reference fasta is provided + pattern: "${prefix}_unaligned.tsv" + - ${prefix}_unaligned.tsv: + type: file + description: | + Report containing unaligned contigs, only when a reference fasta is provided + pattern: "${prefix}_unaligned.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/quilt/quilt/meta.yml b/modules/nf-core/quilt/quilt/meta.yml index e4653983217c..90dbb4caf52e 100644 --- a/modules/nf-core/quilt/quilt/meta.yml +++ b/modules/nf-core/quilt/quilt/meta.yml @@ -1,5 +1,6 @@ name: "quilt_quilt" -description: QUILT is an R and C++ program for rapid genotype imputation from low-coverage sequence using a large reference panel. +description: QUILT is an R and C++ program for rapid genotype imputation from low-coverage + sequence using a large reference panel. keywords: - imputation - low-coverage @@ -8,99 +9,143 @@ keywords: - vcf tools: - "quilt": - description: "Read aware low coverage whole genome sequence imputation from a reference panel" + description: "Read aware low coverage whole genome sequence imputation from a + reference panel" homepage: "https://github.com/rwdavies/quilt" documentation: "https://github.com/rwdavies/quilt" tool_dev_url: "https://github.com/rwdavies/quilt" doi: "10.1038/s41588-021-00877-0" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: (Mandatory) BAM/CRAM files - pattern: "*.{bam,cram,sam}" - - bais: - type: file - description: (Mandatory) BAM/CRAM index files - pattern: "*.{bai}" - - reference_haplotype_file: - type: file - description: (Mandatory) Reference haplotype file in IMPUTE format (file with no header and no rownames, one row per SNP, one column per reference haplotype, space separated, values must be 0 or 1) - pattern: "*.{hap.gz}" - - reference_legend_file: - type: file - description: (Mandatory) Reference haplotype legend file in IMPUTE format (file with one row per SNP, and a header including position for the physical position in 1 based coordinates, a0 for the reference allele, and a1 for the alternate allele). - pattern: "*.{legend.gz}" - - chr: - type: string - description: (Mandatory) What chromosome to run. Should match BAM headers. - - regions_start: - type: integer - description: (Mandatory) When running imputation, where to start from. The 1-based position x is kept if regionStart <= x <= regionEnd. - - regions_end: - type: integer - description: (Mandatory) When running imputation, where to stop. - - buffer: - type: integer - description: Buffer of region to perform imputation over. So imputation is run form regionStart-buffer to regionEnd+buffer, and reported for regionStart to regionEnd, including the bases of regionStart and regionEnd. - - ngen: - type: integer - description: Number of generations since founding or mixing. Note that the algorithm is relatively robust to this. Use nGen = 4 * Ne / K if unsure. - - genetic_map_file: - type: file - description: (Optional) File with genetic map information, a file with 3 white-space delimited entries giving position (1-based), genetic rate map in cM/Mbp, and genetic map in cM. If no file included, rate is based on physical distance and expected rate (expRate). - pattern: "*.{txt.gz}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - posfile: - type: file - description: (Optional) File with positions of where to impute, lining up one-to-one with genfile. File is tab seperated with no header, one row per SNP, with col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), col 3 = reference base, col 4 = alternate base. Bases are capitalized. - pattern: "*.{txt}" - - phasefile: - type: file - description: (Optional) File with truth phasing results. Supersedes genfile if both options given. File has a header row with a name for each sample, matching what is found in the bam file. Each subject is then a tab seperated column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 or 0|1. Note therefore this file has one more row than posfile which has no header. - pattern: "*.{txt}" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: (Optional) File with reference genome. - pattern: "*.{txt.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: (Mandatory) BAM/CRAM files + pattern: "*.{bam,cram,sam}" + - bais: + type: file + description: (Mandatory) BAM/CRAM index files + pattern: "*.{bai}" + - reference_haplotype_file: + type: file + description: (Mandatory) Reference haplotype file in IMPUTE format (file with + no header and no rownames, one row per SNP, one column per reference haplotype, + space separated, values must be 0 or 1) + pattern: "*.{hap.gz}" + - reference_legend_file: + type: file + description: (Mandatory) Reference haplotype legend file in IMPUTE format (file + with one row per SNP, and a header including position for the physical position + in 1 based coordinates, a0 for the reference allele, and a1 for the alternate + allele). + pattern: "*.{legend.gz}" + - chr: + type: string + description: (Mandatory) What chromosome to run. Should match BAM headers. + - regions_start: + type: integer + description: (Mandatory) When running imputation, where to start from. The 1-based + position x is kept if regionStart <= x <= regionEnd. + - regions_end: + type: integer + description: (Mandatory) When running imputation, where to stop. + - ngen: + type: integer + description: Number of generations since founding or mixing. Note that the algorithm + is relatively robust to this. Use nGen = 4 * Ne / K if unsure. + - buffer: + type: integer + description: Buffer of region to perform imputation over. So imputation is run + form regionStart-buffer to regionEnd+buffer, and reported for regionStart + to regionEnd, including the bases of regionStart and regionEnd. + - genetic_map_file: + type: file + description: (Optional) File with genetic map information, a file with 3 white-space + delimited entries giving position (1-based), genetic rate map in cM/Mbp, and + genetic map in cM. If no file included, rate is based on physical distance + and expected rate (expRate). + pattern: "*.{txt.gz}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - posfile: + type: file + description: (Optional) File with positions of where to impute, lining up one-to-one + with genfile. File is tab seperated with no header, one row per SNP, with + col 1 = chromosome, col 2 = physical position (sorted from smallest to largest), + col 3 = reference base, col 4 = alternate base. Bases are capitalized. + pattern: "*.{txt}" + - phasefile: + type: file + description: (Optional) File with truth phasing results. Supersedes genfile + if both options given. File has a header row with a name for each sample, + matching what is found in the bam file. Each subject is then a tab seperated + column, with 0 = ref and 1 = alt, separated by a vertical bar |, e.g. 0|0 + or 0|1. Note therefore this file has one more row than posfile which has no + header. + pattern: "*.{txt}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: (Optional) File with reference genome. + pattern: "*.{txt.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file with both SNP annotation information and per-sample genotype information. - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file with both SNP annotation information and per-sample genotype + information. + pattern: "*.{vcf.gz}" - tbi: - type: file - description: TBI file of the VCF. - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: TBI file of the VCF. + pattern: "*.{vcf.gz.tbi}" - rdata: - type: directory - description: Optional directory path to prepared RData file with reference objects (useful with --save_prepared_reference=TRUE). + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - 'RData", type: "dir': + type: directory + description: Optional directory path to prepared RData file with reference objects + (useful with --save_prepared_reference=TRUE). - plots: - type: directory - description: Optional directory path to save plots. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - 'plots", type: "dir': + type: directory + description: Optional directory path to save plots. + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/racon/meta.yml b/modules/nf-core/racon/meta.yml index 9698c0a8aee6..360a578d4eea 100644 --- a/modules/nf-core/racon/meta.yml +++ b/modules/nf-core/racon/meta.yml @@ -7,44 +7,48 @@ keywords: - polish tools: - racon: - description: Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. + description: Ultrafast consensus module for raw de novo genome assembly of long + uncorrected reads. homepage: https://github.com/lbcb-sci/racon documentation: https://github.com/lbcb-sci/racon tool_dev_url: https://github.com/lbcb-sci/racon doi: 10.1101/gr.214270.116 licence: ["MIT"] + identifier: biotools:Racon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files. Racon expects single end reads - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" - - assembly: - type: file - description: Genome assembly to be improved - pattern: "*.{fasta,fa}" - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files. Racon expects single end reads + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - assembly: + type: file + description: Genome assembly to be improved + pattern: "*.{fasta,fa}" + - paf: + type: file + description: Alignment in PAF format + pattern: "*.paf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - improved_assembly: - type: file - description: Improved genome assembly - pattern: "*_assembly_consensus.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_assembly_consensus.fasta.gz": + type: file + description: Improved genome assembly + pattern: "*_assembly_consensus.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/rapidnj/meta.yml b/modules/nf-core/rapidnj/meta.yml index 0e54b61f1039..84b9a617bdc1 100644 --- a/modules/nf-core/rapidnj/meta.yml +++ b/modules/nf-core/rapidnj/meta.yml @@ -1,35 +1,43 @@ name: rapidnj -description: Produces a Newick format phylogeny from a multiple sequence alignment using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments. +description: Produces a Newick format phylogeny from a multiple sequence alignment + using a Neighbour-Joining algorithm. Capable of bacterial genome size alignments. keywords: - phylogeny - newick - neighbour-joining tools: - rapidnj: - description: RapidNJ is an algorithmic engineered implementation of canonical neighbour-joining. It uses an efficient search heuristic to speed-up the core computations of the neighbour-joining method that enables RapidNJ to outperform other state-of-the-art neighbour-joining implementations. + description: RapidNJ is an algorithmic engineered implementation of canonical + neighbour-joining. It uses an efficient search heuristic to speed-up the core + computations of the neighbour-joining method that enables RapidNJ to outperform + other state-of-the-art neighbour-joining implementations. homepage: https://birc.au.dk/software/rapidnj documentation: https://birc.au.dk/software/rapidnj tool_dev_url: https://github.com/somme89/rapidNJ doi: "10.1007/978-3-540-87361-7_10" licence: ["GPL v2"] + identifier: biotools:rapidnj input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{tre}" - stockholm_alignment: - type: file - description: An alignment in Stockholm format - pattern: "*.{sth}" + - "*.sth": + type: file + description: An alignment in Stockholm format + pattern: "*.{sth}" + - phylogeny: + - "*.tre": + type: file + description: A phylogeny in Newick format + pattern: "*.{tre}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aunderwo" - "@avantonder" diff --git a/modules/nf-core/rasusa/meta.yml b/modules/nf-core/rasusa/meta.yml index 8d80563af6ba..abda9a394a8a 100644 --- a/modules/nf-core/rasusa/meta.yml +++ b/modules/nf-core/rasusa/meta.yml @@ -12,35 +12,38 @@ tools: tool_dev_url: https://github.com/mbhall88/rasusa doi: "10.5281/zenodo.3731394" licence: ["MIT"] + identifier: biotools:rasusa input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files - - genome_size: - type: string - description: Genome size of the species - - depth_cutoff: - type: integer - description: Depth of coverage cutoff + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files + - genome_size: + type: string + description: Genome size of the species + - - depth_cutoff: + type: integer + description: Depth of coverage cutoff output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Reads with subsampled coverage - pattern: "*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Reads with subsampled coverage + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@thanhleviet" maintainers: diff --git a/modules/nf-core/raven/meta.yml b/modules/nf-core/raven/meta.yml index cd962ec3caa3..a017c4f24428 100644 --- a/modules/nf-core/raven/meta.yml +++ b/modules/nf-core/raven/meta.yml @@ -14,34 +14,43 @@ tools: tool_dev_url: https://github.com/lbcb-sci/raven doi: 10.1038/s43588-021-00073-4 licence: ["MIT"] + identifier: biotools:raven input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', suffix:'bacteria' ] - - reads: - type: file - description: Input file in FASTA/FASTQ format. - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - reads: + type: file + description: Input file in FASTA/FASTQ format. + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fa,fq,fa.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', suffix:'bacteria' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Assembled FASTA file - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - "*.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "*.fasta.gz" - gfa: - type: file - description: Repeat graph - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', suffix:'bacteria' ] + - "*.gfa.gz": + type: file + description: Repeat graph + pattern: "*.gfa.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" maintainers: diff --git a/modules/nf-core/raxmlng/meta.yml b/modules/nf-core/raxmlng/meta.yml index f70bfa62e30d..9472081ce587 100644 --- a/modules/nf-core/raxmlng/meta.yml +++ b/modules/nf-core/raxmlng/meta.yml @@ -1,35 +1,41 @@ name: raxmlng -description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. +description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood + (ML) optimality criterion. keywords: - phylogeny - newick - maximum likelihood tools: - raxmlng: - description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. + description: RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood + (ML) optimality criterion. homepage: https://github.com/amkozlov/raxml-ng documentation: https://github.com/amkozlov/raxml-ng/wiki tool_dev_url: https://github.com/amkozlov/raxml-ng doi: 10.1093/bioinformatics/btz305 licence: ["GPL v2-or-later"] + identifier: "" input: - - alignment: - type: file - description: A FASTA format multiple sequence alignment file - pattern: "*.{fasta,fas,fa,mfa}" + - - alignment: + type: file + description: A FASTA format multiple sequence alignment file + pattern: "*.{fasta,fas,fa,mfa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - phylogeny: - type: file - description: A phylogeny in Newick format - pattern: "*.{raxml.bestTree}" + - "*.raxml.bestTree": + type: file + description: A phylogeny in Newick format + pattern: "*.{raxml.bestTree}" - phylogeny_bootstrapped: - type: file - description: A phylogeny in Newick format with bootstrap values - pattern: "*.{raxml.support}" + - "*.raxml.support": + type: file + description: A phylogeny in Newick format with bootstrap values + pattern: "*.{raxml.support}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@avantonder" - "@aunderwo" diff --git a/modules/nf-core/repeatmodeler/builddatabase/meta.yml b/modules/nf-core/repeatmodeler/builddatabase/meta.yml index d3aa9310fb53..cc78cf0f1b44 100644 --- a/modules/nf-core/repeatmodeler/builddatabase/meta.yml +++ b/modules/nf-core/repeatmodeler/builddatabase/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "repeatmodeler_builddatabase" description: Create a database for RepeatModeler @@ -8,36 +7,40 @@ keywords: - repeat tools: - "repeatmodeler": - description: "RepeatModeler is a de-novo repeat family identification and modeling package." + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." homepage: "https://github.com/Dfam-consortium/RepeatModeler" documentation: "https://github.com/Dfam-consortium/RepeatModeler" tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: Fasta file - pattern: "*.{fasta,fsa,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: Fasta file + pattern: "*.{fasta,fsa,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - db: - type: file - description: Database files for repeatmodeler - pattern: "`${prefix}.*`" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Database files for repeatmodeler + pattern: "`${prefix}.*`" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml index 29bb795bf35c..6693ae9a1922 100644 --- a/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml +++ b/modules/nf-core/repeatmodeler/repeatmodeler/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "repeatmodeler_repeatmodeler" -description: Performs de novo transposable element (TE) family identification with RepeatModeler +description: Performs de novo transposable element (TE) family identification with + RepeatModeler keywords: - genomics - fasta @@ -9,43 +9,59 @@ keywords: - transposable element tools: - "repeatmodeler": - description: "RepeatModeler is a de-novo repeat family identification and modeling package." + description: "RepeatModeler is a de-novo repeat family identification and modeling + package." homepage: "https://github.com/Dfam-consortium/RepeatModeler" documentation: "https://github.com/Dfam-consortium/RepeatModeler" tool_dev_url: "https://github.com/Dfam-consortium/RepeatModeler" licence: ["Open Software License v2.1"] + identifier: biotools:repeatmodeler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - db: - type: file - description: RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - db: + type: file + description: RepeatModeler database files generated with REPEATMODELER_BUILDDATABASE + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fasta: - type: file - description: Consensus repeat sequences - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.fa": + type: file + description: Consensus repeat sequences + pattern: "*.fa" - stk: - type: file - description: Seed alignments - pattern: "*.stk" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stk": + type: file + description: Seed alignments + pattern: "*.stk" - log: - type: file - description: A summarized log of the run - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: A summarized log of the run + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/resfinder/run/meta.yml b/modules/nf-core/resfinder/run/meta.yml index aa9ad76b8643..7e81dc152744 100644 --- a/modules/nf-core/resfinder/run/meta.yml +++ b/modules/nf-core/resfinder/run/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "resfinder_run" -description: ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria +description: ResFinder identifies acquired antimicrobial resistance genes in total + or partial sequenced isolates of bacteria keywords: - blastn - kma @@ -10,125 +10,195 @@ keywords: - resistance genes tools: - "resfinder": - description: "ResFinder identifies acquired antimicrobial resistance genes in total or partial sequenced isolates of bacteria" + description: "ResFinder identifies acquired antimicrobial resistance genes in + total or partial sequenced isolates of bacteria" homepage: "https://bitbucket.org/genomicepidemiology/resfinder.git/src" documentation: "https://bitbucket.org/genomicepidemiology/resfinder/src/master/README.md" tool_dev_url: "https://bitbucket.org/genomicepidemiology/resfinder.git/src" doi: "10.1099/mgen.0.000748" licence: ["APACHE-2.0"] + identifier: biotools:resfinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - fastq: - type: file - description: fastq file(s) - pattern: "*.{fastq,fq}{.gz}" - - - fasta: - type: file - description: fasta file - pattern: "*.{fa,fna}" - - - db_point: - type: directory - description: database directory containing known point mutations - - - db_res: - type: directory - description: database directory containing known resistance genes - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: fastq file(s) + pattern: "*.{fastq,fq}{.gz}" + - fasta: + type: file + description: fasta file + pattern: "*.{fa,fna}" + - - db_point: + type: directory + description: database directory containing known point mutations + - - db_res: + type: directory + description: database directory containing known resistance genes output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - json: - type: file - description: CGE standardized json file - pattern: "*.json" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: CGE standardized json file + pattern: "*.json" - disinfinder_kma: - type: directory - description: directory holding kma results - pattern: "disinfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - disinfinder_kma: + type: directory + description: directory holding kma results + pattern: "disinfinder_kma" - pheno_table_species: - type: file - description: table with species specific AMR phenotypes - pattern: "pheno_table_species.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pheno_table_species.txt: + type: file + description: table with species specific AMR phenotypes + pattern: "pheno_table_species.tsv" - pheno_table: - type: file - description: table with all AMR phenotypes - pattern: "pheno_table.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pheno_table.txt: + type: file + description: table with all AMR phenotypes + pattern: "pheno_table.tsv" - pointfinder_kma: - type: directory - description: directory holding kma results - pattern: "pointfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - pointfinder_kma: + type: directory + description: directory holding kma results + pattern: "pointfinder_kma" - pointfinder_prediction: - type: file - description: tab separated table; 1 is given to a predicted resistance against an antibiotic class, 0 is given to not resistance detected - pattern: "PointFinder_prediction.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_prediction.txt: + type: file + description: tab separated table; 1 is given to a predicted resistance against + an antibiotic class, 0 is given to not resistance detected + pattern: "PointFinder_prediction.txt" - pointfinder_results: - type: file - description: tab separated table with predicted point mutations leading to antibiotic resistance - pattern: "PointFinder_results.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_results.txt: + type: file + description: tab separated table with predicted point mutations leading to antibiotic + resistance + pattern: "PointFinder_results.txt" - pointfinder_table: - type: file - description: predicted point mutations grouped into genes to which they belong - pattern: "PointFinder_table.txt" - - - resfinder_blast: - type: directory - description: directory holding blast results - pattern: "resfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - PointFinder_table.txt: + type: file + description: predicted point mutations grouped into genes to which they belong + pattern: "PointFinder_table.txt" - resfinder_hit_in_genome_seq: - type: file - description: fasta sequence of resistance gene hits found in the input data (query) - pattern: "ResFinder_Hit_in_genome_seq.fsa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_Hit_in_genome_seq.fsa: + type: file + description: fasta sequence of resistance gene hits found in the input data + (query) + pattern: "ResFinder_Hit_in_genome_seq.fsa" + - resfinder_blast: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - resfinder_blast: + type: directory + description: directory holding blast results + pattern: "resfinder_kma" - resfinder_kma: - type: directory - description: directory holding kma results - pattern: "resfinder_kma" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - resfinder_kma: + type: directory + description: directory holding kma results + pattern: "resfinder_kma" - resfinder_resistance_gene_seq: - type: file - description: fasta sequence of resistance gene hits found in the database (reference) - pattern: "ResFinder_Resistance_gene_seq.fsa" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_Resistance_gene_seq.fsa: + type: file + description: fasta sequence of resistance gene hits found in the database (reference) + pattern: "ResFinder_Resistance_gene_seq.fsa" - resfinder_results_table: - type: file - description: predicted resistance genes grouped by antibiotic class - pattern: "ResFinder_results_table.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results_table.txt: + type: file + description: predicted resistance genes grouped by antibiotic class + pattern: "ResFinder_results_table.txt" - resfinder_results_tab: - type: file - description: tab separated table with predicted resistance genes - pattern: "ResFinder_results_tab.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results_tab.txt: + type: file + description: tab separated table with predicted resistance genes + pattern: "ResFinder_results_tab.txt" - resfinder_results: - type: file - description: predicted resistance genes grouped by antibiotic class and hit alignments to reference resistance genes - pattern: "ResFinder_results.txt" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ResFinder_results.txt: + type: file + description: predicted resistance genes grouped by antibiotic class and hit + alignments to reference resistance genes + pattern: "ResFinder_results.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@marrip" maintainers: diff --git a/modules/nf-core/rgi/cardannotation/meta.yml b/modules/nf-core/rgi/cardannotation/meta.yml index 97e6911da6a6..8aff020f9528 100644 --- a/modules/nf-core/rgi/cardannotation/meta.yml +++ b/modules/nf-core/rgi/cardannotation/meta.yml @@ -1,37 +1,46 @@ name: rgi_cardannotation -description: Preprocess the CARD database for RGI to predict antibiotic resistance from protein or nucleotide data +description: Preprocess the CARD database for RGI to predict antibiotic resistance + from protein or nucleotide data keywords: - bacteria - fasta - antibiotic resistance tools: - rgi: - description: This module preprocesses the downloaded Comprehensive Antibiotic Resistance Database (CARD) which can then be used as input for RGI. + description: This module preprocesses the downloaded Comprehensive Antibiotic + Resistance Database (CARD) which can then be used as input for RGI. homepage: https://card.mcmaster.ca documentation: https://github.com/arpcard/rgi tool_dev_url: https://github.com/arpcard/rgi doi: "10.1093/nar/gkz935" licence: ["https://card.mcmaster.ca/about"] + identifier: "" input: - - card: - type: directory - description: Directory containing the CARD database - pattern: "*/" + - - card: + type: directory + description: Directory containing the CARD database + pattern: "*/" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: directory - description: Directory containing the processed CARD database files - pattern: "*/" + - card_database_processed: + type: directory + description: Directory containing the processed CARD database files + pattern: "*/" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rgi/main/meta.yml b/modules/nf-core/rgi/main/meta.yml index 7e444c8bbfec..9d9836c0d655 100644 --- a/modules/nf-core/rgi/main/meta.yml +++ b/modules/nf-core/rgi/main/meta.yml @@ -6,59 +6,86 @@ keywords: - antibiotic resistance tools: - rgi: - description: This tool provides a preliminary annotation of your DNA sequence(s) based upon the data available in The Comprehensive Antibiotic Resistance Database (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will be highlighted. As CARD expands to include more pathogens, genomes, plasmids, and ontology terms this tool will grow increasingly powerful in providing first-pass detection of antibiotic resistance associated genes. See license at CARD website + description: This tool provides a preliminary annotation of your DNA sequence(s) + based upon the data available in The Comprehensive Antibiotic Resistance Database + (CARD). Hits to genes tagged with Antibiotic Resistance ontology terms will + be highlighted. As CARD expands to include more pathogens, genomes, plasmids, + and ontology terms this tool will grow increasingly powerful in providing first-pass + detection of antibiotic resistance associated genes. See license at CARD website homepage: https://card.mcmaster.ca documentation: https://github.com/arpcard/rgi tool_dev_url: https://github.com/arpcard/rgi doi: "10.1093/nar/gkz935" licence: ["https://card.mcmaster.ca/about"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" - - card: - type: directory - description: Directory containing the CARD database. This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). - pattern: "*/" - - wildcard: - type: directory - description: Directory containing the WildCARD database (optional). This is expected to be the unarchived but otherwise unaltered download folder (see RGI documentation for download instructions). - pattern: "*/" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - card: + type: directory + description: Directory containing the CARD database. This is expected to be + the unarchived but otherwise unaltered download folder (see RGI documentation + for download instructions). + pattern: "*/" + - - wildcard: + type: directory + description: Directory containing the WildCARD database (optional). This is + expected to be the unarchived but otherwise unaltered download folder (see + RGI documentation for download instructions). + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted file with RGI results - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted file with RGI results + pattern: "*.{json}" - tsv: - type: file - description: Tab-delimited file with RGI results - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tab-delimited file with RGI results + pattern: "*.{txt}" - tmp: - type: directory - description: Directory containing various intermediate files - pattern: "temp/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - temp/: + type: directory + description: Directory containing various intermediate files + pattern: "temp/" - tool_version: - type: string - description: The version of the tool in string format (useful for downstream tools such as hAMRronization) + - RGI_VERSION: + type: string + description: The version of the tool in string format (useful for downstream + tools such as hAMRronization) - db_version: - type: string - description: The version of the used database in string format (useful for downstream tools such as hAMRronization) + - DB_VERSION: + type: string + description: The version of the used database in string format (useful for downstream + tools such as hAMRronization) + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" - "@jfy133" diff --git a/modules/nf-core/rhocall/annotate/meta.yml b/modules/nf-core/rhocall/annotate/meta.yml index 09a64d2591ff..fb041cae88ae 100644 --- a/modules/nf-core/rhocall/annotate/meta.yml +++ b/modules/nf-core/rhocall/annotate/meta.yml @@ -11,47 +11,50 @@ tools: documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: vcf file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: vcf index file - pattern: "*.{tbi}" - - roh: - type: file - description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL - pattern: "*.{roh}" - - bed: - type: file - description: BED file with AZ windows. - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: vcf file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: vcf index file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - roh: + type: file + description: Bcftools roh style TSV file with CHR,POS,AZ,QUAL + pattern: "*.{roh}" + - - bed: + type: file + description: BED file with AZ windows. + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: vcf file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_rhocall.vcf": + type: file + description: vcf file + pattern: "*.{vcf,vcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/rhocall/viz/meta.yml b/modules/nf-core/rhocall/viz/meta.yml index bbcad9ba9705..7efcab02a9b7 100644 --- a/modules/nf-core/rhocall/viz/meta.yml +++ b/modules/nf-core/rhocall/viz/meta.yml @@ -11,41 +11,53 @@ tools: documentation: "https://github.com/dnil/rhocall" tool_dev_url: "https://github.com/dnil" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - roh: - type: file - description: Input RHO file produced from rhocall - pattern: "*.{roh}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - roh: + type: file + description: Input RHO file produced from rhocall + pattern: "*.{roh}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: Bed file containing roh calls - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/${prefix}.bed: + type: file + description: Bed file containing roh calls + pattern: "*.{bed}" - wig: - type: file - description: Wig file containing roh calls - pattern: "*.{wig}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/${prefix}.wig: + type: file + description: Wig file containing roh calls + pattern: "*.{wig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/ribotish/predict/meta.yml b/modules/nf-core/ribotish/predict/meta.yml index f1a84467741d..e8016a2c9d86 100644 --- a/modules/nf-core/ribotish/predict/meta.yml +++ b/modules/nf-core/ribotish/predict/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotish_predict" description: Quality control of riboseq bam data @@ -8,113 +7,127 @@ keywords: - bam tools: - "ribotish": - description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data." + description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using + ribosome profiling data." homepage: "https://github.com/zhpn1024/ribotish" documentation: "https://github.com/zhpn1024/ribotish" tool_dev_url: "https://github.com/zhpn1024/ribotish" doi: "10.1038/s41467-017-01981-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false ] - - bam_ribo: - type: file - description: Sorted riboseq BAM file(s) - pattern: "*.{bam}" - - bai_ribo: - type: file - description: Index for sorted riboseq bam file(s) - pattern: "*.{bai}" - - meta2: - type: map - description: | - Groovy Map containing TI-Seq sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam_ti: - type: file - description: Sorted TI-Seq BAM file(s) - pattern: "*.{bam}" - - bai_ti: - type: file - description: Index for sorted TI-Seq BAM file(s) - pattern: "*.{bai}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - fasta: - type: file - description: | - Fasta-format sequence file for reference sequences used in the bam file - pattern: "*.gtf" - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - - meta4: - type: map - description: | - Groovy Map containing information on candidate ORFs - - candidate_orfs: - type: file - description: | - 3-column (transIDstarttstop) candidate ORFs file - pattern: "*.txt" - - meta5: - type: map - description: | - Groovy Map containing information on riboseq P-site offfset parameter - files - - para_ribo: - type: file - description: | - Input P-site offset parameter files for riboseq bam files - pattern: "*.py" - - meta6: - type: map - description: | - Groovy Map containing information on TI-seq P-site offfset parameter - files - - para_ribo: - type: file - description: | - Input P-site offset parameter files for TI-seq bam files - pattern: "*.py" - + - - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - bam_ribo: + type: file + description: Sorted riboseq BAM file(s) + pattern: "*.{bam}" + - bai_ribo: + type: file + description: Index for sorted riboseq bam file(s) + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing TI-Seq sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam_ti: + type: file + description: Sorted TI-Seq BAM file(s) + pattern: "*.{bam}" + - bai_ti: + type: file + description: Index for sorted TI-Seq BAM file(s) + pattern: "*.{bai}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: | + Fasta-format sequence file for reference sequences used in the bam file + pattern: "*.gtf" + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" + - - meta4: + type: map + description: | + Groovy Map containing information on candidate ORFs + - candidate_orfs: + type: file + description: | + 3-column (transIDstarttstop) candidate ORFs file + pattern: "*.txt" + - - meta5: + type: map + description: | + Groovy Map containing information on riboseq P-site offfset parameter + files + - para_ribo: + type: file + description: | + Input P-site offset parameter files for riboseq bam files + pattern: "*.py" + - - meta6: + type: map + description: | + Groovy Map containing information on TI-seq P-site offfset parameter + files + - para_ti: + type: file + description: | + Input P-site offset parameter files for TI-seq bam files + pattern: "*.py" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - predictions: - type: file - description: | - txt file all possible ORF results that fit the thresholds - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_pred.txt": + type: file + description: | + txt file all possible ORF results that fit the thresholds + pattern: "*.{txt}" - all: - type: file - description: | - txt file similar to the predictions but do not use FDR (q-value) cutoff - pattern: "*.{txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_all.txt": + type: file + description: | + txt file similar to the predictions but do not use FDR (q-value) cutoff + pattern: "*.{txt}" - transprofile: - type: file - description: | - Output RPF P-site profile for each transcript. The profile data is in - python dict format, recording non-zero read counts at different - positions on transcript. - pattern: "*.{py}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_transprofile.py": + type: file + description: | + Output RPF P-site profile for each transcript. The profile data is in + python dict format, recording non-zero read counts at different + positions on transcript. + pattern: "*.{py}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotish/quality/meta.yml b/modules/nf-core/ribotish/quality/meta.yml index 29cf468787c6..99bec9d3f795 100644 --- a/modules/nf-core/ribotish/quality/meta.yml +++ b/modules/nf-core/ribotish/quality/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotish_quality" description: Quality control of riboseq bam data @@ -8,67 +7,79 @@ keywords: - bam tools: - "ribotish": - description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using ribosome profiling data." + description: "Ribo TIS Hunter (Ribo-TISH) identifies translation activities using + ribosome profiling data." homepage: "https://github.com/zhpn1024/ribotish" documentation: "https://github.com/zhpn1024/ribotish" tool_dev_url: "https://github.com/zhpn1024/ribotish" doi: "10.1038/s41467-017-01981-8" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for sorted BAM/CRAM/SAM file - pattern: "*.{bai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for sorted BAM/CRAM/SAM file + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - txt: - type: file - description: | - txt file recording all distribution data in python format for each - group of reads - pattern: "*.{txt}" + - distribution: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.txt": + type: file + description: file containing distribution + pattern: "*.{txt}" - pdf: - type: file - description: | - Pdf figure file is plot of all the distributions and illustration of - quality and P-site offset - pattern: "*.{pdf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pdf": + type: file + description: | + Pdf figure file is plot of all the distributions and illustration of + quality and P-site offset + pattern: "*.{pdf}" - offset: - type: file - description: | - This file saves P-site offsets for different reads lengths in python - code dict format, and can be used in further analysis - pattern: "*.{para.py}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.para.py": + type: file + description: | + This file saves P-site offsets for different reads lengths in python + code dict format, and can be used in further analysis + pattern: "*.{para.py}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotricer/detectorfs/meta.yml b/modules/nf-core/ribotricer/detectorfs/meta.yml index 430f232d0011..6daab6c84eb8 100644 --- a/modules/nf-core/ribotricer/detectorfs/meta.yml +++ b/modules/nf-core/ribotricer/detectorfs/meta.yml @@ -13,86 +13,142 @@ tools: tool_dev_url: "https://github.com/smithlabcode/ribotricer" doi: "10.1093/bioinformatics/btz878" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:ribotricer input: - - meta: - type: map - description: | - Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false, strandedness: 'single' ] - - bam_ribo: - type: file - description: Sorted riboseq BAM file(s) - pattern: "*.{bam}" - - bai_ribo: - type: file - description: Index for sorted riboseq bam file(s) - pattern: "*.{bai}" - - meta2: - type: map - description: | - Map containing reference information for the candidate ORFs - e.g. `[ id:'Ensembl human v.111' ]` - - candidate_orfs: - type: file - description: "TSV file with candidate ORFs from 'ribotricer prepareorfs'" - pattern: "*.tsv" - + - - meta: + type: map + description: | + Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false, strandedness: 'single' ] + - bam: + type: file + description: "BAM/CRAM/SAM file" + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: "Index for sorted BAM/CRAM/SAM file" + pattern: "*.{bai}" + - - meta2: + type: map + description: | + Map containing reference information for the candidate ORFs + e.g. `[ id:'Ensembl human v.111' ]` + - candidate_orfs: + type: file + description: "TSV file with candidate ORFs from 'ribotricer prepareorfs'" + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing riboseq sample information - e.g. `[ id:'sample1', single_end:false ] - protocol: - type: file - description: "txt file containing inferred protocol if it was inferred (not supplied as input)" - pattern: "*_protocol.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_protocol.txt": + type: file + description: "txt file containing inferred protocol if it was inferred (not + supplied as input)" + pattern: "*_protocol.txt" - bam_summary: - type: file - description: "Text summary of reads found in the BAM" - pattern: "*_bam_summary.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_bam_summary.txt": + type: file + description: "Text summary of reads found in the BAM" + pattern: "*_bam_summary.txt" - read_length_dist: - type: file - description: "PDF-format read length distribution as quality control" - pattern: "*_read_length_dist.pdf" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_read_length_dist.pdf": + type: file + description: "PDF-format read length distribution as quality control" + pattern: "*_read_length_dist.pdf" - metagene_profile_5p: - type: file - description: "Metagene profile aligning with the start codon" - pattern: "*_metagene_profiles_5p.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_profiles_5p.tsv": + type: file + description: "Metagene profile aligning with the start codon" + pattern: "*_metagene_profiles_5p.tsv" - metagene_profile_3p: - type: file - description: "Metagene profile aligning with the stop codon" - pattern: "*_metagene_profiles_3p.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_profiles_3p.tsv": + type: file + description: "Metagene profile aligning with the stop codon" + pattern: "*_metagene_profiles_3p.tsv" - metagene_plots: - type: file - description: "Metagene plots for quality control" - pattern: "*_metagene_plots.pdf" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_metagene_plots.pdf": + type: file + description: "Metagene plots for quality control" + pattern: "*_metagene_plots.pdf" - psite_offsets: - type: file - description: | - "If the P-site offsets are not provided, txt file containing the - derived relative offsets" - pattern: "*_psite_offsets.txt" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_psite_offsets.txt": + type: file + description: | + "If the P-site offsets are not provided, txt file containing the + derived relative offsets" + pattern: "*_psite_offsets.txt" - pos_wig: - type: file - description: "Positive strand WIG file for visualization in Genome Browser" - pattern: "*_pos.wig" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_pos.wig": + type: file + description: "Positive strand WIG file for visualization in Genome Browser" + pattern: "*_pos.wig" - neg_wig: - type: file - description: "Negative strand WIG file for visualization in Genome Browser" - pattern: "*_neg.wig" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_neg.wig": + type: file + description: "Negative strand WIG file for visualization in Genome Browser" + pattern: "*_neg.wig" - orfs: - type: file - description: | - "TSV with ORFs assessed as translating in this BAM file. You can output - all ORFs regardless of the translation status with option --report_all" - pattern: "*_translating_ORFs.tsv" + - meta: + type: map + description: | + Groovy Map containing riboseq sample information + e.g. `[ id:'sample1', single_end:false ] + - "*_translating_ORFs.tsv": + type: file + description: | + "TSV with ORFs assessed as translating in this BAM file. You can output + all ORFs regardless of the translation status with option --report_all" + pattern: "*_translating_ORFs.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribotricer/prepareorfs/meta.yml b/modules/nf-core/ribotricer/prepareorfs/meta.yml index 005edd577207..6b92b7dff19f 100644 --- a/modules/nf-core/ribotricer/prepareorfs/meta.yml +++ b/modules/nf-core/ribotricer/prepareorfs/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribotricer_prepareorfs" description: "Accurate detection of short and long active ORFs using Ribo-seq data" @@ -14,39 +13,40 @@ tools: tool_dev_url: "https://github.com/smithlabcode/ribotricer" doi: "10.1093/bioinformatics/btz878" licence: ["GNU General Public v3 (GPL v3)"] + identifier: biotools:ribotricer input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - - fasta: - type: file - description: | - Fasta-format sequence file for reference sequences used in the bam file - pattern: "*.gtf" - - gtf: - type: file - description: | - GTF-format annotation file for reference sequences used in the bam file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: | + Fasta-format sequence file for reference sequences used in the bam file + pattern: "*.gtf" + - gtf: + type: file + description: | + GTF-format annotation file for reference sequences used in the bam file + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'Ensembl human v.111' ]` - candidate_orfs: - type: file - description: "TSV file with candidate ORFs" - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'Ensembl human v.111' ]` + - "*_candidate_orfs.tsv": + type: file + description: "TSV file with candidate ORFs" + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ribowaltz/meta.yml b/modules/nf-core/ribowaltz/meta.yml index 334615984cf8..39f4d836a022 100644 --- a/modules/nf-core/ribowaltz/meta.yml +++ b/modules/nf-core/ribowaltz/meta.yml @@ -1,96 +1,153 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "ribowaltz" -description: Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data +description: Calculation of optimal P-site offsets, diagnostic analysis and visual + inspection of ribosome profiling data keywords: - sort - example - genomics tools: - "ribowaltz": - description: "Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data." + description: "Calculation of optimal P-site offsets, diagnostic analysis and visual + inspection of ribosome profiling data." homepage: "https://github.com/LabTranslationalArchitectomics/riboWaltz" documentation: "https://github.com/LabTranslationalArchitectomics/riboWaltz" tool_dev_url: "https://github.com/LabTranslationalArchitectomics/riboWaltz" doi: "10.1371/journal.pcbi.1006169" licence: ["MIT"] + identifier: biotools:ribowaltz input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - meta2: - type: map - description: | - Map containing reference information for the reference genome GTF file - e.g. `[ id:'Ensembl human v.111' ]` - - meta3: - type: map - description: | - Map containing reference information for the reference genome FASTA file - e.g. `[ id:'Ensembl human v.111' ]` - - bam: - type: file - description: Transcriptome BAM file - pattern: "*.{bam}" - - gtf: - type: file - description: GTF file of reference genome - pattern: "*.{gtf.gz,gtf}" - - fasta: - type: file - description: FASTA file of reference genome - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Transcriptome BAM file + pattern: "*.{bam}" + - - meta2: + type: map + description: | + Map containing reference information for the reference genome GTF file + e.g. `[ id:'Ensembl human v.111' ]` + - gtf: + type: file + description: GTF file of reference genome + pattern: "*.{gtf.gz,gtf}" + - - meta3: + type: map + description: | + Map containing reference information for the reference genome FASTA file + e.g. `[ id:'Ensembl human v.111' ]` + - fasta: + type: file + description: FASTA file of reference genome + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - best_offset: - type: file - description: Text file with the extremity used for the offset correction step and the best offset for each sample (optional, in case no offsets could be determined, usually because no reads pass filtering criteria) - pattern: "*.best_offset.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.best_offset.txt": + type: file + description: Text file with the extremity used for the offset correction step + and the best offset for each sample (optional, in case no offsets could be + determined, usually because no reads pass filtering criteria) + pattern: "*.best_offset.txt" - offset: - type: file - description: TSV file containing P-site offsets for each read length (optional, in case no offsets could be determined, usually because no reads pass filtering criteria) - pattern: "*.psite_offset.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psite_offset.tsv{,.gz}": + type: file + description: TSV file containing P-site offsets for each read length (optional, + in case no offsets could be determined, usually because no reads pass filtering + criteria) + pattern: "*.psite_offset.tsv.gz" - offset_plot: - type: file - description: P-site offset plots for each read length (otional) - pattern: "offset_plot/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - offset_plot/*: + type: file + description: P-site offset plots for each read length (otional) + pattern: "offset_plot/*" - psites: - type: file - description: TSV file containing P-site transcriptomic coordinates and information for each alignment (optional) - pattern: "*.psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.psite.tsv{,.gz}": + type: file + description: TSV file containing P-site transcriptomic coordinates and information + for each alignment (optional) + pattern: "*.psite.tsv.gz" - codon_coverage_rpf: - type: file - description: TSV file with codon-level RPF coverage for each transcript (optional) - pattern: "*.codon_coverage_rpf.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.codon_coverage_rpf.tsv{,.gz}": + type: file + description: TSV file with codon-level RPF coverage for each transcript (optional) + pattern: "*.codon_coverage_rpf.tsv.gz" - codon_coverage_psite: - type: file - description: TSV file with codon-level P-site coverage for each transcript (optional) - pattern: "*.codon_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.codon_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with codon-level P-site coverage for each transcript (optional) + pattern: "*.codon_coverage_psite.tsv.gz" - cds_coverage: - type: file - description: TSV file with CDS P-site in-frame counts for each transcript (optional) - pattern: "*.cds_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.cds_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with CDS P-site in-frame counts for each transcript (optional) + pattern: "*.cds_coverage_psite.tsv.gz" - cds_window_coverage: - type: file - description: TSV file with CDS P-site in-frame counts for each transcript, excluding P-sites within defined distances to start and stop codons (defined by passing --exclude_start and --exclude_stop with the number of nucleotides) (optional) - pattern: "*nt_coverage_psite.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*nt_coverage_psite.tsv{,.gz}": + type: file + description: TSV file with CDS P-site in-frame counts for each transcript, excluding + P-sites within defined distances to start and stop codons (defined by passing + --exclude_start and --exclude_stop with the number of nucleotides) (optional) + pattern: "*nt_coverage_psite.tsv.gz" - ribowaltz_qc: - type: file - description: riboWaltz diagnostic plots (optional) - pattern: "ribowaltz_qc/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ribowaltz_qc/*.pdf: + type: file + description: riboWaltz diagnostic plots (optional) + pattern: "ribowaltz_qc/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@iraiosub" maintainers: diff --git a/modules/nf-core/rmarkdownnotebook/meta.yml b/modules/nf-core/rmarkdownnotebook/meta.yml index 379690f7528a..eeb0eb362c06 100644 --- a/modules/nf-core/rmarkdownnotebook/meta.yml +++ b/modules/nf-core/rmarkdownnotebook/meta.yml @@ -11,6 +11,7 @@ tools: documentation: https://rmarkdown.rstudio.com/lesson-1.html tool_dev_url: https://github.com/rstudio/rmarkdown licence: ["GPL-3"] + identifier: "" params: - parametrize: type: boolean @@ -28,42 +29,70 @@ params: If true, include a parameter `meta` which contains the information specified via the `meta` input channel. input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - notebook: - type: file - description: Rmarkdown file - pattern: "*.{Rmd}" - - parameters: - type: map - description: | - Groovy map with notebook parameters which will be passed to - rmarkdown to generate parametrized reports. - - input_files: - type: file - description: One or multiple files serving as input data for the notebook. - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - notebook: + type: file + description: Rmarkdown file + pattern: "*.{Rmd}" + - - parameters: + type: map + description: | + Groovy map with notebook parameters which will be passed to + rmarkdown to generate parametrized reports. + - - input_files: + type: file + description: One or multiple files serving as input data for the notebook. + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report: - type: file - description: HTML report generated from Rmarkdown - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: HTML report generated from Rmarkdown + pattern: "*.html" + - parameterised_notebook: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.parameterised.Rmd": + type: file + description: Parameterised Rmarkdown file + pattern: "*.parameterised.Rmd" + - artifacts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - artifacts/*: + type: file + description: Artifacts generated by the notebook + pattern: "artifacts/*" - session_info: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - session_info.log: + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/roary/meta.yml b/modules/nf-core/roary/meta.yml index b6c4d124141b..ece578df262d 100644 --- a/modules/nf-core/roary/meta.yml +++ b/modules/nf-core/roary/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: https://github.com/sanger-pathogens/Roary/ doi: "10.1093/bioinformatics/btv421" licence: ["GPL v3"] + identifier: biotools:roary input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff: - type: file - description: A set of GFF3 formatted files - pattern: "*.{gff}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff: + type: file + description: A set of GFF3 formatted files + pattern: "*.{gff}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results: - type: directory - description: Directory containing Roary result files - pattern: "*/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*: + type: directory + description: Directory containing Roary result files + pattern: "*/*" - aln: - type: file - description: Core-genome alignment produced by Roary (Optional) - pattern: "*.{aln}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.aln: + type: file + description: Core-genome alignment produced by Roary (Optional) + pattern: "*.{aln}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/rrnatranscripts/meta.yml b/modules/nf-core/rrnatranscripts/meta.yml index 145506011b2a..93f6a10ef4a6 100644 --- a/modules/nf-core/rrnatranscripts/meta.yml +++ b/modules/nf-core/rrnatranscripts/meta.yml @@ -10,21 +10,24 @@ tools: Extraction of ribosomal RNA homepage: https://github.com/nf-core/rnafusion licence: ["GPL-3.0-or-later"] + identifier: "" input: - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" + - - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" output: # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rrna_gtf: - type: file - description: GTF file with ribosomal RNA only - pattern: "*.{gtf}" + - "*rrna_intervals.gtf": + type: file + description: GTF file with ribosomal RNA only + pattern: "*.{gtf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rannick" maintainers: diff --git a/modules/nf-core/rsem/calculateexpression/meta.yml b/modules/nf-core/rsem/calculateexpression/meta.yml index e6d580e9b357..0a7fbe1b3cf3 100644 --- a/modules/nf-core/rsem/calculateexpression/meta.yml +++ b/modules/nf-core/rsem/calculateexpression/meta.yml @@ -12,53 +12,97 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input reads for quantification - pattern: "*.fastq.gz" - - index: - type: file - description: RSEM index - pattern: "rsem/*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input reads for quantification + pattern: "*.fastq.gz" + - - index: + type: file + description: RSEM index + pattern: "rsem/*" output: - counts_gene: - type: file - description: Expression counts on gene level - pattern: "*.genes.results" - - counts_transctips: - type: file - description: Expression counts on transcript level - pattern: "*.isoforms.results" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.genes.results": + type: file + description: Expression counts on gene level + pattern: "*.genes.results" + - counts_transcript: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.isoforms.results": + type: file + description: Expression counts on transcript level + pattern: "*.isoforms.results" - stat: - type: file - description: RSEM statistics - pattern: "*.stat" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.stat": + type: file + description: RSEM statistics + pattern: "*.stat" - logs: - type: file - description: RSEM logs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.log": + type: file + description: RSEM logs + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - bam_star: - type: file - description: BAM file generated by STAR (optional) - pattern: "*.STAR.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.STAR.genome.bam": + type: file + description: BAM file generated by STAR (optional) + pattern: "*.STAR.genome.bam" - bam_genome: - type: file - description: Genome BAM file (optional) - pattern: "*.genome.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.genome.bam: + type: file + description: Genome BAM file (optional) + pattern: "*.genome.bam" - bam_transcript: - type: file - description: Transcript BAM file (optional) - pattern: "*.transcript.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.transcript.bam: + type: file + description: Transcript BAM file (optional) + pattern: "*.transcript.bam" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rsem/preparereference/meta.yml b/modules/nf-core/rsem/preparereference/meta.yml index 05aa44fe6ca8..e95f4a2ae783 100644 --- a/modules/nf-core/rsem/preparereference/meta.yml +++ b/modules/nf-core/rsem/preparereference/meta.yml @@ -12,28 +12,32 @@ tools: documentation: https://github.com/deweylab/RSEM doi: 10.1186/1471-2105-12-323 licence: ["GPL-3.0-or-later"] + identifier: biotools:rsem input: - - fasta: - type: file - description: The Fasta file of the reference genome - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: The GTF file of the reference genome - pattern: "*.gtf" + - - fasta: + type: file + description: The Fasta file of the reference genome + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: The GTF file of the reference genome + pattern: "*.gtf" output: - - rsem: - type: directory - description: RSEM index directory - pattern: "rsem" + - index: + - rsem: + type: directory + description: RSEM index directory + pattern: "rsem" - transcript_fasta: - type: file - description: Fasta file of transcripts - pattern: "rsem/*transcripts.fa" + - "*transcripts.fa": + type: file + description: Fasta file of transcripts + pattern: "rsem/*transcripts.fa" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/bamstat/meta.yml b/modules/nf-core/rseqc/bamstat/meta.yml index 72745310cf7b..d69f054428bc 100644 --- a/modules/nf-core/rseqc/bamstat/meta.yml +++ b/modules/nf-core/rseqc/bamstat/meta.yml @@ -13,25 +13,32 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" output: - txt: - type: file - description: bam statistics report - pattern: "*.bam_stat.txt" + - meta: + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" + - "*.bam_stat.txt": + type: file + description: bam statistics report + pattern: "*.bam_stat.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/inferexperiment/meta.yml b/modules/nf-core/rseqc/inferexperiment/meta.yml index d9b9ff63eaed..3ac75728946f 100644 --- a/modules/nf-core/rseqc/inferexperiment/meta.yml +++ b/modules/nf-core/rseqc/inferexperiment/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the bam file to calculate statistics of - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the bam file to calculate statistics of + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: infer_experiment results report - pattern: "*.infer_experiment.txt" + - meta: + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" + - "*.infer_experiment.txt": + type: file + description: infer_experiment results report + pattern: "*.infer_experiment.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/innerdistance/meta.yml b/modules/nf-core/rseqc/innerdistance/meta.yml index d0a5bf181914..358e4d160804 100644 --- a/modules/nf-core/rseqc/innerdistance/meta.yml +++ b/modules/nf-core/rseqc/innerdistance/meta.yml @@ -13,45 +13,72 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - distance: - type: file - description: the inner distances - pattern: "*.inner_distance.txt" + - meta: + type: file + description: the inner distances + pattern: "*.inner_distance.txt" + - "*distance.txt": + type: file + description: the inner distances + pattern: "*.inner_distance.txt" - freq: - type: file - description: frequencies of different insert sizes - pattern: "*.inner_distance_freq.txt" + - meta: + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" + - "*freq.txt": + type: file + description: frequencies of different insert sizes + pattern: "*.inner_distance_freq.txt" - mean: - type: file - description: mean/median values of inner distances - pattern: "*.inner_distance_mean.txt" + - meta: + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" + - "*mean.txt": + type: file + description: mean/median values of inner distances + pattern: "*.inner_distance_mean.txt" - pdf: - type: file - description: distribution plot of inner distances - pattern: "*.inner_distance_plot.pdf" + - meta: + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" + - "*.pdf": + type: file + description: distribution plot of inner distances + pattern: "*.inner_distance_plot.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.inner_distance_plot.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.inner_distance_plot.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionannotation/meta.yml b/modules/nf-core/rseqc/junctionannotation/meta.yml index a88aa2db36f1..0622ee43bd33 100644 --- a/modules/nf-core/rseqc/junctionannotation/meta.yml +++ b/modules/nf-core/rseqc/junctionannotation/meta.yml @@ -13,53 +13,90 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: + - xls: + - meta: + type: file + description: xls file with junction information + pattern: "*.xls" + - "*.xls": + type: file + description: xls file with junction information + pattern: "*.xls" + - rscript: + - meta: + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - "*.r": + type: file + description: Rscript to reproduce the plots + pattern: "*.r" + - log: + - meta: + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" + - "*.log": + type: file + description: Log file of execution + pattern: "*.junction_annotation.log" - bed: - type: file - description: bed file of annotated junctions - pattern: "*.junction.bed" + - meta: + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" + - "*.junction.bed": + type: file + description: bed file of annotated junctions + pattern: "*.junction.bed" - interact_bed: - type: file - description: Interact bed file - pattern: "*.Interact.bed" - - xls: - type: file - description: xls file with junction information - pattern: "*.xls" + - meta: + type: file + description: Interact bed file + pattern: "*.Interact.bed" + - "*.Interact.bed": + type: file + description: Interact bed file + pattern: "*.Interact.bed" - pdf: - type: file - description: junction plot - pattern: "*.junction.pdf" + - meta: + type: file + description: junction plot + pattern: "*.junction.pdf" + - "*junction.pdf": + type: file + description: junction plot + pattern: "*.junction.pdf" - events_pdf: - type: file - description: events plot - pattern: "*.events.pdf" - - rscript: - type: file - description: Rscript to reproduce the plots - pattern: "*.r" - - log: - type: file - description: Log file of execution - pattern: "*.junction_annotation.log" + - meta: + type: file + description: events plot + pattern: "*.events.pdf" + - "*events.pdf": + type: file + description: events plot + pattern: "*.events.pdf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/junctionsaturation/meta.yml b/modules/nf-core/rseqc/junctionsaturation/meta.yml index 19ae3f52d924..b6f422dc739b 100644 --- a/modules/nf-core/rseqc/junctionsaturation/meta.yml +++ b/modules/nf-core/rseqc/junctionsaturation/meta.yml @@ -13,33 +13,45 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - pdf: - type: file - description: Junction saturation report - pattern: "*.pdf" + - meta: + type: file + description: Junction saturation report + pattern: "*.pdf" + - "*.pdf": + type: file + description: Junction saturation report + pattern: "*.pdf" - rscript: - type: file - description: Junction saturation R-script - pattern: "*.r" + - meta: + type: file + description: Junction saturation R-script + pattern: "*.r" + - "*.r": + type: file + description: Junction saturation R-script + pattern: "*.r" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readdistribution/meta.yml b/modules/nf-core/rseqc/readdistribution/meta.yml index 989792faa200..578200abb242 100644 --- a/modules/nf-core/rseqc/readdistribution/meta.yml +++ b/modules/nf-core/rseqc/readdistribution/meta.yml @@ -13,29 +13,36 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" + - - bed: + type: file + description: a bed file for the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: the read distribution report - pattern: "*.read_distribution.txt" + - meta: + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" + - "*.read_distribution.txt": + type: file + description: the read distribution report + pattern: "*.read_distribution.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/readduplication/meta.yml b/modules/nf-core/rseqc/readduplication/meta.yml index 4b24d30327d4..ef94122e9017 100644 --- a/modules/nf-core/rseqc/readduplication/meta.yml +++ b/modules/nf-core/rseqc/readduplication/meta.yml @@ -14,41 +14,59 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: the alignment in bam format - pattern: "*.{bam}" - - bed: - type: file - description: a bed file for the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: the alignment in bam format + pattern: "*.{bam}" output: - seq_xls: - type: file - description: Read duplication rate determined from mapping position of read - pattern: "*seq.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" + - "*seq.DupRate.xls": + type: file + description: Read duplication rate determined from mapping position of read + pattern: "*seq.DupRate.xls" - pos_xls: - type: file - description: Read duplication rate determined from sequence of read - pattern: "*pos.DupRate.xls" + - meta: + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" + - "*pos.DupRate.xls": + type: file + description: Read duplication rate determined from sequence of read + pattern: "*pos.DupRate.xls" - pdf: - type: file - description: plot of duplication rate - pattern: "*.pdf" + - meta: + type: file + description: plot of duplication rate + pattern: "*.pdf" + - "*.pdf": + type: file + description: plot of duplication rate + pattern: "*.pdf" - rscript: - type: file - description: script to reproduce the plot - pattern: "*.R" + - meta: + type: file + description: script to reproduce the plot + pattern: "*.R" + - "*.r": + type: file + description: script to reproduce the plot + pattern: "*.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@kevinmenden" diff --git a/modules/nf-core/rseqc/tin/meta.yml b/modules/nf-core/rseqc/tin/meta.yml index f760bb2f4b97..6e363ecd83e2 100644 --- a/modules/nf-core/rseqc/tin/meta.yml +++ b/modules/nf-core/rseqc/tin/meta.yml @@ -13,37 +13,49 @@ tools: documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 licence: ["GPL-3.0-or-later"] + identifier: biotools:rseqc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - bai: - type: file - description: Index for input BAM file - pattern: "*.{bai}" - - bed: - type: file - description: BED file containing the reference gene model - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Index for input BAM file + pattern: "*.{bai}" + - - bed: + type: file + description: BED file containing the reference gene model + pattern: "*.{bed}" output: - txt: - type: file - description: TXT file containing tin.py results summary - pattern: "*.txt" + - meta: + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" + - "*.txt": + type: file + description: TXT file containing tin.py results summary + pattern: "*.txt" - xls: - type: file - description: XLS file containing tin.py results - pattern: "*.xls" + - meta: + type: file + description: XLS file containing tin.py results + pattern: "*.xls" + - "*.xls": + type: file + description: XLS file containing tin.py results + pattern: "*.xls" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index 1991b807d01a..e09aff3af677 100644 --- a/modules/nf-core/rtgtools/format/meta.yml +++ b/modules/nf-core/rtgtools/format/meta.yml @@ -1,5 +1,6 @@ name: "rtgtools_format" -description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into the RTG Sequence Data File (SDF) format. +description: Converts the contents of sequence data files (FASTA/FASTQ/SAM/BAM) into + the RTG Sequence Data File (SDF) format. keywords: - rtg - fasta @@ -8,43 +9,49 @@ keywords: - sam tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input1: - type: file - description: FASTA, FASTQ, BAM or SAM file. This should be the left input file when using paired end FASTQ/FASTA data - pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" - - input2: - type: file - description: The right input file when using paired end FASTQ/FASTA data - pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" - - sam_rg: - type: file - description: A file containing a single readgroup header as a SAM header. This can also be supplied as a string in `task.ext.args` as `--sam-rg `. - pattern: "*.{txt,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input1: + type: file + description: FASTA, FASTQ, BAM or SAM file. This should be the left input file + when using paired end FASTQ/FASTA data + pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz,bam,sam}" + - input2: + type: file + description: The right input file when using paired end FASTQ/FASTA data + pattern: "*.{fasta,fa,fna,fastq,fastq.gz,fq,fq.gz}" + - sam_rg: + type: file + description: A file containing a single readgroup header as a SAM header. This + can also be supplied as a string in `task.ext.args` as `--sam-rg `. + pattern: "*.{txt,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sdf: - type: directory - description: The sequence dictionary format folder created from the input file(s) - pattern: "*.sdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sdf": + type: directory + description: The sequence dictionary format folder created from the input file(s) + pattern: "*.sdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/pedfilter/meta.yml b/modules/nf-core/rtgtools/pedfilter/meta.yml index 4e90fd7bf981..c8eee99d061a 100644 --- a/modules/nf-core/rtgtools/pedfilter/meta.yml +++ b/modules/nf-core/rtgtools/pedfilter/meta.yml @@ -7,37 +7,41 @@ keywords: - ped tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: The input file, can be either a PED or a VCF file - pattern: "*.{vcf,vcf.gz,ped}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: The input file, can be either a PED or a VCF file + pattern: "*.{vcf,vcf.gz,ped}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - output: - type: file - description: | - The output file, can be either a filtered PED file - or a VCF file containing the PED headers (needs --vcf as argument) - pattern: "*.{vcf.gz,ped}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf.gz,ped}": + type: file + description: | + The output file, can be either a filtered PED file + or a VCF file containing the PED headers (needs --vcf as argument) + pattern: "*.{vcf.gz,ped}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/rocplot/meta.yml b/modules/nf-core/rtgtools/rocplot/meta.yml index 2b4d43d7c915..8fccb3181cb5 100644 --- a/modules/nf-core/rtgtools/rocplot/meta.yml +++ b/modules/nf-core/rtgtools/rocplot/meta.yml @@ -1,5 +1,6 @@ name: "rtgtools_rocplot" -description: Plot ROC curves from vcfeval ROC data files, either to an image, or an interactive GUI. The interactive GUI isn't possible for nextflow. +description: Plot ROC curves from vcfeval ROC data files, either to an image, or an + interactive GUI. The interactive GUI isn't possible for nextflow. keywords: - rtgtools - rocplot @@ -7,39 +8,49 @@ keywords: - vcf tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input TSV ROC files created with RTGTOOLS_VCFEVAL - pattern: "*.tsv.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input TSV ROC files created with RTGTOOLS_VCFEVAL + pattern: "*.tsv.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - png: - type: file - description: The resulting rocplot in PNG format - pattern: "*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.png": + type: file + description: The resulting rocplot in PNG format + pattern: "*.png" - svg: - type: file - description: The resulting rocplot in SVG format - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.svg": + type: file + description: The resulting rocplot in SVG format + pattern: "*.svg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 5023ac91822e..9814124ee792 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -1,111 +1,196 @@ name: "rtgtools_vcfeval" -description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set +description: The VCFeval tool of RTG tools. It is used to evaluate called variants + for agreement with a baseline variant set keywords: - benchmarking - vcf - rtg-tools tools: - "rtgtools": - description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation" + description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison + and manipulation" homepage: "https://www.realtimegenomics.com/products/rtg-tools" documentation: "https://github.com/RealTimeGenomics/rtg-tools" tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_vcf: - type: file - description: A VCF with called variants to benchmark against the standard - pattern: "*.{vcf,vcf.gz}" - - query_vcf_index: - type: file - description: The index of the called VCF (optional) - pattern: "*.tbi" - - truth_vcf: - type: file - description: A standard VCF to compare against - pattern: "*.{vcf,vcf.gz}" - - truth_vcf_index: - type: file - description: The index of the standard VCF (optional) - pattern: "*.tbi" - - truth_bed: - type: file - description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) - pattern: "*.bed" - - evaluation_bed: - type: file - description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) - pattern: "*.bed" - - sdf: - type: file - description: The SDF (RTG Sequence Data File) folder of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_vcf: + type: file + description: A VCF with called variants to benchmark against the standard + pattern: "*.{vcf,vcf.gz}" + - query_vcf_tbi: + type: file + description: The index of the VCF file with called variants to benchmark against the standard + pattern: "*.{vcf.gz.tbi, vcf.tbi}" + - truth_vcf: + type: file + description: A standard VCF to compare against + pattern: "*.{vcf,vcf.gz}" + - truth_vcf_tbi: + type: file + description: The index of the standard VCF to compare against + pattern: "*.{vcf.gz.tbi, vcf.tbi}" + - truth_bed: + type: file + description: A BED file containining the strict regions where VCFeval should + only evaluate the fully overlapping variants (optional) + pattern: "*.bed" + - evaluation_bed: + type: file + description: A BED file containing the regions where VCFeval will evaluate every + fully and partially overlapping variant (optional) + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sdf: + type: file + description: The SDF (RTG Sequence Data File) folder of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tp_vcf: - type: file - description: A VCF file for the true positive variants - pattern: "*.tp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp.vcf.gz": + type: file + description: A VCF file for the true positive variants + pattern: "*.tp.vcf.gz" - tp_tbi: - type: file - description: The index of the VCF file for the true positive variants - pattern: "*.tp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp.vcf.gz.tbi": + type: file + description: The index of the VCF file for the true positive variants + pattern: "*.tp.vcf.gz.tbi" - fn_vcf: - type: file - description: A VCF file for the false negative variants - pattern: "*.fn.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fn.vcf.gz": + type: file + description: A VCF file for the false negative variants + pattern: "*.fn.vcf.gz" - fn_tbi: - type: file - description: The index of the VCF file for the false negative variants - pattern: "*.fn.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fn.vcf.gz.tbi": + type: file + description: The index of the VCF file for the false negative variants + pattern: "*.fn.vcf.gz.tbi" - fp_vcf: - type: file - description: A VCF file for the false positive variants - pattern: "*.fp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fp.vcf.gz": + type: file + description: A VCF file for the false positive variants + pattern: "*.fp.vcf.gz" - fp_tbi: - type: file - description: The index of the VCF file for the false positive variants - pattern: "*.fp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fp.vcf.gz.tbi": + type: file + description: The index of the VCF file for the false positive variants + pattern: "*.fp.vcf.gz.tbi" - baseline_vcf: - type: file - description: A VCF file for the true positive variants from the baseline - pattern: "*.tp-baseline.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp-baseline.vcf.gz": + type: file + description: A VCF file for the true positive variants from the baseline + pattern: "*.tp-baseline.vcf.gz" - baseline_tbi: - type: file - description: The index of the VCF file for the true positive variants from the baseline - pattern: "*.tp-baseline.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tp-baseline.vcf.gz.tbi": + type: file + description: The index of the VCF file for the true positive variants from the + baseline + pattern: "*.tp-baseline.vcf.gz.tbi" - snp_roc: - type: file - description: TSV files containing ROC data for the SNPs - pattern: "*.snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.snp_roc.tsv.gz": + type: file + description: TSV files containing ROC data for the SNPs + pattern: "*.snp_roc.tsv.gz" - non_snp_roc: - type: file - description: TSV files containing ROC data for all variants except SNPs - pattern: "*.non_snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.non_snp_roc.tsv.gz": + type: file + description: TSV files containing ROC data for all variants except SNPs + pattern: "*.non_snp_roc.tsv.gz" - weighted_roc: - type: file - description: TSV files containing weighted ROC data for all variants - pattern: "*.weighted_snp_roc.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.weighted_roc.tsv.gz": + type: file + description: TSV files containing weighted ROC data for all variants + pattern: "*.weighted_snp_roc.tsv.gz" - summary: - type: file - description: A TXT file containing the summary of the evaluation - pattern: "*.summary.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary.txt": + type: file + description: A TXT file containing the summary of the evaluation + pattern: "*.summary.txt" - phasing: - type: file - description: A TXT file containing the data on the phasing - pattern: "*.phasing.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.phasing.txt": + type: file + description: A TXT file containing the data on the phasing + pattern: "*.phasing.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/rtn/tni/meta.yml b/modules/nf-core/rtn/tni/meta.yml index b60300bd9e5a..1057cf3d9e1d 100644 --- a/modules/nf-core/rtn/tni/meta.yml +++ b/modules/nf-core/rtn/tni/meta.yml @@ -1,48 +1,76 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "rtn_tni" -description: Uses the RTN R package for transcriptional regulatory network inference (TNI). +description: Uses the RTN R package for transcriptional regulatory network inference + (TNI). keywords: - regulatory network - transcriptomics - transcription factors tools: - "rtn": - description: "RTN: Reconstruction of Transcriptional regulatory Networks and analysis of regulons" + description: "RTN: Reconstruction of Transcriptional regulatory Networks and analysis + of regulons" homepage: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html" documentation: "https://www.bioconductor.org/packages/release/bioc/vignettes/RTN/inst/doc/RTN.html" tool_dev_url: "https://www.bioconductor.org/packages/release/bioc/html/RTN.html" doi: "10.1038/ncomms3464" licence: ["Artistic-2.0"] + identifier: biotools:rtn input: - - expression_matrix: - type: file - description: expression matrix in TSV format - pattern: "*.tsv" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - expression_matrix: + type: file + description: expression matrix in TSV format + pattern: "*.tsv" output: - tni: - type: file - description: RDS R Object with the TNI object - pattern: "tni.rds" + - meta: + type: file + description: RDS R Object with the TNI object + pattern: "tni.rds" + - tni.rds: + type: file + description: RDS R Object with the TNI object + pattern: "tni.rds" - tni_perm: - type: file - description: RDS R Object with the TNI object after permutation - pattern: "tni_permutated.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation + pattern: "tni_permutated.rds" + - tni_permutated.rds: + type: file + description: RDS R Object with the TNI object after permutation + pattern: "tni_permutated.rds" - tni_bootstrap: - type: file - description: RDS R Object with the TNI object after permutation and bootstrap - pattern: "tni_bootstrapped.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation and bootstrap + pattern: "tni_bootstrapped.rds" + - tni_bootstrapped.rds: + type: file + description: RDS R Object with the TNI object after permutation and bootstrap + pattern: "tni_bootstrapped.rds" - tni_filtered: - type: file - description: RDS R Object with the TNI object after permutation, bootstrap and filtering - pattern: "tni_filtered.rds" + - meta: + type: file + description: RDS R Object with the TNI object after permutation, bootstrap and + filtering + pattern: "tni_filtered.rds" + - tni_filtered.rds: + type: file + description: RDS R Object with the TNI object after permutation, bootstrap and + filtering + pattern: "tni_filtered.rds" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mribeirodantas" maintainers: diff --git a/modules/nf-core/sageproteomics/sage/meta.yml b/modules/nf-core/sageproteomics/sage/meta.yml index a62e65c4930e..69bc1f8653ae 100644 --- a/modules/nf-core/sageproteomics/sage/meta.yml +++ b/modules/nf-core/sageproteomics/sage/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sageproteomics_sage" description: sage is a search software for proteomics data @@ -14,67 +13,92 @@ tools: tool_dev_url: "https://github.com/lazear/sage" doi: "10.1021/acs.jproteome.3c00486" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - '"*.mzML"': - type: file - description: mzML open source mass spectrometry raw data format - pattern: "*.{mzML, mzML.gz}" - - meta2: - type: map - description: | - Groovy Map containing information about fasta_proteome - e.g. `[ id:'sample1']` - - fasta_proteome: - type: file - description: proteome database in fasta format - pattern: "*.{fasta, fasta.gz}" - - meta3: - type: map - description: | - Groovy Map containing information about base_config - e.g. `[ id:'sample1']` - - base_config: - type: file - description: sage configuration json - pattern: "*.{json}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - '"*.mzML"': + type: file + description: mzML open source mass spectrometry raw data format + pattern: "*.{mzML, mzML.gz}" + - - meta2: + type: map + description: | + Groovy Map containing information about fasta_proteome + e.g. `[ id:'sample1']` + - fasta_proteome: + type: file + description: proteome database in fasta format + pattern: "*.{fasta, fasta.gz}" + - - meta3: + type: map + description: | + Groovy Map containing information about base_config + e.g. `[ id:'sample1']` + - base_config: + type: file + description: sage configuration json + pattern: "*.{json}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - results_tsv: - type: file - description: tsv output results - pattern: "results.sage.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.sage.tsv: + type: file + description: tsv output results + pattern: "results.sage.tsv" - results_json: - type: file - description: json output results - pattern: "results.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.json: + type: file + description: json output results + pattern: "results.json" - results_pin: - type: file - description: pin format output results - pattern: "results.sage.pin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - results.sage.pin: + type: file + description: pin format output results + pattern: "results.sage.pin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - tmt_tsv: - type: file - description: tandem mass tag quantification - pattern: "tmt.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - tmt.tsv: + type: file + description: tandem mass tag quantification + pattern: "tmt.tsv" - lfq_tsv: - type: file - description: label free quantification - pattern: "lfq.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - lfq.tsv: + type: file + description: label free quantification + pattern: "lfq.tsv" authors: - "@dgemperline-lilly" maintainers: diff --git a/modules/nf-core/salmon/index/meta.yml b/modules/nf-core/salmon/index/meta.yml index fd94dd27472e..48486a2bbf07 100644 --- a/modules/nf-core/salmon/index/meta.yml +++ b/modules/nf-core/salmon/index/meta.yml @@ -13,22 +13,25 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - genome_fasta: - type: file - description: Fasta file of the reference genome - - transcriptome_fasta: - type: file - description: Fasta file of the reference transcriptome + - - genome_fasta: + type: file + description: Fasta file of the reference genome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome output: - index: - type: directory - description: Folder containing the star index files - pattern: "salmon" + - salmon: + type: directory + description: Folder containing the star index files + pattern: "salmon" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salmon/quant/meta.yml b/modules/nf-core/salmon/quant/meta.yml index a2faf589a79c..4cacde0f0a79 100644 --- a/modules/nf-core/salmon/quant/meta.yml +++ b/modules/nf-core/salmon/quant/meta.yml @@ -13,47 +13,69 @@ tools: manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 licence: ["GPL-3.0-or-later"] + identifier: biotools:salmon input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for single-end or paired-end data. - Multiple single-end fastqs or pairs of paired-end fastqs are - handled. - - index: - type: directory - description: Folder containing the star index files - - gtf: - type: file - description: GTF of the reference transcriptome - - transcript_fasta: - type: file - description: Fasta file of the reference transcriptome - - alignment_mode: - type: boolean - description: whether to run salmon in alignment mode - - lib_type: - type: string - description: | - Override library type inferred based on strandedness defined in meta object + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files for single-end or paired-end data. + Multiple single-end fastqs or pairs of paired-end fastqs are + handled. + - - index: + type: directory + description: Folder containing the star index files + - - gtf: + type: file + description: GTF of the reference transcriptome + - - transcript_fasta: + type: file + description: Fasta file of the reference transcriptome + - - alignment_mode: + type: boolean + description: whether to run salmon in alignment mode + - - lib_type: + type: string + description: | + Override library type inferred based on strandedness defined in meta object output: - results: - type: directory - description: Folder containing the quantification results for a specific sample - pattern: "${prefix}" + - meta: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" + - ${prefix}: + type: directory + description: Folder containing the quantification results for a specific sample + pattern: "${prefix}" - json_info: - type: file - description: File containing meta information from Salmon quant - pattern: "*info.json" + - meta: + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - "*info.json": + type: file + description: File containing meta information from Salmon quant + pattern: "*info.json" + - lib_format_counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*lib_format_counts.json": + type: file + description: File containing the library format counts + pattern: "*lib_format_counts.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/salsa2/meta.yml b/modules/nf-core/salsa2/meta.yml index 8729ce064436..7232d1da1a0f 100644 --- a/modules/nf-core/salsa2/meta.yml +++ b/modules/nf-core/salsa2/meta.yml @@ -15,46 +15,73 @@ tools: tool_dev_url: "https://github.com/marbl/SALSA" doi: "10.1186/s12864-017-3879-z" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of assembly. Headers must not contain ':' - pattern: "*.{fa, fasta}" - - index: - type: file - description: Fasta index file of assembly containing the length of contigs. - pattern: "*.{fa.fai, fasta.fai}" - - bed: - type: file - description: BED file of alignments sorted by read names, e.g., from HiC-Pro - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of assembly. Headers must not contain ':' + pattern: "*.{fa, fasta}" + - index: + type: file + description: Fasta index file of assembly containing the length of contigs. + pattern: "*.{fa.fai, fasta.fai}" + - - bed: + type: file + description: BED file of alignments sorted by read names, e.g., from HiC-Pro + pattern: "*.{bed}" + - - gfa: + type: file + description: GFA file of the assembly graph + - - dup: + type: file + description: File containing the duplicated contigs + - - filter_bed: + type: file + description: BED file of the filtered alignments + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Sequences for the scaffolds generated by the algorithm - pattern: "*_scaffolds_FINAL.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_scaffolds_FINAL.fasta": + type: file + description: Sequences for the scaffolds generated by the algorithm + pattern: "*_scaffolds_FINAL.fasta" - agp: - type: file - description: AGP style output for the scaffolds describing the assignment, orientation and ordering of contigs along the scaffolds - pattern: "*_scaffolds_FINAL.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_scaffolds_FINAL.agp": + type: file + description: AGP style output for the scaffolds describing the assignment, orientation + and ordering of contigs along the scaffolds + pattern: "*_scaffolds_FINAL.agp" - agp_original_coordinates: - type: file - description: Secondary output AGP file with names and coordinates matching the original input assembly (optional) - pattern: "*scaffolds_FINAL.original-coordinates.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*scaffolds_FINAL.original-coordinates.agp": + type: file + description: Secondary output AGP file with names and coordinates matching the + original input assembly (optional) + pattern: "*scaffolds_FINAL.original-coordinates.agp" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" maintainers: diff --git a/modules/nf-core/sam2lca/analyze/meta.yml b/modules/nf-core/sam2lca/analyze/meta.yml index aa4f9e310d9a..c3152c780d31 100644 --- a/modules/nf-core/sam2lca/analyze/meta.yml +++ b/modules/nf-core/sam2lca/analyze/meta.yml @@ -1,5 +1,6 @@ name: "sam2lca_analyze" -description: Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM files +description: Calling lowest common ancestors from multi-mapped reads in SAM/BAM/CRAM + files keywords: - LCA - alignment @@ -14,46 +15,62 @@ tools: documentation: "https://sam2lca.readthedocs.io" doi: "10.21105/joss.04360" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM index - pattern: "*.{bai,.crai}" - - database: - type: file - description: Directory containing the sam2lca database - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM index + pattern: "*.{bai,.crai}" + - - database: + type: file + description: Directory containing the sam2lca database + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: CSV file containing the sam2lca results - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: CSV file containing the sam2lca results + pattern: "*.csv" - json: - type: file - description: JSON file containing the sam2lca results - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON file containing the sam2lca results + pattern: "*.json" - bam: - type: file - description: Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic informations - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Optional sorted BAM/CRAM/SAM file annotated with LCA taxonomic + informations + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxibor" maintainers: diff --git a/modules/nf-core/sambamba/flagstat/meta.yml b/modules/nf-core/sambamba/flagstat/meta.yml index 3e68823a5c70..8194d6df143d 100644 --- a/modules/nf-core/sambamba/flagstat/meta.yml +++ b/modules/nf-core/sambamba/flagstat/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" tool_dev_url: "https://github.com/biod/sambamba" licence: ["GPL v2"] + identifier: biotools:sambamba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: Stats file - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: Stats file + pattern: "*.{stats}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/sambamba/markdup/meta.yml b/modules/nf-core/sambamba/markdup/meta.yml index 51b65bd7847b..eeebe38b6021 100644 --- a/modules/nf-core/sambamba/markdup/meta.yml +++ b/modules/nf-core/sambamba/markdup/meta.yml @@ -11,34 +11,43 @@ tools: documentation: "https://lomereiter.github.io/sambamba/docs/sambamba-view.html" tool_dev_url: "https://github.com/biod/sambamba" licence: ["GPL v2"] + identifier: biotools:sambamba input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" - bai: - type: file - description: An optional BAM index file. - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: An optional BAM index file. + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" maintainers: diff --git a/modules/nf-core/samblaster/meta.yml b/modules/nf-core/samblaster/meta.yml index 5c1e5a970023..5faf3a6c3ac5 100644 --- a/modules/nf-core/samblaster/meta.yml +++ b/modules/nf-core/samblaster/meta.yml @@ -23,30 +23,33 @@ tools: tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" licence: ["MIT"] + identifier: biotools:samblaster input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.bam" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.bam" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Tagged or filtered BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Tagged or filtered BAM file + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/ampliconclip/meta.yml b/modules/nf-core/samtools/ampliconclip/meta.yml index 27452f30f67f..fa1e96bd8909 100644 --- a/modules/nf-core/samtools/ampliconclip/meta.yml +++ b/modules/nf-core/samtools/ampliconclip/meta.yml @@ -15,48 +15,63 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bed: - type: file - description: BED file of regions to be removed (e.g. amplicon primers) - pattern: "*.{bed}" - - save_cliprejects: - type: boolean - description: Save filtered reads to a file - - save_clipstats: - type: boolean - description: Save clipping stats to a file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - bed: + type: file + description: BED file of regions to be removed (e.g. amplicon primers) + pattern: "*.{bed}" + - - save_cliprejects: + type: boolean + description: Save filtered reads to a file + - - save_clipstats: + type: boolean + description: Save clipping stats to a file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Clipped reads BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clipallowed.bam": + type: file + description: Clipped reads BAM file + pattern: "*.{bam}" - stats: - type: file - description: Clipping statistics text file - pattern: "*.{clipstats.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clipstats.txt": + type: file + description: Clipping statistics text file + pattern: "*.{clipstats.txt}" - rejects_bam: - type: file - description: Filtered reads BAM file - pattern: "*.{cliprejects.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cliprejects.bam": + type: file + description: Filtered reads BAM file + pattern: "*.{cliprejects.bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/bam2fq/meta.yml b/modules/nf-core/samtools/bam2fq/meta.yml index 7769046b54ae..b17ed608d0ce 100644 --- a/modules/nf-core/samtools/bam2fq/meta.yml +++ b/modules/nf-core/samtools/bam2fq/meta.yml @@ -11,40 +11,43 @@ tools: description: Tools for dealing with SAM, BAM and CRAM files documentation: http://www.htslib.org/doc/1.1/samtools.html licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputbam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - split: - type: boolean - description: | - TRUE/FALSE value to indicate if reads should be separated into - /1, /2 and if present other, or singleton. - Note: choosing TRUE will generate 4 different files. - Choosing FALSE will produce a single file, which will be interleaved in case - the input contains paired reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputbam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - split: + type: boolean + description: | + TRUE/FALSE value to indicate if reads should be separated into + /1, /2 and if present other, or singleton. + Note: choosing TRUE will generate 4 different files. + Choosing FALSE will produce a single file, which will be interleaved in case + the input contains paired reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: | - FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) - or a single interleaved .fq.gz file if the user chooses not to split the reads. - pattern: "*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fq.gz": + type: file + description: | + FASTQ files, which will be either a group of 4 files (read_1, read_2, other and singleton) + or a single interleaved .fq.gz file if the user chooses not to split the reads. + pattern: "*.fq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" maintainers: diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/calmd/meta.yml b/modules/nf-core/samtools/calmd/meta.yml index 857f9b80d39b..c34e1f777b66 100644 --- a/modules/nf-core/samtools/calmd/meta.yml +++ b/modules/nf-core/samtools/calmd/meta.yml @@ -15,34 +15,42 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: FASTA ref file - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA ref file + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JackCurragh" maintainers: diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/cat/meta.yml b/modules/nf-core/samtools/cat/meta.yml index 3541e0c3891b..dfb0f78c4cdb 100644 --- a/modules/nf-core/samtools/cat/meta.yml +++ b/modules/nf-core/samtools/cat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: samtools_cat description: Concatenate BAM or CRAM file @@ -17,34 +16,43 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_files: - type: file - description: BAM/CRAM files - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_files: + type: file + description: BAM/CRAM files + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Concatenated BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: Concatenated BAM file + pattern: "*.{bam}" - cram: - type: file - description: Concatenated CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: Concatenated CRAM file + pattern: "*.{cram}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/collate/meta.yml b/modules/nf-core/samtools/collate/meta.yml index f0aed28a2144..cc54583eea8e 100644 --- a/modules/nf-core/samtools/collate/meta.yml +++ b/modules/nf-core/samtools/collate/meta.yml @@ -13,32 +13,64 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA ref file + pattern: "*.fasta" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM + pattern: "*.{bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM + pattern: "*.{cram}" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: Sorted SAM + pattern: "*.{sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Collated BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index 2bcd47ee161b..b98cbb99092d 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/collatefastq/meta.yml b/modules/nf-core/samtools/collatefastq/meta.yml index 898cdbdad79f..5bc912496e4f 100644 --- a/modules/nf-core/samtools/collatefastq/meta.yml +++ b/modules/nf-core/samtools/collatefastq/meta.yml @@ -11,61 +11,90 @@ tools: description: Tools for dealing with SAM, BAM and CRAM files documentation: http://www.htslib.org/doc/1.1/samtools.html licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference genome fasta file - pattern: "*.{fasta,fa}" - - interleave: - type: boolean - description: | - If true, the output is a single interleaved paired-end FASTQ - If false, the output split paired-end FASTQ - default: false + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference genome fasta file + pattern: "*.{fasta,fa}" + - - interleave: + type: boolean + description: | + If true, the output is a single interleaved paired-end FASTQ + If false, the output split paired-end FASTQ + default: false output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: | - R1 and R2 FASTQ files - pattern: "*_{1,2}.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{1,2}.fq.gz" + - "*_{1,2}.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_{1,2}.fq.gz" - fastq_interleaved: - type: file - description: | - Interleaved paired end FASTQ files - pattern: "*_interleaved.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_interleaved.fq.gz" + - "*_interleaved.fq": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_interleaved.fq.gz" - fastq_other: - type: file - description: | - FASTQ files with reads where the READ1 and READ2 FLAG bits set are either both set or both unset. - pattern: "*_other.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_other.fq.gz" + - "*_other.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_other.fq.gz" - fastq_singleton: - type: file - description: | - FASTQ files with singleton reads. - pattern: "*_singleton.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_singleton.fq.gz" + - "*_singleton.fq.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*_singleton.fq.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lescai" - "@maxulysse" diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index 699c05ce8b66..5a85438e08a8 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -4,5 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - "bioconda::samtools=1.20" diff --git a/modules/nf-core/samtools/consensus/meta.yml b/modules/nf-core/samtools/consensus/meta.yml index 71b96bf368fb..43b993dd615c 100644 --- a/modules/nf-core/samtools/consensus/meta.yml +++ b/modules/nf-core/samtools/consensus/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "samtools_consensus" description: Produces a consensus FASTA/FASTQ/PILEUP @@ -19,35 +18,54 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - + - fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fasta": + type: file + description: Consensus FASTA file + pattern: "*.{fasta}" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq": + type: file + description: Consensus FASTQ file + pattern: "*.{fastq}" + - pileup: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.pileup": + type: file + description: Consensus PILEUP file + pattern: "*.{pileup}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Consensus sequences - pattern: "*.{fasta,fastq,pileup}" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LilyAnderssonLee" maintainers: diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/convert/meta.yml b/modules/nf-core/samtools/convert/meta.yml index 558289715cb6..d5bfa161ba7c 100644 --- a/modules/nf-core/samtools/convert/meta.yml +++ b/modules/nf-core/samtools/convert/meta.yml @@ -15,50 +15,85 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Reference file to create the CRAM file - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference file to create the CRAM file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference index file to create the CRAM file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: filtered/converted BAM file - pattern: "*{.bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: filtered/converted BAM file + pattern: "*{.bam}" - cram: - type: file - description: filtered/converted CRAM file - pattern: "*{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: filtered/converted CRAM file + pattern: "*{cram}" - bai: - type: file - description: filtered/converted BAM index - pattern: "*{.bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: filtered/converted BAM index + pattern: "*{.bai}" - crai: - type: file - description: filtered/converted CRAM index - pattern: "*{.crai}" - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: filtered/converted CRAM index + pattern: "*{.crai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" - "@maxulysse" diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/coverage/meta.yml b/modules/nf-core/samtools/coverage/meta.yml index e74082d93421..fb9ba6f3a1d9 100644 --- a/modules/nf-core/samtools/coverage/meta.yml +++ b/modules/nf-core/samtools/coverage/meta.yml @@ -14,47 +14,56 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Reference genome index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference genome index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - coverage: - type: file - description: Tabulated text containing the coverage at each position or region or an ASCII-art histogram (with --histogram). - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Tabulated text containing the coverage at each position or region + or an ASCII-art histogram (with --histogram). + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/samtools/cramsize/meta.yml b/modules/nf-core/samtools/cramsize/meta.yml index cab8ea441672..0383716dc3f3 100644 --- a/modules/nf-core/samtools/cramsize/meta.yml +++ b/modules/nf-core/samtools/cramsize/meta.yml @@ -14,29 +14,32 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cram: - type: file - description: CRAM file - pattern: "*.cram" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cram: + type: file + description: CRAM file + pattern: "*.cram" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - size: - type: file - description: Size information file - pattern: "*.size" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.size": + type: file + description: Size information file + pattern: "*.size" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@limrp" diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index 2bcd47ee161b..b98cbb99092d 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/depth/meta.yml b/modules/nf-core/samtools/depth/meta.yml index bc51f2648614..2acd645d7913 100644 --- a/modules/nf-core/samtools/depth/meta.yml +++ b/modules/nf-core/samtools/depth/meta.yml @@ -7,45 +7,51 @@ keywords: - coverage tools: - samtools: - description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – computes the read depth at each position or region + description: Tools for dealing with SAM, BAM and CRAM files; samtools depth – + computes the read depth at each position or region homepage: http://www.htslib.org documentation: http://www.htslib.org/doc/samtools-depth.html tool_dev_url: https://github.com/samtools/samtools doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta1: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - intervals: - type: file - description: list of positions or regions in specified bed file - pattern: "*.{bed}" + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - intervals: + type: file + description: list of positions or regions in specified bed file + pattern: "*.{bed}" output: - - meta1: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: The output of samtools depth has three columns - the name of the contig or chromosome, the position and the number of reads aligned at that position - pattern: "*.{tsv}" + - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output of samtools depth has three columns - the name of the + contig or chromosome, the position and the number of reads aligned at that + position + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louperelo" - "@nevinwu" diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/dict/meta.yml b/modules/nf-core/samtools/dict/meta.yml index 61a5d835563d..a84b1cf760a7 100644 --- a/modules/nf-core/samtools/dict/meta.yml +++ b/modules/nf-core/samtools/dict/meta.yml @@ -14,30 +14,33 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - dict: - type: file - description: FASTA dictionary file - pattern: "*.{dict}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.dict": + type: file + description: FASTA dictionary file + pattern: "*.{dict}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@muffato" maintainers: diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index f3c25de20f46..6721b2cb847d 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -14,47 +14,62 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fa: - type: file - description: FASTA file - pattern: "*.{fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fa,fasta}": + type: file + description: FASTA file + pattern: "*.{fa}" - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fai": + type: file + description: FASTA index file + pattern: "*.{fai}" - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gzi": + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index 2bcd47ee161b..b98cbb99092d 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fasta/meta.yml b/modules/nf-core/samtools/fasta/meta.yml index eae26f010144..6ea77632d86c 100644 --- a/modules/nf-core/samtools/fasta/meta.yml +++ b/modules/nf-core/samtools/fasta/meta.yml @@ -13,47 +13,71 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - interleave: - type: boolean - description: Set true for interleaved fasta files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - interleave: + type: boolean + description: Set true for interleaved fasta files output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Compressed FASTA file(s) with reads with either the READ1 or READ2 flag set in separate files. - pattern: "*_{1,2}.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_{1,2}.fasta.gz": + type: file + description: Compressed FASTA file(s) with reads with either the READ1 or READ2 + flag set in separate files. + pattern: "*_{1,2}.fasta.gz" - interleaved: - type: file - description: Compressed FASTA file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file. - pattern: "*_interleaved.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_interleaved.fasta.gz": + type: file + description: Compressed FASTA file with reads with either the READ1 or READ2 + flag set in a combined file. Needs collated input file. + pattern: "*_interleaved.fasta.gz" - singleton: - type: file - description: Compressed FASTA file with singleton reads - pattern: "*_singleton.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_singleton.fasta.gz": + type: file + description: Compressed FASTA file with singleton reads + pattern: "*_singleton.fasta.gz" - other: - type: file - description: Compressed FASTA file with reads with either both READ1 and READ2 flags set or unset - pattern: "*_other.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_other.fasta.gz": + type: file + description: Compressed FASTA file with reads with either both READ1 and READ2 + flags set or unset + pattern: "*_other.fasta.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fastq/meta.yml b/modules/nf-core/samtools/fastq/meta.yml index c4002a45de1b..c15a0b6f84f3 100644 --- a/modules/nf-core/samtools/fastq/meta.yml +++ b/modules/nf-core/samtools/fastq/meta.yml @@ -15,45 +15,69 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - interleave: - type: boolean - description: Set true for interleaved fastq file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - interleave: + type: boolean + description: Set true for interleaved fastq file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 flag set in separate files. - pattern: "*_{1,2}.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_{1,2}.fastq.gz": + type: file + description: Compressed FASTQ file(s) with reads with either the READ1 or READ2 + flag set in separate files. + pattern: "*_{1,2}.fastq.gz" - interleaved: - type: file - description: Compressed FASTQ file with reads with either the READ1 or READ2 flag set in a combined file. Needs collated input file. - pattern: "*_interleaved.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_interleaved.fastq": + type: file + description: Compressed FASTQ file with reads with either the READ1 or READ2 + flag set in a combined file. Needs collated input file. + pattern: "*_interleaved.fastq.gz" - singleton: - type: file - description: Compressed FASTQ file with singleton reads - pattern: "*_singleton.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_singleton.fastq.gz": + type: file + description: Compressed FASTQ file with singleton reads + pattern: "*_singleton.fastq.gz" - other: - type: file - description: Compressed FASTQ file with reads with either both READ1 and READ2 flags set or unset - pattern: "*_other.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_other.fastq.gz": + type: file + description: Compressed FASTQ file with reads with either both READ1 and READ2 + flags set or unset + pattern: "*_other.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" - "@suzannejin" diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/fixmate/meta.yml b/modules/nf-core/samtools/fixmate/meta.yml index f949ce4de3b2..8d4238d4adb7 100644 --- a/modules/nf-core/samtools/fixmate/meta.yml +++ b/modules/nf-core/samtools/fixmate/meta.yml @@ -1,5 +1,8 @@ name: samtools_fixmate -description: Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs. +description: Samtools fixmate is a tool that can fill in information (insert size, + cigar, mapq) about paired end reads onto the corresponding other read. Also has + options to remove secondary/unmapped alignments and recalculate whether reads are + proper pairs. keywords: - fixmate - samtools @@ -19,30 +22,34 @@ tools: tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file, must be sorted by name, not coordinate - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file, must be sorted by name, not coordinate + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: A BAM/CRAM/SAM file with mate information added and/or proper pairs recalled - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: A BAM/CRAM/SAM file with mate information added and/or proper pairs + recalled + pattern: "*.{bam,cram,sam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sppearce" maintainers: diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/flagstat/meta.yml b/modules/nf-core/samtools/flagstat/meta.yml index 97991358e614..cdc4c2544c75 100644 --- a/modules/nf-core/samtools/flagstat/meta.yml +++ b/modules/nf-core/samtools/flagstat/meta.yml @@ -1,5 +1,6 @@ name: samtools_flagstat -description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type +description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG + type keywords: - stats - mapping @@ -17,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.flagstat": + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index 2bcd47ee161b..b98cbb99092d 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/getrg/meta.yml b/modules/nf-core/samtools/getrg/meta.yml index 770960e71a52..31e9cfb981bb 100644 --- a/modules/nf-core/samtools/getrg/meta.yml +++ b/modules/nf-core/samtools/getrg/meta.yml @@ -16,29 +16,29 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - readgroup: - type: file - description: File containing readgroup string(s) + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/idxstats/meta.yml b/modules/nf-core/samtools/idxstats/meta.yml index 344e92a3f8bf..f0a6bcb2a072 100644 --- a/modules/nf-core/samtools/idxstats/meta.yml +++ b/modules/nf-core/samtools/idxstats/meta.yml @@ -18,34 +18,37 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idxstats": + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index 2bcd47ee161b..b98cbb99092d 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.21 - - bioconda::samtools=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/import/meta.yml b/modules/nf-core/samtools/import/meta.yml index 9002e0927161..5c98b8be9570 100644 --- a/modules/nf-core/samtools/import/meta.yml +++ b/modules/nf-core/samtools/import/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "samtools_import" description: converts FASTQ files to unmapped SAM/BAM/CRAM @@ -18,38 +17,53 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - reads: - type: file - description: fastq data to be converted to SAM/BAM/CRAM - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - reads: + type: file + description: fastq data to be converted to SAM/BAM/CRAM + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sam: - type: file - description: SAM file - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.sam": + type: file + description: SAM file + pattern: "*.sam" - bam: - type: file - description: Unaligned BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Unaligned BAM file + pattern: "*.bam" - cram: - type: file - description: Unaligned CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.cram": + type: file + description: Unaligned CRAM file + pattern: "*.cram" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03eb9d..db8df0d50552 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -15,38 +15,52 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: input file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - crai: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - csi: - type: file - description: CSI index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: CSI index file + pattern: "*.{csi}" + - crai: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/markdup/meta.yml b/modules/nf-core/samtools/markdup/meta.yml index 7b3d06124c6a..31cb0c632f26 100644 --- a/modules/nf-core/samtools/markdup/meta.yml +++ b/modules/nf-core/samtools/markdup/meta.yml @@ -13,39 +13,62 @@ tools: tool_dev_url: "https://github.com/samtools/samtools" doi: "10.1093/bioinformatics/btp352" licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: A reference genome in FASTA format - pattern: "*.fasta" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A reference genome in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file + pattern: "*{.bam}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file + pattern: "*{.cram}" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: SAM file + pattern: "*{.sam}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - output: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/merge/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 2e8f3dbbb5bd..235aa2194571 100644 --- a/modules/nf-core/samtools/merge/meta.yml +++ b/modules/nf-core/samtools/merge/meta.yml @@ -15,60 +15,81 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_files: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fai: - type: file - description: Index of the reference file the CRAM was created with (optional) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_files: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fai: + type: file + description: Index of the reference file the CRAM was created with (optional) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file + pattern: "*.{bam}" - cram: - type: file - description: CRAM file - pattern: "*.{cram}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: CRAM file + pattern: "*.{cram}" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@yuukiiwa " diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/mpileup/meta.yml b/modules/nf-core/samtools/mpileup/meta.yml index 13038fbc9bd1..0655e0872772 100644 --- a/modules/nf-core/samtools/mpileup/meta.yml +++ b/modules/nf-core/samtools/mpileup/meta.yml @@ -15,38 +15,41 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - intervals: - type: file - description: Interval FILE - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - intervals: + type: file + description: Interval FILE + pattern: "*.bed" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - mpileup: - type: file - description: mpileup file - pattern: "*.{mpileup}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mpileup.gz": + type: file + description: mpileup file + pattern: "*.{mpileup}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/reheader/meta.yml b/modules/nf-core/samtools/reheader/meta.yml index a5e1591452bd..e9699f5637b2 100644 --- a/modules/nf-core/samtools/reheader/meta.yml +++ b/modules/nf-core/samtools/reheader/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "samtools_reheader" @@ -20,30 +19,33 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: BAM/CRAM file to be reheaded - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: BAM/CRAM file to be reheaded + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Reheaded BAM/CRAM file - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bam": + type: file + description: Reheaded BAM/CRAM file + pattern: "*.{bam,cram}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/sormadup/meta.yml b/modules/nf-core/samtools/sormadup/meta.yml index c37ce759583a..bec58e87cc5d 100644 --- a/modules/nf-core/samtools/sormadup/meta.yml +++ b/modules/nf-core/samtools/sormadup/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "samtools_sormadup" description: Collate/Fixmate/Sort/Markdup SAM/BAM/CRAM file @@ -23,6 +22,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args" + identifier: biotools:samtools - samtools_collate: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -33,6 +33,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args2" + identifier: biotools:samtools - samtools_fixmate: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -43,6 +44,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args3" + identifier: biotools:samtools - samtools_sort: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -53,6 +55,7 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args4" + identifier: biotools:samtools - samtools_markdup: description: | SAMtools is a set of utilities for interacting with and post-processing @@ -63,56 +66,82 @@ tools: doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] args_id: "$args5" + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM files - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome file - pattern: "*.{fasta,fa,fna}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM files + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fna}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted and duplicate marked BAM file - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted and duplicate marked BAM file + pattern: "*.bam" - cram: - type: file - description: Sorted and duplicate marked CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted and duplicate marked CRAM file + pattern: "*.cram" - csi: - type: file - description: Sorted and duplicate marked BAM index file - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Sorted and duplicate marked BAM index file + pattern: "*.csi" - crai: - type: file - description: Sorted and duplicate marked CRAM index file - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: Sorted and duplicate marked CRAM index file + pattern: "*.crai" - metrics: - type: file - description: Duplicate metrics file - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Duplicate metrics file + pattern: "*.metrics" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/sort/meta.yml b/modules/nf-core/samtools/sort/meta.yml index 341a7d0ebf46..a9dbec5a8bf8 100644 --- a/modules/nf-core/samtools/sort/meta.yml +++ b/modules/nf-core/samtools/sort/meta.yml @@ -15,52 +15,73 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file(s) - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta,fna}" - optional: true + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file(s) + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta,fna}" + optional: true output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - cram: - type: file - description: Sorted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: Sorted CRAM file + pattern: "*.{cram}" - crai: - type: file - description: CRAM index file (optional) - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file (optional) + pattern: "*.crai" - csi: - type: file - description: BAM index file (optional) - pattern: "*.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: BAM index file (optional) + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml index 735ff8122ae0..77b020f76ed4 100644 --- a/modules/nf-core/samtools/stats/meta.yml +++ b/modules/nf-core/samtools/stats/meta.yml @@ -16,43 +16,46 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing samtools stats output + pattern: "*.{stats}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@FriederikeHanssen" diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index 09ad4c10750e..b98cbb99092d 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.21 - - bioconda::htslib=1.21 + - bioconda::htslib=1.20 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/samtools/view/meta.yml b/modules/nf-core/samtools/view/meta.yml index 27be60d08cd2..caa7b0150d4b 100644 --- a/modules/nf-core/samtools/view/meta.yml +++ b/modules/nf-core/samtools/view/meta.yml @@ -15,77 +15,120 @@ tools: documentation: http://www.htslib.org/doc/samtools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:samtools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - index: - type: file - description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) - pattern: "*.{.bai,.csi,.crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fasta: - type: file - description: Reference file the CRAM was created with (optional) - pattern: "*.{fasta,fa}" - - qname: - type: file - description: Optional file with read names to output only select alignments - pattern: "*.{txt,list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - index: + type: file + description: BAM.BAI/BAM.CSI/CRAM.CRAI file (optional) + pattern: "*.{.bai,.csi,.crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fasta: + type: file + description: Reference file the CRAM was created with (optional) + pattern: "*.{fasta,fa}" + - - qname: + type: file + description: Optional file with read names to output only select alignments + pattern: "*.{txt,list}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: optional filtered/converted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: optional filtered/converted BAM file + pattern: "*.{bam}" - cram: - type: file - description: optional filtered/converted CRAM file - pattern: "*.{cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.cram: + type: file + description: optional filtered/converted CRAM file + pattern: "*.{cram}" - sam: - type: file - description: optional filtered/converted SAM file - pattern: "*.{sam}" - # bai, csi, and crai are created with `--write-index` + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.sam: + type: file + description: optional filtered/converted SAM file + pattern: "*.{sam}" - bai: - type: file - description: optional BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.bai: + type: file + description: optional BAM file index + pattern: "*.{bai}" - csi: - type: file - description: optional tabix BAM file index - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.csi: + type: file + description: optional tabix BAM file index + pattern: "*.{csi}" - crai: - type: file - description: optional CRAM file index - pattern: "*.{crai}" - # unselected and unselected_index are created when passing a qname + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.${file_type}.crai: + type: file + description: optional CRAM file index + pattern: "*.{crai}" - unselected: - type: file - description: optional file with unselected alignments - pattern: "*.unselected.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}: + type: file + description: optional file with unselected alignments + pattern: "*.unselected.{bam,cram,sam}" - unselected_index: - type: file - description: index for the "unselected" file - pattern: "*.unselected.{bai,csi,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.unselected.${file_type}.{bai,csi,crsi}: + type: file + description: index for the "unselected" file + pattern: "*.unselected.{bai,csi,crai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@joseespinosa" diff --git a/modules/nf-core/samtools/view/tests/main.nf.test.snap b/modules/nf-core/samtools/view/tests/main.nf.test.snap index 29e7aeb08ebd..63849b037b78 100644 --- a/modules/nf-core/samtools/view/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/view/tests/main.nf.test.snap @@ -365,6 +365,26 @@ }, "timestamp": "2024-02-12T19:38:23.322874" }, + "cram_to_bam_index_qname_unselected": { + "content": [ + "test.unselected.bam" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.322874" + }, + "cram_to_bam_index_qname_unselected_csi": { + "content": [ + "test.unselected.bam.csi" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.3" + }, + "timestamp": "2024-02-12T19:38:23.328458" + }, "bam_versions": { "content": [ [ diff --git a/modules/nf-core/scimap/mcmicro/meta.yml b/modules/nf-core/scimap/mcmicro/meta.yml index 4a76e3629c97..55be2f51e5cd 100644 --- a/modules/nf-core/scimap/mcmicro/meta.yml +++ b/modules/nf-core/scimap/mcmicro/meta.yml @@ -11,36 +11,45 @@ tools: documentation: "https://scimap.xyz/All%20Functions/A.%20Pre%20Processing/sm.pp.mcmicro_to_scimap/" tool_dev_url: "https://github.com/labsyspharm/scimap" licence: ["MIT License"] + identifier: biotools:SCIMAP input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - cellbyfeature: - type: file - description: CSV file with cell by feature table - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cellbyfeature: + type: file + description: CSV file with cell by feature table + pattern: "*.{csv}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Sorted CSV file - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Sorted CSV file + pattern: "*.{csv}" - h5ad: - type: file - description: Sorted H5AD file - pattern: "*.{h5ad}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5ad": + type: file + description: Sorted H5AD file + pattern: "*.{h5ad}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luiskuhn" maintainers: diff --git a/modules/nf-core/scimap/spatiallda/meta.yml b/modules/nf-core/scimap/spatiallda/meta.yml index b26932f2bc4f..724b5cc97076 100644 --- a/modules/nf-core/scimap/spatiallda/meta.yml +++ b/modules/nf-core/scimap/spatiallda/meta.yml @@ -1,49 +1,73 @@ name: "scimap_spatiallda" -description: SpatialLDA uses an LDA based approach for the identification of cellular neighborhoods, using cell type identities. +description: SpatialLDA uses an LDA based approach for the identification of cellular + neighborhoods, using cell type identities. keywords: - spatial_neighborhoods - scimap - spatial_omics tools: - "scimap": - description: "Scimap is a scalable toolkit for analyzing spatial molecular data. The underlying framework is generalizable to spatial datasets mapped to XY coordinates. The package uses the anndata framework making it easy to integrate with other popular single-cell analysis toolkits. It includes preprocessing, phenotyping, visualization, clustering, spatial analysis and differential spatial testing. The Python-based implementation efficiently deals with large datasets of millions of cells." + description: "Scimap is a scalable toolkit for analyzing spatial molecular data. + The underlying framework is generalizable to spatial datasets mapped to XY coordinates. + The package uses the anndata framework making it easy to integrate with other + popular single-cell analysis toolkits. It includes preprocessing, phenotyping, + visualization, clustering, spatial analysis and differential spatial testing. + The Python-based implementation efficiently deals with large datasets of millions + of cells." homepage: "https://scimap.xyz/" documentation: "https://scimap.xyz/tutorials/1-scimap-tutorial-getting-started/" tool_dev_url: "https://github.com/labsyspharm/scimap" doi: "10.5281/zenodo.7854095" licence: ["MIT licence"] + identifier: biotools:SCIMAP input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - phenotyped: - type: file - description: Phenotyped CSV file, it must contain the columns, sampleID, X, Y and Phenotype. - pattern: "*.{csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - phenotyped: + type: file + description: Phenotyped CSV file, it must contain the columns, sampleID, X, + Y and Phenotype. + pattern: "*.{csv}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spatial_lda_output: - type: file - description: File with the motifs detected from SpatialLDA - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.csv": + type: file + description: File with the motifs detected from SpatialLDA + pattern: "*.{csv}" - composition_plot: - type: file - description: Plot with the motif composition and the cell type composition of motifs. - pattern: "*.{png}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.png": + type: file + description: Plot with the motif composition and the cell type composition of + motifs. + pattern: "*.{png}" - motif_location_plot: - type: file - description: Plot with the locations of the motifs. - pattern: "*.{html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.html": + type: file + description: Plot with the locations of the motifs. + pattern: "*.{html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" - "@chiarasch" diff --git a/modules/nf-core/scoary/meta.yml b/modules/nf-core/scoary/meta.yml index 842fe3652dcb..507bd22efcd2 100644 --- a/modules/nf-core/scoary/meta.yml +++ b/modules/nf-core/scoary/meta.yml @@ -12,38 +12,41 @@ tools: tool_dev_url: https://github.com/AdmiralenOla/Scoary doi: "10.1186/s13059-016-1108-8" licence: ["GPL v3"] + identifier: biotools:scoary input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genes: - type: file - description: A presence/absence matrix of genes in the pan-genome - pattern: "*.csv" - - traits: - type: file - description: A CSV file containing trait information per-sample - pattern: "*.csv" - - tree: - type: file - description: A Newick formtted tree for phylogenetic analyses - pattern: "*.{dnd,nwk,treefile}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genes: + type: file + description: A presence/absence matrix of genes in the pan-genome + pattern: "*.csv" + - traits: + type: file + description: A CSV file containing trait information per-sample + pattern: "*.csv" + - - tree: + type: file + description: A Newick formtted tree for phylogenetic analyses + pattern: "*.{dnd,nwk,treefile}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: Gene associations in a CSV file per trait - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Gene associations in a CSV file per trait + pattern: "*.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/scramble/clusteranalysis/meta.yml b/modules/nf-core/scramble/clusteranalysis/meta.yml index 4e5200fcc71c..14be2cb42e1b 100644 --- a/modules/nf-core/scramble/clusteranalysis/meta.yml +++ b/modules/nf-core/scramble/clusteranalysis/meta.yml @@ -1,5 +1,6 @@ name: "scramble_clusteranalysis" -description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped clusters found by `cluster_identifier` +description: The Cluster Analysis tool of Scramble analyses and interprets the soft-clipped + clusters found by `cluster_identifier` keywords: - soft-clipped clusters - scramble @@ -12,46 +13,65 @@ tools: documentation: "https://github.com/GeneDx/scramble" tool_dev_url: "https://github.com/GeneDx/scramble" licence: ["CC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - clusters: - type: file - description: Tab-delimited text file containing soft-clipped clusters. Has to be generated using scramble/clusteridentifier - pattern: "*clusters.txt" - - fasta: - type: file - description: Optional fasta reference file. This file is needed to create a VCF file and to evaluate predicted deletions. - pattern: "*.{fasta,fa}" - - mei_ref: - type: file - description: Optional fasta file containing the MEI reference. This file should only be supplied in special occasions where the default isn't correct - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - clusters: + type: file + description: Tab-delimited text file containing soft-clipped clusters. Has to + be generated using scramble/clusteridentifier + pattern: "*clusters.txt" + - - fasta: + type: file + description: Optional fasta reference file. This file is needed to create a + VCF file and to evaluate predicted deletions. + pattern: "*.{fasta,fa}" + - - mei_ref: + type: file + description: Optional fasta file containing the MEI reference. This file should + only be supplied in special occasions where the default isn't correct + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - meis_tab: - type: file - description: Tab-delimited text file containing MEI calls - pattern: "*_MEIs.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_MEIs.txt": + type: file + description: Tab-delimited text file containing MEI calls + pattern: "*_MEIs.txt" - dels_tab: - type: file - description: Tab-delimited text file containing predicted deletions - pattern: "*_PredictedDeletions.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_PredictedDeletions.txt": + type: file + description: Tab-delimited text file containing predicted deletions + pattern: "*_PredictedDeletions.txt" - vcf: - type: file - description: A VCF file containing the MEI calls and/or the predicted deletions (depending on the given arguments) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: A VCF file containing the MEI calls and/or the predicted deletions + (depending on the given arguments) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/scramble/clusteridentifier/meta.yml b/modules/nf-core/scramble/clusteridentifier/meta.yml index 17aab2c08a80..c8973fc8eef9 100644 --- a/modules/nf-core/scramble/clusteridentifier/meta.yml +++ b/modules/nf-core/scramble/clusteridentifier/meta.yml @@ -11,38 +11,41 @@ tools: documentation: "https://github.com/GeneDx/scramble" tool_dev_url: "https://github.com/GeneDx/scramble" licence: ["CC"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: Index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference FASTA file (mandatory when using CRAM files) - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: Index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - fasta: + type: file + description: The reference FASTA file (mandatory when using CRAM files) + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - clusters: - type: file - description: Tab-delimited file containing the soft-clipped clusters - pattern: "*.clusters.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.clusters.txt": + type: file + description: Tab-delimited file containing the soft-clipped clusters + pattern: "*.clusters.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/seacr/callpeak/meta.yml b/modules/nf-core/seacr/callpeak/meta.yml index 9326b02a6c51..2ff21c181701 100644 --- a/modules/nf-core/seacr/callpeak/meta.yml +++ b/modules/nf-core/seacr/callpeak/meta.yml @@ -17,38 +17,41 @@ tools: homepage: https://github.com/FredHutch/SEACR documentation: https://github.com/FredHutch/SEACR licence: ["GPL-2.0-only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: | - The target bedgraph file from which the peaks will be calculated. - - ctrlbedgraph: - type: file - description: | - Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. - - threshold: - type: integer - description: | - Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + The target bedgraph file from which the peaks will be calculated. + - ctrlbedgraph: + type: file + description: | + Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. + - - threshold: + type: integer + description: | + Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: Bed file containing the calculated peaks. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: Bed file containing the calculated peaks. + pattern: "*.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chris-cheshire" maintainers: diff --git a/modules/nf-core/segemehl/align/meta.yml b/modules/nf-core/segemehl/align/meta.yml index fc8e43bab5ba..46b0084b667c 100644 --- a/modules/nf-core/segemehl/align/meta.yml +++ b/modules/nf-core/segemehl/align/meta.yml @@ -1,5 +1,6 @@ name: "segemehl_align" -description: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection +description: A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection keywords: - alignment - circrna @@ -7,65 +8,87 @@ keywords: - fusions tools: - "segemehl": - description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection" + description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection" homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" doi: "10.1186/gb-2014-15-2-r34" licence: ["GPL v3"] + identifier: biotools:segemehl input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTA or FASTQ files - pattern: "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" - - fasta: - type: file - description: Reference genome FASTA file used to construct Segemehl - pattern: "*.{fa,fasta}" - - index: - type: file - description: Segemehl Index file from SEGEMEHL_INDEX - pattern: "*.idx" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTA or FASTQ files + pattern: "*.{fa,fasta,fq,fastq,fq.gz,fastq.gz}" + - - fasta: + type: file + description: Reference genome FASTA file used to construct Segemehl + pattern: "*.{fa,fasta}" + - - index: + type: file + description: Segemehl Index file from SEGEMEHL_INDEX + pattern: "*.idx" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - alignment: - type: file - description: | - File containing genomic alignments in SAM format - (please add "-b" flag to task.ext.args for BAM) - pattern: "*.{sam,bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.${suffix}: + type: file + description: | + File containing genomic alignments in SAM format + (please add "-b" flag to task.ext.args for BAM) + pattern: "*.{sam,bam}" - trans_alignments: - type: file - description: | - Custom text file containing all single split alignments predicted to be in trans - (optional, only if -S flag is set in task.ext.args) - pattern: "*.trns.txt" - - single_bed: - type: file - description: | - Bed file containing all single splice events predicted - in the split read alignments. - (optional, only if -S flag is set in task.ext.args) - pattern: "*.sngl.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.trns.txt: + type: file + description: | + Custom text file containing all single split alignments predicted to be in trans + (optional, only if -S flag is set in task.ext.args) + pattern: "*.trns.txt" - multi_bed: - type: file - description: | - Bed file containing all splice events predicted - in the split read alignments. - (optional, only if -S flag is set in task.ext.args) - pattern: "*.mult.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.mult.bed: + type: file + description: | + Bed file containing all splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.mult.bed" + - single_bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.sngl.bed: + type: file + description: | + Bed file containing all single splice events predicted + in the split read alignments. + (optional, only if -S flag is set in task.ext.args) + pattern: "*.sngl.bed" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" - "@nictru" diff --git a/modules/nf-core/segemehl/index/meta.yml b/modules/nf-core/segemehl/index/meta.yml index a036602da95a..d6c1d983f7b3 100644 --- a/modules/nf-core/segemehl/index/meta.yml +++ b/modules/nf-core/segemehl/index/meta.yml @@ -7,25 +7,29 @@ keywords: - fusions tools: - "segemehl": - description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection" + description: "A multi-split mapping algorithm for circular RNA, splicing, trans-splicing + and fusion detection" homepage: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" documentation: "https://www.bioinf.uni-leipzig.de/Software/segemehl/" doi: "10.1186/gb-2014-15-2-r34" licence: ["GPL v3"] + identifier: biotools:segemehl input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fa,fasta}" + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - index: - type: file - description: Segemehl index file - pattern: "*.{idx}" + - "*.idx": + type: file + description: Segemehl index file + pattern: "*.{idx}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" maintainers: diff --git a/modules/nf-core/semibin/singleeasybin/meta.yml b/modules/nf-core/semibin/singleeasybin/meta.yml index 9e7c491a4614..e1f36adbfc07 100644 --- a/modules/nf-core/semibin/singleeasybin/meta.yml +++ b/modules/nf-core/semibin/singleeasybin/meta.yml @@ -12,50 +12,77 @@ tools: tool_dev_url: "https://github.com/BigDataBiology/SemiBin" doi: "10.1038/s41467-022-29843-y" licence: ["MIT"] + identifier: biotools:semibin input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram}" - - fasta: - type: file - description: Fasta file of the assembled contigs - pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the assembled contigs + pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz}" + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv: - type: file - description: generated files - pattern: "*.csv" - - h5: - type: file - description: trained model - pattern: "*.h5" - - output_prerecluster_bins: - type: file - description: output_prerecluster_bins - pattern: "output_prerecluster_bins/*.fa" - - output_recluster_bins: - type: file - description: output_recluster_bins - pattern: "output_recluster_bins/*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: generated files + pattern: "*.csv" + - model: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.h5": + type: file + description: model file + pattern: "*.h5" + - output_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output_prerecluster_bins/*.fa: + type: file + description: precluster fasta files + pattern: "*.fa" + - recluster_fasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output_recluster_bins/*.fa: + type: file + description: recluster fasta files + pattern: "*.fa" - tsv: - type: file - description: information of bins - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: information of bins + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BigDataBiology" maintainers: diff --git a/modules/nf-core/sentieon/applyvarcal/meta.yml b/modules/nf-core/sentieon/applyvarcal/meta.yml index da92ce343668..e8505a2ae5b4 100644 --- a/modules/nf-core/sentieon/applyvarcal/meta.yml +++ b/modules/nf-core/sentieon/applyvarcal/meta.yml @@ -17,68 +17,80 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - vcf: - type: file - description: VCF file to be recalibrated, this should be the same file as used for the first stage VariantRecalibrator. - pattern: "*.vcf" - - vcf_tbi: - type: file - description: tabix index for the input vcf file. - pattern: "*.vcf.tbi" - - recal: - type: file - description: Recalibration file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: "*.recal" - - recal_index: - type: file - description: Index file for the recalibration file. - pattern: ".recal.idx" - - tranches: - type: file - description: Tranches file produced when the input vcf was run through VariantRecalibrator in stage 1. - pattern: ".tranches" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - vcf: + type: file + description: VCF file to be recalibrated, this should be the same file as used + for the first stage VariantRecalibrator. + pattern: "*.vcf" + - vcf_tbi: + type: file + description: tabix index for the input vcf file. + pattern: "*.vcf.tbi" + - recal: + type: file + description: Recalibration file produced when the input vcf was run through + VariantRecalibrator in stage 1. + pattern: "*.recal" + - recal_index: + type: file + description: Index file for the recalibration file. + pattern: ".recal.idx" + - tranches: + type: file + description: Tranches file produced when the input vcf was run through VariantRecalibrator + in stage 1. + pattern: ".tranches" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: compressed vcf file containing the recalibrated variants. - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.vcf.gz": + type: file + description: compressed vcf file containing the recalibrated variants. + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of recalibrated vcf file. - pattern: "*vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*.tbi": + type: file + description: Index of recalibrated vcf file. + pattern: "*vcf.gz.tbi" - versions: - type: file - description: File containing software versions. - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions. + pattern: "versions.yml" authors: - "@assp8200" maintainers: diff --git a/modules/nf-core/sentieon/bwaindex/meta.yml b/modules/nf-core/sentieon/bwaindex/meta.yml index 0af45ad885c6..acbd14d51afd 100644 --- a/modules/nf-core/sentieon/bwaindex/meta.yml +++ b/modules/nf-core/sentieon/bwaindex/meta.yml @@ -13,29 +13,32 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bwa: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@maxulysse" diff --git a/modules/nf-core/sentieon/bwamem/meta.yml b/modules/nf-core/sentieon/bwamem/meta.yml index 9dad7e68ee0f..b27dd4877f2a 100644 --- a/modules/nf-core/sentieon/bwamem/meta.yml +++ b/modules/nf-core/sentieon/bwamem/meta.yml @@ -15,56 +15,63 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Genome fastq files (single-end or paired-end) - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Genome fastq files (single-end or paired-end) + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - bam_and_bai: - type: file - description: BAM file with corresponding index. - pattern: "*.{bam,bai}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM file with corresponding index. + pattern: "*.{bam,bai}" + - ${prefix}.{bai,crai}: + type: file + description: BAM file with corresponding index. + pattern: "*.{bam,bai}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/collectvcmetrics/meta.yml b/modules/nf-core/sentieon/collectvcmetrics/meta.yml index e81e47bcfcea..9a1867e444bc 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/meta.yml +++ b/modules/nf-core/sentieon/collectvcmetrics/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sentieon_collectvcmetrics" -description: Accelerated implementation of the Picard CollectVariantCallingMetrics tool. +description: Accelerated implementation of the Picard CollectVariantCallingMetrics + tool. keywords: - vcf - sentieon @@ -14,83 +14,90 @@ tools: homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ licence: ["Commercial (requires license for use; redistribution allowed)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta5: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: Sorted VCF file [required] - pattern: "*.vcf" - - tbi: - type: file - description: VCF index file [required] - pattern: "*.vcf{,.gz}.tbi" - - dbsnp: - type: file - description: dbsnp VCF file [required] - pattern: "*.vcf{,.gz}" - - dbsnp_tbi: - type: file - description: dbsnp VCF index file [required] - pattern: "*.vcf{,.gz}.tbi" - - interval: - type: file - description: BED file of genome regions to draw coverage from - pattern: "*.bed" - - fasta: - type: file - description: Genome fasta file [required] - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file [required] - pattern: "*.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: Sorted VCF file [required] + pattern: "*.vcf" + - tbi: + type: file + description: VCF index file [required] + pattern: "*.vcf{,.gz}.tbi" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - dbsnp: + type: file + description: dbsnp VCF file [required] + pattern: "*.vcf{,.gz}" + - dbsnp_tbi: + type: file + description: dbsnp VCF index file [required] + pattern: "*.vcf{,.gz}.tbi" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file [required] + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file [required] + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - interval: + type: file + description: BED file of genome regions to draw coverage from + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - metrics: - type: file - description: | - Metrics file from VCF - pattern: "*.variant_calling_detail_metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.variant_calling_detail_metrics": + type: file + description: | + Metrics file from VCF + pattern: "*.variant_calling_detail_metrics" - summary: - type: file - description: | - Summary of VCF metrics - pattern: "*.collectvcmetrics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.variant_calling_summary_metrics": + type: file + description: | + Summary of VCF metrics + pattern: "*.collectvcmetrics.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/sentieon/coveragemetrics/meta.yml b/modules/nf-core/sentieon/coveragemetrics/meta.yml index 9f6c590cc4a9..e024658ff55f 100644 --- a/modules/nf-core/sentieon/coveragemetrics/meta.yml +++ b/modules/nf-core/sentieon/coveragemetrics/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "sentieon_coveragemetrics" description: Accelerated implementation of the GATK DepthOfCoverage tool. @@ -14,89 +13,129 @@ tools: homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ licence: ["Commercial (requires license for use; redistribution allowed)"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAM/CRAM/SAM file index - pattern: "*.{bai,crai}" - - interval: - type: file - description: BED file of genome regions to draw coverage from - pattern: "*.bed" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - gene_list: - type: file - description: RefSeq file used to aggregate the results - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAM/CRAM/SAM file index + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - interval: + type: file + description: BED file of genome regions to draw coverage from + pattern: "*.bed" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gene_list: + type: file + description: RefSeq file used to aggregate the results + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - per_locus: - type: file - description: The per locus coverage with no partition. - pattern: "${sample_id}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $prefix: + type: file + description: The per locus coverage with no partition. + pattern: "${sample_id}" - sample_summary: - type: file - description: The summary for PARTITION_GROUP sample, aggregated over all bases. - pattern: "${sample_id}.sample_summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_summary: + type: file + description: The summary for PARTITION_GROUP sample, aggregated over all bases. + pattern: "${sample_id}.sample_summary" - statistics: - type: file - description: The statistics for PARTITION_GROUP library, aggregated by interval. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_interval_statistics: + type: file + description: The statistics for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_statistics" - coverage_counts: - type: file - description: Contains the histogram of loci with depth larger than x. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_cumulative_coverage_counts: + type: file + description: Contains the histogram of loci with depth larger than x. + pattern: "${sample_id}.interval_statistics" - coverage_proportions: - type: file - description: Contains the normalized histogram of loci with depth larger than x. - pattern: "${sample_id}.interval_statistics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_cumulative_coverage_proportions: + type: file + description: Contains the normalized histogram of loci with depth larger than + x. + pattern: "${sample_id}.interval_statistics" - interval_summary: - type: file - description: The summary for PARTITION_GROUP library, aggregated by interval. - pattern: "${sample_id}.interval_summary" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}.${partitions_output}_interval_summary: + type: file + description: The summary for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_summary" + - _summary: + type: file + description: The summary for PARTITION_GROUP library, aggregated by interval. + pattern: "${sample_id}.interval_summary" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/sentieon/datametrics/meta.yml b/modules/nf-core/sentieon/datametrics/meta.yml index d2d1450a692a..a72ff866b467 100644 --- a/modules/nf-core/sentieon/datametrics/meta.yml +++ b/modules/nf-core/sentieon/datametrics/meta.yml @@ -11,72 +11,110 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index of th sorted BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of th sorted BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - mq_metrics: - type: file - description: File containing the information about mean base quality score for each sequencing cycle - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*mq_metrics.txt": + type: file + description: File containing the information about mean base quality score for + each sequencing cycle + pattern: "*.txt" - qd_metrics: - type: file - description: File containing the information about number of bases with a specific base quality score - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*qd_metrics.txt": + type: file + description: File containing the information about number of bases with a specific + base quality score + pattern: "*.txt" - gc_summary: - type: file - description: File containing the information about GC bias in the reference and the sample - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*gc_summary.txt": + type: file + description: File containing the information about GC bias in the reference + and the sample + pattern: "*.txt" - gc_metrics: - type: file - description: File containing the information about GC bias in the reference and the sample - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*gc_metrics.txt": + type: file + description: File containing the information about GC bias in the reference + and the sample + pattern: "*.txt" - aln_metrics: - type: file - description: File containing the statistics about the alignment of the reads - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*aln_metrics.txt": + type: file + description: File containing the statistics about the alignment of the reads + pattern: "*.txt" - is_metrics: - type: file - description: File containing the information about statistical distribution of insert sizes - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*is_metrics.txt": + type: file + description: File containing the information about statistical distribution + of insert sizes + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dedup/meta.yml b/modules/nf-core/sentieon/dedup/meta.yml index 0efbb96c2292..003d74befe77 100644 --- a/modules/nf-core/sentieon/dedup/meta.yml +++ b/modules/nf-core/sentieon/dedup/meta.yml @@ -1,5 +1,7 @@ name: sentieon_dedup -description: Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector collects read information that is used by Dedup which in turn marks or removes duplicate reads. +description: Runs the sentieon tool LocusCollector followed by Dedup. LocusCollector + collects read information that is used by Dedup which in turn marks or removes duplicate + reads. keywords: - mem - dedup @@ -14,76 +16,116 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - cram: - type: file - description: CRAM file - pattern: "*.cram" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.cram": + type: file + description: CRAM file + pattern: "*.cram" - crai: - type: file - description: CRAM index file - pattern: "*.crai" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.crai": + type: file + description: CRAM index file + pattern: "*.crai" - bam: - type: file - description: BAM file. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file. + pattern: "*.bam" - bai: - type: file - description: BAI file - pattern: "*.bai" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: BAI file + pattern: "*.bai" - score: - type: file - description: The score file indicates which reads LocusCollector finds are likely duplicates. - pattern: "*.score" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.score": + type: file + description: The score file indicates which reads LocusCollector finds are likely + duplicates. + pattern: "*.score" - metrics: - type: file - description: Output file containing Dedup metrics incl. histogram data. - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: Output file containing Dedup metrics incl. histogram data. + pattern: "*.metrics" - metrics_multiqc_tsv: - type: file - description: Output tsv-file containing Dedup metrics excl. histogram data. - pattern: "*.metrics.multiqc.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.metrics.multiqc.tsv": + type: file + description: Output tsv-file containing Dedup metrics excl. histogram data. + pattern: "*.metrics.multiqc.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/dnamodelapply/meta.yml b/modules/nf-core/sentieon/dnamodelapply/meta.yml index 250765457701..2505aff74e9a 100644 --- a/modules/nf-core/sentieon/dnamodelapply/meta.yml +++ b/modules/nf-core/sentieon/dnamodelapply/meta.yml @@ -12,65 +12,74 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - vcf: - type: file - description: INPUT VCF file - pattern: "*.{vcf,vcf.gz}" - - idx: - type: file - description: Index of the input VCF file - pattern: "*.{tbi}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: INPUT VCF file + pattern: "*.{vcf,vcf.gz}" + - idx: + type: file + description: Index of the input VCF file + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - ml_model: + type: file + description: machine learning model file + pattern: "*.model" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: INPUT VCF file - pattern: "*.{vcf,vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: INPUT VCF file + pattern: "*.{vcf,vcf.gz}" - index: - type: file - description: Index of the input VCF file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Index of the input VCF file + pattern: "*.{tbi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/dnascope/meta.yml b/modules/nf-core/sentieon/dnascope/meta.yml index 6b61cee828f2..e3e0eba8c8ee 100644 --- a/modules/nf-core/sentieon/dnascope/meta.yml +++ b/modules/nf-core/sentieon/dnascope/meta.yml @@ -1,5 +1,6 @@ name: sentieon_dnascope -description: DNAscope algorithm performs an improved version of Haplotype variant calling. +description: DNAscope algorithm performs an improved version of Haplotype variant + calling. keywords: - dnascope - sentieon @@ -11,109 +12,127 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - intervals: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" - - meta2: - type: map - description: | - Groovy Map containing meta information for fasta. - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing meta information for fasta index. - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing meta information for dbsnp. - - dbsnp: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - meta5: - type: map - description: | - Groovy Map containing meta information for dbsnp_tbi. - - dbsnp_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - meta6: - type: map - description: | - Groovy Map containing meta information for machine learning model for Dnascope. - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" - - ml_model: - type: file - description: machine learning model file - pattern: "*.model" - - pcr_indel_model: - type: string - description: | - Controls the option pcr_indel_model for Dnascope. - The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". - See Sentieons documentation for further explanation. - - emit_vcf: - type: string - description: | - Controls the vcf output from Dnascope. - Possible options are "all", "confident" and "variant". - See Sentieons documentation for further explanation. - - emit_gvcf: - type: boolean - description: If true, the haplotyper will output a gvcf + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - intervals: + type: file + description: bed or interval_list file containing interval in the reference + that will be used in the analysis + pattern: "*.{bed,interval_list}" + - - meta2: + type: map + description: | + Groovy Map containing meta information for fasta. + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing meta information for fasta index. + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing meta information for dbsnp. + - dbsnp: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - - meta5: + type: map + description: | + Groovy Map containing meta information for dbsnp_tbi. + - dbsnp_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing meta information for machine learning model for Dnascope. + - ml_model: + type: file + description: machine learning model file + pattern: "*.model" + - - pcr_indel_model: + type: string + description: | + Controls the option pcr_indel_model for Dnascope. + The possible options are "NONE" (used for PCR free samples), and "HOSTILE", "AGGRESSIVE" and "CONSERVATIVE". + See Sentieons documentation for further explanation. + - - emit_vcf: + type: string + description: | + Controls the vcf output from Dnascope. + Possible options are "all", "confident" and "variant". + See Sentieons documentation for further explanation. + - - emit_gvcf: + type: boolean + description: If true, the haplotyper will output a gvcf output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.unfiltered.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.unfiltered.vcf.gz" - vcf_tbi: - type: file - description: Index of VCF file - pattern: "*.unfiltered.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.unfiltered.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz": + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index of GVCF file - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz.tbi": + type: file + description: Index of GVCF file + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/gvcftyper/meta.yml b/modules/nf-core/sentieon/gvcftyper/meta.yml index 5a83eb03082f..f022553711ca 100644 --- a/modules/nf-core/sentieon/gvcftyper/meta.yml +++ b/modules/nf-core/sentieon/gvcftyper/meta.yml @@ -12,59 +12,89 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gvcfs: - type: file - description: | - gVCF(.gz) file - pattern: "*.{vcf,vcf.gz}" - - tbis: - type: file - description: | - index of gvcf file - pattern: "*.tbi" - - intervals: - type: file - description: Interval file with the genomic regions included in the library (optional) - - fasta: - type: file - description: Reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Reference fasta index file - pattern: "*.fai" - - dbsnp: - type: file - description: dbSNP VCF file - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: dbSNP VCF index file - pattern: "*.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gvcfs: + type: file + description: | + gVCF(.gz) file + pattern: "*.{vcf,vcf.gz}" + - tbis: + type: file + description: | + index of gvcf file + pattern: "*.tbi" + - intervals: + type: file + description: Interval file with the genomic regions included in the library + (optional) + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.fasta" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Reference fasta index file + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: dbSNP VCF file + pattern: "*.vcf.gz" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp_tbi: + type: file + description: dbSNP VCF index file + pattern: "*.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Genotyped VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Tbi index for VCF file - pattern: "*.vcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.vcf.gz" + - vcf_gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: VCF index file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/haplotyper/meta.yml b/modules/nf-core/sentieon/haplotyper/meta.yml index e5b3f34a0690..ee0e6152f04f 100644 --- a/modules/nf-core/sentieon/haplotyper/meta.yml +++ b/modules/nf-core/sentieon/haplotyper/meta.yml @@ -11,76 +11,117 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - recal_table: - type: file - description: Recalibration table from sentieon/qualcal (optional) - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" - - dbsnp: - type: file - description: VCF file containing known sites (optional) - - dbsnp_tbi: - type: file - description: VCF index of dbsnp (optional) - - emit_vcf: - type: string - description: | - Controls the vcf output from the haplotyper. - If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". - If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". - If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident". - - emit_gvcf: - type: boolean - description: If true, the haplotyper will output a gvcf + - - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - recal_table: + type: file + description: Recalibration table from sentieon/qualcal (optional) + - - meta1: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp: + type: file + description: VCF file containing known sites (optional) + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - dbsnp_tbi: + type: file + description: VCF index of dbsnp (optional) + - - emit_vcf: + type: string + description: | + Controls the vcf output from the haplotyper. + If emit_vcf is set to "all" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "all". + If emit_vcf is set to "confident" then the haplotyper will output a vcf generated by the haplotyper in emit-mode "confident". + If emit_vcf is set to "variant" then the haplotyper will output a vcf generated by the haplotyper in emit_mode "confident". + - - emit_gvcf: + type: boolean + description: If true, the haplotyper will output a gvcf output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.unfiltered.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.unfiltered.vcf.gz" - vcf_tbi: - type: file - description: Index of VCF file - pattern: "*.unfiltered.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.unfiltered.vcf.gz.tbi": + type: file + description: Index of VCF file + pattern: "*.unfiltered.vcf.gz.tbi" - gvcf: - type: file - description: Compressed GVCF file - pattern: "*.g.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz": + type: file + description: Compressed GVCF file + pattern: "*.g.vcf.gz" - gvcf_tbi: - type: file - description: Index of GVCF file - pattern: "*.g.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.g.vcf.gz.tbi": + type: file + description: Index of GVCF file + pattern: "*.g.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/qualcal/meta.yml b/modules/nf-core/sentieon/qualcal/meta.yml index 76c124b0d87b..7be3b9e77e60 100644 --- a/modules/nf-core/sentieon/qualcal/meta.yml +++ b/modules/nf-core/sentieon/qualcal/meta.yml @@ -1,4 +1,3 @@ ---- name: "sentieon_qualcal" description: Generate recalibration table and optionally perform base quality recalibration keywords: @@ -12,74 +11,125 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - - known_sites: - type: file - description: VCF files with known sites for indels / snps (optional) - pattern: "*.vcf.gz" - - known_sites_tbi: - type: file - description: Tabix index of the known_sites (optional) - pattern: "*.vcf.gz.tbi" - - recalibration_table: - type: file - description: File containing recalibration values (optional) - pattern: "*.table" - - generate_recalibrated_bams: - type: boolean - description: If truem, writes recalibrated bams to disc - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - known_sites: + type: file + description: VCF files with known sites for indels / snps (optional) + pattern: "*.vcf.gz" + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - known_sites_tbi: + type: file + description: Tabix index of the known_sites (optional) + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - recalibration_table: + type: file + description: File containing recalibration values (optional) + pattern: "*.table" + - - generate_recalibrated_bams: + type: boolean + description: If truem, writes recalibrated bams to disc output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - table: - type: file - description: Pre Recalibration table (optional) - pattern: "*.table" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table": + type: file + description: Pre Recalibration table (optional) + pattern: "*.table" - table_post: - type: file - description: Post recalibration table (optional) - pattern: "*.table.post" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.table.post": + type: file + description: Post recalibration table (optional) + pattern: "*.table.post" - recal_alignment: - type: file - description: Recalibrated input files (optional) - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{cram,bam}": + type: file + description: Recalibrated input files (optional) + pattern: "*.{bam,cram}" - csv: - type: file - description: Recalibration results output file used for plotting. (optional) - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: Recalibration results output file used for plotting. (optional) + pattern: "*.csv" - pdf: - type: file - description: PDF file containing graphs (optional) - pattern: "*.pdf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.pdf": + type: file + description: PDF file containing graphs (optional) + pattern: "*.pdf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/sentieon/readwriter/meta.yml b/modules/nf-core/sentieon/readwriter/meta.yml index 9f107663d621..6e79ea190b03 100644 --- a/modules/nf-core/sentieon/readwriter/meta.yml +++ b/modules/nf-core/sentieon/readwriter/meta.yml @@ -1,5 +1,6 @@ name: sentieon_readwriter -description: Merges BAM files, and/or convert them into cram files. Also, outputs the result of applying the Base Quality Score Recalibration to a file. +description: Merges BAM files, and/or convert them into cram files. Also, outputs + the result of applying the Base Quality Score Recalibration to a file. keywords: - merge - convert @@ -12,59 +13,78 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file. - pattern: "*.{bam,cram}" - - index: - type: file - description: BAI/CRAI file. - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: The index of the FASTA reference. - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file. + pattern: "*.{bam,cram}" + - index: + type: file + description: BAI/CRAI file. + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: The index of the FASTA reference. + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - output: - type: file - description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix = .bam", CRAM "ext.prefix = .cram". Defaults to cram - pattern: "*.{bam,cram}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM/CRAM file. Depends on how ext.prefix is set. BAM "ext.prefix + = .bam", CRAM "ext.prefix = .cram". Defaults to cram + pattern: "*.{bam,cram}" - index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}.${index}: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" - output_index: - type: file - description: BAM/CRAM alignment and the corresponding index file + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: file + description: BAM/CRAM alignment and the corresponding index file + - ${prefix}.${index}: + type: file + description: BAM/CRAM alignment and the corresponding index file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/tnfilter/meta.yml b/modules/nf-core/sentieon/tnfilter/meta.yml index d184dd6b7b2e..41dfa94fb6d4 100644 --- a/modules/nf-core/sentieon/tnfilter/meta.yml +++ b/modules/nf-core/sentieon/tnfilter/meta.yml @@ -14,72 +14,90 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - vcf: - type: file - description: compressed vcf file from tnhaplotyper2 - pattern: "*.vcf.gz" - - vcf_tbi: - type: file - description: Tabix index of vcf file - pattern: "*vcf.gz.tbi" - - stats: - type: file - description: Stats file that pairs with output vcf file - pattern: "*vcf.gz.stats" - - contamination: - type: file - description: the location and file name of the file containing the contamination information produced by ContaminationModel. - pattern: "*.contamination_data.tsv" - - segments: - type: file - description: the location and file name of the file containing the tumor segments information produced by ContaminationModel. - pattern: "*.segments" - - orientation_priors: - type: file - description: the location and file name of the file containing the orientation bias information produced by OrientationBias. - pattern: "*.orientation_data.tsv" - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fasta.fai" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: compressed vcf file from tnhaplotyper2 + pattern: "*.vcf.gz" + - vcf_tbi: + type: file + description: Tabix index of vcf file + pattern: "*vcf.gz.tbi" + - stats: + type: file + description: Stats file that pairs with output vcf file + pattern: "*vcf.gz.stats" + - contamination: + type: file + description: the location and file name of the file containing the contamination + information produced by ContaminationModel. + pattern: "*.contamination_data.tsv" + - segments: + type: file + description: the location and file name of the file containing the tumor segments + information produced by ContaminationModel. + pattern: "*.segments" + - orientation_priors: + type: file + description: the location and file name of the file containing the orientation + bias information produced by OrientationBias. + pattern: "*.orientation_data.tsv" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" output: - vcf: - type: file - description: file containing filtered tnhaplotyper2 calls. - pattern: "*.vcf.gz" + - meta: + type: file + description: file containing filtered tnhaplotyper2 calls. + pattern: "*.vcf.gz" + - "*.vcf.gz": + type: file + description: file containing filtered tnhaplotyper2 calls. + pattern: "*.vcf.gz" - vcf_tbi: - type: file - description: tbi file that pairs with vcf. - pattern: "*.vcf.gz.tbi" + - meta: + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" + - "*.vcf.gz.tbi": + type: file + description: tbi file that pairs with vcf. + pattern: "*.vcf.gz.tbi" - stats: - type: file - description: file containing statistics of the tnfilter run. - pattern: "*.stats" + - meta: + type: file + description: file containing statistics of the tnfilter run. + pattern: "*.stats" + - "*.vcf.gz.stats": + type: file + description: file containing statistics of the tnfilter run. + pattern: "*.stats" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" diff --git a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml index 9a0cafd81f74..8e1f481d7b57 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/meta.yml +++ b/modules/nf-core/sentieon/tnhaplotyper2/meta.yml @@ -1,5 +1,6 @@ name: sentieon_tnhaplotyper2 -description: Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched pairs. +description: Tnhaplotyper2 performs somatic variant calling on the tumor-normal matched + pairs. keywords: - tnseq - tnhaplotyper2 @@ -12,122 +13,161 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta6: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta7: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta8: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - intervals: - type: file - description: Bed file with the genomic regions included in the library (optional) - - dict: - type: file - description: GATK sequence dictionary - pattern: "*.dict" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - germline_resource: - type: file - description: Population vcf of germline sequencing, containing allele fractions. - pattern: "*.vcf.gz" - - germline_resource_tbi: - type: file - description: Index file for the germline resource. - pattern: "*.vcf.gz.tbi" - - panel_of_normals: - type: file - description: vcf file to be used as a panel of normals. - pattern: "*.vcf.gz" - - panel_of_normals_tbi: - type: file - description: Index for the panel of normals. - pattern: "*.vcf.gz.tbi" - - emit_orientation_data: - type: boolean - description: If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm OrientationBias. - - emit_contamination_data: - type: boolean - description: If true, the module will run the sentieon algorithm TNhaplotyper2 followed by the sentieon algorithm ContaminationModel. + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - intervals: + type: file + description: Bed file with the genomic regions included in the library (optional) + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - germline_resource: + type: file + description: Population vcf of germline sequencing, containing allele fractions. + pattern: "*.vcf.gz" + - - meta6: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - germline_resource_tbi: + type: file + description: Index file for the germline resource. + pattern: "*.vcf.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - panel_of_normals: + type: file + description: vcf file to be used as a panel of normals. + pattern: "*.vcf.gz" + - - meta8: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - panel_of_normals_tbi: + type: file + description: Index for the panel of normals. + pattern: "*.vcf.gz.tbi" + - - emit_orientation_data: + type: boolean + description: If true, the module will run the sentieon algorithm TNhaplotyper2 + followed by the sentieon algorithm OrientationBias. + - - emit_contamination_data: + type: boolean + description: If true, the module will run the sentieon algorithm TNhaplotyper2 + followed by the sentieon algorithm ContaminationModel. output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - orientation_data: - type: file - description: TSV file from Sentieon's algorithm OrientationBias - pattern: "*.orientation_data.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.orientation_data.tsv": + type: file + description: TSV file from Sentieon's algorithm OrientationBias + pattern: "*.orientation_data.tsv" - contamination_data: - type: file - description: TSV file from Sentieon's algorithm ContaminationModel - pattern: "*.contamination_data.tsv" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.contamination_data.tsv": + type: file + description: TSV file from Sentieon's algorithm ContaminationModel + pattern: "*.contamination_data.tsv" - contamination_segments: - type: file - description: Tumour segments file from Sentieon's algorithm ContaminationModel - pattern: "*.segments" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.segments": + type: file + description: Tumour segments file from Sentieon's algorithm ContaminationModel + pattern: "*.segments" + - stats: + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: Stats file from Sentieon's algorithm + pattern: "*.stats" - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf.gz}" - index: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/tnscope/meta.yml b/modules/nf-core/sentieon/tnscope/meta.yml index 8299888b3bd4..36dcd8d8e688 100644 --- a/modules/nf-core/sentieon/tnscope/meta.yml +++ b/modules/nf-core/sentieon/tnscope/meta.yml @@ -1,5 +1,6 @@ name: sentieon_tnscope -description: TNscope algorithm performs somatic variant calling on the tumor-normal matched pair or the tumor only data, using a Haplotyper algorithm. +description: TNscope algorithm performs somatic variant calling on the tumor-normal + matched pair or the tumor only data, using a Haplotyper algorithm. keywords: - tnscope - sentieon @@ -11,104 +12,114 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information. - e.g. [ id:'test', single_end:false ] - - meta2: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta6: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - meta7: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test' ] - - bam: - type: file - description: BAM file. - pattern: "*.bam" - - bai: - type: file - description: BAI file - pattern: "*.bai" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - cosmic: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - cosmic_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - pon: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - pon_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - dbsnp: - type: file - description: Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: Index of the Single Nucleotide Polymorphism database (dbSNP) file - pattern: "*.vcf.gz.tbi" - - interval: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information. + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file. + pattern: "*.bam" + - bai: + type: file + description: BAI file + pattern: "*.bai" + - - meta2: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - cosmic: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - cosmic_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta5: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - pon: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - pon_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta6: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - dbsnp: + type: file + description: Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz" + - dbsnp_tbi: + type: file + description: Index of the Single Nucleotide Polymorphism database (dbSNP) file + pattern: "*.vcf.gz.tbi" + - - meta7: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test' ] + - interval: + type: file + description: bed or interval_list file containing interval in the reference + that will be used in the analysis + pattern: "*.{bed,interval_list}" output: - - meta: - type: map - description: | - Groovy Map containing reference information. - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file + pattern: "*.{vcf.gz}" - index: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing reference information. + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/sentieon/varcal/meta.yml b/modules/nf-core/sentieon/varcal/meta.yml index cad7ee106f74..4661dc92d8f9 100644 --- a/modules/nf-core/sentieon/varcal/meta.yml +++ b/modules/nf-core/sentieon/varcal/meta.yml @@ -14,60 +14,87 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - vcf: - type: file - description: input vcf file containing the variants to be recalibrated - pattern: "*.vcf.gz" - - tbi: - type: file - description: tbi file matching with -vcf - pattern: "*.vcf.gz.tbi" - - resource_vcf: - type: file - description: all resource vcf files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz" - - resource_tbi: - type: file - description: all resource tbi files that are used with the corresponding '--resource' label - pattern: "*.vcf.gz.tbi" - - labels: - type: string - description: necessary arguments for Sentieon's VarCal. Specified to directly match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm - - fasta: - type: file - description: The reference fasta file - pattern: "*.fasta" - - fai: - type: file - description: Index of reference fasta file - pattern: "fasta.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcf: + type: file + description: input vcf file containing the variants to be recalibrated + pattern: "*.vcf.gz" + - tbi: + type: file + description: tbi file matching with -vcf + pattern: "*.vcf.gz.tbi" + - - resource_vcf: + type: file + description: all resource vcf files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz" + - - resource_tbi: + type: file + description: all resource tbi files that are used with the corresponding '--resource' + label + pattern: "*.vcf.gz.tbi" + - - labels: + type: string + description: necessary arguments for Sentieon's VarCal. Specified to directly + match the resources provided. More information can be found at https://support.sentieon.com/manual/usages/general/#varcal-algorithm + - - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - - fai: + type: file + description: Index of reference fasta file + pattern: "fasta.fai" output: - recal: - type: file - description: Output recal file used by ApplyVQSR - pattern: "*.recal" + - meta: + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" + - "*.recal": + type: file + description: Output recal file used by ApplyVQSR + pattern: "*.recal" - idx: - type: file - description: Index file for the recal output file - pattern: "*.idx" + - meta: + type: file + description: Index file for the recal output file + pattern: "*.idx" + - "*.idx": + type: file + description: Index file for the recal output file + pattern: "*.idx" - tranches: - type: file - description: Output tranches file used by ApplyVQSR - pattern: "*.tranches" + - meta: + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" + - "*.tranches": + type: file + description: Output tranches file used by ApplyVQSR + pattern: "*.tranches" - plots: - type: file - description: Optional output rscript file to aid in visualization of the input data and learned model. - pattern: "*plots.R" - - version: - type: file - description: File containing software versions - pattern: "*.versions.yml" + - meta: + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - "*plots.R": + type: file + description: Optional output rscript file to aid in visualization of the input + data and learned model. + pattern: "*plots.R" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@asp8200" maintainers: diff --git a/modules/nf-core/sentieon/wgsmetrics/meta.yml b/modules/nf-core/sentieon/wgsmetrics/meta.yml index 86431e1c6e3c..a8b64727713e 100644 --- a/modules/nf-core/sentieon/wgsmetrics/meta.yml +++ b/modules/nf-core/sentieon/wgsmetrics/meta.yml @@ -11,61 +11,64 @@ tools: Our software improves upon BWA, STAR, Minimap2, GATK, HaplotypeCaller, Mutect, and Mutect2 based pipelines and is deployable on any generic-CPU-based computing system. homepage: https://www.sentieon.com/ documentation: https://www.sentieon.com/ + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test' ]` - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index of th sorted BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Index of the genome fasta file - pattern: "*.fai" - - interval_list: - type: file - description: bed or interval_list file containing interval in the reference that will be used in the analysis - pattern: "*.{bed,interval_list}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of th sorted BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - fai: + type: file + description: Index of the genome fasta file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test' ]` + - intervals_list: + type: file + description: intervals output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wgs_metrics: - type: file - description: File containing the information about mean base quality score for each sequencing cycle - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: File containing the information about mean base quality score for + each sequencing cycle + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/seqcluster/collapse/meta.yml b/modules/nf-core/seqcluster/collapse/meta.yml index 03e9dc6330bb..e3a6f7e32702 100644 --- a/modules/nf-core/seqcluster/collapse/meta.yml +++ b/modules/nf-core/seqcluster/collapse/meta.yml @@ -1,45 +1,48 @@ name: "seqcluster_collapse" -description: Seqcluster collapse reduces computational complexity by collapsing identical sequences in a FASTQ file. +description: Seqcluster collapse reduces computational complexity by collapsing identical + sequences in a FASTQ file. keywords: - smrnaseq - cluster - mirna tools: - "seqcluster": - description: "Small RNA analysis from NGS data. Seqcluster generates a list of clusters of small RNA sequences, their genome location, their annotation and the abundance in all the sample of the project." + description: "Small RNA analysis from NGS data. Seqcluster generates a list of + clusters of small RNA sequences, their genome location, their annotation and + the abundance in all the sample of the project." homepage: "https://github.com/lpantano/seqcluster" documentation: "https://github.com/lpantano/seqcluster" tool_dev_url: "https://github.com/lpantano/seqcluster" doi: "10.1093/bioinformatics/btr527" licence: ["MIT"] + identifier: biotools:seqcluster input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastq: - type: file - description: FASTQ file - pattern: "*.{fastq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: FASTQ file - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fastq.gz": + type: file + description: FASTQ file + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/seqfu/derep/meta.yml b/modules/nf-core/seqfu/derep/meta.yml index c3ae374a6d3f..8c7741a5e0e3 100644 --- a/modules/nf-core/seqfu/derep/meta.yml +++ b/modules/nf-core/seqfu/derep/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqfu_derep" -description: Dereplicate FASTX sequences, removing duplicate sequences and printing the number of identical sequences in the sequence header. Can dereplicate already dereplicated FASTA files, summing the numbers found in the headers. +description: Dereplicate FASTX sequences, removing duplicate sequences and printing + the number of identical sequences in the sequence header. Can dereplicate already + dereplicated FASTA files, summing the numbers found in the headers. keywords: - dereplicate - fasta @@ -14,30 +15,33 @@ tools: tool_dev_url: "https://telatin.github.io/seqfu2/tools/derep.html" doi: "10.3390/bioengineering8050059" licence: ["GPL v3"] + identifier: biotools:seqfu input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastas: - type: file - description: Input files (mainly FASTA, FASTQ supported) - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastas: + type: file + description: Input files (mainly FASTA, FASTQ supported) + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: dereplicated file (FASTA format) - pattern: "*.{fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_derep.fasta.gz": + type: file + description: dereplicated file (FASTA format) + pattern: "*.{fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@telatin" maintainers: diff --git a/modules/nf-core/seqfu/stats/meta.yml b/modules/nf-core/seqfu/stats/meta.yml index df6093c5120f..f534a3f50fc2 100644 --- a/modules/nf-core/seqfu/stats/meta.yml +++ b/modules/nf-core/seqfu/stats/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqfu_stats" description: Statistics for FASTA or FASTQ files @@ -8,49 +7,53 @@ keywords: - n50 tools: - "seqfu": - description: "Cross-platform compiled suite of tools to manipulate and inspect FASTA and FASTQ files" + description: "Cross-platform compiled suite of tools to manipulate and inspect + FASTA and FASTQ files" homepage: "https://telatin.github.io/seqfu2/" documentation: "https://telatin.github.io/seqfu2/" tool_dev_url: "https://github.com/telatin/seqfu2" doi: "10.3390/bioengineering8050059" licence: ["GPL v3"] + identifier: biotools:seqfu input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - files: - type: file - description: One or more FASTA or FASTQ files - pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - files: + type: file + description: One or more FASTA or FASTQ files + pattern: "*.{fasta,fastq,fasta.gz,fastq.gz,fq,fq.gz}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - stats: - type: file - description: Tab-separated output file with basic sequence statistics. - pattern: "*.{tsv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Tab-separated output file with basic sequence statistics. + pattern: "*.{tsv}" - multiqc: - type: file - description: MultiQC ready table - pattern: "*.{_mqc.txt}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_mqc.txt": + type: file + description: MultiQC ready table + pattern: "*.{_mqc.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@telatin" maintainers: diff --git a/modules/nf-core/seqkit/concat/meta.yml b/modules/nf-core/seqkit/concat/meta.yml index c4511ce0d04b..c5315f255147 100644 --- a/modules/nf-core/seqkit/concat/meta.yml +++ b/modules/nf-core/seqkit/concat/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_concat" description: Concatenating multiple uncompressed sequence files together @@ -16,37 +15,35 @@ tools: tool_dev_url: https://github.com/shenwei356/seqkit doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - input: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: file + description: Sequence file in fasta/q format + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastx: - type: file - description: A concatenated sequence file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{fasta,fastq,fa,fq,fas,fna,faa}": + type: file + description: A concatenated sequence file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqkit/fq2fa/meta.yml b/modules/nf-core/seqkit/fq2fa/meta.yml index d0c55b3c190c..2241fda93a7a 100644 --- a/modules/nf-core/seqkit/fq2fa/meta.yml +++ b/modules/nf-core/seqkit/fq2fa/meta.yml @@ -6,39 +6,39 @@ keywords: - convert tools: - "seqkit": - description: "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen." + description: "Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen." homepage: "https://github.com/shenwei356/seqkit" documentation: "https://bioinf.shenwei.me/seqkit/" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - fastq: - type: file - description: Sequence file in fastq format - pattern: "*.{fastq,fq}.gz" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - fastq: + type: file + description: Sequence file in fastq format + pattern: "*.{fastq,fq}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Sequence file in fasta format - pattern: "*.{fasta,fa}.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fa.gz": + type: file + description: Sequence file in fasta format + pattern: "*.{fasta,fa}.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@d-jch" diff --git a/modules/nf-core/seqkit/fx2tab/meta.yml b/modules/nf-core/seqkit/fx2tab/meta.yml index e403392ce58e..4fb450dca223 100644 --- a/modules/nf-core/seqkit/fx2tab/meta.yml +++ b/modules/nf-core/seqkit/fx2tab/meta.yml @@ -1,5 +1,6 @@ name: seqkit_fx2tab -description: Convert FASTA/Q to tabular format, and provide various information, like sequence length, GC content/GC skew. +description: Convert FASTA/Q to tabular format, and provide various information, like + sequence length, GC content/GC skew. keywords: - fasta - fastq @@ -14,30 +15,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: Sequence file in fasta/q format + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}[.gz,.zst]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - text: - type: file - description: Text file in tabular format - pattern: "*.txt[.gz,.zstd,.zst]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt*": + type: file + description: Text file in tabular format + pattern: "*.txt[.gz,.zstd,.zst]" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seqkit/grep/meta.yml b/modules/nf-core/seqkit/grep/meta.yml index d74dc503c5ae..309f81974862 100644 --- a/modules/nf-core/seqkit/grep/meta.yml +++ b/modules/nf-core/seqkit/grep/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "seqkit_grep" description: Select sequences from a large file based on name/ID @@ -9,46 +8,48 @@ keywords: - grep tools: - "seqkit": - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - sequence: - type: file - description: > - Fasta or fastq file containing sequences to be filtered - - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" - - pattern: - type: file - description: > - pattern file (one record per line). If no pattern is given, a string can be specificied within the args using '-p pattern_string' - - pattern: "*.{txt,tsv}" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - sequence: + type: file + description: > + Fasta or fastq file containing sequences to be filtered + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - pattern: + type: file + description: > + pattern file (one record per line). If no pattern is given, a string can be + specificied within the args using '-p pattern_string' + pattern: "*.{txt,tsv}" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - filter: - type: file - description: > - Fasta or fastq file containing the filtered sequences - - pattern: "*.{fa,fq}[.gz]" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.{fa,fq}.gz": + type: file + description: > + Fasta or fastq file containing the filtered sequences + pattern: "*.{fa,fq}[.gz]" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/seqkit/pair/meta.yml b/modules/nf-core/seqkit/pair/meta.yml index 4a49926ae92e..0bc01bbe5954 100644 --- a/modules/nf-core/seqkit/pair/meta.yml +++ b/modules/nf-core/seqkit/pair/meta.yml @@ -6,40 +6,50 @@ keywords: - fastq tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input paired-end FastQ files. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input paired-end FastQ files. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Paired fastq reads - pattern: "*.paired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paired.fastq.gz": + type: file + description: Paired fastq reads + pattern: "*.paired.fastq.gz" - unpaired_reads: - type: file - description: Unpaired reads (optional) - pattern: "*.unpaired.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unpaired.fastq.gz": + type: file + description: Unpaired reads (optional) + pattern: "*.unpaired.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sateeshperi" - "@mjcipriano" diff --git a/modules/nf-core/seqkit/replace/meta.yml b/modules/nf-core/seqkit/replace/meta.yml index 1763521a0a44..1be01079510d 100644 --- a/modules/nf-core/seqkit/replace/meta.yml +++ b/modules/nf-core/seqkit/replace/meta.yml @@ -8,35 +8,39 @@ keywords: - fasta tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.016396" + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: fasta/q file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: fasta/q file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastx: - type: file - description: fasta/q file with replaced values - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fast*": + type: file + description: fasta/q file with replaced values + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mjcipriano" maintainers: diff --git a/modules/nf-core/seqkit/rmdup/meta.yml b/modules/nf-core/seqkit/rmdup/meta.yml index d0addd4551a1..22e29c117bef 100644 --- a/modules/nf-core/seqkit/rmdup/meta.yml +++ b/modules/nf-core/seqkit/rmdup/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_rmdup" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -16,34 +16,43 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.${extension}: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - log: - type: file - description: Log containing information regarding removed duplicates - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.log": + type: file + description: Log containing information regarding removed duplicates + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/seq/meta.yml b/modules/nf-core/seqkit/seq/meta.yml index 8d4e2b160e48..7d32aba58706 100644 --- a/modules/nf-core/seqkit/seq/meta.yml +++ b/modules/nf-core/seqkit/seq/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_seq" -description: Transforms sequences (extract ID, filter by length, remove gaps, reverse complement...) +description: Transforms sequences (extract ID, filter by length, remove gaps, reverse + complement...) keywords: - genomics - fasta @@ -18,30 +18,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/sliding/meta.yml b/modules/nf-core/seqkit/sliding/meta.yml index dbfa49c458a0..e012ef069501 100644 --- a/modules/nf-core/seqkit/sliding/meta.yml +++ b/modules/nf-core/seqkit/sliding/meta.yml @@ -6,35 +6,39 @@ keywords: - windows tools: - seqkit: - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.016396" + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastx: - type: file - description: fasta/q file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastx: + type: file + description: fasta/q file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastx: - type: file - description: fasta/q window file - pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fast*": + type: file + description: fasta/q window file + pattern: "*.{fasta,fastq,fa,fq,fas,fna,faa}*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqkit/sort/meta.yml b/modules/nf-core/seqkit/sort/meta.yml index 2e61ce1566ff..157ff85ca5b3 100644 --- a/modules/nf-core/seqkit/sort/meta.yml +++ b/modules/nf-core/seqkit/sort/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "seqkit_sort" description: Sorts sequences by id/name/sequence/length @@ -15,30 +14,33 @@ tools: tool_dev_url: "https://github.com/shenwei356/seqkit" doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fastx: - type: file - description: Input fasta/fastq file - pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fsa,fas,fa,fasta,fastq,fq,fsa.gz,fas.gz,fa.gz,fasta.gz,fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - fastx: - type: file - description: Output fasta/fastq file - pattern: "*.{fasta.gz,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Output fasta/fastq file + pattern: "*.{fasta.gz,fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/seqkit/split2/meta.yml b/modules/nf-core/seqkit/split2/meta.yml index 14babd448b6b..c1e6e3def2e9 100644 --- a/modules/nf-core/seqkit/split2/meta.yml +++ b/modules/nf-core/seqkit/split2/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FastQ files - pattern: "*.{fq.gz/fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FastQ files + pattern: "*.{fq.gz/fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Split fastq files - pattern: "*.{fq.gz/fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/*.gz": + type: file + description: Split fastq files + pattern: "*.{fq.gz/fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/seqkit/stats/meta.yml b/modules/nf-core/seqkit/stats/meta.yml index 717ba43c33ff..797712b5bb93 100644 --- a/modules/nf-core/seqkit/stats/meta.yml +++ b/modules/nf-core/seqkit/stats/meta.yml @@ -6,40 +6,42 @@ keywords: - stats tools: - "seqkit": - description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + description: Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, + written by Wei Shen. homepage: https://bioinf.shenwei.me/seqkit/usage/ documentation: https://bioinf.shenwei.me/seqkit/usage/ tool_dev_url: https://github.com/shenwei356/seqkit/ doi: "10.1371/journal.pone.0163962" licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - reads: - type: file - description: > - Either FASTA or FASTQ files. - - pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - reads: + type: file + description: > + Either FASTA or FASTQ files. + pattern: "*.{fa,fna,faa,fasta,fq,fastq}[.gz]" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: > - Tab-separated output file with basic sequence statistics. - - pattern: "*.tsv" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.tsv": + type: file + description: > + Tab-separated output file with basic sequence statistics. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/seqkit/tab2fx/meta.yml b/modules/nf-core/seqkit/tab2fx/meta.yml index 04537148edc6..7c93beb10043 100644 --- a/modules/nf-core/seqkit/tab2fx/meta.yml +++ b/modules/nf-core/seqkit/tab2fx/meta.yml @@ -14,30 +14,33 @@ tools: documentation: https://bioinf.shenwei.me/seqkit/ doi: 10.1371/journal.pone.0163962 licence: ["MIT"] + identifier: biotools:seqkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - text: - type: file - description: Text file in tabular format - pattern: "*.txt[.gz,.zst]" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - text: + type: file + description: Text file in tabular format + pattern: "*.txt[.gz,.zst]" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastx: - type: file - description: Sequence file in fasta/q format - pattern: "*.{fa,fq}[.gz,.zst]" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.f*": + type: file + description: Sequence file in fasta/q format + pattern: "*.{fa,fq}[.gz,.zst]" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seqsero2/meta.yml b/modules/nf-core/seqsero2/meta.yml index 36e98bed954e..9761dd7b6517 100644 --- a/modules/nf-core/seqsero2/meta.yml +++ b/modules/nf-core/seqsero2/meta.yml @@ -13,38 +13,53 @@ tools: tool_dev_url: https://github.com/denglab/SeqSero2 doi: "10.1128/AEM.01746-19" licence: ["GPL v2"] + identifier: biotools:SeqSero2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: FASTQ or FASTA formated sequences - pattern: "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: FASTQ or FASTA formated sequences + pattern: "*.{fq.gz,fastq.gz,fna.gz,fna,fasta.gz,fasta,fa.gz,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: A log of serotype antigen results - pattern: "*_log.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_log.txt: + type: file + description: A log of serotype antigen results + pattern: "*_log.txt" - tsv: - type: file - description: Tab-delimited summary of the SeqSero2 results - pattern: "*_result.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_result.tsv: + type: file + description: Tab-delimited summary of the SeqSero2 results + pattern: "*_result.tsv" - txt: - type: file - description: Detailed summary of the SeqSero2 results - pattern: "*_result.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*_result.txt: + type: file + description: Detailed summary of the SeqSero2 results + pattern: "*_result.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/seqtk/cutn/meta.yml b/modules/nf-core/seqtk/cutn/meta.yml index 1082867938c5..2e39a4775955 100644 --- a/modules/nf-core/seqtk/cutn/meta.yml +++ b/modules/nf-core/seqtk/cutn/meta.yml @@ -6,35 +6,40 @@ keywords: - seqtk tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into + one interleaved file. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: A single fasta file to be split. - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: A single fasta file to be split. + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bed: - type: file - description: The output bed which summarised locations of cuts - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The output bed which summarised locations of cuts + pattern: "*.{bed}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/seqtk/mergepe/meta.yml b/modules/nf-core/seqtk/mergepe/meta.yml index bfe96a12fa56..b318250ae811 100644 --- a/modules/nf-core/seqtk/mergepe/meta.yml +++ b/modules/nf-core/seqtk/mergepe/meta.yml @@ -6,35 +6,43 @@ keywords: - fastx tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into + one interleaved file. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data,respectively. - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data,respectively. + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: If single-end reads, the output is the same as the input, 1 FastQ file for each read. If pair-end reads, the read pairs will be interleaved and output as 1 FastQ file for each read pair. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: If single-end reads, the output is the same as the input, 1 FastQ + file for each read. If pair-end reads, the read pairs will be interleaved + and output as 1 FastQ file for each read pair. + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@emnilsson" maintainers: diff --git a/modules/nf-core/seqtk/rename/meta.yml b/modules/nf-core/seqtk/rename/meta.yml index 7696ef114a9e..5b4682fa65ff 100644 --- a/modules/nf-core/seqtk/rename/meta.yml +++ b/modules/nf-core/seqtk/rename/meta.yml @@ -6,35 +6,40 @@ keywords: - header tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. The seqtk rename command renames sequence names. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - sequences: - type: file - description: A FASTQ or FASTA file - pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - sequences: + type: file + description: A FASTQ or FASTA file + pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, + fna, fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sequences: - type: file - description: FASTQ/FASTA file containing renamed sequences - pattern: "*.{fastq.gz, fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gz": + type: file + description: FASTQ/FASTA file containing renamed sequences + pattern: "*.{fastq.gz, fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hseabolt" - "@mjcipriano" diff --git a/modules/nf-core/seqtk/sample/meta.yml b/modules/nf-core/seqtk/sample/meta.yml index 54a5c2bbe132..42f67d8fe0b5 100644 --- a/modules/nf-core/seqtk/sample/meta.yml +++ b/modules/nf-core/seqtk/sample/meta.yml @@ -6,38 +6,42 @@ keywords: - reads tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk sample command subsamples sequences. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. Seqtk sample command subsamples sequences. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files - pattern: "*.{fastq.gz}" - - sample_size: - type: integer - description: Number of reads to sample. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files + pattern: "*.{fastq.gz}" + - sample_size: + type: integer + description: Number of reads to sample. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Subsampled FastQ files - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Subsampled FastQ files + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" - "@sidorov-si" diff --git a/modules/nf-core/seqtk/seq/meta.yml b/modules/nf-core/seqtk/seq/meta.yml index adb03a0b61da..703b1dd1cb1c 100644 --- a/modules/nf-core/seqtk/seq/meta.yml +++ b/modules/nf-core/seqtk/seq/meta.yml @@ -6,35 +6,41 @@ keywords: - transformation tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk seq command enables common transformation operations on FASTA or FASTQ files. + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format. The seqtk seq command enables common transformation + operations on FASTA or FASTQ files. homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fastx: - type: file - description: A FASTQ or FASTA file - pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fastx: + type: file + description: A FASTQ or FASTA file + pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, + fna, fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastx: - type: file - description: FASTQ/FASTA file containing renamed sequences - pattern: "*.{fastq.gz, fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.gz": + type: file + description: FASTQ/FASTA file containing renamed sequences + pattern: "*.{fastq.gz, fasta.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hseabolt" - "@mjcipriano" diff --git a/modules/nf-core/seqtk/subseq/meta.yml b/modules/nf-core/seqtk/subseq/meta.yml index de4a8413369a..2667f40d680f 100644 --- a/modules/nf-core/seqtk/subseq/meta.yml +++ b/modules/nf-core/seqtk/subseq/meta.yml @@ -6,34 +6,42 @@ keywords: - fastx tools: - seqtk: - description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format + description: Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq,fq.gz,fa,fa.gz}" - - filter_list: - type: file - description: BED file or a text file with a list of sequence names - pattern: "*.{bed,lst}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - sequences: + type: file + description: FASTQ/FASTA file + pattern: "*.{fq,fq.gz,fa,fa.gz}" + - - filter_list: + type: file + description: BED file or a text file with a list of sequence names + pattern: "*.{bed,lst}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sequences: - type: file - description: FASTQ/FASTA file - pattern: "*.{fq.gz,fa.gz}" + - meta: + type: file + description: FASTQ/FASTA file + pattern: "*.{fq.gz,fa.gz}" + - "*.gz": + type: file + description: FASTQ/FASTA file + pattern: "*.{fq.gz,fa.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sidorov-si" maintainers: diff --git a/modules/nf-core/seqtk/trim/meta.yml b/modules/nf-core/seqtk/trim/meta.yml index 11770572e16e..3a0198ac0ab1 100644 --- a/modules/nf-core/seqtk/trim/meta.yml +++ b/modules/nf-core/seqtk/trim/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: seqtk_trim description: Trim low quality bases from FastQ files @@ -8,37 +7,39 @@ keywords: - seqtk tools: - "seqtk": - description: "Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format" + description: "Seqtk is a fast and lightweight tool for processing sequences in + the FASTA or FASTQ format" homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk licence: ["MIT"] + identifier: biotools:seqtk input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input FastQ files - pattern: "*.{fastq.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input FastQ files + pattern: "*.{fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Filtered FastQ files - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Filtered FastQ files + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@laramiellindsey" diff --git a/modules/nf-core/sequencetools/pileupcaller/meta.yml b/modules/nf-core/sequencetools/pileupcaller/meta.yml index c33142844c0b..5c42b3316c1d 100644 --- a/modules/nf-core/sequencetools/pileupcaller/meta.yml +++ b/modules/nf-core/sequencetools/pileupcaller/meta.yml @@ -1,5 +1,6 @@ name: "sequencetools_pileupcaller" -description: PileupCaller is a tool to create genotype calls from bam files using read-sampling methods +description: PileupCaller is a tool to create genotype calls from bam files using + read-sampling methods keywords: - genotyping - mpileup @@ -17,50 +18,84 @@ tools: documentation: "https://github.com/stschiff/sequenceTools#readme" tool_dev_url: "https://github.com/stschiff/sequenceTools" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mpileup: - type: file - description: samtools mpileup output. - - snpfile: - type: file - description: | - Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. - Only alleles matching the Ref and Alt alleles of the provided snp file will be called. - - calling_method: - type: string - description: The desired calling method for pileupcaller. One of 'randomHaploid', 'randomDiploid', or 'majorityCall'. - - output_format: - type: string - description: The desired output format. One of 'PLINK', 'EIGENSTRAT', or 'FREQSUM'. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - mpileup: + type: file + description: samtools mpileup output. + - - snpfile: + type: file + description: | + Eigenstrat format .snp file of the sites in the mpileup file to call genotypes on. + Only alleles matching the Ref and Alt alleles of the provided snp file will be called. + - - sample_names_fn: + type: file + description: File containing the sample names output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - eigenstrat: - type: file - description: A tuple containing the output Eigenstrat-formatted geno, snp and ind files. - pattern: "*.{geno,snp,ind}.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" + - "*.snp": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" + - "*.ind": + type: file + description: A tuple containing the output Eigenstrat-formatted geno, snp and + ind files. + pattern: "*.{geno,snp,ind}.txt" - plink: - type: file - description: A tuple containing the output Plink-formatted bed, bim and fam files. - pattern: "*.{bed,bim,fam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" + - "*.bim": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" + - "*.fam": + type: file + description: A tuple containing the output Plink-formatted bed, bim and fam + files. + pattern: "*.{bed,bim,fam}" - freqsum: - type: file - description: The output freqsum-formatted file. - pattern: "*.freqsum.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.freqsum.gz": + type: file + description: The output freqsum-formatted file. + pattern: "*.freqsum.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/sequenzautils/bam2seqz/meta.yml b/modules/nf-core/sequenzautils/bam2seqz/meta.yml index 45a1fdf419af..eef27d1ca5d4 100644 --- a/modules/nf-core/sequenzautils/bam2seqz/meta.yml +++ b/modules/nf-core/sequenzautils/bam2seqz/meta.yml @@ -1,52 +1,60 @@ name: sequenzautils_bam2seqz -description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz file +description: Sequenza-utils bam2seqz process BAM and Wiggle files to produce a seqz + file keywords: - sequenzautils - copy number - bam2seqz tools: - sequenzautils: - description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program - bam2seqz - process a paired set of BAM/pileup files (tumour and matching normal), and GC-content genome-wide information, to extract the common positions with A and B alleles frequencies. + description: Sequenza-utils provides 3 main command line programs to transform + common NGS file format - such as FASTA, BAM - to input files for the Sequenza + R package. The program - bam2seqz - process a paired set of BAM/pileup files + (tumour and matching normal), and GC-content genome-wide information, to extract + the common positions with A and B alleles frequencies. homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normalbam: - type: file - description: BAM file from the reference/normal sample - pattern: "*.{bam}" - - tumourbam: - type: file - description: BAM file from the tumour sample - pattern: "*.{bam}" - - fasta: - type: file - description: Reference FASTA file - pattern: "*.{fasta}" - - wigfile: - type: file - description: GC content wiggle file - pattern: "*.{wig.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normalbam: + type: file + description: BAM file from the reference/normal sample + pattern: "*.{bam}" + - tumourbam: + type: file + description: BAM file from the tumour sample + pattern: "*.{bam}" + - - fasta: + type: file + description: Reference FASTA file + pattern: "*.{fasta}" + - - wigfile: + type: file + description: GC content wiggle file + pattern: "*.{wig.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - seqz: - type: file - description: Seqz file - pattern: "*.{seqz.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Seqz file + pattern: "*.{seqz.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/sequenzautils/gcwiggle/meta.yml b/modules/nf-core/sequenzautils/gcwiggle/meta.yml index 3ca9afcd4058..e9ee3fdb8e4c 100644 --- a/modules/nf-core/sequenzautils/gcwiggle/meta.yml +++ b/modules/nf-core/sequenzautils/gcwiggle/meta.yml @@ -1,40 +1,47 @@ name: sequenzautils_gcwiggle -description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, and returns a file in the UCSC wiggle format, given a fasta file and a window size. +description: Sequenza-utils gc_wiggle computes the GC percentage across the sequences, + and returns a file in the UCSC wiggle format, given a fasta file and a window size. keywords: - sequenzautils - copy number - gc_wiggle tools: - sequenzautils: - description: Sequenza-utils provides 3 main command line programs to transform common NGS file format - such as FASTA, BAM - to input files for the Sequenza R package. The program -gc_wiggle- takes fasta file as an input, computes GC percentage across the sequences and returns a file in the UCSC wiggle format. + description: Sequenza-utils provides 3 main command line programs to transform + common NGS file format - such as FASTA, BAM - to input files for the Sequenza + R package. The program -gc_wiggle- takes fasta file as an input, computes GC + percentage across the sequences and returns a file in the UCSC wiggle format. homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - wig: - type: file - description: GC Wiggle track file - pattern: "*.{wig.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig.gz": + type: file + description: GC Wiggle track file + pattern: "*.{wig.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kaurravneet4123" maintainers: diff --git a/modules/nf-core/seqwish/induce/meta.yml b/modules/nf-core/seqwish/induce/meta.yml index 562f4014aa32..92d06b938e13 100644 --- a/modules/nf-core/seqwish/induce/meta.yml +++ b/modules/nf-core/seqwish/induce/meta.yml @@ -14,34 +14,37 @@ tools: homepage: https://github.com/ekg/seqwish documentation: https://github.com/ekg/seqwish licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf: - type: list - description: comma-separated PAF file(s) of alignments, single entry allowed - pattern: "[*.{paf,paf.gz},*.{paf,paf.gz},...]" - - fasta: - type: file - description: FASTA file used to generate alignments - pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf: + type: list + description: comma-separated PAF file(s) of alignments, single entry allowed + pattern: "[*.{paf,paf.gz},*.{paf,paf.gz},...]" + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gfa": + type: file + description: Variation graph in GFA 1.0 format + pattern: "*.{gfa}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh" maintainers: diff --git a/modules/nf-core/seroba/run/meta.yml b/modules/nf-core/seroba/run/meta.yml index e0a704ccc227..d78f13e0e5bc 100644 --- a/modules/nf-core/seroba/run/meta.yml +++ b/modules/nf-core/seroba/run/meta.yml @@ -1,45 +1,56 @@ name: "seroba_run" -description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads +description: Determine Streptococcus pneumoniae serotype from Illumina paired-end + reads keywords: - fastq - serotype - Streptococcus pneumoniae tools: - "seroba": - description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina NGS reads for given references." + description: "SeroBA is a k-mer based pipeline to identify the Serotype from Illumina + NGS reads for given references." homepage: "https://sanger-pathogens.github.io/seroba/" documentation: "https://sanger-pathogens.github.io/seroba/" tool_dev_url: "https://github.com/sanger-pathogens/seroba" doi: "10.1099/mgen.0.000186" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input Illunina paired-end FASTQ files - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input Illunina paired-end FASTQ files + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: The predicted serotype in tab-delimited format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.tsv: + type: file + description: The predicted serotype in tab-delimited format + pattern: "*.tsv" - txt: - type: file - description: A detailed description of the predicted serotype - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/detailed_serogroup_info.txt: + type: file + description: A detailed description of the predicted serotype + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/severus/meta.yml b/modules/nf-core/severus/meta.yml index 844eee442a5a..8ada35489ea8 100644 --- a/modules/nf-core/severus/meta.yml +++ b/modules/nf-core/severus/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "severus" -description: Severus is a somatic structural variation (SV) caller for long reads (both PacBio and ONT) +description: Severus is a somatic structural variation (SV) caller for long reads + (both PacBio and ONT) keywords: - structural - variation @@ -16,112 +16,201 @@ tools: tool_dev_url: "https://github.com/KolmogorovLab/Severus" doi: "10.1101/2024.03.22.24304756" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - target_input: - type: file - description: path to one or multiple target BAM/CRAM files (e.g. tumor, must be indexed) - pattern: "*.{bam,cram}" - - target_index: - type: file - description: path to one or multiple target BAM/CRAM index files - pattern: "*.{bai,crai,csi}" - - control_input: - type: file - description: path to the control BAM/CRAM file (e.g. normal, must be indexed) - pattern: "*.{bam,cram}" - - control_index: - type: file - description: path to the control BAM/CRAM file index - pattern: "*.{bai,crai,csi}" - - vcf: - type: file - description: path to vcf file used for phasing (if using haplotype specific SV calling - pattern: "*.{vcf,vcf.gz}" - - meta2: - type: map - description: | - Groovy Map containing tandem repeat regions information - e.g. `[ id:'hg38']` - - bed: - type: file - description: path to bed file for tandem repeat regions (must be ordered) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - target_input: + type: file + description: path to one or multiple target BAM/CRAM files (e.g. tumor, must + be indexed) + pattern: "*.{bam,cram}" + - target_index: + type: file + description: path to one or multiple target BAM/CRAM index files + pattern: "*.{bai,crai,csi}" + - control_input: + type: file + description: path to the control BAM/CRAM file (e.g. normal, must be indexed) + pattern: "*.{bam,cram}" + - control_index: + type: file + description: path to the control BAM/CRAM file index + pattern: "*.{bai,crai,csi}" + - vcf: + type: file + description: path to vcf file used for phasing (if using haplotype specific + SV calling + pattern: "*.{vcf,vcf.gz}" + - - meta2: + type: map + description: | + Groovy Map containing tandem repeat regions information + e.g. `[ id:'hg38']` + - bed: + type: file + description: path to bed file for tandem repeat regions (must be ordered) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: Severus log file - pattern: "${prefix}/severus.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus.log: + type: file + description: Severus log file + pattern: "${prefix}/severus.log" - read_qual: - type: file - description: Severus read_qual file - pattern: "${prefix}/read_qual.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_qual.txt: + type: file + description: Severus read_qual file + pattern: "${prefix}/read_qual.txt" - breakpoints_double: - type: file - description: Severus breakpoints_double file - pattern: "${prefix}/breakpoints_double.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/breakpoints_double.csv: + type: file + description: Severus breakpoints_double file + pattern: "${prefix}/breakpoints_double.csv" - read_alignments: - type: file - description: read alignments file - pattern: "${prefix}/read_alignments" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_alignments: + type: file + description: read alignments file + pattern: "${prefix}/read_alignments" - read_ids: - type: file - description: read IDs for support reads - pattern: "${prefix}/read_ids" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/read_ids.csv: + type: file + description: read IDs for support reads + pattern: "${prefix}/read_ids" - collapsed_dup: - type: file - description: a bed file with identified collapsed duplication regions - pattern: "${prefix}/severus_collaped_dup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_collaped_dup.bed: + type: file + description: a bed file with identified collapsed duplication regions + pattern: "${prefix}/severus_collaped_dup" - loh: - type: file - description: a bed file with predicted LOH regions - pattern: "${prefix}/severus_LOH.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/severus_LOH.bed: + type: file + description: a bed file with predicted LOH regions + pattern: "${prefix}/severus_LOH.bed" - all_vcf: - type: file - description: VCF file with all SVs (somatic + germline) - pattern: "${prefix}/all_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/severus_all.vcf: + type: file + description: VCF file with all SVs (somatic + germline) + pattern: "${prefix}/all_SVs/severus_all.vcf" - all_breakpoints_clusters_list: - type: file - description: Severus breakpoints clusters list file - pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus breakpoints clusters list file + pattern: "${prefix}/all_SVs/breakpoints_clusters_list.tsv" - all_breakpoints_clusters: - type: file - description: Severus breakpoints clusters file - pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/breakpoints_clusters.tsv: + type: file + description: Severus breakpoints clusters file + pattern: "${prefix}/all_SVs/breakpoints_clusters.tsv" - all_plots: - type: file - description: Severus plots - pattern: "${prefix}/all_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/all_SVs/plots/severus_*.html: + type: file + description: Severus plots + pattern: "${prefix}/all_SVs/plots/*.html" - somatic_vcf: - type: file - description: VCF file with somatic SVs - pattern: "${prefix}/somatic_SVs/severus_all.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/severus_all.vcf: + type: file + description: VCF file with somatic SVs + pattern: "${prefix}/somatic_SVs/severus_all.vcf" - somatic_breakpoints_clusters_list: - type: file - description: Severus somatic breakpoints clusters list file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters_list.tsv: + type: file + description: Severus somatic breakpoints clusters list file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters_list.tsv" - somatic_breakpoints_clusters: - type: file - description: Severus somatic breakpoints clusters file - pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/breakpoints_clusters.tsv: + type: file + description: Severus somatic breakpoints clusters file + pattern: "${prefix}/somatic_SVs/breakpoints_clusters.tsv" - somatic_plots: - type: file - description: Severus somatic plots - pattern: "${prefix}/somatic_SVs/plots/*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${prefix}/somatic_SVs/plots/severus_*.html: + type: file + description: Severus somatic plots + pattern: "${prefix}/somatic_SVs/plots/*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/sexdeterrmine/meta.yml b/modules/nf-core/sexdeterrmine/meta.yml index f1b57a8f3ec9..6a2684776780 100644 --- a/modules/nf-core/sexdeterrmine/meta.yml +++ b/modules/nf-core/sexdeterrmine/meta.yml @@ -1,5 +1,6 @@ name: "sexdeterrmine" -description: Calculate the relative coverage on the Gonosomes vs Autosomes from the output of samtools depth, with error bars. +description: Calculate the relative coverage on the Gonosomes vs Autosomes from the + output of samtools depth, with error bars. keywords: - sex determination - genetic sex @@ -7,40 +8,55 @@ keywords: - ancient dna tools: - "sexdeterrmine": - description: "A python script carry out calculate the relative coverage of X and Y chromosomes, and their associated error bars, out of capture data." + description: "A python script carry out calculate the relative coverage of X and + Y chromosomes, and their associated error bars, out of capture data." homepage: "https://github.com/TCLamnidis/Sex.DetERRmine" documentation: "https://github.com/TCLamnidis/Sex.DetERRmine/README.md" tool_dev_url: "https://github.com/TCLamnidis/Sex.DetERRmine" doi: "10.1038/s41467-018-07483-5" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - depth: - type: file - description: Output from samtools depth (with header) - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - depth: + type: file + description: Output from samtools depth (with header) + pattern: "*" + - - sample_list_file: + type: file + description: File containing the list of samples to be processed. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON formatted table of relative coverages on the X and Y, with associated error bars. - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.json": + type: file + description: JSON formatted table of relative coverages on the X and Y, with + associated error bars. + pattern: "*.json" - tsv: - type: file - description: TSV table of relative coverages on the X and Y, with associated error bars. - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: TSV table of relative coverages on the X and Y, with associated + error bars. + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@TCLamnidis" maintainers: diff --git a/modules/nf-core/sgdemux/meta.yml b/modules/nf-core/sgdemux/meta.yml index 1949348ad8fa..3dd52d75aaa7 100644 --- a/modules/nf-core/sgdemux/meta.yml +++ b/modules/nf-core/sgdemux/meta.yml @@ -6,61 +6,96 @@ keywords: - bgzip tools: - "sgdemux": - description: "Tool for demultiplexing sequencing data generated on Singular Genomics' sequencing instruments." + description: "Tool for demultiplexing sequencing data generated on Singular Genomics' + sequencing instruments." homepage: "https://github.com/Singular-Genomics/singular-demux" documentation: "https://github.com/Singular-Genomics/singular-demux#sgdemux" licence: ["For Singular G4™ Sequencing Platform only"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sample_sheet: - type: file - description: sample_sheet file (either a Singular Genomics sample sheet, or a two column csv wih Sample_Barcode and Sample_ID) - pattern: "*.{csv}" - - fastqs_dir: - type: directory - description: "Input directory containing bgzipped (not gzip) FASTQ files" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sample_sheet: + type: file + description: sample_sheet file (either a Singular Genomics sample sheet, or + a two column csv wih Sample_Barcode and Sample_ID) + pattern: "*.{csv}" + - fastqs_dir: + type: directory + description: "Input directory containing bgzipped (not gzip) FASTQ files" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sample_fastq: - type: file - description: Demultiplexed per-sample FASTQ files - pattern: "output/*_R*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/*_R*.fastq.gz: + type: file + description: Demultiplexed per-sample FASTQ files + pattern: "output/*_R*.fastq.gz" - metrics: - type: file - description: | - Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates - pattern: "output/metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/metrics.tsv: + type: file + description: | + Demultiplexing summary stats; control_reads_omitted failing_reads_omitted, total_templates + pattern: "output/metrics.tsv" - most_frequent_unmatched: - type: file - description: | - File containing approx. counts of barcodes that did not match the expected barcodes - pattern: "output/most_frequence_unmatched.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/most_frequent_unmatched.tsv: + type: file + description: | + File containing approx. counts of barcodes that did not match the expected barcodes + pattern: "output/most_frequence_unmatched.tsv" - per_project_metrics: - type: file - description: Summary metrics for samples in the same project - pattern: "output/per_project_metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/per_project_metrics.tsv: + type: file + description: Summary metrics for samples in the same project + pattern: "output/per_project_metrics.tsv" - per_sample_metrics: - type: file - description: Summary metrics for each sample - pattern: "output/per_sample_metrics.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/per_sample_metrics.tsv: + type: file + description: Summary metrics for each sample + pattern: "output/per_sample_metrics.tsv" - sample_barcode_hop_metrics: - type: file - description: | - File output for dual-indexed runs with barcodes which are unexpected combinations of - expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT - pattern: "output/sample_barcode_hop_metrics/tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output/sample_barcode_hop_metrics.tsv: + type: file + description: | + File output for dual-indexed runs with barcodes which are unexpected combinations of + expected barcodes e.g. expected barcodes = AA-TT/GG-CC and observed barcodes = AA-CC/GG-TT + pattern: "output/sample_barcode_hop_metrics/tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nh13" - "@sam-white04" diff --git a/modules/nf-core/shapeit5/ligate/meta.yml b/modules/nf-core/shapeit5/ligate/meta.yml index ed1e5e9efed5..a8d6db145345 100644 --- a/modules/nf-core/shapeit5/ligate/meta.yml +++ b/modules/nf-core/shapeit5/ligate/meta.yml @@ -14,38 +14,41 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867" licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_list: - type: file - description: | - VCF/BCF files containing genotype probabilities (GP field). - The files should be ordered by genomic position. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_list_index: - type: file - description: VCF/BCF files index. - pattern: "*.csi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_list: + type: file + description: | + VCF/BCF files containing genotype probabilities (GP field). + The files should be ordered by genomic position. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_list_index: + type: file + description: VCF/BCF files index. + pattern: "*.csi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_variants: - type: file - description: | - Output VCF/BCF file for the merged regions. - Phased information (HS field) is updated accordingly for the full region. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: | + Output VCF/BCF file for the merged regions. + Phased information (HS field) is updated accordingly for the full region. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@louislenezet" maintainers: diff --git a/modules/nf-core/shapeit5/phasecommon/meta.yml b/modules/nf-core/shapeit5/phasecommon/meta.yml index 47197291ea9b..5aa052320983 100644 --- a/modules/nf-core/shapeit5/phasecommon/meta.yml +++ b/modules/nf-core/shapeit5/phasecommon/meta.yml @@ -1,5 +1,6 @@ name: "shapeit5_phasecommon" -description: Tool to phase common sites, typically SNP array data, or the first step of WES/WGS data. +description: Tool to phase common sites, typically SNP array data, or the first step + of WES/WGS data. keywords: - phasing - haplotype @@ -12,67 +13,85 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: | - Target dataset in VCF/BCF format defined at all variable positions. - The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_index: - type: file - description: Index file of the input VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - region: - type: string - description: | - Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - reference: - type: file - description: Reference panel of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - reference_index: - type: file - description: Index file of the Reference panel file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - scaffold: - type: file - description: Scaffold of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - scaffold_index: - type: file - description: Index file of the scaffold file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: | + Target dataset in VCF/BCF format defined at all variable positions. + The file could possibly be without GT field (for efficiency reasons a file containing only the positions is recommended). + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_index: + type: file + description: Index file of the input VCF/BCF file containing genotype likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - region: + type: string + description: | + Target region, usually a full chromosome (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference panel of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - reference_index: + type: file + description: Index file of the Reference panel file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Scaffold of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - scaffold_index: + type: file + description: Index file of the scaffold file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - phased_variants: - type: file - description: Phased haplotypes in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - phased_variant: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Phased variant dataset in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shapeit5/phaserare/meta.yml b/modules/nf-core/shapeit5/phaserare/meta.yml index dbc0aa13d03b..aaf379c87bd8 100644 --- a/modules/nf-core/shapeit5/phaserare/meta.yml +++ b/modules/nf-core/shapeit5/phaserare/meta.yml @@ -15,64 +15,78 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 requirement: AVX2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_plain: - type: file - description: | - Genotypes to be phased in plain VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - input_plain_index: - type: file - description: Index file of the input_plain VCF/BCF file containing genotype likelihoods. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - input_region: - type: string - description: | - Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20). - For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - scaffold: - type: file - description: Scaffold of haplotypes in VCF/BCF format. - pattern: "*.{vcf.gz,bcf.gz}" - - scaffold_index: - type: file - description: Index file of the scaffold file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" - - scaffold_region: - type: string - description: | - Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - map: - type: file - description: File containing the genetic map. - pattern: "*.gmap" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_plain: + type: file + description: | + Genotypes to be phased in plain VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - input_plain_index: + type: file + description: Index file of the input_plain VCF/BCF file containing genotype + likelihoods. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - input_region: + type: string + description: | + Region to be considered in --input-plain (e.g. chr20:1000000-2000000 or chr20). + For chrX, please treat PAR and non-PAR regions as different choromosome in order to avoid mixing ploidy. + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - scaffold: + type: file + description: Scaffold of haplotypes in VCF/BCF format. + pattern: "*.{vcf.gz,bcf.gz}" + - scaffold_index: + type: file + description: Index file of the scaffold file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - scaffold_region: + type: string + description: | + Region to be considered in --scaffold (e.g. chr20:1000000-2000000 or chr20). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - map: + type: file + description: File containing the genetic map. + pattern: "*.gmap" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - phased_variants: - type: file - description: Phased haplotypes in VCF/BCF format. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - phased_variant: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,bcf,vcf.gz,bcf.gz}": + type: file + description: Phased variants in VCF/BCF format. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shapeit5/switch/meta.yml b/modules/nf-core/shapeit5/switch/meta.yml index 73dd86e49d40..25352305d303 100644 --- a/modules/nf-core/shapeit5/switch/meta.yml +++ b/modules/nf-core/shapeit5/switch/meta.yml @@ -1,5 +1,6 @@ name: "shapeit5_switch" -description: Program to compute switch error rate and genotyping error rate given simulated or trio data. +description: Program to compute switch error rate and genotyping error rate given + simulated or trio data. keywords: - error - phasing @@ -13,59 +14,74 @@ tools: tool_dev_url: "https://github.com/odelaneau/shapeit5" doi: "10.1101/2022.10.19.512867 " licence: ["MIT"] + identifier: biotools:shapeit5 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - estimate: - type: file - description: Imputed data. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - estimate_index: - type: file - description: Index file of the freq VCF/BCF file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - region: - type: string - description: Target region used for imputation, including left and right buffers (e.g. chr20:1000000-2000000). - pattern: "chrXX:leftBufferPosition-rightBufferPosition" - - pedigree: - type: file - description: | - Pedigree information in the following format: offspring father mother. - pattern: "*.{txt, tsv}" - - truth: - type: file - description: Validation dataset called at the same positions as the imputed file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - truth_index: - type: file - description: Index file of the truth VCF/BCF file. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - freq: - type: file - description: File containing allele frequencies at each site. - pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" - - freq_index: - type: file - description: Index file of the freq VCF/BCF file. - pattern: "*.{vcf.gz.csi,bcf.gz.csi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - estimate: + type: file + description: Imputed data. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - estimate_index: + type: file + description: Index file of the freq VCF/BCF file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - region: + type: string + description: Target region used for imputation, including left and right buffers + (e.g. chr20:1000000-2000000). + pattern: "chrXX:leftBufferPosition-rightBufferPosition" + - pedigree: + type: file + description: | + Pedigree information in the following format: offspring father mother. + pattern: "*.{txt, tsv}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - truth: + type: file + description: Validation dataset called at the same positions as the imputed + file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - truth_index: + type: file + description: Index file of the truth VCF/BCF file. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - freq: + type: file + description: File containing allele frequencies at each site. + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - freq_index: + type: file + description: Index file of the freq VCF/BCF file. + pattern: "*.{vcf.gz.csi,bcf.gz.csi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - errors: - type: file - description: Estimates errors from the phased file. - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt.gz": + type: file + description: Estimates errors from the phased file. + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LouisLeNezet" maintainers: diff --git a/modules/nf-core/shasta/meta.yml b/modules/nf-core/shasta/meta.yml index e517e196068f..3bb24cd99214 100644 --- a/modules/nf-core/shasta/meta.yml +++ b/modules/nf-core/shasta/meta.yml @@ -1,5 +1,8 @@ name: shasta -description: The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. Please note Assembler is design to focus on speed, so assembly may be considered somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296. +description: The goal of the Shasta long read assembler is to rapidly produce accurate + assembled sequence using DNA reads generated by Oxford Nanopore flow cells as input. + Please note Assembler is design to focus on speed, so assembly may be considered + somewhat non-deterministic as final assembly may vary across executions. See https://github.com/chanzuckerberg/shasta/issues/296. keywords: - nanopore - de-novo @@ -7,44 +10,60 @@ keywords: - longread tools: - shasta: - description: Rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells. + description: Rapidly produce accurate assembled sequence using as input DNA reads + generated by Oxford Nanopore flow cells. homepage: https://chanzuckerberg.github.io/shasta/index.html documentation: https://chanzuckerberg.github.io/shasta/index.html tool_dev_url: https://github.com/chanzuckerberg/shasta doi: "10.1038/s41587-020-0503-6" licence: ["MIT"] + identifier: biotools:shasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Input file in FASTQ format. - pattern: "*.{fastq,fastq.gz,fq,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Input file in FASTQ format. + pattern: "*.{fastq,fastq.gz,fq,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - assembly: - type: file - description: Assembled FASTA file - pattern: "${prefix}_Assembly.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_Assembly.fasta.gz": + type: file + description: Assembled FASTA file + pattern: "${prefix}_Assembly.fasta.gz" - gfa: - type: file - description: Repeat graph - pattern: "${prefix}_Assembly.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_Assembly.gfa.gz": + type: file + description: Repeat graph + pattern: "${prefix}_Assembly.gfa.gz" - results: - type: directory - description: Resulting assembly directory - pattern: "ShastaRun" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ShastaRun/: + type: directory + description: Resulting assembly directory + pattern: "ShastaRun" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" maintainers: diff --git a/modules/nf-core/shasum/meta.yml b/modules/nf-core/shasum/meta.yml index 2694db9868ae..f89eb3aa612e 100644 --- a/modules/nf-core/shasum/meta.yml +++ b/modules/nf-core/shasum/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://www.gnu.org" documentation: "https://linux.die.net/man/1/shasum" licence: ["GPLv3+"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: Any file - pattern: "*.*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: Any file + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - checksum: - type: file - description: File containing checksum - pattern: "*.sha256" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sha256": + type: file + description: File containing checksum + pattern: "*.sha256" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/shigatyper/meta.yml b/modules/nf-core/shigatyper/meta.yml index 65e1de018905..04e07906f131 100644 --- a/modules/nf-core/shigatyper/meta.yml +++ b/modules/nf-core/shigatyper/meta.yml @@ -12,34 +12,43 @@ tools: tool_dev_url: "https://github.com/CFSAN-Biostatistics/shigatyper" doi: "10.1128/AEM.00165-19" licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, is_ont:false ] - - reads: - type: file - description: Illumina or Nanopore FASTQ file - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, is_ont:false ] + - reads: + type: file + description: Illumina or Nanopore FASTQ file + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV formatted file with ShigaTyper results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tsv: + type: file + description: A TSV formatted file with ShigaTyper results + pattern: "*.tsv" - hits: - type: file - description: A TSV formatted file with individual gene hits - pattern: "*-hits.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}-hits.tsv: + type: file + description: A TSV formatted file with individual gene hits + pattern: "*-hits.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/shigeifinder/meta.yml b/modules/nf-core/shigeifinder/meta.yml index 8951b5299b6d..b2bbb0e9a1e1 100644 --- a/modules/nf-core/shigeifinder/meta.yml +++ b/modules/nf-core/shigeifinder/meta.yml @@ -7,36 +7,40 @@ keywords: - serotype tools: - "shigeifinder": - description: "Cluster informed Shigella and EIEC serotyping tool from Illumina reads and assemblies" + description: "Cluster informed Shigella and EIEC serotyping tool from Illumina + reads and assemblies" homepage: "https://mgtdb.unsw.edu.au/ShigEiFinder/" documentation: "https://github.com/LanLab/ShigEiFinder" tool_dev_url: "https://github.com/LanLab/ShigEiFinder" doi: "10.1099/mgen.0.000704" licence: ["GPL v3"] + identifier: biotools:shigeifinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Assembly or paired-end Illumina reads - pattern: "*.{fasta,fasta.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Assembly or paired-end Illumina reads + pattern: "*.{fasta,fasta.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A TSV formatted file with ShigEiFinder results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A TSV formatted file with ShigEiFinder results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/shinyngs/app/meta.yml b/modules/nf-core/shinyngs/app/meta.yml index 8ff58e9598c0..62a82639460e 100644 --- a/modules/nf-core/shinyngs/app/meta.yml +++ b/modules/nf-core/shinyngs/app/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_app" -description: build and deploy Shiny apps for interactively mining differential abundance data +description: build and deploy Shiny apps for interactively mining differential abundance + data keywords: - differential - expression @@ -7,63 +8,69 @@ keywords: - deseq2 tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. To match meta. - e.g. [ id:'test' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - - contrasts: - type: file - description: | - CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. - - differential_results: - type: file - description: | - List of TSV-format differential analysis outputs, one per row of the contrasts file + - - meta: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta2: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. To match meta. + e.g. [ id:'test' ] + - contrasts: + type: file + description: | + CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. + - differential_results: + type: file + description: | + List of TSV-format differential analysis outputs, one per row of the contrasts file + - - contrast_stats_assay: + type: file + description: contrast statistics output: - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - - data: - type: file - description: | - A shinyngs ExploratorySummarizedExperiment - object serialized with saveRDS(). - pattern: "app/data.rds" - app: - type: file - description: | - The mini R script required build an application from data.rds. - pattern: "app/app.R" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/data.rds": + type: file + description: | + The mini R script required build an application from data.rds. + pattern: "app/app.R" + - "*/app.R": + type: file + description: | + The mini R script required build an application from data.rds. + pattern: "app/app.R" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/staticdifferential/meta.yml b/modules/nf-core/shinyngs/staticdifferential/meta.yml index f49ff70b78d9..f8039ca43293 100644 --- a/modules/nf-core/shinyngs/staticdifferential/meta.yml +++ b/modules/nf-core/shinyngs/staticdifferential/meta.yml @@ -7,62 +7,71 @@ keywords: - shinyngs tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing contrast information, to be passed as reference - and target levels, like '--reference_level $meta.reference - --treatment_level $meta.target' - e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - - meta2: - type: map - description: | - Groovy Map containing information on experiment represented by max, - features and samples, at a minimum an id. - e.g. [ id:'test' ] - - differential_results: - type: file - description: | - CSV or TSV-format tabular file with differential analysis outputs - - sample: - type: file - description: | - CSV or TSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - CSV or TSV-format feature (e.g. gene) metadata - - assay_file: - type: file - description: | - CSV or TSV matrix file to use alongside differential statistics in - interpretation. Usually a normalised form. + - - meta: + type: map + description: | + Groovy Map containing contrast information, to be passed as reference + and target levels, like '--reference_level $meta.reference + --treatment_level $meta.target' + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - differential_result: + type: file + description: statistic differential results + - - meta2: + type: map + description: | + Groovy Map containing information on experiment represented by max, + features and samples, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV or TSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + CSV or TSV-format feature (e.g. gene) metadata + - assay_file: + type: file + description: | + CSV or TSV matrix file to use alongside differential statistics in + interpretation. Usually a normalised form. output: - - meta: - type: map - description: | - Groovy Map containing contrast information - e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] - volcanos_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for a volcano plot built from - the differential result table. + - meta: + type: map + description: | + Groovy Map containing contrast information + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*/png/volcano.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for a volcano plot built from + the differential result table. - volcanos_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for a volcano plot built - from the differential result table. + - meta: + type: map + description: | + Groovy Map containing contrast information + e.g. [ variable:'treatment', reference:'treated', control:'saline', blocking:'' ] + - "*/html/volcano.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for a volcano plot built + from the differential result table. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/staticexploratory/meta.yml b/modules/nf-core/shinyngs/staticexploratory/meta.yml index 5a1b49b2f2c0..180ef25bfad1 100644 --- a/modules/nf-core/shinyngs/staticexploratory/meta.yml +++ b/modules/nf-core/shinyngs/staticexploratory/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_staticexploratory" -description: Make exploratory plots for analysis of matrix data, including PCA, Boxplots and density plots +description: Make exploratory plots for analysis of matrix data, including PCA, Boxplots + and density plots keywords: - exploratory - plot @@ -8,93 +9,162 @@ keywords: - PCA tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on variables for use in plots, - probably experimental information, but at a minimum an id. - e.g. [ id:'treatment' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta: + type: map + description: | + Groovy Map containing information on variables for use in plots, + probably experimental information, but at a minimum an id. + e.g. [ id:'treatment' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). output: - boxplots_png: - type: file - description: | - Meta-keyed tuple containing PNG output for box plots covering input - matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing PNG output for box plots covering input + matrices. + - "*/png/boxplot.png": + type: file + description: | + Meta-keyed tuple containing PNG output for box plots covering input + matrices. - boxplots_html: - type: file - description: | - Meta-keyed tuple containing HTML output for box plots covering input - matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing HTML output for box plots covering input + matrices. + - "*/html/boxplot.html": + type: file + description: | + Meta-keyed tuple containing HTML output for box plots covering input + matrices. - densities_png: - type: file - description: | - Meta-keyed tuple containing PNG output for density plots - covering input matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing PNG output for density plots + covering input matrices. + - "*/png/density.png": + type: file + description: | + Meta-keyed tuple containing PNG output for density plots + covering input matrices. - densities_html: - type: file - description: | - Meta-keyed tuple containing HTML output for density plots - covering input matrices. + - meta: + type: file + description: | + Meta-keyed tuple containing HTML output for density plots + covering input matrices. + - "*/html/density.html": + type: file + description: | + Meta-keyed tuple containing HTML output for density plots + covering input matrices. - pca2d_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for 2D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/png/pca2d.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. - pca2d_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for 2D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing an HTML output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/html/pca2d.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for 2D PCA plots covering + specified input matrix (by default the last one in the input list. - pca3d_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for 3D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/png/pca3d.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. - pca3d_html: - type: file - description: | - Meta-keyed tuple containing an HTML output for 3D PCA plots covering - specified input matrix (by default the last one in the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing an HTML output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. + - "*/html/pca3d.html": + type: file + description: | + Meta-keyed tuple containing an HTML output for 3D PCA plots covering + specified input matrix (by default the last one in the input list. - mad_png: - type: file - description: | - Meta-keyed tuple containing a PNG output for MAD correlation plots - covering specified input matrix (by default the last one in the input - list. - - mad_dendro: - type: file - description: | - Meta-keyed tuple containing an HTML output for MAD correlation plots - covering specified input matrix (by default the last one in the input - list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG output for MAD correlation plots + covering specified input matrix (by default the last one in the input + list. + - "*/png/mad_correlation.png": + type: file + description: | + Meta-keyed tuple containing a PNG output for MAD correlation plots + covering specified input matrix (by default the last one in the input + list. + - mad_html: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/html/mad_correlation.html": + type: file + description: HTML output for MAD correlation plots + pattern: "*{.html}" - dendro: - type: file - description: | - Meta-keyed tuple containing a PNG, for a sample clustering - dendrogramcovering specified input matrix (by default the last one in - the input list. + - meta: + type: file + description: | + Meta-keyed tuple containing a PNG, for a sample clustering + dendrogramcovering specified input matrix (by default the last one in + the input list. + - "*/png/sample_dendrogram.png": + type: file + description: | + Meta-keyed tuple containing a PNG, for a sample clustering + dendrogramcovering specified input matrix (by default the last one in + the input list. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml index 9066ada41b43..f65391dcc3b9 100644 --- a/modules/nf-core/shinyngs/validatefomcomponents/meta.yml +++ b/modules/nf-core/shinyngs/validatefomcomponents/meta.yml @@ -1,5 +1,6 @@ name: "shinyngs_validatefomcomponents" -description: validate consistency of feature and sample annotations with matrices and contrasts +description: validate consistency of feature and sample annotations with matrices + and contrasts keywords: - expression - features @@ -7,75 +8,92 @@ keywords: - validation tools: - "shinyngs": - description: "Provides Shiny applications for various array and NGS applications. Currently very RNA-seq centric, with plans for expansion." + description: "Provides Shiny applications for various array and NGS applications. + Currently very RNA-seq centric, with plans for expansion." homepage: "https://github.com/pinin4fjords/shinyngs" documentation: "https://rawgit.com/pinin4fjords/shinyngs/master/vignettes/shinyngs.html" tool_dev_url: "https://github.com/pinin4fjords/shinyngs" licence: ["AGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing information on features. - e.g. [ id:'test' ] - - meta3: - type: map - description: | - Groovy Map containing information on contrasts. - e.g. [ id:'test' ] - - meta4: - type: map - description: | - Groovy Map containing information on experiment, at a minimum an id. To match meta. - e.g. [ id:'test' ] - - sample: - type: file - description: | - CSV-format sample sheet with sample metadata - - feature_meta: - type: file - description: | - TSV-format feature (e.g. gene) metadata - - assay_files: - type: file - description: | - List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). - - contrasts: - type: file - description: | - CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. + - - meta: + type: map + description: | + Groovy Map containing information on experiment, at a minimum an id. + e.g. [ id:'test' ] + - sample: + type: file + description: | + CSV-format sample sheet with sample metadata + - assay_files: + type: file + description: | + List of TSV-format matrix files representing different measures for the same samples (e.g. raw and normalised). + - - meta2: + type: map + description: | + Groovy Map containing information on features. + e.g. [ id:'test' ] + - feature_meta: + type: file + description: | + TSV-format feature (e.g. gene) metadata + - - meta3: + type: map + description: | + Groovy Map containing information on contrasts. + e.g. [ id:'test' ] + - contrasts: + type: file + description: | + CSV-format file with four columns identifying the sample sheet variable, reference level, treatment level, and optionally a comma-separated list of covariates used as blocking factors. output: - - meta: - type: map - description: | - Groovy Map containing information on experiment. - e.g. [ id:'test' ] - sample_meta: - type: file - description: File containing validated sample metadata - pattern: "/*.sample_metadata.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.sample_metadata.tsv": + type: file + description: File containing validated sample metadata + pattern: "/*.sample_metadata.tsv" - feature_meta: - type: file - description: File containing validated feature metadata - pattern: "/*.feature_metadata.tsv" - optional: true + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.feature_metadata.tsv": + type: file + description: File containing validated feature metadata + pattern: "/*.feature_metadata.tsv" + optional: true - assays: - type: file - description: Files containing validated matrices - pattern: "/*.assay.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.assay.tsv": + type: file + description: Files containing validated matrices + pattern: "/*.assay.tsv" - contrasts: - type: file - description: Files containing validated matrices - pattern: "/*.contrasts_file.tsv" + - meta: + type: map + description: | + Groovy Map containing information on experiment. + e.g. [ id:'test' ] + - "*/*.contrasts_file.tsv": + type: file + description: Files containing validated matrices + pattern: "/*.contrasts_file.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/shovill/meta.yml b/modules/nf-core/shovill/meta.yml index cdeb0152b5be..7f5f33962dfa 100644 --- a/modules/nf-core/shovill/meta.yml +++ b/modules/nf-core/shovill/meta.yml @@ -10,45 +10,73 @@ tools: homepage: https://github.com/tseemann/shovill documentation: https://github.com/tseemann/shovill/blob/master/README.md licence: ["GPL v2"] + identifier: biotools:shovill input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input paired-end FastQ files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input paired-end FastQ files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - contigs: - type: file - description: The final assembly produced by Shovill - pattern: "contigs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs.fa: + type: file + description: The final assembly produced by Shovill + pattern: "contigs.fa" - corrections: - type: file - description: List of post-assembly corrections made by Shovill - pattern: "shovill.corrections" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shovill.corrections: + type: file + description: List of post-assembly corrections made by Shovill + pattern: "shovill.corrections" - log: - type: file - description: Full log file for bug reporting - pattern: "shovill.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shovill.log: + type: file + description: Full log file for bug reporting + pattern: "shovill.log" - raw_contigs: - type: file - description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, or Velvet) - pattern: "{skesa,spades,megahit,velvet}.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "{skesa,spades,megahit,velvet}.fasta": + type: file + description: Raw assembly produced by the assembler (SKESA, SPAdes, MEGAHIT, + or Velvet) + pattern: "{skesa,spades,megahit,velvet}.fasta" - gfa: - type: file - description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet - pattern: "contigs.{fastg,gfa,LastGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - contigs.{fastg,gfa,LastGraph}: + type: file + description: Assembly graph produced by MEGAHIT, SPAdes, or Velvet + pattern: "contigs.{fastg,gfa,LastGraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/sickle/meta.yml b/modules/nf-core/sickle/meta.yml index da94c23d6f6b..03c49e8854a4 100644 --- a/modules/nf-core/sickle/meta.yml +++ b/modules/nf-core/sickle/meta.yml @@ -6,50 +6,75 @@ keywords: - trimming tools: - "sickle": - description: "a tool that determines clipping of reads on 3' end and 5'end based on base quality " + description: "a tool that determines clipping of reads on 3' end and 5'end based + on base quality " homepage: "https://github.com/najoshi/sickle" tool_dev_url: "https://github.com/najoshi/sickle" licence: ["MIT License"] + identifier: biotools:sickle input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false] - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. File of forward reads must be supplied first and reverse reads as the second e.g. ["read.1.fastq.gz","read.2.fastq.gz"] - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - qual_type: - type: string - description: sickle needs a base quality values, which could be either illumina, solexa or sanger - pattern: "illumina or solexa or sanger" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false] + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively. File of forward reads must be supplied first and reverse + reads as the second e.g. ["read.1.fastq.gz","read.2.fastq.gz"] + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - qual_type: + type: string + description: sickle needs a base quality values, which could be either illumina, + solexa or sanger + pattern: "illumina or solexa or sanger" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, qual:'Illumina' ] - single_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) single-end fastq file - pattern: "*.se.trimmed.fastq.gz" - - paired1_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) R1 fastq file - pattern: "*.pe1.trimmed.fastq.gz" - - paired2_trimmed: - type: file - description: 5' or 3' trimmed (based on base quality) R2 fastq file - pattern: "*.pe2.trimmed.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.se.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) single-end fastq file + pattern: "*.se.trimmed.fastq.gz" + - paired_trimmed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.pe{1,2}.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) paired-end fastq files + pattern: "*.pe{1,2}.trimmed.fastq.gz" + - singleton_trimmed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - ${prefix}.singleton.trimmed.fastq.gz: + type: file + description: 5' or 3' trimmed (based on base quality) singleton fastq file + pattern: "*.singleton.trimmed.fastq.gz" - log: - type: file - description: log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, qual:'Illumina' ] + - "*.log": + type: file + description: log file + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BioInf2305" maintainers: diff --git a/modules/nf-core/simpleaf/index/meta.yml b/modules/nf-core/simpleaf/index/meta.yml index 5a23fb8686e0..f90674af1c26 100644 --- a/modules/nf-core/simpleaf/index/meta.yml +++ b/modules/nf-core/simpleaf/index/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: simpleaf_index description: Indexing of transcriptome for gene expression quantification using SimpleAF @@ -13,56 +12,69 @@ tools: SimpleAF is a tool for quantification of gene expression from RNA-seq data homepage: https://github.com/COMBINE-lab/simpleaf licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing information on genome_fasta - - genome_fasta: - type: file - description: | - FASTA file containing the genome sequence - - meta2: - type: map - description: | - Groovy Map containing information on genome_gtf - - genome_gtf: - type: file - description: | - GTF file containing transcript annotations. Optional if transcript FASTA file is provided. - - meta3: - type: map - description: | - Groovy Map containing information on transcript_fasta - - transcript_fasta: - type: file - description: | - FASTA file containing the transcript sequences. Optional if transcript GTF file is provided. + - - meta: + type: map + description: | + Groovy Map containing information on genome_fasta + - genome_fasta: + type: file + description: | + FASTA file containing the genome sequence + - - meta2: + type: map + description: | + Groovy Map containing information on genome_gtf + - genome_gtf: + type: file + description: | + GTF file containing transcript annotations. Optional if transcript FASTA file is provided. + - - meta3: + type: map + description: | + Groovy Map containing information on transcript_fasta + - transcript_fasta: + type: file + description: | + FASTA file containing the transcript sequences. Optional if transcript GTF file is provided. output: - - meta: - type: map - description: | - Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) - index: - type: directory - description: | - Folder containing the Salmon index files - pattern: "salmon/index" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}/index: + type: directory + description: | + Folder containing the Salmon index files + pattern: "salmon/index" - transcript_tsv: - type: file - description: | - Transcript-to-gene mapping file in 3-column TSV format - pattern: "salmon/ref/*_t2g_3col.tsv" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}/ref/t2g_3col.tsv: + type: file + description: | + Transcript-to-gene mapping file in 3-column TSV format + pattern: "salmon/ref/*_t2g_3col.tsv" - salmon: - type: directory - description: | - Folder containing the Salmon files - pattern: "salmon" + - meta: + type: map + description: | + Groovy Map containing information on genome_fasta or transcript_fasta (whichever was used) + - ${prefix}: + type: directory + description: | + Folder containing the Salmon files + pattern: "salmon" - versions: - type: file - description: | - File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: | + File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" - "@maxulysse" diff --git a/modules/nf-core/simpleaf/quant/meta.yml b/modules/nf-core/simpleaf/quant/meta.yml index 545c7d0a3c02..79d7b158e2b4 100644 --- a/modules/nf-core/simpleaf/quant/meta.yml +++ b/modules/nf-core/simpleaf/quant/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: simpleaf_quant -description: simpleaf is a program to simplify and customize the running and configuration of single-cell processing with alevin-fry. +description: simpleaf is a program to simplify and customize the running and configuration + of single-cell processing with alevin-fry. keywords: - quantification - gene expression @@ -12,66 +12,71 @@ tools: SimpleAF is a tool for quantification of gene expression from RNA-seq data homepage: https://github.com/COMBINE-lab/simpleaf licence: ["BSD-3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files for paired-end data. - Reads should be grouped by pairs. - - meta2: - type: map - description: | - Groovy Map containing index information - - index: - type: directory - description: Folder containing the index files - - meta3: - type: map - description: | - Groovy Map containing txp2gene information - - txp2gene: - type: file - description: | - File mapping transcripts to genes. - - chemistry: - type: string - description: | - Chemistry used for library preparation. It can be a string describing - the specific chemistry or the geometry of the barcode, UMI, and - mappable read. For example, "10xv2" and "10xv3" will apply the - appropriate settings for 10x Chromium v2 and v3 protocols, - respectively. Alternatively, you can provide a general geometry string - if your chemistry is not pre-registered. For example, instead of - "10xv2", you could use "1{b[16]u[10]x:}2{r:}", or instead of "10xv3", - you could use "1{b[16]u[12]x:}2{r:}". - - meta4: - type: map - description: | - Groovy Map containing whitelist information - - whitelist: - type: file - description: | - Whitelist file containing valid cell barcodes. Optional. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - chemistry: + type: string + description: | + Chemistry used for library preparation. It can be a string describing + the specific chemistry or the geometry of the barcode, UMI, and + mappable read. For example, "10xv2" and "10xv3" will apply the + appropriate settings for 10x Chromium v2 and v3 protocols, + respectively. Alternatively, you can provide a general geometry string + if your chemistry is not pre-registered. For example, instead of + "10xv2", you could use "1{b[16]u[10]x:}2{r:}", or instead of "10xv3", + you could use "1{b[16]u[12]x:}2{r:}". + - reads: + type: file + description: | + List of input FastQ files for paired-end data. + Reads should be grouped by pairs. + - - meta2: + type: map + description: | + Groovy Map containing index information + - index: + type: directory + description: Folder containing the index files + - - meta3: + type: map + description: | + Groovy Map containing txp2gene information + - txp2gene: + type: file + description: | + File mapping transcripts to genes. + - - resolution: + type: string + description: | + Resolution for the clustering. + - - meta4: + type: map + description: | + Groovy Map containing whitelist information + - whitelist: + type: file + description: | + Whitelist file containing valid cell barcodes. Optional. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alevin_results: - type: directory - description: | - Folder containing the Alevin results for a specific sample - pattern: "*" + - results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}: + type: directory + description: Folder containing the quantification results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fmalmeida" - "@maxulysse" diff --git a/modules/nf-core/sistr/meta.yml b/modules/nf-core/sistr/meta.yml index 77017684636d..4cb907055d02 100644 --- a/modules/nf-core/sistr/meta.yml +++ b/modules/nf-core/sistr/meta.yml @@ -6,48 +6,70 @@ keywords: - salmonella tools: - sistr: - description: Salmonella In Silico Typing Resource (SISTR) commandline tool for serovar prediction + description: Salmonella In Silico Typing Resource (SISTR) commandline tool for + serovar prediction homepage: https://github.com/phac-nml/sistr_cmd documentation: https://github.com/phac-nml/sistr_cmd tool_dev_url: https://github.com/phac-nml/sistr_cmd doi: "10.1371/journal.pone.0147101" licence: ["Apache-2.0"] + identifier: biotools:SISTR input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Nucleotide or protein sequences in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Nucleotide or protein sequences in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: SISTR serovar prediction - pattern: "*.{tsv}" - - allele_json: - type: file - description: Allele sequences and info to JSON - pattern: "*.{json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: SISTR serovar prediction + pattern: "*.{tsv}" - allele_fasta: - type: file - description: FASTA file destination of novel cgMLST alleles - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-allele.fasta": + type: file + description: FASTA file destination of novel cgMLST alleles + pattern: "*.{fasta}" + - allele_json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-allele.json": + type: file + description: Allele sequences and info to JSON + pattern: "*.{json}" - cgmlst_csv: - type: file - description: CSV file destination for cgMLST allelic profiles - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-cgmlst.csv": + type: file + description: CSV file destination for cgMLST allelic profiles + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/slimfastq/meta.yml b/modules/nf-core/slimfastq/meta.yml index 72036d898290..617312ce2834 100644 --- a/modules/nf-core/slimfastq/meta.yml +++ b/modules/nf-core/slimfastq/meta.yml @@ -10,30 +10,33 @@ tools: homepage: "https://github.com/Infinidat/slimfastq" tool_dev_url: "https://github.com/Infinidat/slimfastq" licence: ["BSD-3-clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: Either a single-end FASTQ file or paired-end files. - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: Either a single-end FASTQ file or paired-end files. + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sfq: - type: file - description: Either one or two sequence files in slimfastq compressed format. - pattern: "*.{sfq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sfq": + type: file + description: Either one or two sequence files in slimfastq compressed format. + pattern: "*.{sfq}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/smncopynumbercaller/meta.yml b/modules/nf-core/smncopynumbercaller/meta.yml index f318a2b7a34b..9d91fc096827 100644 --- a/modules/nf-core/smncopynumbercaller/meta.yml +++ b/modules/nf-core/smncopynumbercaller/meta.yml @@ -1,5 +1,7 @@ name: "smncopynumbercaller" -description: tool to call the copy number of full-length SMN1, full-length SMN2, as well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing (WGS) BAM file. +description: tool to call the copy number of full-length SMN1, full-length SMN2, as + well as SMN2Δ7–8 (SMN2 with a deletion of Exon7-8) from a whole-genome sequencing + (WGS) BAM file. keywords: - copy number - BAM @@ -14,38 +16,47 @@ tools: tool_dev_url: "https://github.com/Illumina/SMNCopyNumberCaller" doi: "10.1038/s41436-020-0754-0" licence: ["Apache License Version 2.0"] + identifier: "" input: - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - run_metrics: - type: file - description: File containing run parameters of SMNCopyNumberCaller - pattern: "*.{json}" - smncopynumber: - type: file - description: File containing the output of SMNCopyNumberCaller - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - out/*.tsv: + type: file + description: File containing the output of SMNCopyNumberCaller + pattern: "*.{tsv}" + - run_metrics: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - out/*.json: + type: file + description: File containing run parameters of SMNCopyNumberCaller + pattern: "*.{json}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@peterpru" maintainers: diff --git a/modules/nf-core/smoothxg/meta.yml b/modules/nf-core/smoothxg/meta.yml index 2ba721f89741..3c5de7fea09b 100644 --- a/modules/nf-core/smoothxg/meta.yml +++ b/modules/nf-core/smoothxg/meta.yml @@ -1,5 +1,6 @@ name: smoothxg -description: Linearize and simplify variation graph in GFA format using blocked partial order alignment +description: Linearize and simplify variation graph in GFA format using blocked partial + order alignment keywords: - gfa - graph @@ -14,34 +15,39 @@ tools: homepage: https://github.com/pangenome/smoothxg documentation: https://github.com/pangenome/smoothxg licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA 1.0 format - pattern: "*.{gfa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA 1.0 format + pattern: "*.{gfa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - gfa: - type: file - description: Linearized and simplified graph in GFA 1.0 format - pattern: "*.smoothxg.{gfa}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*smoothxg.gfa": + type: file + description: Linearized and simplified graph in GFA 1.0 format + pattern: "*.smoothxg.{gfa}" - maf: - type: file - description: write the multiple sequence alignments (MSAs) in MAF format in this file (optional) - pattern: "*.{maf}" + - "*.maf": + type: file + description: write the multiple sequence alignments (MSAs) in MAF format in + this file (optional) + pattern: "*.{maf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh, @subwaystation" maintainers: diff --git a/modules/nf-core/smoove/call/meta.yml b/modules/nf-core/smoove/call/meta.yml index bff9916b96f3..379ae6e2daed 100644 --- a/modules/nf-core/smoove/call/meta.yml +++ b/modules/nf-core/smoove/call/meta.yml @@ -1,5 +1,8 @@ name: "smoove_call" -description: smoove simplifies and speeds calling and genotyping SVs for short reads. It also improves specificity by removing many spurious alignment signals that are indicative of low-level noise and often contribute to spurious calls. Developped by Brent Pedersen. +description: smoove simplifies and speeds calling and genotyping SVs for short reads. + It also improves specificity by removing many spurious alignment signals that are + indicative of low-level noise and often contribute to spurious calls. Developped + by Brent Pedersen. keywords: - structural variants - SV @@ -7,51 +10,65 @@ keywords: - wgs tools: - "smoove": - description: "structural variant calling and genotyping with existing tools, but, smoothly" + description: "structural variant calling and genotyping with existing tools, but, + smoothly" homepage: https://github.com/brentp/smoove documentation: https://brentp.github.io/post/smoove/ tool_dev_url: https://github.com/brentp/smoove licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - index: - type: file - description: Index of BAM/CRAM file - pattern: "*.{bai,crai}" - - exclude_beds: - type: file - description: A BED file containing the regions to exclude from the SV calling - pattern: "*.bed" - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fna,fa}" - - fai: - type: file - description: Index of reference fasta file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - index: + type: file + description: Index of BAM/CRAM file + pattern: "*.{bai,crai}" + - exclude_beds: + type: file + description: A BED file containing the regions to exclude from the SV calling + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@scorreard" - "@nvnieuwk" diff --git a/modules/nf-core/snakemake/meta.yml b/modules/nf-core/snakemake/meta.yml index 3da2765988e5..b82abe37f143 100644 --- a/modules/nf-core/snakemake/meta.yml +++ b/modules/nf-core/snakemake/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "snakemake" -description: The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. This module runs a simple Snakemake pipeline based on input snakefile. Expect many limitations." +description: The Snakemake workflow management system is a tool to create reproducible + and scalable data analyses. This module runs a simple Snakemake pipeline based on + input snakefile. Expect many limitations." keywords: - snakemake - workflow @@ -14,45 +15,54 @@ tools: tool_dev_url: "https://github.com/snakemake/snakemake" doi: "10.1093/bioinformatics/bty350" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputs: - type: file - description: Any input file required by Snakemake - pattern: "*" - - meta2: - type: map - description: | - Meta information for Snakefile - e.g. [ id: 'snakefile' ] - - snakefile: - type: file - description: | - Snakefile to use with Snakemake. This is required for proper execution of Snakemake. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputs: + type: file + description: Any input file required by Snakemake + pattern: "*" + - - meta2: + type: map + description: | + Meta information for Snakefile + e.g. [ id: 'snakefile' ] + - snakefile: + type: file + description: | + Snakefile to use with Snakemake. This is required for proper execution of Snakemake. output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - outputs: - type: file - description: | - Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "[!.snakemake|versions.yml]**": + type: file + description: | + Any file generated by Snakemake, excluding the inputs, hidden files and Snakemake log directory (.snakemake). This is set to optional because Snakemake can be used to run arbitrary commands, and we cannot know what files will be generated. - snakemake_dir: - type: directory - description: | - Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - '.snakemake", type: ''dir'', hidden: true': + type: directory + description: | + Snakemake log directory (.snakemake). Can be used to capture logs of Snakemake execution. - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/snapaligner/align/meta.yml b/modules/nf-core/snapaligner/align/meta.yml index 137b67e18aba..37d9078eb1bd 100644 --- a/modules/nf-core/snapaligner/align/meta.yml +++ b/modules/nf-core/snapaligner/align/meta.yml @@ -8,49 +8,60 @@ keywords: - sam tools: - "snapaligner": - description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data" + description: "Scalable Nucleotide Alignment Program -- a fast and accurate read + aligner for high-throughput sequencing data" homepage: "http://snap.cs.berkeley.edu" documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug" tool_dev_url: "https://github.com/amplab/snap" doi: "10.1101/2021.11.23.469039" licence: ["Apache v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: List of input fastq files of size 2 for paired fastq or 1 for bam or single fastq - pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - index: - type: file - description: List of SNAP genome index files - pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: List of input fastq files of size 2 for paired fastq or 1 for bam + or single fastq + pattern: "*.{fastq.gz,fq.gz,fastq,fq,bam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - index: + type: file + description: List of SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Aligned BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Aligned BAM file + pattern: "*.{bam}" - bai: - type: file - description: Optional aligned BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bai": + type: file + description: Optional aligned BAM file index + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/snapaligner/index/meta.yml b/modules/nf-core/snapaligner/index/meta.yml index bf84a6b78ff2..a0d7367daf3b 100644 --- a/modules/nf-core/snapaligner/index/meta.yml +++ b/modules/nf-core/snapaligner/index/meta.yml @@ -7,39 +7,49 @@ keywords: - reference tools: - "snapaligner": - description: "Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for high-throughput sequencing data" + description: "Scalable Nucleotide Alignment Program -- a fast and accurate read + aligner for high-throughput sequencing data" homepage: "http://snap.cs.berkeley.edu" documentation: "https://1drv.ms/b/s!AhuEg_0yZD86hcpblUt-muHKYsG8fA?e=R8ogug" tool_dev_url: "https://github.com/amplab/snap" doi: "10.1101/2021.11.23.469039" licence: ["Apache v2"] + identifier: "" input: - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - - altcontigfile: - type: file - description: Optional file with a list of alt contig names, one per line. - - nonaltcontigfile: - type: file - description: Optional file that contains a list of contigs (one per line) that will not be marked ALT regardless of size. - - altliftoverfile: - type: file - description: Optional file containing ALT-to-REF mappings (SAM format). e.g., hs38DH.fa.alt from bwa-kit. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + - altcontigfile: + type: file + description: Optional file with a list of alt contig names, one per line. + - nonaltcontigfile: + type: file + description: Optional file that contains a list of contigs (one per line) that + will not be marked ALT regardless of size. + - altliftoverfile: + type: file + description: Optional file containing ALT-to-REF mappings (SAM format). e.g., + hs38DH.fa.alt from bwa-kit. output: - index: - type: file - description: SNAP genome index files - pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - meta: + type: file + description: SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" + - snap/*: + type: file + description: SNAP genome index files + pattern: "{Genome,GenomeIndex,GenomeIndexHash,OverflowTable}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/sniffles/meta.yml b/modules/nf-core/sniffles/meta.yml index b747de35ea90..b52d45a304e5 100644 --- a/modules/nf-core/sniffles/meta.yml +++ b/modules/nf-core/sniffles/meta.yml @@ -11,60 +11,84 @@ tools: documentation: https://github.com/fritzsedlazeck/Sniffles#readme tool_dev_url: https://github.com/fritzsedlazeck/Sniffles licence: ["MIT"] + identifier: biotools:sniffles input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - input: - type: file - description: A single .bam/.cram file - OR - one or more .snf files - OR - a single .tsv file containing a list of .snf files and optional sample ids as input - pattern: "*.{bam,cram,snf,tsv}" - - index: - type: file - description: Index of BAM/CAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'fasta' ] - - fasta: - type: file - description: | - Reference database in FASTA format - - meta3: - type: map - description: | - Groovy Map containing tandem repeat information - e.g. [ id:'hg38' ] - - tandem_file: - type: file - description: Tandem repeat file - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - input: + type: file + description: A single .bam/.cram file - OR - one or more .snf files - OR - a + single .tsv file containing a list of .snf files and optional sample ids as + input + pattern: "*.{bam,cram,snf,tsv}" + - index: + type: file + description: Index of BAM/CAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'fasta' ] + - fasta: + type: file + description: | + Reference database in FASTA format + - - meta3: + type: map + description: | + Groovy Map containing tandem repeat information + e.g. [ id:'hg38' ] + - tandem_file: + type: file + description: Tandem repeat file + pattern: "*.bed" + - - vcf_output: + type: file + description: VCF output file + pattern: "*.vcf.gz" + - - snf_output: + type: file + description: SNF output file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Compressed VCF file index - pattern: "*.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz.tbi": + type: file + description: Compressed VCF file index + pattern: "*.tbi" - snf: - type: file - description: SNF file - pattern: "*.snf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.snf": + type: file + description: SNF file + pattern: "*.snf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@christopher-hakkaart" - "@yuukiiwa" diff --git a/modules/nf-core/snippy/core/meta.yml b/modules/nf-core/snippy/core/meta.yml index cd548b67ed42..7d1c39056a77 100644 --- a/modules/nf-core/snippy/core/meta.yml +++ b/modules/nf-core/snippy/core/meta.yml @@ -12,54 +12,84 @@ tools: documentation: "https://github.com/tseemann/snippy" tool_dev_url: "https://github.com/tseemann/snippy" licence: ["GPL v2"] + identifier: biotools:snippy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Annotated variants in VCF format - pattern: "*.vcf.gz" - - aligned_fa: - type: file - description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants) - pattern: "*.aligned.fa.gz" - - reference: - type: file - description: Reference genome in GenBank (preferred) or FASTA format - pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Annotated variants in VCF format + pattern: "*.vcf.gz" + - aligned_fa: + type: file + description: A version of the reference but with - at position with depth=0 + and N for 0 < depth < --mincov (does not have variants) + pattern: "*.aligned.fa.gz" + - - reference: + type: file + description: Reference genome in GenBank (preferred) or FASTA format + pattern: "*.{gbk,gbk.gz,gbff,gbff.gz,fa,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - aln: - type: file - description: A core SNP alignment in FASTA format - pattern: "*.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.aln: + type: file + description: A core SNP alignment in FASTA format + pattern: "*.aln" - full_aln: - type: file - description: A whole genome SNP alignment (includes invariant sites) - pattern: "*.full.aln" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.full.aln: + type: file + description: A whole genome SNP alignment (includes invariant sites) + pattern: "*.full.aln" - tab: - type: file - description: Tab-separated columnar list of core SNP sites with alleles but NO annotations - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.tab: + type: file + description: Tab-separated columnar list of core SNP sites with alleles but + NO annotations + pattern: "*.tab" - vcf: - type: file - description: Multi-sample VCF file with genotype GT tags for all discovered alleles - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.vcf: + type: file + description: Multi-sample VCF file with genotype GT tags for all discovered + alleles + pattern: "*.vcf" - txt: - type: file - description: Tab-separated columnar list of alignment/core-size statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.txt: + type: file + description: Tab-separated columnar list of alignment/core-size statistics + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/snippy/run/meta.yml b/modules/nf-core/snippy/run/meta.yml index e5fafb2f4615..5b3c907d77ba 100644 --- a/modules/nf-core/snippy/run/meta.yml +++ b/modules/nf-core/snippy/run/meta.yml @@ -11,100 +11,202 @@ tools: documentation: "https://github.com/tseemann/snippy" tool_dev_url: "https://github.com/tseemann/snippy" licence: ["GPL v2"] + identifier: biotools:snippy input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fq,fastq,fq.gz,fastq.gz}" - - index: - type: file - description: Reference genome in GenBank (preferred) or FASTA format - pattern: "*.{gbk,gbk.gz,fa,fa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - - reference: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tab: - type: file - description: A simple tab-separated summary of all the variants - pattern: "*.tab" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.tab: + type: file + description: A simple tab-separated summary of all the variants + pattern: "*.tab" - csv: - type: file - description: A comma-separated version of the .tab file - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.csv: + type: file + description: A comma-separated version of the .tab file + pattern: "*.csv" - html: - type: file - description: A HTML version of the .tab file - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.html: + type: file + description: A HTML version of the .tab file + pattern: "*.html" - vcf: - type: file - description: The final annotated variants in VCF format - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf: + type: file + description: The final annotated variants in VCF format + pattern: "*.vcf" - bed: - type: file - description: The variants in BED format - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bed: + type: file + description: The variants in BED format + pattern: "*.bed" - gff: - type: file - description: The variants in GFF3 format - pattern: "*.gff" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.gff: + type: file + description: The variants in GFF3 format + pattern: "*.gff" - bam: - type: file - description: The alignments in BAM format. Includes unmapped, multimapping reads. Excludes duplicates. - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bam: + type: file + description: The alignments in BAM format. Includes unmapped, multimapping reads. + Excludes duplicates. + pattern: "*.bam" - bai: - type: file - description: Index for the .bam file - pattern: "*.bam.bai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.bam.bai: + type: file + description: Index for the .bam file + pattern: "*.bam.bai" - log: - type: file - description: A log file with the commands run and their outputs - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.log: + type: file + description: A log file with the commands run and their outputs + pattern: "*.log" - aligned_fa: - type: file - description: A version of the reference but with - at position with depth=0 and N for 0 < depth < --mincov (does not have variants) - pattern: "*.aligned.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.aligned.fa: + type: file + description: A version of the reference but with - at position with depth=0 + and N for 0 < depth < --mincov (does not have variants) + pattern: "*.aligned.fa" - consensus_fa: - type: file - description: A version of the reference genome with all variants instantiated - pattern: "*.consensus.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.consensus.fa: + type: file + description: A version of the reference genome with all variants instantiated + pattern: "*.consensus.fa" - consensus_subs_fa: - type: file - description: A version of the reference genome with only substitution variants instantiated - pattern: "*.consensus.subs.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.consensus.subs.fa: + type: file + description: A version of the reference genome with only substitution variants + instantiated + pattern: "*.consensus.subs.fa" - raw_vcf: - type: file - description: The unfiltered variant calls from Freebayes - pattern: "*.raw.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.raw.vcf: + type: file + description: The unfiltered variant calls from Freebayes + pattern: "*.raw.vcf" - filt_vcf: - type: file - description: The filtered variant calls from Freebayes - pattern: "*.filt.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.filt.vcf: + type: file + description: The filtered variant calls from Freebayes + pattern: "*.filt.vcf" - vcf_gz: - type: file - description: Compressed .vcf file via BGZIP - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf.gz: + type: file + description: Compressed .vcf file via BGZIP + pattern: "*.vcf.gz" - vcf_csi: - type: file - description: Index for the .vcf.gz via bcftools index - pattern: "*.vcf.gz.csi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.vcf.gz.csi: + type: file + description: Index for the .vcf.gz via bcftools index + pattern: "*.vcf.gz.csi" - txt: - type: file - description: Tab-separated columnar list of statistics - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/${prefix}.txt: + type: file + description: Tab-separated columnar list of statistics + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/snpdists/meta.yml b/modules/nf-core/snpdists/meta.yml index 4991f6e86c42..612638f9ffa6 100644 --- a/modules/nf-core/snpdists/meta.yml +++ b/modules/nf-core/snpdists/meta.yml @@ -12,30 +12,33 @@ tools: documentation: https://github.com/tseemann/snp-dists tool_dev_url: https://github.com/tseemann/snp-dists licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - alignment: - type: file - description: The input FASTA sequence alignment file - pattern: "*.{fasta,fasta.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - alignment: + type: file + description: The input FASTA sequence alignment file + pattern: "*.{fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tsv: - type: file - description: The output TSV file containing SNP distance matrix - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: The output TSV file containing SNP distance matrix + pattern: "*.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" maintainers: diff --git a/modules/nf-core/snpeff/download/meta.yml b/modules/nf-core/snpeff/download/meta.yml index f367c6966481..a3211fc7c93b 100644 --- a/modules/nf-core/snpeff/download/meta.yml +++ b/modules/nf-core/snpeff/download/meta.yml @@ -14,29 +14,35 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome: + type: file + description: Reference genome in FASTA format + pattern: "*.{fasta,fna,fa}" + - cache_version: + type: string + description: Version of the snpEff cache to download output: - cache: - type: file - description: | - snpEff cache + - meta: + type: file + description: | + snpEff cache + - snpeff_cache: + type: file + description: | + snpEff cache - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 7559c3de082e..ef3d495ae74d 100644 --- a/modules/nf-core/snpeff/snpeff/meta.yml +++ b/modules/nf-core/snpeff/snpeff/meta.yml @@ -14,46 +14,76 @@ tools: homepage: https://pcingola.github.io/SnpEff/ documentation: https://pcingola.github.io/SnpEff/se_introduction/ licence: ["MIT"] + identifier: biotools:snpeff input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - db: - type: string - description: | - which db to annotate with - - cache: - type: file - description: | - path to snpEff cache (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to annotate + - - db: + type: string + description: | + which db to annotate with + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - cache: + type: file + description: | + path to snpEff cache (optional) output: - vcf: - type: file - description: | - annotated vcf - pattern: "*.ann.vcf" + - meta: + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" + - "*.ann.vcf": + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" - report: - type: file - description: snpEff report csv file - pattern: "*.csv" + - meta: + type: file + description: snpEff report csv file + pattern: "*.csv" + - "*.csv": + type: file + description: snpEff report csv file + pattern: "*.csv" - summary_html: - type: file - description: snpEff summary statistics in html file - pattern: "*.html" + - meta: + type: file + description: snpEff summary statistics in html file + pattern: "*.html" + - "*.html": + type: file + description: snpEff summary statistics in html file + pattern: "*.html" - genes_txt: - type: file - description: txt (tab separated) file having counts of the number of variants affecting each transcript and gene - pattern: "*.genes.txt" + - meta: + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" + - "*.genes.txt": + type: file + description: txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + pattern: "*.genes.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/snpsift/annotate/meta.yml b/modules/nf-core/snpsift/annotate/meta.yml index da0409e54f48..75970f662f1e 100644 --- a/modules/nf-core/snpsift/annotate/meta.yml +++ b/modules/nf-core/snpsift/annotate/meta.yml @@ -7,53 +7,56 @@ keywords: - cancer genomics tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_introduction/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information regarding vcf file provided - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tbi: - type: file - description: Tabix file for compressed vcf provided - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy map containing sample information regarding database provided - - database: - type: file - description: Database for use to annotate - pattern: "*.{vcf/vcf.gz}" - - dbs_tbi: - type: file - description: Tabix file for compressed database provided - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information regarding vcf file provided + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf, vcf.gz}" + - vcf_tbi: + type: file + description: Tabix file for compressed vcf provided + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy map containing sample information regarding database provided + - database: + type: file + description: Database for use to annotate + pattern: "*.{vcf/vcf.gz}" + - dbs_tbi: + type: file + description: Tabix file for compressed database provided + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - # - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Variant Calling File annotated - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant Calling File annotated + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/snpsift/dbnsfp/meta.yml b/modules/nf-core/snpsift/dbnsfp/meta.yml index 7b9d6f1d5e4b..49ad72d88d88 100644 --- a/modules/nf-core/snpsift/dbnsfp/meta.yml +++ b/modules/nf-core/snpsift/dbnsfp/meta.yml @@ -1,5 +1,6 @@ name: "snpsift_dbnsfp" -description: "The dbNSFP is an integrated database of functional predictions from multiple algorithms" +description: "The dbNSFP is an integrated database of functional predictions from + multiple algorithms" keywords: - variant calling - dbnsfp @@ -8,53 +9,56 @@ keywords: - predictions tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_dbnsfp/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information regarding vcf file provided - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tbi: - type: file - description: Tabix file for compressed vcf provided - pattern: "*.{tbi}" - - meta2: - type: map - description: | - Groovy map containing sample information regarding database provided - - database: - type: file - description: Database for use to annotate - pattern: "*.{vcf/vcf.gz}" - - dbs_tbi: - type: file - description: Tabix file for compressed database provided - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information regarding vcf file provided + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf, vcf.gz}" + - vcf_tbi: + type: file + description: Tabix file for compressed vcf provided + pattern: "*.{tbi}" + - - meta2: + type: map + description: | + Groovy map containing sample information regarding database provided + - database: + type: file + description: Database for use to annotate + pattern: "*.{vcf/vcf.gz}" + - dbs_tbi: + type: file + description: Tabix file for compressed database provided + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Variant Calling File annotated - pattern: "*.{vcf}" - # + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variant Calling File annotated + pattern: "*.{vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/snpsift/split/meta.yml b/modules/nf-core/snpsift/split/meta.yml index 8530461e3e0b..bf1f7236103b 100644 --- a/modules/nf-core/snpsift/split/meta.yml +++ b/modules/nf-core/snpsift/split/meta.yml @@ -6,36 +6,40 @@ keywords: - vcf tools: - snpsift: - description: SnpSift is a toolbox that allows you to filter and manipulate annotated files + description: SnpSift is a toolbox that allows you to filter and manipulate annotated + files homepage: https://pcingola.github.io/SnpEff/ss_introduction/ documentation: https://pcingola.github.io/SnpEff/ss_introduction/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" licence: ["MIT"] + identifier: biotools:snpsift input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file(s) - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file(s) + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - out_vcfs: - type: file - description: Split/Joined VCF file(s) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Split/Joined VCF file(s) + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@SusiJo" - "@jonasscheid" diff --git a/modules/nf-core/snpsites/meta.yml b/modules/nf-core/snpsites/meta.yml index 067294829b16..eafac8e8ff87 100644 --- a/modules/nf-core/snpsites/meta.yml +++ b/modules/nf-core/snpsites/meta.yml @@ -10,28 +10,33 @@ tools: homepage: https://www.sanger.ac.uk/tool/snp-sites/ documentation: https://github.com/sanger-pathogens/snp-sites licence: ["GPL-3.0-or-later"] + identifier: "" input: - - alignment: - type: file - description: fasta alignment file - pattern: "*.{fasta,fas,fa,aln}" + - - alignment: + type: file + description: fasta alignment file + pattern: "*.{fasta,fas,fa,aln}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Variant fasta file - pattern: "*.{fas}" + - "*.fas": + type: file + description: Variant fasta file + pattern: "*.{fas}" - constant_sites: - type: file - description: Text file containing counts of constant sites - pattern: "*.{sites.txt}" + - "*.sites.txt": + type: file + description: Text file containing counts of constant sites + pattern: "*.{sites.txt}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" - constant_sites_string: - type: integer - description: Value with the number of constant sites - pattern: "*.{sites.txt}" + - CONSTANT_SITES: + type: integer + description: Value with the number of constant sites + pattern: "*.{sites.txt}" authors: - "@avantonder" maintainers: diff --git a/modules/nf-core/somalier/ancestry/meta.yml b/modules/nf-core/somalier/ancestry/meta.yml index 6cc67ba6d6ec..7b7dde8d8972 100644 --- a/modules/nf-core/somalier/ancestry/meta.yml +++ b/modules/nf-core/somalier/ancestry/meta.yml @@ -1,5 +1,6 @@ name: "somalier_ancestry" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,53 +15,66 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - query_somalier_files: - type: file - description: Set of somalier files for query samples. Obtained via somalier extract. - pattern: "*.{somalier}" - - meta2: - type: map - description: | - Groovy Map containing labelled samples information - e.g. [ id:'test', single_end:false ] - - labelled_somalier_files: - type: file - description: Set of somalier files for labelled samples. e.g. Somalier files for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1 - pattern: "*.{somalier}" - - labels_tsv: - type: file - description: TSV for labelled samples. e.g. Somalier labels for 1kg https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - query_somalier_files: + type: file + description: Set of somalier files for query samples. Obtained via somalier + extract. + pattern: "*.{somalier}" + - - meta2: + type: map + description: | + Groovy Map containing labelled samples information + e.g. [ id:'test', single_end:false ] + - labels_tsv: + type: file + description: TSV for labelled samples. e.g. Somalier labels for 1kg + https://raw.githubusercontent.com/brentp/somalier/master/scripts/ancestry-labels-1kg.tsv + pattern: "*.{tsv}" + - labelled_somalier_files: + type: file + description: Set of somalier files for labelled samples. e.g. Somalier files + for 1kg https://zenodo.org/record/3479773/files/1kg.somalier.tar.gz?download=1 + pattern: "*.{somalier}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV with ancestry information for query and labelled samples. - pattern: "*.{-ancestry.tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-ancestry.tsv": + type: file + description: TSV with ancestry information for query and labelled samples. + pattern: "*.{-ancestry.tsv}" - html: - type: file - description: html file with ancestry information for query and labelled samples. - pattern: "*.{-ancestry.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*-ancestry.html": + type: file + description: html file with ancestry information for query and labelled samples. + pattern: "*.{-ancestry.html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index aabaf5d6f72b..256216679f7f 100644 --- a/modules/nf-core/somalier/extract/meta.yml +++ b/modules/nf-core/somalier/extract/meta.yml @@ -1,5 +1,6 @@ name: "somalier_extract" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,65 +15,69 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file - - input_index: - type: file - description: index file of the input data, e.g., bam.bai, cram.crai - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fna,fas,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'hg38' ] - - fai: - type: file - description: FASTA index file - pattern: "*.fai" - - meta4: - type: map - description: | - Groovy Map containing sites information - e.g. [ id:'hg38' ] - - sites: - type: file - description: sites file in VCF format which can be taken from https://github.com/brentp/somalier - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM/SAM/BCF/VCF/GVCF or jointly-called VCF file + - input_index: + type: file + description: index file of the input data, e.g., bam.bai, cram.crai + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fna,fas,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'hg38' ] + - fai: + type: file + description: FASTA index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing sites information + e.g. [ id:'hg38' ] + - sites: + type: file + description: sites file in VCF format which can be taken from https://github.com/brentp/somalier + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - extract: - type: file - description: binary output file based on extracted sites - pattern: "*.{somalier}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somalier": + type: file + description: binary output file based on extracted sites + pattern: "*.{somalier}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/somalier/relate/meta.yml b/modules/nf-core/somalier/relate/meta.yml index 42638f4f5878..0da728218b58 100644 --- a/modules/nf-core/somalier/relate/meta.yml +++ b/modules/nf-core/somalier/relate/meta.yml @@ -1,5 +1,6 @@ name: "somalier_relate" -description: Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs +description: Somalier can extract informative sites, evaluate relatedness, and perform + quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs keywords: - relatedness - QC @@ -14,47 +15,67 @@ keywords: - family tools: - "somalier": - description: "Somalier can extract informative sites, evaluate relatedness, and perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" + description: "Somalier can extract informative sites, evaluate relatedness, and + perform quality-control on BAM/CRAM/BCF/VCF/GVCF or from jointly-called VCFs" homepage: "https://github.com/brentp/somalier" documentation: "https://github.com/brentp/somalier/blob/master/README.md" tool_dev_url: "https://github.com/brentp/somalier" doi: "10.1186/s13073-020-00761-2" licence: ["MIT"] + identifier: biotools:somalier input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - extract: - type: file - description: extract file(s) from Somalier extract - pattern: "*.somalier" - - ped: - type: file - description: optional path to a ped or fam file indicating the expected relationships among samples - pattern: "*.{ped,fam}" - - sample_groups: - type: file - description: optional path to expected groups of samples such as tumor normal pairs specified as comma-separated groups per line - pattern: "*.{txt,csv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - extract: + type: file + description: extract file(s) from Somalier extract + pattern: "*.somalier" + - ped: + type: file + description: optional path to a ped or fam file indicating the expected relationships + among samples + pattern: "*.{ped,fam}" + - - sample_groups: + type: file + description: optional path to expected groups of samples such as tumor normal + pairs specified as comma-separated groups per line + pattern: "*.{txt,csv}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - html: - type: file - description: html file - pattern: "*.html" + - meta: + type: file + description: html file + pattern: "*.html" + - "*.html": + type: file + description: html file + pattern: "*.html" - pairs_tsv: - type: file - description: tsv file with output stats for pairs of samples - pattern: "*.pairs.tsv" + - meta: + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" + - "*.pairs.tsv": + type: file + description: tsv file with output stats for pairs of samples + pattern: "*.pairs.tsv" - samples_tsv: - type: file - description: tsv file with sample-level information - pattern: "*.samples.tsv" + - meta: + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - "*.samples.tsv": + type: file + description: tsv file with sample-level information + pattern: "*.samples.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ashotmarg" - "@nvnieuwk" diff --git a/modules/nf-core/sortmerna/meta.yml b/modules/nf-core/sortmerna/meta.yml index c0a2a581fa32..3b43d006d689 100644 --- a/modules/nf-core/sortmerna/meta.yml +++ b/modules/nf-core/sortmerna/meta.yml @@ -8,67 +8,84 @@ keywords: - ribosomal RNA tools: - SortMeRNA: - description: The core algorithm is based on approximate seeds and allows for sensitive analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart aligned and rejected reads into two files. Additional applications include clustering and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. + description: The core algorithm is based on approximate seeds and allows for sensitive + analysis of NGS reads. The main application of SortMeRNA is filtering rRNA from + metatranscriptomic data. SortMeRNA takes as input files of reads (fasta, fastq, + fasta.gz, fastq.gz) and one or multiple rRNA database file(s), and sorts apart + aligned and rejected reads into two files. Additional applications include clustering + and taxonomy assignation available through QIIME v1.9.1. SortMeRNA works with + Illumina, Ion Torrent and PacBio data, and can produce SAM and BLAST-like alignments. homepage: https://hpc.nih.gov/apps/sortmeRNA.html documentation: https://github.com/biocore/sortmerna/wiki/ licence: ["GPL-3.0-or-later"] + identifier: biotools:sortmerna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - fastas: - type: file - description: | - Path to reference file(s) - - meta3: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: directory - description: | - Path to index directory of a previous sortmerna run + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - fastas: + type: file + description: | + Path to reference file(s) + - - meta3: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: directory + description: | + Path to index directory of a previous sortmerna run output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ], or reference information from an - indexing-only run - reads: - type: file - description: The filtered fastq reads - pattern: "*fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*non_rRNA.fastq.gz": + type: file + description: The filtered fastq reads + pattern: "*fastq.gz" - log: - type: file - description: SortMeRNA log file - pattern: "*sortmerna.log" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ], or reference information from an + indexing-only run + - "*.log": + type: file + description: SortMeRNA log file + pattern: "*sortmerna.log" - index: - type: directory - description: | - Path to index directory generated by sortmern + - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - idx: + type: directory + description: | + Path to index directory generated by sortmern - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@mashehu" diff --git a/modules/nf-core/sourmash/compare/meta.yml b/modules/nf-core/sourmash/compare/meta.yml index e9a3eabc29cf..cfd40dbee26b 100644 --- a/modules/nf-core/sourmash/compare/meta.yml +++ b/modules/nf-core/sourmash/compare/meta.yml @@ -10,58 +10,74 @@ keywords: - kmer tools: - "sourmash": - description: "Compute and compare FracMinHash signatures for DNA and protein data sets." + description: "Compute and compare FracMinHash signatures for DNA and protein data + sets." homepage: "https://sourmash.readthedocs.io/" documentation: "https://sourmash.readthedocs.io/" tool_dev_url: "https://github.com/sourmash-bio/sourmash" doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signatures: - type: file - description: Files containing signatures (hash sketches) of samples - pattern: "*.{sig}" - - file_list: - type: file - description: | - An optional file specifying a list of file paths that should be appended to the input signatures. - - save_numpy_matrix: - type: boolean - description: | - If true, output will contain a (dis)similarity matrix numpy binary format. - At least one of save_numpy_matrix or save_csv is required. - - save_csv: - type: boolean - description: | - If true, output will contain a (dis)similarity matrix in CSV format - At least one of save_numpy_matrix or save_csv is required. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signatures: + type: file + description: Files containing signatures (hash sketches) of samples + pattern: "*.{sig}" + - - file_list: + type: file + description: | + An optional file specifying a list of file paths that should be appended to the input signatures. + - - save_numpy_matrix: + type: boolean + description: | + If true, output will contain a (dis)similarity matrix numpy binary format. + At least one of save_numpy_matrix or save_csv is required. + - - save_csv: + type: boolean + description: | + If true, output will contain a (dis)similarity matrix in CSV format + At least one of save_numpy_matrix or save_csv is required. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - matrix: - type: file - description: An optional (dis)similarity matrix numpy binary format - pattern: "*.comp" - - csv: - type: file - description: An optional (dis)similarity matrix in CSV format - pattern: "*.comp.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.npy": + type: file + description: An optional (dis)similarity matrix numpy binary format + pattern: "*.comp" - labels: - type: file - description: A text file that specifies the labels in the output numpy_matrix - pattern: "*.comp.labels.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.npy.labels.txt": + type: file + description: A text file that specifies the labels in the output numpy_matrix + pattern: "*.comp.labels.txt" + - csv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*comp.csv": + type: file + description: An optional (dis)similarity matrix in CSV format + pattern: "*.comp.csv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@taylorreiter" maintainers: diff --git a/modules/nf-core/sourmash/gather/meta.yml b/modules/nf-core/sourmash/gather/meta.yml index 72265fa25b18..f4dd13d89bd3 100644 --- a/modules/nf-core/sourmash/gather/meta.yml +++ b/modules/nf-core/sourmash/gather/meta.yml @@ -1,5 +1,6 @@ name: "sourmash_gather" -description: Search a metagenome sourmash signature against one or many reference databases and return the minimum set of genomes that contain the k-mers in the metagenome. +description: Search a metagenome sourmash signature against one or many reference + databases and return the minimum set of genomes that contain the k-mers in the metagenome. keywords: - FracMinHash sketch - signature @@ -18,73 +19,100 @@ tools: tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signature: - type: file - description: File containing signatures (hash sketches) of a sample - pattern: "*.{sig}" - - db: - type: file - description: Sourmash database (a list of signatures, SBTs, or signature zip files) - - save_unassigned: - type: boolean - description: | - If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query - - save_matches_sig: - type: boolean - description: | - If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query - - save_prefetch: - type: boolean - description: | - If true, output will contain a file with all prefetch-matched signatures from the database - - save_prefetch_csv: - type: boolean - description: | - If true, output will contain a csv file with the names of all prefetch-matched signatures + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signature: + type: file + description: File containing signatures (hash sketches) of a sample + pattern: "*.{sig}" + - - database: + type: file + description: database + - - save_unassigned: + type: boolean + description: | + If true, output will contain a file that is a sourmash signature containing the unassigned hashes from the query + - - save_matches_sig: + type: boolean + description: | + If true, output will contain a file that is a sourmash signature composed of the FracMinHash sketches that were matched in the database and that matched the query + - - save_prefetch: + type: boolean + description: | + If true, output will contain a file with all prefetch-matched signatures from the database + - - save_prefetch_csv: + type: boolean + description: | + If true, output will contain a csv file with the names of all prefetch-matched signatures output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - result: - type: file - description: | - Table with signatures classified as belonging to any of the genomes - in the sourmash database(s). - pattern: "*{csv.gz}" - - matches: - type: file - description: | - A signature containing FracMinHash sketches of genomes - in the sourmash database. - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv.gz": + type: file + description: | + Table with signatures classified as belonging to any of the genomes + in the sourmash database(s). + pattern: "*{csv.gz}" - unassigned: - type: file - description: | - A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes - in the sourmash database(s). - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unassigned.sig.zip": + type: file + description: | + A FracMinHash sketch containing hashes (k-mers) that did not match to any of the genomes + in the sourmash database(s). + pattern: "*{sig.zip}" + - matches: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_matches.sig.zip": + type: file + description: | + A signature containing FracMinHash sketches of genomes + in the sourmash database. + pattern: "*{sig.zip}" - prefetch: - type: file - description: | - All prefetch-matched signatures from the database. - pattern: "*{sig.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_prefetch.sig.zip": + type: file + description: | + All prefetch-matched signatures from the database. + pattern: "*{sig.zip}" - prefetchcsv: - type: file - description: | - The names of all prefetch-matched signatures from the database in CSV format. - pattern: "*{csv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_prefetch.csv.gz": + type: file + description: | + The names of all prefetch-matched signatures from the database in CSV format. + pattern: "*{csv.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vmikk" - "@taylorreiter" diff --git a/modules/nf-core/sourmash/index/meta.yml b/modules/nf-core/sourmash/index/meta.yml index 8639a4589629..dfdffeee128c 100644 --- a/modules/nf-core/sourmash/index/meta.yml +++ b/modules/nf-core/sourmash/index/meta.yml @@ -1,5 +1,6 @@ name: sourmash_index -description: Create a database of sourmash signatures (a group of FracMinHash sketches) to be used as references. +description: Create a database of sourmash signatures (a group of FracMinHash sketches) + to be used as references. keywords: - signatures - sourmash @@ -15,33 +16,36 @@ tools: tool_dev_url: "https://github.com/sourmash-bio/sourmash" doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - signatures: - type: file - description: Files containing signature (hash sketches) of reference genomes - pattern: "*.{sig}" - - ksize: - type: integer - description: ksize value + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - signatures: + type: file + description: Files containing signature (hash sketches) of reference genomes + pattern: "*.{sig}" + - - ksize: + type: integer + description: ksize value output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - signature_index: - type: file - description: Database of signatures - pattern: "*.{sbt.zip}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sbt.zip": + type: file + description: Database of signatures + pattern: "*.{sbt.zip}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@emnilsson" maintainers: diff --git a/modules/nf-core/sourmash/sketch/meta.yml b/modules/nf-core/sourmash/sketch/meta.yml index b0f8145a8837..c759b6695738 100644 --- a/modules/nf-core/sourmash/sketch/meta.yml +++ b/modules/nf-core/sourmash/sketch/meta.yml @@ -1,5 +1,6 @@ name: sourmash_sketch -description: Create a signature (a group of FracMinHash sketches) of a sequence using sourmash +description: Create a signature (a group of FracMinHash sketches) of a sequence using + sourmash keywords: - hash sketch - sourmash @@ -10,36 +11,41 @@ keywords: - kmer tools: - sourmash: - description: Compute and compare FracMinHash signatures for DNA and protein data sets. + description: Compute and compare FracMinHash signatures for DNA and protein data + sets. homepage: https://sourmash.readthedocs.io/ documentation: https://sourmash.readthedocs.io/ tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sequence: - type: file - description: FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) sequence data - pattern: "*.{fna,fa,fasta,fastq,fq,faa}.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence: + type: file + description: FASTA or FASTQ file containing (genomic, transcriptomic, or proteomic) + sequence data + pattern: "*.{fna,fa,fasta,fastq,fq,faa}.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - signatures: - type: file - description: FracMinHash signature of the given sequence - pattern: "*.{sig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sig": + type: file + description: FracMinHash signature of the given sequence + pattern: "*.{sig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/sourmash/taxannotate/meta.yml b/modules/nf-core/sourmash/taxannotate/meta.yml index 764bdb8a5027..7fa10cf6a817 100644 --- a/modules/nf-core/sourmash/taxannotate/meta.yml +++ b/modules/nf-core/sourmash/taxannotate/meta.yml @@ -1,5 +1,6 @@ name: "sourmash_taxannotate" -description: Annotate list of metagenome members (based on sourmash signature matches) with taxonomic information. +description: Annotate list of metagenome members (based on sourmash signature matches) + with taxonomic information. keywords: - fracminhash sketch - signature @@ -18,39 +19,41 @@ tools: tool_dev_url: https://github.com/sourmash-bio/sourmash doi: "10.21105/joss.00027" licence: ["BSD-3-clause"] + identifier: biotools:sourmash ## Description of all of the variables used as input input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gather_results: - type: file - description: | - Mandatory table with signatures classified as belonging to any of the genomes - in the sourmash database(s), result of `sourmash gather` command. - - taxonomy: - type: file - description: One or more databases with lineages (in CSV format, Mandatory) -## Description of all of the variables used as output + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gather_results: + type: file + description: | + Mandatory table with signatures classified as belonging to any of the genomes + in the sourmash database(s), result of `sourmash gather` command. + - - taxonomy: + type: file + description: One or more databases with lineages (in CSV format, Mandatory) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - result: - type: file - description: | - Table with signatures classified as belonging to any of the genomes - in the sourmash database(s) with an additional 'lineage' column - containing the taxonomic information for each database match. - pattern: "*{csv.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.with-lineages.csv.gz": + type: file + description: | + Table with signatures classified as belonging to any of the genomes + in the sourmash database(s) with an additional 'lineage' column + containing the taxonomic information for each database match. + pattern: "*{csv.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@vmikk" - "@taylorreiter" diff --git a/modules/nf-core/spaceranger/count/meta.yml b/modules/nf-core/spaceranger/count/meta.yml index 167ac8c8851f..e1ffcefc9daa 100644 --- a/modules/nf-core/spaceranger/count/meta.yml +++ b/modules/nf-core/spaceranger/count/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_count" -description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics data +description: Module to use the 10x Space Ranger pipeline to process 10x spatial transcriptomics + data keywords: - align - count @@ -22,73 +22,77 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', slide:'10L13-020', area: 'B1'] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', slide:'10L13-020', area: 'B1'] - `id`, `slide` and `area` are mandatory information! - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" - - image: - type: file - description: Brightfield tissue H&E image in JPEG or TIFF format. - pattern: "*.{tif,tiff,jpg,jpeg}" - - cytaimage: - type: file - description: | - CytAssist instrument captured eosin stained Brightfield tissue image with fiducial - frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should - not be modified any way before passing it as input to either Space Ranger or Loupe Browser. - pattern: "*.{tif,tiff}" - - darkimage: - type: file - description: | - Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence - image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files. - pattern: "*.{tif,tiff,jpg,jpeg}" - - colorizedimage: - type: file - description: | - Required for color composite fluorescence microscope image input. - A color composite of one or more fluorescence image channels saved as a single-page, - single-file color TIFF or JPEG. - pattern: "*.{tif,tiff,jpg,jpeg}" - - alignment: - type: file - description: OPTIONAL - Path to manual image alignment. - pattern: "*.json" - - slidefile: - type: file - description: OPTIONAL - Path to slide specifications. - pattern: "*.json" - - reference: - type: directory - description: Folder containing all the reference indices needed by Space Ranger - - probeset: - type: file - description: OPTIONAL - Probe set specification. - pattern: "*.csv" + `id`, `slide` and `area` are mandatory information! + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "${Sample_Name}_S1_L00${Lane_Number}_${I1,I2,R1,R2}_001.fastq.gz" + - image: + type: file + description: Brightfield tissue H&E image in JPEG or TIFF format. + pattern: "*.{tif,tiff,jpg,jpeg}" + - cytaimage: + type: file + description: | + CytAssist instrument captured eosin stained Brightfield tissue image with fiducial + frame in TIFF format. The size of this image is set at 3k in both dimensions and this image should + not be modified any way before passing it as input to either Space Ranger or Loupe Browser. + pattern: "*.{tif,tiff}" + - darkimage: + type: file + description: | + Optional for dark background fluorescence microscope image input. Multi-channel, dark-background fluorescence + image as either a single, multi-layer TIFF file or as multiple TIFF or JPEG files. + pattern: "*.{tif,tiff,jpg,jpeg}" + - colorizedimage: + type: file + description: | + Required for color composite fluorescence microscope image input. + A color composite of one or more fluorescence image channels saved as a single-page, + single-file color TIFF or JPEG. + pattern: "*.{tif,tiff,jpg,jpeg}" + - alignment: + type: file + description: OPTIONAL - Path to manual image alignment. + pattern: "*.json" + - slidefile: + type: file + description: OPTIONAL - Path to slide specifications. + pattern: "*.json" + - - reference: + type: directory + description: Folder containing all the reference indices needed by Space Ranger + - - probeset: + type: file + description: OPTIONAL - Probe set specification. + pattern: "*.csv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - outs: - type: file - description: Files containing the outputs of Space Ranger, see official 10X Genomics documentation for a complete list - pattern: "outs/*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - outs/**: + type: file + description: Files containing the outputs of Space Ranger, see official 10X + Genomics documentation for a complete list + pattern: "outs/*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spaceranger/mkgtf/meta.yml b/modules/nf-core/spaceranger/mkgtf/meta.yml index 125b12622ba1..1294b0c9b162 100644 --- a/modules/nf-core/spaceranger/mkgtf/meta.yml +++ b/modules/nf-core/spaceranger/mkgtf/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_mkgtf" -description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkgtf command. +description: Module to build a filtered GTF needed by the 10x Genomics Space Ranger + tool. Uses the spaceranger mkgtf command. keywords: - reference - mkref @@ -21,20 +21,23 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - gtf: - type: file - description: The reference GTF transcriptome file - pattern: "*.gtf" + - - gtf: + type: file + description: The reference GTF transcriptome file + pattern: "*.gtf" output: - gtf: - type: directory - description: The filtered GTF transcriptome file - pattern: "*.filtered.gtf" + - "*.gtf": + type: directory + description: The filtered GTF transcriptome file + pattern: "*.filtered.gtf" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spaceranger/mkref/meta.yml b/modules/nf-core/spaceranger/mkref/meta.yml index 453a3e56cc65..8360e2f3c100 100644 --- a/modules/nf-core/spaceranger/mkref/meta.yml +++ b/modules/nf-core/spaceranger/mkref/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "spaceranger_mkref" -description: Module to build the reference needed by the 10x Genomics Space Ranger tool. Uses the spaceranger mkref command. +description: Module to build the reference needed by the 10x Genomics Space Ranger + tool. Uses the spaceranger mkref command. keywords: - reference - mkref @@ -21,27 +21,30 @@ tools: tool_dev_url: "https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger" licence: - "10x Genomics EULA" + identifier: "" input: - - fasta: - type: file - description: Reference genome FASTA file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: Reference transcriptome GTF file - pattern: "*.gtf" - - reference_name: - type: string - description: The name to give the new reference folder - pattern: str + - - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fasta,fa}" + - - gtf: + type: file + description: Reference transcriptome GTF file + pattern: "*.gtf" + - - reference_name: + type: string + description: The name to give the new reference folder + pattern: str output: - reference: - type: directory - description: Folder containing all the reference indices needed by Space Ranger + - ${reference_name}: + type: directory + description: Folder containing all the reference indices needed by Space Ranger - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@grst" maintainers: diff --git a/modules/nf-core/spades/meta.yml b/modules/nf-core/spades/meta.yml index 986871be75fd..ec0df43481b4 100644 --- a/modules/nf-core/spades/meta.yml +++ b/modules/nf-core/spades/meta.yml @@ -8,87 +8,139 @@ keywords: - de novo assembler tools: - spades: - description: SPAdes (St. Petersburg genome assembler) is intended for both standard isolates and single-cell MDA bacteria assemblies. + description: SPAdes (St. Petersburg genome assembler) is intended for both standard + isolates and single-cell MDA bacteria assemblies. homepage: http://cab.spbu.ru/files/release3.15.0/manual.html documentation: http://cab.spbu.ru/files/release3.15.0/manual.html tool_dev_url: https://github.com/ablab/spades doi: 10.1089/cmb.2012.0021 licence: ["GPL v2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - illumina: - type: file - description: | - List of input FastQ (Illumina or PacBio CCS reads) files - of size 1 and 2 for single-end and paired-end data, - respectively. This input data type is required. - - pacbio: - type: file - description: | - List of input PacBio CLR FastQ files of size 1. - - nanopore: - type: file - description: | - List of input FastQ files of size 1, originating from Oxford Nanopore technology. - - yml: - type: file - description: | - Path to yml file containing read information. - The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML. - File entries in this yml must contain only the file name and no paths. - pattern: "*.{yml,yaml}" - - hmm: - type: file - description: File or directory with amino acid HMMs for Spades HMM-guided mode. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - illumina: + type: file + description: | + List of input FastQ (Illumina or PacBio CCS reads) files + of size 1 and 2 for single-end and paired-end data, + respectively. This input data type is required. + - pacbio: + type: file + description: | + List of input PacBio CLR FastQ files of size 1. + - nanopore: + type: file + description: | + List of input FastQ files of size 1, originating from Oxford Nanopore technology. + - - yml: + type: file + description: | + Path to yml file containing read information. + The raw FASTQ files listed in this YAML file MUST be supplied to the respective illumina/pacbio/nanopore input channel(s) _in addition_ to this YML. + File entries in this yml must contain only the file name and no paths. + pattern: "*.{yml,yaml}" + - - hmm: + type: file + description: File or directory with amino acid HMMs for Spades HMM-guided mode. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - scaffolds: - type: file - description: | - Fasta file containing scaffolds - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.scaffolds.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - contigs: - type: file - description: | - Fasta file containing contigs - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.contigs.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - transcripts: - type: file - description: | - Fasta file containing transcripts - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.transcripts.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - gene_clusters: - type: file - description: | - Fasta file containing gene_clusters - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" + - "*.gene_clusters.fa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.fa.gz" - gfa: - type: file - description: | - gfa file containing assembly - pattern: "*.gfa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.gfa.gz" + - "*.assembly.gfa.gz": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.gfa.gz" + - warnings: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.warnings.log": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - log: - type: file - description: | - Spades log file - pattern: "*.spades.log" - - log: - type: file - description: | - Spades warning log file - pattern: "*.warning.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.spades.log" + - "*.spades.log": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "*.spades.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@drpatelh" diff --git a/modules/nf-core/spatyper/meta.yml b/modules/nf-core/spatyper/meta.yml index 2af1abca8a51..4efc3f75ca60 100644 --- a/modules/nf-core/spatyper/meta.yml +++ b/modules/nf-core/spatyper/meta.yml @@ -12,38 +12,41 @@ tools: tool_dev_url: https://github.com/HCGB-IGTP/spaTyper doi: 10.5281/zenodo.4063625 licence: ["LGPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" - - repeats: - type: file - description: spa repeat sequences in FASTA format (Optional) - pattern: "*.{fasta}" - - repeat_order: - type: file - description: spa types and order of repeats (Optional) - pattern: "*.{txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - repeats: + type: file + description: spa repeat sequences in FASTA format (Optional) + pattern: "*.{fasta}" + - - repeat_order: + type: file + description: spa types and order of repeats (Optional) + pattern: "*.{txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/splitubam/meta.yml b/modules/nf-core/splitubam/meta.yml index 3d11eaaebc75..6469135712dd 100644 --- a/modules/nf-core/splitubam/meta.yml +++ b/modules/nf-core/splitubam/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "splitubam" description: split one ubam into multiple, per line, fast @@ -13,33 +12,34 @@ tools: documentation: "https://github.com/fellen31/splitubam" tool_dev_url: "https://github.com/fellen31/splitubam" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:true ]` - - bam: - type: file - description: (u)BAM file - pattern: "*.{bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:true ]` + - bam: + type: file + description: (u)BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Split (u)BAM file - pattern: "*.{bam}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.bam": + type: file + description: Split (u)BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" maintainers: diff --git a/modules/nf-core/spotiflow/meta.yml b/modules/nf-core/spotiflow/meta.yml index fe521caa8a1d..96d3d0016142 100644 --- a/modules/nf-core/spotiflow/meta.yml +++ b/modules/nf-core/spotiflow/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "spotiflow" description: Spotiflow, accurate and efficient spot detection with stereographic flow. @@ -9,43 +8,42 @@ keywords: - detection tools: - "spotiflow": - description: "Spotiflow allows for accurate and efficient spot detection with stereographic flow" + description: "Spotiflow allows for accurate and efficient spot detection with + stereographic flow" homepage: "https://weigertlab.github.io/spotiflow/" documentation: "https://weigertlab.github.io/spotiflow/" tool_dev_url: "https://github.com/weigertlab/spotiflow" doi: "10.1101/2024.02.01.578426" licence: ["BSD-3"] + identifier: "" ## Spotiflow requires only an input image file input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - image_2d: - type: file - description: 2D TIF Image file with the spots to be detected - pattern: "*.{tif,tiff,png,jpg,jpeg}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - image_2d: + type: file + description: 2D TIF Image file with the spots to be detected + pattern: "*.{tif,tiff,png,jpg,jpeg}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - spots: - type: file - description: CSV file with the X, Y positions of the detected spots. - pattern: "*.{csv}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.csv": + type: file + description: CSV file with the X, Y positions of the detected spots. + pattern: "*.{csv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" maintainers: diff --git a/modules/nf-core/spring/compress/meta.yml b/modules/nf-core/spring/compress/meta.yml index 8b52160940c1..1235f6d83481 100644 --- a/modules/nf-core/spring/compress/meta.yml +++ b/modules/nf-core/spring/compress/meta.yml @@ -6,40 +6,44 @@ keywords: - lossless tools: - "spring": - description: "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)" + description: "SPRING is a compression tool for Fastq files (containing up to 4.29 + Billion reads)" homepage: "https://github.com/shubhamchandak94/Spring" documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" tool_dev_url: "https://github.com/shubhamchandak94/Spring" doi: "10.1093/bioinformatics/bty1015" licence: ["Free for non-commercial use"] + identifier: biotools:spring input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq1: - type: file - description: FASTQ file to compress. - pattern: "*.{fq.gz,fastq.gz}" - - fastq2: - type: file - description: Parired FASTQ file fon non single-end experiments. - pattern: "*.{fq.gz,fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq1: + type: file + description: FASTQ file to compress. + pattern: "*.{fq.gz,fastq.gz}" + - fastq2: + type: file + description: Parired FASTQ file fon non single-end experiments. + pattern: "*.{fq.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spring: - type: file - description: One sequence file in spring compressed format. - pattern: "*.{spring}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.spring": + type: file + description: One sequence file in spring compressed format. + pattern: "*.{spring}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/spring/decompress/meta.yml b/modules/nf-core/spring/decompress/meta.yml index a3449b4fb3db..72b72b75da7c 100644 --- a/modules/nf-core/spring/decompress/meta.yml +++ b/modules/nf-core/spring/decompress/meta.yml @@ -6,41 +6,45 @@ keywords: - lossless tools: - "spring": - description: "SPRING is a compression tool for Fastq files (containing up to 4.29 Billion reads)" + description: "SPRING is a compression tool for Fastq files (containing up to 4.29 + Billion reads)" homepage: "https://github.com/shubhamchandak94/Spring" documentation: "https://github.com/shubhamchandak94/Spring/blob/master/README.md" tool_dev_url: "https://github.com/shubhamchandak94/Spring" doi: "10.1093/bioinformatics/bty1015" licence: ["Free for non-commercial use"] + identifier: biotools:spring input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - spring: - type: file - description: Spring file to decompress. - pattern: "*.{spring}" - - write_one_fastq_gz: - type: boolean - description: | - Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions - pattern: "true or false" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - spring: + type: file + description: Spring file to decompress. + pattern: "*.{spring}" + - - write_one_fastq_gz: + type: boolean + description: | + Controls whether spring should write one fastq.gz file with reads from both directions or two fastq.gz files with reads from distinct directions + pattern: "true or false" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Decompressed FASTQ file(s). - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: Decompressed FASTQ file(s). + pattern: "*.{fastq.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@xec-cm" maintainers: diff --git a/modules/nf-core/sratools/fasterqdump/meta.yml b/modules/nf-core/sratools/fasterqdump/meta.yml index 6a2151a87a2a..42e2c07ccff8 100644 --- a/modules/nf-core/sratools/fasterqdump/meta.yml +++ b/modules/nf-core/sratools/fasterqdump/meta.yml @@ -1,5 +1,6 @@ name: sratools_fasterqdump -description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read Archive (SRA). +description: Extract sequencing reads in FASTQ format from a given NCBI Sequence Read + Archive (SRA). keywords: - sequencing - FASTQ @@ -11,42 +12,44 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - sra: - type: directory - description: Directory containing ETL data for the given SRA. - pattern: "*/*.sra" - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - sra: + type: directory + description: Directory containing ETL data for the given SRA. + pattern: "*/*.sra" + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - reads: - type: file - description: Extracted FASTQ file or files if the sequencing reads are paired-end. - pattern: "*.fastq.gz" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - "*.fastq.gz": + type: file + description: Extracted FASTQ file or files if the sequencing reads are paired-end. + pattern: "*.fastq.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/sratools/prefetch/meta.yml b/modules/nf-core/sratools/prefetch/meta.yml index 7ed42d499836..3a537bfeacca 100644 --- a/modules/nf-core/sratools/prefetch/meta.yml +++ b/modules/nf-core/sratools/prefetch/meta.yml @@ -11,45 +11,47 @@ tools: documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools licence: ["Public Domain"] + identifier: "" input: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - - id: - type: string - description: > - A string denoting an SRA id. - - - ncbi_settings: - type: file - description: > - An NCBI user settings file. - - pattern: "*.mkfg" - - certificate: - type: file - description: > - Path to a JWT cart file used to access protected dbGAP data on SRA using the sra-toolkit - - pattern: "*.cart" + - - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + - id: + type: string + description: > + A string denoting an SRA id. + - - ncbi_settings: + type: file + description: > + An NCBI user settings file. + pattern: "*.mkfg" + - - certificate: + type: file + description: > + Path to a JWT cart file used to access protected dbGAP data on SRA using the + sra-toolkit + pattern: "*.cart" output: - - meta: - type: map - description: > - Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - sra: - type: directory - description: > - Directory containing the ETL data for the given SRA id. - - pattern: "*/*.sra" + - meta: + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" + - "id, type: 'dir": + type: map + description: > + Groovy Map containing sample information e.g. [ id:'test', single_end:false + ] + pattern: "*/*.sra" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/srst2/srst2/meta.yml b/modules/nf-core/srst2/srst2/meta.yml index 5d5a6876a6e0..f7f51ba4468b 100644 --- a/modules/nf-core/srst2/srst2/meta.yml +++ b/modules/nf-core/srst2/srst2/meta.yml @@ -15,56 +15,80 @@ tools: tool_dev_url: "https://github.com/katholt/srst2" doi: "10.1186/s13073-014-0090-6" licence: ["BSD"] + identifier: biotools:srst2 input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: should be the identification number or sample name - single_end: should be true for single end data and false for paired in data - db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option - e.g. [ id:'sample', single_end:false , db:'gene'] - - fasta: - type: file - description: | - gzipped fasta file. If files are NOT in - MiSeq format sample_S1_L001_R1_001.fastq.gz uses --forward and --reverse parameters; otherwise - default is _1, i.e. expect forward reads as sample_1.fastq.gz). - pattern: "*.fastq.gz" - - db: - type: file - description: Database in FASTA format - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + id: should be the identification number or sample name + single_end: should be true for single end data and false for paired in data + db: should be either 'gene' to use the --gene_db option or "mlst" to use the --mlst_db option + e.g. [ id:'sample', single_end:false , db:'gene'] + - fastq_s: + type: file + description: input FastQ files + pattern: "*.{fq,fastq,fq.gz,fastq.gz}" + - db: + type: file + description: Database in FASTA format + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'sample', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - txt: - type: file - description: A detailed report, with one row per gene per sample described here github.com/katholt/srst2#gene-typing - pattern: "*_fullgenes_*_results.txt" - - txt: - type: file - description: A tabulated summary report of samples x genes. - pattern: "*_genes_*_results.txt" - - txt: - type: file - description: A tabulated summary report of mlst subtyping. - pattern: "*_mlst_*_results.txt" - - bam: - type: file - description: Sorted BAM file - pattern: "*.sorted.bam" + - gene_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_genes_*_results.txt": + type: file + description: SRST2 gene results + pattern: "*_genes_*_results.txt" + - fullgene_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_fullgenes_*_results.txt": + type: file + description: SRST2 full gene results + pattern: "*_fullgenes_*_results.txt" + - mlst_results: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*_mlst_*_results.txt": + type: file + description: SRST2 MLST results + pattern: "*_mlst_*_results.txt" - pileup: - type: file - description: SAMtools pileup file - pattern: "*.pileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*.pileup": + type: file + description: SAMtools pileup file + pattern: "*.pileup" + - sorted_bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'sample', single_end:false ] + - "*.sorted.bam": + type: file + description: Sorted BAM file + pattern: "*.sorted.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jvhagey" maintainers: diff --git a/modules/nf-core/ssuissero/meta.yml b/modules/nf-core/ssuissero/meta.yml index d10881867aea..36f0c8d5020f 100644 --- a/modules/nf-core/ssuissero/meta.yml +++ b/modules/nf-core/ssuissero/meta.yml @@ -11,30 +11,33 @@ tools: documentation: https://github.com/jimmyliu1326/SsuisSero tool_dev_url: https://github.com/jimmyliu1326/SsuisSero licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly in FASTA format - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Assembly in FASTA format + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz,faa,faa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited serotype prediction - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited serotype prediction + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/stadeniolib/scramble/meta.yml b/modules/nf-core/stadeniolib/scramble/meta.yml index 8e3d6f270d86..610f859f28b5 100644 --- a/modules/nf-core/stadeniolib/scramble/meta.yml +++ b/modules/nf-core/stadeniolib/scramble/meta.yml @@ -7,51 +7,57 @@ keywords: - compression tools: - "scramble": - description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read by distributions). This contains code for reading and writing a variety of Bioinformatics / DNA Sequence formats." + description: "Staden Package 'io_lib' (sometimes referred to as libstaden-read + by distributions). This contains code for reading and writing a variety of Bioinformatics + / DNA Sequence formats." homepage: "https://github.com/jkbonfield/io_lib" documentation: "https://github.com/jkbonfield/io_lib/blob/master/README.md" tool_dev_url: "https://github.com/jkbonfield/io_lib" licence: ["BSD"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: Reference genome in FASTA format - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FASTA index file from samtools faidx - pattern: "*.{fai}" - - gzi: - type: file - description: Optional gzip index file for BAM inputs - pattern: "*.gzi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - fasta: + type: file + description: Reference genome in FASTA format + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: FASTA index file from samtools faidx + pattern: "*.{fai}" + - - gzi: + type: file + description: Optional gzip index file for BAM inputs + pattern: "*.gzi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - reads: - type: file - description: Converted reads - pattern: "*.{sam, bam, cram}" + - cram: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{cram,bam}": + type: file + description: Compressed BAM/CRAM file + pattern: "*.{cram,bam}" - gzi: - type: file - description: gzip index file for BAM outputs - pattern: ".{bam.gzi}" + - "*.gzi": + type: file + description: gzip index file for BAM outputs + pattern: ".{bam.gzi}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@matthdsm" maintainers: diff --git a/modules/nf-core/staphopiasccmec/meta.yml b/modules/nf-core/staphopiasccmec/meta.yml index e67b78fd218c..584554194c02 100644 --- a/modules/nf-core/staphopiasccmec/meta.yml +++ b/modules/nf-core/staphopiasccmec/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: https://github.com/staphopia/staphopia-sccmec doi: 10.7717/peerj.5261 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA assembly file - pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA assembly file + pattern: "*.{fasta,fasta.gz,fa,fa.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: Tab-delimited results - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Tab-delimited results + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/star/align/environment.yml b/modules/nf-core/star/align/environment.yml index e3d1c714d30d..1debc4c9b943 100644 --- a/modules/nf-core/star/align/environment.yml +++ b/modules/nf-core/star/align/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::star=2.7.10a - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 + - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index e80dbb7dd3ed..d30556b515a9 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -14,97 +14,189 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - index: - type: directory - description: STAR genome index - pattern: "star" - - meta3: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: Annotation GTF file - pattern: "*.{gtf}" - - star_ignore_sjdbgtf: - type: boolean - description: Ignore annotation GTF file - - seq_platform: - type: string - description: Sequencing platform - - seq_center: - type: string - description: Sequencing center + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - index: + type: directory + description: STAR genome index + pattern: "star" + - - meta3: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: Annotation GTF file + pattern: "*.{gtf}" + - - star_ignore_sjdbgtf: + type: boolean + description: Ignore annotation GTF file + - - seq_platform: + type: string + description: Sequencing platform + - - seq_center: + type: string + description: Sequencing center output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: file + description: STAR final log file + pattern: "*Log.final.out" + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: file + description: STAR lot out file + pattern: "*Log.out" + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: file + description: STAR log progress file + pattern: "*Log.progress.out" + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + - bam: + - meta: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - "*d.out.bam": + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" - bam_sorted: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + - meta: + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" + - "*sortedByCoord.out.bam": + type: file + description: Sorted BAM file of read alignments (optional) + pattern: "*sortedByCoord.out.bam" - bam_transcript: - type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + - meta: + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" + - "*toTranscriptome.out.bam": + type: file + description: Output BAM file of transcriptome alignment (optional) + pattern: "*toTranscriptome.out.bam" - bam_unsorted: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + - meta: + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" + - "*Aligned.unsort.out.bam": + type: file + description: Unsorted BAM file of read alignments (optional) + pattern: "*Aligned.unsort.out.bam" - fastq: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + - meta: + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" + - "*fastq.gz": + type: file + description: Unmapped FastQ files (optional) + pattern: "*fastq.gz" - tab: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + - meta: + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - "*.tab": + type: file + description: STAR output tab file(s) (optional) + pattern: "*.tab" + - spl_junc_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.SJ.out.tab": + type: file + description: STAR output splice junction tab file + pattern: "*.SJ.out.tab" + - read_per_gene_tab: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" - junction: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" + - meta: + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - "*.out.junction": + type: file + description: STAR chimeric junction output file (optional) + pattern: "*.out.junction" + - sam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.out.sam": + type: file + description: STAR output SAM file + pattern: "*.out.sam" - wig: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" + - meta: + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" + - "*.wig": + type: file + description: STAR output wiggle format file(s) (optional) + pattern: "*.wig" - bedgraph: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + - meta: + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" + - "*.bg": + type: file + description: STAR output bedGraph format file(s) (optional) + pattern: "*.bg" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/genomegenerate/environment.yml b/modules/nf-core/star/genomegenerate/environment.yml index 38611dfa26e6..1debc4c9b943 100644 --- a/modules/nf-core/star/genomegenerate/environment.yml +++ b/modules/nf-core/star/genomegenerate/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::samtools=1.18 - bioconda::htslib=1.18 + - bioconda::samtools=1.18 - bioconda::star=2.7.10a - conda-forge::gawk=5.1.0 diff --git a/modules/nf-core/star/genomegenerate/meta.yml b/modules/nf-core/star/genomegenerate/meta.yml index 1061e1b8dc0a..33c1f65f3d49 100644 --- a/modules/nf-core/star/genomegenerate/meta.yml +++ b/modules/nf-core/star/genomegenerate/meta.yml @@ -14,37 +14,40 @@ tools: manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Fasta file of the reference genome - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - gtf: - type: file - description: GTF file of the reference genome + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Fasta file of the reference genome + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - gtf: + type: file + description: GTF file of the reference genome output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - index: - type: directory - description: Folder containing the star index files - pattern: "star" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - star: + type: directory + description: Folder containing the star index files + pattern: "star" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@drpatelh" diff --git a/modules/nf-core/star/starsolo/meta.yml b/modules/nf-core/star/starsolo/meta.yml index c3e7c42cfc79..d9297f012a45 100644 --- a/modules/nf-core/star/starsolo/meta.yml +++ b/modules/nf-core/star/starsolo/meta.yml @@ -1,5 +1,6 @@ name: "starsolo" -description: Create a counts matrix for single-cell data using STARSolo, handling cell barcodes and UMI information. +description: Create a counts matrix for single-cell data using STARSolo, handling + cell barcodes and UMI information. keywords: - align - count @@ -12,60 +13,102 @@ tools: documentation: "https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md" doi: "10.1101/2021.05.05.442755" licence: ["MIT"] + identifier: biotools:star input: - - meta: - type: map - description: | - Groovy Map containing sample information. - Here, you should add all the specific barcode/umi - information for each sample. - e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` - - solotype: - type: string - description: | - Type of single-cell library. - It can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3, - CB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq. - - meta2: - type: map - description: Groovy Map containing the STAR index information. - - index: - type: directory - description: STAR genome index - pattern: "star" - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - solotype: + type: string + description: | + Type of single-cell library. + It can be CB_UMI_Simple for most common ones such as 10xv2 and 10xv3, + CB_UMI_Complex for method such as inDrop and SmartSeq for SMART-Seq. + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - opt_whitelist: + type: file + description: Optional whitelist file + - - meta2: + type: map + description: Groovy Map containing the STAR index information. + - index: + type: directory + description: STAR genome index + pattern: "star" output: - - meta: - type: map - description: | - Groovy Map containing sample information. - Here, you should add all the specific barcode/umi - information for each sample. - e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - counts: + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*.Solo.out": + type: file + description: STARSolo counts matrix + pattern: "*.Solo.out" - log_final: - type: file - description: STAR final log file - pattern: "*Log.final.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.final.out": + type: file + description: STAR final log file + pattern: "*Log.final.out" - log_out: - type: file - description: STAR lot out file - pattern: "*Log.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.out": + type: file + description: STAR lot out file + pattern: "*Log.out" - log_progress: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*Log.progress.out": + type: file + description: STAR log progress file + pattern: "*Log.progress.out" - summary: - type: file - description: STARSolo metrics summary CSV file. - pattern: "*/Gene/Summary.csv" + - meta: + type: map + description: | + Groovy Map containing sample information. + Here, you should add all the specific barcode/umi + information for each sample. + e.g. `[ id:'test_starsolo', umi_len:'12', cb_start:1 ]` + - "*/Gene/Summary.csv": + type: file + description: STARSolo metrics summary CSV file. + pattern: "*/Gene/Summary.csv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kevinmenden" - "@ggabernet" diff --git a/modules/nf-core/staramr/search/meta.yml b/modules/nf-core/staramr/search/meta.yml index 909dd070c647..be0e60a37245 100644 --- a/modules/nf-core/staramr/search/meta.yml +++ b/modules/nf-core/staramr/search/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "staramr_search" -description: "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases." +description: "Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder + databases." keywords: - amr - plasmid @@ -16,65 +16,123 @@ tools: tool_dev_url: "https://github.com/phac-nml/staramr" doi: "10.3390/microorganisms10020292" licence: ["Apache Software License"] + identifier: biotools:staramr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - genome_fasta: - type: file - description: | - Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids. - pattern: "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - genome_fasta: + type: file + description: | + Assembled/complete genome(s) in FASTA format to search for AMR/MLST/Plasmids. + pattern: "*.{fasta,fna,fsa,fa,fasta.gz,fna.gz,fsa.gz,fa.gz}" output: - results_xlsx: - type: file - description: Excel spreadsheet containing summary of StarAMR results. - pattern: "*_results/results.xlsx" + - meta: + type: file + description: Excel spreadsheet containing summary of StarAMR results. + pattern: "*_results/results.xlsx" + - "*_results/results.xlsx": + type: file + description: Excel spreadsheet containing summary of StarAMR results. + pattern: "*_results/results.xlsx" - summary_tsv: - type: file - description: | - A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. - A series of descriptive statistics is also provided for each genome, - as well as feedback for whether or not the genome passes several quality metrics and if not, - feedback on why the genome fails. - pattern: "*_results/summary.tsv" + - meta: + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/summary.tsv" + - "*_results/summary.tsv": + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/summary.tsv" - detailed_summary_tsv: - type: file - description: | - A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. - A series of descriptive statistics is also provided for each genome, - as well as feedback for whether or not the genome passes several quality metrics and if not, - feedback on why the genome fails. - pattern: "*_results/detailed_summary.tsv" + - meta: + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/detailed_summary.tsv" + - "*_results/detailed_summary.tsv": + type: file + description: | + A summary of all detected AMR genes/mutations/plasmids/sequence type in each genome, one genome per line. + A series of descriptive statistics is also provided for each genome, + as well as feedback for whether or not the genome passes several quality metrics and if not, + feedback on why the genome fails. + pattern: "*_results/detailed_summary.tsv" - resfinder_tsv: - type: file - description: A tabular file of each AMR gene and additional BLAST information from the ResFinder database, one gene per line. - pattern: "*_results/resfinder.tsv" + - meta: + type: file + description: A tabular file of each AMR gene and additional BLAST information + from the ResFinder database, one gene per line. + pattern: "*_results/resfinder.tsv" + - "*_results/resfinder.tsv": + type: file + description: A tabular file of each AMR gene and additional BLAST information + from the ResFinder database, one gene per line. + pattern: "*_results/resfinder.tsv" - plasmidfinder_tsv: - type: file - description: A tabular file of each AMR plasmid type and additional BLAST information from the PlasmidFinder database, one plasmid type per line. - pattern: "*_results/plasmidfinder.tsv" + - meta: + type: file + description: A tabular file of each AMR plasmid type and additional BLAST information + from the PlasmidFinder database, one plasmid type per line. + pattern: "*_results/plasmidfinder.tsv" + - "*_results/plasmidfinder.tsv": + type: file + description: A tabular file of each AMR plasmid type and additional BLAST information + from the PlasmidFinder database, one plasmid type per line. + pattern: "*_results/plasmidfinder.tsv" - mlst_tsv: - type: file - description: A tabular file of each multi-locus sequence type (MLST) and it's corresponding locus/alleles, one genome per line. - pattern: "*_results/mlst.tsv" + - meta: + type: file + description: A tabular file of each multi-locus sequence type (MLST) and it's + corresponding locus/alleles, one genome per line. + pattern: "*_results/mlst.tsv" + - "*_results/mlst.tsv": + type: file + description: A tabular file of each multi-locus sequence type (MLST) and it's + corresponding locus/alleles, one genome per line. + pattern: "*_results/mlst.tsv" - settings_txt: - type: file - description: The command-line, database versions, and other settings used to run staramr. - pattern: "*_results/settings.txt" + - meta: + type: file + description: The command-line, database versions, and other settings used to + run staramr. + pattern: "*_results/settings.txt" + - "*_results/settings.txt": + type: file + description: The command-line, database versions, and other settings used to + run staramr. + pattern: "*_results/settings.txt" - pointfinder_tsv: - type: file - description: An optional tabular file of each AMR point mutation and additional BLAST information from the PointFinder database, one gene per line. - pattern: "*_results/pointfinder.tsv" + - meta: + type: file + description: An optional tabular file of each AMR point mutation and additional + BLAST information from the PointFinder database, one gene per line. + pattern: "*_results/pointfinder.tsv" + - "*_results/pointfinder.tsv": + type: file + description: An optional tabular file of each AMR point mutation and additional + BLAST information from the PointFinder database, one gene per line. + pattern: "*_results/pointfinder.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apetkau" maintainers: diff --git a/modules/nf-core/stardist/meta.yml b/modules/nf-core/stardist/meta.yml index a6514d2febdf..70e60b75db07 100644 --- a/modules/nf-core/stardist/meta.yml +++ b/modules/nf-core/stardist/meta.yml @@ -6,42 +6,41 @@ keywords: - image tools: - "stardist": - description: "Stardist is an cell segmentation tool developed in Python by Martin Weigert and Uwe Schmidt" + description: "Stardist is an cell segmentation tool developed in Python by Martin + Weigert and Uwe Schmidt" homepage: "https://stardist.net/" documentation: "https://stardist.net/faq/" tool_dev_url: "https://github.com/stardist/stardist" doi: "10.1109/ISBIC56247.2022.9854534" licence: ["BSD 3-Clause"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - image: - type: file - description: Single channel nuclear image - pattern: "*.{tiff,tif}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - image: + type: file + description: Single channel nuclear image + pattern: "*.{tiff,tif}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - mask: - type: file - description: labelled mask output from stardist in tif format. - pattern: "*.{tiff,tif}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.stardist.tif": + type: file + description: labelled mask output from stardist in tif format. + pattern: "*.{tiff,tif}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@migueLib" maintainers: diff --git a/modules/nf-core/stecfinder/meta.yml b/modules/nf-core/stecfinder/meta.yml index a4efed3190dc..1d8452129e10 100644 --- a/modules/nf-core/stecfinder/meta.yml +++ b/modules/nf-core/stecfinder/meta.yml @@ -7,36 +7,40 @@ keywords: - fasta tools: - "stecfinder": - description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping tool from Illumina reads and assemblies" + description: "Cluster informed Shigatoxin producing E. coli (STEC) serotyping + tool from Illumina reads and assemblies" homepage: "https://github.com/LanLab/STECFinder" documentation: "https://github.com/LanLab/STECFinder" tool_dev_url: "https://github.com/LanLab/STECFinder" doi: "10.3389/fcimb.2021.772574" licence: ["GPL v3"] + identifier: biotools:stecfinder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - seqs: - type: file - description: Illumina paired-end reads or an assembly - pattern: "*.{fastq.gz,fasta.gz,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - seqs: + type: file + description: Illumina paired-end reads or an assembly + pattern: "*.{fastq.gz,fasta.gz,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: A tab-delimited report of results - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited report of results + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/stitch/meta.yml b/modules/nf-core/stitch/meta.yml index 2596fa379282..48a21c4996f0 100644 --- a/modules/nf-core/stitch/meta.yml +++ b/modules/nf-core/stitch/meta.yml @@ -1,7 +1,9 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "stitch" -description: "STITCH is an R program for reference panel free, read aware, low coverage sequencing genotype imputation. STITCH runs on a set of samples with sequencing reads in BAM format, as well as a list of positions to genotype, and outputs imputed genotypes in VCF format." +description: "STITCH is an R program for reference panel free, read aware, low coverage + sequencing genotype imputation. STITCH runs on a set of samples with sequencing + reads in BAM format, as well as a list of positions to genotype, and outputs imputed + genotypes in VCF format." keywords: - imputation - genomics @@ -18,102 +20,136 @@ tools: tool_dev_url: "https://github.com/rwdavies/stitch" doi: "10.1038/ng.3594" licence: ["GPL v3"] + identifier: biotools:stitch-snijderlab input: - - meta: - type: map - description: | - Groovy Map containing information about the set of positions to run the imputation over - e.g. `[ id:'test' ]` - - posfile: - type: file - description: | - Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information. - pattern: "*.tsv" - - input: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "input" - - rdata: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "RData" - - chromosome_name: - type: string - description: Name of the chromosome to impute. Should match a chromosome name in the reference genome. - - K: - type: integer - description: Number of ancestral haplotypes to use for imputation. Refer to the documentation for the `--K` argument of STITCH for more information. - - nGen: - type: integer - description: Number of generations since founding of the population to use for imputation. Refer to the documentation for the `--nGen` argument of STITCH for more information. - - meta2: - type: map - description: | - Groovy Map containing information about the set of samples - e.g. `[ id:'test' ]` - - collected_crams: - type: file - description: List of sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - collected_crais: - type: file - description: List of BAM/CRAM/SAM index files - pattern: "*.{bai,crai,sai}" - - cramlist: - type: file - description: | - Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. - pattern: "*.txt" - - meta3: - type: map - description: | - Groovy Map containing information about the reference genome used - e.g. `[ id:'test' ]` - - fasta: - type: file - description: FASTA reference genome file - pattern: "*.{fa,fasta}" - - fasta_fai: - type: file - description: FASTA index file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing information about the set of positions to run the imputation over + e.g. `[ id:'test' ]` + - posfile: + type: file + description: | + Tab-separated file describing the variable positions to be used for imputation. Refer to the documentation for the `--posfile` argument of STITCH for more information. + pattern: "*.tsv" + - input: + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "input" + - rdata: + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "RData" + - chromosome_name: + type: string + description: Name of the chromosome to impute. Should match a chromosome name + in the reference genome. + - K: + type: integer + description: Number of ancestral haplotypes to use for imputation. Refer to + the documentation for the `--K` argument of STITCH for more information. + - nGen: + type: integer + description: Number of generations since founding of the population to use for + imputation. Refer to the documentation for the `--nGen` argument of STITCH + for more information. + - - meta2: + type: map + description: | + Groovy Map containing information about the set of samples + e.g. `[ id:'test' ]` + - collected_crams: + type: file + description: List of sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - collected_crais: + type: file + description: List of BAM/CRAM/SAM index files + pattern: "*.{bai,crai,sai}" + - cramlist: + type: file + description: | + Text file with the path to the cram files to use in imputation, one per line. Since the cram files are staged to the working directory for the process, this file should just contain the file names without any pre-pending path. + pattern: "*.txt" + - - meta3: + type: map + description: | + Groovy Map containing information about the reference genome used + e.g. `[ id:'test' ]` + - fasta: + type: file + description: FASTA reference genome file + pattern: "*.{fa,fasta}" + - fasta_fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - - seed: + type: integer + description: Seed for random number generation output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - input: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "input" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'input", type: "dir': + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "input" - rdata: - type: directory - description: | - Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. - pattern: "RData" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'RData", type: "dir': + type: directory + description: | + Folder of pre-generated input RData objects used when STITCH is called with the `--regenerateInput FALSE` flag. It is generated by running STITCH with the `--generateInputOnly TRUE` flag. + pattern: "RData" - plots: - type: directory - description: | - Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH. - pattern: "plots" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - 'plots", type: "dir': + type: directory + description: | + Folder containing plots produced by STITCH during imputation. Which plots are produced depends on the command-line arguments passed to STITCH. + pattern: "plots" - vcf: - type: file - description: | - Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output. - pattern: ".vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.vcf.gz": + type: file + description: | + Imputed genotype calls for the positions in `posfile`, in vcf format. This is the default output. + pattern: ".vcf.gz" - bgen: - type: file - description: | - Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified. - pattern: ".bgen" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - "*.bgen": + type: file + description: | + Imputed genotype calls for the positions in `posfile`, in vcf format. This is the produced if `--output_format bgen` is specified. + pattern: ".bgen" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@saulpierotti" maintainers: diff --git a/modules/nf-core/stranger/meta.yml b/modules/nf-core/stranger/meta.yml index 5e0bc0bb0cae..a5486dbdbfc8 100644 --- a/modules/nf-core/stranger/meta.yml +++ b/modules/nf-core/stranger/meta.yml @@ -1,5 +1,6 @@ name: stranger -description: Annotates output files from ExpansionHunter with the pathologic implications of the repeat sizes. +description: Annotates output files from ExpansionHunter with the pathologic implications + of the repeat sizes. keywords: - STR - repeat_expansions @@ -13,39 +14,42 @@ tools: tool_dev_url: https://github.com/moonso/stranger doi: "10.5281/zenodo.4548873" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF with repeat expansions - pattern: "*.{vcf.gz,vcf}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - variant_catalog: - type: file - description: json file with repeat expansion sites to genotype - pattern: "*.{json}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF with repeat expansions + pattern: "*.{vcf.gz,vcf}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - variant_catalog: + type: file + description: json file with repeat expansion sites to genotype + pattern: "*.{json}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: annotated VCF with keys STR_STATUS, NormalMax and PathologicMin + pattern: "*.{vcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ljmesi" maintainers: diff --git a/modules/nf-core/strelka/germline/meta.yml b/modules/nf-core/strelka/germline/meta.yml index 9a597ef01fdb..5536dd8a5665 100644 --- a/modules/nf-core/strelka/germline/meta.yml +++ b/modules/nf-core/strelka/germline/meta.yml @@ -1,5 +1,6 @@ name: strelka_germline -description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation +description: Strelka2 is a fast and accurate small variant caller optimized for analysis + of germline variation keywords: - variantcalling - germline @@ -8,68 +9,90 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing reads + description: Strelka calls somatic and germline small variants from mapped sequencing + reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] + identifier: biotools:strelka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAI index file - pattern: "*.{bai,crai}" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_index: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAI index file + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_index: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - vcf: - type: file - description: gzipped germline variant file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*variants.vcf.gz": + type: file + description: gzipped germline variant file + pattern: "*.{vcf.gz}" - vcf_tbi: - type: file - description: index file for the vcf file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*variants.vcf.gz.tbi": + type: file + description: index file for the vcf file + pattern: "*.vcf.gz.tbi" - genome_vcf: - type: file - description: variant records and compressed non-variant blocks - pattern: "*_genome.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*genome.vcf.gz": + type: file + description: variant records and compressed non-variant blocks + pattern: "*_genome.vcf.gz" - genome_vcf_tbi: - type: file - description: index file for the genome_vcf file - pattern: "*_genome.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - "*genome.vcf.gz.tbi": + type: file + description: index file for the genome_vcf file + pattern: "*_genome.vcf.gz.tbi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@arontommi" maintainers: diff --git a/modules/nf-core/strelka/somatic/meta.yml b/modules/nf-core/strelka/somatic/meta.yml index 428bcb3f843b..6f2caaa3e7f7 100644 --- a/modules/nf-core/strelka/somatic/meta.yml +++ b/modules/nf-core/strelka/somatic/meta.yml @@ -1,5 +1,7 @@ name: strelka_somatic -description: Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs +description: Strelka2 is a fast and accurate small variant caller optimized for analysis + of germline variation in small cohorts and somatic variation in tumor/normal sample + pairs keywords: - variant calling - germline @@ -8,84 +10,106 @@ keywords: - variants tools: - strelka: - description: Strelka calls somatic and germline small variants from mapped sequencing reads + description: Strelka calls somatic and germline small variants from mapped sequencing + reads homepage: https://github.com/Illumina/strelka documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x licence: ["GPL v3"] + identifier: biotools:strelka input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input_normal: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_normal: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - input_tumor: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - input_index_tumor: - type: file - description: BAM/CRAM/SAM index file - pattern: "*.{bai,crai,sai}" - - manta_candidate_small_indels: - type: file - description: VCF.gz file - pattern: "*.{vcf.gz}" - - manta_candidate_small_indels_tbi: - type: file - description: VCF.gz index file - pattern: "*.tbi" - - fasta: - type: file - description: Genome reference FASTA file - pattern: "*.{fa,fasta}" - - fai: - type: file - description: Genome reference FASTA index file - pattern: "*.{fa.fai,fasta.fai}" - - target_bed: - type: file - description: BED file containing target regions for variant calling - pattern: "*.{bed}" - - target_bed_index: - type: file - description: Index for BED file containing target regions for variant calling - pattern: "*.{bed.tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input_normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_normal: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - input_tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - input_index_tumor: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - manta_candidate_small_indels: + type: file + description: VCF.gz file + pattern: "*.{vcf.gz}" + - manta_candidate_small_indels_tbi: + type: file + description: VCF.gz index file + pattern: "*.tbi" + - target_bed: + type: file + description: BED file containing target regions for variant calling + pattern: "*.{bed}" + - target_bed_index: + type: file + description: Index for BED file containing target regions for variant calling + pattern: "*.{bed.tbi}" + - - fasta: + type: file + description: Genome reference FASTA file + pattern: "*.{fa,fasta}" + - - fai: + type: file + description: Genome reference FASTA index file + pattern: "*.{fa.fai,fasta.fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf_indels: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_indels.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - vcf_indels_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_indels.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - vcf_snvs: - type: file - description: Gzipped VCF file containing variants - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_snvs.vcf.gz": + type: file + description: Gzipped VCF file containing variants + pattern: "*.{vcf.gz}" - vcf_snvs_tbi: - type: file - description: Index for gzipped VCF file containing variants - pattern: "*.{vcf.gz.tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.somatic_snvs.vcf.gz.tbi": + type: file + description: Index for gzipped VCF file containing variants + pattern: "*.{vcf.gz.tbi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/stringtie/merge/meta.yml b/modules/nf-core/stringtie/merge/meta.yml index 5d02d678617e..cf6902b321d3 100644 --- a/modules/nf-core/stringtie/merge/meta.yml +++ b/modules/nf-core/stringtie/merge/meta.yml @@ -11,27 +11,29 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - stringtie_gtf: - type: file - description: | - Stringtie transcript gtf output(s). - pattern: "*.gtf" - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). - pattern: "*.gtf" + - - stringtie_gtf: + type: file + description: | + Stringtie transcript gtf output(s). + pattern: "*.gtf" + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). + pattern: "*.gtf" output: - - merged_gtf: - type: map - description: | - Merged gtf from annotation and stringtie output gtfs. - pattern: "*.gtf" + - gtf: + - stringtie.merged.gtf: + type: file + description: Merged gtf file + pattern: "stringtie.merged.gtf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yuukiiwa" maintainers: diff --git a/modules/nf-core/stringtie/stringtie/meta.yml b/modules/nf-core/stringtie/stringtie/meta.yml index d8ebdd88aa04..e55b2abfcb18 100644 --- a/modules/nf-core/stringtie/stringtie/meta.yml +++ b/modules/nf-core/stringtie/stringtie/meta.yml @@ -12,46 +12,67 @@ tools: homepage: https://ccb.jhu.edu/software/stringtie/index.shtml documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual licence: ["MIT"] + identifier: biotools:stringtie input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Stringtie transcript gtf output(s). - - annotation_gtf: - type: file - description: | - Annotation gtf file (optional). + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Stringtie transcript gtf output(s). + - - annotation_gtf: + type: file + description: | + Annotation gtf file (optional). output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - transcript_gtf: - type: file - description: transcript gtf - pattern: "*.{transcripts.gtf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transcripts.gtf": + type: file + description: transcript gtf + pattern: "*.{transcripts.gtf}" + - abundance: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abundance.txt": + type: file + description: abundance + pattern: "*.{abundance.txt}" - coverage_gtf: - type: file - description: coverage gtf - pattern: "*.{coverage.gtf}" - - abudance: - type: file - description: abudance - pattern: "*.{abudance.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.coverage.gtf": + type: file + description: coverage gtf + pattern: "*.{coverage.gtf}" - ballgown: - type: file - description: for running ballgown - pattern: "*.{ballgown}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ballgown": + type: file + description: for running ballgown + pattern: "*.{ballgown}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/subread/featurecounts/meta.yml b/modules/nf-core/subread/featurecounts/meta.yml index 38a379456316..a9b045b7dce3 100644 --- a/modules/nf-core/subread/featurecounts/meta.yml +++ b/modules/nf-core/subread/featurecounts/meta.yml @@ -7,43 +7,55 @@ keywords: - reference tools: - featurecounts: - description: featureCounts is a highly efficient general-purpose read summarization program that counts mapped reads for genomic features such as genes, exons, promoter, gene bodies, genomic bins and chromosomal locations. It can be used to count both RNA-seq and genomic DNA-seq reads. + description: featureCounts is a highly efficient general-purpose read summarization + program that counts mapped reads for genomic features such as genes, exons, + promoter, gene bodies, genomic bins and chromosomal locations. It can be used + to count both RNA-seq and genomic DNA-seq reads. homepage: http://bioinf.wehi.edu.au/featureCounts/ documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf doi: "10.1093/bioinformatics/btt656" licence: ["GPL v3"] + identifier: biotools:subread input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file containing read alignments - pattern: "*.{bam}" - - annotation: - type: file - description: Genomic features annotation in GTF or SAF - pattern: "*.{gtf,saf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: BAM files containing mapped reads + pattern: "*.bam" + - annotation: + type: file + description: Genomic features annotation in GTF or SAF + pattern: "*.{gtf,saf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - counts: - type: file - description: Counts of reads mapping to features - pattern: "*featureCounts.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt": + type: file + description: Counts of reads mapping to features + pattern: "*featureCounts.txt" - summary: - type: file - description: Summary log file - pattern: "*.featureCounts.txt.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*featureCounts.txt.summary": + type: file + description: Summary log file + pattern: "*.featureCounts.txt.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ntoda03" maintainers: diff --git a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml index e5118d289482..820d4f163caf 100644 --- a/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml +++ b/modules/nf-core/summarizedexperiment/summarizedexperiment/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "summarizedexperiment_summarizedexperiment" description: | @@ -11,68 +10,77 @@ keywords: - assay tools: - "summarizedexperiment": - description: "The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples." + description: "The SummarizedExperiment container contains one or more assays, + each represented by a matrix-like object of numeric or other mode. The rows + typically represent genomic ranges of interest and the columns represent samples." homepage: "https://bioconductor.org/packages/release/bioc/html/SummarizedExperiment.html" documentation: "https://bioconductor.org/packages/release/bioc/vignettes/SummarizedExperiment/inst/doc/SummarizedExperiment.html" tool_dev_url: "https://github.com/Bioconductor/SummarizedExperiment" doi: "10.18129/B9.bioc.SummarizedExperiment" licence: ["Artistic-2.0"] + identifier: biotools:summarizedexperiment input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - matrix_files: - type: directory - description: | - One or more paths to CSV or TSV matrix files. All files must have the - same rows and columns. - pattern: "*.{csv,tsv}" - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference from which matrix rows are derived e.g. `[ id:'yeast' ]` - - rowdata: - type: file - description: | - Metadata on matrix features. One column must contain all matrix row - IDs. - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole, - as represented by the matrix columns and the sample sheet e.g. - `[id:'SRP123456' ]` - - coldata: - type: file - description: | - Metadata on matrix columns. One column must contain all matrix column - IDs. - pattern: "*.{csv,tsv}" - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - matrix_files: + type: directory + description: | + One or more paths to CSV or TSV matrix files. All files must have the + same rows and columns. + pattern: "*.{csv,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference from which matrix rows are derived e.g. `[ id:'yeast' ]` + - rowdata: + type: file + description: | + Metadata on matrix features. One column must contain all matrix row + IDs. + pattern: "*.{csv,tsv}" + - - meta3: + type: map + description: | + Groovy Map containing information related to the experiment as a whole, + as represented by the matrix columns and the sample sheet e.g. + `[id:'SRP123456' ]` + - coldata: + type: file + description: | + Metadata on matrix columns. One column must contain all matrix column + IDs. + pattern: "*.{csv,tsv}" output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - rds: - type: file - description: Serialised SummarizedExperiment object - pattern: "*.SummarizedExperiment.rds" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.rds": + type: file + description: Serialised SummarizedExperiment object + pattern: "*.SummarizedExperiment.rds" - log: - type: file - description: dump of R SessionInfo - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*.R_sessionInfo.log": + type: file + description: dump of R SessionInfo + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/survivor/bedpetovcf/meta.yml b/modules/nf-core/survivor/bedpetovcf/meta.yml index 6045d4fbc1a7..8a1b4f941f17 100644 --- a/modules/nf-core/survivor/bedpetovcf/meta.yml +++ b/modules/nf-core/survivor/bedpetovcf/meta.yml @@ -13,29 +13,32 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedpe: - type: file - description: BEDPE file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedpe: + type: file + description: BEDPE file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Output VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Output VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/survivor/filter/meta.yml b/modules/nf-core/survivor/filter/meta.yml index 64565408d306..cc6c8d61ad6f 100644 --- a/modules/nf-core/survivor/filter/meta.yml +++ b/modules/nf-core/survivor/filter/meta.yml @@ -13,45 +13,47 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file to filter - pattern: "*.{vcf}" - - bed: - type: file - description: BED file with regions to ignore (NA to disable) - - minsv: - type: integer - description: Min SV size (-1 to disable) - - maxsv: - type: integer - description: Max SV size (-1 to disable) - - minallelefreq: - type: float - description: Min allele frequency (0-1) - - minnumreads: - type: integer - description: Min number of reads support [RE flag (-1 to disable)] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf_file: + type: file + description: VCF file to filter + - bed: + type: file + description: BED file with regions to ignore (NA to disable) + - - minsv: + type: integer + description: Min SV size (-1 to disable) + - - maxsv: + type: integer + description: Max SV size (-1 to disable) + - - minallelefreq: + type: float + description: Min allele frequency (0-1) + - - minnumreads: + type: integer + description: Min number of reads support [RE flag (-1 to disable)] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Filtered VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Filtered VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@LlaneroHiboreo" maintainers: diff --git a/modules/nf-core/survivor/merge/meta.yml b/modules/nf-core/survivor/merge/meta.yml index 529e9175dde3..f60f68bc7678 100644 --- a/modules/nf-core/survivor/merge/meta.yml +++ b/modules/nf-core/survivor/merge/meta.yml @@ -1,5 +1,6 @@ name: "survivor_merge" -description: Compare or merge VCF files to generate a consensus or multi sample VCF files. +description: Compare or merge VCF files to generate a consensus or multi sample VCF + files. keywords: - survivor - merge @@ -13,50 +14,54 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: list - description: | - The VCF files to be merged - Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158 - pattern: "*.vcf" - - max_distance_breakpoints: - type: integer - description: Max distance between breakpoints (0-1 percent of length, 1- number of bp) - - min_supporting_callers: - type: integer - description: Minimum number of supporting caller - - account_for_type: - type: integer - description: Take the type into account (1==yes, else no) - - account_for_sv_strands: - type: integer - description: Take the strands of SVs into account (1==yes, else no) - - estimate_distanced_by_sv_size: - type: integer - description: Estimate distance based on the size of SV (1==yes, else no) - - min_sv_size: - type: integer - description: Minimum size of SVs to be taken into account + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: list + description: | + The VCF files to be merged + Gzipped VCF files are not supported: https://github.com/fritzsedlazeck/SURVIVOR/issues/158 + pattern: "*.vcf" + - - max_distance_breakpoints: + type: integer + description: Max distance between breakpoints (0-1 percent of length, 1- number + of bp) + - - min_supporting_callers: + type: integer + description: Minimum number of supporting caller + - - account_for_type: + type: integer + description: Take the type into account (1==yes, else no) + - - account_for_sv_strands: + type: integer + description: Take the strands of SVs into account (1==yes, else no) + - - estimate_distanced_by_sv_size: + type: integer + description: Estimate distance based on the size of SV (1==yes, else no) + - - min_sv_size: + type: integer + description: Minimum size of SVs to be taken into account output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The merged VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: The merged VCF file + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/survivor/simsv/meta.yml b/modules/nf-core/survivor/simsv/meta.yml index 80b6d1c918ab..504b6ae2a351 100644 --- a/modules/nf-core/survivor/simsv/meta.yml +++ b/modules/nf-core/survivor/simsv/meta.yml @@ -1,4 +1,3 @@ ---- name: "survivor_simsv" description: Simulate an SV VCF file based on a reference genome keywords: @@ -14,70 +13,98 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing fasta information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: The reference genome - pattern: "*.{fasta,fna,fa}" - - meta2: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The index of the reference genome - pattern: "*.fai" - - meta3: - type: map - description: | - Groovy Map containing parameters information - e.g. `[ id:'test', single_end:false ]` - - parameters: - type: file - description: A text file containing the parameters to be used for the simulation. Gets automatically generated using defaults when this is not supplied - pattern: "*.txt" - - snp_mutation_frequency: - type: float - description: The SNP mutation frequency in the output VCF (0-1) - - sim_reads: - type: integer - description: Whether or not to simulate reads (1==yes, else no) + - - meta: + type: map + description: | + Groovy Map containing fasta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: The reference genome + pattern: "*.{fasta,fna,fa}" + - - meta2: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The index of the reference genome + pattern: "*.fai" + - - meta3: + type: map + description: | + Groovy Map containing parameters information + e.g. `[ id:'test', single_end:false ]` + - parameters: + type: file + description: A text file containing the parameters to be used for the simulation. + Gets automatically generated using defaults when this is not supplied + pattern: "*.txt" + - - snp_mutation_frequency: + type: float + description: The SNP mutation frequency in the output VCF (0-1) + - - sim_reads: + type: integer + description: Whether or not to simulate reads (1==yes, else no) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - parameters: - type: file - description: The created parameters file - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.txt": + type: file + description: The created parameters file + pattern: "*.txt" - vcf: - type: file - description: A VCF containing the simulated variants - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf": + type: file + description: A VCF containing the simulated variants + pattern: "*.vcf" - bed: - type: file - description: A BED file of the simulated structural variants - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.bed": + type: file + description: A BED file of the simulated structural variants + pattern: "*.bed" - fasta: - type: file - description: A Fasta file file containing the variants from the output VCF - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fasta": + type: file + description: A Fasta file file containing the variants from the output VCF + pattern: "*.fasta" - insertions: - type: file - description: A Fasta file file containing insertion sequences - pattern: "*.insertions.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.insertions.fa": + type: file + description: A Fasta file file containing insertion sequences + pattern: "*.insertions.fa" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/survivor/stats/meta.yml b/modules/nf-core/survivor/stats/meta.yml index ba450a727279..cc89f0aead6e 100644 --- a/modules/nf-core/survivor/stats/meta.yml +++ b/modules/nf-core/survivor/stats/meta.yml @@ -13,39 +13,42 @@ tools: tool_dev_url: "https://github.com/fritzsedlazeck/SURVIVOR" doi: "10.1038/NCOMMS14061" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file to filter - pattern: "*.{vcf}" - - minsv: - type: integer - description: Min SV size (-1 to disable) - - maxsv: - type: integer - description: Max SV size (-1 to disable) - - minnumreads: - type: integer - description: Min number of reads support [RE flag (-1 to disable)] + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file to filter + pattern: "*.{vcf}" + - - minsv: + type: integer + description: Min SV size (-1 to disable) + - - maxsv: + type: integer + description: Max SV size (-1 to disable) + - - minnumreads: + type: integer + description: Min number of reads support [RE flag (-1 to disable)] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - stats: - type: file - description: File containing statistics given input VCF file - pattern: "*.{stats}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.stats": + type: file + description: File containing statistics given input VCF file + pattern: "*.{stats}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svaba/meta.yml b/modules/nf-core/svaba/meta.yml index d78ea0e8c991..24753c6a56a6 100644 --- a/modules/nf-core/svaba/meta.yml +++ b/modules/nf-core/svaba/meta.yml @@ -1,5 +1,6 @@ name: "svaba" -description: SvABA is an efficient and accurate method for detecting SVs from short-read sequencing data using genome-wide local assembly with low memory and computing requirements +description: SvABA is an efficient and accurate method for detecting SVs from short-read + sequencing data using genome-wide local assembly with low memory and computing requirements keywords: - sv - structural variants @@ -13,147 +14,248 @@ tools: tool_dev_url: "https://github.com/walaj/svaba" doi: "10.1101/gr.221028.117" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - id: should be the identification number or sample name. If there is normal file meta should be common - e.g. [ id:'test' ] - - meta2: - type: map - description: | - Groovy Map containing FASTA information - id: should be the identification number for alignment file and should be the same used to create BWA index files - e.g. [ id:'fasta' ] - - meta3: - type: map - description: | - Groovy Map containing BWA information - id: should be the identification number same as fasta file - e.g. [ id:'bwa' ] - - meta4: - type: map - description: | - Groovy Map containing dbSNP information - id: should be the identification number for dbSNP files - e.g. [ id:'test' ] - - meta5: - type: map - description: | - Groovy Map containing regions information - id: should be the identification number for regions - e.g. [ id:'test' ] - - tumorbam: - type: file - description: Tumor or metastatic sample, BAM, SAM or CRAM file - pattern: "*.{bam,cram,sam}" - - tummorbai: - type: file - description: Index - pattern: "*.{bai,crai,sai}" - - normalbam: - type: file - description: Control (or normal) of matching tumor/metastatic sample, BAM, SAM or CRAM file - pattern: "*.{bam,cram,sam}" - - normalbai: - type: file - description: Index - pattern: "*.{bai,crai,sai}" - - bwa_index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - fasta: - type: file - description: FASTA file - pattern: "*.{fasta|fa}" - - fasta_fai: - type: file - description: Index of FASTA file - pattern: "*.{fai}" - - dbsnp: - type: file - description: VCF file including dbSNP variants - pattern: "*.vcf.gz" - - dbsnp_tbi: - type: file - description: Index of VCF file including dbSNP variants - pattern: "*.vcf.gz.tbi" - - regions: - type: file - description: Targeted intervals. Accepts BED file or Samtools-style string - pattern: "*.bed|*.txt|*.tab" + - - meta: + type: map + description: | + Groovy Map containing sample information + id: should be the identification number or sample name. If there is normal file meta should be common + e.g. [ id:'test' ] + - tumorbam: + type: file + description: Tumor or metastatic sample, BAM, SAM or CRAM file + pattern: "*.{bam,cram,sam}" + - tumorbai: + type: file + description: Index of the tumor or metastatic sample + pattern: "*.{bai,crai,sai}" + - normalbam: + type: file + description: Control (or normal) of matching tumor/metastatic sample, BAM, SAM + or CRAM file + pattern: "*.{bam,cram,sam}" + - normalbai: + type: file + description: Index + pattern: "*.{bai,crai,sai}" + - - meta2: + type: map + description: | + Groovy Map containing FASTA information + id: should be the identification number for alignment file and should be the same used to create BWA index files + e.g. [ id:'fasta' ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta|fa}" + - - meta2: + type: map + description: | + Groovy Map containing FASTA information + id: should be the identification number for alignment file and should be the same used to create BWA index files + e.g. [ id:'fasta' ] + - fasta_fai: + type: file + description: Index of FASTA file + pattern: "*.{fai}" + - - meta3: + type: map + description: | + Groovy Map containing BWA information + id: should be the identification number same as fasta file + e.g. [ id:'bwa' ] + - bwa_index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta4: + type: map + description: | + Groovy Map containing dbSNP information + id: should be the identification number for dbSNP files + e.g. [ id:'test' ] + - dbsnp: + type: file + description: VCF file including dbSNP variants + pattern: "*.vcf.gz" + - - meta4: + type: map + description: | + Groovy Map containing dbSNP information + id: should be the identification number for dbSNP files + e.g. [ id:'test' ] + - dbsnp_tbi: + type: file + description: Index of VCF file including dbSNP variants + pattern: "*.vcf.gz.tbi" + - - meta5: + type: map + description: | + Groovy Map containing regions information + id: should be the identification number for regions + e.g. [ id:'test' ] + - regions: + type: file + description: Targeted intervals. Accepts BED file or Samtools-style string + pattern: "*.bed|*.txt|*.tab" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - sv: - type: file - description: Filtered SVs for tumor only cases - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.sv.vcf.gz": + type: file + description: Filtered SVs for tumor only cases + pattern: "*.vcf.gz" - indel: - type: file - description: Filtered Indels for tumor only cases - pattern: "*.vcf.gz" - - som_sv: - type: file - description: Somatic filtered SVs for tumor/normal paired samples - pattern: "*.vcf.gz" - - som_indel: - type: file - description: Somatic filtered Indels for tumor/normal paired samples - pattern: "*.vcf.gz" - - germ_sv: - type: file - description: Germline filtered SVs for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.indel.vcf.gz": + type: file + description: Filtered Indels for tumor only cases + pattern: "*.vcf.gz" - germ_indel: - type: file - description: Germline filtered Indels for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.germline.indel.vcf.gz": + type: file + description: Germline filtered Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - germ_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.germline.sv.vcf.gz": + type: file + description: Germline filtered SVs for tumor/normal paired samples + pattern: "*.vcf.gz" + - som_indel: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.somatic.indel.vcf.gz": + type: file + description: Somatic filtered Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - som_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.somatic.sv.vcf.gz": + type: file + description: Somatic filtered SVs for tumor/normal paired samples + pattern: "*.vcf.gz" - unfiltered_sv: - type: file - description: Unfiltered SVs for tumor only cases - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.sv.vcf.gz": + type: file + description: Unfiltered SVs for tumor only cases + pattern: "*.vcf.gz" - unfiltered_indel: - type: file - description: Unfiltered Indels for tumor only cases - pattern: "*.vcf.gz" - - unfiltered_som_sv: - type: file - description: Unfiltered somatic SVs for tumor/normal paired samples - pattern: "*.vcf.gz" - - unfiltered_som_indel: - type: file - description: Unfiltered somatic Indels for tumor/normal paired samples - pattern: "*.vcf.gz" - - unfiltered_germ_sv: - type: file - description: Unfiltered germline SVs for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.indel.vcf.gz": + type: file + description: Unfiltered Indels for tumor only cases + pattern: "*.vcf.gz" - unfiltered_germ_indel: - type: file - description: Unfiltered germline Indels for tumor/normal paired samples - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.germline.indel.vcf.gz": + type: file + description: Unfiltered germline Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_germ_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.germline.sv.vcf.gz": + type: file + description: Unfiltered germline SVs for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_som_indel: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.somatic.indel.vcf.gz": + type: file + description: Unfiltered somatic Indels for tumor/normal paired samples + pattern: "*.vcf.gz" + - unfiltered_som_sv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.svaba.unfiltered.somatic.sv.vcf.gz": + type: file + description: Unfiltered somatic SVs for tumor/normal paired samples + pattern: "*.vcf.gz" - raw_calls: - type: file - description: Raw, unfiltered variants - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bps.txt.gz": + type: file + description: Raw, unfiltered variants + pattern: "*.txt.gz" - discordants: - type: file - description: Information on all clusters of discordant reads identified with 2+ reads - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.discordants.txt.gz": + type: file + description: Information on all clusters of discordant reads identified with + 2+ reads + pattern: "*.txt.gz" - log: - type: file - description: Log file - pattern: "*.txt.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.log": + type: file + description: Log file + pattern: "*.txt.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svanalyzer/svbenchmark/meta.yml b/modules/nf-core/svanalyzer/svbenchmark/meta.yml index c8a76ac19962..8f5d652bbdf6 100644 --- a/modules/nf-core/svanalyzer/svbenchmark/meta.yml +++ b/modules/nf-core/svanalyzer/svbenchmark/meta.yml @@ -1,7 +1,8 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "svanalyzer_svbenchmark" -description: "SVbenchmark compares a set of “test” structural variants in VCF format to a known truth set (also in VCF format) and outputs estimates of sensitivity and specificity." +description: "SVbenchmark compares a set of “test” structural variants in VCF format + to a known truth set (also in VCF format) and outputs estimates of sensitivity and + specificity." keywords: - structural variant - sv @@ -14,75 +15,110 @@ tools: tool_dev_url: "https://github.com/nhansen/SVanalyzer" license: "['CC0']" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing test sample information - e.g. `[ id:'test' ]` - - meta2: - type: map - description: | - Groovy Map containing reference genome information for fasta - e.g. `[ id:'test2' ]` - - meta3: - type: map - description: | - Groovy Map containing reference genome information for fai - e.g. `[ id:'test3' ]` - - test: - type: file - description: A VCF-formatted file of structural variants to test (required) - pattern: "*.{vcf,vcf.gz}" - - test_tbi: - type: file - description: A VCF-formatted file index of structural variants to test only for zipped files - pattern: "*.{vcf.gz.tbi}" - - truth: - type: file - description: A VCF-formatted file of variants to compare against (required) - pattern: "*.{vcf,vcf.gz}" - - truth_tbi: - type: file - description: A VCF-formatted file of variants to compare against only for zipped files - pattern: "*.{vcf.gz.tbi}" - - fasta: - type: file - description: The reference FASTA file for the supplied VCF file or files (required) - pattern: "*.{fa,fasta,fa.gz,fasta.gz}" - - bed: - type: file - description: BED File of regions from which to include variants. Used to filter both test and truth variants. - pattern: "*.{bed}" + - - meta: + type: map + description: | + Groovy Map containing test sample information + e.g. `[ id:'test' ]` + - test: + type: file + description: A VCF-formatted file of structural variants to test (required) + pattern: "*.{vcf,vcf.gz}" + - test_tbi: + type: file + description: A VCF-formatted file index of structural variants to test only + for zipped files + pattern: "*.{vcf.gz.tbi}" + - truth: + type: file + description: A VCF-formatted file of variants to compare against (required) + pattern: "*.{vcf,vcf.gz}" + - truth_tbi: + type: file + description: A VCF-formatted file of variants to compare against only for zipped + files + pattern: "*.{vcf.gz.tbi}" + - bed: + type: file + description: BED File of regions from which to include variants. Used to filter + both test and truth variants. + pattern: "*.{bed}" + - - meta2: + type: map + description: | + Groovy Map containing reference genome information for fasta + e.g. `[ id:'test2' ]` + - fasta: + type: file + description: The reference FASTA file for the supplied VCF file or files (required) + pattern: "*.{fa,fasta,fa.gz,fasta.gz}" + - - meta3: + type: map + description: | + Groovy Map containing reference genome information for fai + e.g. `[ id:'test3' ]` + - fai: + type: file + description: The reference FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information inherited from test vcf - e.g. `[ id:'test']` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fns: - type: file - description: VCF file with False Negatives - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.falsenegatives.vcf.gz": + type: file + description: VCF file with False Negatives + pattern: "*.{vcf.gz}" - fps: - type: file - description: VCF file with False Positives - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.falsepositives.vcf.gz": + type: file + description: VCF file with False Positives + pattern: "*.{vcf.gz}" - distances: - type: file - description: TSV file with genomic distances and size differences between structural variants compared - pattern: "*.{distances}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.distances": + type: file + description: TSV file with genomic distances and size differences between structural + variants compared + pattern: "*.{distances}" - log: - type: file - description: LOG file of the run - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.log": + type: file + description: LOG file of the run + pattern: "*.{log}" - report: - type: file - description: Text file reporting RECALL, PRECISION and F1. - pattern: "*.{report}" + - meta: + type: map + description: | + Groovy Map containing sample information inherited from test vcf + e.g. `[ id:'test']` + - "*.report": + type: file + description: Text file reporting RECALL, PRECISION and F1. + pattern: "*.{report}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" diff --git a/modules/nf-core/svdb/build/meta.yml b/modules/nf-core/svdb/build/meta.yml index c5c5a99265db..dd3789d43f4b 100644 --- a/modules/nf-core/svdb/build/meta.yml +++ b/modules/nf-core/svdb/build/meta.yml @@ -10,29 +10,35 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: Input VCF file(s) or folder - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input VCF file(s) or folder + pattern: "*" + - - input_type: + type: string + description: input type output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: SVDB database + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.db": + type: file + description: SVDB database + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@fellen31" diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml index bf44cd967b36..f725b65248d5 100644 --- a/modules/nf-core/svdb/merge/environment.yml +++ b/modules/nf-core/svdb/merge/environment.yml @@ -1,8 +1,8 @@ channels: - conda-forge - bioconda + dependencies: - - svdb=2.8.1 - # renovate: datasource=conda depName=bioconda/samtools - - samtools=1.19.2 - htslib=1.19.1 + - samtools=1.19.2 + - svdb=2.8.1 diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index e53e61fe7437..7dc7c67588ad 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -10,33 +10,37 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - priority: - type: list - description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator'] - - vcfs: - type: list - description: Two or more VCF files. Order of files should correspond to the order of tags used for priority. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - vcfs: + type: list + description: Two or more VCF files. Order of files should correspond to the + order of tags used for priority. + pattern: "*.{vcf,vcf.gz}" + - - priority: + type: list + description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator'] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: merged VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: merged VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" maintainers: diff --git a/modules/nf-core/svdb/query/meta.yml b/modules/nf-core/svdb/query/meta.yml index d11c51e6412e..f8cd33c8d802 100644 --- a/modules/nf-core/svdb/query/meta.yml +++ b/modules/nf-core/svdb/query/meta.yml @@ -10,52 +10,54 @@ tools: homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - in_occs: - type: list - description: A list of allele count tags - - in_frqs: - type: list - description: A list of allele frequency tags - - vcf: - type: file - description: query vcf file - pattern: "*.{vcf,vcf.gz}" - - vcf_dbs: - type: file - description: path to a database vcf, or a comma separated list of vcfs - pattern: "*.{vcf,vcf.gz}" - - bedpe_dbs: - type: file - description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, or a comma separated list of files - pattern: "*.{bedpe}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query vcf file + pattern: "*.{vcf,vcf.gz}" + - - in_occs: + type: list + description: A list of allele count tags + - - in_frqs: + type: list + description: A list of allele frequency tags + - - out_occs: + type: list + description: A list of allele count tags + - - out_frqs: + type: list + description: A list of allele frequency tags + - - vcf_dbs: + type: file + description: path to a database vcf, or a comma separated list of vcfs + pattern: "*.{vcf,vcf.gz}" + - - bedpe_dbs: + type: file + description: path to a SV database of the following format chrA-posA-chrB-posB-type-count-frequency, + or a comma separated list of files + pattern: "*.{bedpe}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - out_occs: - type: list - description: A list of allele count tags - - out_frqs: - type: list - description: A list of allele frequency tags - vcf: - type: file - description: Annotated output VCF file - pattern: "*_query.vcf" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*_query.vcf": + type: file + description: Annotated output VCF file + pattern: "*_query.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ramprasadn" diff --git a/modules/nf-core/svtk/baftest/meta.yml b/modules/nf-core/svtk/baftest/meta.yml index fcae45bd8dd2..1d1519317b96 100644 --- a/modules/nf-core/svtk/baftest/meta.yml +++ b/modules/nf-core/svtk/baftest/meta.yml @@ -9,47 +9,51 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: A BED file created with `svtk vcf2bed` - pattern: "*.bed" - - baf: - type: file - description: A BAF file created with `gatk PrintSVEvidence` - pattern: "*.baf.txt.gz" - - baf_index: - type: file - description: The index of the BAF file - pattern: "*.baf.txt.gz.tbi" - - batch: - type: file - description: A text file containing information about the sample(s) - pattern: "*.txt" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: A BED file created with `svtk vcf2bed` + pattern: "*.bed" + - baf: + type: file + description: A BAF file created with `gatk PrintSVEvidence` + pattern: "*.baf.txt.gz" + - baf_index: + type: file + description: The index of the BAF file + pattern: "*.baf.txt.gz.tbi" + - batch: + type: file + description: A text file containing information about the sample(s) + pattern: "*.txt" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - metrics: - type: file - description: The results file from the BAF test - pattern: "*.metrics" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.metrics": + type: file + description: The results file from the BAF test + pattern: "*.metrics" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/countsvtypes/meta.yml b/modules/nf-core/svtk/countsvtypes/meta.yml index bc398ec1e728..70b333899f8f 100644 --- a/modules/nf-core/svtk/countsvtypes/meta.yml +++ b/modules/nf-core/svtk/countsvtypes/meta.yml @@ -7,36 +7,40 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" doi: "10.1038/s41586-020-2287-8" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: The VCF file containing structural variants - pattern: "*.vcf.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: The VCF file containing structural variants + pattern: "*.vcf.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - counts: - type: file - description: A tab-delimited file containing the counts of the SV types - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: A tab-delimited file containing the counts of the SV types + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/rdtest2vcf/meta.yml b/modules/nf-core/svtk/rdtest2vcf/meta.yml index c1851f5738d2..8a702f9f82fb 100644 --- a/modules/nf-core/svtk/rdtest2vcf/meta.yml +++ b/modules/nf-core/svtk/rdtest2vcf/meta.yml @@ -8,48 +8,59 @@ keywords: - vcf tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" doi: "10.1038/s41586-020-2287-8" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: An RdTest-formatted bed - pattern: "*.bed" - - samples: - type: file - description: A text file containing the names of all samples that need to be added to the VCF - pattern: "*.txt" - - fasta_fai: - type: file - description: The reference file of a FASTA file containing the contigs - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: An RdTest-formatted bed + pattern: "*.bed" + - samples: + type: file + description: A text file containing the names of all samples that need to be + added to the VCF + pattern: "*.txt" + - - fasta_fai: + type: file + description: The reference file of a FASTA file containing the contigs + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The converted VCF - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: The converted VCF + pattern: "*.vcf.gz" - tbi: - type: file - description: The index of the converted VCF - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: The index of the converted VCF + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/standardize/meta.yml b/modules/nf-core/svtk/standardize/meta.yml index e0d35cf4dde7..84090cbacdd6 100644 --- a/modules/nf-core/svtk/standardize/meta.yml +++ b/modules/nf-core/svtk/standardize/meta.yml @@ -8,51 +8,44 @@ keywords: - standardization tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - args: - type: map - description: | - Groovy Map containing tool parameters. MUST follow the structure/keywords below and be provided via modules.config. Parameters must be set between quotes. - ``` - { - [ - "args": "", - "caller": "delly" // Should be either delly, lumpy, manta, wham or melt - ] - } - ``` - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A gzipped VCF file to be standardized - pattern: "*.vcf.gz" - - fasta_fai: - type: file - description: Optional fasta index file that specifies the contigs to be used in the VCF header (defaults to all contigs of GRCh37) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A gzipped VCF file to be standardized + pattern: "*.vcf.gz" + - - fasta_fai: + type: file + description: Optional fasta index file that specifies the contigs to be used + in the VCF header (defaults to all contigs of GRCh37) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - standardized_vcf: - type: file - description: A gzipped version of the standardized VCF file - pattern: "*.std.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.std.vcf.gz": + type: file + description: A gzipped version of the standardized VCF file + pattern: "*.std.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtk/vcf2bed/meta.yml b/modules/nf-core/svtk/vcf2bed/meta.yml index 4b1d2e63e13c..7cc6d23362b4 100644 --- a/modules/nf-core/svtk/vcf2bed/meta.yml +++ b/modules/nf-core/svtk/vcf2bed/meta.yml @@ -8,39 +8,43 @@ keywords: - structural variants tools: - "svtk": - description: "Utilities for consolidating, filtering, resolving, and annotating structural variants." + description: "Utilities for consolidating, filtering, resolving, and annotating + structural variants." homepage: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" documentation: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" tool_dev_url: "https://github.com/broadinstitute/gatk-sv/tree/master/src/svtk" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: A VCF file created with a structural variant caller - pattern: "*.vcf.gz" - - tbi: - type: file - description: The index for the VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: A VCF file created with a structural variant caller + pattern: "*.vcf.gz" + - tbi: + type: file + description: The index for the VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: The created BED file - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The created BED file + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/svtyper/svtyper/meta.yml b/modules/nf-core/svtyper/svtyper/meta.yml index 2184620d36b9..6846e2ec7224 100644 --- a/modules/nf-core/svtyper/svtyper/meta.yml +++ b/modules/nf-core/svtyper/svtyper/meta.yml @@ -1,5 +1,6 @@ name: "svtyper_svtyper" -description: SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data +description: SVTyper performs breakpoint genotyping of structural variants (SVs) using + whole genome sequencing data keywords: - sv - structural variants @@ -12,55 +13,79 @@ tools: tool_dev_url: "https://github.com/hall-lab/svtyper" doi: "10.1038/nmeth.3505" licence: ["MIT"] + identifier: biotools:svtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for FASTA file - e.g. [ id:'fasta'] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - vcf: - type: file - description: Matching VCF of alignments - pattern: "*.vcf" - - fasta: - type: file - description: FASTA file used to generate alignments - pattern: "*.{fa,fasta}" - - fai: - type: file - description: FAI file used to generate alignments - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bam_index: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - vcf: + type: file + description: Matching VCF of alignments + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information for FASTA file + e.g. [ id:'fasta'] + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing sample information for FASTA file + e.g. [ id:'fasta'] + - fai: + type: file + description: FAI file used to generate alignments + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - json: - type: file - description: JSON file including Library information - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: JSON file including Library information + pattern: "*.json" - gt_vcf: - type: file - description: Genotyped SVs - pattern: "*.vcf" - - relevant_bam: - type: file - description: Relevant alignments - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Genotyped SVs + pattern: "*.vcf" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: BAM file with + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/svtyper/svtypersso/meta.yml b/modules/nf-core/svtyper/svtypersso/meta.yml index edbf8e3ce5cc..d89b1035fa34 100644 --- a/modules/nf-core/svtyper/svtypersso/meta.yml +++ b/modules/nf-core/svtyper/svtypersso/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "svtyper_svtypersso" -description: SVTyper-sso computes structural variant (SV) genotypes based on breakpoint depth on a SINGLE sample +description: SVTyper-sso computes structural variant (SV) genotypes based on breakpoint + depth on a SINGLE sample keywords: - sv - structural variants @@ -15,53 +15,61 @@ tools: tool_dev_url: "https://github.com/hall-lab/svtyper" doi: "10.1038/nmeth.3505" licence: ["MIT"] + identifier: biotools:svtyper input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test'] - - meta2: - type: map - description: | - Groovy Map containing sample information for reference FASTA file - e.g. [ id:'fasta'] - - bam: - type: file - description: BAM or CRAM file with alignments - pattern: "*.{bam,cram}" - - bam_index: - type: file - description: BAI file matching the BAM file - pattern: "*.{bai}" - - vcf: - type: file - description: Matching VCF of alignments - pattern: "*.vcf" - - fasta: - type: file - description: indexed reference FASTA file (recommended for reading CRAM files) - pattern: "*.{fa,fasta}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - bam: + type: file + description: BAM or CRAM file with alignments + pattern: "*.{bam,cram}" + - bam_index: + type: file + description: BAI file matching the BAM file + pattern: "*.{bai}" + - vcf: + type: file + description: Matching VCF of alignments + pattern: "*.vcf" + - - meta2: + type: map + description: | + Groovy Map containing sample information for reference FASTA file + e.g. [ id:'fasta'] + - fasta: + type: file + description: indexed reference FASTA file (recommended for reading CRAM files) + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - json: - type: file - description: JSON file including library information - pattern: "*.json" - gt_vcf: - type: file - description: Genotyped SVs - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf": + type: file + description: Genotyped SVs + pattern: "*.vcf" + - json: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.json": + type: file + description: JSON file including library information + pattern: "*.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tstoeriko" maintainers: diff --git a/modules/nf-core/svync/meta.yml b/modules/nf-core/svync/meta.yml index dacc5738ba50..cad35715cdd0 100644 --- a/modules/nf-core/svync/meta.yml +++ b/modules/nf-core/svync/meta.yml @@ -1,4 +1,3 @@ ---- name: "svync" description: A tool to standardize VCF files from structural variant callers keywords: @@ -14,41 +13,42 @@ tools: documentation: "https://github.com/nvnieuwk/svync" tool_dev_url: "https://github.com/nvnieuwk/svync" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - vcf: - type: file - description: The input VCF file containing structural variants - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: The index of the input VCF file containing structural variants - pattern: "*.tbi" - - config: - type: file - description: The config stating how the standardization should happen - pattern: "*.{yml,yaml}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - vcf: + type: file + description: The input VCF file containing structural variants + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: The index of the input VCF file containing structural variants + pattern: "*.tbi" + - config: + type: file + description: The config stating how the standardization should happen + pattern: "*.{yml,yaml}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The standardized VCF file - pattern: "*.vcf.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: The standardized VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index c863e9207c07..017c259da1cb 100644 --- a/modules/nf-core/tabix/bgzip/environment.yml +++ b/modules/nf-core/tabix/bgzip/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml index 621d49ea0ea8..131e92cfdbd0 100644 --- a/modules/nf-core/tabix/bgzip/meta.yml +++ b/modules/nf-core/tabix/bgzip/meta.yml @@ -13,33 +13,42 @@ tools: documentation: http://www.htslib.org/doc/bgzip.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: file to compress or to decompress + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: file to compress or to decompress output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - output: - type: file - description: Output compressed/decompressed file - pattern: "*." + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: Output compressed/decompressed file + pattern: "*." - gzi: - type: file - description: Optional gzip index file for compressed inputs - pattern: "*.gzi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}.gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index c863e9207c07..017c259da1cb 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 438aba4d18d5..806fbc121fc1 100644 --- a/modules/nf-core/tabix/bgziptabix/meta.yml +++ b/modules/nf-core/tabix/bgziptabix/meta.yml @@ -13,38 +13,50 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file - pattern: "*.{bed,gff,sam,vcf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Sorted tab-delimited genome file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gz: - type: file - description: Output compressed file - pattern: "*.{gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{gz.tbi}" - - csi: - type: file - description: tabix alternate index file - pattern: "*.{gz.csi}" + - gz_tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.tbi": + type: file + description: tabix index file + pattern: "*.tbi" + - gz_csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: bgzipped tab-delimited genome file + pattern: "*.gz" + - "*.csi": + type: file + description: csi index file + pattern: "*.csi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" - "@DLBPointon" diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index ae5b4f439f19..7864832d93ce 100644 --- a/modules/nf-core/tabix/tabix/meta.yml +++ b/modules/nf-core/tabix/tabix/meta.yml @@ -11,34 +11,43 @@ tools: documentation: https://www.htslib.org/doc/tabix.1.html doi: 10.1093/bioinformatics/btq671 licence: ["MIT"] + identifier: biotools:tabix input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tab: - type: file - description: TAB-delimited genome position file compressed with bgzip - pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - tab: + type: file + description: TAB-delimited genome position file compressed with bgzip + pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: tabix index file + pattern: "*.{tbi}" - csi: - type: file - description: coordinate sorted index file - pattern: "*.{csi}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: coordinate sorted index file + pattern: "*.{csi}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tailfindr/meta.yml b/modules/nf-core/tailfindr/meta.yml index 47cc2a370209..f221e0fc4e70 100644 --- a/modules/nf-core/tailfindr/meta.yml +++ b/modules/nf-core/tailfindr/meta.yml @@ -1,41 +1,46 @@ name: "tailfindr" -description: Estimating poly(A)-tail lengths from basecalled fast5 files produced by Nanopore sequencing of RNA and DNA +description: Estimating poly(A)-tail lengths from basecalled fast5 files produced + by Nanopore sequencing of RNA and DNA keywords: - polya tail - fast5 - nanopore tools: - "tailfindr": - description: "An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads." + description: "An R package for estimating poly(A)-tail lengths in Oxford Nanopore + RNA and DNA reads." homepage: "https://github.com/adnaniazi/tailfindr" documentation: "https://github.com/adnaniazi/tailfindr/blob/master/README.md" tool_dev_url: "https://github.com/adnaniazi/tailfindr" doi: "10.1261/rna.071332.119" licence: ["AGPL v3"] + identifier: biotools:tailfindr input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - fast5: - type: file - description: fast5 file - pattern: "*.fast5" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - fast5: + type: file + description: fast5 file + pattern: "*.fast5" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - csv_gz: - type: file - description: Compressed csv file - pattern: "*.csv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.csv.gz": + type: file + description: Compressed csv file + pattern: "*.csv.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucacozzuto" maintainers: diff --git a/modules/nf-core/taxonkit/name2taxid/meta.yml b/modules/nf-core/taxonkit/name2taxid/meta.yml index e96c8993ac72..7a8d16e801ee 100644 --- a/modules/nf-core/taxonkit/name2taxid/meta.yml +++ b/modules/nf-core/taxonkit/name2taxid/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "taxonkit_name2taxid" description: Convert taxon names to TaxIds @@ -15,38 +14,40 @@ tools: tool_dev_url: "https://github.com/shenwei356/taxonkit" doi: "10.1016/j.jgg.2021.03.006" licence: ["MIT"] + identifier: biotools:taxonkit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - name: - type: string - description: Taxon name to look up (provide either this or names.txt, not both) - - names_txt: - type: file - description: File with taxon names to look up, each on their own line (provide either this or name, not both) - - taxdb: - type: file - description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - name: + type: string + description: Taxon name to look up (provide either this or names.txt, not both) + - names_txt: + type: file + description: File with taxon names to look up, each on their own line (provide + either this or name, not both) + - - taxdb: + type: file + description: Taxonomy database unpacked from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsv: - type: file - description: TSV file of Taxon names and their taxon ID - pattern: "*.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: TSV file of Taxon names and their taxon ID + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mahesh-panchal" maintainers: diff --git a/modules/nf-core/taxpasta/merge/meta.yml b/modules/nf-core/taxpasta/merge/meta.yml index a4cbed946c11..5e2d7ab0d150 100644 --- a/modules/nf-core/taxpasta/merge/meta.yml +++ b/modules/nf-core/taxpasta/merge/meta.yml @@ -15,46 +15,55 @@ tools: documentation: "https://taxpasta.readthedocs.io/" tool_dev_url: "https://github.com/taxprofiler/taxpasta" licence: ["Apache-2.0"] + identifier: biotools:taxpasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profiles: - type: file - description: A list of taxonomic profiler output files (typically in text format, mandatory) - pattern: "*.{tsv,csv,arrow,parquet,biom}" - - profiler: - type: string - description: Name of the profiler used to generate the profile (mandatory) - pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - - format: - type: string - description: Type of output file to be generated - pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" - - taxonomy: - type: directory - description: Directory containing at a minimum nodes.dmp and names.dmp files (optional) - pattern: "*/" - - samplesheet: - type: file - description: A samplesheet describing the sample name and a filepath to a taxonomic abundance profile that needs to be relative from the Nextflow work directory of the executed process. The profiles must be provided even if you give a samplesheet as argument (optional) - pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profiles: + type: file + description: A list of taxonomic profiler output files (typically in text format, + mandatory) + pattern: "*.{tsv,csv,arrow,parquet,biom}" + - - profiler: + type: string + description: Name of the profiler used to generate the profile (mandatory) + pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + - - format: + type: string + description: Type of output file to be generated + pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" + - - taxonomy: + type: directory + description: Directory containing at a minimum nodes.dmp and names.dmp files + (optional) + pattern: "*/" + - - samplesheet: + type: file + description: A samplesheet describing the sample name and a filepath to a taxonomic + abundance profile that needs to be relative from the Nextflow work directory + of the executed process. The profiles must be provided even if you give a + samplesheet as argument (optional) + pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - merged_profiles: - type: file - description: Output file with standardised multiple profiles in one go and have all profiles combined into a single table. - pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tsv,csv,arrow,parquet,biom}": + type: file + description: Output file with standardised multiple profiles in one go and have + all profiles combined into a single table. + pattern: "*.{tsv,csv,ods,xlsx,arrow,parquet,biom}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" - "@jfy133" diff --git a/modules/nf-core/taxpasta/standardise/meta.yml b/modules/nf-core/taxpasta/standardise/meta.yml index b855905a7ce4..ca7a28ecad89 100644 --- a/modules/nf-core/taxpasta/standardise/meta.yml +++ b/modules/nf-core/taxpasta/standardise/meta.yml @@ -15,42 +15,46 @@ tools: documentation: "https://taxpasta.readthedocs.io/" tool_dev_url: "https://github.com/taxprofiler/taxpasta" licence: ["Apache-2.0"] + identifier: biotools:taxpasta input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - profile: - type: file - description: profiler output file (mandatory) - pattern: "*" - - profiler: - type: string - description: Name of the profiler used to generate the profile (mandatory) - pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" - - format: - type: string - description: Type of output file to be generated - pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" - - taxonomy: - type: directory - description: Directory containing at a minimum nodes.dmp and names.dmp files (optional) - pattern: "*/" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - profile: + type: file + description: profiler output file (mandatory) + pattern: "*" + - - profiler: + type: string + description: Name of the profiler used to generate the profile (mandatory) + pattern: "bracken|centrifuge|diamond|ganon|kaiju|kmcp|kraken2|krakenuniq|megan6|metaphlan|motus" + - - format: + type: string + description: Type of output file to be generated + pattern: "tsv|csv|ods|xlsx|arrow|parquet|biom" + - - taxonomy: + type: directory + description: Directory containing at a minimum nodes.dmp and names.dmp files + (optional) + pattern: "*/" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - standardised_profile: - type: file - description: Standardised taxonomic profile - pattern: "*.{tsv,csv,arrow,parquet,biom}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{tsv,csv,arrow,parquet,biom}": + type: file + description: Standardised taxonomic profile + pattern: "*.{tsv,csv,arrow,parquet,biom}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Midnighter" maintainers: diff --git a/modules/nf-core/tbprofiler/profile/meta.yml b/modules/nf-core/tbprofiler/profile/meta.yml index a53aa3e3bc78..98989dda1077 100644 --- a/modules/nf-core/tbprofiler/profile/meta.yml +++ b/modules/nf-core/tbprofiler/profile/meta.yml @@ -6,52 +6,80 @@ keywords: - serotype tools: - tbprofiler: - description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance and lineage from WGS data + description: Profiling tool for Mycobacterium tuberculosis to detect drug resistance + and lineage from WGS data homepage: https://github.com/jodyphelan/TBProfiler documentation: https://jodyphelan.gitbook.io/tb-profiler/ tool_dev_url: https://github.com/jodyphelan/TBProfiler doi: "10.1186/s13073-019-0650-x" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ file - pattern: "*.{fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file + pattern: "*.{fastq.gz,fq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: BAM file with alignment details - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam/*.bam: + type: file + description: BAM file with alignment details + pattern: "*.bam" - csv: - type: file - description: Optional CSV formated result file of resistance and strain type - pattern: "*.csv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.csv: + type: file + description: Optional CSV formated result file of resistance and strain type + pattern: "*.csv" - json: - type: file - description: JSON formated result file of resistance and strain type - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.json: + type: file + description: JSON formated result file of resistance and strain type + pattern: "*.json" - txt: - type: file - description: Optional text file of resistance and strain type - pattern: "*.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results/*.txt: + type: file + description: Optional text file of resistance and strain type + pattern: "*.txt" - vcf: - type: file - description: VCF with variant info again refernce genomes - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf/*.vcf.gz: + type: file + description: VCF with variant info again refernce genomes + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@rpetit3" maintainers: diff --git a/modules/nf-core/tcoffee/align/meta.yml b/modules/nf-core/tcoffee/align/meta.yml index 4125d1ed2c24..518be2b39d51 100644 --- a/modules/nf-core/tcoffee/align/meta.yml +++ b/modules/nf-core/tcoffee/align/meta.yml @@ -6,69 +6,84 @@ keywords: - genomics tools: - "tcoffee": - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - meta3: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_infos']` - - template: - type: file - description: T_coffee template file that maps sequences to the accessory information files to be used. - pattern: "*" - - accessory_informations: - type: file - description: Accessory files to be used in the alignment. For example, it could be protein structures or secondary structures. - pattern: "*" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - meta3: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_infos']` + - template: + type: file + description: T_coffee template file that maps sequences to the accessory information + files to be used. + pattern: "*" + - accessory_informations: + type: file + description: Accessory files to be used in the alignment. For example, it could + be protein structures or secondary structures. + pattern: "*" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file in FASTA format. May be gzipped. - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file in FASTA format. May be gzipped. + pattern: "*.aln{.gz,}" - lib: - type: file - description: optional output, the library generated from the MSA file. - pattern: "*.*lib" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.*lib": + type: file + description: optional output, the library generated from the MSA file. + pattern: "*.*lib" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/tcoffee/alncompare/meta.yml b/modules/nf-core/tcoffee/alncompare/meta.yml index 31502555d9ed..0dd0c9ee97aa 100644 --- a/modules/nf-core/tcoffee/alncompare/meta.yml +++ b/modules/nf-core/tcoffee/alncompare/meta.yml @@ -6,47 +6,52 @@ keywords: - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. Can be gzipped or uncompressed - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - ref_msa: - type: file - description: fasta file containing the reference alignment used for the evaluation. Can be gzipped or uncompressed - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - msa: + type: file + description: fasta file containing the alignment to be evaluated. Can be gzipped + or uncompressed + pattern: "*.{aln,fa,fasta,fas}{.gz,}" + - ref_msa: + type: file + description: fasta file containing the reference alignment used for the evaluation. + Can be gzipped or uncompressed + pattern: "*.{aln,fa,fasta,fas}{.gz,}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scores: - type: file - description: a file containing the score of the alignment - pattern: "*.scores" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scores": + type: file + description: a file containing the score of the alignment + pattern: "*.scores" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@l-mansouri" - "@luisas" diff --git a/modules/nf-core/tcoffee/consensus/meta.yml b/modules/nf-core/tcoffee/consensus/meta.yml index 54d608300a05..c485e06a41d3 100644 --- a/modules/nf-core/tcoffee/consensus/meta.yml +++ b/modules/nf-core/tcoffee/consensus/meta.yml @@ -6,57 +6,61 @@ keywords: - genomics tools: - tcoffee: - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - pigz: description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - aln: - type: file - description: List of multiple sequence alignments in FASTA format to be used to compute the consensus - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. Compression is done using pigz, and is multithreaded. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - aln: + type: file + description: List of multiple sequence alignments in FASTA format to be used + to compute the consensus + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - alignment: - type: file - description: Consensus alignment in FASTA format - pattern: "*.{fa,fasta,aln}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.{aln,aln.gz}": + type: file + description: Consensus alignment in FASTA format + pattern: "*.{fa,fasta,aln}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/tcoffee/irmsd/meta.yml b/modules/nf-core/tcoffee/irmsd/meta.yml index e13e7ddadf34..cf930ea038bb 100644 --- a/modules/nf-core/tcoffee/irmsd/meta.yml +++ b/modules/nf-core/tcoffee/irmsd/meta.yml @@ -6,58 +6,46 @@ keywords: - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - - meta2: - type: map - description: | - Groovy Map containing information about the structures - e.g. [ id:'test', ... ] - - - template: - type: file - description: Template file matching the structures to the sequences in the alignment. - pattern: "*" - - - structures: - type: directory - description: Directory containing the structures file matching the sequences in the alignment in PDB format - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - irmsd: - type: file - description: File containing the irmsd of the alignment - pattern: "*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.irmsd: + type: file + description: File containing the irmsd of the alignment + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" diff --git a/modules/nf-core/tcoffee/seqreformat/meta.yml b/modules/nf-core/tcoffee/seqreformat/meta.yml index 0571c7d875dc..17111df376dc 100644 --- a/modules/nf-core/tcoffee/seqreformat/meta.yml +++ b/modules/nf-core/tcoffee/seqreformat/meta.yml @@ -6,41 +6,39 @@ keywords: - genomics tools: - "tcoffee": - description: "A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - infile: - type: file - description: Input file to be reformatted - pattern: "*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - infile: + type: file + description: Input file to be reformatted output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - formatted_file: - type: file - description: Formatted file - pattern: "*" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test' ]` + - ${prefix}.txt: + type: file + description: Formatted file + pattern: "*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" - "@JoseEspinosa" diff --git a/modules/nf-core/tcoffee/tcs/environment.yml b/modules/nf-core/tcoffee/tcs/environment.yml index 26a17e709832..615d140e6bb7 100644 --- a/modules/nf-core/tcoffee/tcs/environment.yml +++ b/modules/nf-core/tcoffee/tcs/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::t-coffee=13.46.0.919e8c6b + - "bioconda::t-coffee=13.46.0.919e8c6b" - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/tcs/meta.yml b/modules/nf-core/tcoffee/tcs/meta.yml index 7a13e79a8b61..2846d4ba188c 100644 --- a/modules/nf-core/tcoffee/tcs/meta.yml +++ b/modules/nf-core/tcoffee/tcs/meta.yml @@ -1,62 +1,72 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tcoffee_tcs" -description: Compute the TCS score for a MSA or for a MSA plus a library file. Outputs the tcs as it is and a csv with just the total TCS score. +description: Compute the TCS score for a MSA or for a MSA plus a library file. Outputs + the tcs as it is and a csv with just the total TCS score. keywords: - alignment - MSA - evaluation tools: - "tcoffee": - description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein Sequence" + description: "A collection of tools for Multiple Alignments of DNA, RNA, Protein + Sequence" homepage: "http://www.tcoffee.org/Projects/tcoffee/" documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" tool_dev_url: "https://github.com/cbcrg/tcoffee" doi: "10.1006/jmbi.2000.4042" licence: ["GPL v3"] + identifier: "" - "pigz": description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', ... ] - - msa: - type: file - description: fasta file containing the alignment to be evaluated. May be gzipped or uncompressed. - pattern: "*.{aln,fa,fasta,fas}{.gz,}" - - meta2: - type: map - description: | - Groovy Map containing library information - e.g. [ id:'test', ... ] - - lib: - type: file - description: lib file containing the alignment library of the given msa. - pattern: "*{.tc_lib,*_lib}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', ... ] + - msa: + type: file + description: fasta file containing the alignment to be evaluated. May be gzipped + or uncompressed. + pattern: "*.{aln,fa,fasta,fas}{.gz,}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - lib: + type: file + description: lib file containing the alignment library of the given msa. + pattern: "*{.tc_lib,*_lib}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tcs: - type: file - description: The msa represented in tcs format, prepended with TCS scores - pattern: "*.tcs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tcs": + type: file + description: The msa represented in tcs format, prepended with TCS scores + pattern: "*.tcs" - scores: - type: file - description: a file containing the score of the alignment in csv format - pattern: "*.scores" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.scores": + type: file + description: a file containing the score of the alignment in csv format + pattern: "*.scores" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alessiovignoli" diff --git a/modules/nf-core/thermorawfileparser/meta.yml b/modules/nf-core/thermorawfileparser/meta.yml index 5c604c63cf24..7235bc31ac59 100644 --- a/modules/nf-core/thermorawfileparser/meta.yml +++ b/modules/nf-core/thermorawfileparser/meta.yml @@ -9,39 +9,41 @@ keywords: - proteomics tools: - thermorawfileparser: - description: "Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library for running on Linux with mono" + description: "Wrapper around the .net (C#) ThermoFisher ThermoRawFileReader library + for running on Linux with mono" homepage: "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md" documentation: "https://github.com/compomics/ThermoRawFileParser/blob/master/README.md" tool_dev_url: "https://github.com/compomics/ThermoRawFileParser" doi: "10.1021/acs.jproteome.9b00328" licence: ["Apache Software"] + identifier: biotools:ThermoRawFileParser input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - raw: - type: file - description: Thermo RAW file - pattern: "*.{raw,RAW}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw: + type: file + description: Thermo RAW file + pattern: "*.{raw,RAW}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - spectra: - type: file - description: Mass spectra in open format - pattern: "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}": + type: file + description: Mass spectra in open format + pattern: "*.{mzML,mzML.gz,mgf,mgf.gz,parquet,parquet.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jonasscheid" maintainers: diff --git a/modules/nf-core/tiara/tiara/meta.yml b/modules/nf-core/tiara/tiara/meta.yml index e9d6b0553d7d..8d86ae9fde52 100644 --- a/modules/nf-core/tiara/tiara/meta.yml +++ b/modules/nf-core/tiara/tiara/meta.yml @@ -1,50 +1,69 @@ name: "tiara_tiara" -description: Domain-level classification of contigs to bacterial, archaeal, eukaryotic, or organelle +description: Domain-level classification of contigs to bacterial, archaeal, eukaryotic, + or organelle keywords: - contigs - metagenomics - classify tools: - "tiara": - description: "Deep-learning-based approach for identification of eukaryotic sequences in the metagenomic data powered by PyTorch." + description: "Deep-learning-based approach for identification of eukaryotic sequences + in the metagenomic data powered by PyTorch." homepage: "https://ibe-uw.github.io/tiara/" documentation: https://ibe-uw.github.io/tiara/" tool_dev_url: "https://github.com/ibe-uw/tiara" doi: "10.1093/bioinformatics/btab672" licence: ["MIT"] + identifier: biotools:tiara-metagenomics input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file of assembled contigs. - pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file of assembled contigs. + pattern: "*.{fa,fa.gz,fasta,fasta.gz,fna,fna.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - classifications: - type: file - description: TSV file containing per-contig classification probabilities and overall classifications. Gzipped if flag --gz is set. - pattern: "*.{txt,txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.{txt,txt.gz}: + type: file + description: TSV file containing per-contig classification probabilities and + overall classifications. Gzipped if flag --gz is set. + pattern: "*.{txt,txt.gz}" - log: - type: file - description: Log file containing tiara model parameters. Gzipped if flag --gz is set. - pattern: "log_*.{txt,txt.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - log_*.{txt,txt.gz}: + type: file + description: Log file containing tiara model parameters. Gzipped if flag --gz + is set. + pattern: "log_*.{txt,txt.gz}" - fasta: - type: file - description: | - (optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs - pattern: "*.{fasta,fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{fasta,fasta.gz}": + type: file + description: | + (optional) - fasta files for each domain category specified in command flag `-tf`, containing classified contigs + pattern: "*.{fasta,fasta.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@prototaxites" maintainers: diff --git a/modules/nf-core/tiddit/cov/meta.yml b/modules/nf-core/tiddit/cov/meta.yml index c28546cc8243..88b72641dbda 100644 --- a/modules/nf-core/tiddit/cov/meta.yml +++ b/modules/nf-core/tiddit/cov/meta.yml @@ -12,45 +12,54 @@ tools: documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: "10.12688/f1000research.11168.1" licence: ["GPL v3"] + identifier: biotools:tiddit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'genome' ] - - fasta: - type: file - description: | - Reference genome file. Only needed when passing in CRAM instead of BAM. - If not using CRAM, please pass an empty file instead. - pattern: "*.fasta" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: | + Reference genome file. Only needed when passing in CRAM instead of BAM. + If not using CRAM, please pass an empty file instead. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - cov: - type: file - description: The coverage of different regions in bed format. Optional. - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: The coverage of different regions in bed format. Optional. + pattern: "*.bed" - wig: - type: file - description: The coverage of different regions in WIG format. Optional. - pattern: "*.wig" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.wig": + type: file + description: The coverage of different regions in WIG format. Optional. + pattern: "*.wig" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@ramprasadn" diff --git a/modules/nf-core/tiddit/sv/meta.yml b/modules/nf-core/tiddit/sv/meta.yml index bfcbc4e3fd89..21527baf13d8 100644 --- a/modules/nf-core/tiddit/sv/meta.yml +++ b/modules/nf-core/tiddit/sv/meta.yml @@ -11,56 +11,65 @@ tools: documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md doi: 10.12688/f1000research.11168.1 licence: ["GPL-3.0-or-later"] + identifier: biotools:tiddit input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test_fasta']` - - fasta: - type: file - description: Input FASTA file - pattern: "*.{fasta,fa}" - - meta3: - type: map - description: | - Groovy Map containing sample information from bwa index - e.g. `[ id:'test_bwa-index' ]` - - bwa_index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test_fasta']` + - fasta: + type: file + description: Input FASTA file + pattern: "*.{fasta,fa}" + - - meta3: + type: map + description: | + Groovy Map containing sample information from bwa index + e.g. `[ id:'test_bwa-index' ]` + - bwa_index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: vcf - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: vcf + pattern: "*.{vcf}" - ploidy: - type: file - description: tab - pattern: "*.{ploidies.tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ploidies.tab": + type: file + description: tab + pattern: "*.{ploidies.tab}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@maxulysse" maintainers: diff --git a/modules/nf-core/tidk/explore/meta.yml b/modules/nf-core/tidk/explore/meta.yml index 582aaf56cda0..72d15954b98d 100644 --- a/modules/nf-core/tidk/explore/meta.yml +++ b/modules/nf-core/tidk/explore/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_explore" description: | @@ -10,42 +9,52 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - explore_tsv: - type: file - description: Telomeres and their frequencies in TSV format - pattern: "*.tidk.explore.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tidk.explore.tsv": + type: file + description: Telomeres and their frequencies in TSV format + pattern: "*.tidk.explore.tsv" - top_sequence: - type: file - description: | - The most frequent telomere sequence if one or more - sequences are identified by the toolkit - pattern: "*.top.sequence.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.top.sequence.txt": + type: file + description: | + The most frequent telomere sequence if one or more + sequences are identified by the toolkit + pattern: "*.top.sequence.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/plot/meta.yml b/modules/nf-core/tidk/plot/meta.yml index 451195c85474..75289b28434c 100644 --- a/modules/nf-core/tidk/plot/meta.yml +++ b/modules/nf-core/tidk/plot/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_plot" description: | @@ -11,36 +10,40 @@ keywords: - plot tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - tsv: - type: file - description: Search results in TSV format from `tidk search` - pattern: "*.tsv" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - tsv: + type: file + description: Search results in TSV format from `tidk search` + pattern: "*.tsv" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - svg: - type: file - description: Telomere search plot - pattern: "*.svg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.svg": + type: file + description: Telomere search plot + pattern: "*.svg" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tidk/search/meta.yml b/modules/nf-core/tidk/search/meta.yml index 8ba073501580..9a30ff1545d6 100644 --- a/modules/nf-core/tidk/search/meta.yml +++ b/modules/nf-core/tidk/search/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tidk_search" description: Searches a genome for a telomere string such as TTAGGG @@ -8,43 +7,53 @@ keywords: - search tools: - "tidk": - description: tidk is a toolkit to identify and visualise telomeric repeats in genomes + description: tidk is a toolkit to identify and visualise telomeric repeats in + genomes homepage: "https://github.com/tolkit/telomeric-identifier" documentation: "https://github.com/tolkit/telomeric-identifier" tool_dev_url: "https://github.com/tolkit/telomeric-identifier" doi: "10.5281/zenodo.10091385" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - fasta: - type: file - description: The input fasta file - pattern: "*.{fsa,fa,fasta}" - - string: - type: string - description: Search string such as TTAGGG + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fasta: + type: file + description: The input fasta file + pattern: "*.{fsa,fa,fasta}" + - - string: + type: string + description: Search string such as TTAGGG output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - tsv: - type: file - description: Search results in TSV format - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: Search results in TSV format + pattern: "*.tsv" - bedgraph: - type: file - description: Search results in BEDGRAPH format - pattern: "*.bedgraph" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.bedgraph": + type: file + description: Search results in BEDGRAPH format + pattern: "*.bedgraph" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/topas/gencons/meta.yml b/modules/nf-core/topas/gencons/meta.yml index 4bef8632826c..c6ec267664c8 100644 --- a/modules/nf-core/topas/gencons/meta.yml +++ b/modules/nf-core/topas/gencons/meta.yml @@ -1,68 +1,114 @@ name: "topas_gencons" -description: Create fasta consensus with TOPAS toolkit with options to penalize substitutions for typical DNA damage present in ancient DNA +description: Create fasta consensus with TOPAS toolkit with options to penalize substitutions + for typical DNA damage present in ancient DNA keywords: - consensus - fasta - ancient DNA tools: - "topas": - description: "This toolkit allows the efficient manipulation of sequence data in various ways. It is organized into modules: The FASTA processing modules, the FASTQ processing modules, the GFF processing modules and the VCF processing modules." + description: "This toolkit allows the efficient manipulation of sequence data + in various ways. It is organized into modules: The FASTA processing modules, + the FASTQ processing modules, the GFF processing modules and the VCF processing + modules." homepage: "https://github.com/subwaystation/TOPAS" documentation: "https://github.com/subwaystation/TOPAS/wiki/Overview-Modules" tool_dev_url: "https://github.com/subwaystation/TOPAS" doi: "10.1038/s41598-017-17723-1" licence: ["CC-BY"] + identifier: biotools:TOPAS input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called snps - pattern: "*.vcf.gz" - - vcf_indels: - type: file - description: Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper containing the called indels - pattern: "*.vcf.gz" - - reference: - type: file - description: Fasta file of reference genome - pattern: "*.fasta" - - fai: - type: file - description: Optional index for the fasta file of reference genome - pattern: "*.fai" - - vcf_output: - type: boolean - description: Boolean value to indicate if a compressed vcf file with the consensus calls included as SNPs should be produced + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Gzipped compressed vcf file generated with GATK UnifiedGenotyper + containing the called snps + pattern: "*.vcf.gz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf_indels: + type: file + description: Optional gzipped compressed vcf file generated with GATK UnifiedGenotyper + containing the called indels + pattern: "*.vcf.gz" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Fasta file of reference genome + pattern: "*.fasta" + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Optional index for the fasta file of reference genome + pattern: "*.fai" + - - vcf_output: + type: boolean + description: Boolean value to indicate if a compressed vcf file with the consensus + calls included as SNPs should be produced output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Gzipped consensus fasta file with bases under threshold replaced with Ns - pattern: "*.fasta.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta.gz": + type: file + description: Gzipped consensus fasta file with bases under threshold replaced + with Ns + pattern: "*.fasta.gz" - vcf: - type: file - description: Gzipped vcf file with updated calls for the SNPs used in the consensus generation and for bases under threshold replaced with Ns - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Gzipped vcf file with updated calls for the SNPs used in the consensus + generation and for bases under threshold replaced with Ns + pattern: "*.vcf.gz" - ccf: - type: file - description: Statistics file containing information about the consensus calls in the fasta file - pattern: "*.ccf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ccf": + type: file + description: Statistics file containing information about the consensus calls + in the fasta file + pattern: "*.ccf" - log: - type: file - description: Log file - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log file + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@aidaanva" maintainers: diff --git a/modules/nf-core/toulligqc/meta.yml b/modules/nf-core/toulligqc/meta.yml index 61c69794c292..b269eccf8018 100644 --- a/modules/nf-core/toulligqc/meta.yml +++ b/modules/nf-core/toulligqc/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "toulligqc" description: "A post sequencing QC tool for Oxford Nanopore sequencers" @@ -13,45 +12,64 @@ tools: documentation: https://github.com/GenomiqueENS/toulligQC tool_dev_url: https://github.com/GenomiqueENS/toulligQC licence: ["CECILL-2.1"] + identifier: biotools:ToulligQC input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ontfile: - type: file - description: Input ONT file - pattern: "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ontfile: + type: file + description: Input ONT file + pattern: "*.{fastq,fastq.gz,fq,fq.gz,txt,txt.gz,bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - report_data: - type: file - description: Report data emitted from toulligqc - pattern: "*.data" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.data": + type: file + description: Report data emitted from toulligqc + pattern: "*.data" - report_html: - type: file - description: Report data in html format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/*.html": + type: file + description: Report data in html format + pattern: "*.html" - plots_html: - type: file - description: Plots emitted in html format - pattern: "*.html" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/images/*.html": + type: file + description: Plots emitted in html format + pattern: "*.html" - plotly_js: - type: file - description: Plots emitted from toulligqc - pattern: "plotly.min.js" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*/images/plotly.min.js": + type: file + description: Plots emitted from toulligqc + pattern: "plotly.min.js" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Salome-Brunon" maintainers: diff --git a/modules/nf-core/transdecoder/longorf/meta.yml b/modules/nf-core/transdecoder/longorf/meta.yml index 49f0baeb149a..05225e812c98 100644 --- a/modules/nf-core/transdecoder/longorf/meta.yml +++ b/modules/nf-core/transdecoder/longorf/meta.yml @@ -1,5 +1,6 @@ name: transdecoder_longorf -description: TransDecoder identifies candidate coding regions within transcript sequences. it is used to build gff file. +description: TransDecoder identifies candidate coding regions within transcript sequences. + it is used to build gff file. keywords: - eucaryotes - gff @@ -7,50 +8,76 @@ keywords: - coding tools: - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + description: TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript assembly using + Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat + and Cufflinks. homepage: https://github.com/TransDecoder documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder licence: ["Broad Institute"] + identifier: biotools:TransDecoder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pep: - type: file - description: all ORFs meeting the minimum length criteria, regardless of coding potential. file - pattern: "*.{pep}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.pep: + type: file + description: all ORFs meeting the minimum length criteria, regardless of coding + potential. file + pattern: "*.{pep}" - gff3: - type: file - description: positions of all ORFs as found in the target transcripts. file - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.gff3: + type: file + description: positions of all ORFs as found in the target transcripts. file + pattern: "*.{gff3}" - cds: - type: file - description: the nucleotide coding sequence for all detected ORFs. file - pattern: "*{cds}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.cds: + type: file + description: the nucleotide coding sequence for all detected ORFs. file + pattern: "*{cds}" - dat: - type: file - description: nucleotide frequencies - pattern: "*{dat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output_dir_name}/*.dat: + type: file + description: nucleotide frequencies + pattern: "*{dat}" - folder: - type: directory - description: contains all the files from the run + - ${output_dir_name}: + type: directory + description: contains all the files from the run + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Danilo2771" maintainers: diff --git a/modules/nf-core/transdecoder/predict/meta.yml b/modules/nf-core/transdecoder/predict/meta.yml index b3bd9da1e99c..b6ba5174a64f 100644 --- a/modules/nf-core/transdecoder/predict/meta.yml +++ b/modules/nf-core/transdecoder/predict/meta.yml @@ -1,5 +1,6 @@ name: transdecoder_predict -description: TransDecoder identifies candidate coding regions within transcript sequences. It is used to build gff file. You can use this module after transdecoder_longorf +description: TransDecoder identifies candidate coding regions within transcript sequences. + It is used to build gff file. You can use this module after transdecoder_longorf keywords: - eukaryotes - gff @@ -7,51 +8,76 @@ keywords: - transcroder tools: - transdecoder: - description: TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. + description: TransDecoder identifies candidate coding regions within transcript + sequences, such as those generated by de novo RNA-Seq transcript assembly using + Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat + and Cufflinks. homepage: https://github.com/TransDecoder documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder licence: ["Broad Institute"] + identifier: biotools:TransDecoder input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: fasta file - pattern: "*.{fasta}" - - fold: - type: directory - description: Output from the module transdecoder_longorf - pattern: "*" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: fasta file + pattern: "*.{fasta}" + - - fold: + type: directory + description: Output from the module transdecoder_longorf + pattern: "*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - pep: - type: file - description: All ORFs meeting the minimum length criteria, regardless of coding potential - pattern: "*.{pep}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.pep": + type: file + description: All ORFs meeting the minimum length criteria, regardless of coding + potential + pattern: "*.{pep}" - gff3: - type: file - description: Positions of all ORFs as found in the target transcripts - pattern: "*.{gff3}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.gff3": + type: file + description: Positions of all ORFs as found in the target transcripts + pattern: "*.{gff3}" - cds: - type: file - description: the nucleotide coding sequence for all detected ORFs - pattern: "*{cds}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.cds": + type: file + description: the nucleotide coding sequence for all detected ORFs + pattern: "*{cds}" - bed: - type: file - description: bed file - pattern: "*{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.transdecoder.bed": + type: file + description: bed file + pattern: "*{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Danilo2771" maintainers: diff --git a/modules/nf-core/trimgalore/meta.yml b/modules/nf-core/trimgalore/meta.yml index e649088cee0a..576cb4c59632 100644 --- a/modules/nf-core/trimgalore/meta.yml +++ b/modules/nf-core/trimgalore/meta.yml @@ -14,50 +14,77 @@ tools: homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. - pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*{3prime,5prime,trimmed,val}*.fq.gz": + type: file + description: | + List of input adapter trimmed FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. + pattern: "*{3prime,5prime,trimmed,val}*.fq.gz" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*report.txt": + type: file + description: Trim Galore! trimming report + pattern: "*_{report.txt}" - unpaired: - type: file - description: | - FastQ files containing unpaired reads from read 1 or read 2 - pattern: "*unpaired*.fq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*unpaired*.fq.gz": + type: file + description: | + FastQ files containing unpaired reads from read 1 or read 2 + pattern: "*unpaired*.fq.gz" - html: - type: file - description: FastQC report (optional) - pattern: "*_{fastqc.html}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.html": + type: file + description: FastQC report (optional) + pattern: "*_{fastqc.html}" - zip: - type: file - description: FastQC report archive (optional) - pattern: "*_{fastqc.zip}" - - log: - type: file - description: Trim Galore! trimming report - pattern: "*_{report.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.zip": + type: file + description: FastQC report archive (optional) + pattern: "*_{fastqc.zip}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@ewels" diff --git a/modules/nf-core/trimmomatic/meta.yml b/modules/nf-core/trimmomatic/meta.yml index 2d38bf50f393..e74014d5d97b 100644 --- a/modules/nf-core/trimmomatic/meta.yml +++ b/modules/nf-core/trimmomatic/meta.yml @@ -11,47 +11,74 @@ tools: documentation: "https://github.com/usadellab/Trimmomatic" doi: "10.1093/bioinformatics/btu170" licence: ["GPL v3"] + identifier: biotools:trimmomatic input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively. - pattern: "*.fastq.gz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Input FastQ files of size 1 or 2 for single-end and paired-end data, respectively. + pattern: "*.fastq.gz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - trimmed_reads: - type: file - description: The trimmed/modified paired end fastq reads - pattern: "*.paired.trim*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paired.trim*.fastq.gz": + type: file + description: The trimmed/modified paired end fastq reads + pattern: "*.paired.trim*.fastq.gz" - unpaired_reads: - type: file - description: The trimmed/modified unpaired end fastq reads - pattern: "*.unpaired.trim_*.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unpaired.trim_*.fastq.gz": + type: file + description: The trimmed/modified unpaired end fastq reads + pattern: "*.unpaired.trim_*.fastq.gz" - trim_log: - type: file - description: trimmomatic log file, from the trim_log parameter - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_trim.log": + type: file + description: trimmomatic log file, from the trim_log parameter + pattern: "*.log" - out_log: - type: file - description: log of output from the standard out - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_out.log": + type: file + description: log of output from the standard out + pattern: "*.log" - summary: - type: file - description: trimmomatic summary file of surviving and dropped reads - pattern: "*.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.summary": + type: file + description: trimmomatic summary file of surviving and dropped reads + pattern: "*.summary" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alyssa-ab" maintainers: diff --git a/modules/nf-core/trinity/meta.yml b/modules/nf-core/trinity/meta.yml index 963043240d5f..564ed65d353d 100644 --- a/modules/nf-core/trinity/meta.yml +++ b/modules/nf-core/trinity/meta.yml @@ -13,35 +13,44 @@ tools: tool_dev_url: "https://github.com/trinityrnaseq/trinityrnaseq/" doi: "10.1038/nbt.1883" licence: ["BSD-3-clause"] + identifier: biotools:trinity input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input fasta/fastq reads to be assembled into a transcriptome. - pattern: "*.{fa|fasta|fq|fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input fasta/fastq reads to be assembled into a transcriptome. + pattern: "*.{fa|fasta|fq|fastq}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - transcript_fasta: - type: file - description: de novo assembled transcripts fasta file compressed - pattern: "*.fa.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fa.gz": + type: file + description: de novo assembled transcripts fasta file compressed + pattern: "*.fa.gz" - log: - type: file - description: Log from trinity - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Log from trinity + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@timslittle" - "@gallvp" diff --git a/modules/nf-core/trust4/meta.yml b/modules/nf-core/trust4/meta.yml index 89bc4d296798..da2a5ff43fc1 100644 --- a/modules/nf-core/trust4/meta.yml +++ b/modules/nf-core/trust4/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "trust4" description: Run TRUST4 on RNA-seq data @@ -13,62 +12,139 @@ tools: documentation: "https://github.com/liulab-dfci/TRUST4" tool_dev_url: "https://github.com/liulab-dfci/TRUST4" licence: ["GPL v3"] + identifier: biotools:trust4 input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - bam: - type: file - description: BAM file from bulk or single-cell RNA-seq data - pattern: "*.bam" - - reads: - type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively - - fasta: - type: file - description: Path to the fasta file coordinate and sequence of V/D/J/C genes - - ref: - type: file - description: Path to detailed V/D/J/C gene reference file, such as from IMGT database. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: BAM file from bulk or single-cell RNA-seq data + pattern: "*.bam" + - reads: + type: file + description: List of input FastQ files of size 1 and 2 for single-end and paired-end + data, respectively + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Path to the fasta file coordinate and sequence of V/D/J/C genes + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vdj_reference: + type: file + description: reference file of V/D/J genes + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - barcode_read: + type: file + description: barcode read file + - - meta5: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - umi_read: + type: file + description: umi read file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - tsv: - type: file - description: tsv files created by TRUST4 - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: tsv files created by TRUST4 + pattern: "*.tsv" + - airr_files: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_airr.tsv": + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" - airr_tsv: - type: file - description: TRUST4 results in AIRR format - pattern: "*_airr.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - ${meta.id}_airr.tsv: + type: file + description: TRUST4 results in AIRR format + pattern: "*_airr.tsv" - report_tsv: - type: file - description: TRUST4 report in tsv format - pattern: "*_report.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*_report.tsv": + type: file + description: TRUST4 report in tsv format + pattern: "*_report.tsv" - fasta: - type: file - description: Fasta files created by TRUST4 - pattern: "*.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fa": + type: file + description: Fasta files created by TRUST4 + pattern: "*.fa" - out: - type: file - description: Further report files - pattern: "*.out" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.out": + type: file + description: Further report files + pattern: "*.out" - fq: - type: file - description: Fastq files created by TRUST4 - pattern: "*.fq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fq": + type: file + description: Fastq files created by TRUST4 + pattern: "*.fq" + - outs: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "**": + type: file + description: outputt files - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mapo9, @Joaodemeirelles" maintainers: diff --git a/modules/nf-core/truvari/bench/meta.yml b/modules/nf-core/truvari/bench/meta.yml index 1d8cf5bb2373..85f2f97fbc02 100644 --- a/modules/nf-core/truvari/bench/meta.yml +++ b/modules/nf-core/truvari/bench/meta.yml @@ -1,4 +1,3 @@ ---- name: "truvari_bench" description: Given baseline and comparison sets of variants, calculate the recall/precision/f-measure keywords: @@ -15,96 +14,147 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: Input SV VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Input SV VCF index file - pattern: "*.vcf.gz.tbi" - - truth_vcf: - type: file - description: Input VCF file with truth SVs - pattern: "*.vcf.gz" - - tbi: - type: file - description: Input VCF index file with truth SVs - pattern: "*.vcf.gz.tbi" - - bed: - type: file - description: BED file containing regions to compare - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: Reference FASTA file - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing fasta index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: Reference FASTA index file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: Input SV VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Input SV VCF index file + pattern: "*.vcf.gz.tbi" + - truth_vcf: + type: file + description: Input VCF file with truth SVs + pattern: "*.vcf.gz" + - truth_tbi: + type: file + description: Input VCF index file with truth SVs + pattern: "*.vcf.gz.tbi" + - bed: + type: file + description: BED file containing regions to compare + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: Reference FASTA file + pattern: "*.{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing fasta index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: Reference FASTA index file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fn_vcf: - type: file - description: VCF file with false negatives - pattern: "*.fn.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fn.vcf.gz": + type: file + description: VCF file with false negatives + pattern: "*.fn.vcf.gz" - fn_tbi: - type: file - description: VCF index file with false negatives - pattern: "*.fn.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fn.vcf.gz.tbi": + type: file + description: VCF index file with false negatives + pattern: "*.fn.vcf.gz.tbi" - fp_vcf: - type: file - description: VCF file with false positives - pattern: "*.fp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fp.vcf.gz": + type: file + description: VCF file with false positives + pattern: "*.fp.vcf.gz" - fp_tbi: - type: file - description: VCF index file with false positives - pattern: "*.fp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.fp.vcf.gz.tbi": + type: file + description: VCF index file with false positives + pattern: "*.fp.vcf.gz.tbi" - tp_base_vcf: - type: file - description: VCF file with base true positives - pattern: "*.tp-base.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-base.vcf.gz": + type: file + description: VCF file with base true positives + pattern: "*.tp-base.vcf.gz" - tp_base_tbi: - type: file - description: VCF index file with base true positives - pattern: "*.tp-base.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-base.vcf.gz.tbi": + type: file + description: VCF index file with base true positives + pattern: "*.tp-base.vcf.gz.tbi" - tp_comp_vcf: - type: file - description: VCF file with compared true positives - pattern: "*.tp-comp.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-comp.vcf.gz": + type: file + description: VCF file with compared true positives + pattern: "*.tp-comp.vcf.gz" - tp_comp_tbi: - type: file - description: VCF index file with compared true positives - pattern: "*.tp-comp.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.tp-comp.vcf.gz.tbi": + type: file + description: VCF index file with compared true positives + pattern: "*.tp-comp.vcf.gz.tbi" - summary: - type: file - description: Summary JSON file with results from the benchmark - pattern: "*.summary.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.summary.json": + type: file + description: Summary JSON file with results from the benchmark + pattern: "*.summary.json" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/truvari/consistency/meta.yml b/modules/nf-core/truvari/consistency/meta.yml index 6e3baf863fa6..9a7c6fe1c48d 100644 --- a/modules/nf-core/truvari/consistency/meta.yml +++ b/modules/nf-core/truvari/consistency/meta.yml @@ -14,30 +14,33 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - vcfs: - type: file - description: two or more VCF files to compare - pattern: "*.{vcf,gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - vcfs: + type: file + description: two or more VCF files to compare + pattern: "*.{vcf,gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - consistency: - type: file - description: Output report in txt or json format - pattern: "*.{txt,json}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.{txt,json}": + type: file + description: Output report in txt or json format + pattern: "*.{txt,json}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/truvari/segment/meta.yml b/modules/nf-core/truvari/segment/meta.yml index eb554706856b..cf5ab12552de 100644 --- a/modules/nf-core/truvari/segment/meta.yml +++ b/modules/nf-core/truvari/segment/meta.yml @@ -14,30 +14,33 @@ tools: tool_dev_url: "https://github.com/ACEnglish/truvari" doi: "10.1186/s13059-022-02840-6" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - vcf: - type: file - description: Input VCF file - pattern: "*.{vcf,gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - vcf: + type: file + description: Input VCF file + pattern: "*.{vcf,gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Segmented VCF file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.vcf": + type: file + description: Segmented VCF file + pattern: "*.{vcf}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kubranarci" maintainers: diff --git a/modules/nf-core/trycycler/cluster/meta.yml b/modules/nf-core/trycycler/cluster/meta.yml index a17357b93412..ba5539e61e8c 100644 --- a/modules/nf-core/trycycler/cluster/meta.yml +++ b/modules/nf-core/trycycler/cluster/meta.yml @@ -8,47 +8,41 @@ keywords: - genomics tools: - "trycycler": - description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + description: Trycycler is a tool for generating consensus long-read assemblies + for bacterial genomes homepage: https://github.com/rrwick/Trycycler documentation: https://github.com/rrwick/Trycycler/wiki doi: 10.1186/s13059-021-02483-z licence: ["GPL v3"] + identifier: biotools:trycycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Long-read FASTQ file, optionally gzip compressed - - - assemblies: - type: file - description: Input assemblies whose contigs will be clustered - - - out_dir: - type: directory - description: Output directory for clustering results - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - contigs: + type: file + description: Contigs file + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - cluster_dir: - type: directory - description: Output directory containing clustering results - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*": + type: directory + description: Output directory containing clustering results - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@watsonar" maintainers: diff --git a/modules/nf-core/trycycler/subsample/meta.yml b/modules/nf-core/trycycler/subsample/meta.yml index 38c7f9b232f4..5a0fed8ff412 100644 --- a/modules/nf-core/trycycler/subsample/meta.yml +++ b/modules/nf-core/trycycler/subsample/meta.yml @@ -6,44 +6,39 @@ keywords: - genomics tools: - "trycycler": - description: Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes + description: Trycycler is a tool for generating consensus long-read assemblies + for bacterial genomes homepage: https://github.com/rrwick/Trycycler documentation: https://github.com/rrwick/Trycycler/wiki doi: 10.1186/s13059-021-02483-z licence: ["GPL v3"] + identifier: biotools:trycycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - reads: - type: file - description: Long-read FASTQ file, optionally gzip compressed - - - out_dir: - type: directory - description: Output directory for subsampled read sets - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Long-read FASTQ file, optionally gzip compressed output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - subreads: - type: file - description: Subsampled read sets - pattern: "*.{fastq.gz}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*/*.fastq.gz": + type: file + description: Subsampled read sets + pattern: "*.{fastq.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@watsonar" maintainers: diff --git a/modules/nf-core/tsebra/meta.yml b/modules/nf-core/tsebra/meta.yml index 18660d49e175..b7808efe05e9 100644 --- a/modules/nf-core/tsebra/meta.yml +++ b/modules/nf-core/tsebra/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tsebra" -description: Transcript Selector for BRAKER TSEBRA combines gene predictions by selecing transcripts based on their extrisic evidence support +description: Transcript Selector for BRAKER TSEBRA combines gene predictions by selecing + transcripts based on their extrisic evidence support keywords: - genomics - transcript @@ -11,55 +11,66 @@ keywords: - evidence tools: - "tsebra": - description: TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons + description: TSEBRA is a combiner tool that selects transcripts from gene predictions + based on the support by extrisic evidence in form of introns and start/stop + codons homepage: "https://github.com/Gaius-Augustus/TSEBRA" documentation: "https://github.com/Gaius-Augustus/TSEBRA" tool_dev_url: "https://github.com/Gaius-Augustus/TSEBRA" doi: "10.1186/s12859-021-04482-0" licence: ["Artistic-2.0"] + identifier: biotools:tsebra input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - gtfs: - type: list - description: List of gene prediction files in gtf - pattern: "*.gtf" - - hints_files: - type: list - description: List of files containing extrinsic evidence in gff - pattern: "*.gff" - - keep_gtfs: - type: list - description: | - List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all - transcripts from these gene sets are included in the output - pattern: "*.gtf" - - config: - type: file - description: Configuration file that sets the parameter for TSEBRA - pattern: "*.cfg" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - gtfs: + type: list + description: List of gene prediction files in gtf + pattern: "*.gtf" + - - hints_files: + type: list + description: List of files containing extrinsic evidence in gff + pattern: "*.gff" + - - keep_gtfs: + type: list + description: | + List of gene prediction files in gtf. These gene sets are used the same way as other inputs, but TSEBRA ensures that all + transcripts from these gene sets are included in the output + pattern: "*.gtf" + - - config: + type: file + description: Configuration file that sets the parameter for TSEBRA + pattern: "*.cfg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tsebra_gtf: - type: file - description: Output file for the combined gene predictions in gtf - pattern: "*.gtf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.gtf": + type: file + description: Output file for the combined gene predictions in gtf + pattern: "*.gtf" - tsebra_scores: - type: file - description: Transcript scores as a table - pattern: "*.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.tsv": + type: file + description: Transcript scores as a table + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@GallVp" maintainers: diff --git a/modules/nf-core/tximeta/tximport/meta.yml b/modules/nf-core/tximeta/tximport/meta.yml index 9ee5fd365d8f..d4c6a5492553 100644 --- a/modules/nf-core/tximeta/tximport/meta.yml +++ b/modules/nf-core/tximeta/tximport/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "tximeta_tximport" description: | @@ -18,102 +17,131 @@ tools: tool_dev_url: "https://github.com/thelovelab/tximeta" doi: "10.1371/journal.pcbi.1007664" licence: ["GPL-2"] + identifier: biotools:tximeta input: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - quants: - type: directory - description: Paths to subdirectories corresponding to - sample-wise runs of Salmon or Kallisto - - meta2: - type: map - description: | - Groovy Map containing reference information related to the species - reference e.g. `[ id:'yeast' ]` - - tx2gene: - type: file - description: A transcript to gene mapping table such as those generated - by custom/tx2gene - pattern: "*.{csv,tsv}" - - meta3: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - - coldata: - type: file - description: | - Optional 'coldata' file equivalent to a sample sheet where the first - column corresponds to the sample names (directory names in the input - salmon/ kallisto results) - pattern: "*.{csv,tsv}" - - quant_type: - type: string - description: Quantification type, 'kallisto' or 'salmon' - + - - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - '"quants/*"': + type: directory + description: Directory containing quantification files + - - meta2: + type: map + description: | + Groovy Map containing reference information related to the species + reference e.g. `[ id:'yeast' ]` + - tx2gene: + type: file + description: A transcript to gene mapping table such as those generated by custom/tx2gene + pattern: "*.{csv,tsv}" + - - quant_type: + type: string + description: Quantification type, 'kallisto' or 'salmon' output: - - meta: - type: map - description: | - Groovy Map containing information related to the experiment as a whole - e.g. `[ id:'SRP123456' ]` - tpm_gene: - type: file - description: | - Abundance (TPM) values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_tpm.tsv" - counts_gene: - type: file - description: | - Count values derived from tximport output after - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*gene_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts.tsv": + type: file + description: | + Count values derived from tximport output after + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*gene_counts.tsv" - counts_gene_length_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'lengthScaledTPM' - pattern: "*gene_counts_length_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_length_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'lengthScaledTPM' + pattern: "*gene_counts_length_scaled.tsv" - counts_gene_scaled: - type: file - description: | - Count values derived from tximport output after summarizeToGene(), with - a 'countsFromAbundance' specification of 'scaledTPM' - pattern: "*gene_counts_scaled.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_counts_scaled.tsv": + type: file + description: | + Count values derived from tximport output after summarizeToGene(), with + a 'countsFromAbundance' specification of 'scaledTPM' + pattern: "*gene_counts_scaled.tsv" - lengths_gene: - type: file - description: | - Length values derived from tximport output after summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*gene_lengths.tsv": + type: file + description: | + Length values derived from tximport output after summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - tpm_transcript: - type: file - description: | - Abundance (TPM) values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_tpm.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_tpm.tsv": + type: file + description: | + Abundance (TPM) values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_tpm.tsv" - counts_transcript: - type: file - description: | - Count values derived from tximport output without - summarizeToGene(), without a 'countsFromAbundance' specification - pattern: "*transcript_counts.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_counts.tsv": + type: file + description: | + Count values derived from tximport output without + summarizeToGene(), without a 'countsFromAbundance' specification + pattern: "*transcript_counts.tsv" - lengths_transcript: - type: file - description: | - Length values derived from tximport output without summarizeToGene(), - without a 'countsFromAbundance' specification - pattern: "*gene_lengths.tsv" + - meta: + type: map + description: | + Groovy Map containing information related to the experiment as a whole + e.g. `[ id:'SRP123456' ]` + - "*transcript_lengths.tsv": + type: file + description: | + Length values derived from tximport output without summarizeToGene(), + without a 'countsFromAbundance' specification + pattern: "*gene_lengths.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@pinin4fjords" maintainers: diff --git a/modules/nf-core/ucsc/bedclip/meta.yml b/modules/nf-core/ucsc/bedclip/meta.yml index 2467a28f2195..9222d31d20b0 100644 --- a/modules/nf-core/ucsc/bedclip/meta.yml +++ b/modules/nf-core/ucsc/bedclip/meta.yml @@ -9,30 +9,36 @@ tools: description: Remove lines from bed file that refer to off-chromosome locations. homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - - sizes: + type: file + description: Chromosome sizes file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedgraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bedGraph": + type: file + description: bedGraph file + pattern: "*.{bedgraph}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml index a60118abe5b6..5d42cbde78cc 100755 --- a/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/meta.yml @@ -12,34 +12,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file - pattern: "*.{bedGraph}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: bedGraph file + pattern: "*.{bedGraph}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigwig: - type: file - description: bigWig file - pattern: "*.{bigWig}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigWig": + type: file + description: bigWig file + pattern: "*.{bigWig}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bedtobigbed/meta.yml b/modules/nf-core/ucsc/bedtobigbed/meta.yml index aae1996f4fc4..6afc3148ef02 100755 --- a/modules/nf-core/ucsc/bedtobigbed/meta.yml +++ b/modules/nf-core/ucsc/bedtobigbed/meta.yml @@ -12,38 +12,41 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: https://genome.ucsc.edu/goldenPath/help/bigBed.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed file - pattern: "*.{bed}" - - sizes: - type: file - description: chromosome sizes file - pattern: "*.{sizes}" - - autosql: - type: file - description: autoSql file to describe the columns of the BED file - pattern: "*.{as}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed file + pattern: "*.{bed}" + - - sizes: + type: file + description: chromosome sizes file + pattern: "*.{sizes}" + - - autosql: + type: file + description: autoSql file to describe the columns of the BED file + pattern: "*.{as}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bigbed: - type: file - description: bigBed file - pattern: "*.{bigBed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bigBed": + type: file + description: bigBed file + pattern: "*.{bigBed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml b/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml index 9b2884477d85..c215f36266c8 100644 --- a/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml +++ b/modules/nf-core/ucsc/bigwigaverageoverbed/meta.yml @@ -10,34 +10,37 @@ tools: homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ documentation: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: bed file - pattern: "*.{bed}" - - bigwig: - type: file - description: bigwig file - pattern: "*.{bigwig,bw}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: bed file + pattern: "*.{bed}" + - - bigwig: + type: file + description: bigwig file + pattern: "*.{bigwig,bw}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - tab: - type: file - description: tab file - pattern: "*.{tab}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tab": + type: file + description: tab file + pattern: "*.{tab}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" maintainers: diff --git a/modules/nf-core/ucsc/gtftogenepred/meta.yml b/modules/nf-core/ucsc/gtftogenepred/meta.yml index 02122e4101e9..cf04154d4a15 100644 --- a/modules/nf-core/ucsc/gtftogenepred/meta.yml +++ b/modules/nf-core/ucsc/gtftogenepred/meta.yml @@ -11,34 +11,43 @@ tools: description: Convert GTF files to GenePred format homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gtf: - type: file - description: GTF file - pattern: "*.{gtf}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gtf: + type: file + description: GTF file + pattern: "*.{gtf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - genepred: - type: file - description: genepred file - pattern: "*.{genepred}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.genepred": + type: file + description: genepred file + pattern: "*.{genepred}" - refflat: - type: file - description: refflat file - pattern: "*.{refflat}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.refflat": + type: file + description: refflat file + pattern: "*.{refflat}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@BarryDigby" - "@anoronh4" diff --git a/modules/nf-core/ucsc/liftover/meta.yml b/modules/nf-core/ucsc/liftover/meta.yml index c1c40d966259..9905b6870a64 100644 --- a/modules/nf-core/ucsc/liftover/meta.yml +++ b/modules/nf-core/ucsc/liftover/meta.yml @@ -9,38 +9,47 @@ tools: description: Move annotations from one assembly to another homepage: http://hgdownload.cse.ucsc.edu/admin/exe/ licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Browser Extensible Data (BED) file - pattern: "*.{bed}" - - chain: - type: file - description: Chain file - pattern: "*.{chain,chain.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Browser Extensible Data (BED) file + pattern: "*.{bed}" + - - chain: + type: file + description: Chain file + pattern: "*.{chain,chain.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software version - pattern: "versions.yml" - lifted: - type: file - description: BED file containing successfully lifted variants - pattern: "*.{lifted.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lifted.bed": + type: file + description: BED file containing successfully lifted variants + pattern: "*.{lifted.bed}" - unlifted: - type: file - description: BED file containing variants that couldn't be lifted - pattern: "*.{unlifted.bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.unlifted.bed": + type: file + description: BED file containing variants that couldn't be lifted + pattern: "*.{unlifted.bed}" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@nebfield" maintainers: diff --git a/modules/nf-core/ucsc/wigtobigwig/meta.yml b/modules/nf-core/ucsc/wigtobigwig/meta.yml index f747648065fd..97bf98b16ad9 100644 --- a/modules/nf-core/ucsc/wigtobigwig/meta.yml +++ b/modules/nf-core/ucsc/wigtobigwig/meta.yml @@ -11,28 +11,35 @@ tools: or bedGraph format) to binary big wig format homepage: http://www.genome.ucsc.edu/goldenPath/help/bigWig.html licence: ["varies; see http://genome.ucsc.edu/license"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - wig: - type: file - description: wig file - pattern: "*.{wig}" - - chromsizes: - type: file - description: chromosome sizes file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - wig: + type: file + description: wig file + pattern: "*.{wig}" + - - sizes: + type: file + description: Chromosome sizes file output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bw: - type: file - description: bigwig file - pattern: "*.{bw}" + - meta: + type: file + description: bigwig file + pattern: "*.{bw}" + - "*.bw": + type: file + description: bigwig file + pattern: "*.{bw}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jianhong" - "@projectoriented" diff --git a/modules/nf-core/ultra/align/environment.yml b/modules/nf-core/ultra/align/environment.yml index 39d65509991f..23c5097c14f0 100644 --- a/modules/nf-core/ultra/align/environment.yml +++ b/modules/nf-core/ultra/align/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::ultra_bioinformatics=0.1 - bioconda::samtools=1.17 + - bioconda::ultra_bioinformatics=0.1 diff --git a/modules/nf-core/ultra/align/meta.yml b/modules/nf-core/ultra/align/meta.yml index 79b9e30aadb6..bb5298d1451a 100644 --- a/modules/nf-core/ultra/align/meta.yml +++ b/modules/nf-core/ultra/align/meta.yml @@ -1,5 +1,6 @@ name: "ultra_align" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Map reads on genome +description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection + - Map reads on genome keywords: - uLTRA - align @@ -15,42 +16,45 @@ tools: tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A fasta or fastq file of reads to align - pattern: "*.{fa,fasta,fastq}" - - genome: - type: file - description: A fasta file of reference genome - pattern: "*.{fa,fasta}" - - pickle: - type: file - description: Pickle files generated by uLTRA index - pattern: "*.pickle" - - db: - type: file - description: Database generated by uLTRA index - pattern: "*.db" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A fasta or fastq file of reads to align + pattern: "*.{fa,fasta,fastq}" + - - genome: + type: file + description: A fasta file of reference genome + pattern: "*.{fa,fasta}" + - - pickle: + type: file + description: Pickle files generated by uLTRA index + pattern: "*.pickle" + - db: + type: file + description: Database generated by uLTRA index + pattern: "*.db" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: The aligned reads in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: The aligned reads in bam format + pattern: "*.bam" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/index/meta.yml b/modules/nf-core/ultra/index/meta.yml index 1bf59abab07b..236bcc2d5882 100644 --- a/modules/nf-core/ultra/index/meta.yml +++ b/modules/nf-core/ultra/index/meta.yml @@ -1,5 +1,6 @@ name: "ultra_index" -description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection - Index gtf file for reads alignment +description: uLTRA aligner - A wrapper around minimap2 to improve small exon detection + - Index gtf file for reads alignment keywords: - uLTRA - index @@ -15,28 +16,31 @@ tools: tool_dev_url: "https://github.com/ksahlin/uLTRA" doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - fasta: - type: file - description: A fasta file of the genome to use as reference for mapping - pattern: "*.{fasta, fa}" - - gtf: - type: file - description: An annotation file of the reference genome in GTF format - pattern: "*.gtf" + - - fasta: + type: file + description: A fasta file of the genome to use as reference for mapping + pattern: "*.{fasta, fa}" + - - gtf: + type: file + description: An annotation file of the reference genome in GTF format + pattern: "*.gtf" output: + - index: + - "*.pickle": + type: file + description: Index file + pattern: "*.pickle" + - "*.db": + type: file + description: Index database + pattern: "*.db" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - pickle: - type: file - description: Index files generated by uLTRA index - pattern: "*.pickle" - - pickle: - type: file - description: database file generated by uLTRA index - pattern: "*.db" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" maintainers: diff --git a/modules/nf-core/ultra/pipeline/meta.yml b/modules/nf-core/ultra/pipeline/meta.yml index 7e51a5e63a1b..4c26b6d137c4 100644 --- a/modules/nf-core/ultra/pipeline/meta.yml +++ b/modules/nf-core/ultra/pipeline/meta.yml @@ -15,38 +15,41 @@ tools: tool_dev_url: https://github.com/ksahlin/uLTRA doi: "10.1093/bioinformatics/btab540" licence: ["GNU GPLV3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: A fasta or fastq file of reads to align - pattern: "*.{fasta,fastq}" - - genome: - type: file - description: fasta file of reference genome - pattern: "*.fasta" - - gtf: - type: file - description: A annotation of use the genome - pattern: "*.gtf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: A fasta or fastq file of reads to align + pattern: "*.{fasta,fastq}" + - - genome: + type: file + description: fasta file of reference genome + pattern: "*.fasta" + - - gtf: + type: file + description: A annotation of use the genome + pattern: "*.gtf" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - sam: - type: file - description: The aligned reads in sam format - pattern: "*.sam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sam": + type: file + description: The aligned reads in sam format + pattern: "*.sam" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sguizard" - "@lassefolkersen" diff --git a/modules/nf-core/ultraplex/meta.yml b/modules/nf-core/ultraplex/meta.yml index 66659aac6690..581c64c12d83 100644 --- a/modules/nf-core/ultraplex/meta.yml +++ b/modules/nf-core/ultraplex/meta.yml @@ -1,5 +1,6 @@ name: "ultraplex" -description: Ultraplex is an all-in-one software package for processing and demultiplexing fastq files. +description: Ultraplex is an all-in-one software package for processing and demultiplexing + fastq files. keywords: - demultiplex - fastq @@ -12,38 +13,53 @@ tools: tool_dev_url: https://github.com/ulelab/ultraplex doi: "10.5281/zenodo.465128" licence: ["MIT"] + identifier: biotools:ultraplex input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: Zipped FASTQ file - pattern: "*.{fastq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ file(s) to demultiplex + - - barcode_file: + type: file + description: FASTQ file containing barcode sequences + - - adapter_seq: + type: string + description: adapter sequence output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fastq: - type: file - description: Demultiplexed sample FASTQ files - pattern: "*[!no_match].fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*[!no_match].fastq.gz": + type: file + description: Demultiplexed sample FASTQ files + pattern: "*[!no_match].fastq.gz" - no_match_fastq: - type: file - description: FASTQ file containing reads that could not be demultiplexed - pattern: "*no_match.fastq.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*no_match.fastq.gz": + type: file + description: FASTQ file containing reads that could not be demultiplexed + pattern: "*no_match.fastq.gz" - report: - type: file - description: File containing demultiplexing log - pattern: "*.log" + - "*.log": + type: file + description: File containing demultiplexing log + pattern: "*.log" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CharlotteAnne" - "@oscarwilkins" diff --git a/modules/nf-core/umicollapse/meta.yml b/modules/nf-core/umicollapse/meta.yml index c1361f9ad12d..8b366c24438c 100644 --- a/modules/nf-core/umicollapse/meta.yml +++ b/modules/nf-core/umicollapse/meta.yml @@ -1,58 +1,76 @@ ---- name: "umicollapse" -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umicollapse - deduplication - genomics tools: - "umicollapse": - description: "UMICollapse contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs)." + description: "UMICollapse contains tools for dealing with Unique Molecular Identifiers + (UMIs)/Random Molecular Tags (RMTs)." homepage: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" documentation: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" tool_dev_url: "https://github.com/Daniel-Liu-c0deb0t/UMICollapse" doi: "10.7717/peerj.8275" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input. - pattern: "*.{bai}" - - mode: - type: string - description: | - Selects the mode of Umicollapse - either fastq or bam need to be provided. - pattern: "{fastq,bam}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: Input bam file + pattern: "*.bam" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. Optionally can be skipped using [] when using FastQ input. + pattern: "*.{bai}" + - - mode: + type: string + description: | + Selects the mode of Umicollapse - either fastq or bam need to be provided. + pattern: "{fastq,bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" + - fastq: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*dedup*fastq.gz": + type: file + description: FASTQ file with deduplicated UMIs. + pattern: "*dedup*fastq.gz" - log: - type: file - description: A log file with the deduplication statistics. - pattern: "*_{UMICollapse.log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_UMICollapse.log": + type: file + description: A log file with the deduplication statistics. + pattern: "*_{UMICollapse.log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CharlotteAnne" - "@chris-cheshire" diff --git a/modules/nf-core/umitools/dedup/meta.yml b/modules/nf-core/umitools/dedup/meta.yml index 38d3fd46542f..6cbd84116d5c 100644 --- a/modules/nf-core/umitools/dedup/meta.yml +++ b/modules/nf-core/umitools/dedup/meta.yml @@ -1,5 +1,6 @@ name: umitools_dedup -description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. +description: Deduplicate reads based on the mapping co-ordinate and the UMI attached + to the read. keywords: - umitools - deduplication @@ -7,60 +8,89 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - get_output_stats: - type: boolean - description: | - Whether or not to generate output stats. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - get_output_stats: + type: boolean + description: | + Whether or not to generate output stats. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - tsv_edit_distance: - type: file - description: Reports the (binned) average edit distance between the UMIs at each position. - pattern: "*edit_distance.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*edit_distance.tsv": + type: file + description: Reports the (binned) average edit distance between the UMIs at + each position. + pattern: "*edit_distance.tsv" - tsv_per_umi: - type: file - description: UMI-level summary statistics. - pattern: "*per_umi.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_umi.tsv": + type: file + description: UMI-level summary statistics. + pattern: "*per_umi.tsv" - tsv_umi_per_position: - type: file - description: Tabulates the counts for unique combinations of UMI and position. - pattern: "*per_position.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*per_position.tsv": + type: file + description: Tabulates the counts for unique combinations of UMI and position. + pattern: "*per_position.tsv" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/extract/meta.yml b/modules/nf-core/umitools/extract/meta.yml index 7695b2717622..648ffbd26f38 100644 --- a/modules/nf-core/umitools/extract/meta.yml +++ b/modules/nf-core/umitools/extract/meta.yml @@ -1,5 +1,6 @@ name: umitools_extract -description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place +description: Extracts UMI barcode from a read and add it to the read name, leaving + any sample barcode in place keywords: - UMI - barcode @@ -8,38 +9,49 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: "MIT" + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FASTQ files whose UMIs will be extracted. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - reads: - type: file - description: > - Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. - pattern: "*.{fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq.gz": + type: file + description: > + Extracted FASTQ files. | For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. + | For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" - log: - type: file - description: Logfile for umi_tools - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Logfile for umi_tools + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@grst" diff --git a/modules/nf-core/umitools/group/meta.yml b/modules/nf-core/umitools/group/meta.yml index c989836f7fa5..e755684aa82c 100644 --- a/modules/nf-core/umitools/group/meta.yml +++ b/modules/nf-core/umitools/group/meta.yml @@ -9,52 +9,73 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" - - create_bam: - type: boolean - description: | - Whether or not to create a read group tagged BAM file. - - get_group_info: - type: boolean - description: | - Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" + - - create_bam: + type: boolean + description: | + Whether or not to create a read group tagged BAM file. + - - get_group_info: + type: boolean + description: | + Whether or not to generate the flatfile describing the read groups, see docs for complete info of all columns output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: a read group tagged BAM file. - pattern: "${prefix}.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.bam: + type: file + description: a read group tagged BAM file. + pattern: "${prefix}.{bam}" - tsv: - type: file - description: Flatfile describing the read groups, see docs for complete info of all columns - pattern: "*.{tsv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tsv": + type: file + description: Flatfile describing the read groups, see docs for complete info + of all columns + pattern: "*.{tsv}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Joon-Klaps" maintainers: diff --git a/modules/nf-core/umitools/prepareforrsem/meta.yml b/modules/nf-core/umitools/prepareforrsem/meta.yml index 8b85366cc4ad..3e8ead2576ed 100644 --- a/modules/nf-core/umitools/prepareforrsem/meta.yml +++ b/modules/nf-core/umitools/prepareforrsem/meta.yml @@ -8,43 +8,53 @@ keywords: tools: - umi_tools: description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random + Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes documentation: https://umi-tools.readthedocs.io/en/latest/ license: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - bam: - type: file - description: Prepared BAM file. - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Prepared BAM file. + pattern: "*.{bam}" - log: - type: file - description: File with logging information - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: File with logging information + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" - "@pinin4fjords" diff --git a/modules/nf-core/unicycler/meta.yml b/modules/nf-core/unicycler/meta.yml index 406b14703ed0..5bd8583fc180 100644 --- a/modules/nf-core/unicycler/meta.yml +++ b/modules/nf-core/unicycler/meta.yml @@ -13,47 +13,58 @@ tools: tool_dev_url: https://github.com/rrwick/Unicycler doi: 10.1371/journal.pcbi.1005595 licence: ["GPL v3"] + identifier: biotools:unicycler input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - shortreads: - type: file - description: | - List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - longreads: - type: file - description: | - List of input FastQ files of size 1, PacBio or Nanopore long reads. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - shortreads: + type: file + description: | + List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - longreads: + type: file + description: | + List of input FastQ files of size 1, PacBio or Nanopore long reads. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds: - type: file - description: Fasta file containing scaffolds - pattern: "*.{scaffolds.fa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.scaffolds.fa.gz": + type: file + description: Fasta file containing scaffolds + pattern: "*.{scaffolds.fa.gz}" - gfa: - type: file - description: gfa file containing assembly - pattern: "*.{assembly.gfa.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.assembly.gfa.gz": + type: file + description: gfa file containing assembly + pattern: "*.{assembly.gfa.gz}" - log: - type: file - description: unicycler log file - pattern: "*.{log}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: unicycler log file + pattern: "*.{log}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@JoseEspinosa" - "@drpatelh" diff --git a/modules/nf-core/universc/meta.yml b/modules/nf-core/universc/meta.yml index 92a46bc6f4b3..af350b380ede 100644 --- a/modules/nf-core/universc/meta.yml +++ b/modules/nf-core/universc/meta.yml @@ -1,5 +1,6 @@ name: "universc" -description: Module to run UniverSC an open-source pipeline to demultiplex and process single-cell RNA-Seq data +description: Module to run UniverSC an open-source pipeline to demultiplex and process + single-cell RNA-Seq data keywords: - demultiplex - align @@ -9,31 +10,42 @@ keywords: - umi tools: - "universc": - description: "UniverSC: a flexible cross-platform single-cell data processing pipeline" + description: "UniverSC: a flexible cross-platform single-cell data processing + pipeline" homepage: "https://hub.docker.com/r/tomkellygenetics/universc" documentation: "https://raw.githubusercontent.com/minoda-lab/universc/master/man/launch_universc.sh" tool_dev_url: "https://github.com/minoda-lab/universc" doi: "10.1101/2021.01.19.427209" licence: ["GPL-3.0-or-later"] + identifier: biotools:universc input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FASTQ or FASTQ.GZ file, list of 2 files for paired-end data + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - reference: + type: file + description: Reference genome file output: - outs: - type: file - description: Files containing the outputs of Cell Ranger - pattern: "sample-${meta.id}/outs/*" + - meta: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "sample-${meta.id}/outs/*" + - sample-${meta.id}/outs/*: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "sample-${meta.id}/outs/*" - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@kbattenb" - "@tomkellygenetics" diff --git a/modules/nf-core/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f55da..290346b3fa7c 100644 --- a/modules/nf-core/untar/meta.yml +++ b/modules/nf-core/untar/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - untar: - type: directory - description: Directory containing contents of archive - pattern: "*/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/untarfiles/meta.yml b/modules/nf-core/untarfiles/meta.yml index 3810882641b6..1d23eb257217 100644 --- a/modules/nf-core/untarfiles/meta.yml +++ b/modules/nf-core/untarfiles/meta.yml @@ -10,30 +10,33 @@ tools: Extract tar.gz files. documentation: https://www.gnu.org/software/tar/manual/ licence: ["GPL-3.0-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - files: - type: string - description: A list containing references to individual archive files - pattern: "*/**" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/**: + type: string + description: A list containing references to individual archive files + pattern: "*/**" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/unzip/meta.yml b/modules/nf-core/unzip/meta.yml index e8e377e2af85..426fccb76b0d 100644 --- a/modules/nf-core/unzip/meta.yml +++ b/modules/nf-core/unzip/meta.yml @@ -7,35 +7,39 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: ZIP file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: ZIP file + pattern: "*.zip" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - unzipped_archive: - type: directory - description: Directory contents of the unzipped archive - pattern: "${archive.baseName}/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/: + type: directory + description: Directory contents of the unzipped archive + pattern: "${archive.baseName}/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" maintainers: diff --git a/modules/nf-core/unzipfiles/meta.yml b/modules/nf-core/unzipfiles/meta.yml index 20020ad651fc..7735c0cd63b0 100644 --- a/modules/nf-core/unzipfiles/meta.yml +++ b/modules/nf-core/unzipfiles/meta.yml @@ -7,35 +7,39 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: ZIP file - pattern: "*.zip" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: ZIP file + pattern: "*.zip" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - files: - type: list - description: A list containing references to individual archive files - pattern: "*/**" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}/**: + type: list + description: A list containing references to individual archive files + pattern: "*/**" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@pinin4fjords" diff --git a/modules/nf-core/upd/meta.yml b/modules/nf-core/upd/meta.yml index 9375d56d4c8b..a0e900632894 100644 --- a/modules/nf-core/upd/meta.yml +++ b/modules/nf-core/upd/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "upd" description: Simple software to call UPD regions from germline exome/wgs trios. @@ -13,31 +12,34 @@ tools: documentation: https://github.com/bjhall/upd tool_dev_url: https://github.com/bjhall/upd licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bed: - type: file - description: BED file - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED file + pattern: "*.{bed}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@hrydbeck" maintainers: diff --git a/modules/nf-core/upp/align/meta.yml b/modules/nf-core/upp/align/meta.yml index a5470c2c087e..08781fa6fc32 100644 --- a/modules/nf-core/upp/align/meta.yml +++ b/modules/nf-core/upp/align/meta.yml @@ -13,44 +13,48 @@ tools: tool_dev_url: "https://github.com/smirarab/sepp/tree/master" doi: "10.1093/bioinformatics/btad007" licence: ["GPL v3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - - fasta: - type: file - description: Input sequences in FASTA format - pattern: "*.{fa,fasta}" - - meta2: - type: map - description: | - Groovy Map containing tree information - e.g. `[ id:'test_tree']` - - tree: - type: file - description: Input guide tree in Newick format - pattern: "*.{dnd}" - - compress: - type: boolean - description: Flag representing whether the output MSA should be compressed. Set to true to enable/false to disable compression. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test']` - alignment: - type: file - description: Alignment file, in FASTA format. May be gzipped or uncompressed, depending on if compress is set to true or false - pattern: "*.aln{.gz,}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file, in FASTA format. May be gzipped or uncompressed, + depending on if compress is set to true or false + pattern: "*.aln{.gz,}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@luisas" maintainers: diff --git a/modules/nf-core/vardictjava/meta.yml b/modules/nf-core/vardictjava/meta.yml index 5c2fc921aca6..801db6fa7f3f 100644 --- a/modules/nf-core/vardictjava/meta.yml +++ b/modules/nf-core/vardictjava/meta.yml @@ -14,56 +14,60 @@ tools: tool_dev_url: "https://github.com/AstraZeneca-NGS/VarDictJava" doi: "10.1093/nar/gkw227 " licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bams: - type: file - description: One or two BAM files. Supply two BAM files to run Vardict in paired mode. - pattern: "*.bam" - - bais: - type: file - description: Index/indices of the BAM file(s) - pattern: "*.bai" - - bed: - type: file - description: BED with the regions of interest - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA of the reference genome - pattern: "*.{fa,fasta}" - - meta3: - type: map - description: | - Groovy Map containing fasta information - e.g. [ id:'test', single_end:false ] - - fasta_fai: - type: file - description: The index of the FASTA of the reference genome - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bams: + type: file + description: One or two BAM files. Supply two BAM files to run Vardict in paired + mode. + pattern: "*.bam" + - bais: + type: file + description: Index/indices of the BAM file(s) + pattern: "*.bai" + - bed: + type: file + description: BED with the regions of interest + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA of the reference genome + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing fasta information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the FASTA of the reference genome + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: VCF file output - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: VCF file output + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/variantbam/meta.yml b/modules/nf-core/variantbam/meta.yml index 817dccb5c245..d470d7a4df9e 100644 --- a/modules/nf-core/variantbam/meta.yml +++ b/modules/nf-core/variantbam/meta.yml @@ -9,36 +9,40 @@ keywords: - subsample bam tools: - variantbam: - description: Filtering and profiling of next-generational sequencing data using region-specific rules + description: Filtering and profiling of next-generational sequencing data using + region-specific rules homepage: https://github.com/walaj/VariantBam documentation: https://github.com/walaj/VariantBam#table-of-contents tool_dev_url: https://github.com/walaj/VariantBam doi: 10.1093/bioinformatics/btw111 licence: ["Apache-2.0"] + identifier: biotools:variantbam input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Filtered or downsampled BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bam": + type: file + description: Filtered or downsampled BAM file + pattern: "*.{bam}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@bjohnnyd" maintainers: diff --git a/modules/nf-core/varlociraptor/callvariants/meta.yml b/modules/nf-core/varlociraptor/callvariants/meta.yml index 85ef816d34f3..a72d90c8c3f0 100644 --- a/modules/nf-core/varlociraptor/callvariants/meta.yml +++ b/modules/nf-core/varlociraptor/callvariants/meta.yml @@ -1,65 +1,87 @@ name: "varlociraptor_callvariants" -description: Call variants for a given scenario specified with the varlociraptor calling grammar, preprocessed by varlociraptor preprocessing +description: Call variants for a given scenario specified with the varlociraptor calling + grammar, preprocessed by varlociraptor preprocessing keywords: - observations - variants - calling tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - normal_vcf: - type: file - description: Sorted VCF/BCF file (list) - pattern: "*.{bcf,vcf,vcf.gz}" - - tumor_vcf: - type: file - description: Sorted VCF/BCF file (optional) - pattern: "*.{bcf,bcf.gz,vcf,vcf.gz}" - - scenario: - type: file - description: Yaml file containing scenario information (optional) - pattern: "*.{yml,yaml}" - - scenario_sample: - type: string - description: (List of) sample name(s) to be processed as named in the scenario yml (optional) - pattern: "*.{bcf,vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal_vcf: + type: file + description: Sorted VCF/BCF file (list) + pattern: "*.{bcf,vcf,vcf.gz}" + - tumor_vcf: + type: file + description: Sorted VCF/BCF file (optional) + pattern: "*.{bcf,bcf.gz,vcf,vcf.gz}" + - - scenario: + type: file + description: Yaml file containing scenario information (optional) + pattern: "*.{yml,yaml}" + - - scenario_sample_name: + type: string + description: Sample name for the scenario output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf_gz: - type: file - description: Compressed VCF file containing sample observations - pattern: "*.vcf.gz" - bcf_gz: - type: file - description: BCF file containing sample observations - pattern: "*.bcf.gz" - - vcf: - type: file - description: VCF file containing sample observations - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF file containing sample observations + pattern: "*.bcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file containing sample observations + pattern: "*.vcf.gz" - bcf: - type: file - description: BCF file containing sample observations - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF file containing sample observations + pattern: "*.bcf" + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF file containing sample observations + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml index 624b0754fa39..1c48146ab747 100644 --- a/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml +++ b/modules/nf-core/varlociraptor/estimatealignmentproperties/meta.yml @@ -1,59 +1,65 @@ name: "varlociraptor_estimatealignmentproperties" -description: In order to judge about candidate indel and structural variants, Varlociraptor needs to know about certain properties of the underlying sequencing experiment in combination with the used read aligner. +description: In order to judge about candidate indel and structural variants, Varlociraptor + needs to know about certain properties of the underlying sequencing experiment in + combination with the used read aligner. keywords: - estimation - alignment - variants tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/estimating/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index for reference fasta file (must be with samtools index) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index for reference fasta file (must be with samtools index) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - alignment_properties_json: - type: file - description: File containing alignment properties - pattern: "*.alignment-properties.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.alignment-properties.json": + type: file + description: File containing alignment properties + pattern: "*.alignment-properties.json" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/varlociraptor/preprocess/meta.yml b/modules/nf-core/varlociraptor/preprocess/meta.yml index 7fd3de5bb8f2..0cd13723026c 100644 --- a/modules/nf-core/varlociraptor/preprocess/meta.yml +++ b/modules/nf-core/varlociraptor/preprocess/meta.yml @@ -1,79 +1,106 @@ name: "varlociraptor_preprocess" -description: Obtains per-sample observations for the actual calling process with varlociraptor calls +description: Obtains per-sample observations for the actual calling process with varlociraptor + calls keywords: - observations - variants - preprocessing tools: - "varlociraptor": - description: "Flexible, uncertainty-aware variant calling with parameter free filtration via FDR control." + description: "Flexible, uncertainty-aware variant calling with parameter free + filtration via FDR control." homepage: "https://varlociraptor.github.io/docs/estimating/" documentation: "https://varlociraptor.github.io/docs/calling/" tool_dev_url: "https://github.com/varlociraptor/varlociraptor" doi: "10.1186/s13059-020-01993-6" licence: ["GPL v3"] + identifier: biotools:varlociraptor input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - candidates: - type: file - description: Sorted BCF/VCF file - pattern: "*.{bcf,vcf,vcf.gz}" - - alignment_json: - type: file - description: File containing alignment properties obtained with varlociraptor/estimatealignmentproperties - pattern: "*.json" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Reference fasta file - pattern: "*.{fasta}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: Index for reference fasta file (must be with samtools index) - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index of the BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" + - candidates: + type: file + description: Sorted BCF/VCF file + pattern: "*.{bcf,vcf,vcf.gz}" + - alignment_json: + type: file + description: File containing alignment properties obtained with varlociraptor/estimatealignmentproperties + pattern: "*.json" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference fasta file + pattern: "*.{fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. [ id:'test', single_end:false ] + - fai: + type: file + description: Index for reference fasta file (must be with samtools index) + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - vcf_gz: - type: file - description: Compressed VCF file containing sample observations - pattern: "*.vcf.gz" - bcf_gz: - type: file - description: BCF file containing sample observations - pattern: "*.bcf.gz" - - vcf: - type: file - description: VCF file containing sample observations - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf.gz": + type: file + description: BCF file containing sample observations + pattern: "*.bcf.gz" + - vcf_gz: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file containing sample observations + pattern: "*.vcf.gz" - bcf: - type: file - description: BCF file containing sample observations - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: BCF file containing sample observations + pattern: "*.bcf" + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: VCF file containing sample observations + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FriederikeHanssen" maintainers: diff --git a/modules/nf-core/vcf2cytosure/meta.yml b/modules/nf-core/vcf2cytosure/meta.yml index 2430f1aee416..0c38d9c8de64 100644 --- a/modules/nf-core/vcf2cytosure/meta.yml +++ b/modules/nf-core/vcf2cytosure/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json name: "vcf2cytosure" description: Convert VCF with structural variations to CytoSure format @@ -14,64 +13,65 @@ tools: documentation: "https://github.com/NBISweden/vcf2cytosure" tool_dev_url: "https://github.com/NBISweden/vcf2cytosure" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta2: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - meta4: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - sv_vcf: - type: file - description: VCF file with structural variants - pattern: "*.{vcf,vcf.gz}" - - coverage_bed: - type: file - description: Bed file with coverage data - pattern: "*.bed" - - cns: - type: file - description: CN file from CNVkit, not compatible with coverage_bed file - - snv_vcf: - type: file - description: | - VCF file with SNVs to calculate probe coverage, - not compatible with coverage_bed + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - sv_vcf: + type: file + description: VCF file with structural variants pattern: "*.{vcf,vcf.gz}" - - blacklist_bed: - type: file - description: Bed file with regions to exclude - pattern: "*.bed" - + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - coverage_bed: + type: file + description: Bed file with coverage data + pattern: "*.bed" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - cns: + type: file + description: CN file from CNVkit, not compatible with coverage_bed file + - - meta4: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - snv_vcf: + type: file + description: | + VCF file with SNVs to calculate probe coverage, + not compatible with coverage_bed + pattern: "*.{vcf,vcf.gz}" + - - blacklist_bed: + type: file + description: Bed file with regions to exclude + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - cgh: - type: file - description: SV:s in CytoSure format - pattern: "*.cgh" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.cgh": + type: file + description: SV:s in CytoSure format + pattern: "*.cgh" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jemten" diff --git a/modules/nf-core/vcf2db/meta.yml b/modules/nf-core/vcf2db/meta.yml index b6529a6ae054..48795c216854 100644 --- a/modules/nf-core/vcf2db/meta.yml +++ b/modules/nf-core/vcf2db/meta.yml @@ -11,34 +11,37 @@ tools: documentation: "https://github.com/quinlan-lab/vcf2db" tool_dev_url: "https://github.com/quinlan-lab/vcf2db" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.vcf.gz" - - ped: - type: file - description: PED file - pattern: "*.ped" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.vcf.gz" + - ped: + type: file + description: PED file + pattern: "*.ped" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - db: - type: file - description: Gemini-compatible database file - pattern: "*.db" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.db": + type: file + description: Gemini-compatible database file + pattern: "*.db" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml index b091f2b10153..e5ce08381319 100644 --- a/modules/nf-core/vcf2maf/meta.yml +++ b/modules/nf-core/vcf2maf/meta.yml @@ -13,34 +13,41 @@ tools: tool_dev_url: "https://github.com/mskcc/vcf2maf" doi: "10.5281/zenodo.593251" licence: ["Apache-2.0"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to convert to MAF format. Must be uncompressed. - - vep_cache: - type: file - description: | - Path to VEP cache dir. Required for correct running of VEP. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + vcf to convert to MAF format. Must be uncompressed. + - - fasta: + type: file + description: | + Path to reference genome fasta file. + - - vep_cache: + type: file + description: | + Path to VEP cache dir. Required for correct running of VEP. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - maf: - type: file - description: MAF file produced from VCF - pattern: "*.maf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.maf": + type: file + description: MAF file produced from VCF + pattern: "*.maf" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@adamrtalbot" maintainers: diff --git a/modules/nf-core/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml index 89c781ad1666..18d27127c22c 100644 --- a/modules/nf-core/vcfanno/meta.yml +++ b/modules/nf-core/vcfanno/meta.yml @@ -1,5 +1,6 @@ name: vcfanno -description: quickly annotate your VCF with any number of INFO fields from any number of VCFs or BED files +description: quickly annotate your VCF with any number of INFO fields from any number + of VCFs or BED files keywords: - vcf - bed @@ -14,48 +15,53 @@ tools: tool_dev_url: https://github.com/brentp/vcfanno doi: "10.1186/s13059-016-0973-5" license: ["MIT"] + identifier: biotools:vcfanno input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: query VCF file - pattern: "*.{vcf, vcf.gz}" - - vcf_tabix: - type: file - description: tabix index of query VCF - only needed if vcf is compressed - pattern: "*.vcf.gz.tbi" - - specific_resources: - type: map - description: A list of sample specific reference files defined in toml config, must also include indices if bgzipped. - - toml: - type: file - description: configuration file with reference file basenames - pattern: "*.toml" - - lua: - type: file - description: Lua file for custom annotations - pattern: "*.lua" - - resources: - type: map - description: List of reference files defined in toml config, must also include indices if bgzipped. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: query VCF file + pattern: "*.{vcf, vcf.gz}" + - tbi: + type: file + description: tabix index file for the query VCF + pattern: "*.tbi" + - specific_resources: + type: map + description: A list of sample specific reference files defined in toml config, + must also include indices if bgzipped. + - - toml: + type: file + description: configuration file with reference file basenames + pattern: "*.toml" + - - lua: + type: file + description: Lua file for custom annotations + pattern: "*.lua" + - - resources: + type: map + description: List of reference files defined in toml config, must also include + indices if bgzipped. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Annotated VCF file - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Annotated VCF file + pattern: "*.vcf" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@projectoriented" - "@matthdsm" diff --git a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml index 42a50ce47048..08dec641e37b 100644 --- a/modules/nf-core/vcflib/vcfbreakmulti/meta.yml +++ b/modules/nf-core/vcflib/vcfbreakmulti/meta.yml @@ -1,5 +1,6 @@ name: "vcflib_vcfbreakmulti" -description: If multiple alleles are specified in a single record, break the record into several lines preserving allele-specific INFO fields +description: If multiple alleles are specified in a single record, break the record + into several lines preserving allele-specific INFO fields keywords: - vcflib - vcfbreakmulti @@ -11,34 +12,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.{.vcf.gz,vcf}" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.{.vcf.gz,vcf}" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@lucpen" maintainers: diff --git a/modules/nf-core/vcflib/vcffilter/meta.yml b/modules/nf-core/vcflib/vcffilter/meta.yml index f9fe81b52c02..359770651bd9 100644 --- a/modules/nf-core/vcflib/vcffilter/meta.yml +++ b/modules/nf-core/vcflib/vcffilter/meta.yml @@ -13,34 +13,37 @@ tools: tool_dev_url: "https://github.com/vcflib/vcflib" doi: "10.1371/journal.pcbi.1009123" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test_sample_1' ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf,vcf.gz}" - - tbi: - type: file - description: Index file - pattern: "*.{tbi}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test_sample_1' ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf,vcf.gz}" + - tbi: + type: file + description: Index file + pattern: "*.{tbi}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - vcf: - type: file - description: Filtered VCF file - pattern: "*.{vcf.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.vcf.gz": + type: file + description: Filtered VCF file + pattern: "*.{vcf.gz}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@zachary-foster" maintainers: diff --git a/modules/nf-core/vcflib/vcffixup/meta.yml b/modules/nf-core/vcflib/vcffixup/meta.yml index be7eac6a960e..4d95e4f0d4a9 100644 --- a/modules/nf-core/vcflib/vcffixup/meta.yml +++ b/modules/nf-core/vcflib/vcffixup/meta.yml @@ -1,5 +1,6 @@ name: "vcflib_vcffixup" -description: Generates a VCF stream where AC and NS have been generated for each record using sample genotypes. +description: Generates a VCF stream where AC and NS have been generated for each record + using sample genotypes. keywords: - vcf - vcflib @@ -12,34 +13,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.{.vcf.gz,vcf}" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.{.vcf.gz,vcf}" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@atrigila" maintainers: diff --git a/modules/nf-core/vcflib/vcfuniq/meta.yml b/modules/nf-core/vcflib/vcfuniq/meta.yml index 8adf6b62b4dd..407b729f58c6 100644 --- a/modules/nf-core/vcflib/vcfuniq/meta.yml +++ b/modules/nf-core/vcflib/vcfuniq/meta.yml @@ -1,5 +1,6 @@ name: vcflib_vcfuniq -description: List unique genotypes. Like GNU uniq, but for VCF records. Remove records which have the same position, ref, and alt as the previous record. +description: List unique genotypes. Like GNU uniq, but for VCF records. Remove records + which have the same position, ref, and alt as the previous record. keywords: - vcf - uniq @@ -11,34 +12,37 @@ tools: documentation: https://github.com/vcflib/vcflib#USAGE doi: "10.1101/2021.05.21.445151" licence: ["MIT"] + identifier: biotools:vcflib input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" - - tbi: - type: file - description: Index of VCF file - pattern: "*.vcf.gz.tbi" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - tbi: + type: file + description: Index of VCF file + pattern: "*.vcf.gz.tbi" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@drpatelh" maintainers: diff --git a/modules/nf-core/vcftools/meta.yml b/modules/nf-core/vcftools/meta.yml index 09ad5908abca..b4c564ecaf2d 100644 --- a/modules/nf-core/vcftools/meta.yml +++ b/modules/nf-core/vcftools/meta.yml @@ -6,287 +6,681 @@ keywords: - sort tools: - vcftools: - description: A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries + description: A set of tools written in Perl and C++ for working with VCF files. + This package only contains the C++ libraries whereas the package perl-vcftools-vcf + contains the perl libraries homepage: http://vcftools.sourceforge.net/ documentation: http://vcftools.sourceforge.net/man_latest.html licence: ["LGPL"] + identifier: biotools:vcftools input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - variant_file: - type: file - description: variant input file which can be vcf, vcf.gz, or bcf format. - - bed: - type: file - description: bed file which can be used with different arguments in vcftools (optional) - - diff_variant_file: - type: file - description: secondary variant file which can be used with the 'diff' suite of tools (optional) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - variant_file: + type: file + description: variant input file which can be vcf, vcf.gz, or bcf format. + - - bed: + type: file + description: bed file which can be used with different arguments in vcftools + (optional) + - - diff_variant_file: + type: file + description: secondary variant file which can be used with the 'diff' suite + of tools (optional) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: vcf file (optional) - pattern: "*.vcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: vcf file (optional) + pattern: "*.vcf" - bcf: - type: file - description: bcf file (optional) - pattern: "*.bcf" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bcf": + type: file + description: bcf file (optional) + pattern: "*.bcf" - frq: - type: file - description: Allele frequency for each site (optional) - pattern: "*.frq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.frq": + type: file + description: Allele frequency for each site (optional) + pattern: "*.frq" - frq_count: - type: file - description: Allele counts for each site (optional) - pattern: "*.frq.count" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.frq.count": + type: file + description: Allele counts for each site (optional) + pattern: "*.frq.count" - idepth: - type: file - description: mean depth per individual (optional) - pattern: "*.idepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.idepth": + type: file + description: mean depth per individual (optional) + pattern: "*.idepth" - ldepth: - type: file - description: depth per site summed across individuals (optional) - pattern: "*.ildepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldepth": + type: file + description: depth per site summed across individuals (optional) + pattern: "*.ildepth" - ldepth_mean: - type: file - description: mean depth per site calculated across individuals (optional) - pattern: "*.ldepth.mean" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldepth.mean": + type: file + description: mean depth per site calculated across individuals (optional) + pattern: "*.ldepth.mean" - gdepth: - type: file - description: depth for each genotype in vcf file (optional) - pattern: "*.gdepth" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.gdepth": + type: file + description: depth for each genotype in vcf file (optional) + pattern: "*.gdepth" - hap_ld: - type: file - description: r2, D, and D’ statistics using phased haplotypes (optional) - pattern: "*.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hap.ld": + type: file + description: r2, D, and D’ statistics using phased haplotypes (optional) + pattern: "*.hap.ld" - geno_ld: - type: file - description: squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional) - pattern: "*.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno.ld": + type: file + description: squared correlation coefficient between genotypes encoded as 0, + 1 and 2 to represent the number of non-reference alleles in each individual + (optional) + pattern: "*.geno.ld" - geno_chisq: - type: file - description: test for genotype independence via the chi-squared statistic (optional) - pattern: "*.geno.chisq" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.geno.chisq": + type: file + description: test for genotype independence via the chi-squared statistic (optional) + pattern: "*.geno.chisq" - list_hap_ld: - type: file - description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) - pattern: "*.list.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list.hap.ld": + type: file + description: r2 statistics of the sites contained in the provided input file + verses all other sites (optional) + pattern: "*.list.hap.ld" - list_geno_ld: - type: file - description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) - pattern: "*.list.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.list.geno.ld": + type: file + description: r2 statistics of the sites contained in the provided input file + verses all other sites (optional) + pattern: "*.list.geno.ld" - interchrom_hap_ld: - type: file - description: r2 statistics for sites (haplotypes) on different chromosomes (optional) - pattern: "*.interchrom.hap.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interchrom.hap.ld": + type: file + description: r2 statistics for sites (haplotypes) on different chromosomes (optional) + pattern: "*.interchrom.hap.ld" - interchrom_geno_ld: - type: file - description: r2 statistics for sites (genotypes) on different chromosomes (optional) - pattern: "*.interchrom.geno.ld" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.interchrom.geno.ld": + type: file + description: r2 statistics for sites (genotypes) on different chromosomes (optional) + pattern: "*.interchrom.geno.ld" - tstv: - type: file - description: Transition / Transversion ratio in bins of size defined in options (optional) - pattern: "*.TsTv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv": + type: file + description: Transition / Transversion ratio in bins of size defined in options + (optional) + pattern: "*.TsTv" - tstv_summary: - type: file - description: Summary of all Transitions and Transversions (optional) - pattern: "*.TsTv.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.summary": + type: file + description: Summary of all Transitions and Transversions (optional) + pattern: "*.TsTv.summary" - tstv_count: - type: file - description: Transition / Transversion ratio as a function of alternative allele count (optional) - pattern: "*.TsTv.count" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.count": + type: file + description: Transition / Transversion ratio as a function of alternative allele + count (optional) + pattern: "*.TsTv.count" - tstv_qual: - type: file - description: Transition / Transversion ratio as a function of SNP quality threshold (optional) - pattern: "*.TsTv.qual" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.TsTv.qual": + type: file + description: Transition / Transversion ratio as a function of SNP quality threshold + (optional) + pattern: "*.TsTv.qual" - filter_summary: - type: file - description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional) - pattern: "*.FILTER.summary" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.FILTER.summary": + type: file + description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category + (optional) + pattern: "*.FILTER.summary" - sites_pi: - type: file - description: Nucleotide divergency on a per-site basis (optional) - pattern: "*.sites.pi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.sites.pi": + type: file + description: Nucleotide divergency on a per-site basis (optional) + pattern: "*.sites.pi" - windowed_pi: - type: file - description: Nucleotide diversity in windows, with window size determined by options (optional) - pattern: "*windowed.pi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.windowed.pi": + type: file + description: Nucleotide diversity in windows, with window size determined by + options (optional) + pattern: "*windowed.pi" - weir_fst: - type: file - description: Fst estimate from Weir and Cockerham’s 1984 paper (optional) - pattern: "*.weir.fst" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.weir.fst": + type: file + description: Fst estimate from Weir and Cockerham’s 1984 paper (optional) + pattern: "*.weir.fst" - heterozygosity: - type: file - description: Heterozygosity on a per-individual basis (optional) - pattern: "*.het" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.het": + type: file + description: Heterozygosity on a per-individual basis (optional) + pattern: "*.het" - hwe: - type: file - description: Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional) - pattern: "*.hwe" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hwe": + type: file + description: Contains the Observed numbers of Homozygotes and Heterozygotes + and the corresponding Expected numbers under HWE (optional) + pattern: "*.hwe" - tajima_d: - type: file - description: Tajima’s D statistic in bins with size of the specified number in options (optional) - pattern: "*.Tajima.D" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Tajima.D": + type: file + description: Tajima’s D statistic in bins with size of the specified number + in options (optional) + pattern: "*.Tajima.D" - freq_burden: - type: file - description: Number of variants within each individual of a specific frequency in options (optional) - pattern: "*.ifreqburden" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ifreqburden": + type: file + description: Number of variants within each individual of a specific frequency + in options (optional) + pattern: "*.ifreqburden" - lroh: - type: file - description: Long Runs of Homozygosity (optional) - pattern: "*.LROH" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.LROH": + type: file + description: Long Runs of Homozygosity (optional) + pattern: "*.LROH" - relatedness: - type: file - description: Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional) - pattern: "*.relatedness" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.relatedness": + type: file + description: Relatedness statistic based on the method of Yang et al, Nature + Genetics 2010 (doi:10.1038/ng.608) (optional) + pattern: "*.relatedness" - relatedness2: - type: file - description: Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional) - pattern: "*.relatedness2" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.relatedness2": + type: file + description: Relatedness statistic based on the method of Manichaikul et al., + BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional) + pattern: "*.relatedness2" - lqual: - type: file - description: per-site SNP quality (optional) - pattern: "*.lqual" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lqual": + type: file + description: per-site SNP quality (optional) + pattern: "*.lqual" - missing_individual: - type: file - description: Missingness on a per-individual basis (optional) - pattern: "*.imiss" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.imiss": + type: file + description: Missingness on a per-individual basis (optional) + pattern: "*.imiss" - missing_site: - type: file - description: Missingness on a per-site basis (optional) - pattern: "*.lmiss" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.lmiss": + type: file + description: Missingness on a per-site basis (optional) + pattern: "*.lmiss" - snp_density: - type: file - description: Number and density of SNPs in bins of size defined by option (optional) - pattern: "*.snpden" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.snpden": + type: file + description: Number and density of SNPs in bins of size defined by option (optional) + pattern: "*.snpden" - kept_sites: - type: file - description: All sites that have been kept after filtering (optional) - pattern: "*.kept.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.kept.sites": + type: file + description: All sites that have been kept after filtering (optional) + pattern: "*.kept.sites" - removed_sites: - type: file - description: All sites that have been removed after filtering (optional) - pattern: "*.removed.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.removed.sites": + type: file + description: All sites that have been removed after filtering (optional) + pattern: "*.removed.sites" - singeltons: - type: file - description: Location of singletons, and the individual they occur in (optional) - pattern: "*.singeltons" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.singletons": + type: file + description: Location of singletons, and the individual they occur in (optional) + pattern: "*.singeltons" - indel_hist: - type: file - description: Histogram file of the length of all indels (including SNPs) (optional) - pattern: "*.indel_hist" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.indel.hist": + type: file + description: Histogram file of the length of all indels (including SNPs) (optional) + pattern: "*.indel_hist" - hapcount: - type: file - description: Unique haplotypes within user specified bins (optional) - pattern: "*.hapcount" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.hapcount": + type: file + description: Unique haplotypes within user specified bins (optional) + pattern: "*.hapcount" - mendel: - type: file - description: Mendel errors identified in trios (optional) - pattern: "*.mendel" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mendel": + type: file + description: Mendel errors identified in trios (optional) + pattern: "*.mendel" - format: - type: file - description: Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional) - pattern: "*.FORMAT" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.FORMAT": + type: file + description: Extracted information from the genotype fields in the VCF file + relating to a specfied FORMAT identifier (optional) + pattern: "*.FORMAT" - info: - type: file - description: Extracted information from the INFO field in the VCF file (optional) - pattern: "*.INFO" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.INFO": + type: file + description: Extracted information from the INFO field in the VCF file (optional) + pattern: "*.INFO" - genotypes_matrix: - type: file - description: | - Genotypes output as large matrix. - Genotypes of each individual on a separate line. - Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles. - Missing genotypes are represented by -1 (optional) - pattern: "*.012" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012": + type: file + description: | + Genotypes output as large matrix. + Genotypes of each individual on a separate line. + Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles. + Missing genotypes are represented by -1 (optional) + pattern: "*.012" - genotypes_matrix_individual: - type: file - description: Details the individuals included in the main genotypes_matrix file (optional) - pattern: "*.012.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012.indv": + type: file + description: Details the individuals included in the main genotypes_matrix file + (optional) + pattern: "*.012.indv" - genotypes_matrix_position: - type: file - description: Details the site locations included in the main genotypes_matrix file (optional) - pattern: "*.012.pos" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.012.pos": + type: file + description: Details the site locations included in the main genotypes_matrix + file (optional) + pattern: "*.012.pos" - impute_hap: - type: file - description: Phased haplotypes in IMPUTE reference-panel format (optional) - pattern: "*.impute.hap" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap": + type: file + description: Phased haplotypes in IMPUTE reference-panel format (optional) + pattern: "*.impute.hap" - impute_hap_legend: - type: file - description: Impute haplotype legend file (optional) - pattern: "*.impute.hap.legend" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap.legend": + type: file + description: Impute haplotype legend file (optional) + pattern: "*.impute.hap.legend" - impute_hap_indv: - type: file - description: Impute haplotype individuals file (optional) - pattern: "*.impute.hap.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.impute.hap.indv": + type: file + description: Impute haplotype individuals file (optional) + pattern: "*.impute.hap.indv" - ldhat_sites: - type: file - description: Output data in LDhat format, sites (optional) - pattern: "*.ldhat.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldhat.sites": + type: file + description: Output data in LDhat format, sites (optional) + pattern: "*.ldhat.sites" - ldhat_locs: - type: file - description: output data in LDhat format, locations (optional) - pattern: "*.ldhat.locs" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ldhat.locs": + type: file + description: output data in LDhat format, locations (optional) + pattern: "*.ldhat.locs" - beagle_gl: - type: file - description: Genotype likelihoods for biallelic sites (optional) - pattern: "*.BEAGLE.GL" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.BEAGLE.GL": + type: file + description: Genotype likelihoods for biallelic sites (optional) + pattern: "*.BEAGLE.GL" - beagle_pl: - type: file - description: Genotype likelihoods for biallelic sites (optional) - pattern: "*.BEAGLE.PL" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.BEAGLE.PL": + type: file + description: Genotype likelihoods for biallelic sites (optional) + pattern: "*.BEAGLE.PL" - ped: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.ped" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ped": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.ped" - map_: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.map" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.map": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.map" - tped: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.tped" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tped": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.tped" - tfam: - type: file - description: output the genotype data in PLINK PED format (optional) - pattern: "*.tfam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tfam": + type: file + description: output the genotype data in PLINK PED format (optional) + pattern: "*.tfam" - diff_sites_in_files: - type: file - description: Sites that are common / unique to each file specified in optional inputs (optional) - pattern: "*.diff.sites.in.files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.sites_in_files": + type: file + description: Sites that are common / unique to each file specified in optional + inputs (optional) + pattern: "*.diff.sites.in.files" - diff_indv_in_files: - type: file - description: Individuals that are common / unique to each file specified in optional inputs (optional) - pattern: "*.diff.indv.in.files" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.indv_in_files": + type: file + description: Individuals that are common / unique to each file specified in + optional inputs (optional) + pattern: "*.diff.indv.in.files" - diff_sites: - type: file - description: Discordance on a site by site basis, specified in optional inputs (optional) - pattern: "*.diff.sites" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.sites": + type: file + description: Discordance on a site by site basis, specified in optional inputs + (optional) + pattern: "*.diff.sites" - diff_indv: - type: file - description: Discordance on a individual by individual basis, specified in optional inputs (optional) - pattern: "*.diff.indv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.indv": + type: file + description: Discordance on a individual by individual basis, specified in optional + inputs (optional) + pattern: "*.diff.indv" - diff_discd_matrix: - type: file - description: Discordance matrix between files specified in optional inputs (optional) - pattern: "*.diff.discordance.matrix" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.discordance.matrix": + type: file + description: Discordance matrix between files specified in optional inputs (optional) + pattern: "*.diff.discordance.matrix" - diff_switch_error: - type: file - description: Switch errors found between sites (optional) - pattern: "*.diff.switch" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.diff.switch": + type: file + description: Switch errors found between sites (optional) + pattern: "*.diff.switch" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Mark-S-Hill" maintainers: diff --git a/modules/nf-core/velocyto/meta.yml b/modules/nf-core/velocyto/meta.yml index b5c0cacc6250..9c4a8f77486b 100644 --- a/modules/nf-core/velocyto/meta.yml +++ b/modules/nf-core/velocyto/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "velocyto" description: | @@ -36,49 +35,53 @@ tools: tool_dev_url: https://github.com/velocyto-team/velocyto.py doi: "10.1038/s41586-018-0414-6" licence: ["MIT"] + identifier: "" input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - barcodes: - type: file - description: Valid barcodes file, to filter the bam - pattern: "*.tsv.gz" - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - sorted_bam: - type: file - description: Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam` - pattern: "*.bam" - - gtf: - type: file - description: genome annotation file - pattern: "*.gtf" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - barcodes: + type: file + description: Valid barcodes file, to filter the bam + pattern: "*.tsv.gz" + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - sorted_bam: + type: file + description: Cell sorted BAM/CRAM/SAM file generated with `samtools sort -t + CB -O BAM -o cellsorted_possorted_genome_bam.bam possorted_genome_bam.bam` + pattern: "*.bam" + - - gtf: + type: file + description: genome annotation file + pattern: "*.gtf" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - loom: - type: file - description: Loom file with counts divided in spliced/unspliced/ambiguous. - pattern: "*.loom" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*.loom": + type: file + description: Loom file with counts divided in spliced/unspliced/ambiguous. + pattern: "*.loom" + - "*.velocyto.log": + type: file + description: Loom file with counts divided in spliced/unspliced/ambiguous. + pattern: "*.loom" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@tucano" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid/meta.yml b/modules/nf-core/verifybamid/verifybamid/meta.yml index 1897edd15294..82cedad03b48 100644 --- a/modules/nf-core/verifybamid/verifybamid/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid/meta.yml @@ -1,79 +1,127 @@ name: "verifybamid_verifybamid" -description: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. +description: Detecting and estimating inter-sample DNA contamination became a crucial + quality assessment step to ensure high quality sequence reads and reliable downstream + analysis. keywords: - qc - contamination - bam tools: - "verifybamid": - description: "verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples." + description: "verifyBamID is a software that verifies whether the reads in particular + file match previously known genotypes for an individual (or group of individuals), + and checks whether the reads are contaminated as a mixture of two samples." homepage: "https://genome.sph.umich.edu/wiki/VerifyBamID" documentation: "http://genome.sph.umich.edu/wiki/VerifyBamID" tool_dev_url: "https://github.com/statgen/verifyBamID" doi: "10.1016/j.ajhg.2012.09.004" licence: ["GPL v3"] + identifier: biotools:verifybamid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file. - It also requires to contain "@RG" header lines to annotation different readGroups (sequencing runs and lanes). - The SM tag in the "@RG" header should match with one of the genotyped sample. - pattern: "*.bam" - - bai: - type: file - description: BAM index file BAI - pattern: "*.bai" - - refvcf: - type: file - description: | - The input VCF file contains - (1) external genotype information and/or - (2) allele frequency information as AF entry or AC/AN entries in the INFO field. - pattern: "*.{vcf,vcf.gz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file, a sorted, indexed, base quality recalibrated, and duplication-marked BAM file. + It also requires to contain "@RG" header lines to annotation different readGroups (sequencing runs and lanes). + The SM tag in the "@RG" header should match with one of the genotyped sample. + pattern: "*.bam" + - bai: + type: file + description: BAM index file BAI + pattern: "*.bai" + - - refvcf: + type: file + description: | + The input VCF file contains + (1) external genotype information and/or + (2) allele frequency information as AF entry or AC/AN entries in the INFO field. + pattern: "*.{vcf,vcf.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - log: - type: file - description: Detailed summary of the verifyBamID result. - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Detailed summary of the verifyBamID result. + pattern: "*.log" - selfsm: - type: file - description: Per-sample statistics describing how well the sample matches to the annotated sample. - pattern: "*.selfSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfSM": + type: file + description: Per-sample statistics describing how well the sample matches to + the annotated sample. + pattern: "*.selfSM" - depthsm: - type: file - description: The depth distribution of the sequence reads per sample - pattern: "*.depthSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthSM": + type: file + description: The depth distribution of the sequence reads per sample + pattern: "*.depthSM" - selfrg: - type: file - description: Per-readGroup statistics describing how well each lane matches to the annotated sample. (available only without --ignoreRG option) - pattern: "*.selfRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfRG": + type: file + description: Per-readGroup statistics describing how well each lane matches + to the annotated sample. (available only without --ignoreRG option) + pattern: "*.selfRG" - depthrg: - type: file - description: The depth distribution of the sequence reads per readGroup. (available only without --ignoreRG option) - pattern: "*.depthRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.depthRG": + type: file + description: The depth distribution of the sequence reads per readGroup. (available + only without --ignoreRG option) + pattern: "*.depthRG" - bestsm: - type: file - description: Per-sample best-match statistics with best-matching sample among the genotyped sample (available only with --best option) - pattern: "*.bestSM" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bestSM": + type: file + description: Per-sample best-match statistics with best-matching sample among + the genotyped sample (available only with --best option) + pattern: "*.bestSM" - bestrg: - type: file - description: Per-readgroup best-match statistics with best-matching sample among the genotyped sample (available only with --best and without --ignoreRG option) - pattern: "*.bestRG" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bestRG": + type: file + description: Per-readgroup best-match statistics with best-matching sample among + the genotyped sample (available only with --best and without --ignoreRG option) + pattern: "*.bestRG" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/verifybamid/verifybamid2/meta.yml b/modules/nf-core/verifybamid/verifybamid2/meta.yml index 313047deb64e..b511fc3cd016 100644 --- a/modules/nf-core/verifybamid/verifybamid2/meta.yml +++ b/modules/nf-core/verifybamid/verifybamid2/meta.yml @@ -1,5 +1,7 @@ name: "VERIFYBAMID_VERIFYBAMID2" -description: Detecting and estimating inter-sample DNA contamination became a crucial quality assessment step to ensure high quality sequence reads and reliable downstream analysis. +description: Detecting and estimating inter-sample DNA contamination became a crucial + quality assessment step to ensure high quality sequence reads and reliable downstream + analysis. keywords: - contamination - bam @@ -7,80 +9,117 @@ keywords: - DNA contamination estimation tools: - "verifybamid2": - description: "A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method." + description: "A robust tool for DNA contamination estimation from sequence reads + using ancestry-agnostic method." homepage: "http://griffan.github.io/VerifyBamID" documentation: "http://griffan.github.io/VerifyBamID" tool_dev_url: "https://github.com/Griffan/VerifyBamID" doi: "10.1101/gr.246934.118" licence: ["MIT"] + identifier: biotools:verifybamid input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: BAI/CRAI/CSI index file - pattern: "*.{bai,crai,csi}" - - svd_ud: - type: file - description: .UD matrix file from SVD result of genotype matrix - pattern: "*.UD" - - svd_mu: - type: file - description: .mu matrix file of genotype matrix - pattern: "*.mu" - - svd_bed: - type: file - description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] - pattern: "*.bed" - - references: - type: file - description: reference file [Required] - pattern: "*.fasta" - - refvcf: - type: file - description: Reference panel VCF with genotype information, for generation of .UD .mu .bed files [Optional] - pattern: "*.vcf" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: BAI/CRAI/CSI index file + pattern: "*.{bai,crai,csi}" + - - svd_ud: + type: file + description: .UD matrix file from SVD result of genotype matrix + pattern: "*.UD" + - svd_mu: + type: file + description: .mu matrix file of genotype matrix + pattern: "*.mu" + - svd_bed: + type: file + description: .Bed file for markers used in this analysis,format(chr\tpos-1\tpos\trefAllele\taltAllele)[Required] + pattern: "*.bed" + - - refvcf: + type: file + description: Reference panel VCF with genotype information, for generation of + .UD .mu .bed files [Optional] + pattern: "*.vcf" + - - references: + type: file + description: reference file [Required] + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mu: - type: file - description: .mu matrix file of genotype matrix from customized reference vcf input - pattern: "*.mu" + - log: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.log": + type: file + description: Detailed summary of the VerifyBamId2 results + pattern: "*.log" - ud: - type: file - description: .UD matrix file from customized reference vcf input - pattern: "*.UD" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.UD": + type: file + description: .UD matrix file from customized reference vcf input + pattern: "*.UD" - bed: - type: file - description: .Bed file from customized reference marker vcf input - pattern: "*.bed" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - log: - type: file - description: Detailed summary of the VerifyBamId2 results - pattern: "*.log" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: .Bed file from customized reference marker vcf input + pattern: "*.bed" + - mu: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mu": + type: file + description: .mu matrix file of genotype matrix from customized reference vcf + input + pattern: "*.mu" - self_sm: - type: file - description: Shares the same format as legacy VB1 and the key information FREEMIX indicates the estimated contamination level. - pattern: "*.selfSM" - - ancenstry: - type: file - description: PC coordinates for both intended sample and contaminating sample, with each row being one PC. - pattern: "*.Ancestry" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.selfSM": + type: file + description: Shares the same format as legacy VB1 and the key information FREEMIX + indicates the estimated contamination level. + pattern: "*.selfSM" + - ancestry: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.Ancestry": + type: file + description: Ancestry information + pattern: "*.Ancestry" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@manifestoso" maintainers: diff --git a/modules/nf-core/vg/construct/meta.yml b/modules/nf-core/vg/construct/meta.yml index 0f1c2b84ff13..e8ef6ad962c5 100644 --- a/modules/nf-core/vg/construct/meta.yml +++ b/modules/nf-core/vg/construct/meta.yml @@ -1,5 +1,6 @@ name: "vg_construct" -description: Constructs a graph from a reference and variant calls or a multiple sequence alignment file +description: Constructs a graph from a reference and variant calls or a multiple sequence + alignment file keywords: - vg - graph @@ -15,47 +16,62 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: list - description: | - Either one or more VCF files containing different contigs or a multiple sequence alignment file - pattern: "*.{vcf.gz,fa,fasta,fna,clustal}" - - tbis: - type: list - description: The index files for the VCF files - pattern: "*.tbi" - - insertions_fasta: - type: file - description: A FASTA file containing insertion sequences (referred to in the VCF file(s)) - pattern: "*.{fa,fasta,fna}" - - fasta: - type: file - description: The reference FASTA file (cannot be used in combination with `msa`, but is required when using `vcfs`) - pattern: "*.{fa,fasta,fna}" - - fasta_fai: - type: file - description: The index of the reference FASTA file - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: list + description: | + Either one or more VCF files containing different contigs or a multiple sequence alignment file + pattern: "*.{vcf.gz,fa,fasta,fna,clustal}" + - tbis: + type: list + description: The index files for the VCF files + pattern: "*.tbi" + - insertions_fasta: + type: file + description: A FASTA file containing insertion sequences (referred to in the + VCF file(s)) + pattern: "*.{fa,fasta,fna}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: The reference FASTA file (cannot be used in combination with `msa`, + but is required when using `vcfs`) + pattern: "*.{fa,fasta,fna}" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_fai: + type: file + description: The index of the reference FASTA file + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - graph: - type: file - description: The constructed graph - pattern: "*.vg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vg": + type: file + description: The constructed graph + pattern: "*.vg" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vg/deconstruct/meta.yml b/modules/nf-core/vg/deconstruct/meta.yml index e1275e47eab3..86e8ef229058 100644 --- a/modules/nf-core/vg/deconstruct/meta.yml +++ b/modules/nf-core/vg/deconstruct/meta.yml @@ -1,5 +1,6 @@ name: vg_deconstruct -description: Deconstruct snarls present in a variation graph in GFA format to variants in VCF format +description: Deconstruct snarls present in a variation graph in GFA format to variants + in VCF format keywords: - vcf - gfa @@ -15,38 +16,43 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA format - pattern: "*.{gfa}" - - pb: - type: file - description: Optional snarls file (from vg snarls) to avoid recomputing. Usually ends with "pb". See "vg snarls". - pattern: "*.{pb}" - - gbwt: - type: file - description: Optional GBWT file (from vg gbwt) so to only consider alt traversals that correspond to GBWT threads FILE. - pattern: "*.{gbwt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Variation graph in GFA format + pattern: "*.{gfa}" + - - pb: + type: file + description: Optional snarls file (from vg snarls) to avoid recomputing. Usually + ends with "pb". See "vg snarls". + pattern: "*.{pb}" + - - gbwt: + type: file + description: Optional GBWT file (from vg gbwt) so to only consider alt traversals + that correspond to GBWT threads FILE. + pattern: "*.{gbwt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - vcf: - type: file - description: Variants in VCF format - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf": + type: file + description: Variants in VCF format + pattern: "*.{vcf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@heuermh, @subwaystation" maintainers: diff --git a/modules/nf-core/vg/index/meta.yml b/modules/nf-core/vg/index/meta.yml index 1761ac6aea19..c929349e8130 100644 --- a/modules/nf-core/vg/index/meta.yml +++ b/modules/nf-core/vg/index/meta.yml @@ -13,34 +13,44 @@ tools: homepage: https://github.com/vgteam/vg documentation: https://github.com/vgteam/vg/wiki licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: list - description: One or more input graph files created with `vg/construct` - pattern: "*.vg" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: list + description: One or more input graph files created with `vg/construct` + pattern: "*.vg" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - xg: - type: file - description: File containing a succint, queryable version of the input graph(s) or read for GCSA or distance indexing - pattern: "*.xg" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.xg": + type: file + description: File containing a succint, queryable version of the input graph(s) + or read for GCSA or distance indexing + pattern: "*.xg" - vg_index: - type: file - description: An index of the graph(s) created when `--index-sorted-vg` is supplied. - pattern: "*.vgi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vgi": + type: file + description: An index of the graph(s) created when `--index-sorted-vg` is supplied. + pattern: "*.vgi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/viennarna/rnacofold/meta.yml b/modules/nf-core/viennarna/rnacofold/meta.yml index fa68573698e4..61d512995f4d 100644 --- a/modules/nf-core/viennarna/rnacofold/meta.yml +++ b/modules/nf-core/viennarna/rnacofold/meta.yml @@ -31,37 +31,47 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - rnacofold_fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - rnacofold_fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - rnacofold_csv: - type: file - description: The CSV Output of RNAcofold that has the predicted structure and energies - pattern: "*.{csv}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csv": + type: file + description: The CSV Output of RNAcofold that has the predicted structure and + energies + pattern: "*.{csv}" - rnacofold_ps: - type: file - description: The text Output of RNAfold that contains the predicted secondary structure in postscript format - pattern: "*.{ps}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.ps": + type: file + description: The text Output of RNAfold that contains the predicted secondary + structure in postscript format + pattern: "*.{ps}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/viennarna/rnafold/meta.yml b/modules/nf-core/viennarna/rnafold/meta.yml index 0081b30a0b5e..ef7bf479d194 100644 --- a/modules/nf-core/viennarna/rnafold/meta.yml +++ b/modules/nf-core/viennarna/rnafold/meta.yml @@ -1,7 +1,7 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "viennarna_rnafold" -description: Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate minimum free energy secondary structures and partition function of RNAs. +description: Predict RNA secondary structure using the ViennaRNA RNAfold tools. Calculate + minimum free energy secondary structures and partition function of RNAs. keywords: - RNA - fasta @@ -21,25 +21,46 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rnafold_txt: - type: file - description: The text Output of RNAfold that - pattern: "*.{fold}" + - meta: + type: file + description: The text Output of RNAfold that + pattern: "*.{fold}" + - "*.fold": + type: file + description: The text Output of RNAfold that + pattern: "*.{fold}" - rnafold_ps: - type: file - description: The text Output of RNAfold that - pattern: "*.ss" + - meta: + type: file + description: The text Output of RNAfold that + pattern: "*.ss" + - "*.ps": + type: file + description: The text Output of RNAfold that + pattern: "*.ss" + - versions: + - meta: + type: file + description: File containing software versions + pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/viennarna/rnalfold/meta.yml b/modules/nf-core/viennarna/rnalfold/meta.yml index 7c7d24a1890a..b642745a6983 100644 --- a/modules/nf-core/viennarna/rnalfold/meta.yml +++ b/modules/nf-core/viennarna/rnalfold/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "viennarna_rnalfold" description: calculate locally stable secondary structures of RNAs @@ -22,23 +21,25 @@ tools: documentation: "https://viennarna.readthedocs.io/en/latest/" doi: 10.1186/1748-7188-6-26 licence: ["custom"] + identifier: biotools:viennarna input: - - fasta: - type: file - description: | - A fasta file containing RNA or transcript sequences - pattern: "*.{fasta,fa}" + - - fasta: + type: file + description: | + A fasta file containing RNA or transcript sequences + pattern: "*.{fasta,fa}" output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - rnalfold_txt: - type: file - description: The text Output of RNALfold - pattern: "*.{lfold}" - + - "*.lfold": + type: file + description: The text Output of RNALfold + pattern: "*.{lfold}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@kokul-atx" maintainers: diff --git a/modules/nf-core/vireo/meta.yml b/modules/nf-core/vireo/meta.yml index 43c491235a98..77e5fa42072f 100644 --- a/modules/nf-core/vireo/meta.yml +++ b/modules/nf-core/vireo/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "vireo" description: Use vireo to perform donor deconvolution for multiplexed scRNA-seq data @@ -14,61 +13,75 @@ tools: tool_dev_url: "https://github.com/single-cell-genetics/vireo" doi: "10.1186/s13059-019-1865-2" licence: ["Apache-2.0"] + identifier: biotools:Vireo input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1']` - - - cell_data: - type: file - description: The cell genotype file in VCF format or cellSNP folder with sparse matrices. - pattern: "*.vcf|*/" - - n_donor: - type: integer - description: Number of donors to demultiplex. - - donor_file: - type: file - description: The optional donor genotype file in VCF format. - pattern: "*.vcf" - - vartrix_data: - type: file - description: The optional cell genotype files in vartrix outputs. - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1']` + - cell_data: + type: file + description: The cell genotype file in VCF format or cellSNP folder with sparse + matrices. + pattern: "*.vcf|*/" + - n_donor: + type: integer + description: Number of donors to demultiplex. + - donor_file: + type: file + description: The optional donor genotype file in VCF format. + pattern: "*.vcf" + - vartrix_data: + type: file + description: The optional cell genotype files in vartrix outputs. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1' ]` - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - summary: - type: file - description: Summary tsv file of deconvolution result. - pattern: "*_summary.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_summary.tsv": + type: file + description: Summary tsv file of deconvolution result. + pattern: "*_summary.tsv" - donor_ids: - type: file - description: Donor assignment with detailed statistics. - pattern: "*_donor_ids.tsv" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_donor_ids.tsv": + type: file + description: Donor assignment with detailed statistics. + pattern: "*_donor_ids.tsv" - prob_singlets: - type: file - description: contains probability of classifing singlets - pattern: "*_prob_singlet.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_prob_singlet.tsv.gz": + type: file + description: contains probability of classifing singlets + pattern: "*_prob_singlet.tsv.gz" - prob_doublets: - type: file - description: contains probability of classifing doublets - pattern: "*_prob_doublet.tsv.gz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - "*_prob_doublet.tsv.gz": + type: file + description: contains probability of classifing doublets + pattern: "*_prob_doublet.tsv.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mari-ga" - "@maxozo" diff --git a/modules/nf-core/vrhyme/extractunbinned/meta.yml b/modules/nf-core/vrhyme/extractunbinned/meta.yml index ef52cf111c54..c9a9b941d595 100644 --- a/modules/nf-core/vrhyme/extractunbinned/meta.yml +++ b/modules/nf-core/vrhyme/extractunbinned/meta.yml @@ -8,40 +8,51 @@ keywords: - extractunbinned tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3 license", "GPL v3"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file containing contigs/scaffolds input into vRhyme - pattern: "*.{fasta,fna,fa}" - - membership: - type: file - description: TSV file containing information regarding which bins input sequences were placed information - pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - membership: + type: file + description: TSV file containing information regarding which bins input sequences + were placed information + pattern: "*.{tsv}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file containing contigs/scaffolds input into vRhyme + pattern: "*.{fasta,fna,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - unbinned_sequences: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_unbinned_sequences.fasta": + type: file + description: FASTA file containing unbinned sequences + pattern: "*_unbinned_sequences.fasta" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - unbinnned_sequences: - type: file - description: FASTA file containing sequences unbinned by vRhyme - pattern: "*_unbinned_sequences.fasta" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vrhyme/linkbins/meta.yml b/modules/nf-core/vrhyme/linkbins/meta.yml index df8aea7c9bb0..1302b2ea24fe 100644 --- a/modules/nf-core/vrhyme/linkbins/meta.yml +++ b/modules/nf-core/vrhyme/linkbins/meta.yml @@ -8,35 +8,41 @@ keywords: - linkbins tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3 license", "GPL v3"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bins: - type: directory - description: Directory file containing bin FASTA files output by vRhyme (each bin having multiple sequences) + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bins: + type: directory + description: Directory file containing bin FASTA files output by vRhyme (each + bin having multiple sequences) output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - linked_bins: - type: file - description: FASTA file containing all bins that have been linked by N's - pattern: "*_linked_bins.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_linked_bins.fasta": + type: file + description: FASTA file containing all bins that have been linked by N's + pattern: "*_linked_bins.fasta" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vrhyme/vrhyme/environment.yml b/modules/nf-core/vrhyme/vrhyme/environment.yml index c343a66a1655..b4f66fea2124 100644 --- a/modules/nf-core/vrhyme/vrhyme/environment.yml +++ b/modules/nf-core/vrhyme/vrhyme/environment.yml @@ -1,8 +1,9 @@ channels: - conda-forge - bioconda + dependencies: - bioconda::vrhyme=1.1.0 - - conda-forge::python=3.10.8 # Locked with the container - - conda-forge::numpy=1.23.5 # Locked with the container - - conda-forge::scikit-learn=1.2.2 # Locked with the container + - conda-forge::numpy=1.23.5 + - conda-forge::python=3.10.8 + - conda-forge::scikit-learn=1.2.2 diff --git a/modules/nf-core/vrhyme/vrhyme/meta.yml b/modules/nf-core/vrhyme/vrhyme/meta.yml index 659d805b88c7..e020a1acde04 100644 --- a/modules/nf-core/vrhyme/vrhyme/meta.yml +++ b/modules/nf-core/vrhyme/vrhyme/meta.yml @@ -8,48 +8,70 @@ keywords: - vrhyme tools: - "vrhyme": - description: "vRhyme functions by utilizing coverage variance comparisons and supervised machine learning classification of sequence features to construct viral metagenome-assembled genomes (vMAGs)." + description: "vRhyme functions by utilizing coverage variance comparisons and + supervised machine learning classification of sequence features to construct + viral metagenome-assembled genomes (vMAGs)." homepage: https://github.com/AnantharamanLab/vRhyme documentation: https://github.com/AnantharamanLab/vRhyme tool_dev_url: https://github.com/AnantharamanLab/vRhyme doi: 10.1093/nar/gkac341 licence: ["GPL v3", "GPL v3 license"] + identifier: biotools:vrhyme input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Preprocessed FASTQ file containing sample reads - pattern: "*.{fastq}" - - fasta: - type: file - description: Contigs/scaffolds identified as viral - pattern: "*.{fna,fasta,fa}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Preprocessed FASTQ file containing sample reads + pattern: "*.{fastq}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Contigs/scaffolds identified as viral + pattern: "*.{fna,fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bins: - type: directory - description: Directory containing bin FASTA files - pattern: "**/vRhyme_best_bins_fasta/" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vRhyme_best_bins_fasta/: + type: directory + description: Directory containing bin FASTA files + pattern: "**/vRhyme_best_bins_fasta/" - membership: - type: file - description: TSV file describing the contig/scaffold membership of each bin - pattern: "vRhyme_best_bins.*.membership.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/vRhyme_best_bins.*.membership.tsv": + type: file + description: TSV file describing the contig/scaffold membership of each bin + pattern: "vRhyme_best_bins.*.membership.tsv" - summary: - type: file - description: TSV file summarizing the attributes of each bin - pattern: "vRhyme_best_bins.*.summary.tsv" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "**/vRhyme_best_bins.*.summary.tsv": + type: file + description: TSV file summarizing the attributes of each bin + pattern: "vRhyme_best_bins.*.summary.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@CarsonJM" maintainers: diff --git a/modules/nf-core/vsearch/cluster/meta.yml b/modules/nf-core/vsearch/cluster/meta.yml index 60d64347c509..5013feb55e2b 100644 --- a/modules/nf-core/vsearch/cluster/meta.yml +++ b/modules/nf-core/vsearch/cluster/meta.yml @@ -1,67 +1,160 @@ name: "vsearch_cluster" -description: Cluster sequences using a single-pass, greedy centroid-based clustering algorithm. +description: Cluster sequences using a single-pass, greedy centroid-based clustering + algorithm. keywords: - vsearch - clustering - microbiome tools: - vsearch: - description: VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative) + description: VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative) homepage: https://github.com/torognes/vsearch documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to cluster in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to cluster in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - aln: - type: file - description: Results in pairwise alignment format - pattern: "*.aln.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.aln.gz": + type: file + description: Results in pairwise alignment format + pattern: "*.aln.gz" - biom: - type: file - description: Results in an OTU table in the biom version 1.0 file format - pattern: "*.biom.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.biom.gz": + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.biom.gz" - mothur: - type: file - description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format - pattern: "*.mothur.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.mothur.tsv.gz": + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.mothur.tsv.gz" - otu: - type: file - description: Results in an OTU table in the classic tab-separated plain text format - pattern: "*.otu.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.otu.tsv.gz": + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.otu.tsv.gz" - bam: - type: file - description: Results written in bam format - pattern: "*.bam" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.bam": + type: file + description: Results written in bam format + pattern: "*.bam" - out: - type: file - description: Results in tab-separated output, columns defined by user - pattern: "*.out.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.out.tsv.gz": + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.out.tsv.gz" - blast: - type: file - description: Tab delimited results in blast-like tabular format - pattern: "*.blast.tsv.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.blast.tsv.gz": + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.blast.tsv.gz" - uc: - type: file - description: Tab delimited results in a uclust-like format with 10 columns - pattern: "*.uc.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.uc.tsv.gz": + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.uc.gz" + - centroids: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.centroids.fasta.gz": + type: file + description: Centroid sequences in FASTA format + pattern: "*.centroids.fasta.gz" + - clusters: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.clusters.fasta*.gz": + type: file + description: Clustered sequences in FASTA format + pattern: "*.clusters.fasta*.gz" + - profile: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.profile.txt.gz": + type: file + description: Profile of the clustering results + pattern: "*.profile.txt.gz" + - msa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*.msa.fasta.gz": + type: file + description: Multiple sequence alignment of the centroids + pattern: "*.msa.fasta.gz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/vsearch/dereplicate/meta.yml b/modules/nf-core/vsearch/dereplicate/meta.yml index 061f34346af9..5023f81cf717 100644 --- a/modules/nf-core/vsearch/dereplicate/meta.yml +++ b/modules/nf-core/vsearch/dereplicate/meta.yml @@ -1,5 +1,7 @@ name: "vsearch_dereplicate" -description: Merge strictly identical sequences contained in filename. Identical sequences are defined as having the same length and the same string of nucleotides (case insensitive, T and U are considered the same). +description: Merge strictly identical sequences contained in filename. Identical sequences + are defined as having the same length and the same string of nucleotides (case insensitive, + T and U are considered the same). keywords: - vsearch/dereplicate - vsearch @@ -16,34 +18,42 @@ tools: tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to be sorted in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to be sorted in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz,.fna,.fna.gz}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: dereplicated fasta - pattern: "*.fasta" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ]` + - "*.derep.fasta": + type: file + description: dereplicated fasta + pattern: "*.fasta" - clustering: - type: file - description: dereplicated derep.uc file - pattern: "*.uc" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ]` + - "*.derep.uc": + type: file + description: dereplicated derep.uc file + pattern: "*.uc" - log: - type: file - description: a log file of the run - pattern: "*.derep.log" + - "*.derep.log": + type: file + description: a log file of the run + pattern: "*.derep.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@chriswyatt1" maintainers: diff --git a/modules/nf-core/vsearch/fastqfilter/meta.yml b/modules/nf-core/vsearch/fastqfilter/meta.yml index 02ac685eeba4..b91fc90d6097 100644 --- a/modules/nf-core/vsearch/fastqfilter/meta.yml +++ b/modules/nf-core/vsearch/fastqfilter/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_fastqfilter" -description: Performs quality filtering and / or conversion of a FASTQ file to FASTA format. +description: Performs quality filtering and / or conversion of a FASTQ file to FASTA + format. keywords: - vsearch/fastqfilter - vsearch @@ -10,35 +11,44 @@ keywords: - population genetics tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'sample1'] - - fastq: - type: file - description: FASTQ file to filter - pattern: "*.{fastq,fq,fastq.gz,fq.gz}" + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'sample1'] + - fastq: + type: file + description: FASTQ file to filter + pattern: "*.{fastq,fq,fastq.gz,fq.gz}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'sample1'] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fasta: - type: file - description: Filtered FASTA file - pattern: "*.fasta" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'sample1'] + - "*.fasta": + type: file + description: Filtered FASTA file + pattern: "*.fasta" - log: - type: file - description: Log file of the run - pattern: "*.log" + - "*.log": + type: file + description: Log file of the run + pattern: "*.log" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@FernandoDuarteF" maintainers: diff --git a/modules/nf-core/vsearch/sintax/meta.yml b/modules/nf-core/vsearch/sintax/meta.yml index 97cd5ebe8a74..7b387b903c19 100644 --- a/modules/nf-core/vsearch/sintax/meta.yml +++ b/modules/nf-core/vsearch/sintax/meta.yml @@ -6,32 +6,44 @@ keywords: - taxonomy tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing query file information e.g. [ id:'test' ] - - queryfasta: - type: file - description: Query sequences in FASTA or FASTQ format - pattern: "*.{fasta,fa,fna,faa,fastq,fq}" - - db: - type: file - description: Reference database file in FASTA or UDB format - pattern: "*" + - - meta: + type: map + description: Groovy Map containing query file information e.g. [ id:'test' ] + - queryfasta: + type: file + description: Query sequences in FASTA or FASTQ format + pattern: "*.{fasta,fa,fna,faa,fastq,fq}" + - - db: + type: file + description: Reference database file in FASTA or UDB format + pattern: "*" output: - tsv: - type: file - description: Results written to tab-delimited file - pattern: "*.{tsv}" + - meta: + type: file + description: Results written to tab-delimited file + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Results written to tab-delimited file + pattern: "*.{tsv}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jtangrot" maintainers: diff --git a/modules/nf-core/vsearch/sort/meta.yml b/modules/nf-core/vsearch/sort/meta.yml index ddf28a307875..62a7b31619d8 100644 --- a/modules/nf-core/vsearch/sort/meta.yml +++ b/modules/nf-core/vsearch/sort/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_sort" -description: Sort fasta entries by decreasing abundance (--sortbysize) or sequence length (--sortbylength). +description: Sort fasta entries by decreasing abundance (--sortbysize) or sequence + length (--sortbylength). keywords: - vsearch/sort - vsearch @@ -10,38 +11,47 @@ keywords: - population genetics tools: - vsearch: - description: VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative) + description: VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative) homepage: https://github.com/torognes/vsearch documentation: https://github.com/torognes/vsearch/releases/download/v2.21.1/vsearch_manual.pdf tool_dev_url: https://github.com/torognes/vsearch doi: 10.7717/peerj.2584 licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - fasta: - type: file - description: Sequences to be sorted in FASTA format - pattern: "*.{fasta,fa,fasta.gz,fa.gz}" - - sort_arg: - type: string - description: Argument to provide to sort algorithm. Sort by abundance with --sortbysize or by sequence length with --sortbylength. - enum: ["--sortbysize", "--sortbylength"] + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - fasta: + type: file + description: Sequences to be sorted in FASTA format + pattern: "*.{fasta,fa,fasta.gz,fa.gz}" + - - sort_arg: + type: string + description: Argument to provide to sort algorithm. Sort by abundance with --sortbysize + or by sequence length with --sortbylength. + enum: ["--sortbysize", "--sortbylength"] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Sorted FASTA file - pattern: "*.{fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fasta": + type: file + description: Sorted FASTA file + pattern: "*.{fasta}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@mirpedrol" maintainers: diff --git a/modules/nf-core/vsearch/usearchglobal/meta.yml b/modules/nf-core/vsearch/usearchglobal/meta.yml index ba56f1778e42..9f4b4203efa6 100644 --- a/modules/nf-core/vsearch/usearchglobal/meta.yml +++ b/modules/nf-core/vsearch/usearchglobal/meta.yml @@ -1,5 +1,6 @@ name: "vsearch_usearchglobal" -description: Compare target sequences to fasta-formatted query sequences using global pairwise alignment. +description: Compare target sequences to fasta-formatted query sequences using global + pairwise alignment. keywords: - vsearch - usearch @@ -7,74 +8,136 @@ keywords: - fasta tools: - "vsearch": - description: "VSEARCH is a versatile open-source tool for microbiome analysis, including chimera detection, clustering, dereplication and rereplication, extraction, FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH alternative)" + description: "VSEARCH is a versatile open-source tool for microbiome analysis, + including chimera detection, clustering, dereplication and rereplication, extraction, + FASTA/FASTQ/SFF file processing, masking, orienting, pair-wise alignment, restriction + site cutting, searching, shuffling, sorting, subsampling, and taxonomic classification + of amplicon sequences for metagenomics, genomics, and population genetics. (USEARCH + alternative)" homepage: "https://github.com/torognes/vsearch" tool_dev_url: "https://github.com/torognes/vsearch" doi: "10.7717/peerj.2584" licence: ["GPL v3-or-later OR BSD-2-clause"] + identifier: biotools:vsearch input: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test' ] - - queryfasta: - type: file - description: Query sequences in FASTA format - pattern: "*.{fasta,fa,fna,faa}" - - db: - type: file - description: Reference database file in FASTA or UDB format - pattern: "*" - - idcutoff: - type: float - description: Reject the sequence match if the pairwise identity is lower than the given id cutoff value (value ranging from 0.0 to 1.0 included) - - outoption: - type: string - description: Specify the type of output file to be generated by selecting one of the vsearch output file options - pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" - - user_columns: - type: string - description: If using the `userout` option, specify which columns to include in output, with fields separated with `+` (e.g. query+target+id). See USEARCH manual for valid options. For other output options, use an empty string. + - - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test' ] + - queryfasta: + type: file + description: Query sequences in FASTA format + pattern: "*.{fasta,fa,fna,faa}" + - - db: + type: file + description: Reference database file in FASTA or UDB format + pattern: "*" + - - idcutoff: + type: float + description: Reject the sequence match if the pairwise identity is lower than + the given id cutoff value (value ranging from 0.0 to 1.0 included) + - - outoption: + type: string + description: Specify the type of output file to be generated by selecting one + of the vsearch output file options + pattern: "alnout|biomout|blast6out|mothur_shared_out|otutabout|samout|uc|userout|lcaout" + - - user_columns: + type: string + description: If using the `userout` option, specify which columns to include + in output, with fields separated with `+` (e.g. query+target+id). See USEARCH + manual for valid options. For other output options, use an empty string. output: - aln: - type: file - description: Results in pairwise alignment format - pattern: "*.{aln}" + - meta: + type: file + description: Results in pairwise alignment format + pattern: "*.{aln}" + - "*.aln": + type: file + description: Results in pairwise alignment format + pattern: "*.{aln}" - biom: - type: file - description: Results in an OTU table in the biom version 1.0 file format - pattern: "*.{biom}" + - meta: + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.{biom}" + - "*.biom": + type: file + description: Results in an OTU table in the biom version 1.0 file format + pattern: "*.{biom}" - lca: - type: file - description: Last common ancestor (LCA) information about the hits of each query in tab-separated format - pattern: "*.{lca}" + - meta: + type: file + description: Last common ancestor (LCA) information about the hits of each query + in tab-separated format + pattern: "*.{lca}" + - "*.lca": + type: file + description: Last common ancestor (LCA) information about the hits of each query + in tab-separated format + pattern: "*.{lca}" - mothur: - type: file - description: Results in an OTU table in the mothur ’shared’ tab-separated plain text file format - pattern: "*.{mothur}" + - meta: + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.{mothur}" + - "*.mothur": + type: file + description: Results in an OTU table in the mothur ’shared’ tab-separated plain + text file format + pattern: "*.{mothur}" - otu: - type: file - description: Results in an OTU table in the classic tab-separated plain text format - pattern: "*.{otu}" + - meta: + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.{otu}" + - "*.otu": + type: file + description: Results in an OTU table in the classic tab-separated plain text + format + pattern: "*.{otu}" - sam: - type: file - description: Results written in sam format - pattern: "*.{sam}" + - meta: + type: file + description: Results written in sam format + pattern: "*.{sam}" + - "*.sam": + type: file + description: Results written in sam format + pattern: "*.{sam}" - tsv: - type: file - description: Results in tab-separated output, columns defined by user - pattern: "*.{tsv}" + - meta: + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.{tsv}" + - "*.tsv": + type: file + description: Results in tab-separated output, columns defined by user + pattern: "*.{tsv}" - txt: - type: file - description: Tab delimited results in blast-like tabular format - pattern: "*.{txt}" + - meta: + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.{txt}" + - "*.txt": + type: file + description: Tab delimited results in blast-like tabular format + pattern: "*.{txt}" - uc: - type: file - description: Tab delimited results in a uclust-like format with 10 columns - pattern: "*.{uc}" + - meta: + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.{uc}" + - "*.uc": + type: file + description: Tab delimited results in a uclust-like format with 10 columns + pattern: "*.{uc}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jtangrot" maintainers: diff --git a/modules/nf-core/vt/decompose/meta.yml b/modules/nf-core/vt/decompose/meta.yml index 0a08d8767309..d9c75de331cb 100644 --- a/modules/nf-core/vt/decompose/meta.yml +++ b/modules/nf-core/vt/decompose/meta.yml @@ -1,4 +1,3 @@ ---- name: "vt_decompose" description: decomposes multiallelic variants into biallelic in a VCF file. keywords: @@ -14,34 +13,37 @@ tools: documentation: "https://genome.sph.umich.edu/wiki/Vt" tool_dev_url: "https://github.com/atks/vt" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: The VCF file to decompose - pattern: "*.vcf(.gz)?" - - intervals: - type: file - description: The intervals of the variants of decompose - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: The VCF file to decompose + pattern: "*.vcf(.gz)?" + - intervals: + type: file + description: The intervals of the variants of decompose + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The decomposed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The decomposed VCF file + pattern: "*.vcf.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/vt/normalize/meta.yml b/modules/nf-core/vt/normalize/meta.yml index 37e7bca1612b..845baa489db4 100644 --- a/modules/nf-core/vt/normalize/meta.yml +++ b/modules/nf-core/vt/normalize/meta.yml @@ -1,4 +1,3 @@ ---- name: "vt_normalize" description: normalizes variants in a VCF file keywords: @@ -13,60 +12,70 @@ tools: documentation: "https://genome.sph.umich.edu/wiki/Vt" tool_dev_url: "https://github.com/atks/vt" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - vcf: - type: file - description: The VCF file to normalize - pattern: "*.vcf(.gz)?" - - tbi: - type: file - description: The tabix index of the VCF file when bgzipped - pattern: "*.tbi" - - intervals: - type: file - description: The intervals of the variants of normalize - pattern: "*.bed" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. `[ id:'test', single_end:false ]` - - fasta: - type: file - description: The reference fasta file - pattern: "*.{fasta,fn,fna,fa}" - - meta3: - type: map - description: | - Groovy Map containing reference index information - e.g. `[ id:'test', single_end:false ]` - - fai: - type: file - description: The index of the reference fasta file (OPTIONAL) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - vcf: + type: file + description: The VCF file to normalize + pattern: "*.vcf(.gz)?" + - tbi: + type: file + description: The tabix index of the VCF file when bgzipped + pattern: "*.tbi" + - intervals: + type: file + description: The intervals of the variants of normalize + pattern: "*.bed" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. `[ id:'test', single_end:false ]` + - fasta: + type: file + description: The reference fasta file + pattern: "*.{fasta,fn,fna,fa}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. `[ id:'test', single_end:false ]` + - fai: + type: file + description: The index of the reference fasta file (OPTIONAL) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: The normalized VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*.vcf.gz": + type: file + description: The normalized VCF file + pattern: "*.vcf.gz" - fai: - type: file - description: The created index of the reference fasta file (only when the fai wasn't supplied) - pattern: "*.fai" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - ${fasta}.fai: + type: file + description: The created index of the reference fasta file (only when the fai + wasn't supplied) + pattern: "*.fai" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wfmash/meta.yml b/modules/nf-core/wfmash/meta.yml index dc5cd5a8fd8c..df9024fdb391 100644 --- a/modules/nf-core/wfmash/meta.yml +++ b/modules/nf-core/wfmash/meta.yml @@ -14,49 +14,55 @@ tools: tool_dev_url: https://github.com/waveygang/wfmash doi: 10.5281/zenodo.6949373 licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta_gz: - type: file - description: BGZIPPED FASTA target file to create the mappings from. - pattern: "{fa.gz,fna.gz,fasta.gz}" - - paf: - type: file - description: Optional inpute file in PAF format to derive the precise alignments for. - pattern: "*.{paf}" - - query_self: - type: boolean - description: If set to true, the input FASTA will also be used as the query FASTA. - - gzi: - type: file - description: The GZI index of the input FASTA file. - pattern: "*.{gzi}" - - fai: - type: file - description: The FASTA index of the input FASTA file. - pattern: "*.{fai}" - - fasta_query_list: - type: file - description: Optional inpute file in FASTA format specifying the query sequences as a list. - pattern: "*.{fa,fna,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta_gz: + type: file + description: BGZIPPED FASTA target file to create the mappings from. + pattern: "{fa.gz,fna.gz,fasta.gz}" + - paf: + type: file + description: Optional inpute file in PAF format to derive the precise alignments + for. + pattern: "*.{paf}" + - gzi: + type: file + description: The GZI index of the input FASTA file. + pattern: "*.{gzi}" + - fai: + type: file + description: The FASTA index of the input FASTA file. + pattern: "*.{fai}" + - - query_self: + type: boolean + description: If set to true, the input FASTA will also be used as the query + FASTA. + - - fasta_query_list: + type: file + description: Optional inpute file in FASTA format specifying the query sequences + as a list. + pattern: "*.{fa,fna,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - paf: - type: file - description: Alignments in PAF format - pattern: "*.{paf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.paf": + type: file + description: Alignments in PAF format + pattern: "*.{paf}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@subwaystation" maintainers: diff --git a/modules/nf-core/wgsim/meta.yml b/modules/nf-core/wgsim/meta.yml index b57c67b8d186..018d60fb8725 100644 --- a/modules/nf-core/wgsim/meta.yml +++ b/modules/nf-core/wgsim/meta.yml @@ -11,30 +11,33 @@ tools: documentation: "https://github.com/lh3/wgsim" tool_dev_url: "https://github.com/lh3/wgsim" licence: ["MIT"] + identifier: biotools:wgsim input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Genome fasta file - pattern: "*.{fa,fasta}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - fastq: - type: file - description: Simulated FASTQ read files - pattern: "*.{fastq}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.fastq": + type: file + description: Simulated FASTQ read files + pattern: "*.{fastq}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@priyanka-surana" maintainers: diff --git a/modules/nf-core/whamg/meta.yml b/modules/nf-core/whamg/meta.yml index fc19fce9b892..55f6a304df05 100644 --- a/modules/nf-core/whamg/meta.yml +++ b/modules/nf-core/whamg/meta.yml @@ -1,5 +1,7 @@ name: "whamg" -description: The wham suite consists of two programs, wham and whamg. wham, the original tool, is a very sensitive method with a high false discovery rate. The second program, whamg, is more accurate and better suited for general structural variant (SV) discovery. +description: The wham suite consists of two programs, wham and whamg. wham, the original + tool, is a very sensitive method with a high false discovery rate. The second program, + whamg, is more accurate and better suited for general structural variant (SV) discovery. keywords: - whamg - wham @@ -14,46 +16,65 @@ tools: tool_dev_url: "https://github.com/zeeev/wham" doi: "10.1371/journal.pcbi.1004572" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/SAM file - pattern: "*.{bam,sam}" - - bai: - type: file - description: BAM index file - pattern: "*.bai" - - fasta: - type: file - description: Reference Fasta file - pattern: "*.{fasta,fa}" - - fasta_fai: - type: file - description: Index of the reference Fasta - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/SAM file + pattern: "*.{bam,sam}" + - bai: + type: file + description: BAM index file + pattern: "*.bai" + - - fasta: + type: file + description: Reference Fasta file + pattern: "*.{fasta,fa}" + - - fasta_fai: + type: file + description: Index of the reference Fasta + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - vcf: - type: file - description: Compressed VCF file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz": + type: file + description: Compressed VCF file + pattern: "*.vcf.gz" - tbi: - type: file - description: Index of the VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.vcf.gz.tbi": + type: file + description: Index of the VCF file + pattern: "*.vcf.gz.tbi" + - graph: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: Graph file + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/windowmasker/convert/meta.yml b/modules/nf-core/windowmasker/convert/meta.yml index d9e46e798228..e163f8bd1ff9 100644 --- a/modules/nf-core/windowmasker/convert/meta.yml +++ b/modules/nf-core/windowmasker/convert/meta.yml @@ -6,35 +6,38 @@ keywords: - windowmasker tools: - windowmasker: - description: "A program to mask highly repetitive and low complexity DNA sequences within a genome." + description: "A program to mask highly repetitive and low complexity DNA sequences + within a genome." homepage: "https://blast.ncbi.nlm.nih.gov/Blast.cgi" documentation: "ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/windowmasker/README.windowmasker" doi: 10.1016/S0022-2836(05)80360-2 licence: ["US-Government-Work"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - counts: - type: file - description: valid unit counts file - pattern: "*.{ascii,binary,oascii,obinary,txt}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - counts: + type: file + description: valid unit counts file + pattern: "*.{ascii,binary,oascii,obinary,txt}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - counts: - type: file - description: valid unit counts file - pattern: "*.{ascii,binary,oascii,obinary}" + - converted: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: converted file - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@alxndrdiaz" maintainers: diff --git a/modules/nf-core/windowmasker/mkcounts/meta.yml b/modules/nf-core/windowmasker/mkcounts/meta.yml index 436ed7a50529..825a0674e44f 100644 --- a/modules/nf-core/windowmasker/mkcounts/meta.yml +++ b/modules/nf-core/windowmasker/mkcounts/meta.yml @@ -11,31 +11,32 @@ tools: homepage: https://github.com/ncbi/ncbi-cxx-toolkit-public documentation: https://ncbi.github.io/cxx-toolkit/ licence: ["MIT"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: An input nucleotide fasta file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: An input nucleotide fasta file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: | - An output file containing genomic locations of low - complexity and highly repetitive regions - pattern: "${prefix}.txt" + - counts: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.txt": + type: file + description: A file containing frequency counts of repetitive units. + pattern: "*.txt" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/windowmasker/ustat/meta.yml b/modules/nf-core/windowmasker/ustat/meta.yml index 6a07c9352396..bc51a9340c17 100644 --- a/modules/nf-core/windowmasker/ustat/meta.yml +++ b/modules/nf-core/windowmasker/ustat/meta.yml @@ -1,5 +1,6 @@ name: windowmasker_ustat -description: A program to take a counts file and creates a file of genomic co-ordinates to be masked. +description: A program to take a counts file and creates a file of genomic co-ordinates + to be masked. keywords: - fasta - interval @@ -11,39 +12,39 @@ tools: homepage: https://github.com/ncbi/ncbi-cxx-toolkit-public documentation: https://ncbi.github.io/cxx-toolkit/ licence: ["MIT"] + identifier: biotools:windowmasker input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - counts: - type: file - description: Contains count data of repetitive regions. - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - ref: - type: file - description: An input nucleotide fasta file. + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - counts: + type: file + description: Contains count data of repetitive regions. + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ref: + type: file + description: An input nucleotide fasta file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - wm_intervals: - type: file - description: | - An output file containing genomic locations of low - complexity and highly repetitive regions - pattern: "${output}" + - intervals: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${output}: + type: file + description: intervals - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@DLBPointon" maintainers: diff --git a/modules/nf-core/wisecondorx/convert/meta.yml b/modules/nf-core/wisecondorx/convert/meta.yml index d70d9d69ab23..07233d2953d1 100644 --- a/modules/nf-core/wisecondorx/convert/meta.yml +++ b/modules/nf-core/wisecondorx/convert/meta.yml @@ -12,52 +12,56 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Reads in BAM/CRAM format - pattern: "*.{bam,cram}" - - bai: - type: file - description: index of the BAM/CRAM file - pattern: "*.{bai,crai}" - - meta2: - type: map - description: | - Groovy Map containing reference fasta meta information - e.g. [ id:'test' ] - - fasta: - type: file - description: The reference FASTA file (mandatory when using CRAM files) - pattern: "*.{fasta,fa,fna}" - - meta3: - type: map - description: | - Groovy Map containing reference fasta index meta information - e.g. [ id:'test' ] - - fasta_fai: - type: file - description: The index of the reference FASTA file (mandatory when using CRAM files) - pattern: "*.fai" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Reads in BAM/CRAM format + pattern: "*.{bam,cram}" + - bai: + type: file + description: index of the BAM/CRAM file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference fasta meta information + e.g. [ id:'test' ] + - fasta: + type: file + description: The reference FASTA file (mandatory when using CRAM files) + pattern: "*.{fasta,fa,fna}" + - - meta3: + type: map + description: | + Groovy Map containing reference fasta index meta information + e.g. [ id:'test' ] + - fasta_fai: + type: file + description: The index of the reference FASTA file (mandatory when using CRAM + files) + pattern: "*.fai" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npz: - type: file - description: The output NPZ file - pattern: "*.npz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: The output NPZ file + pattern: "*.npz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/gender/meta.yml b/modules/nf-core/wisecondorx/gender/meta.yml index cd4da24f7bc0..ccf1052ee198 100644 --- a/modules/nf-core/wisecondorx/gender/meta.yml +++ b/modules/nf-core/wisecondorx/gender/meta.yml @@ -1,5 +1,6 @@ name: "wisecondorx_gender" -description: Returns the gender of a .npz resulting from convert, based on a Gaussian mixture model trained during the newref phase +description: Returns the gender of a .npz resulting from convert, based on a Gaussian + mixture model trained during the newref phase keywords: - copy number analysis - gender determination @@ -12,34 +13,38 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - npz: - type: file - description: Single sample NPZ file (from which to determine the gender) - pattern: "*.npz" - - reference: - type: file - description: Reference NPZ file - pattern: "*.npz" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - npz: + type: file + description: Single sample NPZ file (from which to determine the gender) + pattern: "*.npz" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: Reference NPZ file + pattern: "*.npz" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - gender: - type: string - description: The gender of the input NPZ file - pattern: "(fe)?male" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/newref/meta.yml b/modules/nf-core/wisecondorx/newref/meta.yml index d5efefeb53f5..d05b18200017 100644 --- a/modules/nf-core/wisecondorx/newref/meta.yml +++ b/modules/nf-core/wisecondorx/newref/meta.yml @@ -12,30 +12,33 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - inputs: - type: file - description: Multiple NPZ files from healthy patients - pattern: "*.{npz}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - inputs: + type: file + description: Multiple NPZ files from healthy patients + pattern: "*.{npz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - npz: - type: file - description: The reference NPZ file - pattern: "*.{npz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.npz": + type: file + description: The reference NPZ file + pattern: "*.{npz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wisecondorx/predict/meta.yml b/modules/nf-core/wisecondorx/predict/meta.yml index 0f347ee36d4e..ae17554578b3 100644 --- a/modules/nf-core/wisecondorx/predict/meta.yml +++ b/modules/nf-core/wisecondorx/predict/meta.yml @@ -13,68 +13,107 @@ tools: tool_dev_url: "https://github.com/CenterForMedicalGeneticsGhent/WisecondorX" doi: "10.1093/nar/gky1263" licence: ["Attribution-NonCommercial-ShareAlike CC BY-NC-SA"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - npz: - type: file - description: An NPZ file created with WisecondorX convert - pattern: "*.npz" - - meta2: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test', single_end:false ] - - reference: - type: file - description: A reference NPZ file created with WisecondorX newref - pattern: "*.npz" - - meta3: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - blacklist: - type: file - description: OPTIONAL - A BED file containing blacklist regions (used mainly when the reference is small) - pattern: "*.bed" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - npz: + type: file + description: An NPZ file created with WisecondorX convert + pattern: "*.npz" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test', single_end:false ] + - reference: + type: file + description: A reference NPZ file created with WisecondorX newref + pattern: "*.npz" + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - blacklist: + type: file + description: OPTIONAL - A BED file containing blacklist regions (used mainly + when the reference is small) + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - aberrations_bed: - type: file - description: OPTIONAL - Output abberations in BED format. This gets created with the `--bed` option - pattern: "*_aberrations.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_aberrations.bed": + type: file + description: OPTIONAL - Output abberations in BED format. This gets created + with the `--bed` option + pattern: "*_aberrations.bed" - bins_bed: - type: file - description: OPTIONAL - Output bins in BED format. This gets created with the `--bed` option - pattern: "*_bins.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_bins.bed": + type: file + description: OPTIONAL - Output bins in BED format. This gets created with the + `--bed` option + pattern: "*_bins.bed" - segments_bed: - type: file - description: OPTIONAL - Output segments in BED format. This gets created with the `--bed` option - pattern: "*_segments.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_segments.bed": + type: file + description: OPTIONAL - Output segments in BED format. This gets created with + the `--bed` option + pattern: "*_segments.bed" - chr_statistics: - type: file - description: OPTIONAL - Statistics per chromosome in TXT format. This gets created with the `--bed` option - pattern: "*_chr_statistics.txt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_chr_statistics.txt": + type: file + description: OPTIONAL - Statistics per chromosome in TXT format. This gets created + with the `--bed` option + pattern: "*_chr_statistics.txt" - chr_plots: - type: list - description: OPTIONAL - A list containing the CNV plots of each chromosome. This gets created with the `--plot` option - pattern: "[!genome_wide]*.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "[!genome_wide]*.png": + type: list + description: OPTIONAL - A list containing the CNV plots of each chromosome. + This gets created with the `--plot` option + pattern: "[!genome_wide]*.png" - genome_plot: - type: file - description: OPTIONAL - A plot containing the CNV information of the whole genome - pattern: "genome_wide.png" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genome_wide.png: + type: file + description: OPTIONAL - A plot containing the CNV information of the whole genome + pattern: "genome_wide.png" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@nvnieuwk" maintainers: diff --git a/modules/nf-core/wittyer/meta.yml b/modules/nf-core/wittyer/meta.yml index cda7f751b3c6..40110aa24476 100644 --- a/modules/nf-core/wittyer/meta.yml +++ b/modules/nf-core/wittyer/meta.yml @@ -12,52 +12,67 @@ tools: documentation: "https://github.com/Illumina/witty.er" tool_dev_url: "https://github.com/Illumina/witty.er" licence: ["BSD-2"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - query_vcf: - type: file - description: A VCF with called variants to benchmark against the standard - pattern: "*.{vcf}" - - truth_vcf: - type: file - description: A standard VCF to compare against - pattern: "*.{vcf}" - - bed: - type: file - description: A BED file specifying regions to be included in the analysis (optional) - pattern: "*.bed" - - wittyer_config: - type: file - description: | - Config file in json format used to specify per variant type settings. - Used in place of include bed arguments. (optional) - pattern: "*.json" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - query_vcf: + type: file + description: A VCF with called variants to benchmark against the standard + pattern: "*.{vcf}" + - truth_vcf: + type: file + description: A standard VCF to compare against + pattern: "*.{vcf}" + - bed: + type: file + description: A BED file specifying regions to be included in the analysis (optional) + pattern: "*.bed" + - wittyer_config: + type: file + description: | + Config file in json format used to specify per variant type settings. + Used in place of include bed arguments. (optional) + pattern: "*.json" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - report: - type: file - description: Detailed per-sample-pair, per-svtype, per-bin stats - pattern: "*.json" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.json": + type: file + description: Detailed per-sample-pair, per-svtype, per-bin stats + pattern: "*.json" - bench_vcf: - type: file - description: Updated query and truth entries merged into one file - pattern: "*.vcf.gz" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz": + type: file + description: Updated query and truth entries merged into one file + pattern: "*.vcf.gz" - bench_vcf_tbi: - type: file - description: Index of merged query and truth entries VCF file - pattern: "*.vcf.gz.tbi" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.vcf.gz.tbi": + type: file + description: Index of merged query and truth entries VCF file + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@famosab" maintainers: diff --git a/modules/nf-core/xengsort/index/meta.yml b/modules/nf-core/xengsort/index/meta.yml index 570c781d09be..145d15f075ec 100644 --- a/modules/nf-core/xengsort/index/meta.yml +++ b/modules/nf-core/xengsort/index/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xengsort_index" description: Fast lightweight accurate xenograft sorting @@ -18,43 +17,45 @@ tools: tool_dev_url: "https://gitlab.com/genomeinformatics/xengsort" doi: "10.4230/LIPIcs.WABI.2020.4" licence: ["MIT"] + identifier: "" input: - - host_fasta: - type: file - description: | - Reference genome fasta file from host, compressed or uncompressed. - - graft_fasta: - type: file - description: | - Reference genome fasta file from graft, compressed or uncompressed. - - index: - type: string - description: | - File name prefix to store index files. - - nobjects: - type: string - description: | - Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000. - - mask: - type: string - description: | - Gapped k-mer mask (quoted string like '#__##_##__#'). - + - - host_fasta: + type: file + description: | + Reference genome fasta file from host, compressed or uncompressed. + - - graft_fasta: + type: file + description: | + Reference genome fasta file from graft, compressed or uncompressed. + - - index: + type: string + description: | + File name prefix to store index files. + - - nobjects: + type: string + description: | + Number of k-mers that will be stored in the hash table. Underscore should be used, i.e for 1000000, it should be typed 1_000_000. + - - mask: + type: string + description: | + Gapped k-mer mask (quoted string like '#__##_##__#'). output: - hash: - type: file - description: File with index hash file. - pattern: "*hash" + - ${index}.hash: + type: file + description: File with index hash file. + pattern: "*hash" - info: - type: file - description: File with index info file. - pattern: "*info" + - ${index}.info: + type: file + description: File with index info file. + pattern: "*info" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@diegomscoelho" maintainers: diff --git a/modules/nf-core/xz/compress/meta.yml b/modules/nf-core/xz/compress/meta.yml index bdc002ad4a04..27be72969cbb 100644 --- a/modules/nf-core/xz/compress/meta.yml +++ b/modules/nf-core/xz/compress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xz_compress" description: Compresses files with xz. @@ -8,41 +7,40 @@ keywords: - archive tools: - "xz": - description: "xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2." + description: "xz is a general-purpose data compression tool with command line + syntax similar to gzip and bzip2." homepage: "https://tukaani.org/xz/" documentation: "https://tukaani.org/xz/man/xz.1.html" tool_dev_url: "https://github.com/tukaani-project/xz" licence: ["GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - raw_file: - type: file - description: File to be compressed - pattern: "*.*" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - raw_file: + type: file + description: File to be compressed + pattern: "*.*" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - archive: - type: file - description: The compressed file - pattern: "*.xz" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $archive: + type: file + description: The compressed file + pattern: "*.xz" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/xz/decompress/meta.yml b/modules/nf-core/xz/decompress/meta.yml index 831f9f6ee63e..89b87ed301c7 100644 --- a/modules/nf-core/xz/decompress/meta.yml +++ b/modules/nf-core/xz/decompress/meta.yml @@ -1,4 +1,3 @@ ---- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "xz_decompress" description: Decompresses files with xz. @@ -8,39 +7,40 @@ keywords: - compression tools: - "xz": - description: "xz is a general-purpose data compression tool with command line syntax similar to gzip and bzip2." + description: "xz is a general-purpose data compression tool with command line + syntax similar to gzip and bzip2." homepage: "https://tukaani.org/xz/" documentation: "https://tukaani.org/xz/man/xz.1.html" tool_dev_url: "https://github.com/tukaani-project/xz" licence: ["GNU LGPLv2.1", "GNU GPLv2", "GNU GPLv3"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - - archive: - type: file - description: File to be decompressed - pattern: "*.{xz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - archive: + type: file + description: File to be decompressed + pattern: "*.{xz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - file: - type: file - description: The decompressed file - pattern: "*.*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - $decompressed_file: + type: file + description: The decompressed file + pattern: "*.*" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@leoisl" maintainers: diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml index 7ddcc7781ee9..bb3112e80387 100644 --- a/modules/nf-core/yahs/meta.yml +++ b/modules/nf-core/yahs/meta.yml @@ -13,49 +13,64 @@ tools: tool_dev_url: "https://github.com/c-zhou/yahs" doi: "10.1093/bioinformatics/btac808" licence: ["MIT"] + identifier: biotools:yahs input: # Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - # - - hic_map: - type: file - description: BED file containing coordinates of read alignments - pattern: "*.{bed,bam,bin}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: index of the reference file - pattern: "*.{fai}" + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - hic_map: + type: file + description: BED file containing coordinates of read alignments + pattern: "*.{bed,bam,bin}" + - - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - - fai: + type: file + description: index of the reference file + pattern: "*.{fai}" output: #Only when we have meta - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test' ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - scaffolds_fasta: - type: file - description: FASTA file with resulting contigs - pattern: "*scaffolds_final.fa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*scaffolds_final.fa": + type: file + description: FASTA file with resulting contigs + pattern: "*scaffolds_final.fa" - scaffolds_agp: - type: file - description: AGP file containing contigs placing coordinates - pattern: "*scaffolds_final.agp" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*scaffolds_final.agp": + type: file + description: AGP file containing contigs placing coordinates + pattern: "*scaffolds_final.agp" - binary: - type: file - description: BIN file with alignment results of Hi-C reads to the contigs in internal YaHS binary format - pattern: "*bin" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - "*bin": + type: file + description: BIN file with alignment results of Hi-C reads to the contigs in + internal YaHS binary format + pattern: "*bin" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@ksenia-krasheninnikova" maintainers: diff --git a/modules/nf-core/yak/count/meta.yml b/modules/nf-core/yak/count/meta.yml index c5e35302eb49..b8c519e8b987 100644 --- a/modules/nf-core/yak/count/meta.yml +++ b/modules/nf-core/yak/count/meta.yml @@ -14,33 +14,34 @@ tools: documentation: "https://github.com/lh3/yak/blob/master/README.md" tool_dev_url: "https://github.com/lh3/yak" licence: ["MIT"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - fastq: - type: file - description: reads fastq/fasta file - pattern: "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" - + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fastq: + type: file + description: reads fastq/fasta file + pattern: "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'sample1', single_end:false ]` - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - yak: - type: file - description: k-mer hash table of input - pattern: "*.{yak}" - + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.yak": + type: file + description: k-mer hash table of input + pattern: "*.{yak}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@yumisims" maintainers: diff --git a/modules/nf-core/yara/index/meta.yml b/modules/nf-core/yara/index/meta.yml index c2a1a95bccf8..7c4a9eb7d615 100644 --- a/modules/nf-core/yara/index/meta.yml +++ b/modules/nf-core/yara/index/meta.yml @@ -8,29 +8,37 @@ keywords: - reference tools: - yara: - description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + description: Yara is an exact tool for aligning DNA sequencing reads to reference + genomes. homepage: https://github.com/seqan/seqan documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + identifier: biotools:yara input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file output: - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - index: - type: file - description: YARA genome index files - pattern: "yara.*" + - meta: + type: file + description: YARA genome index files + pattern: "yara.*" + - ${fasta}*: + type: file + description: YARA genome index files + pattern: "yara.*" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/yara/mapper/meta.yml b/modules/nf-core/yara/mapper/meta.yml index c6f060322fab..d4f68eebf86e 100644 --- a/modules/nf-core/yara/mapper/meta.yml +++ b/modules/nf-core/yara/mapper/meta.yml @@ -6,48 +6,58 @@ keywords: - reference tools: - yara: - description: Yara is an exact tool for aligning DNA sequencing reads to reference genomes. + description: Yara is an exact tool for aligning DNA sequencing reads to reference + genomes. homepage: https://github.com/seqan/seqan documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan licence: ["https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE"] + identifier: biotools:yara input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - meta2: - type: map - description: | - Groovy Map containing index information - e.g. [ id:'test' ] - - index: - type: file - description: YARA genome index files + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - - meta2: + type: map + description: | + Groovy Map containing index information + e.g. [ id:'test' ] + - index: + type: file + description: YARA genome index files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - bam: - type: file - description: Sorted BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.bam": + type: file + description: Sorted BAM file + pattern: "*.{bam}" - bai: - type: file - description: Sorted BAM file index - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.mapped.bam.bai": + type: file + description: Sorted BAM file index + pattern: "*.{bai}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@apeltzer" maintainers: diff --git a/modules/nf-core/zip/meta.yml b/modules/nf-core/zip/meta.yml index f4bfcd043894..c2b87259f654 100644 --- a/modules/nf-core/zip/meta.yml +++ b/modules/nf-core/zip/meta.yml @@ -7,34 +7,38 @@ keywords: - archiving tools: - unzip: - description: p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip, see www.7-zip.org) for Unix. + description: p7zip is a quick port of 7z.exe and 7za.exe (command line version + of 7zip, see www.7-zip.org) for Unix. homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" licence: ["LGPL-2.1-or-later"] + identifier: "" input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - files: - type: file - description: File or list of files to be zipped + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - files: + type: file + description: File or list of files to be zipped output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - zipped_archive: - type: file - description: ZIP file - pattern: "*.zip" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.zip: + type: file + description: ZIP file + pattern: "*.zip" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" - "@pinin4fjords" From 196062335bb9ec979075bf2212f64a369b927b0d Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Fri, 20 Sep 2024 10:54:32 -0300 Subject: [PATCH 078/486] Update mirtop version (#6663) * update mirtop to 0.4.28 * add prefix to gff outputs * update tests --- modules/nf-core/mirtop/counts/environment.yml | 10 ++++-- modules/nf-core/mirtop/counts/main.nf | 4 +-- .../nf-core/mirtop/counts/tests/main.nf.test | 7 +--- .../mirtop/counts/tests/main.nf.test.snap | 35 ++++++++++++++---- modules/nf-core/mirtop/export/environment.yml | 13 +++---- modules/nf-core/mirtop/export/main.nf | 4 +-- .../mirtop/export/tests/main.nf.test.snap | 12 +++---- modules/nf-core/mirtop/gff/environment.yml | 9 +++-- modules/nf-core/mirtop/gff/main.nf | 6 ++-- modules/nf-core/mirtop/gff/tests/main.nf.test | 8 +---- .../mirtop/gff/tests/main.nf.test.snap | 36 ++++++++++++++----- modules/nf-core/mirtop/stats/environment.yml | 9 +++-- modules/nf-core/mirtop/stats/main.nf | 4 +-- .../mirtop/stats/tests/main.nf.test.snap | 20 +++++------ .../tests/main.nf.test.snap | 14 ++++---- 15 files changed, 114 insertions(+), 77 deletions(-) diff --git a/modules/nf-core/mirtop/counts/environment.yml b/modules/nf-core/mirtop/counts/environment.yml index ed1198d82609..1f5deb375a8a 100644 --- a/modules/nf-core/mirtop/counts/environment.yml +++ b/modules/nf-core/mirtop/counts/environment.yml @@ -4,6 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/counts/main.nf b/modules/nf-core/mirtop/counts/main.nf index 9b623bff8f3b..a4ca1889fb11 100644 --- a/modules/nf-core/mirtop/counts/main.nf +++ b/modules/nf-core/mirtop/counts/main.nf @@ -3,9 +3,7 @@ process MIRTOP_COUNTS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test b/modules/nf-core/mirtop/counts/tests/main.nf.test index 52b31db1eb29..5048c166ab81 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test @@ -54,12 +54,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.versions - ).match() - }, - // md5sum is not stable, order of elements in column "variant" change - { assert file(process.out.tsv[0][1]).readLines().findAll { it.contains("iso-22-I0S21NSLN") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap index d05798b0bb6c..104acf131db0 100644 --- a/modules/nf-core/mirtop/counts/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/counts/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ], "tsv": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" ] } ], @@ -30,18 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T13:24:41.148536938" + "timestamp": "2024-09-18T15:05:22.556134542" }, "isomir - bam": { "content": [ - [ - "versions.yml:md5,16430682c2080d67387e7d5e9caf69a7" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "1": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ], + "tsv": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.tsv:md5,43f8a525104c2d9b5a8937564c3a14f6" + ] + ], + "versions": [ + "versions.yml:md5,a9b4901761f70f5a2c9aa3718dd361b8" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T18:39:50.607483472" + "timestamp": "2024-09-18T16:05:58.332523272" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/export/environment.yml b/modules/nf-core/mirtop/export/environment.yml index 4b5ae03a45a3..17572707529b 100644 --- a/modules/nf-core/mirtop/export/environment.yml +++ b/modules/nf-core/mirtop/export/environment.yml @@ -1,10 +1,11 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" - - "conda-forge::r-base=4.1.1" - - "conda-forge::r-data.table=1.14.2" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/export/main.nf b/modules/nf-core/mirtop/export/main.nf index 33f6c3032623..b99333def69c 100644 --- a/modules/nf-core/mirtop/export/main.nf +++ b/modules/nf-core/mirtop/export/main.nf @@ -3,9 +3,7 @@ process MIRTOP_EXPORT { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/export/tests/main.nf.test.snap b/modules/nf-core/mirtop/export/tests/main.nf.test.snap index f8c668a62fbb..ea272199f4a0 100644 --- a/modules/nf-core/mirtop/export/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/export/tests/main.nf.test.snap @@ -22,7 +22,7 @@ ] ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ [ @@ -44,7 +44,7 @@ ] ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -52,7 +52,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T15:25:40.531010949" + "timestamp": "2024-09-18T14:54:17.653801164" }, "isomir - bam": { "content": [ @@ -72,7 +72,7 @@ ], "3": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ], "fasta": [ @@ -89,7 +89,7 @@ ], "versions": [ - "versions.yml:md5,2dbbe262efcd19a681b803812d0e4c8c" + "versions.yml:md5,f107a819b949304d703be77d60d97ae9" ] } ], @@ -97,6 +97,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:12:49.612315132" + "timestamp": "2024-09-18T16:06:37.626754369" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/gff/environment.yml b/modules/nf-core/mirtop/gff/environment.yml index 6e57308ae1cd..1f5deb375a8a 100644 --- a/modules/nf-core/mirtop/gff/environment.yml +++ b/modules/nf-core/mirtop/gff/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "bioconda::samtools=1.15.1" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/gff/main.nf b/modules/nf-core/mirtop/gff/main.nf index 453b624b9f6f..aeb26bcc64a6 100644 --- a/modules/nf-core/mirtop/gff/main.nf +++ b/modules/nf-core/mirtop/gff/main.nf @@ -3,9 +3,7 @@ process MIRTOP_GFF { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(bam, arity:'1..*') @@ -14,7 +12,7 @@ process MIRTOP_GFF { output: tuple val(meta), path("mirtop/*mirtop.gff") , emit: gff - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test b/modules/nf-core/mirtop/gff/tests/main.nf.test index 3ce7ef855234..85977b436651 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test @@ -33,13 +33,7 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.bam, - process.out.versions, - ).match() - }, - // md5sum is not stable, order of elements in section "variant" may change - { assert file(process.out.gff[0][1]).readLines().findAll { it.contains("iso-24-5URPV39QFB") }} + { assert snapshot(process.out).match() } ) } diff --git a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap index a9e6f852e6ff..0dddae2d318f 100644 --- a/modules/nf-core/mirtop/gff/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/gff/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ], "gff": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" ] } ], @@ -30,19 +30,39 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:40:30.542921953" + "timestamp": "2024-09-18T14:31:04.976117723" }, "isomir - bam": { "content": [ - null, - [ - "versions.yml:md5,d16ade25d46f8d12e200e124205afefc" - ] + { + "0": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "1": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ], + "gff": [ + [ + { + "id": "sample_sim_isomir_bam" + }, + "sample_sim_isomir_bam_mirtop.gff:md5,da04f476c3fb8670e861fd8dd83418f9" + ] + ], + "versions": [ + "versions.yml:md5,4413a2adbdafd7b63e8db3c18bd73314" + ] + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T22:38:09.903017316" + "timestamp": "2024-09-18T16:07:04.203181613" } } \ No newline at end of file diff --git a/modules/nf-core/mirtop/stats/environment.yml b/modules/nf-core/mirtop/stats/environment.yml index 3c24c43e8052..1f5deb375a8a 100644 --- a/modules/nf-core/mirtop/stats/environment.yml +++ b/modules/nf-core/mirtop/stats/environment.yml @@ -4,5 +4,10 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::mirtop=0.4.25" - - "conda-forge::pandas=1.3.5" + - "bioconda::mirtop=0.4.28" + - "bioconda::samtools=1.21" + - "conda-forge::python=3.11" + - "conda-forge::biopython=1.83" + - "bioconda::pysam=0.22.1" + - "bioconda::pybedtools=0.10.0" + - "conda-forge::pandas=2.2.2" diff --git a/modules/nf-core/mirtop/stats/main.nf b/modules/nf-core/mirtop/stats/main.nf index 51d33019a99b..4742448b8c10 100644 --- a/modules/nf-core/mirtop/stats/main.nf +++ b/modules/nf-core/mirtop/stats/main.nf @@ -4,9 +4,7 @@ process MIRTOP_STATS { label 'process_single' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' : - 'biocontainers/mulled-v2-0c13ef770dd7cc5c76c2ce23ba6669234cf03385:63be019f50581cc5dfe4fc0f73ae50f2d4d661f7-0' }" + container "community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools_pruned:60b8208f3dbb2910" input: tuple val(meta), path(mirtop_gff) diff --git a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap index ba9633d12a2c..2904830d59ee 100644 --- a/modules/nf-core/mirtop/stats/tests/main.nf.test.snap +++ b/modules/nf-core/mirtop/stats/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:49:32.73944037" + "timestamp": "2024-09-18T15:02:00.325615537" }, "isomir - bam": { "content": [ @@ -56,7 +56,7 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "1": [ @@ -64,18 +64,18 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "2": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ], "log": [ [ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.log:md5,c5ecfb62e732021795df17306a0fb99b" + "mirtop_stats.log:md5,8fa28ad20bb1b1a91245f2c1e6613f85" ] ], "txt": [ @@ -83,11 +83,11 @@ { "id": "mirtop_gff_sample1" }, - "mirtop_stats.txt:md5,952f4face50f16ae54bc17eeba787535" + "mirtop_stats.txt:md5,006f8767fe5afd6f66c83a28a1caba63" ] ], "versions": [ - "versions.yml:md5,53f4ce15bd9c3321676f960d89a30aca" + "versions.yml:md5,e894f8aff6fda2b94339ecd04fb25aed" ] } ], @@ -95,6 +95,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-03T17:47:39.121648755" + "timestamp": "2024-09-18T15:01:49.621322368" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap index 2a0e41a3439a..513f11be483b 100644 --- a/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_stats_mirna_mirtop/tests/main.nf.test.snap @@ -14,7 +14,7 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.txt:md5,e89c014047ffffed65f1ec4fb328e3bc" + "mirtop_stats.txt:md5,3db542a532cf3f3c8b4efda134bd6202" ] ], [ @@ -22,20 +22,20 @@ { "id": "sample_sim_isomir_bam" }, - "mirtop_stats.log:md5,49b85517828253858cc60a0390567585" + "mirtop_stats.log:md5,676d0cedfb4770f7862bc0601c2a7f15" ] ], [ - "versions.yml:md5,04fed9539a0164a116d37bf090613d42", - "versions.yml:md5,13a50e3cef16f8bb981197bbc9a46d8e", - "versions.yml:md5,5f6bea8a46cdfec82b3d8f1b6c906ac7", - "versions.yml:md5,976382d50b05cded89483e2415fde415" + "versions.yml:md5,60caed2a2383e82ed06867a75d5a50e2", + "versions.yml:md5,87d473a6cb931a2032357c3272b3249d", + "versions.yml:md5,91c635a35016586e75b620c7f33e6461", + "versions.yml:md5,b314282e0db6b00dc8acaffe182f2b80" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-12T23:13:48.308574263" + "timestamp": "2024-09-19T21:09:04.079276367" } } \ No newline at end of file From 49057d33fa714bcc7c6c420ad4452d5c660fae8a Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Fri, 20 Sep 2024 16:00:37 +0200 Subject: [PATCH 079/486] Display message when error 132 found (#6675) * Display message when error 132 found * Update snapshots * Make lint happy * Add call to the function with trap * Make nf-core lint happy * More linting * Make lint happy --- modules/nf-core/kalign/align/main.nf | 12 +++++++++++ modules/nf-core/kalign/align/meta.yml | 4 ++-- .../kalign/align/tests/main.nf.test.snap | 20 +++++++++++++------ 3 files changed, 28 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf index 5d575dc71ea9..59998df1adc8 100644 --- a/modules/nf-core/kalign/align/main.nf +++ b/modules/nf-core/kalign/align/main.nf @@ -23,6 +23,18 @@ process KALIGN_ALIGN { def prefix = task.ext.prefix ?: "${meta.id}" def write_output = compress ? ">(pigz -cp ${task.cpus} > ${prefix}.aln.gz)" : "${prefix}.aln" """ + error_handler() { + exit_code=\$? + if [ \$exit_code -eq 132 ]; then + echo "\n\nKALIGN failed because is incompatible with some CPU types, see https://github.com/TimoLassmann/kalign/issues/46.\n\n" + else + trap - ERR + return \$exit_code + fi + } + + trap 'error_handler' ERR + unpigz -cdf $fasta | \\ kalign \\ $args \\ diff --git a/modules/nf-core/kalign/align/meta.yml b/modules/nf-core/kalign/align/meta.yml index 8e9f5f137eed..66c5ca8af955 100644 --- a/modules/nf-core/kalign/align/meta.yml +++ b/modules/nf-core/kalign/align/meta.yml @@ -12,13 +12,13 @@ tools: tool_dev_url: "https://github.com/TimoLassmann/kalign" doi: "10.1093/bioinformatics/btz795" licence: ["GPL v3"] - identifier: "" + identifier: "biotools:kalign" input: - - meta: type: map description: | Groovy Map containing sample information - e.g. `[ id:'test']` + e.g. [ id:'test'] - fasta: type: file description: Input sequences in FASTA format. May be gzipped or uncompressed. diff --git a/modules/nf-core/kalign/align/tests/main.nf.test.snap b/modules/nf-core/kalign/align/tests/main.nf.test.snap index da6fc94c52e7..cee655899ecb 100644 --- a/modules/nf-core/kalign/align/tests/main.nf.test.snap +++ b/modules/nf-core/kalign/align/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" + "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" ], "alignment": [ [ @@ -22,11 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" + "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" ] } ], - "timestamp": "2024-03-22T16:42:01.934768" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-09-20T12:44:18.067352" }, "SARS-CoV-2 scaffolds fasta - compressed": { "content": [ @@ -40,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" + "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" ], "alignment": [ [ @@ -51,10 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" + "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" ] } ], - "timestamp": "2024-03-22T16:42:07.734293" + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-09-20T12:44:31.031883" } } \ No newline at end of file From 2da71b7a52a7c6609cb8f29d316ed3fd90d0f7cc Mon Sep 17 00:00:00 2001 From: Friederike Hanssen Date: Fri, 20 Sep 2024 17:43:12 +0200 Subject: [PATCH 080/486] Sentieon/datametrics: Add plots optionally for each quality metric (#6676) * add plots optionally for each quality metric * switch to nf-test * add snapshots * [automated] Fix linting with Prettier * update meta.yml * exclude conda --------- Co-authored-by: nf-core-bot Co-authored-by: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> --- .github/workflows/test.yml | 2 + modules/nf-core/sentieon/datametrics/main.nf | 21 + modules/nf-core/sentieon/datametrics/meta.yml | 44 ++ .../sentieon/datametrics/tests/main.nf.test | 109 ++++ .../datametrics/tests/main.nf.test.snap | 545 ++++++++++++++++++ .../datametrics/tests/nextflow.config | 16 + .../nf-core/sentieon/datametrics/main.nf | 24 - .../sentieon/datametrics/nextflow.config | 20 - .../nf-core/sentieon/datametrics/test.yml | 13 - 9 files changed, 737 insertions(+), 57 deletions(-) create mode 100644 modules/nf-core/sentieon/datametrics/tests/main.nf.test create mode 100644 modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap create mode 100644 modules/nf-core/sentieon/datametrics/tests/nextflow.config delete mode 100644 tests/modules/nf-core/sentieon/datametrics/main.nf delete mode 100644 tests/modules/nf-core/sentieon/datametrics/nextflow.config delete mode 100644 tests/modules/nf-core/sentieon/datametrics/test.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index c8dc9cbc5180..6d486992e07f 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -606,6 +606,8 @@ jobs: path: modules/nf-core/sentieon/bwaindex - profile: conda path: modules/nf-core/sentieon/bwamem + - profile: conda + path: modules/nf-core/sentieon/datametrics - profile: conda path: modules/nf-core/sentieon/dedup - profile: conda diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf index e430f1e53ecf..6567cc7218fa 100644 --- a/modules/nf-core/sentieon/datametrics/main.nf +++ b/modules/nf-core/sentieon/datametrics/main.nf @@ -12,6 +12,7 @@ process SENTIEON_DATAMETRICS { tuple val(meta), path(bam), path(bai) tuple val(meta2), path(fasta) tuple val(meta3), path(fai) + val plot_results output: tuple val(meta), path('*mq_metrics.txt') , emit: mq_metrics @@ -20,6 +21,10 @@ process SENTIEON_DATAMETRICS { tuple val(meta), path('*gc_metrics.txt') , emit: gc_metrics tuple val(meta), path('*aln_metrics.txt'), emit: aln_metrics tuple val(meta), path('*is_metrics.txt') , emit: is_metrics + tuple val(meta), path('*mq_metrics.pdf') , emit: mq_plot, optional: true + tuple val(meta), path('*qd_metrics.pdf') , emit: qd_plot, optional: true + tuple val(meta), path('*is_metrics.pdf') , emit: is_plot, optional: true + tuple val(meta), path('*gc_metrics.pdf') , emit: gc_plot, optional: true path "versions.yml" , emit: versions when: @@ -47,6 +52,14 @@ process SENTIEON_DATAMETRICS { --algo InsertSizeMetricAlgo ${prefix}_is_metrics.txt \\ --algo AlignmentStat ${prefix}_aln_metrics.txt + if $plot_results + then + sentieon plot GCBias -o ${prefix}_gc_metrics.pdf ${prefix}_gc_metrics.txt + sentieon plot MeanQualityByCycle -o ${prefix}_mq_metrics.pdf ${prefix}_mq_metrics.txt + sentieon plot QualDistribution -o ${prefix}_qd_metrics.pdf ${prefix}_qd_metrics.txt + sentieon plot InsertSizeMetricAlgo -o ${prefix}_is_metrics.pdf ${prefix}_is_metrics.txt + fi + cat <<-END_VERSIONS > versions.yml "${task.process}": sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") @@ -63,6 +76,14 @@ process SENTIEON_DATAMETRICS { touch ${prefix}_aln_metrics.txt touch ${prefix}_is_metrics.txt + if $plot_results + then + touch ${prefix}_gc_metrics.pdf + touch ${prefix}_mq_metrics.pdf + touch ${prefix}_qd_metrics.pdf + touch ${prefix}_is_metrics.pdf + fi + cat <<-END_VERSIONS > versions.yml "${task.process}": sentieon: \$(echo \$(sentieon driver --version 2>&1) | sed -e "s/sentieon-genomics-//g") diff --git a/modules/nf-core/sentieon/datametrics/meta.yml b/modules/nf-core/sentieon/datametrics/meta.yml index a72ff866b467..2b59da39c8a0 100644 --- a/modules/nf-core/sentieon/datametrics/meta.yml +++ b/modules/nf-core/sentieon/datametrics/meta.yml @@ -44,6 +44,10 @@ input: type: file description: Index of the genome fasta file pattern: "*.fai" + - - plot_results: + type: boolean + description: Boolean to determine whether plots should be generated + pattern: "true or false" output: - mq_metrics: - meta: @@ -110,6 +114,46 @@ output: description: File containing the information about statistical distribution of insert sizes pattern: "*.txt" + - mq_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*mq_metrics.pdf": + type: file + description: "PDF containting plot of mean base quality scores" + pattern: "*.pdf" + - qd_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*qd_metrics.pdf": + type: file + description: "PDF containting plot of specific base quality score" + pattern: "*.pdf" + - is_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*is_metrics.pdf": + type: file + description: "PDF containting plot of insert sizes" + pattern: "*.pdf" + - gc_plot: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + - "*gc_metrics.pdf": + type: file + description: "PDF containting plot of GC bias" + pattern: "*.pdf" - versions: - versions.yml: type: file diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test b/modules/nf-core/sentieon/datametrics/tests/main.nf.test new file mode 100644 index 000000000000..a13d68e6ef3a --- /dev/null +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test @@ -0,0 +1,109 @@ +nextflow_process { + + name "Test Process SENTIEON_DATAMETRICS" + script "../main.nf" + process "SENTIEON_DATAMETRICS" + + tag "modules" + tag "modules_nfcore" + tag "sentieon" + tag "sentieon/datametrics" + config "./nextflow.config" + + test("metrics - no plots") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input [1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + input [2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true), + ] + input [3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("metrics - with plots") { + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input [1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + input [2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true), + ] + input [3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + ] + input [1] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + input [2] = [ + [id:'genome'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true), + ] + input [3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap new file mode 100644 index 000000000000..25b1ae128fb0 --- /dev/null +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap @@ -0,0 +1,545 @@ +{ + "sarscov2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "aln_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "gc_summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "is_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "is_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mq_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "mq_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "qd_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "qd_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.pdf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T12:01:01.974389137" + }, + "metrics - with plots": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + ] + ], + "10": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + ] + ], + "6": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.pdf:md5,c04212fac971c67066082dcb63fa08ce" + ] + ], + "7": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.pdf:md5,4edab3779660668a7cfd203196912ace" + ] + ], + "8": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.pdf:md5,068232633e0f93ea2b53f4c698bd8a54" + ] + ], + "9": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.pdf:md5,950372106204ff4d2fbe5ca413ac8300" + ] + ], + "aln_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + ] + ], + "gc_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + ] + ], + "gc_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.pdf:md5,950372106204ff4d2fbe5ca413ac8300" + ] + ], + "gc_summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + ] + ], + "is_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + ] + ], + "is_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.pdf:md5,068232633e0f93ea2b53f4c698bd8a54" + ] + ], + "mq_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + ] + ], + "mq_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.pdf:md5,c04212fac971c67066082dcb63fa08ce" + ] + ], + "qd_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + ] + ], + "qd_plot": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.pdf:md5,4edab3779660668a7cfd203196912ace" + ] + ], + "versions": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T12:00:41.711146115" + }, + "metrics - no plots": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + ] + ], + "10": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + ] + ], + "6": [ + + ], + "7": [ + + ], + "8": [ + + ], + "9": [ + + ], + "aln_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + ] + ], + "gc_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + ] + ], + "gc_plot": [ + + ], + "gc_summary": [ + [ + { + "id": "test", + "single_end": false + }, + "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + ] + ], + "is_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + ] + ], + "is_plot": [ + + ], + "mq_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + ] + ], + "mq_plot": [ + + ], + "qd_metrics": [ + [ + { + "id": "test", + "single_end": false + }, + "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + ] + ], + "qd_plot": [ + + ], + "versions": [ + "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T12:00:27.37021578" + } +} \ No newline at end of file diff --git a/modules/nf-core/sentieon/datametrics/tests/nextflow.config b/modules/nf-core/sentieon/datametrics/tests/nextflow.config new file mode 100644 index 000000000000..dead4e3238c1 --- /dev/null +++ b/modules/nf-core/sentieon/datametrics/tests/nextflow.config @@ -0,0 +1,16 @@ +env { + // NOTE This is how pipeline users will use Sentieon in real world use + SENTIEON_LICENSE = "$SENTIEON_LICSRVR_IP" + // NOTE This should only happen in GitHub actions or nf-core MegaTests + SENTIEON_AUTH_MECH = "$SENTIEON_AUTH_MECH" + SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA + // NOTE This is how pipeline users will test out Sentieon with a license file + // nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat | base64 -w 0) +} + +process { + withLabel: 'sentieon' { + ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 + ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 + } +} diff --git a/tests/modules/nf-core/sentieon/datametrics/main.nf b/tests/modules/nf-core/sentieon/datametrics/main.nf deleted file mode 100644 index be7c607f383b..000000000000 --- a/tests/modules/nf-core/sentieon/datametrics/main.nf +++ /dev/null @@ -1,24 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { SENTIEON_DATAMETRICS } from '../../../../../modules/nf-core/sentieon/datametrics/main.nf' - -workflow test_sentieon_datametrics { - - input = [ - [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) - ] - fasta = [ - [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ] - fai = [ - [id:'genome'], - file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - ] - - SENTIEON_DATAMETRICS ( input, fasta, fai ) -} diff --git a/tests/modules/nf-core/sentieon/datametrics/nextflow.config b/tests/modules/nf-core/sentieon/datametrics/nextflow.config deleted file mode 100644 index 578ce50b6a5a..000000000000 --- a/tests/modules/nf-core/sentieon/datametrics/nextflow.config +++ /dev/null @@ -1,20 +0,0 @@ -env { - // NOTE This is how nf-core/sarek users will use Sentieon in real world use - SENTIEON_LICENSE = $SENTIEON_LICSRVR_IP - // NOTE This should only happen in GitHub actions or nf-core MegaTests - SENTIEON_AUTH_MECH = $SENTIEON_AUTH_MECH - SENTIEON_AUTH_DATA = secrets.SENTIEON_AUTH_DATA - // NOTE This is how nf-core/sarek users will test out Sentieon in Sarek with a license file - // nextflow secrets set SENTIEON_LICENSE_BASE64 $(cat | base64 -w 0) -} - -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withLabel: 'sentieon' { - ext.sentieon_auth_mech_base64 = secrets.SENTIEON_AUTH_MECH_BASE64 - ext.sentieon_auth_data_base64 = secrets.SENTIEON_AUTH_DATA_BASE64 - } - -} diff --git a/tests/modules/nf-core/sentieon/datametrics/test.yml b/tests/modules/nf-core/sentieon/datametrics/test.yml deleted file mode 100644 index c13434ee9800..000000000000 --- a/tests/modules/nf-core/sentieon/datametrics/test.yml +++ /dev/null @@ -1,13 +0,0 @@ -- name: sentieon datametrics - command: nextflow run ./tests/modules/nf-core/sentieon/datametrics -entry test_sentieon_datametrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/sentieon/datametrics/nextflow.config - tags: - - sentieon - - sentieon/datametrics - files: - - path: ./output/sentieon/test_mq_metrics.txt - - path: ./output/sentieon/test_qd_metrics.txt - - path: ./output/sentieon/test_gc_summary.txt - - path: ./output/sentieon/test_gc_metrics.txt - - path: ./output/sentieon/test_aln_metrics.txt - - path: ./output/sentieon/test_is_metrics.txt - - path: ./output/sentieon/versions.yml From cadb9bbfe56001ac421e0ee87808b0ccc754593a Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Fri, 20 Sep 2024 18:26:04 +0200 Subject: [PATCH 081/486] KALIGN - fix bug in error catching: remove new lines (#6681) * remove new lines * fix test --- modules/nf-core/kalign/align/main.nf | 2 +- .../kalign/align/tests/main.nf.test.snap | 20 +++++++++---------- 2 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules/nf-core/kalign/align/main.nf b/modules/nf-core/kalign/align/main.nf index 59998df1adc8..d1e0668928c2 100644 --- a/modules/nf-core/kalign/align/main.nf +++ b/modules/nf-core/kalign/align/main.nf @@ -26,7 +26,7 @@ process KALIGN_ALIGN { error_handler() { exit_code=\$? if [ \$exit_code -eq 132 ]; then - echo "\n\nKALIGN failed because is incompatible with some CPU types, see https://github.com/TimoLassmann/kalign/issues/46.\n\n" + echo "KALIGN failed because is incompatible with some CPU types, see https://github.com/TimoLassmann/kalign/issues/46." else trap - ERR return \$exit_code diff --git a/modules/nf-core/kalign/align/tests/main.nf.test.snap b/modules/nf-core/kalign/align/tests/main.nf.test.snap index cee655899ecb..016894ac04f1 100644 --- a/modules/nf-core/kalign/align/tests/main.nf.test.snap +++ b/modules/nf-core/kalign/align/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" + "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" ], "alignment": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" + "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T12:44:18.067352" + "timestamp": "2024-09-20T16:18:52.609498249" }, "SARS-CoV-2 scaffolds fasta - compressed": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" + "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" ], "alignment": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,b5ef6a09110c24f552fcddb1af13ff94" + "versions.yml:md5,0764ff5c30fd8befd86baa9026493ffe" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T12:44:31.031883" + "timestamp": "2024-09-20T16:19:03.641722069" } } \ No newline at end of file From 8af81e4f81833fb4f98e0746a10e230a849648e8 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Fri, 20 Sep 2024 19:14:42 +0200 Subject: [PATCH 082/486] new module: jvarkit vcf2table (#6631) * 1st * vcf2table * fix tests.snap * rm name * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * test content * fix meta * update tools 3.0.0 * update env.yml --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../nf-core/jvarkit/vcf2table/environment.yml | 8 ++ modules/nf-core/jvarkit/vcf2table/main.nf | 63 +++++++++++++++ modules/nf-core/jvarkit/vcf2table/meta.yml | 75 ++++++++++++++++++ .../jvarkit/vcf2table/tests/main.nf.test | 76 +++++++++++++++++++ .../jvarkit/vcf2table/tests/main.nf.test.snap | 30 ++++++++ .../jvarkit/vcf2table/tests/nextflow.config | 7 ++ .../nf-core/jvarkit/vcf2table/tests/tags.yml | 2 + 7 files changed, 261 insertions(+) create mode 100644 modules/nf-core/jvarkit/vcf2table/environment.yml create mode 100644 modules/nf-core/jvarkit/vcf2table/main.nf create mode 100644 modules/nf-core/jvarkit/vcf2table/meta.yml create mode 100644 modules/nf-core/jvarkit/vcf2table/tests/main.nf.test create mode 100644 modules/nf-core/jvarkit/vcf2table/tests/main.nf.test.snap create mode 100644 modules/nf-core/jvarkit/vcf2table/tests/nextflow.config create mode 100644 modules/nf-core/jvarkit/vcf2table/tests/tags.yml diff --git a/modules/nf-core/jvarkit/vcf2table/environment.yml b/modules/nf-core/jvarkit/vcf2table/environment.yml new file mode 100644 index 000000000000..18aee65ed611 --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/environment.yml @@ -0,0 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda:bcftools=1.20" + - "bioconda::jvarkit=2024.08.25" diff --git a/modules/nf-core/jvarkit/vcf2table/main.nf b/modules/nf-core/jvarkit/vcf2table/main.nf new file mode 100644 index 000000000000..f701a6b487ef --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/main.nf @@ -0,0 +1,63 @@ +process JVARKIT_VCF2TABLE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(vcf), path(tbi), path(regions_file) + tuple val(meta2), path(pedigree) + output: + tuple val(meta), path("*.${extension}"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args1 = task.ext.args1 ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def ped = pedigree?"--pedigree \"${pedigree}\"":"" + def regions_file = regions_file? (tbi ? " --regions-file" : " --targets-file")+" \"${regions_file}\" ":"" + extension = getFileExtension(args2); /* custom function, see below */ + + if ("$vcf" == "${prefix}.${extension}") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + mkdir -p TMP + + bcftools view ${regions_file} -O v ${args1} "${vcf}" |\\ + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP vcf2table ${ped} ${args2} > "${prefix}.${extension}" + + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def args2 = task.ext.args2 ?: '' + extension = getFileExtension(args2); /* custom function, see below */ + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.${extension}" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} + + +// Custom Function to get VCF extension +String getFileExtension(String args) { + return args.contains("--format html") ? "html" : "txt" +} diff --git a/modules/nf-core/jvarkit/vcf2table/meta.yml b/modules/nf-core/jvarkit/vcf2table/meta.yml new file mode 100644 index 000000000000..4170d11f7751 --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/meta.yml @@ -0,0 +1,75 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "jvarkit_vcf2table" +description: Convert VCF to a user friendly table +keywords: + - vcf + - bcf + - text + - html + - visualization +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.6084/m9.figshare.1425030" + licence: ["MIT"] + args_id: "$args2" + identifier: "" + - "bcftools": + description: | + View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF + homepage: "http://samtools.github.io/bcftools/bcftools.html" + documentation: "http://www.htslib.org/doc/bcftools.html" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args1" + identifier: "biotools:samtools" +input: + - - "meta": + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'genome' ] + - vcf: + type: file + description: Input vcf/bcf file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - tbi: + type: file + description: Optional index file for the VCF + pattern: "*.{tbi,csi}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{bed,bed.gz,txt,tsv}" + - - meta2: + type: map + description: | + Groovy Map containing pedigree information + - pedigree: + type: file + description: Optional pedigree for jvarkit + pattern: "*.{ped,pedigree}" +output: + - output: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.${extension}": + type: file + description: Output file + pattern: "*.{txt,html}" + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test new file mode 100644 index 000000000000..0a0c41607cb4 --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test @@ -0,0 +1,76 @@ +nextflow_process { + + name "Test Process JVARKIT_VCF2TABLE" + script "../main.nf" + process "JVARKIT_VCF2TABLE" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/vcf2table" + + test("sarscov2 - vcf") { + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] + ] + input[1] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.output[0][1]).text.startsWith(">>MT192765.1:197/G (n. 1)")}, + { assert snapshot( + path(process.out.output[0][1]), + process.out.versions + ).match() + } + ) + } + + } + + + + test("sarscov2 - vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"vcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [], + [] + ] + input[1] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.output[0][1]), + process.out.versions + ).match() + } + ) + } + + } + +} diff --git a/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test.snap b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test.snap new file mode 100644 index 000000000000..de05e2fd64f6 --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + "sarscov2 - vcf": { + "content": [ + "vcf_test.txt:md5,91513583ed7c0d0e63bb046c03419460", + [ + "versions.yml:md5,0c4f207f3c21b881974f056ea9f863c7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + + "sarscov2 - vcf - stub": { + "content": [ + "vcf_test.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "versions.yml:md5,0c4f207f3c21b881974f056ea9f863c7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + } + +} diff --git a/modules/nf-core/jvarkit/vcf2table/tests/nextflow.config b/modules/nf-core/jvarkit/vcf2table/tests/nextflow.config new file mode 100644 index 000000000000..a7272c8356ef --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: JVARKIT_VCF2TABLE { + ext.args2=" --hide NO_CALL " + } + +} diff --git a/modules/nf-core/jvarkit/vcf2table/tests/tags.yml b/modules/nf-core/jvarkit/vcf2table/tests/tags.yml new file mode 100644 index 000000000000..de823e3f6b30 --- /dev/null +++ b/modules/nf-core/jvarkit/vcf2table/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/vcf2table: + - "modules/nf-core/jvarkit/vcf2table/**" From 163f8ba5ab8dc54bc68099844b3b7fb5c9cba570 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Fri, 20 Sep 2024 19:42:48 +0200 Subject: [PATCH 083/486] add module telseq (#6678) * add module telseq * lint code * fix quote in meta * fix lint * fix_indent * fix_indent * fix_indent * fix_indent * fix_indent * fix_indent * add bed test * fix snap --- modules/nf-core/telseq/environment.yml | 6 + modules/nf-core/telseq/main.nf | 62 +++++++++ modules/nf-core/telseq/meta.yml | 89 +++++++++++++ modules/nf-core/telseq/tests/main.nf.test | 122 ++++++++++++++++++ .../nf-core/telseq/tests/main.nf.test.snap | 54 ++++++++ modules/nf-core/telseq/tests/tags.yml | 2 + 6 files changed, 335 insertions(+) create mode 100644 modules/nf-core/telseq/environment.yml create mode 100644 modules/nf-core/telseq/main.nf create mode 100644 modules/nf-core/telseq/meta.yml create mode 100644 modules/nf-core/telseq/tests/main.nf.test create mode 100644 modules/nf-core/telseq/tests/main.nf.test.snap create mode 100644 modules/nf-core/telseq/tests/tags.yml diff --git a/modules/nf-core/telseq/environment.yml b/modules/nf-core/telseq/environment.yml new file mode 100644 index 000000000000..5502308b97c1 --- /dev/null +++ b/modules/nf-core/telseq/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::samtools=1.20 + - bioconda::telseq=0.0.2 diff --git a/modules/nf-core/telseq/main.nf b/modules/nf-core/telseq/main.nf new file mode 100644 index 000000000000..4bfeac5aba4e --- /dev/null +++ b/modules/nf-core/telseq/main.nf @@ -0,0 +1,62 @@ +process TELSEQ { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-5ce2a0c04652b0d0cc87f012a2240e1e5a90bc90:eb084e8aa92146f3987d00af8d38b36214d1f39f-0': + 'biocontainers/mulled-v2-5ce2a0c04652b0d0cc87f012a2240e1e5a90bc90:eb084e8aa92146f3987d00af8d38b36214d1f39f-0' }" + + input: + tuple val(meta ), path(bam), path(bai) + tuple val(meta2), path(fasta) + tuple val(meta3), path(fai) + tuple val(meta4), path(bed) + + output: + tuple val(meta), path("*.telseq.tsv"), emit: output + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def exome = bed ? " --exomebed=${bed}" : "" + """ + # telseq doesn't support CRAM. See https://github.com/zd1/telseq/issues/26 + if ${bam.name.endsWith(".cram")} + then + samtools view -T ${fasta} -O BAM --uncompressed ${bam} |\\ + telseq ${args} ${exome} - > tmp.tsv + else + telseq ${args} ${exome} ${bam} > tmp.tsv + fi + + # + # 'bug' in telseq, messages that should be printed on stderr are printed on stdout + # We remove them with awk + # + awk '/^ReadGroup/ {ok=1;} {if(ok) print;}' tmp.tsv > ${prefix}.telseq.tsv + rm tmp.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + telseq: \$(telseq --help 2>&1 | grep "^Version" -m1 | cut -d ' ' -f2) + samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.telseq.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + telseq: \$(telseq --help 2>&1 | grep "^Version" -m1 | cut -d ' ' -f2) + samtools: \$(samtools --version |& sed '1!d ; s/samtools //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/telseq/meta.yml b/modules/nf-core/telseq/meta.yml new file mode 100644 index 000000000000..092567432fbd --- /dev/null +++ b/modules/nf-core/telseq/meta.yml @@ -0,0 +1,89 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "telseq" +description: "Telseq: a software for calculating telomere length" +keywords: + - bam + - cram + - genomics + - samtools + - telomere + - telseq +tools: + - "telseq": + description: "A software for calculating telomere length" + homepage: "https://github.com/zd1/telseq" + documentation: "https://github.com/zd1/telseq" + tool_dev_url: "https://github.com/zd1/telseq" + doi: "10.1093/nar/gku181" + licence: ["GPL v3"] + args_id: "$args" + identifier: "" + - samtools: + description: Tools for dealing with SAM, BAM and CRAM files + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + tool_dev_url: https://github.com/samtools/samtools + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] + identifier: "biotools:samtools" +input: + - - "meta ": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'genome' ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: bam index file + pattern: "*.{bai,crai}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'genome' ] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fa,fasta}" + - - meta3: + type: map + description: | + Groovy Map containing reference index information + e.g. [ id:'genome' ] + - fai: + type: file + description: Fasta index file + pattern: "*.fai" + - - meta4: + type: map + description: | + Groovy Map containing bed information + e.g. [ id:'genome' ] + - bed: + type: file + description: Optional exome regions in BED format. These regions will be excluded + pattern: "*.bed" +output: + - output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.telseq.tsv": + type: file + description: Telseq output + pattern: "*.tsv" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/telseq/tests/main.nf.test b/modules/nf-core/telseq/tests/main.nf.test new file mode 100644 index 000000000000..02a4e0815b1d --- /dev/null +++ b/modules/nf-core/telseq/tests/main.nf.test @@ -0,0 +1,122 @@ +// nf-core modules test telseq +nextflow_process { + + name "Test Process TELSEQ" + script "../main.nf" + process "TELSEQ" + + tag "modules" + tag "modules_nfcore" + tag "telseq" + + test("sarscov2 - cram") { + when { + process { + """ + input[0] = [ + [ id:'cram' ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true) + ] + input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.output[0][1], + process.out.versions).match() } + ) + } + } + + test("sarscov2 - bam") { + when { + process { + """ + input[0] = [ + [ id:'bam' ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.output[0][1], + process.out.versions).match() } + ) + } + } + + test("sarscov2 - bam - bed") { + when { + process { + """ + input[0] = [ + [ id:'bambed' ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.output[0][1], + process.out.versions).match() } + ) + } + } + + + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'stub', single_end:false ], // meta map + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + input[1] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + input[2] = [ [] , file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) ] + input[3] = [ [] , [] ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.output[0][1], + process.out.versions).match() } + ) + } + + } + +} diff --git a/modules/nf-core/telseq/tests/main.nf.test.snap b/modules/nf-core/telseq/tests/main.nf.test.snap new file mode 100644 index 000000000000..4ca41fd6646b --- /dev/null +++ b/modules/nf-core/telseq/tests/main.nf.test.snap @@ -0,0 +1,54 @@ +{ + "sarscov2 - bam - stub": { + "content": [ + "stub.telseq.tsv:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T14:09:45.936712383" + }, + "sarscov2 - cram": { + "content": [ + "cram.telseq.tsv:md5,82005b49e17f114e8ad759dd9d520912", + [ + "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T14:09:09.775504172" + }, + "sarscov2 - bam": { + "content": [ + "bam.telseq.tsv:md5,82005b49e17f114e8ad759dd9d520912", + [ + "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T14:09:27.747371336" + }, + "sarscov2 - bam - bed": { + "content": [ + "bambed.telseq.tsv:md5,58374f99d395fa64ea561aca73fd6c89", + [ + "versions.yml:md5,f0569759735b18ce1064c9ed2ddc9610" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T14:09:27.747371336" + } +} diff --git a/modules/nf-core/telseq/tests/tags.yml b/modules/nf-core/telseq/tests/tags.yml new file mode 100644 index 000000000000..5776bda0406c --- /dev/null +++ b/modules/nf-core/telseq/tests/tags.yml @@ -0,0 +1,2 @@ +telseq: + - "modules/nf-core/telseq/**" From 009760978ef780cb08f7eccb8847f181ffa29eb0 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 20 Sep 2024 17:50:48 +0000 Subject: [PATCH 084/486] chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.6.6 (#6671) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 595734b39a2f..2387066d67f8 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.5 + rev: v0.6.6 hooks: - id: ruff files: \.py$ From 589abc5edfdb6c7f8faf3df098f8d11d33b9b487 Mon Sep 17 00:00:00 2001 From: Pierre Lindenbaum <33838+lindenb@users.noreply.github.com> Date: Mon, 23 Sep 2024 16:55:19 +0200 Subject: [PATCH 085/486] new module jvarkit/dict2bed (#6683) * dict2bed * fix snap * fix-snap * fix meta names * args1 to args * remove dict_files from output * change test * fixtest * fixtest * reverse change from https://github.com/nf-core/modules/pull/6683#pullrequestreview-2321835180 --- .../nf-core/jvarkit/dict2bed/environment.yml | 7 ++ modules/nf-core/jvarkit/dict2bed/main.nf | 47 +++++++++++ modules/nf-core/jvarkit/dict2bed/meta.yml | 51 ++++++++++++ .../jvarkit/dict2bed/tests/main.nf.test | 78 +++++++++++++++++++ .../jvarkit/dict2bed/tests/main.nf.test.snap | 30 +++++++ .../jvarkit/dict2bed/tests/nextflow.config | 5 ++ .../nf-core/jvarkit/dict2bed/tests/tags.yml | 2 + 7 files changed, 220 insertions(+) create mode 100644 modules/nf-core/jvarkit/dict2bed/environment.yml create mode 100644 modules/nf-core/jvarkit/dict2bed/main.nf create mode 100644 modules/nf-core/jvarkit/dict2bed/meta.yml create mode 100644 modules/nf-core/jvarkit/dict2bed/tests/main.nf.test create mode 100644 modules/nf-core/jvarkit/dict2bed/tests/main.nf.test.snap create mode 100644 modules/nf-core/jvarkit/dict2bed/tests/nextflow.config create mode 100644 modules/nf-core/jvarkit/dict2bed/tests/tags.yml diff --git a/modules/nf-core/jvarkit/dict2bed/environment.yml b/modules/nf-core/jvarkit/dict2bed/environment.yml new file mode 100644 index 000000000000..14d0e3387c56 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::jvarkit=2024.08.25" diff --git a/modules/nf-core/jvarkit/dict2bed/main.nf b/modules/nf-core/jvarkit/dict2bed/main.nf new file mode 100644 index 000000000000..ca8afd2f80fd --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/main.nf @@ -0,0 +1,47 @@ +process JVARKIT_DICT2BED { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(dict_files) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' /* give a chance to run a command like '| cut -f1,2,3 |sort | uniq' */ + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir TMP + + jvarkit -Xmx${task.memory.giga}g -XX:-UsePerfData -Djava.io.tmpdir=TMP dict2bed ${args} ${dict_files} ${args2} > ${prefix}.bed + + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.bed" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} diff --git a/modules/nf-core/jvarkit/dict2bed/meta.yml b/modules/nf-core/jvarkit/dict2bed/meta.yml new file mode 100644 index 000000000000..0bba699f69c4 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/meta.yml @@ -0,0 +1,51 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "jvarkit_dict2xml" +description: Extract BED file from hts files containing a dictionary (VCF,BAM, CRAM, DICT, etc...) +keywords: + - vcf + - bcf + - bed + - dict + - dictionary + - fasta + - fai +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.6084/m9.figshare.1425030" + licence: ["MIT License"] + args_id: "$args" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing dict file information + e.g. [ id:'test_reference' ] + - dict_files: + type: file + description: File(s) containing a dictionary VCF/BCF/BAM/DICT etc... + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz,dict,fai,bam,cram,interval_list}" +output: + - bed: + - meta: + type: map + description: | + Groovy Map containing VCF information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: BED output file + pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lindenb" +maintainers: + - "@lindenb" diff --git a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test new file mode 100644 index 000000000000..ff9eb040e350 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test @@ -0,0 +1,78 @@ +// nf-core modules test jvarkit/dict2bed +nextflow_process { + + name "Test Process JVARKIT_DICT2BED" + script "../main.nf" + process "JVARKIT_DICT2BED" + config "./nextflow.config" + + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/dict2bed" + + test("sarscov2 - dict") { + + when { + process { + """ + input[0] =[ + [id:"dict_test"], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.bed[0][1]), + process.out.versions + ).match() + } + ) + } + + } + + test("sarscov2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"dict_stub"], + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true) + ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.bed[0][1]), + process.out.versions + ).match() + } + ) + } + + } +} diff --git a/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test.snap b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test.snap new file mode 100644 index 000000000000..535acba5e726 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/tests/main.nf.test.snap @@ -0,0 +1,30 @@ +{ + + "sarscov2 - dict": { + "content": [ + "dict_test.bed:md5,296a58ee6d26a13ceed194d3f5286c64", + [ + "versions.yml:md5,53252028d7bd745cb0720a242d7851d7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + }, + "sarscov2 - stub": { + "content": [ + "dict_stub.bed:md5,d41d8cd98f00b204e9800998ecf8427e", + [ + "versions.yml:md5,53252028d7bd745cb0720a242d7851d7" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-03T14:00:13.118369362" + } + +} diff --git a/modules/nf-core/jvarkit/dict2bed/tests/nextflow.config b/modules/nf-core/jvarkit/dict2bed/tests/nextflow.config new file mode 100644 index 000000000000..10753a2b9d78 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: JVARKIT_DICT2BED { + ext.args2 =" | cut -f1,2,3 " + } +} diff --git a/modules/nf-core/jvarkit/dict2bed/tests/tags.yml b/modules/nf-core/jvarkit/dict2bed/tests/tags.yml new file mode 100644 index 000000000000..82b4d2676d66 --- /dev/null +++ b/modules/nf-core/jvarkit/dict2bed/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/dict2bed: + - "modules/nf-core/jvarkit/dict2bed/**" From 4eecd9a0c06fa508ae314c06ac952c161c019679 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Mon, 23 Sep 2024 17:23:51 +0200 Subject: [PATCH 086/486] mtmalign/align - clean tests and fix output (#6684) * clean * Update modules/nf-core/mtmalign/align/main.nf Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> * update align --------- Co-authored-by: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> --- modules/nf-core/mtmalign/align/main.nf | 10 ++-- .../nf-core/mtmalign/align/tests/main.nf.test | 60 +++++++++++-------- .../mtmalign/align/tests/main.nf.test.snap | 53 +++++++++++++--- 3 files changed, 85 insertions(+), 38 deletions(-) diff --git a/modules/nf-core/mtmalign/align/main.nf b/modules/nf-core/mtmalign/align/main.nf index 933d2c74a8f6..54c9c5213fc6 100644 --- a/modules/nf-core/mtmalign/align/main.nf +++ b/modules/nf-core/mtmalign/align/main.nf @@ -37,18 +37,16 @@ process MTMALIGN_ALIGN { mtm-align -i input_list.txt -o ${prefix}.pdb # -o does not affect the fasta naming, so move it to the new name - mv ./mTM_result/result.fasta ./mTM_result/${prefix}.aln + mv ./mTM_result/result.fasta ${prefix}.aln + mv ./mTM_result/${prefix}.pdb ${prefix}.pdb # Remove ".pdb" from the ids in the alignment file - sed -i 's/\\.pdb//g' ./mTM_result/${prefix}.aln + sed -i 's/\\.pdb//g' ${prefix}.aln # compress both output files if ${compress}; then - pigz -p ${task.cpus} ./mTM_result/${prefix}.aln ./mTM_result/${prefix}.pdb + pigz -p ${task.cpus} ${prefix}.aln ${prefix}.pdb fi - # move everything in mTM_result to the working directory - mv ./mTM_result/* . - # mtm-align -v prints the wrong version 20180725, so extract it from the cosmetic output in the help message cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test b/modules/nf-core/mtmalign/align/tests/main.nf.test index ada32c39baae..0dc8b885699b 100644 --- a/modules/nf-core/mtmalign/align/tests/main.nf.test +++ b/modules/nf-core/mtmalign/align/tests/main.nf.test @@ -9,19 +9,20 @@ nextflow_process { tag "mtmalign/align" tag "untar" - test("Test on seatoxin dataset - uncompressed") { - setup { + setup { - run("UNTAR") { - script "../../../../../modules/nf-core/untar/main.nf" - process { - """ - archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) - input[0] = Channel.of(tuple([id:'test'], archive)) - """ - } - } + run("UNTAR") { + script "../../../../../modules/nf-core/untar/main.nf" + process { + """ + archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) + input[0] = Channel.of(tuple([id:'test'], archive)) + """ + } } + } + + test("seatoxin - uncompressed") { when { params { @@ -49,19 +50,7 @@ nextflow_process { } } - test("Test on seatoxin dataset - compressed") { - setup { - - run("UNTAR") { - script "../../../../../modules/nf-core/untar/main.nf" - process { - """ - archive = file("https://raw.githubusercontent.com/nf-core/test-datasets/multiplesequencealign/testdata/structures/seatoxin-ref.tar.gz", checkIfExists: true) - input[0] = Channel.of(tuple([id:'test'], archive)) - """ - } - } - } + test("seatoxin - compressed") { when { params { @@ -87,4 +76,27 @@ nextflow_process { ) } } + + test("seatoxin - uncompressed - stub") { + + options '-stub' + when { + params { + } + process { + """ + input[0] = UNTAR.out.untar.map { meta,dir -> [[ id:'test' ], file(dir).listFiles().collect()]} + input[1] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } \ No newline at end of file diff --git a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap index 0eefb1919fc6..548ced89f304 100644 --- a/modules/nf-core/mtmalign/align/tests/main.nf.test.snap +++ b/modules/nf-core/mtmalign/align/tests/main.nf.test.snap @@ -5,10 +5,6 @@ "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-06-03T11:01:13.729263689" }, "versions1": { @@ -17,10 +13,51 @@ "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, "timestamp": "2024-06-03T11:01:37.28539854" + }, + "seatoxin - uncompressed - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.pdb:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10" + ], + "alignment": [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "structure": [ + [ + { + "id": "test" + }, + "test.pdb:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,7cbacec15bb9e0c8cbb27610bde74c10" + ] + } + ], + "timestamp": "2024-09-23T16:51:04.027375" } } \ No newline at end of file From 757f60e5656283122cd6ec37d4679483bebb7312 Mon Sep 17 00:00:00 2001 From: Anabella Trigila <18577080+atrigila@users.noreply.github.com> Date: Mon, 23 Sep 2024 13:48:52 -0300 Subject: [PATCH 087/486] Add nf-core module and subworkflow `mirdeep2` (#6662) * first design mirdeep * fix prettier * fix linting * reformat subworkflow structure * fix linting * allow paths to files or replace with 'none' * fix linting * capture unstable outputs in snapshot * update meta --------- Co-authored-by: Alexander Peltzer Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .../nf-core/mirdeep2/mapper/environment.yml | 7 + modules/nf-core/mirdeep2/mapper/main.nf | 53 +++++++ modules/nf-core/mirdeep2/mapper/meta.yml | 50 +++++++ .../mirdeep2/mapper/tests/main.nf.test | 141 ++++++++++++++++++ .../mirdeep2/mapper/tests/main.nf.test.snap | 51 +++++++ .../mirdeep2/mapper/tests/nextflow.config | 11 ++ .../nf-core/mirdeep2/mirdeep2/environment.yml | 7 + modules/nf-core/mirdeep2/mirdeep2/main.nf | 64 ++++++++ modules/nf-core/mirdeep2/mirdeep2/meta.yml | 76 ++++++++++ .../mirdeep2/mirdeep2/tests/main.nf.test | 111 ++++++++++++++ .../mirdeep2/mirdeep2/tests/main.nf.test.snap | 60 ++++++++ .../mirdeep2/mirdeep2/tests/nextflow.config | 5 + .../nf-core/fastq_find_mirna_mirdeep2/main.nf | 33 ++++ .../fastq_find_mirna_mirdeep2/meta.yml | 51 +++++++ .../tests/main.nf.test | 80 ++++++++++ .../tests/main.nf.test.snap | 20 +++ .../tests/nextflow.config | 11 ++ 17 files changed, 831 insertions(+) create mode 100644 modules/nf-core/mirdeep2/mapper/environment.yml create mode 100644 modules/nf-core/mirdeep2/mapper/main.nf create mode 100644 modules/nf-core/mirdeep2/mapper/meta.yml create mode 100644 modules/nf-core/mirdeep2/mapper/tests/main.nf.test create mode 100644 modules/nf-core/mirdeep2/mapper/tests/main.nf.test.snap create mode 100644 modules/nf-core/mirdeep2/mapper/tests/nextflow.config create mode 100644 modules/nf-core/mirdeep2/mirdeep2/environment.yml create mode 100644 modules/nf-core/mirdeep2/mirdeep2/main.nf create mode 100644 modules/nf-core/mirdeep2/mirdeep2/meta.yml create mode 100644 modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test create mode 100644 modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test.snap create mode 100644 modules/nf-core/mirdeep2/mirdeep2/tests/nextflow.config create mode 100644 subworkflows/nf-core/fastq_find_mirna_mirdeep2/main.nf create mode 100644 subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml create mode 100644 subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test create mode 100644 subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap create mode 100644 subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/nextflow.config diff --git a/modules/nf-core/mirdeep2/mapper/environment.yml b/modules/nf-core/mirdeep2/mapper/environment.yml new file mode 100644 index 000000000000..fafc66632553 --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirdeep2=2.0.1.2" diff --git a/modules/nf-core/mirdeep2/mapper/main.nf b/modules/nf-core/mirdeep2/mapper/main.nf new file mode 100644 index 000000000000..d52820a362bb --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/main.nf @@ -0,0 +1,53 @@ +process MIRDEEP2_MAPPER { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.2--0': + 'biocontainers/mirdeep2:2.0.1.2--0' }" + + input: + tuple val(meta), path(reads) + tuple val(meta2), path(index, stageAs: '*') + + output: + tuple val(meta), path('*.fa'), path('*.arf'), emit: outputs + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.1' + + """ + mapper.pl \\ + ${reads} \\ + $args \\ + -p ${index}/${meta2.id} \\ + -s ${prefix}_collapsed.fa \\ + -t ${prefix}_reads_collapsed_vs_${meta2.id}_genome.arf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirdeep2: \$(echo "$VERSION") + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.1' + """ + touch ${prefix}.fa + touch ${prefix}reads_vs_refdb.arf + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirdeep2: \$(echo "$VERSION") + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirdeep2/mapper/meta.yml b/modules/nf-core/mirdeep2/mapper/meta.yml new file mode 100644 index 000000000000..5844344cf97f --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/meta.yml @@ -0,0 +1,50 @@ +name: "mirdeep2_mapper" +description: | + miRDeep2 Mapper is a tool that prepares deep sequencing reads for downstream miRNA detection by collapsing reads, mapping them to a genome, and outputting the required files for miRNA discovery. +keywords: + - mirdeep2 + - mapper + - RNA sequencing +tools: + - "mirdeep2": + description: | + miRDeep2 Mapper (`mapper.pl`) is part of the miRDeep2 suite. It collapses identical reads, maps them to a reference genome, and outputs both collapsed FASTA and ARF files for downstream miRNA detection and analysis. + homepage: "https://www.mdc-berlin.de/content/mirdeep2-documentation" + documentation: "https://www.mdc-berlin.de/content/mirdeep2-documentation" + tool_dev_url: "https://github.com/rajewsky-lab/mirdeep2" + doi: "10.1093/nar/gkn491" + licence: ["GPL V3"] + identifier: biotools:mirdeep2 + +input: + - - meta: + type: map + description: Groovy Map containing sample information, e.g. `[ id:'sample1', + single_end:false ]` + - reads: + type: file + description: File containing the raw sequencing reads that need to be collapsed + and mapped to a reference genome. + pattern: "*.fa" + - - meta2: + type: map + description: Groovy Map containing information about the genome index. + - index: + type: file + description: Path to the genome index file used for mapping the reads to the + genome. + pattern: "*" +output: + - outputs: + - meta: {} + - "*.fa": {} + - "*.arf": {} + - versions: + - versions.yml: + type: file + description: File containing software versions for tracking. + pattern: "versions.yml" +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirdeep2/mapper/tests/main.nf.test b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test new file mode 100644 index 000000000000..62e3e615abc6 --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test @@ -0,0 +1,141 @@ + +nextflow_process { + + name "Test Process MIRDEEP2_MAPPER" + script "../main.nf" + process "MIRDEEP2_MAPPER" + + tag "modules" + tag "modules_nfcore" + tag "mirdeep2" + tag "bowtie/build" + tag "mirdeep2/mapper" + tag "seqkit/fq2fa" + tag "seqkit/replace" + + + setup { + run("BOWTIE_BUILD") { + script "../../../bowtie/build/main.nf" + process { + """ + input[0] = [ + [ id:'genome_cel_cluster' ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/cel_cluster.fa', checkIfExists: true) + ] + """ + } + } + + run("SEQKIT_FQ2FA") { + script "../../../seqkit/fq2fa/main.nf" + process { + """ + input[0] = [ + [ id:'small_Clone1_N1' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz', checkIfExists: true) + ] + """ + } + } + + run("SEQKIT_REPLACE") { + script "../../../seqkit/replace/main.nf" + config "./nextflow.config" + process { + """ + input[0] = SEQKIT_FQ2FA.out.fasta + """ + } + } + + } + + test("mirdeep2 - mapper - fasta celegans") { + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'test_reads', single_end:false ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/reads.fa', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match() }, + + // md5sum not stable - IDs change while sequences are the same + + // Assert TCACCGGGGGTACATCAGCTAA occurs once + { assert file(process.out.outputs[0][1]).readLines().findAll { it.contains("TCACCGGGGGTACATCAGCTAA") }.size() == 1 }, + + // Assert seq_347479_x287 occurs once + { assert file(process.out.outputs[0][1]).readLines().findAll { it.contains("seq_347479_x287") }.size() == 1 }, + + // Assert that specific content occurs 4 times + { assert file(process.out.outputs[0][2]).readLines().findAll { it.contains("21\t1\t21\ttcaccgggtgtaaatcagctt\tchrII:11534525-11540624\t21\t3535\t3555\ttcaccgggtgtaaatcagctt\t+\t0\tmmmmmmmmmmmmmmmmmmmmm") }.size() == 4 } + ) + } + + } + + test("mirdeep2 - mapper - fasta smrnaseq") { + config "./nextflow.config" + + when { + process { + """ + input[0] = SEQKIT_REPLACE.out.fastx + input[1] = BOWTIE_BUILD.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + + // Assert reads occurs once + { assert file(process.out.outputs[0][1]).readLines().findAll { it.contains("TACCTGAGGTAGCAGGTTGTATAGTTGGGG") }.size() == 1 }, + + // Assert ID occurs once + { assert file(process.out.outputs[0][1]).readLines().findAll { it.contains("seq_996152_x1") }.size() == 1 } + + ) + } + + } + + test("mirdeep2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test_reads', single_end:false ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/reads.fa', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mirdeep2/mapper/tests/main.nf.test.snap b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test.snap new file mode 100644 index 000000000000..4c3697d976ed --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/tests/main.nf.test.snap @@ -0,0 +1,51 @@ +{ + "mirdeep2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_reads", + "single_end": false + }, + "test_reads.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_readsreads_vs_refdb.arf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,33c794292d6772d67fa8001439394614" + ], + "outputs": [ + [ + { + "id": "test_reads", + "single_end": false + }, + "test_reads.fa:md5,d41d8cd98f00b204e9800998ecf8427e", + "test_readsreads_vs_refdb.arf:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,33c794292d6772d67fa8001439394614" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T20:58:19.544297445" + }, + "mirdeep2 - mapper - fasta celegans": { + "content": [ + [ + "versions.yml:md5,33c794292d6772d67fa8001439394614" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-17T17:41:05.101661825" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirdeep2/mapper/tests/nextflow.config b/modules/nf-core/mirdeep2/mapper/tests/nextflow.config new file mode 100644 index 000000000000..ec097561e602 --- /dev/null +++ b/modules/nf-core/mirdeep2/mapper/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: 'MIRDEEP2_MAPPER' { + ext.args = "-c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -v" + } + + withName: 'SEQKIT_REPLACE' { + ext.args = "-p '\s.+'" + ext.suffix = "fasta" + } + +} diff --git a/modules/nf-core/mirdeep2/mirdeep2/environment.yml b/modules/nf-core/mirdeep2/mirdeep2/environment.yml new file mode 100644 index 000000000000..fafc66632553 --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::mirdeep2=2.0.1.2" diff --git a/modules/nf-core/mirdeep2/mirdeep2/main.nf b/modules/nf-core/mirdeep2/mirdeep2/main.nf new file mode 100644 index 000000000000..66c859683ace --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/main.nf @@ -0,0 +1,64 @@ +process MIRDEEP2_MIRDEEP2 { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mirdeep2:2.0.1.2--0': + 'biocontainers/mirdeep2:2.0.1.2--0' }" + + input: + tuple val(meta), path(processed_reads), path(genome_mappings) + tuple val(meta2), path(fasta) + tuple val(meta3), path(mature), path(hairpin), path(mature_other_species) + + output: + tuple val(meta), path("result*.{bed,csv,html}") , emit: outputs + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.1' + def mature_species = mature ? "${mature}" : "none" + def mature_other = mature_other_species ? "${mature_other_species}": "none" + def precursors = hairpin ? "${hairpin}" : "none" + + """ + miRDeep2.pl \\ + $processed_reads \\ + $fasta \\ + $genome_mappings \\ + $mature_species \\ + $mature_other \\ + $precursors \\ + $args + + mv result_*.bed result_${prefix}.bed + mv result_*.csv result_${prefix}.csv + mv result_*.html result_${prefix}.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirdeep2: \$(echo "$VERSION") + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '2.0.1' + """ + touch result_${prefix}.html + touch result_${prefix}.bed + touch result_${prefix}.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mirdeep2: \$(echo "$VERSION") + END_VERSIONS + """ +} diff --git a/modules/nf-core/mirdeep2/mirdeep2/meta.yml b/modules/nf-core/mirdeep2/mirdeep2/meta.yml new file mode 100644 index 000000000000..adf1410195bf --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/meta.yml @@ -0,0 +1,76 @@ +name: "mirdeep2_mirdeep2" +description: | + miRDeep2 is a tool for identifying known and novel miRNAs in deep sequencing data by analyzing sequenced RNAs. It integrates the mapping of sequencing reads to the genome and predicts miRNA precursors and mature miRNAs. +keywords: + - mirdeep2 + - miRNA + - RNA sequencing +tools: + - "mirdeep2": + description: | + miRDeep2 is a tool that discovers microRNA genes by analyzing sequenced RNAs. + It includes three main scripts: `miRDeep2.pl`, `mapper.pl`, and `quantifier.pl` for comprehensive miRNA detection and quantification. + homepage: "https://www.mdc-berlin.de/content/mirdeep2-documentation" + documentation: "https://www.mdc-berlin.de/content/mirdeep2-documentation" + tool_dev_url: "https://github.com/rajewsky-lab/mirdeep2" + doi: "10.1093/nar/gkn491" + licence: ["GPL V3"] + identifier: biotools:mirdeep2 + +input: + - - meta: + type: map + description: Groovy Map containing sample information, e.g. `[ id:'sample1', + single_end:false ]` + - processed_reads: + type: file + description: FASTA file containing the processed sequencing reads. + pattern: "*.fa" + - genome_mappings: + type: file + description: ARF format file with mapped reads to the genome. + pattern: "*.arf" + - - meta2: + type: map + description: Groovy Map for genome FASTA file metadata, e.g. `[ id:'genome']` + - fasta: + type: file + description: FASTA file of the corresponding genome. + pattern: "*.fa" + - - meta3: + type: map + description: Groovy Map for miRNA metadata, e.g. `[ id:'mirbase', single_end:false + ]` + - mature: + type: file + description: FASTA file containing known mature miRNAs of the species being + analyzed. + pattern: "*.fa" + - hairpin: + type: file + description: FASTA file containing hairpin sequences (miRNA precursors). + pattern: "*.fa" + - mature_other_species: + type: file + description: FASTA file containing known mature miRNAs of other species. + pattern: "*.fa" +output: + - outputs: + - meta: + type: map + description: Groovy Map containing sample information e.g. `[ id:'sample1', + single_end:false ]` + - result*.{bed,csv,html}: + type: file + description: Output files, including BED, CSV, and HTML results files with an + overview of detected miRNAs. + pattern: "result*.{bed,csv,html}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test new file mode 100644 index 000000000000..b7b73ec123d9 --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test @@ -0,0 +1,111 @@ +nextflow_process { + + name "Test Process MIRDEEP2_MIRDEEP2" + script "../main.nf" + process "MIRDEEP2_MIRDEEP2" + + tag "modules" + tag "modules_nfcore" + tag "mirdeep2" + tag "mirdeep2/mirdeep2" + tag "bowtie/build" + tag "mirdeep2/mapper" + + + setup { + run("BOWTIE_BUILD") { + script "../../../bowtie/build/main.nf" + process { + """ + input[0] = [ + [ id:'genome_cel_cluster' ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/cel_cluster.fa', checkIfExists: true) + ] + """ + } + } + + run("MIRDEEP2_MAPPER") { + script "../../../mirdeep2/mapper/main.nf" + config "./nextflow.config" + + process { + """ + input[0] = [ + [ id:'test_reads', single_end:false ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/reads.fa', checkIfExists: true) + ] + input[1] = BOWTIE_BUILD.out.index + """ + } + } + + } + + test("mirdeep2 - mirdeep2 - fa") { + + when { + process { + """ + input[0] = MIRDEEP2_MAPPER.out.outputs + input[1] = [ + [ id:'genome_cel_cluster' ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/cel_cluster.fa', checkIfExists: true) + ] + input[2] = [ + [ id:'hairpin_mature'], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/mature_ref_this_species.fa', checkIfExists: true), + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/precursors_ref_this_species.fa', checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions, + path(process.out.outputs.get(0).get(1)[2]).readLines().last().contains(''), + process.out.outputs.get(0).get(1)[0], + path(process.out.outputs.get(0).get(1)[1]).readLines().first().contains('miRDeep2 score') + ).match() }, + // Assert .html + { assert path(process.out.outputs.get(0).get(1)[2]).readLines().last().contains('') } + ) + } + + } + + test("mirdeep - mirdeep2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = MIRDEEP2_MAPPER.out.outputs + input[1] = [ + [ id:'genome_cel_cluster' ], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/cel_cluster.fa', checkIfExists: true) + ] + input[2] = [ + [ id:'hairpin_mature'], // meta map + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/mature_ref_this_species.fa', checkIfExists: true), + file('https://github.com/rajewsky-lab/mirdeep2/raw/master/tutorial_dir/mature_ref_other_species.fa', checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test.snap b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test.snap new file mode 100644 index 000000000000..f8ffcf019dbf --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "mirdeep - mirdeep2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_reads", + "single_end": false + }, + [ + "result_test_reads.bed:md5,d41d8cd98f00b204e9800998ecf8427e", + "result_test_reads.csv:md5,d41d8cd98f00b204e9800998ecf8427e", + "result_test_reads.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,8984ad2f1e8bdd148da051e2e6b569bf" + ], + "outputs": [ + [ + { + "id": "test_reads", + "single_end": false + }, + [ + "result_test_reads.bed:md5,d41d8cd98f00b204e9800998ecf8427e", + "result_test_reads.csv:md5,d41d8cd98f00b204e9800998ecf8427e", + "result_test_reads.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,8984ad2f1e8bdd148da051e2e6b569bf" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T21:04:53.304188615" + }, + "mirdeep2 - mirdeep2 - fa": { + "content": [ + [ + "versions.yml:md5,8984ad2f1e8bdd148da051e2e6b569bf" + ], + true, + "result_test_reads.bed:md5,ba5ef5782e40d7219ca064dd68865d74", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-23T15:08:50.660562955" + } +} \ No newline at end of file diff --git a/modules/nf-core/mirdeep2/mirdeep2/tests/nextflow.config b/modules/nf-core/mirdeep2/mirdeep2/tests/nextflow.config new file mode 100644 index 000000000000..6a33ae05eede --- /dev/null +++ b/modules/nf-core/mirdeep2/mirdeep2/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'MIRDEEP2_MAPPER' { + ext.args = "-c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -v" + } +} diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/main.nf b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/main.nf new file mode 100644 index 000000000000..f8c3da931134 --- /dev/null +++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/main.nf @@ -0,0 +1,33 @@ +include { SEQKIT_FQ2FA } from '../../../modules/nf-core/seqkit/fq2fa/main' +include { SEQKIT_REPLACE } from '../../../modules/nf-core/seqkit/replace/main' +include { MIRDEEP2_MAPPER } from '../../../modules/nf-core/mirdeep2/mapper/main' +include { MIRDEEP2_MIRDEEP2 } from '../../../modules/nf-core/mirdeep2/mirdeep2/main' + +workflow FASTQ_FIND_MIRNA_MIRDEEP2 { + + take: + ch_reads // channel: [ val(meta), fastq ] + ch_genome_fasta // channel: [ val(meta), genome_fasta ] + ch_bowtie_index // channel: [ val(meta), index ] + ch_mirna_mature_hairpin // channel: [ val(meta), mature_mirna, hairpin_mirna ] + + main: + + ch_versions = Channel.empty() + + SEQKIT_FQ2FA ( ch_reads ) + ch_versions = ch_versions.mix(SEQKIT_FQ2FA.out.versions) + + SEQKIT_REPLACE ( SEQKIT_FQ2FA.out.fasta ) + ch_versions = ch_versions.mix(SEQKIT_REPLACE.out.versions) + + MIRDEEP2_MAPPER ( SEQKIT_REPLACE.out.fastx, ch_bowtie_index ) + ch_versions = ch_versions.mix(MIRDEEP2_MAPPER.out.versions) + + MIRDEEP2_MIRDEEP2 ( MIRDEEP2_MAPPER.out.outputs, ch_genome_fasta, ch_mirna_mature_hairpin ) + ch_versions = ch_versions.mix(MIRDEEP2_MIRDEEP2.out.versions) + + emit: + outputs = MIRDEEP2_MIRDEEP2.out.outputs // channel: [ val(meta), [ bed, csv, html ] ] + versions = ch_versions // channel: [ versions.yml ] +} diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml new file mode 100644 index 000000000000..22a475b36f72 --- /dev/null +++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/meta.yml @@ -0,0 +1,51 @@ +name: "fastq_find_mirna_mirdeep2" +description: | + This subworkflow identifies miRNAs from FASTQ files using miRDeep2. The workflow converts FASTQ to FASTA, processes and replaces any whitespace in sequence IDs, builds a Bowtie index of the genome, and then maps reads using miRDeep2 mapper before identifying known and novel miRNAs. +keywords: + - miRNA + - FASTQ + - FASTA + - Bowtie + - miRDeep2 +components: + - seqkit/fq2fa + - seqkit/replace + - bowtie/build + - mirdeep2/mapper + - mirdeep2/mirdeep2 +input: + - ch_reads: + type: file + description: | + The input channel containing the FASTQ files to process and identify miRNAs. + Structure: [ val(meta), path(fastq) ] + pattern: "*.fastq.gz" + - ch_genome_fasta: + type: file + description: | + The input channel containing the genome FASTA files used to build the Bowtie index. + Structure: [ val(meta), path(fasta) ] + pattern: "*.fa" + - ch_mirna_mature_hairpin: + type: file + description: | + The input channel containing the mature and hairpin miRNA sequences for miRNA identification. + Structure: [ val(meta), path(mature_fasta), path(hairpin_fasta) ] + pattern: "*.fa" +output: + - outputs: + type: file + description: | + The output channel containing the BED, CSV, and HTML files with the identified miRNAs. + Structure: [ val(meta), path(bed), path(csv), path(html) ] + pattern: "*.{bed,csv,html}" + - versions: + type: file + description: | + File containing software versions + Structure: [ path(versions.yml) ] + pattern: "versions.yml" +authors: + - "@atrigila" +maintainers: + - "@atrigila" diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test new file mode 100644 index 000000000000..13c10e52658f --- /dev/null +++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_workflow { + + name "Test Subworkflow FASTQ_FIND_MIRNA_MIRDEEP2" + script "../main.nf" + workflow "FASTQ_FIND_MIRNA_MIRDEEP2" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/fastq_find_mirna_mirdeep2" + tag "mirdeep2/mapper" + tag "mirdeep2/mirdeep2" + tag "seqkit/fq2fa" + tag "seqkit/replace" + tag "bowtie/build" + + + test("smrnaseq - fasta - single_end") { + config "./nextflow.config" + + setup { + run("SEQKIT_REPLACE") { + script "modules/nf-core/seqkit/replace/main.nf" + config "./nextflow.config" + + process { + """ + input[0] = [ + [ id:'genome' ], // meta map + file('https://github.com/nf-core/test-datasets/raw/smrnaseq/reference/genome.fa', checkIfExists: true) + ] + """ + } + } + + run("BOWTIE_BUILD") { + script "modules/nf-core/bowtie/build/main.nf" + process { + """ + input[0] = SEQKIT_REPLACE.out.fastx + """ + } + } + } + + when { + workflow { + """ + input[0] = [ + [ id:'small_Clone1_N1', single_end:false ], // meta map + file('https://github.com/nf-core/test-datasets/raw/smrnaseq/testdata/trimmed/small_Clone1_N1.fastp.fastq.gz', checkIfExists: true) + ] + + input[1] = SEQKIT_REPLACE.out.fastx + + input[2] = BOWTIE_BUILD.out.index + + input[3] = [ + [ id:'mirna_mature_hairpin'], // meta map + file('https://github.com/nf-core/test-datasets/raw/smrnaseq/MirGeneDB/mirgenedb_hsa_mature.fa', checkIfExists: true), + file('https://github.com/nf-core/test-datasets/raw/smrnaseq/MirGeneDB/mirgenedb_hsa_hairpin.fa', checkIfExists: true), + [] + ] + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot(workflow.out.versions, + path(workflow.out.outputs.get(0).get(1)[2]).readLines().last().contains(''), + workflow.out.outputs.get(0).get(1)[0], + path(workflow.out.outputs.get(0).get(1)[1]).readLines().first().contains('miRDeep2 score') + ).match()}, + // Assert .html + { assert path(workflow.out.outputs.get(0).get(1)[2]).readLines().last().contains('') } + ) + } + } +} diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap new file mode 100644 index 000000000000..c48df3d7ed9b --- /dev/null +++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/main.nf.test.snap @@ -0,0 +1,20 @@ +{ + "smrnaseq - fasta - single_end": { + "content": [ + [ + "versions.yml:md5,10138b74aed5b2658c26ddf80ff391d5", + "versions.yml:md5,631c0428c28d5355f0e3e9bd790bd77d", + "versions.yml:md5,706a3f609ec9d66162576d93a6f6a67b", + "versions.yml:md5,756eee52b4a45f7a9effe33b1cd3cb92" + ], + true, + "result_small_Clone1_N1.bed:md5,98a74ac6dd16ee876e9a3f54d2695c88", + true + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-23T14:56:03.274059331" + } +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/nextflow.config b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/nextflow.config new file mode 100644 index 000000000000..ec097561e602 --- /dev/null +++ b/subworkflows/nf-core/fastq_find_mirna_mirdeep2/tests/nextflow.config @@ -0,0 +1,11 @@ +process { + withName: 'MIRDEEP2_MAPPER' { + ext.args = "-c -j -k TCGTATGCCGTCTTCTGCTTGT -l 18 -m -v" + } + + withName: 'SEQKIT_REPLACE' { + ext.args = "-p '\s.+'" + ext.suffix = "fasta" + } + +} From b13f07be4c508d6ff6312d354d09f2493243e208 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 24 Sep 2024 11:49:28 +0200 Subject: [PATCH 088/486] restore samtools modules version bump (#6685) * restore samtools modules version bump * add htslib * same environment.yml file for each samtools modules --- modules/nf-core/samtools/ampliconclip/environment.yml | 7 ++++--- modules/nf-core/samtools/bam2fq/environment.yml | 7 ++++--- modules/nf-core/samtools/calmd/environment.yml | 7 ++++--- modules/nf-core/samtools/cat/environment.yml | 7 ++++--- modules/nf-core/samtools/collate/environment.yml | 7 ++++--- modules/nf-core/samtools/collatefastq/environment.yml | 7 ++++--- modules/nf-core/samtools/consensus/environment.yml | 3 ++- modules/nf-core/samtools/convert/environment.yml | 7 ++++--- modules/nf-core/samtools/coverage/environment.yml | 7 ++++--- modules/nf-core/samtools/cramsize/environment.yml | 3 ++- modules/nf-core/samtools/depth/environment.yml | 7 ++++--- modules/nf-core/samtools/dict/environment.yml | 7 ++++--- modules/nf-core/samtools/faidx/environment.yml | 3 ++- modules/nf-core/samtools/fasta/environment.yml | 7 ++++--- modules/nf-core/samtools/fastq/environment.yml | 7 ++++--- modules/nf-core/samtools/fixmate/environment.yml | 7 ++++--- modules/nf-core/samtools/flagstat/environment.yml | 7 ++++--- modules/nf-core/samtools/getrg/environment.yml | 7 ++++--- modules/nf-core/samtools/idxstats/environment.yml | 7 ++++--- modules/nf-core/samtools/import/environment.yml | 7 ++++--- modules/nf-core/samtools/index/environment.yml | 7 ++++--- modules/nf-core/samtools/markdup/environment.yml | 7 ++++--- modules/nf-core/samtools/merge/environment.yml | 7 ++++--- modules/nf-core/samtools/mpileup/environment.yml | 7 ++++--- modules/nf-core/samtools/reheader/environment.yml | 7 ++++--- modules/nf-core/samtools/sormadup/environment.yml | 7 ++++--- modules/nf-core/samtools/sort/environment.yml | 7 ++++--- modules/nf-core/samtools/stats/environment.yml | 7 ++++--- modules/nf-core/samtools/view/environment.yml | 7 ++++--- 29 files changed, 110 insertions(+), 81 deletions(-) diff --git a/modules/nf-core/samtools/ampliconclip/environment.yml b/modules/nf-core/samtools/ampliconclip/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/ampliconclip/environment.yml +++ b/modules/nf-core/samtools/ampliconclip/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/bam2fq/environment.yml +++ b/modules/nf-core/samtools/bam2fq/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/calmd/environment.yml b/modules/nf-core/samtools/calmd/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/calmd/environment.yml +++ b/modules/nf-core/samtools/calmd/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/cat/environment.yml b/modules/nf-core/samtools/cat/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/cat/environment.yml +++ b/modules/nf-core/samtools/cat/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/collate/environment.yml b/modules/nf-core/samtools/collate/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/collate/environment.yml +++ b/modules/nf-core/samtools/collate/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/collatefastq/environment.yml +++ b/modules/nf-core/samtools/collatefastq/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/consensus/environment.yml b/modules/nf-core/samtools/consensus/environment.yml index 5a85438e08a8..62054fc97acb 100644 --- a/modules/nf-core/samtools/consensus/environment.yml +++ b/modules/nf-core/samtools/consensus/environment.yml @@ -4,4 +4,5 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::samtools=1.20" + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/coverage/environment.yml b/modules/nf-core/samtools/coverage/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/coverage/environment.yml +++ b/modules/nf-core/samtools/coverage/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/cramsize/environment.yml b/modules/nf-core/samtools/cramsize/environment.yml index 2bcd47ee161b..62054fc97acb 100644 --- a/modules/nf-core/samtools/cramsize/environment.yml +++ b/modules/nf-core/samtools/cramsize/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - bioconda::htslib=1.21 - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/depth/environment.yml b/modules/nf-core/samtools/depth/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/depth/environment.yml +++ b/modules/nf-core/samtools/depth/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/dict/environment.yml b/modules/nf-core/samtools/dict/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/dict/environment.yml +++ b/modules/nf-core/samtools/dict/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index 2bcd47ee161b..62054fc97acb 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - bioconda::htslib=1.21 - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fasta/environment.yml b/modules/nf-core/samtools/fasta/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/fasta/environment.yml +++ b/modules/nf-core/samtools/fasta/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fastq/environment.yml b/modules/nf-core/samtools/fastq/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/fastq/environment.yml +++ b/modules/nf-core/samtools/fastq/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/fixmate/environment.yml b/modules/nf-core/samtools/fixmate/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/fixmate/environment.yml +++ b/modules/nf-core/samtools/fixmate/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/flagstat/environment.yml b/modules/nf-core/samtools/flagstat/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/flagstat/environment.yml +++ b/modules/nf-core/samtools/flagstat/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/getrg/environment.yml b/modules/nf-core/samtools/getrg/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/getrg/environment.yml +++ b/modules/nf-core/samtools/getrg/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/idxstats/environment.yml b/modules/nf-core/samtools/idxstats/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/idxstats/environment.yml +++ b/modules/nf-core/samtools/idxstats/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/import/environment.yml b/modules/nf-core/samtools/import/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/import/environment.yml +++ b/modules/nf-core/samtools/import/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/markdup/environment.yml b/modules/nf-core/samtools/markdup/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/markdup/environment.yml +++ b/modules/nf-core/samtools/markdup/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/mpileup/environment.yml b/modules/nf-core/samtools/mpileup/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/mpileup/environment.yml +++ b/modules/nf-core/samtools/mpileup/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/reheader/environment.yml b/modules/nf-core/samtools/reheader/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/reheader/environment.yml +++ b/modules/nf-core/samtools/reheader/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sormadup/environment.yml b/modules/nf-core/samtools/sormadup/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/sormadup/environment.yml +++ b/modules/nf-core/samtools/sormadup/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/sort/environment.yml b/modules/nf-core/samtools/sort/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/sort/environment.yml +++ b/modules/nf-core/samtools/sort/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/stats/environment.yml b/modules/nf-core/samtools/stats/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/stats/environment.yml +++ b/modules/nf-core/samtools/stats/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/view/environment.yml b/modules/nf-core/samtools/view/environment.yml index b98cbb99092d..62054fc97acb 100644 --- a/modules/nf-core/samtools/view/environment.yml +++ b/modules/nf-core/samtools/view/environment.yml @@ -1,7 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 From c3a2705bff298ffd2972bdb1b925b362491e2ee3 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 24 Sep 2024 15:01:27 +0200 Subject: [PATCH 089/486] update wisecondorx predict output (#6687) * update wisecondorx predict output * fix linting --- modules/nf-core/wisecondorx/predict/main.nf | 4 +- modules/nf-core/wisecondorx/predict/meta.yml | 49 ++++++++++++------- .../predict/tests/main.nf.test.snap | 4 +- 3 files changed, 35 insertions(+), 22 deletions(-) diff --git a/modules/nf-core/wisecondorx/predict/main.nf b/modules/nf-core/wisecondorx/predict/main.nf index 70005fc030a3..c4f682535758 100644 --- a/modules/nf-core/wisecondorx/predict/main.nf +++ b/modules/nf-core/wisecondorx/predict/main.nf @@ -17,7 +17,7 @@ process WISECONDORX_PREDICT { tuple val(meta), path("*_aberrations.bed") , emit: aberrations_bed, optional:true tuple val(meta), path("*_bins.bed") , emit: bins_bed, optional:true tuple val(meta), path("*_segments.bed") , emit: segments_bed, optional:true - tuple val(meta), path("*_chr_statistics.txt") , emit: chr_statistics, optional:true + tuple val(meta), path("*_statistics.txt") , emit: chr_statistics, optional:true tuple val(meta), path("[!genome_wide]*.png") , emit: chr_plots, optional:true tuple val(meta), path("genome_wide.png") , emit: genome_plot, optional:true path "versions.yml" , emit: versions @@ -55,7 +55,7 @@ process WISECONDORX_PREDICT { def prefix = task.ext.prefix ?: "${meta.id}" def VERSION = '1.2.9' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. - def bed = args.contains("--bed") ? "touch ${prefix}_aberrations.bed && touch ${prefix}_bins.bed && touch ${prefix}_chr_statistics.txt && touch ${prefix}_segments.bed" : "" + def bed = args.contains("--bed") ? "touch ${prefix}_aberrations.bed && touch ${prefix}_bins.bed && touch ${prefix}_statistics.txt && touch ${prefix}_segments.bed" : "" def plot = args.contains("--plot") ? "touch genome_wide.png && touch chr22.png && touch chr1.png" : "" """ diff --git a/modules/nf-core/wisecondorx/predict/meta.yml b/modules/nf-core/wisecondorx/predict/meta.yml index ae17554578b3..65b62b8fa4c0 100644 --- a/modules/nf-core/wisecondorx/predict/meta.yml +++ b/modules/nf-core/wisecondorx/predict/meta.yml @@ -50,10 +50,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*_aberrations.bed" - "*_aberrations.bed": - type: file - description: OPTIONAL - Output abberations in BED format. This gets created - with the `--bed` option + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*_aberrations.bed" - bins_bed: - meta: @@ -61,10 +63,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*_bins.bed" - "*_bins.bed": - type: file - description: OPTIONAL - Output bins in BED format. This gets created with the - `--bed` option + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*_bins.bed" - segments_bed: - meta: @@ -72,10 +76,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*_segments.bed" - "*_segments.bed": - type: file - description: OPTIONAL - Output segments in BED format. This gets created with - the `--bed` option + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*_segments.bed" - chr_statistics: - meta: @@ -83,10 +89,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*_chr_statistics.txt": - type: file - description: OPTIONAL - Statistics per chromosome in TXT format. This gets created - with the `--bed` option + pattern: "*_chr_statistics.txt" + - "*_statistics.txt": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*_chr_statistics.txt" - chr_plots: - meta: @@ -94,10 +102,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "[!genome_wide]*.png" - "[!genome_wide]*.png": - type: list - description: OPTIONAL - A list containing the CNV plots of each chromosome. - This gets created with the `--plot` option + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "[!genome_wide]*.png" - genome_plot: - meta: @@ -105,9 +115,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "genome_wide.png" - genome_wide.png: - type: file - description: OPTIONAL - A plot containing the CNV information of the whole genome + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "genome_wide.png" - versions: - versions.yml: diff --git a/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap b/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap index 9381ba13418a..ce09d8b890a0 100644 --- a/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap +++ b/modules/nf-core/wisecondorx/predict/tests/main.nf.test.snap @@ -33,7 +33,7 @@ { "id": "test" }, - "test_chr_statistics.txt" + "test_statistics.txt" ] ], [ @@ -60,6 +60,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-29T13:48:50.058254" + "timestamp": "2024-09-24T14:47:28.342417115" } } \ No newline at end of file From 6b3bf38285d94cc1ea3cd9fa93310d54b04c3819 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20B=C3=A4uerle?= <45968370+famosab@users.noreply.github.com> Date: Wed, 25 Sep 2024 10:04:29 +0200 Subject: [PATCH 090/486] add stubs gatk4 (#6672) * add stubs * run lint --fix * fix formatting --- modules/nf-core/gatk4/applybqsr/main.nf | 13 + .../gatk4/applybqsr/tests/main.nf.test | 59 +++++ .../gatk4/applybqsr/tests/main.nf.test.snap | 78 ++++++ .../nf-core/gatk4/collectsvevidence/main.nf | 18 ++ .../nf-core/gatk4/collectsvevidence/meta.yml | 4 +- .../collectsvevidence/tests/main.nf.test | 60 +++++ .../collectsvevidence/tests/main.nf.test.snap | 226 ++++++++++++++++++ modules/nf-core/gatk4/combinegvcfs/main.nf | 11 + .../gatk4/combinegvcfs/tests/main.nf.test | 31 ++- .../combinegvcfs/tests/main.nf.test.snap | 35 +++ 10 files changed, 531 insertions(+), 4 deletions(-) diff --git a/modules/nf-core/gatk4/applybqsr/main.nf b/modules/nf-core/gatk4/applybqsr/main.nf index 78db9d7f009d..4e91c311b0ee 100644 --- a/modules/nf-core/gatk4/applybqsr/main.nf +++ b/modules/nf-core/gatk4/applybqsr/main.nf @@ -48,4 +48,17 @@ process GATK4_APPLYBQSR { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def input_extension = input.getExtension() + def output_extension = input_extension == 'bam' ? 'bam' : 'cram' + """ + touch ${prefix}.${output_extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test index 3d9c6204f78f..acb41ce1e47d 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test @@ -92,4 +92,63 @@ nextflow_process { } } + test("sarscov2 - cram - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/gatk/test.baserecalibrator.table', checkIfExists: true), + [] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + } diff --git a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap index a387039d6ad9..19b37d0636d8 100644 --- a/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/applybqsr/tests/main.nf.test.snap @@ -1,4 +1,43 @@ { + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + ], + "bam": [ + [ + { + "id": "test" + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "cram": [ + + ], + "versions": [ + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:25:00.314573" + }, "sarscov2 - bam - intervals": { "content": [ { @@ -60,6 +99,45 @@ }, "timestamp": "2023-12-09T03:10:46.70859771" }, + "sarscov2 - cram - stub": { + "content": [ + { + "0": [ + + ], + "1": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + ], + "bam": [ + + ], + "cram": [ + [ + { + "id": "test" + }, + "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,bb2a060a0280c812fba3c74b1707b350" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:24:52.761169" + }, "sarscov2 - bam": { "content": [ { diff --git a/modules/nf-core/gatk4/collectsvevidence/main.nf b/modules/nf-core/gatk4/collectsvevidence/main.nf index 5c96232f79ff..9e6dd4a284b8 100644 --- a/modules/nf-core/gatk4/collectsvevidence/main.nf +++ b/modules/nf-core/gatk4/collectsvevidence/main.nf @@ -54,4 +54,22 @@ process GATK4_COLLECTSVEVIDENCE { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def sd_vcf = site_depth_vcf ? "echo '' | gzip > ${prefix}.sd.txt.gz" : "" + def sd_vcf_tbi = site_depth_vcf_tbi ? "touch ${prefix}.sd.txt.gz.tbi" : "" + """ + echo "" | gzip > ${prefix}.sr.txt.gz + touch ${prefix}.sr.txt.gz.tbi + echo "" | gzip > ${prefix}.pe.txt.gz + touch ${prefix}.pe.txt.gz.tbi + ${sd_vcf} + ${sd_vcf_tbi} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/collectsvevidence/meta.yml b/modules/nf-core/gatk4/collectsvevidence/meta.yml index 2a8b6fc46433..a9d64d30e509 100644 --- a/modules/nf-core/gatk4/collectsvevidence/meta.yml +++ b/modules/nf-core/gatk4/collectsvevidence/meta.yml @@ -37,8 +37,8 @@ input: pattern: "*.vcf.gz" - site_depth_vcf_tbi: type: file - description: tbi index of the input VCF of SNPs marking loci for site - depths + description: Optional - input VCF TBI of SNPs marking loci for site depths, needed + for the site depths output pattern: "*.vcf.gz.tbi" - - fasta: type: file diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test index 308fc7f678e9..418554bb3456 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test @@ -118,4 +118,64 @@ nextflow_process { } } + test("test-gatk4-collectsvevidence-cram - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai', checkIfExists: true), + [], + [] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-gatk4-collectsvevidence-allele-count - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test_haplotcaller.cnn.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = [] + input[2] = [] + input[3] = [] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } diff --git a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap index 5143cf3c0bee..1f6992b8c64c 100644 --- a/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/collectsvevidence/tests/main.nf.test.snap @@ -15,6 +15,107 @@ }, "timestamp": "2024-08-26T12:51:11.44656" }, + "test-gatk4-collectsvevidence-cram - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + + ], + "5": [ + + ], + "6": [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ], + "paired_end_evidence": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "paired_end_evidence_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "site_depths": [ + + ], + "site_depths_index": [ + + ], + "split_read_evidence": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "split_read_evidence_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:36:35.045647" + }, "test-gatk4-collectsvevidence-allele-count": { "content": [ "chr22\t2008\tleft\t1\tnormal", @@ -33,6 +134,131 @@ }, "timestamp": "2024-08-26T12:48:13.663238" }, + "test-gatk4-collectsvevidence-allele-count - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ], + "paired_end_evidence": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "paired_end_evidence_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.pe.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "site_depths": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "site_depths_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "split_read_evidence": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "split_read_evidence_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sr.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,eb641a78898f7bfe135ef01b77647079" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:36:43.992644" + }, "test-gatk4-collectsvevidence-bam": { "content": [ "chr22\t2008\tleft\t1\tnormal", diff --git a/modules/nf-core/gatk4/combinegvcfs/main.nf b/modules/nf-core/gatk4/combinegvcfs/main.nf index df8ade11bfc8..56db0c12c868 100644 --- a/modules/nf-core/gatk4/combinegvcfs/main.nf +++ b/modules/nf-core/gatk4/combinegvcfs/main.nf @@ -45,4 +45,15 @@ process GATK4_COMBINEGVCFS { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.combined.g.vcf.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test index 56f54d0f1b53..df2d5b4e5eff 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test @@ -13,10 +13,10 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = [ [ id:'test', single_end:false ], // meta map file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) ] input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) @@ -35,4 +35,31 @@ nextflow_process { ) } } + + test("test_gatk4_combinegvcfs - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.idx', checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } \ No newline at end of file diff --git a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap index 1f04b8bd4328..dfbd1ac1ef77 100644 --- a/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/combinegvcfs/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "test_gatk4_combinegvcfs - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.combined.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + ], + "combined_gvcf": [ + [ + { + "id": "test", + "single_end": false + }, + "test.combined.g.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,d6331ea8e97541d1d439707fe3dd41b2" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:35:25.18434" + }, "test_gatk4_combinegvcfs": { "content": [ [ From 679f45cae4f603f12d7c38c042afee11150574a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Famke=20B=C3=A4uerle?= <45968370+famosab@users.noreply.github.com> Date: Wed, 25 Sep 2024 10:12:05 +0200 Subject: [PATCH 091/486] add more stubs gatk4 (#6673) * add stubs * run lint --fix * fix formatting --- .../gatk4/condensedepthevidence/main.nf | 12 +++++ .../condensedepthevidence/tests/main.nf.test | 29 ++++++++++ .../tests/main.nf.test.snap | 53 +++++++++++++++++++ modules/nf-core/gatk4/fastqtosam/main.nf | 11 ++++ .../gatk4/fastqtosam/tests/main.nf.test | 23 +++++++- .../gatk4/fastqtosam/tests/main.nf.test.snap | 35 ++++++++++++ .../gatk4/gatherpileupsummaries/main.nf | 11 ++++ .../gatherpileupsummaries/tests/main.nf.test | 25 +++++++++ .../tests/main.nf.test.snap | 35 ++++++++++++ 9 files changed, 233 insertions(+), 1 deletion(-) diff --git a/modules/nf-core/gatk4/condensedepthevidence/main.nf b/modules/nf-core/gatk4/condensedepthevidence/main.nf index dba1462f5b7b..a37b6693f39f 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/main.nf +++ b/modules/nf-core/gatk4/condensedepthevidence/main.nf @@ -50,4 +50,16 @@ process GATK4_CONDENSEDEPTHEVIDENCE { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.rd.txt.gz + touch ${prefix}.rd.txt.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test index 0f65f5428916..e681d0bddaa0 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test @@ -41,4 +41,33 @@ nextflow_process { } } + test("test-gatk4-condensdepthevidence - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/condensedepthevidence/testN.rd.txt.gz.tbi", checkIfExists: true) + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + } + } diff --git a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap index d8da0978b2b6..b9dddfbb9895 100644 --- a/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/condensedepthevidence/tests/main.nf.test.snap @@ -1,4 +1,57 @@ { + "test-gatk4-condensdepthevidence - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + ], + "condensed_evidence": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rd.txt.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "condensed_evidence_index": [ + [ + { + "id": "test", + "single_end": false + }, + "test.rd.txt.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d1d29007b92a10b3e50bdd25335013a8" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:42:07.848497" + }, "test-gatk4-condensdepthevidence": { "content": [ [ diff --git a/modules/nf-core/gatk4/fastqtosam/main.nf b/modules/nf-core/gatk4/fastqtosam/main.nf index e0331f744960..452d1ca1f351 100644 --- a/modules/nf-core/gatk4/fastqtosam/main.nf +++ b/modules/nf-core/gatk4/fastqtosam/main.nf @@ -42,4 +42,15 @@ process GATK4_FASTQTOSAM { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test index 2e3688a779d4..8ba0ff044c54 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test @@ -44,7 +44,6 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - """ } } @@ -61,4 +60,26 @@ nextflow_process { } } + test("test-gatk4-fastqtosam-single-end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } diff --git a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap index 554480a24b7e..a4b44520dc55 100644 --- a/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/fastqtosam/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "test-gatk4-fastqtosam-single-end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + ], + "bam": [ + [ + { + "id": "test", + "single_end": true + }, + "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,ac3f2cf1b686e56d72f1dd4a5977f7ab" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:43:37.316141" + }, "test-gatk4-fastqtosam-single-end": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf index c784d59ab263..bcafd544b434 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/main.nf +++ b/modules/nf-core/gatk4/gatherpileupsummaries/main.nf @@ -44,4 +44,15 @@ process GATK4_GATHERPILEUPSUMMARIES { gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.pileups.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test index 8497e64db378..f33c6a0d9488 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test @@ -34,4 +34,29 @@ nextflow_process { } } + test("test-gatk4-gatherpileupsummaries - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/test.pileups.table', checkIfExists: true) ] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.dict', checkIfExists: true) + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } diff --git a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap index f05a7ef0d111..fd9f25834402 100644 --- a/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap +++ b/modules/nf-core/gatk4/gatherpileupsummaries/tests/main.nf.test.snap @@ -1,4 +1,39 @@ { + "test-gatk4-gatherpileupsummaries - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + ], + "table": [ + [ + { + "id": "test", + "single_end": false + }, + "test.out.pileups.table:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,d3772ab0d5963a88a2748fd83af76c02" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T10:44:42.759098" + }, "test-gatk4-gatherpileupsummaries": { "content": [ { From f448e846bdadd80fc8be31fbbc78d9f5b5131a45 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 25 Sep 2024 15:28:51 +0200 Subject: [PATCH 092/486] update stubs for tabix/bgziptabix (#6692) update modules --- modules/nf-core/tabix/bgziptabix/main.nf | 5 +- .../tabix/bgziptabix/tests/main.nf.test | 29 ++++++++ .../tabix/bgziptabix/tests/main.nf.test.snap | 73 ++++++++++++++----- 3 files changed, 88 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 05041f495322..22f37a7739b3 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${meta.id}" + def args2 = task.ext.args2 ?: '' + def index = args2.contains("-C ") || args2.contains("--csi") ? "csi" : "tbi" """ echo "" | gzip > ${prefix}.${input.getExtension()}.gz - touch ${prefix}.${input.getExtension()}.gz.tbi - touch ${prefix}.${input.getExtension()}.gz.csi + touch ${prefix}.${input.getExtension()}.gz.${index} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 1a84d74fc0d8..4d4130dc07dc 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test @@ -91,4 +91,33 @@ nextflow_process { } + test("sarscov2_bed_tbi_stub") { + config "./tabix_tbi.config" + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert snapshot( + file(process.out.gz_tbi[0][1]).name + ).match("tbi_stub") + } + ) + } + + } + } diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap index c166ea7288fa..fb87799b2030 100644 --- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap +++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap @@ -91,6 +91,47 @@ }, "timestamp": "2024-02-19T14:51:00.548801" }, + "sarscov2_bed_tbi_stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ], + "gz_csi": [ + + ], + "gz_tbi": [ + [ + { + "id": "test" + }, + "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.533169949" + }, "csi_stub": { "content": [ "test.bed.gz" @@ -101,6 +142,16 @@ }, "timestamp": "2024-02-19T14:51:09.218454" }, + "tbi_stub": { + "content": [ + "test.bed.gz" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-25T14:45:18.550930179" + }, "tbi_test": { "content": [ "tbi_test.bed.gz" @@ -115,13 +166,7 @@ "content": [ { "0": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "1": [ [ @@ -145,13 +190,7 @@ ] ], "gz_tbi": [ - [ - { - "id": "test" - }, - "test.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + ], "versions": [ "versions.yml:md5,736e7c3b16a3ac525253e5b5f5d8fdfa" @@ -159,9 +198,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-19T11:29:45.105209991" + "timestamp": "2024-09-25T14:44:19.786135972" } } \ No newline at end of file From e17652681c856afaf2e240ba4c98bf4631a0fe2d Mon Sep 17 00:00:00 2001 From: "Diego Alvarez S." Date: Wed, 25 Sep 2024 16:18:16 -0300 Subject: [PATCH 093/486] Refactor checkm2/databasedownload using aria2 (#6654) * Use aria2 for CHECKM2_DATABASEDOWNLOAD, update snaps * Fix linting * Add bioconda to environment.yml * Add zenodo_id as input to select which version to download * Add input param to the test * Add process input for predict * Fix databasedownload meta * Improve field description --------- Co-authored-by: James A. Fellows Yates --- .../checkm2/databasedownload/environment.yml | 2 +- .../nf-core/checkm2/databasedownload/main.nf | 31 +++++++++++-------- .../nf-core/checkm2/databasedownload/meta.yml | 5 +++ .../databasedownload/tests/main.nf.test | 8 +++++ .../databasedownload/tests/main.nf.test.snap | 8 ++--- modules/nf-core/checkm2/predict/main.nf | 2 +- .../checkm2/predict/tests/main.nf.test | 5 +++ .../checkm2/predict/tests/main.nf.test.snap | 6 +--- 8 files changed, 41 insertions(+), 26 deletions(-) diff --git a/modules/nf-core/checkm2/databasedownload/environment.yml b/modules/nf-core/checkm2/databasedownload/environment.yml index 18fd1f51a80c..52d11ba96bab 100644 --- a/modules/nf-core/checkm2/databasedownload/environment.yml +++ b/modules/nf-core/checkm2/databasedownload/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::checkm2=1.0.2 + - conda-forge::aria2=1.36.0 diff --git a/modules/nf-core/checkm2/databasedownload/main.nf b/modules/nf-core/checkm2/databasedownload/main.nf index cea2c9c6cd02..6144067b27d7 100644 --- a/modules/nf-core/checkm2/databasedownload/main.nf +++ b/modules/nf-core/checkm2/databasedownload/main.nf @@ -3,10 +3,13 @@ import groovy.json.JsonSlurper process CHECKM2_DATABASEDOWNLOAD { label 'process_single' - conda "bioconda::checkm2=1.0.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/checkm2:1.0.2--pyh7cba7a3_0': - 'biocontainers/checkm2:1.0.2--pyh7cba7a3_0' }" + 'https://depot.galaxyproject.org/singularity/aria2:1.36.0': + 'biocontainers/aria2:1.36.0' }" + + input: + val(db_zenodo_id) output: tuple val(meta), path("checkm2_db_v${db_version}.dmnd"), emit: database @@ -16,25 +19,27 @@ process CHECKM2_DATABASEDOWNLOAD { task.ext.when == null || task.ext.when script: - zenodo_id = 5571251 - def jsonSlurper = new JsonSlurper() - db_version = jsonSlurper.parseText(file("https://zenodo.org/api/records/${zenodo_id}").text).metadata.version - meta = [id: 'checkm2_db', version: db_version] + def args = task.ext.args ?: '' + zenodo_id = db_zenodo_id ?: 5571251 // Default to latest version if no ID provided + api_data = (new JsonSlurper()).parseText(file("https://zenodo.org/api/records/${zenodo_id}").text) + db_version = api_data.metadata.version + checksum = api_data.files[0].checksum.replaceFirst(/^md5:/, "md5=") + meta = [id: 'checkm2_db', version: db_version] """ # Automatic download is broken when using singularity/apptainer (https://github.com/chklovski/CheckM2/issues/73) - # So we download the database manually - wget https://zenodo.org/records/${zenodo_id}/files/checkm2_database.tar.gz + # So it's necessary to download the database manually + aria2c \ + ${args} \ + --checksum ${checksum} \ + https://zenodo.org/records/${zenodo_id}/files/checkm2_database.tar.gz tar -xzf checkm2_database.tar.gz db_path=\$(find -name *.dmnd) - MD5=\$(grep -o '\\.dmnd": "[^"]*"' CONTENTS.json | cut -d '"' -f 3) - - md5sum -c <<< "\$MD5 \$db_path" mv \$db_path checkm2_db_v${db_version}.dmnd cat <<-END_VERSIONS > versions.yml "${task.process}": - checkm2: \$(checkm2 --version) + aria2: \$(echo \$(aria2c --version 2>&1) | grep 'aria2 version' | cut -f3 -d ' ') END_VERSIONS """ diff --git a/modules/nf-core/checkm2/databasedownload/meta.yml b/modules/nf-core/checkm2/databasedownload/meta.yml index 09c69c923f59..632b492218b4 100644 --- a/modules/nf-core/checkm2/databasedownload/meta.yml +++ b/modules/nf-core/checkm2/databasedownload/meta.yml @@ -17,6 +17,11 @@ tools: licence: ["GPL v3"] identifier: "" +input: + - - db_zenodo_id: + type: integer + description: Zenodo ID of the CheckM2 database to download + output: - database: - meta: diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test index 5673a6c5302f..2a98f0510ce9 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test @@ -10,6 +10,14 @@ nextflow_process { test("Test CheckM2 Database Download") { + when { + process { + """ + input[0] = [] + """ + } + } + then { assertAll( { assert process.success }, diff --git a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap index a8e201456ab8..403d26fd7301 100644 --- a/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/databasedownload/tests/main.nf.test.snap @@ -2,13 +2,9 @@ "Test CheckM2 Database Download": { "content": [ [ - "versions.yml:md5,a0f7b47476ffc62ce27870f0503e6c04" + "versions.yml:md5,6201d5ac7aca6e32b98daf4f8656aa2a" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-12T06:29:33.222099893" + "timestamp": "2024-09-16T22:23:54.183040031" } } \ No newline at end of file diff --git a/modules/nf-core/checkm2/predict/main.nf b/modules/nf-core/checkm2/predict/main.nf index 4bcddb36dfad..25271ba986a8 100644 --- a/modules/nf-core/checkm2/predict/main.nf +++ b/modules/nf-core/checkm2/predict/main.nf @@ -2,7 +2,7 @@ process CHECKM2_PREDICT { tag "${meta.id}" label 'process_medium' - conda "bioconda::checkm2=1.0.2" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/checkm2:1.0.2--pyh7cba7a3_0': 'biocontainers/checkm2:1.0.2--pyh7cba7a3_0' }" diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test b/modules/nf-core/checkm2/predict/tests/main.nf.test index cd7dda4ed253..e825f74c9a0c 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test @@ -14,6 +14,11 @@ nextflow_process { setup { run("CHECKM2_DATABASEDOWNLOAD") { script "../../databasedownload/main.nf" + process { + """ + input[0] = [] + """ + } } } diff --git a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap index dcb34a4a9fc7..6fd2e918975d 100644 --- a/modules/nf-core/checkm2/predict/tests/main.nf.test.snap +++ b/modules/nf-core/checkm2/predict/tests/main.nf.test.snap @@ -13,10 +13,6 @@ "versions.yml:md5,088ec2d8a46efd530c11019328064bff" ] ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-12T06:34:56.335651565" + "timestamp": "2024-09-16T22:43:50.787486798" } } \ No newline at end of file From 01ec8bfdf3980b12d706db0408cb3c86227e5628 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Thu, 26 Sep 2024 11:18:22 +0200 Subject: [PATCH 094/486] chore(deps): update actions/setup-java digest to b36c23c (#6688) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/test.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 6d486992e07f..8be6d86d95de 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -166,7 +166,7 @@ jobs: - name: Install pip run: python -m pip install --upgrade pip - - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: distribution: "temurin" java-version: "17" @@ -204,7 +204,7 @@ jobs: - name: Install pip run: python -m pip install --upgrade pip - - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: distribution: "temurin" java-version: "17" @@ -416,7 +416,7 @@ jobs: - name: Install Python dependencies run: python -m pip install --upgrade pip pytest-workflow cryptography - - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: distribution: "temurin" java-version: "17" @@ -655,7 +655,7 @@ jobs: steps: - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 - - uses: actions/setup-java@2dfa2011c5b2a0f1489bf9e433881c92c1631f88 # v4 + - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: distribution: "temurin" java-version: "17" From d1e0ec7670fa77905a378627232566ce54c3c26d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Thu, 26 Sep 2024 17:01:35 +0200 Subject: [PATCH 095/486] create indices when missing (#6697) * create indices when missing * fix meta yaml --- modules/nf-core/bcftools/concat/main.nf | 16 +- modules/nf-core/bcftools/concat/meta.yml | 27 ++- .../bcftools/concat/tests/main.nf.test | 18 +- .../bcftools/concat/tests/main.nf.test.snap | 158 +++++++++--------- 4 files changed, 116 insertions(+), 103 deletions(-) diff --git a/modules/nf-core/bcftools/concat/main.nf b/modules/nf-core/bcftools/concat/main.nf index e2337eff2579..a94b28d86d76 100644 --- a/modules/nf-core/bcftools/concat/main.nf +++ b/modules/nf-core/bcftools/concat/main.nf @@ -11,18 +11,22 @@ process BCFTOOLS_CONCAT { tuple val(meta), path(vcfs), path(tbi) output: - tuple val(meta), path("*.gz") , emit: vcf - tuple val(meta), path("*.tbi"), emit: tbi, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("${prefix}.vcf.gz") , emit: vcf + tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true + tuple val(meta), path("${prefix}.vcf.gz.csi"), emit: csi, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" + def tbi_names = tbi.findAll { file -> !(file instanceof List) }.collect { file -> file.name } + def create_input_index = vcfs.collect { vcf -> tbi_names.contains(vcf.name + ".tbi") ? "" : "tabix ${vcf}" }.join("\n ") """ + ${create_input_index} + bcftools concat \\ --output ${prefix}.vcf.gz \\ $args \\ @@ -37,7 +41,7 @@ process BCFTOOLS_CONCAT { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : args.contains("--write-index") || args.contains("-W") ? "csi" : diff --git a/modules/nf-core/bcftools/concat/meta.yml b/modules/nf-core/bcftools/concat/meta.yml index b5d1f5b2cefd..d2565b289fba 100644 --- a/modules/nf-core/bcftools/concat/meta.yml +++ b/modules/nf-core/bcftools/concat/meta.yml @@ -37,9 +37,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.gz": - type: file - description: VCF concatenated output file + pattern: "*.{vcf.gz}" + - ${prefix}.vcf.gz: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.{vcf.gz}" - tbi: - meta: @@ -47,9 +50,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.tbi": - type: file - description: Alternative VCF file index + pattern: "*.tbi" + - ${prefix}.vcf.gz.tbi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.tbi" - csi: - meta: @@ -57,9 +63,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.csi": - type: file - description: Default VCF file index + pattern: "*.csi" + - ${prefix}.vcf.gz.csi: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.csi" - versions: - versions.yml: diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test b/modules/nf-core/bcftools/concat/tests/main.nf.test index cea386e3bd38..cb4642b29cd4 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test @@ -10,7 +10,7 @@ nextflow_process { tag "bcftools/concat" - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]") { config "./nextflow.config" @@ -41,7 +41,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index") { config "./vcf_gz_index.config" @@ -78,7 +78,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi") { config "./vcf_gz_index_csi.config" @@ -115,7 +115,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi") { config "./vcf_gz_index_tbi.config" @@ -153,7 +153,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], []]") { + test("homo_sapiens - [[vcf1, vcf2], []]") { config "./nextflow.config" @@ -181,7 +181,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub") { config "./nextflow.config" options "-stub" @@ -213,7 +213,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub") { config "./vcf_gz_index.config" options "-stub" @@ -246,7 +246,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub") { config "./vcf_gz_index_csi.config" options "-stub" @@ -279,7 +279,7 @@ nextflow_process { } - test("sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { + test("homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub") { config "./vcf_gz_index_tbi.config" options "-stub" diff --git a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap index 1182854f9478..09e87cd3e5dd 100644 --- a/modules/nf-core/bcftools/concat/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/concat/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index - stub": { "content": [ { "0": [ @@ -49,12 +49,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T08:09:13.734103412" + "timestamp": "2024-09-26T11:04:11.178539482" }, - "sarscov2 - [[vcf1, vcf2], []]": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]]": { "content": [ { "0": [ @@ -94,12 +94,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:09.213249578" + "timestamp": "2024-09-26T11:03:08.765639958" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index": { "content": [ [ [ @@ -125,12 +125,12 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T08:08:23.981388325" + "timestamp": "2024-09-26T11:03:21.607274757" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { "content": [ { "0": [ @@ -142,29 +142,29 @@ ] ], "1": [ - - ], - "2": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "2": [ + ], "3": [ "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ], "csi": [ + + ], + "tbi": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "tbi": [ - ], "vcf": [ [ @@ -180,12 +180,43 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T11:04:27.332133878" + }, + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" + ] + ], + [ + [ + { + "id": "test3" + }, + "test3_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:01:24.419027693" + "timestamp": "2024-09-26T11:03:36.575719606" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]]": { + "homo_sapiens - [[vcf1, vcf2], []]": { "content": [ { "0": [ @@ -225,43 +256,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:03.597061078" + "timestamp": "2024-09-26T11:03:54.069826178" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi": { - "content": [ - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz:md5,5f6796c3ae109a1a5b87353954693f5a" - ] - ], - [ - [ - { - "id": "test3" - }, - "test3_vcf.vcf.gz.csi" - ] - ], - [ - - ], - [ - "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" - }, - "timestamp": "2024-06-05T14:00:10.868487669" - }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - stub": { "content": [ { "0": [ @@ -301,12 +301,12 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-04T15:19:14.836256897" + "timestamp": "2024-09-26T11:04:02.45346063" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi": { "content": [ [ [ @@ -332,12 +332,12 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:00:31.061411617" + "timestamp": "2024-09-26T11:03:44.618596639" }, - "sarscov2 - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_tbi - stub": { + "homo_sapiens - [[vcf1, vcf2], [tbi1, tbi2]] - vcf_gz_index_csi - stub": { "content": [ { "0": [ @@ -349,29 +349,29 @@ ] ], "1": [ + + ], + "2": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] - ], - "2": [ - ], "3": [ "versions.yml:md5,c6e19f105510a46af1c5da9064e2e659" ], "csi": [ - - ], - "tbi": [ [ { "id": "test3" }, - "test3_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + "test3_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "tbi": [ + ], "vcf": [ [ @@ -387,9 +387,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-05T14:01:35.209746508" + "timestamp": "2024-09-26T11:04:19.745768656" } } \ No newline at end of file From a90a8863a3408e15d5a339b06413e57cf9ca9860 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?= <90359308+nschcolnicov@users.noreply.github.com> Date: Thu, 26 Sep 2024 18:32:48 -0300 Subject: [PATCH 096/486] Updated stub mkfastq (#6700) --- modules/nf-core/cellranger/mkfastq/main.nf | 27 +++++-------------- .../mkfastq/tests/main.nf.test.snap | 14 +++++++--- 2 files changed, 16 insertions(+), 25 deletions(-) diff --git a/modules/nf-core/cellranger/mkfastq/main.nf b/modules/nf-core/cellranger/mkfastq/main.nf index 06c15bbc1517..09480345aac1 100644 --- a/modules/nf-core/cellranger/mkfastq/main.nf +++ b/modules/nf-core/cellranger/mkfastq/main.nf @@ -48,34 +48,19 @@ process CELLRANGER_MKFASTQ { } def prefix = task.ext.prefix ?: "${meta.id}" """ - mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/" - # data with something to avoid breaking nf-test java I/O stream, fastq - cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/fake_file.fastq - @SEQ_ID - GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT - + - !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 - FAKE_FQ - gzip -n ${prefix}_outs/outs/fastq_path/fake_file.fastq - - # data with something to avoid breaking nf-test java I/O stream, fastq_undetermined - cat <<-FAKE_FQ > ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq - @SEQ_ID - GATTTGGGGTTCAAAGCAGTATCGATCAAATAGTAAATCCATTTGTTCAACTCACAGTTT - + - !''*((((***+))%%%++)(%%%%).1***-+*''))**55CCF>>>>>>CCCCCCC65 - FAKE_FQ - gzip -n ${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq - # data for reports output channel mkdir -p "${prefix}_outs/outs/fastq_path/Reports" - # data for stats output channel mkdir -p "${prefix}_outs/outs/fastq_path/Stats" - # data for interops output channel mkdir -p "${prefix}_outs/outs/interop_path/" touch "${prefix}_outs/outs/interop_path/IndexMetricsOut.bin" + # data for fastq channels + mkdir -p "${prefix}_outs/outs/fastq_path/sample/files/" + touch "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq" + touch "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq" + gzip "${prefix}_outs/outs/fastq_path/Undetermined_fake_file.fastq" + gzip "${prefix}_outs/outs/fastq_path/sample/files/fake_file.fastq" cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap index b12246889ddc..f2c1b325862f 100644 --- a/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap +++ b/modules/nf-core/cellranger/mkfastq/tests/main.nf.test.snap @@ -54,11 +54,17 @@ "id": "test", "lane": 1 }, - "fake_file.fastq.gz:md5,8e16c1f4a441cbb3b7de374d2c924da7" + "fake_file.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], [ - + [ + { + "id": "test", + "lane": 1 + }, + "Undetermined_fake_file.fastq.gz:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ], [ [ @@ -75,9 +81,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-15T20:01:48.013075" + "timestamp": "2024-09-26T18:47:18.168033527" }, "cellranger - tiny - illumina": { "content": [ From d3a3d04073af68437f07e0fb9b88aa6172c3f678 Mon Sep 17 00:00:00 2001 From: YSims Date: Fri, 27 Sep 2024 07:51:38 +0100 Subject: [PATCH 097/486] yahs release update (#6695) * update yahs version and output options * update yahs version and output options * add correct datatype in nf-test, new version yahs would attempt scaffolding based on alignment file * add samtools tag --- modules/nf-core/yahs/main.nf | 8 +-- modules/nf-core/yahs/meta.yml | 1 + modules/nf-core/yahs/tests/main.nf.test | 32 +++++++++--- modules/nf-core/yahs/tests/main.nf.test.snap | 52 +++++--------------- 4 files changed, 41 insertions(+), 52 deletions(-) diff --git a/modules/nf-core/yahs/main.nf b/modules/nf-core/yahs/main.nf index 470e5e2c3b58..6475fd91ad87 100644 --- a/modules/nf-core/yahs/main.nf +++ b/modules/nf-core/yahs/main.nf @@ -4,8 +4,8 @@ process YAHS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/yahs:1.2a.2--h7132678_0': - 'biocontainers/yahs:1.2a.2--h7132678_0' }" + 'https://depot.galaxyproject.org/singularity/yahs:1.2--he4a0461_1': + 'biocontainers/yahs:1.2--he4a0461_1' }" input: tuple val(meta), path(hic_map) @@ -13,8 +13,8 @@ process YAHS { path fai output: - tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta - tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp + tuple val(meta), path("*scaffolds_final.fa") , emit: scaffolds_fasta, optional: true + tuple val(meta), path("*scaffolds_final.agp"), emit: scaffolds_agp, optional: true tuple val(meta), path("*bin") , emit: binary path "versions.yml" , emit: versions diff --git a/modules/nf-core/yahs/meta.yml b/modules/nf-core/yahs/meta.yml index bb3112e80387..38869045f392 100644 --- a/modules/nf-core/yahs/meta.yml +++ b/modules/nf-core/yahs/meta.yml @@ -75,3 +75,4 @@ authors: - "@ksenia-krasheninnikova" maintainers: - "@ksenia-krasheninnikova" + - "@yy5" diff --git a/modules/nf-core/yahs/tests/main.nf.test b/modules/nf-core/yahs/tests/main.nf.test index 6e09ff0054b7..ee53a110d92b 100644 --- a/modules/nf-core/yahs/tests/main.nf.test +++ b/modules/nf-core/yahs/tests/main.nf.test @@ -9,18 +9,36 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "yahs" + tag "samtools/view" - test("sarscov2-bed-fasta-fai") { + setup { + run("SAMTOOLS_VIEW") { + script "../../samtools/view" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram', checkIfExists: true), + [] + ]) + input[1] = Channel.of([ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = [] + """ + } + } + } + + test("homo_sapiens-bam-fasta-fai") { when { process { """ - input[0] = [ [ id:'test' ], - file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) - ] - input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true) - + input[0] = SAMTOOLS_VIEW.out.bam + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) """ } } diff --git a/modules/nf-core/yahs/tests/main.nf.test.snap b/modules/nf-core/yahs/tests/main.nf.test.snap index a98c16fbec2e..c62caa91904e 100644 --- a/modules/nf-core/yahs/tests/main.nf.test.snap +++ b/modules/nf-core/yahs/tests/main.nf.test.snap @@ -1,67 +1,37 @@ { - "test-yahs": { + "homo_sapiens-bam-fasta-fai": { "content": [ { "0": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442" - ] + ], "1": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168" - ] + ], "2": [ - [ - { - "id": "test" - }, - "test.bin:md5,c60503a616a0f7726176febdad3ae186" - ] + ], "3": [ - "versions.yml:md5,007c44dd06fe8686b6f8068314601462" + ], "binary": [ - [ - { - "id": "test" - }, - "test.bin:md5,c60503a616a0f7726176febdad3ae186" - ] + ], "scaffolds_agp": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.agp:md5,7134a33534816100a84a6d32351c2168" - ] + ], "scaffolds_fasta": [ - [ - { - "id": "test" - }, - "test_scaffolds_final.fa:md5,a7673a43fb4e3f0a87d2ca2fe48bd442" - ] + ], "versions": [ - "versions.yml:md5,007c44dd06fe8686b6f8068314601462" + ] } ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.04.4" + "nextflow": "24.04.2" }, - "timestamp": "2024-08-23T08:47:14.869961" + "timestamp": "2024-09-26T22:35:24.103271222" } } \ No newline at end of file From 5c2ab5de7e8de33ac7cab83a4cd28a4d29a84049 Mon Sep 17 00:00:00 2001 From: Lorena Pantano Date: Fri, 27 Sep 2024 03:30:28 -0400 Subject: [PATCH 098/486] add alignmentSieve (#6693) * add alignmentSieve * longer keywords * add three keywords * possible solution with size * using logs instead of bam files * fix meta * Update modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * update snapshot * fix keywords Co-authored-by: Jose Espinosa-Carrasco * fix authors Co-authored-by: Jose Espinosa-Carrasco * fix authors names Co-authored-by: Jose Espinosa-Carrasco * add to maintainers Co-authored-by: Jose Espinosa-Carrasco --------- Co-authored-by: Alexander Peltzer Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: Jose Espinosa-Carrasco --- .../deeptools/alignmentsieve/environment.yml | 6 ++ .../nf-core/deeptools/alignmentsieve/main.nf | 49 +++++++++++++++ .../nf-core/deeptools/alignmentsieve/meta.yml | 56 +++++++++++++++++ .../alignmentsieve/tests/main.nf.test | 60 +++++++++++++++++++ .../alignmentsieve/tests/main.nf.test.snap | 59 ++++++++++++++++++ .../deeptools/alignmentsieve/tests/tags.yml | 2 + 6 files changed, 232 insertions(+) create mode 100644 modules/nf-core/deeptools/alignmentsieve/environment.yml create mode 100644 modules/nf-core/deeptools/alignmentsieve/main.nf create mode 100644 modules/nf-core/deeptools/alignmentsieve/meta.yml create mode 100644 modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test create mode 100644 modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap create mode 100644 modules/nf-core/deeptools/alignmentsieve/tests/tags.yml diff --git a/modules/nf-core/deeptools/alignmentsieve/environment.yml b/modules/nf-core/deeptools/alignmentsieve/environment.yml new file mode 100644 index 000000000000..d8e208ca8302 --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::deeptools=3.5.5 + - bioconda::samtools=1.20 diff --git a/modules/nf-core/deeptools/alignmentsieve/main.nf b/modules/nf-core/deeptools/alignmentsieve/main.nf new file mode 100644 index 000000000000..3223399c2439 --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/main.nf @@ -0,0 +1,49 @@ +process DEEPTOOLS_ALIGNMENTSIEVE { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0': + 'biocontainers/mulled-v2-eb9e7907c7a753917c1e4d7a64384c047429618a:41defd13a6f2ce014549fcc05d0b051f655777f9-0' }" + + input: + tuple val(meta), path(input), path(input_index) + + output: + tuple val(meta), path("*_as.bam") , emit: bam + path "versions.yml" , emit: versions + path "*_log.txt" , emit: logs + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + alignmentSieve \\ + $args \\ + -b $input \\ + -o ${prefix}_as.bam \\ + --filterMetrics ${prefix}_log.txt \\ + --numberOfProcessors $task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deeptools: \$(alignmentSieve --version | sed -e "s/alignmentSieve //g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}_as.bam + touch ${prefix}_log.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deeptools: \$(alignmentSieve --version | sed -e "s/alignmentSieve //g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/deeptools/alignmentsieve/meta.yml b/modules/nf-core/deeptools/alignmentsieve/meta.yml new file mode 100644 index 000000000000..37d381ca41d2 --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/meta.yml @@ -0,0 +1,56 @@ +name: deeptools_alignmentSieve +description: This tool filters alignments in a BAM/CRAM file according the the specified parameters. +keywords: + - ATACseq + - filter + - shift + - ATACshift +tools: + - deeptools: + description: A set of user-friendly tools for normalization and visualzation of + deep-sequencing data + homepage: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html + documentation: https://deeptools.readthedocs.io/en/develop/content/tools/alignmentSieve.html + tool_dev_url: https://github.com/deeptools/deepTools/ + doi: "10.1093/nar/gkw257" + licence: ["GPL v3"] + identifier: biotools:deeptools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM file + pattern: "*.{bam}" + - input_index: + type: file + description: BAM index file + pattern: "*.{bai}" +output: + - bam: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*_as.bam": + type: file + description: BAM file + pattern: "*.bam" + - logs: + - "*_log.txt": + type: file + description: TXT file + pattern: "*.txt" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lpantano" +maintainers: + - "@lpantano" diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test new file mode 100644 index 000000000000..2d3b61b93d8e --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test @@ -0,0 +1,60 @@ +nextflow_process { + + name "Test Process DEEPTOOLS_ALIGNMENTSIEVE" + script "../main.nf" + process "DEEPTOOLS_ALIGNMENTSIEVE" + + tag "modules" + tag "modules_nfcore" + tag "deeptools" + tag "deeptools/alignmentsieve" + + test("homo_sampiens - bam") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.logs, + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions) + .match() + } + ) + } + } + test("homo_sampiens - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap new file mode 100644 index 000000000000..ad1c635d92de --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/tests/main.nf.test.snap @@ -0,0 +1,59 @@ +{ + "homo_sampiens - bam": { + "content": [ + [ + "test_log.txt:md5,39f97a6a2ff83330d5c93411113df63a" + ], + "463ac3b905fbf4ddf113a94dbfa8d69f", + [ + "versions.yml:md5,baf8080ab016b89a27483809252bc803" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T12:59:06.183167" + }, + "homo_sampiens - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_as.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,baf8080ab016b89a27483809252bc803" + ], + "2": [ + "test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test_as.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "logs": [ + "test_log.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ], + "versions": [ + "versions.yml:md5,baf8080ab016b89a27483809252bc803" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-26T12:59:10.273315" + } +} \ No newline at end of file diff --git a/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml b/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml new file mode 100644 index 000000000000..fd24baa97d1d --- /dev/null +++ b/modules/nf-core/deeptools/alignmentsieve/tests/tags.yml @@ -0,0 +1,2 @@ +deeptools/bamcoverage: + - "modules/nf-core/deeptools/alignmentsieve/**" From e8e7ac1e4ead5adb59002b568b9d9744cc6d6393 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 30 Sep 2024 08:51:14 +0200 Subject: [PATCH 099/486] maxbin2: fix missing meta.yml content (#6710) fix missing meta.yml content --- modules/nf-core/maxbin2/meta.yml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/nf-core/maxbin2/meta.yml b/modules/nf-core/maxbin2/meta.yml index 6b5a98c766d8..538ba07f3fd3 100644 --- a/modules/nf-core/maxbin2/meta.yml +++ b/modules/nf-core/maxbin2/meta.yml @@ -108,6 +108,9 @@ output: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - "*_bin.tar.gz": + type: file + description: Marker bins + pattern: "*_bin.tar.gz" - marker_genes: - meta: type: map From ec48f56f6e1571e23800aaaba41cceda13408e02 Mon Sep 17 00:00:00 2001 From: Jose Espinosa-Carrasco Date: Mon, 30 Sep 2024 11:56:53 +0200 Subject: [PATCH 100/486] Switch from oras to https in phantompeakqualtools module (#6711) Switch from oras to https --- modules/nf-core/phantompeakqualtools/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/phantompeakqualtools/main.nf b/modules/nf-core/phantompeakqualtools/main.nf index f0f7dc634a0e..e1f22699685a 100644 --- a/modules/nf-core/phantompeakqualtools/main.nf +++ b/modules/nf-core/phantompeakqualtools/main.nf @@ -5,7 +5,7 @@ process PHANTOMPEAKQUALTOOLS { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/phantompeakqualtools:1.2.2--50be7727b2a72700' : + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/4a/4a1cddfad5b503ee347cc5de17d172e1876c547fca00aa844559c9e764fb400f/data' : 'community.wave.seqera.io/library/phantompeakqualtools:1.2.2--f8026fe2526a5e18' }" input: From 26757a6a54d05c3133c01c564c192ff617c5ea33 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 30 Sep 2024 12:53:54 +0200 Subject: [PATCH 101/486] Fix mirdeep2_mapper meta.yml (#6712) * fix missing meta.yml content * fix meta.yml for mirdeep2_mapper * fix hierarchy --- modules/nf-core/mirdeep2/mapper/meta.yml | 15 ++++++++++++--- 1 file changed, 12 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/mirdeep2/mapper/meta.yml b/modules/nf-core/mirdeep2/mapper/meta.yml index 5844344cf97f..a482c4805c57 100644 --- a/modules/nf-core/mirdeep2/mapper/meta.yml +++ b/modules/nf-core/mirdeep2/mapper/meta.yml @@ -36,9 +36,18 @@ input: pattern: "*" output: - outputs: - - meta: {} - - "*.fa": {} - - "*.arf": {} + - meta: + type: map + description: Groovy Map containing sample information, e.g. `[ id:'sample1', single_end:false ]` + - "*.fa": + type: file + description: Collapsed reads in FASTA format. + pattern: "*.fa" + - "*.arf": + type: file + description: Alignment Read Format (ARF) file containing the mapping of reads + to the genome. + pattern: "*.arf" - versions: - versions.yml: type: file From 83e2df1e4ec594beb8a575b4db0b4197900f4ebd Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 30 Sep 2024 16:23:30 +0200 Subject: [PATCH 102/486] update vcfeval inputs + nf-test conversion (#6714) update vcfeval inputs --- .../rtgtools/rocplot/tests/main.nf.test | 4 +- modules/nf-core/rtgtools/vcfeval/main.nf | 20 +- modules/nf-core/rtgtools/vcfeval/meta.yml | 4 +- .../rtgtools/vcfeval/tests/main.nf.test | 113 +++ .../rtgtools/vcfeval/tests/main.nf.test.snap | 677 ++++++++++++++++++ .../rtgtools/vcfeval/tests/nextflow.config | 4 + tests/config/pytest_modules.yml | 3 - .../modules/nf-core/rtgtools/vcfeval/main.nf | 50 -- .../nf-core/rtgtools/vcfeval/nextflow.config | 8 - .../modules/nf-core/rtgtools/vcfeval/test.yml | 67 -- 10 files changed, 809 insertions(+), 141 deletions(-) create mode 100644 modules/nf-core/rtgtools/vcfeval/tests/main.nf.test create mode 100644 modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap create mode 100644 modules/nf-core/rtgtools/vcfeval/tests/nextflow.config delete mode 100644 tests/modules/nf-core/rtgtools/vcfeval/main.nf delete mode 100644 tests/modules/nf-core/rtgtools/vcfeval/nextflow.config delete mode 100644 tests/modules/nf-core/rtgtools/vcfeval/test.yml diff --git a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index c7c37084e528..52c5386d16ce 100644 --- a/modules/nf-core/rtgtools/rocplot/tests/main.nf.test +++ b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test @@ -35,8 +35,8 @@ nextflow_process { file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists: true) ] input[1] = UNTAR.out.untar println(projectDir) diff --git a/modules/nf-core/rtgtools/vcfeval/main.nf b/modules/nf-core/rtgtools/vcfeval/main.nf index 98f9adb18dd3..330a1f3d9643 100644 --- a/modules/nf-core/rtgtools/vcfeval/main.nf +++ b/modules/nf-core/rtgtools/vcfeval/main.nf @@ -8,7 +8,7 @@ process RTGTOOLS_VCFEVAL { 'biocontainers/rtg-tools:3.12.1--hdfd78af_0' }" input: - tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(evaluation_bed) + tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(truth_bed), path(regions_bed) tuple val(meta2), path(sdf) output: @@ -33,8 +33,8 @@ process RTGTOOLS_VCFEVAL { script: def args = task.ext.args ?: "" def prefix = task.ext.prefix ?: "${meta.id}" - def bed_regions = truth_bed ? "--bed-regions=${truth_bed}" : "" - def eval_regions = evaluation_bed ? "--evaluation-regions=${evaluation_bed}" : "" + def bed_regions = regions_bed ? "--bed-regions=${regions_bed}" : "" + def eval_regions = truth_bed ? "--evaluation-regions=${truth_bed}" : "" def truth_index = truth_vcf_tbi ? "" : "rtg index ${truth_vcf}" def query_index = query_vcf_tbi ? "" : "rtg index ${query_vcf}" def avail_mem = task.memory.toGiga() + "G" @@ -68,17 +68,17 @@ process RTGTOOLS_VCFEVAL { def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.tp.vcf.gz + echo | gzip > ${prefix}.tp.vcf.gz touch ${prefix}.tp.vcf.gz.tbi - touch ${prefix}.fn.vcf.gz + echo | gzip > ${prefix}.fn.vcf.gz touch ${prefix}.fn.vcf.gz.tbi - touch ${prefix}.fp.vcf.gz + echo | gzip > ${prefix}.fp.vcf.gz touch ${prefix}.fp.vcf.gz.tbi - touch ${prefix}.tp-baseline.vcf.gz + echo | gzip > ${prefix}.tp-baseline.vcf.gz touch ${prefix}.tp-baseline.vcf.gz.tbi - touch ${prefix}.snp_roc.tsv.gz - touch ${prefix}.non_snp_roc.tsv.gz - touch ${prefix}.weighted_roc.tsv.gz + echo | gzip > ${prefix}.snp_roc.tsv.gz + echo | gzip > ${prefix}.non_snp_roc.tsv.gz + echo | gzip > ${prefix}.weighted_roc.tsv.gz touch ${prefix}.summary.txt touch ${prefix}.phasing.txt diff --git a/modules/nf-core/rtgtools/vcfeval/meta.yml b/modules/nf-core/rtgtools/vcfeval/meta.yml index 9814124ee792..4c59bab5216f 100644 --- a/modules/nf-core/rtgtools/vcfeval/meta.yml +++ b/modules/nf-core/rtgtools/vcfeval/meta.yml @@ -40,11 +40,13 @@ input: type: file description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional) + This input should be used to provide the golden truth BED files. pattern: "*.bed" - - evaluation_bed: + - regions_bed: type: file description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional) + This input should be used to provide the regions used by the analysis pattern: "*.bed" - - meta2: type: map diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test new file mode 100644 index 000000000000..55abc8427597 --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test @@ -0,0 +1,113 @@ +nextflow_process { + + name "Test Process RTGTOOLS_VCFEVAL" + script "../main.nf" + process "RTGTOOLS_VCFEVAL" + + tag "modules" + tag "modules_nfcore" + tag "rtgtools" + tag "rtgtools/vcfeval" + tag "untar" + + setup { + run("UNTAR") { + script "../../../untar/main.nf" + process { + """ + input[0] = Channel.value([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz', checkIfExists:true) + ]) + """ + } + } + } + + test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf") { + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true) + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, [], truth, [], [], []], sdf") { + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + [], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + [], + [], + [] + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [id:'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists:true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed', checkIfExists:true) + ]) + input[1] = UNTAR.out.untar + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap new file mode 100644 index 000000000000..4f39e2d46418 --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/main.nf.test.snap @@ -0,0 +1,677 @@ +{ + "homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + ] + ], + "11": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f4c8df93c8bdab603036bbc27b4a28c3" + ] + ], + "12": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,31988234bee208cacb3de90dabe1797f" + ] + ], + "13": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "2": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + ] + ], + "baseline_tbi": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "baseline_vcf": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "fn_tbi": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fn_vcf": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,fc419367818700d47df073615aeb9077" + ] + ], + "fp_tbi": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fp_vcf": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "non_snp_roc": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,eb0910409b8b088655defbd152103b81" + ] + ], + "phasing": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,31988234bee208cacb3de90dabe1797f" + ] + ], + "snp_roc": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,11d7393a16c25ac0a092382fecafee9b" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f4c8df93c8bdab603036bbc27b4a28c3" + ] + ], + "tp_tbi": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "tp_vcf": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5171021307097220337dbcaccc860495" + ] + ], + "versions": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "weighted_roc": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,de36bf613b3dacf4a043311336bb4a94" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:17:31.564974666" + }, + "homo_sapiens - [vcf, [], truth, [], [], []], sdf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5125ee41457c9d93f46b19e32788edb4" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,a0e9ac2d38c04bd591ab8f857c5c9133" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + ] + ], + "11": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f33feb32f84958fb931063044fba369b" + ] + ], + "12": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,133677dbd8be657439ea2b03fdfb8795" + ] + ], + "13": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "2": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,df96e4e4014cdb3050cb6f221f0cdca9" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,d4bfa2c7271351ca19589f0f57f210b7" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,920af25c3c18a438b11440702562fa35" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,95938320b425e28cf06c45ab45ad0360" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + ] + ], + "baseline_tbi": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,95938320b425e28cf06c45ab45ad0360" + ] + ], + "baseline_vcf": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,920af25c3c18a438b11440702562fa35" + ] + ], + "fn_tbi": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fn_vcf": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,df96e4e4014cdb3050cb6f221f0cdca9" + ] + ], + "fp_tbi": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,092a7a3162e7cff25d273525751eb284" + ] + ], + "fp_vcf": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,d4bfa2c7271351ca19589f0f57f210b7" + ] + ], + "non_snp_roc": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,30283ede3bcc5dd247f8a84bf345bf9a" + ] + ], + "phasing": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,133677dbd8be657439ea2b03fdfb8795" + ] + ], + "snp_roc": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,85edc0101bb9e8d3edc11abe4fdcda93" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,f33feb32f84958fb931063044fba369b" + ] + ], + "tp_tbi": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,a0e9ac2d38c04bd591ab8f857c5c9133" + ] + ], + "tp_vcf": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,5125ee41457c9d93f46b19e32788edb4" + ] + ], + "versions": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "weighted_roc": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,5dfacd641b080cc8ad22eebec015c698" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:18:04.344989466" + }, + "homo_sapiens - [vcf, tbi, truth, truth_tbi, truth_bed, regions_bed], sdf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "11": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "12": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "13": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "2": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "baseline_tbi": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "baseline_vcf": [ + [ + { + "id": "test" + }, + "test.tp-baseline.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "fn_tbi": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fn_vcf": [ + [ + { + "id": "test" + }, + "test.fn.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "fp_tbi": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "fp_vcf": [ + [ + { + "id": "test" + }, + "test.fp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "non_snp_roc": [ + [ + { + "id": "test" + }, + "test.non_snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "phasing": [ + [ + { + "id": "test" + }, + "test.phasing.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "snp_roc": [ + [ + { + "id": "test" + }, + "test.snp_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "summary": [ + [ + { + "id": "test" + }, + "test.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tp_tbi": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tp_vcf": [ + [ + { + "id": "test" + }, + "test.tp.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,a228f0d9e8b205b4cc7c485151a77bb0" + ], + "weighted_roc": [ + [ + { + "id": "test" + }, + "test.weighted_roc.tsv.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T15:23:21.165461388" + } +} \ No newline at end of file diff --git a/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config b/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config new file mode 100644 index 000000000000..7563521514f8 --- /dev/null +++ b/modules/nf-core/rtgtools/vcfeval/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + withName: UNTAR { + } +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index c5ede631186f..485641f1da0c 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -578,9 +578,6 @@ roary: rtgtools/format: - modules/nf-core/rtgtools/format/** - tests/modules/nf-core/rtgtools/format/** -rtgtools/vcfeval: - - modules/nf-core/rtgtools/vcfeval/** - - tests/modules/nf-core/rtgtools/vcfeval/** scramble/clusteranalysis: - modules/nf-core/scramble/clusteranalysis/** - tests/modules/nf-core/scramble/clusteranalysis/** diff --git a/tests/modules/nf-core/rtgtools/vcfeval/main.nf b/tests/modules/nf-core/rtgtools/vcfeval/main.nf deleted file mode 100644 index 7ca921fcaed7..000000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/main.nf +++ /dev/null @@ -1,50 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { RTGTOOLS_VCFEVAL } from '../../../../../modules/nf-core/rtgtools/vcfeval/main.nf' -include { UNTAR } from '../../../../modules/nf-core/untar/main.nf' - -workflow test_rtgtools_vcfeval { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true), - file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) - ] - - compressed_sdf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) - ] - - sdf = UNTAR( compressed_sdf ).untar - - RTGTOOLS_VCFEVAL ( input, sdf ) -} - -workflow test_rtgtools_vcfeval_no_optional_inputs { - - input = [ - [ id:'test' ], // meta map - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true), - [], - file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true), - [], - [], - [] - ] - - compressed_sdf = [ - [ id:'test' ], - file(params.test_data['homo_sapiens']['genome']['genome_21_sdf']) - ] - - sdf = UNTAR( compressed_sdf ).untar - - RTGTOOLS_VCFEVAL ( input, sdf ) -} diff --git a/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config b/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config deleted file mode 100644 index 4ced2e3b2ab1..000000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: UNTAR { - publishDir = [enabled:false] - } -} diff --git a/tests/modules/nf-core/rtgtools/vcfeval/test.yml b/tests/modules/nf-core/rtgtools/vcfeval/test.yml deleted file mode 100644 index 8f89d2b44b61..000000000000 --- a/tests/modules/nf-core/rtgtools/vcfeval/test.yml +++ /dev/null @@ -1,67 +0,0 @@ -- name: rtgtools vcfeval test_rtgtools_vcfeval - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rtgtools/vcfeval/nextflow.config - tags: - - rtgtools/vcfeval - - rtgtools - files: - - path: output/rtgtools/test.fn.vcf.gz - md5sum: 65142f7398361eebb00028255c4645f9 - - path: output/rtgtools/test.fn.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.fp.vcf.gz - md5sum: 459988c1aa5206214587044971db2518 - - path: output/rtgtools/test.fp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.non_snp_roc.tsv.gz - md5sum: 0ccf995d071c7d27812e9e899b67050a - - path: output/rtgtools/test.phasing.txt - md5sum: 31988234bee208cacb3de90dabe1797f - - path: output/rtgtools/test.snp_roc.tsv.gz - md5sum: cff421e8b15db7d92355fbef0be5ec93 - - path: output/rtgtools/test.summary.txt - md5sum: f4c8df93c8bdab603036bbc27b4a28c3 - - path: output/rtgtools/test.tp-baseline.vcf.gz - md5sum: 65142f7398361eebb00028255c4645f9 - - path: output/rtgtools/test.tp-baseline.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.tp.vcf.gz - md5sum: 459988c1aa5206214587044971db2518 - - path: output/rtgtools/test.tp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.weighted_roc.tsv.gz - md5sum: 946dd5b0a6f33993bc2f7378c503c5cc - - path: output/rtgtools/versions.yml - -- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs - command: nextflow run ./tests/modules/nf-core/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/rtgtools/vcfeval/nextflow.config - tags: - - rtgtools/vcfeval - - rtgtools - files: - - path: output/rtgtools/test.fn.vcf.gz - md5sum: 6a148698fa6c20d6e5bbe384d962363a - - path: output/rtgtools/test.fn.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.fp.vcf.gz - md5sum: 9c1606449d3c256233bdd2b6c8016776 - - path: output/rtgtools/test.fp.vcf.gz.tbi - md5sum: 092a7a3162e7cff25d273525751eb284 - - path: output/rtgtools/test.non_snp_roc.tsv.gz - md5sum: 9990107a5d8951e124d452f6cac26062 - - path: output/rtgtools/test.phasing.txt - md5sum: 133677dbd8be657439ea2b03fdfb8795 - - path: output/rtgtools/test.snp_roc.tsv.gz - md5sum: cde86d34fa86475194e29a74dfc9090c - - path: output/rtgtools/test.summary.txt - md5sum: f33feb32f84958fb931063044fba369b - - path: output/rtgtools/test.tp-baseline.vcf.gz - md5sum: 5d9bb9b55b03d42c1726c0c32498b624 - - path: output/rtgtools/test.tp-baseline.vcf.gz.tbi - md5sum: 95938320b425e28cf06c45ab45ad0360 - - path: output/rtgtools/test.tp.vcf.gz - md5sum: d771fa4d28b42b43e698cee93c92cf65 - - path: output/rtgtools/test.tp.vcf.gz.tbi - md5sum: a0e9ac2d38c04bd591ab8f857c5c9133 - - path: output/rtgtools/test.weighted_roc.tsv.gz - md5sum: 005c2e8bacaaab0b409da449301d67fd - - path: output/rtgtools/versions.yml From 023b45c4bb222b85a12b1bdc36d45b941d308702 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Mon, 30 Sep 2024 17:18:20 +0200 Subject: [PATCH 103/486] chore(deps): update pre-commit hook python-jsonschema/check-jsonschema to v0.29.3 (#6715) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 2387066d67f8..d195d3d90444 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: additional_dependencies: - prettier@3.2.5 - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.2 + rev: 0.29.3 hooks: - id: check-jsonschema # match meta.ymls in one of the subdirectories of modules/nf-core From bfa8975eefb8df3e480a44ac9e594f23f52b2963 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 30 Sep 2024 18:31:48 +0200 Subject: [PATCH 104/486] bedtools/genomecov - Update main.nf to use https over oras (#6713) Update main.nf to use https over oras --- modules/nf-core/bedtools/genomecov/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/bedtools/genomecov/main.nf b/modules/nf-core/bedtools/genomecov/main.nf index 8403c5303800..35e2ab14b34d 100644 --- a/modules/nf-core/bedtools/genomecov/main.nf +++ b/modules/nf-core/bedtools/genomecov/main.nf @@ -4,7 +4,7 @@ process BEDTOOLS_GENOMECOV { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/bedtools_coreutils:ba273c06a3909a15': + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/63/6397750e9730a3fbcc5b4c43f14bd141c64c723fd7dad80e47921a68a7c3cd21/data': 'community.wave.seqera.io/library/bedtools_coreutils:a623c13f66d5262b' }" input: From eb7b70119bfb1877334c996d13e520c61b21067d Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 2 Oct 2024 13:19:06 +0200 Subject: [PATCH 105/486] update sentieon to version 202308.03 (#6722) * update sentieon to version 202308.03 * update snapshot --- .../sentieon/applyvarcal/environment.yml | 2 +- modules/nf-core/sentieon/applyvarcal/main.nf | 4 +- .../nf-core/sentieon/bwaindex/environment.yml | 2 +- modules/nf-core/sentieon/bwaindex/main.nf | 4 +- .../nf-core/sentieon/bwamem/environment.yml | 2 +- modules/nf-core/sentieon/bwamem/main.nf | 4 +- .../sentieon/bwamem/tests/main.nf.test.snap | 50 +++++++------- .../sentieon/collectvcmetrics/environment.yml | 2 +- .../nf-core/sentieon/collectvcmetrics/main.nf | 4 +- .../collectvcmetrics/tests/main.nf.test.snap | 20 +++--- .../sentieon/coveragemetrics/environment.yml | 2 +- .../nf-core/sentieon/coveragemetrics/main.nf | 4 +- .../coveragemetrics/tests/main.nf.test.snap | 36 +++++----- .../sentieon/datametrics/environment.yml | 2 +- modules/nf-core/sentieon/datametrics/main.nf | 4 +- .../datametrics/tests/main.nf.test.snap | 66 +++++++++---------- .../nf-core/sentieon/dedup/environment.yml | 2 +- modules/nf-core/sentieon/dedup/main.nf | 4 +- .../sentieon/dedup/tests/main.nf.test.snap | 56 ++++++++-------- .../sentieon/dnamodelapply/environment.yml | 2 +- .../nf-core/sentieon/dnamodelapply/main.nf | 4 +- .../nf-core/sentieon/dnascope/environment.yml | 2 +- modules/nf-core/sentieon/dnascope/main.nf | 4 +- .../sentieon/gvcftyper/environment.yml | 2 +- modules/nf-core/sentieon/gvcftyper/main.nf | 4 +- .../gvcftyper/tests/main.nf.test.snap | 38 +++++------ .../sentieon/haplotyper/environment.yml | 2 +- modules/nf-core/sentieon/haplotyper/main.nf | 4 +- .../haplotyper/tests/main.nf.test.snap | 50 +++++++------- modules/nf-core/sentieon/qualcal/main.nf | 4 +- .../sentieon/qualcal/tests/main.nf.test.snap | 44 ++++++------- .../sentieon/readwriter/environment.yml | 2 +- modules/nf-core/sentieon/readwriter/main.nf | 4 +- .../readwriter/tests/main.nf.test.snap | 32 ++++----- .../nf-core/sentieon/tnfilter/environment.yml | 2 +- modules/nf-core/sentieon/tnfilter/main.nf | 4 +- .../sentieon/tnhaplotyper2/environment.yml | 2 +- .../nf-core/sentieon/tnhaplotyper2/main.nf | 4 +- .../nf-core/sentieon/tnscope/environment.yml | 2 +- modules/nf-core/sentieon/tnscope/main.nf | 4 +- .../nf-core/sentieon/varcal/environment.yml | 2 +- modules/nf-core/sentieon/varcal/main.nf | 4 +- .../sentieon/wgsmetrics/environment.yml | 2 +- modules/nf-core/sentieon/wgsmetrics/main.nf | 4 +- 44 files changed, 249 insertions(+), 249 deletions(-) diff --git a/modules/nf-core/sentieon/applyvarcal/environment.yml b/modules/nf-core/sentieon/applyvarcal/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/applyvarcal/environment.yml +++ b/modules/nf-core/sentieon/applyvarcal/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/applyvarcal/main.nf b/modules/nf-core/sentieon/applyvarcal/main.nf index 9f64f5a2f32e..724912d689e2 100644 --- a/modules/nf-core/sentieon/applyvarcal/main.nf +++ b/modules/nf-core/sentieon/applyvarcal/main.nf @@ -5,8 +5,8 @@ process SENTIEON_APPLYVARCAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(recal), path(recal_index), path(tranches) diff --git a/modules/nf-core/sentieon/bwaindex/environment.yml b/modules/nf-core/sentieon/bwaindex/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/bwaindex/environment.yml +++ b/modules/nf-core/sentieon/bwaindex/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/bwaindex/main.nf b/modules/nf-core/sentieon/bwaindex/main.nf index 2d3f1afa61f4..4372cc04baeb 100644 --- a/modules/nf-core/sentieon/bwaindex/main.nf +++ b/modules/nf-core/sentieon/bwaindex/main.nf @@ -5,8 +5,8 @@ process SENTIEON_BWAINDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/sentieon/bwamem/environment.yml b/modules/nf-core/sentieon/bwamem/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/bwamem/environment.yml +++ b/modules/nf-core/sentieon/bwamem/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/bwamem/main.nf b/modules/nf-core/sentieon/bwamem/main.nf index 76e364decac1..c038a857bf5d 100644 --- a/modules/nf-core/sentieon/bwamem/main.nf +++ b/modules/nf-core/sentieon/bwamem/main.nf @@ -5,8 +5,8 @@ process SENTIEON_BWAMEM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap index 0dc67a9a5b64..77070ccc45b5 100644 --- a/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/bwamem/tests/main.nf.test.snap @@ -8,12 +8,12 @@ "id": "test", "single_end": true }, - "test.bam:md5,58bc2194d084cf8462a3a7f6114c303a", - "test.bam.bai:md5,4fd9b026ff2306cc292cd695e11d5628" + "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b", + "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18" ] ], "1": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ], "bam_and_bai": [ [ @@ -21,12 +21,12 @@ "id": "test", "single_end": true }, - "test.bam:md5,58bc2194d084cf8462a3a7f6114c303a", - "test.bam.bai:md5,4fd9b026ff2306cc292cd695e11d5628" + "test.bam:md5,7b62831cb67d6d4a8e33b3cb788dfb1b", + "test.bam.bai:md5,6fc1dff58fab0491ecfa48f016041a18" ] ], "versions": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ] } ], @@ -34,7 +34,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T08:58:40.112926615" + "timestamp": "2024-10-02T10:25:33.275731212" }, "Paired-End - stub": { "content": [ @@ -50,7 +50,7 @@ ] ], "1": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ], "bam_and_bai": [ [ @@ -63,7 +63,7 @@ ] ], "versions": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ] } ], @@ -71,7 +71,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T08:59:20.476791905" + "timestamp": "2024-10-02T10:26:16.58588651" }, "Paired-End": { "content": [ @@ -82,12 +82,12 @@ "id": "test", "single_end": false }, - "test.bam:md5,3418d864f42215d1c0c8d604d9571b0d", + "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268", "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919" ] ], "1": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ], "bam_and_bai": [ [ @@ -95,12 +95,12 @@ "id": "test", "single_end": false }, - "test.bam:md5,3418d864f42215d1c0c8d604d9571b0d", + "test.bam:md5,b0c8606d660dbe50a34cf80a376bb268", "test.bam.bai:md5,be4ad85790468042f7fc01ca2e36a919" ] ], "versions": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ] } ], @@ -108,7 +108,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T08:59:00.346034062" + "timestamp": "2024-10-02T10:25:55.068934639" }, "Single-End - stub": { "content": [ @@ -124,7 +124,7 @@ ] ], "1": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ], "bam_and_bai": [ [ @@ -137,7 +137,7 @@ ] ], "versions": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ] } ], @@ -145,7 +145,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T08:59:10.054146084" + "timestamp": "2024-10-02T10:26:05.151760076" }, "Single-End Output CRAM": { "content": [ @@ -156,12 +156,12 @@ "id": "test", "single_end": true }, - "test.cram:md5,04d88bd709dc0bc27ca81a09e80d4a1b", - "test.cram.crai:md5,ac34c713fe95aa8a1fd6291bdbb76dcf" + "test.cram:md5,817cf0847ae0c89062e2ee4be312101a", + "test.cram.crai:md5,60f801c550a18982e55207adb31ec351" ] ], "1": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ], "bam_and_bai": [ [ @@ -169,12 +169,12 @@ "id": "test", "single_end": true }, - "test.cram:md5,04d88bd709dc0bc27ca81a09e80d4a1b", - "test.cram.crai:md5,ac34c713fe95aa8a1fd6291bdbb76dcf" + "test.cram:md5,817cf0847ae0c89062e2ee4be312101a", + "test.cram.crai:md5,60f801c550a18982e55207adb31ec351" ] ], "versions": [ - "versions.yml:md5,6095ad80036c5d876c2616504a21efcc" + "versions.yml:md5,755d24c7416c1408313ec93814cef759" ] } ], @@ -182,6 +182,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T08:58:49.962693499" + "timestamp": "2024-10-02T10:25:44.360755915" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/collectvcmetrics/environment.yml b/modules/nf-core/sentieon/collectvcmetrics/environment.yml index f065ece32f49..d1a652d95867 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/environment.yml +++ b/modules/nf-core/sentieon/collectvcmetrics/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sentieon=202308.02" + - "bioconda::sentieon=202308.03" diff --git a/modules/nf-core/sentieon/collectvcmetrics/main.nf b/modules/nf-core/sentieon/collectvcmetrics/main.nf index 47038ca82f9e..c4897a9ba982 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/main.nf +++ b/modules/nf-core/sentieon/collectvcmetrics/main.nf @@ -5,8 +5,8 @@ process SENTIEON_COLLECTVCMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta) , path(vcf), path(tbi) diff --git a/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test.snap index 1769bf458ad2..66598400e901 100644 --- a/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/collectvcmetrics/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,3598e0348efd4895a499bcca3c121577" + "versions.yml:md5,b323d4c67c15a60c781d0b693058b80b" ], "metrics": [ [ @@ -38,15 +38,15 @@ ] ], "versions": [ - "versions.yml:md5,3598e0348efd4895a499bcca3c121577" + "versions.yml:md5,b323d4c67c15a60c781d0b693058b80b" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-12T14:04:32.056180428" + "timestamp": "2024-10-02T10:26:43.851386846" }, "Test VCF with intervals": { "content": [ @@ -61,14 +61,14 @@ "" ], [ - "versions.yml:md5,3598e0348efd4895a499bcca3c121577" + "versions.yml:md5,b323d4c67c15a60c781d0b693058b80b" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-12T13:27:27.277407951" + "timestamp": "2024-10-02T10:26:36.744267657" }, "Test VCF": { "content": [ @@ -83,13 +83,13 @@ "" ], [ - "versions.yml:md5,3598e0348efd4895a499bcca3c121577" + "versions.yml:md5,b323d4c67c15a60c781d0b693058b80b" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-12T13:27:19.639784594" + "timestamp": "2024-10-02T10:26:27.119501631" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/coveragemetrics/environment.yml b/modules/nf-core/sentieon/coveragemetrics/environment.yml index f065ece32f49..d1a652d95867 100644 --- a/modules/nf-core/sentieon/coveragemetrics/environment.yml +++ b/modules/nf-core/sentieon/coveragemetrics/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::sentieon=202308.02" + - "bioconda::sentieon=202308.03" diff --git a/modules/nf-core/sentieon/coveragemetrics/main.nf b/modules/nf-core/sentieon/coveragemetrics/main.nf index cf9afca190ea..1ff7b07af11e 100644 --- a/modules/nf-core/sentieon/coveragemetrics/main.nf +++ b/modules/nf-core/sentieon/coveragemetrics/main.nf @@ -5,8 +5,8 @@ process SENTIEON_COVERAGEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta) , path(bam), path(bai) diff --git a/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test.snap index cae0395fd71f..31d11a34fa1a 100644 --- a/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/coveragemetrics/tests/main.nf.test.snap @@ -26,7 +26,7 @@ ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ @@ -52,7 +52,7 @@ ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -60,7 +60,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T10:43:42.344116091" + "timestamp": "2024-10-02T10:27:12.750615072" }, "Test with interval": { "content": [ @@ -114,7 +114,7 @@ ] ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ [ @@ -165,7 +165,7 @@ ] ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -173,7 +173,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T10:43:35.316973881" + "timestamp": "2024-10-02T10:27:02.629834795" }, "Test multiple BAMs": { "content": [ @@ -227,7 +227,7 @@ ] ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ [ @@ -278,7 +278,7 @@ ] ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -286,7 +286,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T10:43:57.275424452" + "timestamp": "2024-10-02T10:27:30.422776076" }, "Test - stub": { "content": [ @@ -310,7 +310,7 @@ ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ @@ -331,7 +331,7 @@ ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -339,7 +339,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T15:36:05.272586496" + "timestamp": "2024-10-02T10:27:36.672912519" }, "Test per sample": { "content": [ @@ -393,7 +393,7 @@ ] ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ [ @@ -444,7 +444,7 @@ ] ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -452,7 +452,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T10:43:28.382765881" + "timestamp": "2024-10-02T10:26:52.908981157" }, "Test readgroup partition": { "content": [ @@ -506,7 +506,7 @@ ] ], "6": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ], "coverage_counts": [ [ @@ -557,7 +557,7 @@ ] ], "versions": [ - "versions.yml:md5,f929dc12581c3a297a974e3eda9057b0" + "versions.yml:md5,ba376730b2ae7f9f177a079f07f5e2f4" ] } ], @@ -565,6 +565,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-07T10:43:49.706927947" + "timestamp": "2024-10-02T10:27:20.950349637" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/datametrics/environment.yml b/modules/nf-core/sentieon/datametrics/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/datametrics/environment.yml +++ b/modules/nf-core/sentieon/datametrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/datametrics/main.nf b/modules/nf-core/sentieon/datametrics/main.nf index 6567cc7218fa..85bf6b507e6d 100644 --- a/modules/nf-core/sentieon/datametrics/main.nf +++ b/modules/nf-core/sentieon/datametrics/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DATAMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap index 25b1ae128fb0..d31612106bb1 100644 --- a/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/datametrics/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "10": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ], "2": [ [ @@ -186,7 +186,7 @@ ] ], "versions": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ] } ], @@ -194,7 +194,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T12:01:01.974389137" + "timestamp": "2024-10-02T10:22:45.899449567" }, "metrics - with plots": { "content": [ @@ -205,7 +205,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" ] ], "1": [ @@ -214,11 +214,11 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" ] ], "10": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ], "2": [ [ @@ -226,7 +226,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" ] ], "3": [ @@ -235,7 +235,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" ] ], "4": [ @@ -244,7 +244,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" ] ], "5": [ @@ -253,7 +253,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" ] ], "6": [ @@ -298,7 +298,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" ] ], "gc_metrics": [ @@ -307,7 +307,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" ] ], "gc_plot": [ @@ -325,7 +325,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" ] ], "is_metrics": [ @@ -334,7 +334,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" ] ], "is_plot": [ @@ -352,7 +352,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" ] ], "mq_plot": [ @@ -370,7 +370,7 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" ] ], "qd_plot": [ @@ -383,7 +383,7 @@ ] ], "versions": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ] } ], @@ -391,7 +391,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T12:00:41.711146115" + "timestamp": "2024-10-02T10:22:36.981327826" }, "metrics - no plots": { "content": [ @@ -402,7 +402,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" ] ], "1": [ @@ -411,11 +411,11 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" ] ], "10": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ], "2": [ [ @@ -423,7 +423,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" ] ], "3": [ @@ -432,7 +432,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" ] ], "4": [ @@ -441,7 +441,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" ] ], "5": [ @@ -450,7 +450,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" ] ], "6": [ @@ -471,7 +471,7 @@ "id": "test", "single_end": false }, - "test_aln_metrics.txt:md5,1cf61ba2d564cf427976d2543fd770ac" + "test_aln_metrics.txt:md5,1950af402ff3751023761de5bb649b43" ] ], "gc_metrics": [ @@ -480,7 +480,7 @@ "id": "test", "single_end": false }, - "test_gc_metrics.txt:md5,1ed8166e64c9a44e40ab6e5173489ef2" + "test_gc_metrics.txt:md5,42d6ee7ce81858329b66c38e6558d66d" ] ], "gc_plot": [ @@ -492,7 +492,7 @@ "id": "test", "single_end": false }, - "test_gc_summary.txt:md5,33e6d54497ac882486c38ec05b2ca60a" + "test_gc_summary.txt:md5,367143e0f7680555bb68173561919e5f" ] ], "is_metrics": [ @@ -501,7 +501,7 @@ "id": "test", "single_end": false }, - "test_is_metrics.txt:md5,be543f33974d1ed4663ef2676a416669" + "test_is_metrics.txt:md5,0ce93baa9d470f9b6344094218d74e59" ] ], "is_plot": [ @@ -513,7 +513,7 @@ "id": "test", "single_end": false }, - "test_mq_metrics.txt:md5,4f4540509edee8dc3ad78caf1733e206" + "test_mq_metrics.txt:md5,159ed897b11e7621703365134f60c1f7" ] ], "mq_plot": [ @@ -525,14 +525,14 @@ "id": "test", "single_end": false }, - "test_qd_metrics.txt:md5,f53e8b0da374aa35908cfd2180bf1406" + "test_qd_metrics.txt:md5,fa86f2f5cc195ea48565401f68ba0730" ] ], "qd_plot": [ ], "versions": [ - "versions.yml:md5,7c769d886e94ed56a45445ac1c9ebcdf" + "versions.yml:md5,aa6e267932a3f74d88a7bce286a1493a" ] } ], @@ -540,6 +540,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-20T12:00:27.37021578" + "timestamp": "2024-10-02T10:22:26.909097428" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dedup/environment.yml b/modules/nf-core/sentieon/dedup/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/dedup/environment.yml +++ b/modules/nf-core/sentieon/dedup/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/dedup/main.nf b/modules/nf-core/sentieon/dedup/main.nf index f0b387f64f60..5735df734068 100644 --- a/modules/nf-core/sentieon/dedup/main.nf +++ b/modules/nf-core/sentieon/dedup/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DEDUP { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap index c1cd83ec3478..26117a7cdf48 100644 --- a/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/dedup/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test.cram:md5,d2993113f4614f5196fc74d489412fc4" + "test.cram:md5,e46e97256846338e1cff32d862105491" ] ], "1": [ @@ -34,7 +34,7 @@ { "id": "test" }, - "test.score:md5,a97459ff2939682091bac3c3912402dc" + "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" ] ], "5": [ @@ -42,7 +42,7 @@ { "id": "test" }, - "test.cram.metrics:md5,ccd45ea1f2397184e3ab271b1ba8bb2a" + "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc" ] ], "6": [ @@ -50,11 +50,11 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,ccd45ea1f2397184e3ab271b1ba8bb2a" + "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc" ] ], "7": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ], "bai": [ [ @@ -80,7 +80,7 @@ { "id": "test" }, - "test.cram:md5,d2993113f4614f5196fc74d489412fc4" + "test.cram:md5,e46e97256846338e1cff32d862105491" ] ], "metrics": [ @@ -88,7 +88,7 @@ { "id": "test" }, - "test.cram.metrics:md5,ccd45ea1f2397184e3ab271b1ba8bb2a" + "test.cram.metrics:md5,208f7c5fa2f489cfaaffbce116fed0bc" ] ], "metrics_multiqc_tsv": [ @@ -96,7 +96,7 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,ccd45ea1f2397184e3ab271b1ba8bb2a" + "test.cram.metrics.multiqc.tsv:md5,208f7c5fa2f489cfaaffbce116fed0bc" ] ], "score": [ @@ -104,19 +104,19 @@ { "id": "test" }, - "test.score:md5,a97459ff2939682091bac3c3912402dc" + "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" ] ], "versions": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-26T13:02:23.640202" + "timestamp": "2024-10-02T10:28:10.570152622" }, "Test removing duplicates": { "content": [ @@ -126,7 +126,7 @@ { "id": "test" }, - "test.cram:md5,e67398ab64430191f9d15cb8a8f425c7" + "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4" ] ], "1": [ @@ -153,7 +153,7 @@ { "id": "test" }, - "test.score:md5,a97459ff2939682091bac3c3912402dc" + "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" ] ], "5": [ @@ -161,7 +161,7 @@ { "id": "test" }, - "test.cram.metrics:md5,7fc2ddc6b21838bdc42aff146549cea2" + "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65" ] ], "6": [ @@ -169,11 +169,11 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,7fc2ddc6b21838bdc42aff146549cea2" + "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65" ] ], "7": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ], "bai": [ [ @@ -199,7 +199,7 @@ { "id": "test" }, - "test.cram:md5,e67398ab64430191f9d15cb8a8f425c7" + "test.cram:md5,8075d3e7c66d36fdbb81270eefc996d4" ] ], "metrics": [ @@ -207,7 +207,7 @@ { "id": "test" }, - "test.cram.metrics:md5,7fc2ddc6b21838bdc42aff146549cea2" + "test.cram.metrics:md5,2a41239de0275a8321f4658286d97d65" ] ], "metrics_multiqc_tsv": [ @@ -215,7 +215,7 @@ { "id": "test" }, - "test.cram.metrics.multiqc.tsv:md5,7fc2ddc6b21838bdc42aff146549cea2" + "test.cram.metrics.multiqc.tsv:md5,2a41239de0275a8321f4658286d97d65" ] ], "score": [ @@ -223,19 +223,19 @@ { "id": "test" }, - "test.score:md5,a97459ff2939682091bac3c3912402dc" + "test.score:md5,835f05ecc5d3ef5d4e31ba7f831d9a8b" ] ], "versions": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-26T13:02:33.698037" + "timestamp": "2024-10-02T10:28:19.377946074" }, "Test stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "7": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ], "bai": [ [ @@ -346,14 +346,14 @@ ] ], "versions": [ - "versions.yml:md5,f057aca19107ce54f0cec1e42edd097e" + "versions.yml:md5,763463853476be96846b6da5aecfacf4" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-26T13:02:41.360148" + "timestamp": "2024-10-02T10:28:28.792696026" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/dnamodelapply/environment.yml b/modules/nf-core/sentieon/dnamodelapply/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/dnamodelapply/environment.yml +++ b/modules/nf-core/sentieon/dnamodelapply/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/dnamodelapply/main.nf b/modules/nf-core/sentieon/dnamodelapply/main.nf index b4b10ce4d09d..85fd601b3933 100644 --- a/modules/nf-core/sentieon/dnamodelapply/main.nf +++ b/modules/nf-core/sentieon/dnamodelapply/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DNAMODELAPPLY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(vcf), path(idx) diff --git a/modules/nf-core/sentieon/dnascope/environment.yml b/modules/nf-core/sentieon/dnascope/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/dnascope/environment.yml +++ b/modules/nf-core/sentieon/dnascope/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/dnascope/main.nf b/modules/nf-core/sentieon/dnascope/main.nf index 63d7d23b8a27..bdeb62521a33 100644 --- a/modules/nf-core/sentieon/dnascope/main.nf +++ b/modules/nf-core/sentieon/dnascope/main.nf @@ -5,8 +5,8 @@ process SENTIEON_DNASCOPE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(bam), path(bai), path(intervals) diff --git a/modules/nf-core/sentieon/gvcftyper/environment.yml b/modules/nf-core/sentieon/gvcftyper/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/gvcftyper/environment.yml +++ b/modules/nf-core/sentieon/gvcftyper/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/gvcftyper/main.nf b/modules/nf-core/sentieon/gvcftyper/main.nf index e2e5d2434d9b..6817c6dbe277 100644 --- a/modules/nf-core/sentieon/gvcftyper/main.nf +++ b/modules/nf-core/sentieon/gvcftyper/main.nf @@ -5,8 +5,8 @@ process SENTIEON_GVCFTYPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(gvcfs), path(tbis), path(intervals) diff --git a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap index 5e7e40fb6bed..627b62fd872d 100644 --- a/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/gvcftyper/tests/main.nf.test.snap @@ -2,58 +2,58 @@ "sentieon gvcftyper dbsnp": { "content": [ [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "test.genotyped.vcf.gz.tbi", "21606383c760bf676d4c1f747b97d118" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:12:47.508154" + "timestamp": "2024-10-02T10:29:01.102534193" }, "sentieon gvcftyper dbsnp intervals": { "content": [ [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "test.genotyped.vcf.gz.tbi", "21606383c760bf676d4c1f747b97d118" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:13:05.636172" + "timestamp": "2024-10-02T10:29:20.933217951" }, "sentieon gvcftyper vcf.gz": { "content": [ [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "test.genotyped.vcf.gz.tbi", "d13216836f1452e200b215b796606671" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:12:38.720056" + "timestamp": "2024-10-02T10:28:50.937002394" }, "sentieon gvcftyper intervals": { "content": [ [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "test.genotyped.vcf.gz.tbi", "d13216836f1452e200b215b796606671" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:12:56.700687" + "timestamp": "2024-10-02T10:29:11.029924476" }, "sentieon gvcftyper - stub": { "content": [ @@ -75,7 +75,7 @@ ] ], "2": [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "vcf_gz": [ [ @@ -94,28 +94,28 @@ ] ], "versions": [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:03:46.379477" + "timestamp": "2024-10-02T10:29:30.788262037" }, "sentieon gvcftyper vcf": { "content": [ [ - "versions.yml:md5,bc9039ece9061340830a80ac2b171f3b" + "versions.yml:md5,03a2696e8be5117cccfe48a9bfd8c68a" ], "test.genotyped.vcf.gz.tbi", "d13216836f1452e200b215b796606671" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T14:12:29.24482" + "timestamp": "2024-10-02T10:28:41.276698125" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/haplotyper/environment.yml b/modules/nf-core/sentieon/haplotyper/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/haplotyper/environment.yml +++ b/modules/nf-core/sentieon/haplotyper/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/haplotyper/main.nf b/modules/nf-core/sentieon/haplotyper/main.nf index 33122d86b2f9..a04b342caf08 100644 --- a/modules/nf-core/sentieon/haplotyper/main.nf +++ b/modules/nf-core/sentieon/haplotyper/main.nf @@ -5,8 +5,8 @@ process SENTIEON_HAPLOTYPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(input), path(input_index), path(intervals), path(recal_table) diff --git a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap index 5b77a02f5ee3..0527f0fcbe44 100644 --- a/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/haplotyper/tests/main.nf.test.snap @@ -2,49 +2,49 @@ "Sentieon Haplotyper VCF": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.unfiltered.vcf.gz.tbi", "cea0045051da7877b38a1e25df812a91" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:16:51.711057" + "timestamp": "2024-10-02T10:29:42.675527558" }, "Sentieon Haplotyper Recalibration": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.unfiltered.vcf.gz.tbi", "10faa3b669c49826098e09784d8a4716" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T15:21:57.012186" + "timestamp": "2024-10-02T10:30:38.708688756" }, "Sentieon Haplotyper GVCF": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.g.vcf.gz.tbi", "338fc3c37b208d6595948576833eb665" ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:17:01.797501" + "timestamp": "2024-10-02T10:29:53.99302993" }, "Sentieon Haplotyper BOTH": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.g.vcf.gz.tbi", "338fc3c37b208d6595948576833eb665", @@ -53,14 +53,14 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:17:12.021226" + "timestamp": "2024-10-02T10:30:03.323463525" }, "Sentieon Haplotyper DBSNP BOTH": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.g.vcf.gz.tbi", "228556b7921205f023fec51098feeb97", @@ -69,14 +69,14 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:30:48.065511" + "timestamp": "2024-10-02T10:30:25.917634004" }, "Sentieon Haplotyper Intervals BOTH": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.g.vcf.gz.tbi", "338fc3c37b208d6595948576833eb665", @@ -85,9 +85,9 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:17:22.554336" + "timestamp": "2024-10-02T10:30:14.249175276" }, "Sentieon Haplotyper - stub": { "content": [ @@ -125,7 +125,7 @@ ] ], "4": [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "gvcf": [ [ @@ -160,28 +160,28 @@ ] ], "versions": [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-31T10:47:33.117516" + "timestamp": "2024-10-02T10:30:56.435076872" }, "Sentieon Haplotyper multiple CRAMs": { "content": [ [ - "versions.yml:md5,b58c15c81619894cdbab1f2edf694190" + "versions.yml:md5,1a7b41acc44d0724c8dca247e6323877" ], "test.unfiltered.vcf.gz.tbi", "b5d6e09e336438e38f7bf5531799e3a" ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T17:04:30.67684393" + "timestamp": "2024-10-02T10:30:49.266709749" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/qualcal/main.nf b/modules/nf-core/sentieon/qualcal/main.nf index 91785ce52a33..de4287e19706 100644 --- a/modules/nf-core/sentieon/qualcal/main.nf +++ b/modules/nf-core/sentieon/qualcal/main.nf @@ -4,8 +4,8 @@ process SENTIEON_QUALCAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(input), path(input_index) diff --git a/modules/nf-core/sentieon/qualcal/tests/main.nf.test.snap b/modules/nf-core/sentieon/qualcal/tests/main.nf.test.snap index 860131a7d012..676768d5de66 100644 --- a/modules/nf-core/sentieon/qualcal/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/qualcal/tests/main.nf.test.snap @@ -18,7 +18,7 @@ { "id": "test" }, - "test.recalibrated.bam:md5,f77f009ae183d0985e301ca43f0d8bc9" + "test.recalibrated.bam:md5,4fb1bab59ea9b0e04415a319f26622fb" ] ], "3": [ @@ -38,7 +38,7 @@ ] ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ [ @@ -61,7 +61,7 @@ { "id": "test" }, - "test.recalibrated.bam:md5,f77f009ae183d0985e301ca43f0d8bc9" + "test.recalibrated.bam:md5,4fb1bab59ea9b0e04415a319f26622fb" ] ], "table": [ @@ -76,7 +76,7 @@ ] ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -84,7 +84,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:40:58.953198101" + "timestamp": "2024-10-02T10:31:32.425231469" }, "BAM - stub": { "content": [ @@ -130,7 +130,7 @@ ] ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ [ @@ -173,7 +173,7 @@ ] ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -181,7 +181,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:41:20.102366914" + "timestamp": "2024-10-02T10:31:54.72910232" }, "Generate recalibration table - CRAM": { "content": [ @@ -207,7 +207,7 @@ ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ @@ -230,7 +230,7 @@ ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -238,7 +238,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:40:45.702266837" + "timestamp": "2024-10-02T10:31:19.033117607" }, "no recal BAM - stub": { "content": [ @@ -279,7 +279,7 @@ ] ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ [ @@ -317,7 +317,7 @@ ] ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -325,7 +325,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:41:27.713572216" + "timestamp": "2024-10-02T10:32:01.710216891" }, "Recalibrate - CRAM": { "content": [ @@ -346,7 +346,7 @@ { "id": "test" }, - "test.recalibrated.cram:md5,a092db2ad452a51f95c43e768dfe498d" + "test.recalibrated.cram:md5,9a51a1fd90e0a7cbec18762c6917c3d2" ] ], "3": [ @@ -366,7 +366,7 @@ ] ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ [ @@ -389,7 +389,7 @@ { "id": "test" }, - "test.recalibrated.cram:md5,a092db2ad452a51f95c43e768dfe498d" + "test.recalibrated.cram:md5,9a51a1fd90e0a7cbec18762c6917c3d2" ] ], "table": [ @@ -404,7 +404,7 @@ ] ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -412,7 +412,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:41:12.389107209" + "timestamp": "2024-10-02T10:31:46.677277887" }, "Generate recalibration table - BAM": { "content": [ @@ -438,7 +438,7 @@ ], "5": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ], "csv": [ @@ -461,7 +461,7 @@ ], "versions": [ - "versions.yml:md5,aa4db95f935851225e5a7c3bc18f0ba4" + "versions.yml:md5,9343aad4eaf20c1fe4ba1848f0b2461c" ] } ], @@ -469,6 +469,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-13T16:40:37.232122352" + "timestamp": "2024-10-02T10:31:08.50547086" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/readwriter/environment.yml b/modules/nf-core/sentieon/readwriter/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/readwriter/environment.yml +++ b/modules/nf-core/sentieon/readwriter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/readwriter/main.nf b/modules/nf-core/sentieon/readwriter/main.nf index 1011c7b2e132..7e00b9e98f5d 100644 --- a/modules/nf-core/sentieon/readwriter/main.nf +++ b/modules/nf-core/sentieon/readwriter/main.nf @@ -5,8 +5,8 @@ process SENTIEON_READWRITER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(input), path(index) diff --git a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap index 6e71a1d2bf51..0af607892b96 100644 --- a/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap +++ b/modules/nf-core/sentieon/readwriter/tests/main.nf.test.snap @@ -4,56 +4,56 @@ "2f11e4fe3390b8ad0a1852616fd1da04", "test.bam.bai", [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-01T13:14:43.34615" + "timestamp": "2024-10-02T10:32:10.696224516" }, "cram": { "content": [ "2f11e4fe3390b8ad0a1852616fd1da04", "test.cram.crai", [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-01T13:14:53.60186" + "timestamp": "2024-10-02T10:32:23.080911465" }, "merging - output bam": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.bam.bai", [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-01T13:15:03.780064" + "timestamp": "2024-10-02T10:32:36.741074568" }, "merging - output bam to cram": { "content": [ "ed89d81d2d6adafdbb819a1a4ec86493", "test.cram.crai", [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-01T13:15:15.313494" + "timestamp": "2024-10-02T10:33:50.523887508" }, "sentieon readwriter - stub": { "content": [ @@ -84,7 +84,7 @@ ] ], "3": [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ], "index": [ [ @@ -112,14 +112,14 @@ ] ], "versions": [ - "versions.yml:md5,7e0e065f92de4419098841b16968fbed" + "versions.yml:md5,914cac5a1fad066362698afc9419ecb2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-01T13:15:23.88137" + "timestamp": "2024-10-02T10:34:00.856232997" } } \ No newline at end of file diff --git a/modules/nf-core/sentieon/tnfilter/environment.yml b/modules/nf-core/sentieon/tnfilter/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/tnfilter/environment.yml +++ b/modules/nf-core/sentieon/tnfilter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/tnfilter/main.nf b/modules/nf-core/sentieon/tnfilter/main.nf index 57f8f20f57a2..e1de21d534d6 100644 --- a/modules/nf-core/sentieon/tnfilter/main.nf +++ b/modules/nf-core/sentieon/tnfilter/main.nf @@ -5,8 +5,8 @@ process SENTIEON_TNFILTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(vcf), path(vcf_tbi), path(stats), path(contamination), path(segments), path(orientation_priors) diff --git a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/environment.yml +++ b/modules/nf-core/sentieon/tnhaplotyper2/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/tnhaplotyper2/main.nf b/modules/nf-core/sentieon/tnhaplotyper2/main.nf index dfa9796754a5..4a001cd1a6e7 100644 --- a/modules/nf-core/sentieon/tnhaplotyper2/main.nf +++ b/modules/nf-core/sentieon/tnhaplotyper2/main.nf @@ -5,8 +5,8 @@ process SENTIEON_TNHAPLOTYPER2 { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/nf-core/sentieon/tnscope/environment.yml b/modules/nf-core/sentieon/tnscope/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/tnscope/environment.yml +++ b/modules/nf-core/sentieon/tnscope/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/tnscope/main.nf b/modules/nf-core/sentieon/tnscope/main.nf index ac13542f978d..b588aeb419d0 100644 --- a/modules/nf-core/sentieon/tnscope/main.nf +++ b/modules/nf-core/sentieon/tnscope/main.nf @@ -5,8 +5,8 @@ process SENTIEON_TNSCOPE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/sentieon/varcal/environment.yml b/modules/nf-core/sentieon/varcal/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/varcal/environment.yml +++ b/modules/nf-core/sentieon/varcal/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/varcal/main.nf b/modules/nf-core/sentieon/varcal/main.nf index 7c85c1210203..d78eacb44a02 100644 --- a/modules/nf-core/sentieon/varcal/main.nf +++ b/modules/nf-core/sentieon/varcal/main.nf @@ -5,8 +5,8 @@ process SENTIEON_VARCAL { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(vcf), path(tbi) // input vcf and tbi of variants to recalibrate diff --git a/modules/nf-core/sentieon/wgsmetrics/environment.yml b/modules/nf-core/sentieon/wgsmetrics/environment.yml index 185d95bde824..d7abf668ea9e 100644 --- a/modules/nf-core/sentieon/wgsmetrics/environment.yml +++ b/modules/nf-core/sentieon/wgsmetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::sentieon=202308.02 + - bioconda::sentieon=202308.03 diff --git a/modules/nf-core/sentieon/wgsmetrics/main.nf b/modules/nf-core/sentieon/wgsmetrics/main.nf index fad8d071700e..9f268f5a8580 100644 --- a/modules/nf-core/sentieon/wgsmetrics/main.nf +++ b/modules/nf-core/sentieon/wgsmetrics/main.nf @@ -5,8 +5,8 @@ process SENTIEON_WGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/sentieon:202308.02--ffce1b7074ce9924' : - 'nf-core/sentieon:202308.02--c641bc397cbf79d5' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/a6/a64461f38d76bebea8e21441079e76e663e1168b0c59dafee6ee58440ad8c8ac/data' : + 'community.wave.seqera.io/library/sentieon:202308.03--59589f002351c221' }" input: tuple val(meta), path(bam), path(bai) From b8d36829fa84b6e404364abff787e8b07f6d058c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?= <90359308+nschcolnicov@users.noreply.github.com> Date: Wed, 2 Oct 2024 17:19:05 -0300 Subject: [PATCH 106/486] Bumped MQC to 1.25.1 (#6726) Co-authored-by: zxBIB Schcolnicov --- modules/nf-core/multiqc/environment.yml | 2 +- modules/nf-core/multiqc/main.nf | 4 +-- .../nf-core/multiqc/tests/main.nf.test.snap | 26 +++++++++---------- 3 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index f1cd99b07923..6f5b867b768a 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.24.1 + - bioconda::multiqc=1.25.1 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index b9ccebdbbc0f..9724d2f34efa 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,8 +3,8 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.25--pyhdfd78af_0' : - 'biocontainers/multiqc:1.25--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.25.1--pyhdfd78af_0' : + 'biocontainers/multiqc:1.25.1--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index b779e46924bb..2fcbb5ff7d1d 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "multiqc_versions_single": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T12:41:34.562023" + "timestamp": "2024-10-02T17:51:46.317523" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:27:11.933869532" + "timestamp": "2024-10-02T17:52:20.680978" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,8c8724363a5efe0c6f43ab34faa57efd" + "versions.yml:md5,41f391dcedce7f93ca188f3a3ffa0916" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T11:26:56.709849369" + "timestamp": "2024-10-02T17:52:09.185842" } -} +} \ No newline at end of file From 3cf419b5480c5ca8893f5ea6e1746d2b3a7c326d Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Thu, 3 Oct 2024 08:57:52 +0200 Subject: [PATCH 107/486] Update motus merge module (#6701) * Update motus merge module * Add stub test * Update modules/nf-core/motus/merge/tests/main.nf.test * Review suggestions * Remove old pytest * Update pytest_modules.yml * remove the extra output --------- Co-authored-by: Lili Andersson-Li <64467552+LilyAnderssonLee@users.noreply.github.com> Co-authored-by: Lili Andersson-Li --- modules/nf-core/motus/merge/main.nf | 22 ++++- .../nf-core/motus/merge/tests/main.nf.test | 89 +++++++++++++++++++ .../motus/merge/tests/main.nf.test.snap | 63 +++++++++++++ modules/nf-core/motus/merge/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/motus/merge/main.nf | 51 ----------- .../nf-core/motus/merge/nextflow.config | 8 -- tests/modules/nf-core/motus/merge/test.yml | 19 ---- 8 files changed, 174 insertions(+), 83 deletions(-) create mode 100644 modules/nf-core/motus/merge/tests/main.nf.test create mode 100644 modules/nf-core/motus/merge/tests/main.nf.test.snap create mode 100644 modules/nf-core/motus/merge/tests/tags.yml delete mode 100644 tests/modules/nf-core/motus/merge/main.nf delete mode 100644 tests/modules/nf-core/motus/merge/nextflow.config delete mode 100644 tests/modules/nf-core/motus/merge/test.yml diff --git a/modules/nf-core/motus/merge/main.nf b/modules/nf-core/motus/merge/main.nf index 06cb93cc7c1f..392024aed6a6 100644 --- a/modules/nf-core/motus/merge/main.nf +++ b/modules/nf-core/motus/merge/main.nf @@ -4,8 +4,8 @@ process MOTUS_MERGE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/motus:3.0.3--pyhdfd78af_0': - 'biocontainers/motus:3.0.3--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0': + 'biocontainers/motus:3.1.0--pyhdfd78af_0' }" input: tuple val(meta), path(input) @@ -42,4 +42,22 @@ process MOTUS_MERGE { motus: \$VERSION END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def cmd_input = input.size() > 1 ? "-i ${input.join(',')}" : input.isDirectory() ? "-d ${input}" : "-i ${input}" + def suffix = task.ext.args?.contains("-B") ? "biom" : "txt" + + """ + touch ${prefix}.txt + + VERSION=\$(cat ${profile_version_yml} | grep '/*motus:.*' | sed 's/.*otus: //g') + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + motus: \$VERSION + END_VERSIONS + """ + } diff --git a/modules/nf-core/motus/merge/tests/main.nf.test b/modules/nf-core/motus/merge/tests/main.nf.test new file mode 100644 index 000000000000..13f0121ec3eb --- /dev/null +++ b/modules/nf-core/motus/merge/tests/main.nf.test @@ -0,0 +1,89 @@ +nextflow_process { + name "Test Process MOTUS_MERGE" + script "../main.nf" + process "MOTUS_MERGE" + tag "modules" + tag "modules_nfcore" + tag "motus" + tag "motus/downloaddb" + tag "motus/profile" + tag "motus/merge" + + + setup { + run("MOTUS_DOWNLOADDB") { + script "modules/nf-core/motus/downloaddb/main.nf" + process { + """ + input[0] = Channel.of([ + file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') + ]) + """ + } + } + + run("MOTUS_PROFILE") { + script "modules/nf-core/motus/profile/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true ), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true ) + ] + ] + + input[1] = MOTUS_DOWNLOADDB.out.db + """ + } + } + } + + test("sarscov2 - illumina paired end [fastq]") { + + + when { + process { + """ + input[0] = MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple() + input[1] = MOTUS_DOWNLOADDB.out.db + input[2] = MOTUS_PROFILE.out.versions.first() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + path(process.out.txt[0][1]).readLines()[3..10], + process.out.versions, + ).match() + } + ) + } + } + + test("sarscov2 - illumina paired end [fastq] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple() + input[1] = MOTUS_DOWNLOADDB.out.db + input[2] = MOTUS_PROFILE.out.versions.first() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( process.out ).match() } + ) + } + } +} diff --git a/modules/nf-core/motus/merge/tests/main.nf.test.snap b/modules/nf-core/motus/merge/tests/main.nf.test.snap new file mode 100644 index 000000000000..a8d75f4f1aa8 --- /dev/null +++ b/modules/nf-core/motus/merge/tests/main.nf.test.snap @@ -0,0 +1,63 @@ +{ + "sarscov2 - illumina paired end [fastq]": { + "content": [ + [ + "Leptospira alexanderi [ref_mOTU_v31_00001]\t0.0000000000", + "Leptospira weilii [ref_mOTU_v31_00002]\t0.0000000000", + "Chryseobacterium sp. [ref_mOTU_v31_00004]\t0.0000000000", + "Chryseobacterium gallinarum [ref_mOTU_v31_00005]\t0.0000000000", + "Chryseobacterium indologenes [ref_mOTU_v31_00006]\t0.0000000000", + "Chryseobacterium artocarpi/ureilyticum [ref_mOTU_v31_00007]\t0.0000000000", + "Chryseobacterium jejuense [ref_mOTU_v31_00008]\t0.0000000000", + "Chryseobacterium sp. G972 [ref_mOTU_v31_00009]\t0.0000000000" + ], + [ + "versions.yml:md5,fb03dc5dcf4912bd54b06f9ee59a7eef" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-03T06:11:21.297394816" + }, + "sarscov2 - illumina paired end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,fb03dc5dcf4912bd54b06f9ee59a7eef" + ], + "biom": [ + + ], + "txt": [ + [ + { + "id": "test" + }, + "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,fb03dc5dcf4912bd54b06f9ee59a7eef" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.1" + }, + "timestamp": "2024-10-02T12:18:09.391582" + } +} \ No newline at end of file diff --git a/modules/nf-core/motus/merge/tests/tags.yml b/modules/nf-core/motus/merge/tests/tags.yml new file mode 100644 index 000000000000..44edb8d0758d --- /dev/null +++ b/modules/nf-core/motus/merge/tests/tags.yml @@ -0,0 +1,2 @@ +motus/merge: + - modules/nf-core/motus/merge/** diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 485641f1da0c..2d544dfd48c0 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -437,9 +437,6 @@ mmseqs/tsv2exprofiledb: motus/downloaddb: - modules/nf-core/motus/downloaddb/** - tests/modules/nf-core/motus/downloaddb/** -motus/merge: - - modules/nf-core/motus/merge/** - - tests/modules/nf-core/motus/merge/** msisensor/msi: - modules/nf-core/msisensor/msi/** - tests/modules/nf-core/msisensor/msi/** diff --git a/tests/modules/nf-core/motus/merge/main.nf b/tests/modules/nf-core/motus/merge/main.nf deleted file mode 100644 index 22260b3f4331..000000000000 --- a/tests/modules/nf-core/motus/merge/main.nf +++ /dev/null @@ -1,51 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { MOTUS_DOWNLOADDB } from '../../../../../modules/nf-core/motus/downloaddb/main.nf' -include { MOTUS_PROFILE } from '../../../../../modules/nf-core/motus/profile/main.nf' -include { MOTUS_MERGE } from '../../../../../modules/nf-core/motus/merge/main.nf' -include { MOTUS_MERGE as MOTUS_MERGE_BIOM } from '../../../../../modules/nf-core/motus/merge/main.nf' - -workflow test_motus_merge { - - input = Channel.fromList( - [ - [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ], - [ - [ id:'test2', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] - ) - - MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') ) - MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db ) - MOTUS_MERGE ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() ) - -} - -workflow test_motus_merge_biom { - - input = Channel.fromList( - [ - [ - [ id:'test', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ], - [ - [ id:'test2', single_end:true ], // meta map - file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) - ] - ] - ) - - MOTUS_DOWNLOADDB ( file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') ) - MOTUS_PROFILE ( input, MOTUS_DOWNLOADDB.out.db ) - MOTUS_MERGE_BIOM ( MOTUS_PROFILE.out.out.map{ [[id:"test"], it[1]] }.groupTuple(), MOTUS_DOWNLOADDB.out.db, MOTUS_PROFILE.out.versions.first() ) - -} - diff --git a/tests/modules/nf-core/motus/merge/nextflow.config b/tests/modules/nf-core/motus/merge/nextflow.config deleted file mode 100644 index d5b9187c2fe1..000000000000 --- a/tests/modules/nf-core/motus/merge/nextflow.config +++ /dev/null @@ -1,8 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: MOTUS_MERGE_BIOM { - ext.args = "-B" - } -} diff --git a/tests/modules/nf-core/motus/merge/test.yml b/tests/modules/nf-core/motus/merge/test.yml deleted file mode 100644 index aa786fecd2a5..000000000000 --- a/tests/modules/nf-core/motus/merge/test.yml +++ /dev/null @@ -1,19 +0,0 @@ -- name: motus merge test_motus_merge - command: nextflow run ./tests/modules/nf-core/motus/merge -entry test_motus_merge -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/motus/merge/nextflow.config - tags: - - motus - - motus/merge - files: - - path: output/motus/test.txt - contains: - - "consensus_taxonomy" - -- name: motus merge test_motus_merge_biom - command: nextflow run ./tests/modules/nf-core/motus/merge -entry test_motus_merge_biom -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/motus/merge/nextflow.config - tags: - - motus - - motus/merge - files: - - path: output/motus/test.biom - contains: - - "Biological Observation Matrix 1.0.0" From 5212d5eff3e0e216f66c6de13e1c7fbca02cb307 Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Thu, 3 Oct 2024 09:33:54 +0200 Subject: [PATCH 108/486] pypgx/createinputvcf (#6720) * pypgx/createinputvcf * add pgx_genes and assembly_version value channels * improved vcf testing --------- Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com> --- .../pypgx/createinputvcf/environment.yml | 7 ++ modules/nf-core/pypgx/createinputvcf/main.nf | 59 ++++++++++++++ modules/nf-core/pypgx/createinputvcf/meta.yml | 76 +++++++++++++++++++ .../pypgx/createinputvcf/tests/main.nf.test | 76 +++++++++++++++++++ .../createinputvcf/tests/main.nf.test.snap | 65 ++++++++++++++++ .../pypgx/createinputvcf/tests/tags.yml | 2 + 6 files changed, 285 insertions(+) create mode 100644 modules/nf-core/pypgx/createinputvcf/environment.yml create mode 100644 modules/nf-core/pypgx/createinputvcf/main.nf create mode 100644 modules/nf-core/pypgx/createinputvcf/meta.yml create mode 100644 modules/nf-core/pypgx/createinputvcf/tests/main.nf.test create mode 100644 modules/nf-core/pypgx/createinputvcf/tests/main.nf.test.snap create mode 100644 modules/nf-core/pypgx/createinputvcf/tests/tags.yml diff --git a/modules/nf-core/pypgx/createinputvcf/environment.yml b/modules/nf-core/pypgx/createinputvcf/environment.yml new file mode 100644 index 000000000000..36c4150bd259 --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::pypgx=0.25.0 diff --git a/modules/nf-core/pypgx/createinputvcf/main.nf b/modules/nf-core/pypgx/createinputvcf/main.nf new file mode 100644 index 000000000000..6de30339a659 --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/main.nf @@ -0,0 +1,59 @@ +process PYPGX_CREATEINPUTVCF { + tag "$meta.id" + label "process_single" + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0': + 'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }" + + input: + tuple val(meta), path(bam), path(bai) + tuple val(meta2), path(fasta) + val(pgx_genes) + val(assembly_version) + + + + output: + tuple val(meta), path("*.vcf.gz"), emit: vcf + tuple val(meta), path("*.vcf.gz.tbi"), emit: tbi + path("versions.yml"), emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def assembly = "${assembly_version}" ?: "GRCh38" + def prefix = task.ext.prefix ?: "${meta.id}" + def pgx_genes = "--genes ${pgx_genes.join(' ')}" ?: '' + + """ + pypgx create-input-vcf \\ + ${args} \\ + ${pgx_genes} \\ + --assembly ${assembly} \\ + ${prefix}.vcf.gz \\ + ${fasta} \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip > ${prefix}.vcf.gz + touch ${prefix}.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pypgx/createinputvcf/meta.yml b/modules/nf-core/pypgx/createinputvcf/meta.yml new file mode 100644 index 000000000000..3e95800769b9 --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/meta.yml @@ -0,0 +1,76 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pypgx_createinputvcf" +description: Call SNVs/indels from BAM files for all target genes. +keywords: + - pypgx + - Pharmacogenetics + - variants +tools: + - "pypgx": + description: "A Python package for pharmacogenomics research" + homepage: "https://pypgx.readthedocs.io/en/latest/" + documentation: "https://pypgx.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/sbslee/pypgx" + doi: "10.1371/journal.pone.0272129" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [id: 'test'] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Input BAM index file + pattern: "*.{bam.bai}" + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [id: 'test'] + - fasta: + type: file + description: Reference genome file + pattern: "*.{fasta,fa,fna,fasta.gz,fa.gz,fna.gz}" + - - pgx_genes: + type: list + description: List of PGx genes supported by PyPGx to include in variant calling. + - - assembly_version: + type: string + description: Genome assembly version to use for variant calling. + pattern: "{GRCh37,GRCh38}" +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [id: 'test'] + - "*.vcf.gz": + type: file + description: VCF file containing called SNVs/indels + pattern: "*.vcf.gz" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [id: 'test'] + - "*.vcf.gz.tbi": + type: file + description: File containing the VCF tabix index + pattern: "*.vcf.gz.tbi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jorisvansteenbrugge" +maintainers: + - "@jorisvansteenbrugge" diff --git a/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test b/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test new file mode 100644 index 000000000000..1faef5d16b98 --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test @@ -0,0 +1,76 @@ +// nf-core modules test pypgx/createinputvcf +nextflow_process { + + name "Test Process PYPGX_CREATEINPUTVCF" + script "../main.nf" + process "PYPGX_CREATEINPUTVCF" + + tag "modules" + tag "modules_nfcore" + tag "pypgx" + tag "pypgx/createinputvcf" + + + test("human paired end bam CYP2D6 locus - GR37_chr22.fasta") { + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam.bai', checkIfExists: true) + ] + input[1] = [ + [id: 'GRCh37'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/GRCh37_chr22.fasta.gz', checkIfExists: true) + ] + input[2] = ["CYP2D6"] + input[3] = "GRCh37" + """ + } + } + + then { + def vcfFile = path(process.out.vcf[0][1]).vcf + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.versions, + vcfFile.variantsMD5).match() }, + {assert vcfFile.chromosomes == ['22'] as Set}, + {assert vcfFile.sampleCount == 1} + ) + } + } + + + test("stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + [], + [] + ] + input[1] = [ + [id: 'test_genome'], + [] + ] + input[2] = [] + input[3] = "" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test.snap b/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test.snap new file mode 100644 index 000000000000..f41606648d01 --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/tests/main.nf.test.snap @@ -0,0 +1,65 @@ +{ + "human paired end bam CYP2D6 locus - GR37_chr22.fasta": { + "content": [ + "test.vcf.gz", + [ + "versions.yml:md5,6afe5f69d9cb49f74eb1958a8ba2e990" + ], + "3a4fe74d4e0b45036ebd91bdae36b225" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-03T08:47:44.853651" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,6afe5f69d9cb49f74eb1958a8ba2e990" + ], + "tbi": [ + [ + { + "id": "test" + }, + "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6afe5f69d9cb49f74eb1958a8ba2e990" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-03T08:47:53.567926" + } +} \ No newline at end of file diff --git a/modules/nf-core/pypgx/createinputvcf/tests/tags.yml b/modules/nf-core/pypgx/createinputvcf/tests/tags.yml new file mode 100644 index 000000000000..9bab1c03b35a --- /dev/null +++ b/modules/nf-core/pypgx/createinputvcf/tests/tags.yml @@ -0,0 +1,2 @@ +pypgx/createinputvcf: + - "modules/nf-core/pypgx/createinputvcf/**" From cc60acf0fe70fc1293f5aa34d6ca05b7a044f034 Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Thu, 3 Oct 2024 13:31:24 +0200 Subject: [PATCH 109/486] Support nft-compress in nf-test.config (#6727) * Load nft-compress for nf-test support for compressed files in nf-test * alphabetic order --- nf-test.config | 1 + 1 file changed, 1 insertion(+) diff --git a/nf-test.config b/nf-test.config index 194d44e83179..e09675184571 100644 --- a/nf-test.config +++ b/nf-test.config @@ -14,6 +14,7 @@ config { // load the necessary plugins plugins { load "nft-bam@0.3.0" + load "nft-compress@0.1.0" load "nft-vcf@1.0.7" } } From f351fad4807767e8b88b1844c94efa28ff12c645 Mon Sep 17 00:00:00 2001 From: Eric Wei Date: Thu, 3 Oct 2024 08:57:20 -0700 Subject: [PATCH 110/486] Add bcftools/pluginsetgt (#6718) * Create module from template * Fill in main.nf * Fill in meta.yml * Add tests * Add description * Add non-file mandatory command arguments --- .../bcftools/pluginsetgt/environment.yml | 7 + modules/nf-core/bcftools/pluginsetgt/main.nf | 80 +++++ modules/nf-core/bcftools/pluginsetgt/meta.yml | 108 ++++++ .../bcftools/pluginsetgt/tests/main.nf.test | 308 ++++++++++++++++ .../pluginsetgt/tests/main.nf.test.snap | 333 ++++++++++++++++++ .../pluginsetgt/tests/nextflow.config | 4 + .../pluginsetgt/tests/vcf_gz_index.config | 5 + .../pluginsetgt/tests/vcf_gz_index_csi.config | 5 + .../pluginsetgt/tests/vcf_gz_index_tbi.config | 5 + 9 files changed, 855 insertions(+) create mode 100644 modules/nf-core/bcftools/pluginsetgt/environment.yml create mode 100644 modules/nf-core/bcftools/pluginsetgt/main.nf create mode 100644 modules/nf-core/bcftools/pluginsetgt/meta.yml create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config create mode 100644 modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config diff --git a/modules/nf-core/bcftools/pluginsetgt/environment.yml b/modules/nf-core/bcftools/pluginsetgt/environment.yml new file mode 100644 index 000000000000..a394b0263278 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::bcftools=1.21" diff --git a/modules/nf-core/bcftools/pluginsetgt/main.nf b/modules/nf-core/bcftools/pluginsetgt/main.nf new file mode 100644 index 000000000000..489b563a5dc0 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/main.nf @@ -0,0 +1,80 @@ +process BCFTOOLS_PLUGINSETGT { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bcftools:1.21--h8b25389_0': + 'biocontainers/bcftools:1.21--h8b25389_0' }" + + input: + tuple val(meta), path(vcf), path(index) + val(target_gt) + val(new_gt) + path(regions) + path(targets) + + output: + tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf + tuple val(meta), path("*.tbi") , emit: tbi, optional: true + tuple val(meta), path("*.csi") , emit: csi, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def regions_file = regions ? "--regions-file ${regions}" : "" + def targets_file = targets ? "--targets-file ${targets}" : "" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + """ + bcftools plugin setGT \\ + --output ${prefix}.${extension} \\ + ${regions_file} \\ + ${targets_file} \\ + $args \\ + --threads $task.cpus \\ + ${vcf} \\ + -- \\ + --target-gt ${target_gt} \\ + --new-gt ${new_gt} \\ + $args2 + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = args.contains("--output-type b") || args.contains("-Ob") ? "bcf.gz" : + args.contains("--output-type u") || args.contains("-Ou") ? "bcf" : + args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : + args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : + "vcf" + def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" + def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" + def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + + """ + ${create_cmd} ${prefix}.${extension} + ${create_index} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bcftools: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/bcftools/pluginsetgt/meta.yml b/modules/nf-core/bcftools/pluginsetgt/meta.yml new file mode 100644 index 000000000000..820ea48cea16 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/meta.yml @@ -0,0 +1,108 @@ +--- +name: "bcftools_pluginsetgt" +description: Sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that. +keywords: + - setgt + - bcftools + - genotype + - vcf +tools: + - "bcftools": + description: "BCFtools is a set of utilities that manipulate variant calls in + the Variant Call Format (VCF) and its binary counterpart BCF. All commands work + transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\ + \ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically + even when streaming from a pipe. Indexed VCF and BCF will work in all situations. + Un-indexed VCF and BCF and streams will work in most, but not all situations." + homepage: "https://samtools.github.io/bcftools/howtos/index.html" + documentation: "https://samtools.github.io/bcftools/bcftools.html" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args" + identifier: biotools:bcftools + - "bcftools plugin setGT": + description: "Bcftools plugins are tools that can be used with bcftools to manipulate + variant calls in Variant Call Format (VCF) and BCF. The setGT plugin sets genotypes according to the specified criteria and filtering expressions. For example, missing genotypes can be set to ref, but much more than that." + homepage: "https://samtools.github.io/bcftools/howtos/plugins.html" + documentation: "https://samtools.github.io/bcftools/howtos/plugin.setGT.html" + tool_dev_url: "https://github.com/samtools/bcftools" + doi: "10.1093/bioinformatics/btp352" + licence: ["MIT"] + args_id: "$args2" + identifier: biotools:bcftools + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - - target_gt: + type: string + description: | + Genotypes to change + - - new_gt: + type: string + description: | + Genotypes to set + - - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' +output: + - vcf: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.{vcf,vcf.gz,bcf,bcf.gz}": + type: file + description: VCF output file containing set genotypes + pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}" + - tbi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.tbi": + type: file + description: Alternative VCF file index + pattern: "*.tbi" + - csi: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.csi": + type: file + description: Default VCF file index + pattern: "*.csi" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@eweizy" +maintainers: + - "@eweizy" diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test new file mode 100644 index 000000000000..ab915458cfc3 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test @@ -0,0 +1,308 @@ +nextflow_process { + + name "Test Process BCFTOOLS_PLUGINSETGT" + script "../main.nf" + process "BCFTOOLS_PLUGINSETGT" + + tag "modules" + tag "modules_nfcore" + tag "bcftools" + tag "bcftools/pluginsetgt" + + test("sarscov2 - [vcf, tbi], [], []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index") { + + config "./vcf_gz_index.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi") { + + config "./vcf_gz_index_csi.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi") { + + config "./vcf_gz_index_tbi.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.tbi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], vcf, tsv, []") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.targets.tsv.gz', checkIfExists: true) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.vcf, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - stub") { + + config "./nextflow.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.vcf[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub") { + + config "./vcf_gz_index.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub") { + + config "./vcf_gz_index_csi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.csi[0][1].endsWith(".csi") } + ) + } + + } + + test("sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub") { + + config "./vcf_gz_index_tbi.config" + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'out', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + input[1] = "a" + input[2] = "p" + input[3] = [] + input[4] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + { assert process.out.tbi[0][1].endsWith(".tbi") } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap new file mode 100644 index 000000000000..d7bd1c430fc2 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/main.nf.test.snap @@ -0,0 +1,333 @@ +{ + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:20:17.908216187" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi" + ] + ], + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:19:20.519406077" + }, + "sarscov2 - [vcf, tbi], [], []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out.vcf:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:10:46.935219433" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + + ], + "2": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ], + "csi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:20:01.440738039" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_tbi - stub": { + "content": [ + { + "0": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ], + "csi": [ + + ], + "tbi": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "vcf": [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:20:30.745502548" + }, + "sarscov2 - [vcf, tbi], vcf, tsv, []": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out.vcf:md5,55e955c359bf9094bb692660f3c1c677" + ] + ], + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:19:35.097141661" + }, + "sarscov2 - [vcf, tbi], [], [], [] - stub": { + "content": [ + "out.vcf", + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:19:47.7899858" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:18:49.513524959" + }, + "sarscov2 - [vcf, tbi], [], [], [] - vcf_gz_index_csi": { + "content": [ + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz:md5,9fb75c9fdb304b49c3895476666a85bb" + ] + ], + [ + [ + { + "id": "out", + "single_end": false + }, + "out_vcf.vcf.gz.csi" + ] + ], + [ + + ], + [ + "versions.yml:md5,f5e31da0a117751eb1d951d0c2a09c75" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-30T21:19:04.133512404" + } +} \ No newline at end of file diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config b/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config new file mode 100644 index 000000000000..eb8000d60bba --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/nextflow.config @@ -0,0 +1,4 @@ +process { + ext.args = '--no-version --output-type v' + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config new file mode 100644 index 000000000000..9507854d716c --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index --no-version" + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config new file mode 100644 index 000000000000..9e53fe2596dd --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_csi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=csi --no-version" + ext.args2 = "-s 42" +} diff --git a/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config new file mode 100644 index 000000000000..38abb7860dd3 --- /dev/null +++ b/modules/nf-core/bcftools/pluginsetgt/tests/vcf_gz_index_tbi.config @@ -0,0 +1,5 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z --write-index=tbi --no-version" + ext.args2 = "-s 42" +} From ac55541b663c35e9ff50f79d32049ce7492a6ea5 Mon Sep 17 00:00:00 2001 From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Date: Thu, 3 Oct 2024 11:15:18 -0500 Subject: [PATCH 111/486] pints 1.1.13 (#6709) * build(pints): Switch to PyPI The bioconda builds aren't getting updated, and the biocontainers containers aren't getting updated. They're publishing to PyPI consistently, so we'll meet them where they're at. Really need the stuff in https://github.com/hyulab/PINTS/pull/19/commits/101c0cb1f5bd1e31d6f2d72fe6fa0246d22bec56 like yesterday. * chore: Add renovate comment * build: Include pybedtools manually And htslib for bgzip. pybedtools wiht pip needs gcc to install. * chore: Copy code from @ewels https://github.com/nf-core/modules/issues/6694#issuecomment-2376197663 Co-authored-by: ewels * build: Fix uv shebang * fix(#6694): Remove async code * style: Run ruff * fix(#6694): Clean up some errors And by that I mean comment out the code. Seriously anyone reading these? * chore: Clean up httpx * refactor: Simplify script * fix: Remove oras * fix: containerimage => containerImage * fix: Remove oras and mediatype => mediaType * style: Run ruff --------- Co-authored-by: ewels --- .github/scripts/wave_singularity.py | 54 +++++++++++++++++++ modules/nf-core/pints/caller/environment.yml | 9 +++- modules/nf-core/pints/caller/main.nf | 4 +- .../nf-core/pints/caller/tests/main.nf.test | 5 +- .../pints/caller/tests/main.nf.test.snap | 37 ++++++++++--- 5 files changed, 96 insertions(+), 13 deletions(-) create mode 100755 .github/scripts/wave_singularity.py diff --git a/.github/scripts/wave_singularity.py b/.github/scripts/wave_singularity.py new file mode 100755 index 000000000000..5e97395674f6 --- /dev/null +++ b/.github/scripts/wave_singularity.py @@ -0,0 +1,54 @@ +#!/usr/bin/env -S uv run +# /// script +# requires-python = ">=3.10" +# dependencies = [ +# "httpx", +# ] +# /// + +import logging + +import httpx + +logger = logging.getLogger(__name__) + +image_url = "oras://community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:aa20de1f1b5ddb30" + +if image_url.startswith("oras://"): + image_url = image_url.replace("oras://", "") + +wave_api_url = "https://wave.seqera.io" +url = f"{wave_api_url}/v1alpha1/inspect" + +# if platform_pat: +# data["toweraccesstoken"] = platform_pat +# else: +# TODO +logger.warning("'platform_pat' not set, no auth to wave back end") + +try: + logger.info(f"calling image inspect at {url} for image url {image_url}") + response = httpx.post( + url=url, + json={"containerImage": image_url}, + headers={"content-type": "application/json"}, + ) + + data = response.json() + logger.debug(data) + layers = data.get("container", {}).get("manifest", {}).get("layers", []) + is_singularity = len(layers) == 1 and layers[0].get("mediaType", "").endswith(".sif") + if not is_singularity: + print(layers) + raise ValueError("not a singularity image") + if "digest" not in layers[0]: + print(layers) + raise ValueError("no 'digest' in first layer found") + + digest = layers[0]["digest"].replace("sha256:", "") + container_url = f"https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/{digest[:2]}/{digest}/data" + print(container_url) + +except httpx.RequestError as exc: + print(f"An error occurred while requesting {exc.request.url!r}.") + print("No singularity image for you") diff --git a/modules/nf-core/pints/caller/environment.yml b/modules/nf-core/pints/caller/environment.yml index afcdc7eb7f3f..1c29653cc0a2 100644 --- a/modules/nf-core/pints/caller/environment.yml +++ b/modules/nf-core/pints/caller/environment.yml @@ -2,4 +2,11 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::pypints=1.1.10 + - pybedtools + - bedtools + - htslib + - pip + - pip: # FIXME https://github.com/nf-core/modules/issues/5814 + # NOTE PINTS isn't adding conda builds and is a few versions behind. + # renovate: datasource=pypi depName=pypints + - pypints==1.1.13 diff --git a/modules/nf-core/pints/caller/main.nf b/modules/nf-core/pints/caller/main.nf index 2c0ede18afea..7f927c9dd282 100644 --- a/modules/nf-core/pints/caller/main.nf +++ b/modules/nf-core/pints/caller/main.nf @@ -5,8 +5,8 @@ process PINTS_CALLER { conda "${moduleDir}/environment.yml" // NOTE Stopped publishing at 1.1.9 https://quay.io/repository/biocontainers/pypints?tab=tags container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'oras://community.wave.seqera.io/library/pints_caller:650ef63c9768bb5a' : - 'community.wave.seqera.io/library/pints_caller:b1e6404513917871' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/f1/f1a9e30012e1b41baf9acd1ff94e01161138d8aa17f4e97aa32f2dc4effafcd1/data' : + 'community.wave.seqera.io/library/pybedtools_bedtools_htslib_pip_pypints:39699b96998ec5f6' }" input: tuple val(meta), path(bams), path(bais) diff --git a/modules/nf-core/pints/caller/tests/main.nf.test b/modules/nf-core/pints/caller/tests/main.nf.test index 0bb2a7cb1bf2..e0e2f8ea3f99 100644 --- a/modules/nf-core/pints/caller/tests/main.nf.test +++ b/modules/nf-core/pints/caller/tests/main.nf.test @@ -35,7 +35,7 @@ nextflow_process { process.out.divergent_TREs, process.out.bidirectional_TREs, file(process.out.unidirectional_TREs.get(0).get(1).get(0)).name, - process.out.versions, + path(process.out.versions.get(0)).yaml, ).match("bams") }, ) @@ -65,9 +65,10 @@ nextflow_process { process.out.divergent_TREs, process.out.bidirectional_TREs, file(process.out.unidirectional_TREs[0][1]).name, - process.out.versions, + path(process.out.versions.get(0)).yaml, ).match("single_bam") }, + { assert snapshot(path(process.out.versions.get(0)).yaml).match("versions") }, ) } } diff --git a/modules/nf-core/pints/caller/tests/main.nf.test.snap b/modules/nf-core/pints/caller/tests/main.nf.test.snap index 767aa4970cec..d6d2a14bab51 100644 --- a/modules/nf-core/pints/caller/tests/main.nf.test.snap +++ b/modules/nf-core/pints/caller/tests/main.nf.test.snap @@ -1,4 +1,19 @@ { + "versions": { + "content": [ + { + "PINTS_CALLER": { + "python": "3.12.6", + "pints": "1.1.13" + } + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-29T22:22:29.559913" + }, "bams": { "content": [ [ @@ -24,15 +39,18 @@ ] ], "test_1_unidirectional_peaks.bed", - [ - "versions.yml:md5,6142633d4306c8a74b9716c4aac7e956" - ] + { + "PINTS_CALLER": { + "python": "3.12.6", + "pints": "1.1.13" + } + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:17:21.517020581" + "timestamp": "2024-09-29T22:19:23.738834" }, "single_bam": { "content": [ @@ -55,14 +73,17 @@ ] ], "test_1_unidirectional_peaks.bed", - [ - "versions.yml:md5,6142633d4306c8a74b9716c4aac7e956" - ] + { + "PINTS_CALLER": { + "python": "3.12.6", + "pints": "1.1.13" + } + } ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:07:12.112579276" + "timestamp": "2024-09-29T22:22:29.544608" } } \ No newline at end of file From 2d82007b83328343d0e2a9cec087b628eef7e3d1 Mon Sep 17 00:00:00 2001 From: herpov <54803557+herpov@users.noreply.github.com> Date: Thu, 3 Oct 2024 21:13:54 +0200 Subject: [PATCH 112/486] Update bam2fastq10x to handle multiplexed samples (#6702) * update output dir for bamtofastq10x * update path for output fastq * update snapshot * update stub * update output definition in meta.yml --------- Co-authored-by: Helle Rus Povlsen --- modules/nf-core/bamtofastq10x/main.nf | 9 ++++---- modules/nf-core/bamtofastq10x/meta.yml | 4 ++-- .../bamtofastq10x/tests/main.nf.test.snap | 22 ++++++++----------- 3 files changed, 16 insertions(+), 19 deletions(-) diff --git a/modules/nf-core/bamtofastq10x/main.nf b/modules/nf-core/bamtofastq10x/main.nf index be1b14415bee..bff379c19ee3 100644 --- a/modules/nf-core/bamtofastq10x/main.nf +++ b/modules/nf-core/bamtofastq10x/main.nf @@ -11,8 +11,8 @@ process BAMTOFASTQ10X { tuple val(meta), path(bam) output: - tuple val(meta), path("*.fastq.gz"), emit: fastq - path "versions.yml" , emit: versions + tuple val(meta), path("**/*.fastq.gz"), emit: fastq + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -24,7 +24,7 @@ process BAMTOFASTQ10X { bamtofastq \\ $args \\ $bam \\ - ${prefix}.fastq.gz + $prefix cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -35,7 +35,8 @@ process BAMTOFASTQ10X { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.fastq.gz + mkdir -p ${prefix}/bamtofastq10x + touch ${prefix}/bamtofastq10x/bamtofastq.fastq.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bamtofastq10x/meta.yml b/modules/nf-core/bamtofastq10x/meta.yml index ace49c251829..f3e5dfcaa244 100644 --- a/modules/nf-core/bamtofastq10x/meta.yml +++ b/modules/nf-core/bamtofastq10x/meta.yml @@ -37,10 +37,10 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1', single_end:false ]` - - "*.fastq.gz": + - "**/*.fastq.gz": type: file description: fastq compressed file - pattern: "*.fastq.gz" + pattern: "**/*.fastq.gz" - versions: - versions.yml: type: file diff --git a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap index d534674592d6..fd5310910176 100644 --- a/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap +++ b/modules/nf-core/bamtofastq10x/tests/main.nf.test.snap @@ -8,11 +8,9 @@ "id": "test" }, [ - [ - "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", - "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", - "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" - ] + "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", + "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", + "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" ] ] ], @@ -25,11 +23,9 @@ "id": "test" }, [ - [ - "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", - "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", - "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" - ] + "bamtofastq_S1_L000_I1_001.fastq.gz:md5,a33682ac881de7a7453d79721b7621a0", + "bamtofastq_S1_L000_R1_001.fastq.gz:md5,5ccebf77d8636d7a7cdfc59737aea79f", + "bamtofastq_S1_L000_R2_001.fastq.gz:md5,2ee7c90e4307deba74065cfd00a65002" ] ] ], @@ -39,9 +35,9 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-22T16:43:24.999397" + "timestamp": "2024-10-02T12:56:21.808042" } } \ No newline at end of file From 22fc6d90be8eca2cf6afe5d10b3c5cffcdbcb19c Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Fri, 4 Oct 2024 14:05:26 +0200 Subject: [PATCH 113/486] Remove `params` from longphase (#6732) * Remove params * tests --- modules/nf-core/longphase/haplotag/main.nf | 4 ++-- .../haplotag/tests/main.nf.test.snap | 8 ++++---- modules/nf-core/longphase/phase/main.nf | 4 ++-- .../longphase/phase/tests/main.nf.test.snap | 20 +++++++++---------- 4 files changed, 18 insertions(+), 18 deletions(-) diff --git a/modules/nf-core/longphase/haplotag/main.nf b/modules/nf-core/longphase/haplotag/main.nf index 701af31fe54a..86ba05925569 100644 --- a/modules/nf-core/longphase/haplotag/main.nf +++ b/modules/nf-core/longphase/haplotag/main.nf @@ -24,8 +24,8 @@ process LONGPHASE_HAPLOTAG { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sv_file = params.svs ? "--sv-file ${svs}" : "" - def mod_file = params.mods ? "--mod-file ${mods}" : "" + def sv_file = svs ? "--sv-file ${svs}" : "" + def mod_file = mods ? "--mod-file ${mods}" : "" """ longphase \\ diff --git a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap index 225a4f7ed859..3cf35dc32ffd 100644 --- a/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap +++ b/modules/nf-core/longphase/haplotag/tests/main.nf.test.snap @@ -119,15 +119,15 @@ "@RG\tID:test\tSM:test", "@PG\tID:minimap2\tPN:minimap2\tVN:2.28-r1209\tCL:minimap2 -y -x map-ont --secondary=no -R @RG\\tID:test\\tSM:test -t 30 -a genome.mmi test.bam_other.fastq.gz", "@PG\tID:samtools\tPN:samtools\tPP:minimap2\tVN:1.19.2\tCL:samtools sort -@ 29 -o test.bam_other.fastq.gz.bam --write-index", - "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam " + "@PG\tID:longphase\tPN:longphase\tPP:samtools\tVN:1.7.3\tCL:longphase haplotag --threads 2 -o test --reference genome.fasta --snp-file test.genome.vcf.gz --bam test.sorted.bam --sv-file NA24385_sv.vcf.gz " ], "721264eb2824a3146b331f2532d10180" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-25T09:13:39.901419316" + "timestamp": "2024-10-04T13:39:33.50395694" }, "[ bam, bai, snps, [], [] ], fasta, fai - log & cram": { "content": [ diff --git a/modules/nf-core/longphase/phase/main.nf b/modules/nf-core/longphase/phase/main.nf index ad29d9972887..f121f4b6dd65 100644 --- a/modules/nf-core/longphase/phase/main.nf +++ b/modules/nf-core/longphase/phase/main.nf @@ -24,8 +24,8 @@ process LONGPHASE_PHASE { def args = task.ext.args ?: '' def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sv_file = params.svs ? "--sv-file ${svs}" : "" - def mod_file = params.mods ? "--mod-file ${mods}" : "" + def sv_file = svs ? "--sv-file ${svs}" : "" + def mod_file = mods ? "--mod-file ${mods}" : "" def bamList = [] for (file in bam) { diff --git a/modules/nf-core/longphase/phase/tests/main.nf.test.snap b/modules/nf-core/longphase/phase/tests/main.nf.test.snap index 02e2bb1731f6..8a38c1caa5ce 100644 --- a/modules/nf-core/longphase/phase/tests/main.nf.test.snap +++ b/modules/nf-core/longphase/phase/tests/main.nf.test.snap @@ -40,7 +40,7 @@ { "id": "test" }, - "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a" + "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c" ] ], "1": [ @@ -51,7 +51,7 @@ { "id": "test" }, - "test.vcf.gz:md5,fd2d21056b2de4722f12d5e883d9cb0a" + "test.vcf.gz:md5,b0a3effd6e076edbe7e2f1f7cfff547c" ] ], "versions": [ @@ -60,10 +60,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:14:39.961315592" + "timestamp": "2024-10-04T13:37:16.921910004" }, "[ bam x2, bai x2, snps, svs, [] ], fasta, fai": { "content": [ @@ -73,7 +73,7 @@ { "id": "test" }, - "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687" + "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c" ] ], "1": [ @@ -84,7 +84,7 @@ { "id": "test" }, - "test.vcf.gz:md5,3ced25dc8c1ec0a7c64481c8a163d687" + "test.vcf.gz:md5,04905b6042998e592c9f3b887ae9e09c" ] ], "versions": [ @@ -93,10 +93,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:15:07.970597495" + "timestamp": "2024-10-04T13:37:23.41768963" }, "[ bam, bai, snps, [], [] ], fasta, fai - stub": { "content": [ From 8a36181859504560ef333c299f6773c7b99a801f Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Fri, 4 Oct 2024 14:37:42 +0200 Subject: [PATCH 114/486] Fix copy paste tag mistake (#6734) Fix copy paste mistake --- modules/nf-core/severus/tests/main.nf.test | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/modules/nf-core/severus/tests/main.nf.test b/modules/nf-core/severus/tests/main.nf.test index 1b85a109f048..ab700a4c12c8 100644 --- a/modules/nf-core/severus/tests/main.nf.test +++ b/modules/nf-core/severus/tests/main.nf.test @@ -7,7 +7,6 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "severus" - tag "deepvariant" test("homo_sapiens - [ bam, bai, [], [], [] ], [[],[]]") { @@ -206,4 +205,4 @@ nextflow_process { } -} \ No newline at end of file +} From 1f19c093c86ae49d1899e234d4aa4d56c57be780 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 4 Oct 2024 14:40:05 +0200 Subject: [PATCH 115/486] fails nf-validation with lenient strategy (#6733) fails with lenient strategy --- .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 5784a33f2f51..07ff7afdd9ec 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -169,7 +169,7 @@ nextflow_workflow { params { monochrome_logs = true test_data = '' - outdir = 1 + outdir = true } workflow { """ From 11680c37e2a185d006e9ba289d2254ccac9f4bb4 Mon Sep 17 00:00:00 2001 From: Sofia Stamouli <91951607+sofstam@users.noreply.github.com> Date: Fri, 4 Oct 2024 15:23:53 +0200 Subject: [PATCH 116/486] Add motus prep_long (#6590) * Add motus prep_long * Prettier * Update meta * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/motus/preplong/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/motus/preplong/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/motus/preplong/meta.yml Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update modules/nf-core/motus/preplong/tests/main.nf.test Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> * Update snap file * Fix linting * Update meta.yml * Update modules/nf-core/motus/preplong/main.nf Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Fix formatting * Update meta.yaml * Update meta.yml * Update meta.yaml * Fix formatting for meta.yaml * Try to fix linting * Remove unnecessary output * Fix linting * Update meta.yml with version.yml --------- Co-authored-by: Felix Lenner <52530259+fellen31@users.noreply.github.com> Co-authored-by: James A. Fellows Yates Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../nf-core/motus/preplong/environment.yml | 5 ++ modules/nf-core/motus/preplong/main.nf | 53 +++++++++++++ modules/nf-core/motus/preplong/meta.yml | 52 +++++++++++++ .../nf-core/motus/preplong/tests/main.nf.test | 75 +++++++++++++++++++ .../motus/preplong/tests/main.nf.test.snap | 72 ++++++++++++++++++ modules/nf-core/motus/preplong/tests/tags.yml | 2 + 6 files changed, 259 insertions(+) create mode 100644 modules/nf-core/motus/preplong/environment.yml create mode 100644 modules/nf-core/motus/preplong/main.nf create mode 100644 modules/nf-core/motus/preplong/meta.yml create mode 100644 modules/nf-core/motus/preplong/tests/main.nf.test create mode 100644 modules/nf-core/motus/preplong/tests/main.nf.test.snap create mode 100644 modules/nf-core/motus/preplong/tests/tags.yml diff --git a/modules/nf-core/motus/preplong/environment.yml b/modules/nf-core/motus/preplong/environment.yml new file mode 100644 index 000000000000..b8ef520eaa2a --- /dev/null +++ b/modules/nf-core/motus/preplong/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::motus=3.1.0 diff --git a/modules/nf-core/motus/preplong/main.nf b/modules/nf-core/motus/preplong/main.nf new file mode 100644 index 000000000000..3fffc1496485 --- /dev/null +++ b/modules/nf-core/motus/preplong/main.nf @@ -0,0 +1,53 @@ +process MOTUS_PREPLONG { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/motus:3.1.0--pyhdfd78af_0': + 'biocontainers/motus:3.1.0--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads) + path db + + output: + tuple val(meta), path("*.gz"), emit: out + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def refdb = db ? "-db ${db}" : "" + + """ + motus \\ + prep_long \\ + $args \\ + -i $reads \\ + $refdb \\ + -t $task.cpus \\ + -o ${prefix}.gz \\ + 2> >(tee ${prefix}.log >&2) + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo '' | gzip > ${prefix}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + motus: \$(motus --version 2>&1 | sed 's/.* \\([0-9]*\\.[0-9]*\\.[0-9]*\\) .*/\\1/') + END_VERSIONS + """ +} diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml new file mode 100644 index 000000000000..6ef63949a04d --- /dev/null +++ b/modules/nf-core/motus/preplong/meta.yml @@ -0,0 +1,52 @@ +name: "motus_preplong" +description: Taxonomic meta-omics profiling using universal marker genes +keywords: + - classify + - metagenomics + - fastq + - taxonomic profiling +tools: + - "motus": + description: "Marker gene-based operational taxonomic unit (mOTU) profiling" + homepage: "https://motu-tool.org/" + documentation: "https://github.com/motu-tool/mOTUs/wiki" + tool_dev_url: "https://github.com/motu-tool/mOTUs" + doi: "10.1186/s40168-022-01410-z" + licence: ["GPL v3"] + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - reads: + type: file + description: Long read file to convert, can be fasta(.gz) or fastq(.gz) + pattern: "*.{gz}" + - - db: + type: directory + description: | + mOTUs database downloaded by `motus downloadDB` + pattern: "db_mOTU/" +output: + - out: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.gz": + type: file + description: converted file (gzipped), ready to be used by motus profile + pattern: "*.gz" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@sofstam" +maintainers: + - "@sofstam" diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test b/modules/nf-core/motus/preplong/tests/main.nf.test new file mode 100644 index 000000000000..5ad8e7487f19 --- /dev/null +++ b/modules/nf-core/motus/preplong/tests/main.nf.test @@ -0,0 +1,75 @@ +nextflow_process { + + name "Test Process MOTUS_PREPLONG" + script "../main.nf" + process "MOTUS_PREPLONG" + + tag "modules" + tag "modules_nfcore" + tag "motus" + tag "motus/downloaddb" + tag "motus/preplong" + + setup { + run("MOTUS_DOWNLOADDB") { + script "modules/nf-core/motus/downloaddb/main.nf" + process { + """ + input[0] = Channel.of([ + file('https://raw.githubusercontent.com/motu-tool/mOTUs/master/motus/downloadDB.py') + ]) + """ + } + } + } + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true) + ] + input[1] = MOTUS_DOWNLOADDB.out.db + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/nanopore/fastq/test_2.fastq.gz', checkIfExists: true) + ] + input[1] = MOTUS_DOWNLOADDB.out.db + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + + } + +} diff --git a/modules/nf-core/motus/preplong/tests/main.nf.test.snap b/modules/nf-core/motus/preplong/tests/main.nf.test.snap new file mode 100644 index 000000000000..5ed72ec8a9a5 --- /dev/null +++ b/modules/nf-core/motus/preplong/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb" + ], + "out": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.1" + }, + "timestamp": "2024-09-06T16:29:18.602046" + }, + "sarscov2 - fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c" + ] + ], + "1": [ + "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb" + ], + "out": [ + [ + { + "id": "test", + "single_end": false + }, + "test.gz:md5,37be4a7321bcb2fdae60affb21a1737c" + ] + ], + "versions": [ + "versions.yml:md5,8fc614f9fe354b0811def13c772bc6fb" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "23.04.1" + }, + "timestamp": "2024-09-06T15:55:48.439664" + } +} \ No newline at end of file diff --git a/modules/nf-core/motus/preplong/tests/tags.yml b/modules/nf-core/motus/preplong/tests/tags.yml new file mode 100644 index 000000000000..bdaae3b2032a --- /dev/null +++ b/modules/nf-core/motus/preplong/tests/tags.yml @@ -0,0 +1,2 @@ +motus/preplong: + - "modules/nf-core/motus/preplong/**" From e6c055a7bb7551ef18436a8ef410dd0e27393c61 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 4 Oct 2024 15:25:25 +0200 Subject: [PATCH 117/486] Really fails nf-validation with lenient strategy (#6735) Update main.nf.test I'm sure I tested true and it failed as expected, but I cannot reproduce, so I'm resorting to false as I know it'll fail for good --- .../nf-core/utils_nfvalidation_plugin/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test index 07ff7afdd9ec..c50b1fb53232 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/tests/main.nf.test @@ -169,7 +169,7 @@ nextflow_workflow { params { monochrome_logs = true test_data = '' - outdir = true + outdir = false } workflow { """ From 55692e15e2ef8be6b37ad1475944a338770b4b3e Mon Sep 17 00:00:00 2001 From: Daniel Schmitz Date: Fri, 4 Oct 2024 16:25:08 +0200 Subject: [PATCH 118/486] Update Genmod to 3.8.3 (#6736) * Updated genmod to 3.8.3 * Fixed typos in version --- modules/nf-core/genmod/annotate/environment.yml | 2 +- modules/nf-core/genmod/annotate/main.nf | 4 ++-- modules/nf-core/genmod/compound/environment.yml | 2 +- modules/nf-core/genmod/compound/main.nf | 4 ++-- modules/nf-core/genmod/models/environment.yml | 2 +- modules/nf-core/genmod/models/main.nf | 4 ++-- modules/nf-core/genmod/score/environment.yml | 2 +- modules/nf-core/genmod/score/main.nf | 4 ++-- 8 files changed, 12 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml index 1eca76fad2ca..bbc3fd973a9e 100644 --- a/modules/nf-core/genmod/annotate/environment.yml +++ b/modules/nf-core/genmod/annotate/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf index eb161187687d..033caa9ae93d 100644 --- a/modules/nf-core/genmod/annotate/main.nf +++ b/modules/nf-core/genmod/annotate/main.nf @@ -4,8 +4,8 @@ process GENMOD_ANNOTATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml index 1eca76fad2ca..bbc3fd973a9e 100644 --- a/modules/nf-core/genmod/compound/environment.yml +++ b/modules/nf-core/genmod/compound/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf index 1731b7222242..4831da855faf 100644 --- a/modules/nf-core/genmod/compound/main.nf +++ b/modules/nf-core/genmod/compound/main.nf @@ -4,8 +4,8 @@ process GENMOD_COMPOUND { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml index 1eca76fad2ca..bbc3fd973a9e 100644 --- a/modules/nf-core/genmod/models/environment.yml +++ b/modules/nf-core/genmod/models/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf index 0504574a1943..90c1fd482334 100644 --- a/modules/nf-core/genmod/models/main.nf +++ b/modules/nf-core/genmod/models/main.nf @@ -4,8 +4,8 @@ process GENMOD_MODELS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml index 1eca76fad2ca..bbc3fd973a9e 100644 --- a/modules/nf-core/genmod/score/environment.yml +++ b/modules/nf-core/genmod/score/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::genmod=3.8.2 + - bioconda::genmod=3.8.3 diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf index 15be5f744b3d..522e05b65814 100644 --- a/modules/nf-core/genmod/score/main.nf +++ b/modules/nf-core/genmod/score/main.nf @@ -4,8 +4,8 @@ process GENMOD_SCORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/genmod:3.8.2--pyhdfd78af_0': - 'biocontainers/genmod:3.8.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/genmod:3.8.3--pyhdfd78af_0': + 'biocontainers/genmod:3.8.3--pyhdfd78af_0' }" input: tuple val(meta), path(input_vcf) From f8ee14db9bef612a48cf8d4d89359111ea943a9d Mon Sep 17 00:00:00 2001 From: Edmund Miller <20095261+edmundmiller@users.noreply.github.com> Date: Mon, 7 Oct 2024 02:39:25 -0500 Subject: [PATCH 119/486] Remove CODEOWNERS (#6738) * chore: Remove all autogenerated module references * chore: Opt-in @edmundmiller to CODEOWNERS * Update .github/CODEOWNERS --------- Co-authored-by: Maxime U Garcia --- .github/CODEOWNERS | 1116 +------------------------------------------- 1 file changed, 13 insertions(+), 1103 deletions(-) diff --git a/.github/CODEOWNERS b/.github/CODEOWNERS index d2286a7018ca..3893bf75737c 100644 --- a/.github/CODEOWNERS +++ b/.github/CODEOWNERS @@ -1,1104 +1,14 @@ -*.nf.test* @nf-core/nf-test -.github/workflows/test.yml @nf-core/nf-test -tags.yml @nf-core/nf-test -tests/config @nf-core/nf-test -modules/nf-core/abacas/** @joseespinosa @drpatelh -modules/nf-core/abricate/run/** @rpetit3 -modules/nf-core/abricate/summary/** @rpetit3 -modules/nf-core/abritamr/run/** @rpetit3 -modules/nf-core/adapterremovalfixprefix/** @jfy133 -modules/nf-core/adapterremoval/** @maxibor @jfy133 -modules/nf-core/admixture/** @atrigila -modules/nf-core/affy/justrma/** @pinin4fjords -modules/nf-core/agat/convertspgff2gtf/** @toniher -modules/nf-core/agat/convertspgxf2gxf/** @toniher -modules/nf-core/agat/spstatistics/** @toniher -modules/nf-core/agat/sqstatbasic/** @toniher -modules/nf-core/agrvate/** @abhi18av -modules/nf-core/allelecounter/** @fullama @fbdtemme -modules/nf-core/ampcombi/** @darcy220606 @louperelo -modules/nf-core/ampir/** @jasmezz -modules/nf-core/amplify/predict/** @louperelo -modules/nf-core/amps/** @jfy133 -modules/nf-core/amrfinderplus/run/** @rpetit3 @louperelo @jfy133 -modules/nf-core/amrfinderplus/update/** @rpetit3 -modules/nf-core/angsd/contamination/** @jbv2 -modules/nf-core/angsd/docounts/** @jfy133 -modules/nf-core/annotsv/annotsv/** @nvnieuwk -modules/nf-core/annotsv/installannotations/** @nvnieuwk -modules/nf-core/antismash/antismashlitedownloaddatabases/** @jasmezz -modules/nf-core/antismash/antismashlite/** @jasmezz -modules/nf-core/arcashla/extract/** @christopher-mohr -modules/nf-core/aria2/** @JoseEspinosa -modules/nf-core/ariba/getref/** @rpetit3 -modules/nf-core/ariba/run/** @rpetit3 -modules/nf-core/arriba/arriba/** @praveenraj2018,@rannick -modules/nf-core/artic/guppyplex/** @joseespinosa @drpatelh -modules/nf-core/artic/minion/** @joseespinosa @drpatelh -modules/nf-core/art/illumina/** @MarieLataretu -modules/nf-core/ascat/** @aasNGC @lassefolkersen @FriederikeHanssen @maxulysse @SusiJo -modules/nf-core/ashlar/** @RobJY @jmuhlich -modules/nf-core/assemblyscan/** @sateeshperi @mjcipriano -modules/nf-core/ataqv/ataqv/** @i-pletenev -modules/nf-core/ataqv/mkarv/** @bjlang -modules/nf-core/atlas/call/** @jfy133 -modules/nf-core/atlasgeneannotationmanipulation/gtf2featureannotation/** @pinin4fjords -modules/nf-core/atlas/pmd/** @maxibor @merszym -modules/nf-core/atlas/recal/** @ltcrod -modules/nf-core/atlas/splitmerge/** @merszym -modules/nf-core/authentict/deam2cont/** @scarlhoff @StephanePeyregne -modules/nf-core/backsub/** @kbestak -modules/nf-core/bacphlip/** @CarsonJM -modules/nf-core/bakta/baktadbdownload/** @jfy133 @jasmezz -modules/nf-core/bakta/bakta/** @rpetit3 @oschwengers @jfy133 -modules/nf-core/bamaligncleaner/** @jfy133 -modules/nf-core/bamcmp/** @kmurat1 @sppearce -modules/nf-core/bamtools/convert/** @sguizard -modules/nf-core/bamtools/split/** @sguizard @matthdsm -modules/nf-core/bamtools/stats/** @lescai -modules/nf-core/bamutil/trimbam/** @jfy133 -modules/nf-core/bandage/image/** @heuermh -modules/nf-core/barrnap/** @danilodileo -modules/nf-core/bases2fastq/** @edmundmiller -modules/nf-core/basicpy/** @FloWuenne -modules/nf-core/bbmap/align/** @erikrikarddaniel -modules/nf-core/bbmap/bbduk/** @MGordon09 -modules/nf-core/bbmap/bbnorm/** @danilodileo -modules/nf-core/bbmap/bbsplit/** @joseespinosa @drpatelh -modules/nf-core/bbmap/clumpify/** @tamuanand -modules/nf-core/bbmap/index/** @daniellundin -modules/nf-core/bbmap/pileup/** @edmundmiller -modules/nf-core/bbmap/sendsketch/** @phanhung2 -modules/nf-core/bcftools/annotate/** @projectoriented @ramprasadn -modules/nf-core/bcftools/call/** @abhi18av @LouisLeNezet -modules/nf-core/bcftools/concat/** @abhi18av @nvnieuwk -modules/nf-core/bcftools/consensus/** @joseespinosa @drpatelh -modules/nf-core/bcftools/convert/** @nvnieuwk @ramprasadn @atrigila -modules/nf-core/bcftools/filter/** @joseespinosa @drpatelh -modules/nf-core/bcftools/index/** @jfy133 -modules/nf-core/bcftools/isec/** @joseespinosa @drpatelh -modules/nf-core/bcftools/merge/** @joseespinosa @drpatelh @nvnieuwk @ramprasadn -modules/nf-core/bcftools/mpileup/** @joseespinosa @drpatelh -modules/nf-core/bcftools/norm/** @abhi18av @ramprasadn -modules/nf-core/bcftools/pluginscatter/** @nvnieuwk -modules/nf-core/bcftools/pluginsplit/** @nvnieuwk -modules/nf-core/bcftools/query/** @abhi18av @drpatelh -modules/nf-core/bcftools/reheader/** @bjohnnyd @jemten @ramprasadn -modules/nf-core/bcftools/roh/** @ramprasadn -modules/nf-core/bcftools/sort/** @Gwennid -modules/nf-core/bcftools/split/** @matthdsm @atrigila -modules/nf-core/bcftools/stats/** @joseespinosa @drpatelh @SusiJo @TCLamnidis -modules/nf-core/bcftools/view/** @abhi18av -modules/nf-core/bcl2fastq/** @matthdsm -modules/nf-core/bclconvert/** @matthdsm -modules/nf-core/beagle5/beagle/** @ashotmarg -modules/nf-core/bedtools/bamtobed/** @yuukiiwa @drpatelh -modules/nf-core/bedtools/closest/** @nvnieuwk -modules/nf-core/bedtools/complement/** @edmundmiller @sruthipsuresh @drpatelh -modules/nf-core/bedtools/coverage/** @priyanka-surana -modules/nf-core/bedtools/genomecov/** @edmundmiller @sruthipsuresh @drpatelh @sidorov-si @chris-cheshire -modules/nf-core/bedtools/getfasta/** @joseespinosa @drpatelh -modules/nf-core/bedtools/groupby/** @mashehu -modules/nf-core/bedtools/intersect/** @edmundmiller @sruthipsuresh @drpatelh @sidorov-si -modules/nf-core/bedtools/jaccard/** @nvnieuwk -modules/nf-core/bedtools/makewindows/** @kevbrick @nvnieuwk -modules/nf-core/bedtools/map/** @ekushele -modules/nf-core/bedtools/maskfasta/** @joseespinosa @drpatelh -modules/nf-core/bedtools/merge/** @edmundmiller @sruthipsuresh @drpatelh -modules/nf-core/bedtools/multiinter/** @matthdsm -modules/nf-core/bedtools/shift/** @ekushele -modules/nf-core/bedtools/slop/** @edmundmiller @sruthipsuresh @drpatelh -modules/nf-core/bedtools/sort/** @edmundmiller @sruthipsuresh @drpatelh @chris-cheshire @adamrtalbot -modules/nf-core/bedtools/split/** @nvnieuwk -modules/nf-core/bedtools/subtract/** @sidorov-si -modules/nf-core/bedtools/unionbedg/** @ekushele -modules/nf-core/bioawk/** @jfy133 -modules/nf-core/biobambam/bammarkduplicates2/** @muffato -modules/nf-core/biobambam/bammerge/** @matthdsm -modules/nf-core/biobambam/bamsormadup/** @matthdsm -modules/nf-core/biohansel/** @rpetit3 -modules/nf-core/biscuit/align/** @njspix -modules/nf-core/biscuit/biscuitblaster/** @njspix -modules/nf-core/biscuit/bsconv/** @njspix -modules/nf-core/biscuit/epiread/** @njspix -modules/nf-core/biscuit/index/** @njspix -modules/nf-core/biscuit/mergecg/** @njspix -modules/nf-core/biscuit/pileup/** @njspix -modules/nf-core/biscuit/qc/** @njspix -modules/nf-core/biscuit/vcf2bed/** @njspix -modules/nf-core/bismark/align/** @phue @FelixKrueger @ewels -modules/nf-core/bismark/coverage2cytosine/** @FelixKrueger @ewels -modules/nf-core/bismark/deduplicate/** @phue @FelixKrueger @ewels -modules/nf-core/bismark/genomepreparation/** @phue @FelixKrueger @ewels -modules/nf-core/bismark/methylationextractor/** @phue @FelixKrueger @ewels -modules/nf-core/bismark/report/** @phue @FelixKrueger @ewels -modules/nf-core/bismark/summary/** @phue @FelixKrueger @ewels -modules/nf-core/blast/blastn/** @joseespinosa @drpatelh @vagkaratzas -modules/nf-core/blast/blastp/** @vagkaratzas -modules/nf-core/blast/makeblastdb/** @joseespinosa @drpatelh @vagkaratzas -modules/nf-core/blast/tblastn/** @yumisims @gq2 @vagkaratzas -modules/nf-core/blat/** @d-jch -modules/nf-core/bowtie2/align/** @joseespinosa @drpatelh -modules/nf-core/bowtie2/build/** @joseespinosa @drpatelh -modules/nf-core/bowtie/align/** @kevinmenden -modules/nf-core/bowtie/build/** @kevinmenden @drpatelh -modules/nf-core/bracken/bracken/** @Midnighter -modules/nf-core/bracken/combinebrackenoutputs/** @jfy133 -modules/nf-core/busco/** @priyanka-surana @charles-plessy @mahesh-panchal @muffato @jvhagey -modules/nf-core/bwa/aln/** @jfy133 -modules/nf-core/bwa/index/** @drpatelh @maxulysse -modules/nf-core/bwamem2/index/** @maxulysse -modules/nf-core/bwamem2/mem/** @maxulysse -modules/nf-core/bwa/mem/** @drpatelh @jeremy1805 -modules/nf-core/bwameth/align/** @phue -modules/nf-core/bwameth/index/** @phue -modules/nf-core/bwa/sampe/** @jfy133 -modules/nf-core/bwa/samse/** @jfy133 -modules/nf-core/cadd/** @ramprasadn -modules/nf-core/calder2/** @lucananni93 -modules/nf-core/canu/** @scorreard -modules/nf-core/cat/cat/** @erikrikarddaniel @FriederikeHanssen -modules/nf-core/cat/fastq/** @joseespinosa @drpatelh -modules/nf-core/cdhit/cdhitest/** @Joon-Klaps -modules/nf-core/cdhit/cdhit/** @timslittle -modules/nf-core/cellpose/** @josenimo -modules/nf-core/cellrangeratac/count/** @ggabernet @edmundmiller @heylf -modules/nf-core/cellrangeratac/mkfastq/** @ggabernet @edmundmiller @RHReynolds @heylf -modules/nf-core/cellrangeratac/mkref/** @ggabernet @heylf -modules/nf-core/cellranger/count/** @ggabernet @edmundmiller -modules/nf-core/cellranger/mkfastq/** @ggabernet @edmundmiller @RHReynolds -modules/nf-core/cellranger/mkgtf/** @ggabernet @edmundmiller -modules/nf-core/cellranger/mkref/** @ggabernet -modules/nf-core/cellranger/mkvdjref/** @ggabernet @klkeys -modules/nf-core/cellranger/multi/** @klkeys -modules/nf-core/cellranger/vdj/** @ggabernet @edmundmiller @klkeys -modules/nf-core/centrifuge/centrifuge/** @sofstam @jfy133 @sateeshperi -modules/nf-core/centrifuge/kreport/** @sofstam @jfy133 -modules/nf-core/checkm/lineagewf/** @jfy133 -modules/nf-core/checkm/qa/** @jfy133 -modules/nf-core/checkv/downloaddatabase/** @Joon-Klaps -modules/nf-core/checkv/endtoend/** @Joon-Klaps -modules/nf-core/checkv/updatedatabase/** @Joon-Klaps -modules/nf-core/chopper/** @FynnFreyer -modules/nf-core/chromap/chromap/** @mahesh-panchal @joseespinosa -modules/nf-core/chromap/index/** @mahesh-panchal @joseespinosa -modules/nf-core/chromograph/** @ramprasadn -modules/nf-core/circexplorer2/annotate/** @BarryDigby -modules/nf-core/circexplorer2/parse/** @BarryDigby -modules/nf-core/clippy/** @marc-jones @CharlotteAnne -modules/nf-core/clonalframeml/** @rpetit3 -modules/nf-core/clustalo/align/** @luisas -modules/nf-core/clustalo/guidetree/** @luisas -modules/nf-core/cmseq/polymut/** @maxibor -modules/nf-core/cnvkit/access/** @adamrtalbot @priesgo -modules/nf-core/cnvkit/antitarget/** @adamrtalbot @priesgo @SusiJo -modules/nf-core/cnvkit/batch/** @adamrtalbot @drpatelh @fbdtemme @kaurravneet4123 @KevinMenden @lassefolkersen @MaxUlysse @priesgo @SusiJo -modules/nf-core/cnvkit/call/** @adamrtalbot @priesgo -modules/nf-core/cnvkit/export/** @adamrtalbot @priesgo -modules/nf-core/cnvkit/genemetrics/** @adamrtalbot @marrip @priesgo -modules/nf-core/cnvkit/reference/** @adamrtalbot @priesgo @SusiJo -modules/nf-core/cnvkit/target/** @adamrtalbot @priesgo -modules/nf-core/cnvnator/cnvnator/** @ramprasadn -modules/nf-core/cnvnator/convert2vcf/** @ramprasadn -modules/nf-core/cnvpytor/callcnvs/** @sima-r -modules/nf-core/cnvpytor/histogram/** @sima-r @ramprasadn -modules/nf-core/cnvpytor/importreaddepth/** @sima-r @ramprasadn -modules/nf-core/cnvpytor/partition/** @sima-r @ramprasadn -modules/nf-core/cnvpytor/view/** @sima-r @ramprasadn -modules/nf-core/concoct/concoctcoveragetable/** @jfy133 -modules/nf-core/concoct/concoct/** @jfy133 -modules/nf-core/concoct/cutupfasta/** @jfy133 -modules/nf-core/concoct/extractfastabins/** @jfy133 -modules/nf-core/concoct/mergecutupclustering/** @jfy133 -modules/nf-core/conifer/** @icaromsc @rpetit3 -modules/nf-core/controlfreec/assesssignificance/** @FriederikeHanssen -modules/nf-core/controlfreec/freec2bed/** @FriederikeHanssen -modules/nf-core/controlfreec/freec2circos/** @FriederikeHanssen -modules/nf-core/controlfreec/freec/** @FriederikeHanssen -modules/nf-core/controlfreec/makegraph/** @FriederikeHanssen -modules/nf-core/cooler/balance/** @nservant @muffato -modules/nf-core/cooler/cload/** @jianhong @muffato -modules/nf-core/cooler/digest/** @jianhong -modules/nf-core/cooler/dump/** @jianhong @muffato -modules/nf-core/cooler/makebins/** @nservant @muffato -modules/nf-core/cooler/merge/** @jianhong -modules/nf-core/cooler/zoomify/** @jianhong -modules/nf-core/coreograph/** @arozhada @MargotCh -modules/nf-core/crisprcleanr/normalize/** @LaurenceKuhl -modules/nf-core/crumble/** @priyanka-surana -modules/nf-core/csvtk/concat/** @rpetit3 -modules/nf-core/csvtk/join/** @anoronh4 -modules/nf-core/csvtk/split/** @SusiJo -modules/nf-core/custom/dumpsoftwareversions/** @drpatelh @grst -modules/nf-core/custom/getchromsizes/** @tamara-hodgetts @chris-cheshire @muffato -modules/nf-core/custom/matrixfilter/** @pinin4fjords -modules/nf-core/custom/sratoolsncbisettings/** @Midnighter -modules/nf-core/custom/tabulartogseacls/** @pinin4fjords -modules/nf-core/custom/tabulartogseagct/** @pinin4fjords -modules/nf-core/cutadapt/** @drpatelh @kevinmenden -modules/nf-core/cutesv/** @christopher-hakkaart @yuukiiwa -modules/nf-core/damageprofiler/** @jfy133 -modules/nf-core/dastool/dastool/** @maxibor @jfy133 -modules/nf-core/dastool/fastatocontig2bin/** @maxibor @jfy133 -modules/nf-core/dastool/scaffolds2bin/** @maxibor -modules/nf-core/dedup/** @jfy133 -modules/nf-core/deeparg/downloaddata/** @jfy133 -modules/nf-core/deeparg/predict/** @jfy133 -modules/nf-core/deepbgc/download/** @louperelo -modules/nf-core/deepbgc/pipeline/** @louperelo @jfy133 -modules/nf-core/deepcell/mesmer/** @migueLib @chiarasch -modules/nf-core/deeptmhmm/** @vagkaratzas -modules/nf-core/deeptools/bamcoverage/** @FriederikeHanssen @SusiJo -modules/nf-core/deeptools/computematrix/** @jeremy1805 @edmundmiller @drpatelh @joseespinosa -modules/nf-core/deeptools/multibamsummary/** @tamara-hodgetts @chris-cheshire -modules/nf-core/deeptools/plotcorrelation/** @tamara-hodgetts @chris-cheshire -modules/nf-core/deeptools/plotfingerprint/** @edmundmiller @drpatelh @joseespinosa -modules/nf-core/deeptools/plotheatmap/** @edmundmiller @drpatelh @joseespinosa -modules/nf-core/deeptools/plotpca/** @tamara-hodgetts @chris-cheshire -modules/nf-core/deeptools/plotprofile/** @edmundmiller @drpatelh @joseespinosa -modules/nf-core/deepvariant/** @abhi18av @ramprasadn -modules/nf-core/delly/call/** @projectoriented @nvnieuwk -modules/nf-core/deseq2/differential/** @pinin4fjords -modules/nf-core/diamond/blastp/** @spficklin @jfy133 -modules/nf-core/diamond/blastx/** @spficklin @jfy133 @mjamy -modules/nf-core/diamond/makedb/** @spficklin -modules/nf-core/dragmap/align/** @edmundmiller -modules/nf-core/dragmap/hashtable/** @edmundmiller -modules/nf-core/dragonflye/** @rpetit3 -modules/nf-core/dshbio/exportsegments/** @heuermh -modules/nf-core/dshbio/filterbed/** @heuermh -modules/nf-core/dshbio/filtergff3/** @heuermh -modules/nf-core/dshbio/splitbed/** @heuermh -modules/nf-core/dshbio/splitgff3/** @heuermh -modules/nf-core/duphold/** @nvnieuwk -modules/nf-core/ectyper/** @rpetit3 -modules/nf-core/eido/convert/** @rafalstepien -modules/nf-core/eido/validate/** @rafalstepien -modules/nf-core/eigenstratdatabasetools/eigenstratsnpcoverage/** @TCLamnidis -modules/nf-core/eklipse/** @Lucpen -modules/nf-core/elprep/filter/** @matthdsm -modules/nf-core/elprep/merge/** @matthdsm -modules/nf-core/elprep/split/** @matthdsm -modules/nf-core/emboss/cons/** @Joon-Klaps -modules/nf-core/emboss/revseq/** @erikrikarddaniel -modules/nf-core/emboss/seqret/** @MillironX -modules/nf-core/emmtyper/** @rpetit3 -modules/nf-core/endorspy/** @aidaanva -modules/nf-core/ensemblvep/download/** @maxulysse -modules/nf-core/ensemblvep/filtervep/** @ramprasadn -modules/nf-core/ensemblvep/vep/** @maxulysse @matthdsm @nvnieuwk -modules/nf-core/entrezdirect/esearch/** @alxndrdiaz -modules/nf-core/entrezdirect/esummary/** @alxndrdiaz -modules/nf-core/entrezdirect/xtract/** @alxndrdiaz -modules/nf-core/epang/place/** @erikrikarddaniel -modules/nf-core/epang/split/** @erikrikarddaniel -modules/nf-core/expansionhunterdenovo/merge/** @nvnieuwk -modules/nf-core/expansionhunterdenovo/profile/** @nvnieuwk -modules/nf-core/expansionhunter/** @jemten -modules/nf-core/falco/** @lucacozzuto -modules/nf-core/famsa/align/** @luisas -modules/nf-core/famsa/guidetree/** @luisas -modules/nf-core/faqcs/** @mjcipriano @sateeshperi @hseabolt -modules/nf-core/fargene/** @louperelo -modules/nf-core/fastani/** @abhi18av -modules/nf-core/fastawindows/** @muffato -modules/nf-core/fastk/fastk/** @mahesh-panchal -modules/nf-core/fastk/histex/** @mahesh-panchal -modules/nf-core/fastk/merge/** @mahesh-panchal -modules/nf-core/fastp/** @drpatelh @kevinmenden -modules/nf-core/fastqc/** @drpatelh @grst @FelixKrueger -modules/nf-core/fastqscan/** @rpetit3 -modules/nf-core/fasttree/** @aunderwo -modules/nf-core/fcs/fcsadaptor/** @d4straub -modules/nf-core/fcs/fcsgx/** @tillenglert -modules/nf-core/ffq/** @drpatelh -modules/nf-core/fgbio/callduplexconsensusreads/** @lescai -modules/nf-core/fgbio/callmolecularconsensusreads/** @sruthipsuresh -modules/nf-core/fgbio/fastqtobam/** @lescai @matthdsm -modules/nf-core/fgbio/filterconsensusreads/** @lescai -modules/nf-core/fgbio/groupreadsbyumi/** @lescai -modules/nf-core/fgbio/sortbam/** @sruthipsuresh -modules/nf-core/fgbio/zipperbams/** @lescai -modules/nf-core/filtlong/** @d4straub @sofstam -modules/nf-core/flash/** @Erkison -modules/nf-core/flye/** @mirpedrol -modules/nf-core/fq/generate/** @adamrtalbot -modules/nf-core/fq/lint/** @adamrtalbot -modules/nf-core/fq/subsample/** @adamrtalbot -modules/nf-core/fqtk/** @nh13 @sam-white04 -modules/nf-core/freebayes/** @maxibor @FriederikeHanssen @maxulysse -modules/nf-core/freyja/boot/** @Joon-Klaps -modules/nf-core/freyja/demix/** @Joon-Klaps -modules/nf-core/freyja/update/** @Joon-Klaps -modules/nf-core/freyja/variants/** @Joon-Klaps -modules/nf-core/galah/** @prototaxites -modules/nf-core/gamma/gamma/** @sateeshperi @rastanton @jvhagey -modules/nf-core/gangstr/** @nvnieuwk -modules/nf-core/ganon/buildcustom/** @jfy133 -modules/nf-core/ganon/classify/** @jfy133 -modules/nf-core/ganon/report/** @jfy133 -modules/nf-core/ganon/table/** @jfy133 -modules/nf-core/gappa/examineassign/** @erikrikarddaniel -modules/nf-core/gappa/examinegraft/** @erikrikarddaniel -modules/nf-core/gappa/examineheattree/** @erikrikarddaniel -modules/nf-core/gatk4/annotateintervals/** @nvnieuwk -modules/nf-core/gatk4/applybqsrspark/** @yocra3 @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/applybqsr/** @yocra3 @FriederikeHanssen -modules/nf-core/gatk4/applyvqsr/** @GCJMackenzie -modules/nf-core/gatk4/asereadcounter/** @Lucpen -modules/nf-core/gatk4/baserecalibratorspark/** @yocra3 @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/baserecalibrator/** @yocra3 @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/bedtointervallist/** @kevinmenden @ramprasadn -modules/nf-core/gatk4/calculatecontamination/** @GCJMackenzie @maxulysse -modules/nf-core/gatk4/calibratedragstrmodel/** @nvnieuwk -modules/nf-core/gatk4/cnnscorevariants/** @FriederikeHanssen -modules/nf-core/gatk4/collectreadcounts/** @nvnieuwk -modules/nf-core/gatk4/collectsvevidence/** @nvnieuwk -modules/nf-core/gatk4/combinegvcfs/** @sateeshperi @mjcipriano @hseabolt @maxulysse -modules/nf-core/gatk4/composestrtablefile/** @nvnieuwk -modules/nf-core/gatk4/condensedepthevidence/** @nvnieuwk -modules/nf-core/gatk4/createreadcountpanelofnormals/** @ramprasadn -modules/nf-core/gatk4/createsequencedictionary/** @maxulysse @ramprasadn -modules/nf-core/gatk4/createsomaticpanelofnormals/** @GCJMackenzie -modules/nf-core/gatk4/denoisereadcounts/** @ramprasadn -modules/nf-core/gatk4/determinegermlinecontigploidy/** @nvnieuwk -modules/nf-core/gatk4/estimatelibrarycomplexity/** @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/fastqtosam/** @ntoda03 -modules/nf-core/gatk4/filterintervals/** @ryanjameskennedy @ViktorHy -modules/nf-core/gatk4/filtermutectcalls/** @GCJMackenzie @maxulysse @ramprasadn -modules/nf-core/gatk4/filtervarianttranches/** @FriederikeHanssen -modules/nf-core/gatk4/gatherbqsrreports/** @FriederikeHanssen -modules/nf-core/gatk4/gatherpileupsummaries/** @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/genomicsdbimport/** @GCJMackenzie -modules/nf-core/gatk4/genotypegvcfs/** @santiagorevale @maxulysse -modules/nf-core/gatk4/germlinecnvcaller/** @ryanjameskennedy @ViktorHy -modules/nf-core/gatk4/getpileupsummaries/** @GCJMackenzie -modules/nf-core/gatk4/haplotypecaller/** @suzannejin @FriederikeHanssen -modules/nf-core/gatk4/indexfeaturefile/** @santiagorevale -modules/nf-core/gatk4/intervallisttobed/** @FriederikeHanssen -modules/nf-core/gatk4/intervallisttools/** @praveenraj2018 -modules/nf-core/gatk4/learnreadorientationmodel/** @GCJMackenzie -modules/nf-core/gatk4/leftalignandtrimvariants/** @adamrtalbot -modules/nf-core/gatk4/markduplicates/** @ajodeh-juma @FriederikeHanssen @maxulysse -modules/nf-core/gatk4/markduplicatesspark/** @ajodeh-juma @FriederikeHanssen @maxulysse @SusiJo -modules/nf-core/gatk4/mergebamalignment/** @kevinmenden @ramprasadn -modules/nf-core/gatk4/mergemutectstats/** @FriederikeHanssen -modules/nf-core/gatk4/mergevcfs/** @kevinmenden -modules/nf-core/gatk4/mutect2/** @GCJMackenzie @ramprasadn -modules/nf-core/gatk4/postprocessgermlinecnvcalls/** @ryanjameskennedy -modules/nf-core/gatk4/preprocessintervals/** @ryanjameskennedy @ViktorHy @ramprasadn -modules/nf-core/gatk4/printreads/** @ramprasadn -modules/nf-core/gatk4/printsvevidence/** @nvnieuwk -modules/nf-core/gatk4/reblockgvcf/** @nvnieuwk -modules/nf-core/gatk4/revertsam/** @kevinmenden -modules/nf-core/gatk4/samtofastq/** @kevinmenden -modules/nf-core/gatk4/selectvariants/** @mjcipriano @ramprasadn -modules/nf-core/gatk4/shiftfasta/** @ramprasadn -modules/nf-core/gatk4/sitedepthtobaf/** @nvnieuwk -modules/nf-core/gatk4/splitcram/** @nvnieuwk -modules/nf-core/gatk4/splitintervals/** @nvnieuwk @ramprasadn -modules/nf-core/gatk4/splitncigarreads/** @kevinmenden -modules/nf-core/gatk4/svannotate/** @nvnieuwk -modules/nf-core/gatk4/svcluster/** @nvnieuwk -modules/nf-core/gatk4/variantfiltration/** @kevinmenden @ramprasadn -modules/nf-core/gatk4/variantrecalibrator/** @GCJMackenzie @nickhsmith -modules/nf-core/gatk/indelrealigner/** @jfy133 -modules/nf-core/gatk/realignertargetcreator/** @jfy133 -modules/nf-core/gatk/unifiedgenotyper/** @ilight1542 @jfy133 -modules/nf-core/gawk/** @nvnieuwk -modules/nf-core/gecco/run/** @jfy133 -modules/nf-core/gem2/gem2bedmappability/** @nvnieuwk -modules/nf-core/gem2/gemindexer/** @nvnieuwk -modules/nf-core/gem2/gemmappability/** @nvnieuwk -modules/nf-core/gem3/gem3indexer/** @miqalvarez -modules/nf-core/genescopefk/** @mahesh-panchal -modules/nf-core/genmap/index/** @jianhong @nvnieuwk -modules/nf-core/genmap/map/** @jianhong @nvnieuwk -modules/nf-core/genmod/annotate/** @ramprasadn -modules/nf-core/genmod/compound/** @ramprasadn -modules/nf-core/genmod/models/** @ramprasadn -modules/nf-core/genmod/score/** @ramprasadn -modules/nf-core/genomad/download/** @CarsonJM -modules/nf-core/genomad/endtoend/** @CarsonJM -modules/nf-core/genomescope2/** @mahesh-panchal -modules/nf-core/genotyphi/parse/** @rpetit3 -modules/nf-core/genrich/** @JoseEspinosa @samuelruizperez -modules/nf-core/geoquery/getgeo/** @azedinez @pinin4fjords -modules/nf-core/gfaffix/** @heuermh -modules/nf-core/gfastats/** @mahesh-panchal -modules/nf-core/gfatools/gfa2fa/** @mahesh-panchal -modules/nf-core/gfatools/stat/** @mahesh-panchal -modules/nf-core/gffcompare/** @jemten -modules/nf-core/gffread/** @edmundmiller -modules/nf-core/gget/gget/** @adamrtalbot -modules/nf-core/glimpse2/chunk/** @louislenezet -modules/nf-core/glimpse2/concordance/** @louislenezet -modules/nf-core/glimpse2/ligate/** @louislenezet -modules/nf-core/glimpse2/phase/** @LouisLeNezet -modules/nf-core/glimpse2/splitreference/** @LouisLeNezet -modules/nf-core/glimpse/chunk/** @louislenezet -modules/nf-core/glimpse/concordance/** @louislenezet -modules/nf-core/glimpse/ligate/** @louislenezet -modules/nf-core/glimpse/phase/** @louislenezet -modules/nf-core/glimpse/sample/** @louislenezet -modules/nf-core/glnexus/** @ramprasadn -modules/nf-core/gnu/sort/** @DLBPointon -modules/nf-core/goat/taxonsearch/** @alxndrdiaz @muffato -modules/nf-core/goleft/indexcov/** @lindenb -modules/nf-core/goleft/indexsplit/** @matthdsm -modules/nf-core/graphmap2/align/** @yuukiiwa @drpatelh -modules/nf-core/graphmap2/index/** @yuukiiwa @drpatelh -modules/nf-core/graphtyper/genotype/** @zachary-foster -modules/nf-core/graphtyper/vcfconcatenate/** @zachary-foster -modules/nf-core/gridss/gridss/** @nvnieuwk -modules/nf-core/gsea/gsea/** @pinin4fjords -modules/nf-core/gstama/collapse/** @sguizard -modules/nf-core/gstama/merge/** @sguizard -modules/nf-core/gstama/polyacleanup/** @sguizard -modules/nf-core/gtdbtk/classifywf/** @skrakau @abhi18av -modules/nf-core/gubbins/** @avantonder -modules/nf-core/gunc/downloaddb/** @jfy133 -modules/nf-core/gunc/mergecheckm/** @jfy133 -modules/nf-core/gunc/run/** @jfy133 -modules/nf-core/gunzip/** @joseespinosa @drpatelh @jfy133 -modules/nf-core/gvcftools/extractvariants/** @nvnieuwk -modules/nf-core/hamronization/abricate/** @jasmezz -modules/nf-core/hamronization/amrfinderplus/** @louperelo -modules/nf-core/hamronization/deeparg/** @jfy133 -modules/nf-core/hamronization/fargene/** @jfy133 -modules/nf-core/hamronization/rgi/** @louperelo -modules/nf-core/hamronization/summarize/** @jfy133 -modules/nf-core/hapibd/** @ashotmarg -modules/nf-core/haplocheck/** @lmtani -modules/nf-core/haplogrep2/classify/** @lucpen -modules/nf-core/happy/happy/** @nvnieuwk -modules/nf-core/happy/prepy/** @nvnieuwk -modules/nf-core/hicap/** @rpetit3 -modules/nf-core/hicexplorer/hicpca/** @jianhong -modules/nf-core/hifiasm/** @sidorov-si @scorreard -modules/nf-core/hisat2/align/** @ntoda03 @ramprasadn -modules/nf-core/hisat2/build/** @ntoda03 -modules/nf-core/hisat2/extractsplicesites/** @ntoda03 @ramprasadn -modules/nf-core/hlala/preparegraph/** @mapo9 -modules/nf-core/hlala/typing/** @mapo9 -modules/nf-core/hmmcopy/gccounter/** @sppearce @adamrtalbot -modules/nf-core/hmmcopy/generatemap/** @sppearce @adamrtalbot -modules/nf-core/hmmcopy/mapcounter/** @sppearce -modules/nf-core/hmmcopy/readcounter/** @sppearce -modules/nf-core/hmmer/eslalimask/** @erikrikarddaniel -modules/nf-core/hmmer/eslreformat/** @erikrikarddaniel -modules/nf-core/hmmer/hmmalign/** @erikrikarddaniel @jfy133 -modules/nf-core/hmmer/hmmbuild/** @erikrikarddaniel -modules/nf-core/hmmer/hmmfetch/** @erikrikarddaniel -modules/nf-core/hmmer/hmmsearch/** @Midnighter -modules/nf-core/hmtnote/annotate/** @sysbiocoder -modules/nf-core/homer/annotatepeaks/** @drpatelh @kevinmenden -modules/nf-core/homer/findpeaks/** @edmundmiller -modules/nf-core/homer/maketagdirectory/** @edmundmiller -modules/nf-core/homer/makeucscfile/** @edmundmiller -modules/nf-core/homer/pos2bed/** @edmundmiller -modules/nf-core/hpsuissero/** @rpetit3 -modules/nf-core/htseq/count/** @zehrahazalsezer -modules/nf-core/hypo/** @remiolsen -modules/nf-core/ichorcna/createpon/** @sppearce -modules/nf-core/ichorcna/run/** @sppearce -modules/nf-core/icountmini/metagene/** @marc-jones @chris-cheshire @charlotteanne -modules/nf-core/icountmini/peaks/** @marc-jones @chris-cheshire @charlotteanne -modules/nf-core/icountmini/segment/** @marc-jones @chris-cheshire @charlotteanne -modules/nf-core/icountmini/sigxls/** @marc-jones @chris-cheshire @charlotteanne -modules/nf-core/icountmini/summary/** @marc-jones @chris-cheshire @charlotteanne -modules/nf-core/idr/** @drpatelh @joseespinosa -modules/nf-core/igv/js/** @mirpedrol -modules/nf-core/ilastik/multicut/** @FloWuenne -modules/nf-core/ilastik/pixelclassification/** @FloWuenne -modules/nf-core/instrain/compare/** @margotl9 @CarsonJM -modules/nf-core/instrain/profile/** @mrolm -modules/nf-core/interproscan/** @toniher -modules/nf-core/iphop/download/** @CarsonJM -modules/nf-core/iphop/predict/** @CarsonJM -modules/nf-core/iqtree/** @avantonder @aunderwo -modules/nf-core/islandpath/** @jvfe -modules/nf-core/ismapper/** @rpetit3 -modules/nf-core/isoseq3/cluster/** @sguizard -modules/nf-core/isoseq3/refine/** @sguizard -modules/nf-core/ivar/consensus/** @andersgs @drpatelh -modules/nf-core/ivar/trim/** @andersgs @drpatelh -modules/nf-core/ivar/variants/** @andersgs @drpatelh -modules/nf-core/jasminesv/** @nvnieuwk -modules/nf-core/jupyternotebook/** @grst -modules/nf-core/kaiju/kaiju2krona/** @MillironX -modules/nf-core/kaiju/kaiju2table/** @sofstam @talnor @jfy133 -modules/nf-core/kaiju/kaiju/** @talnor @sofstam @jfy133 -modules/nf-core/kalign/align/** @luisas -modules/nf-core/kallistobustools/count/** @flowuenne -modules/nf-core/kallistobustools/ref/** @flowuenne -modules/nf-core/kallisto/index/** @ggabernet -modules/nf-core/kallisto/quant/** @anoronh4 -modules/nf-core/kat/hist/** @mahesh-panchal -modules/nf-core/khmer/normalizebymedian/** @erikrikarddaniel -modules/nf-core/khmer/uniquekmers/** @JoseEspinosa -modules/nf-core/kleborate/** @abhi18av @rpetit3 -modules/nf-core/kmcp/compute/** @sofstam -modules/nf-core/kmcp/index/** @sofstam -modules/nf-core/kmcp/merge/** @sofstam -modules/nf-core/kmcp/profile/** @sofstam -modules/nf-core/kmcp/search/** @sofstam -modules/nf-core/kofamscan/** @toniher -modules/nf-core/kraken2/kraken2/** @joseespinosa @drpatelh -modules/nf-core/krakentools/combinekreports/** @jfy133 -modules/nf-core/krakentools/kreport2krona/** @MillironX -modules/nf-core/krakenuniq/build/** @jfy133 -modules/nf-core/krakenuniq/download/** @jfy133 -modules/nf-core/krakenuniq/preloadedkrakenuniq/** @mjamy @Midnighter -modules/nf-core/krona/kronadb/** @mjakobs -modules/nf-core/krona/ktimporttaxonomy/** @mjakobs -modules/nf-core/krona/ktimporttext/** @jianhong -modules/nf-core/krona/ktupdatetaxonomy/** @mjakobs -modules/nf-core/last/dotplot/** @charles-plessy -modules/nf-core/last/lastal/** @charles-plessy -modules/nf-core/last/lastdb/** @charles-plessy -modules/nf-core/last/mafconvert/** @aleksandrabliznina -modules/nf-core/last/mafswap/** @charles-plessy -modules/nf-core/last/postmask/** @charles-plessy -modules/nf-core/last/split/** @aleksandrabliznina -modules/nf-core/last/train/** @aleksandrabliznina -modules/nf-core/learnmsa/align/** @luisas -modules/nf-core/leehom/** @jfy133 -modules/nf-core/legsta/** @rpetit3 -modules/nf-core/lima/** @sguizard -modules/nf-core/limma/differential/** @pinin4fjords -modules/nf-core/lissero/** @rpetit3 -modules/nf-core/lofreq/call/** @bjohnnyd -modules/nf-core/lofreq/callparallel/** @kaurravneet4123 @bjohnnyd -modules/nf-core/lofreq/filter/** @bjohnnyd -modules/nf-core/lofreq/indelqual/** @kaurravneet4123 -modules/nf-core/lofreq/somatic/** @nevinwu -modules/nf-core/macrel/contigs/** @darcy220606 -modules/nf-core/macs2/callpeak/** @ntoda03 @JoseEspinosa @jianhong -modules/nf-core/mafft/** @MillironX -modules/nf-core/mageck/count/** @LaurenceKuhl -modules/nf-core/mageck/mle/** @LaurenceKuhl -modules/nf-core/mageck/test/** @LaurenceKuhl -modules/nf-core/malt/build/** @jfy133 -modules/nf-core/maltextract/** @jfy133 -modules/nf-core/malt/run/** @jfy133 -modules/nf-core/manta/convertinversion/** @FriederikeHanssen -modules/nf-core/manta/germline/** @maxulysse @ramprasadn @nvnieuwk -modules/nf-core/manta/somatic/** @FriederikeHanssen @nvnieuwk -modules/nf-core/manta/tumoronly/** @maxulysse @nvnieuwk -modules/nf-core/mapad/index/** @jch-13 -modules/nf-core/mapad/map/** @jch-13 -modules/nf-core/mapdamage2/** @darcy220606 -modules/nf-core/mash/dist/** @rpetit3 -modules/nf-core/mash/screen/** @mahesh-panchal -modules/nf-core/mash/sketch/** @thanhleviet -modules/nf-core/mashtree/** @rpetit3 -modules/nf-core/maxbin2/** @jfy133 -modules/nf-core/maxquant/lfq/** @veitveit -modules/nf-core/mcquant/** @FloWuenne -modules/nf-core/mcroni/** @rpetit3 -modules/nf-core/md5sum/** @matthdsm -modules/nf-core/medaka/** @avantonder -modules/nf-core/megahit/** @jfy133 -modules/nf-core/megan/daa2info/** @jfy133 -modules/nf-core/megan/rma2info/** @jfy133 -modules/nf-core/meningotype/** @rpetit3 -modules/nf-core/merquryfk/katcomp/** @mahesh-panchal -modules/nf-core/merquryfk/katgc/** @mahesh-panchal -modules/nf-core/merquryfk/merquryfk/** @mahesh-panchal -modules/nf-core/merquryfk/ploidyplot/** @mahesh-panchal -modules/nf-core/merqury/** @mahesh-panchal -modules/nf-core/meryl/count/** @mahesh-panchal -modules/nf-core/meryl/histogram/** @mahesh-panchal -modules/nf-core/meryl/unionsum/** @mahesh-panchal -modules/nf-core/metabat2/jgisummarizebamcontigdepths/** @maxibor -modules/nf-core/metabat2/metabat2/** @maxibor @jfy133 -modules/nf-core/metaeuk/easypredict/** @prototaxites -modules/nf-core/metaphlan3/mergemetaphlantables/** @jfy133 -modules/nf-core/metaphlan3/metaphlan3/** @MGordon09 -modules/nf-core/metaphlan/makedb/** @LilyAnderssonLee -modules/nf-core/metaphlan/mergemetaphlantables/** @jfy133 @LilyAnderssonLee -modules/nf-core/metaphlan/metaphlan/** @MGordon09 @LilyAnderssonLee -modules/nf-core/methyldackel/extract/** @phue -modules/nf-core/methyldackel/mbias/** @phue -modules/nf-core/midas/run/** @rpetit3 -modules/nf-core/mindagap/mindagap/** @ViriatoII @flowuenne -modules/nf-core/minia/** @drpatelh @kevinmenden -modules/nf-core/miniasm/** @avantonder -modules/nf-core/minimap2/align/** @heuermh @sofstam @sateeshperi @jfy133 -modules/nf-core/minimap2/index/** @yuukiiwa @drpatelh -modules/nf-core/miniprot/align/** @yumisims @muffato -modules/nf-core/miniprot/index/** @yumisims @muffato -modules/nf-core/miranda/** @BarryDigby -modules/nf-core/mitohifi/findmitoreference/** @verku -modules/nf-core/mitohifi/mitohifi/** @ksenia-krasheninnikova -modules/nf-core/mlst/** @lskatz @tseemann -modules/nf-core/mmseqs/cluster/** @Joon-Klaps -modules/nf-core/mmseqs/createdb/** @Joon-Klaps -modules/nf-core/mmseqs/createindex/** @JoseEspinosa -modules/nf-core/mmseqs/createtsv/** @Joon-Klaps -modules/nf-core/mmseqs/databases/** @prototaxites -modules/nf-core/mmseqs/easysearch/** @luisas -modules/nf-core/mmseqs/linclust/** @vagkaratzas -modules/nf-core/mmseqs/search/** @Joon-Klaps -modules/nf-core/mmseqs/tsv2exprofiledb/** @JoseEspinosa -modules/nf-core/mobsuite/recon/** @rpetit3 -modules/nf-core/mosdepth/** @joseespinosa @drpatelh @ramprasadn @matthdsm -modules/nf-core/motus/downloaddb/** @jianhong -modules/nf-core/motus/merge/** @jfy133 -modules/nf-core/motus/profile/** @jianhong -modules/nf-core/msisensor2/msi/** @adamrtalbot -modules/nf-core/msisensor2/scan/** @adamrtalbot -modules/nf-core/msisensor/msi/** @kevbrick -modules/nf-core/msisensorpro/msisomatic/** @FriederikeHanssen -modules/nf-core/msisensorpro/scan/** @FriederikeHanssen -modules/nf-core/msisensor/scan/** @kevbrick -modules/nf-core/mtnucratio/** @louperelo -modules/nf-core/multiqc/** @abhi18av @bunop @drpatelh @jfy133 @ewels -modules/nf-core/multivcfanalyzer/** @jfy133 -modules/nf-core/mummer/** @mjcipriano @sateeshperi -modules/nf-core/muscle5/super5/** @alessiovignoli -modules/nf-core/muscle/** @MGordon -modules/nf-core/mykrobe/predict/** @rpetit3 -modules/nf-core/nanocomp/** @paulwolk -modules/nf-core/nanolyse/** @yuukiiwa -modules/nf-core/nanomonsv/parse/** @awgymer -modules/nf-core/nanoplot/** @drpatelh @yuukiiwa -modules/nf-core/ncbigenomedownload/** @rpetit3 -modules/nf-core/nextclade/datasetget/** @antunderwood @drpatelh -modules/nf-core/nextclade/run/** @antunderwood @drpatelh -modules/nf-core/nextgenmap/** @cmatkhan -modules/nf-core/ngmaster/** @rpetit3 -modules/nf-core/ngmerge/** @charlotteanne @jsh58 -modules/nf-core/ngsbits/samplegender/** @nvnieuwk -modules/nf-core/ngscheckmate/fastq/** @sppearce -modules/nf-core/ngscheckmate/ncm/** @sppearce -modules/nf-core/ngscheckmate/patterngenerator/** @sppearce -modules/nf-core/ngscheckmate/vafncm/** @sppearce -modules/nf-core/nonpareil/nonpareil/** @jfy133 -modules/nf-core/nonpareil/curve/** @jfy133 -modules/nf-core/nucmer/** @sateeshperi @mjcipriano -modules/nf-core/odgi/build/** @subwaystation -modules/nf-core/odgi/draw/** @subwaystation -modules/nf-core/odgi/layout/** @subwaystation -modules/nf-core/odgi/sort/** @subwaystation -modules/nf-core/odgi/squeeze/** @subwaystation -modules/nf-core/odgi/stats/** @subwaystation -modules/nf-core/odgi/unchop/** @subwaystation -modules/nf-core/odgi/view/** @subwaystation -modules/nf-core/odgi/viz/** @subwaystation -modules/nf-core/oncocnv/** @marrip -modules/nf-core/openms/decoydatabase/** @jonasscheid -modules/nf-core/optitype/** @apeltzer -modules/nf-core/paftools/sam2paf/** @DLBPointon -modules/nf-core/pairix/** @jianhong -modules/nf-core/pairtools/dedup/** @jianhong -modules/nf-core/pairtools/flip/** @jianhong -modules/nf-core/pairtools/merge/** @nservant -modules/nf-core/pairtools/parse/** @jianhong -modules/nf-core/pairtools/restrict/** @jianhong -modules/nf-core/pairtools/select/** @jianhong -modules/nf-core/pairtools/sort/** @jianhong @nservant -modules/nf-core/pairtools/stats/** @nservant -modules/nf-core/panaroo/run/** @rpetit3 -modules/nf-core/pangolin/** @kevinmenden @drpatelh -modules/nf-core/parabricks/applybqsr/** @bsiranosian -modules/nf-core/parabricks/fq2bam/** @bsiranosian @adamrtalbot -modules/nf-core/paraclu/** @mashehu -modules/nf-core/paragraph/idxdepth/** @nvnieuwk -modules/nf-core/paragraph/multigrmpy/** @nvnieuwk -modules/nf-core/paragraph/vcf2paragraph/** @nvnieuwk -modules/nf-core/pasty/** @rpetit3 -modules/nf-core/pbbam/pbmerge/** @sguizard -modules/nf-core/pbccs/** @sguizard -modules/nf-core/pbptyper/** @rpetit3 -modules/nf-core/pear/** @mirpedrol -modules/nf-core/peddy/** @rannick -modules/nf-core/peka/** @kkuret @codeprimate123 @chris-cheshire @charlotteanne -modules/nf-core/phantompeakqualtools/** @drpatelh @edmundmiller @JoseEspinosa -modules/nf-core/phispy/** @jvfe -modules/nf-core/phyloflash/** @abhi18av -modules/nf-core/picard/addorreplacereadgroups/** @sateeshperi @mjcipriano @hseabolt @cmatKhan @muffato -modules/nf-core/picard/bedtointervallist/** @kevinmenden @matthdsm -modules/nf-core/picard/cleansam/** @sateeshperi @mjcipriano @hseabolt -modules/nf-core/picard/collecthsmetrics/** @projectoriented @matthdsm -modules/nf-core/picard/collectinsertsizemetrics/** @FerriolCalvet -modules/nf-core/picard/collectmultiplemetrics/** @drpatelh -modules/nf-core/picard/collectrnaseqmetrics/** @anoronh4 -modules/nf-core/picard/collectwgsmetrics/** @drpatelh @flowuenne @lassefolkersen @ramprasadn -modules/nf-core/picard/createsequencedictionary/** @sateeshperi @mjcipriano @hseabolt -modules/nf-core/picard/crosscheckfingerprints/** @matthdsm -modules/nf-core/picard/fastqtosam/** @matthdsm -modules/nf-core/picard/filtersamreads/** @jfy133 -modules/nf-core/picard/fixmateinformation/** @sateeshperi @mjcipriano @hseabolt -modules/nf-core/picard/liftovervcf/** @lucpen @ramprasadn -modules/nf-core/picard/markduplicates/** @drpatelh @projectoriented @ramprasadn -modules/nf-core/picard/mergesamfiles/** @drpatelh -modules/nf-core/picard/renamesampleinvcf/** @Lucpen -modules/nf-core/picard/scatterintervalsbyns/** @nvnieuwk -modules/nf-core/picard/sortsam/** @jfy133 -modules/nf-core/picard/sortvcf/** @ramprasadn -modules/nf-core/pilon/** @scorreard -modules/nf-core/pindel/pindel/** @marrip +.github/workflows/** @nf-core/a-team +tests/config @nf-core/a-team + +# Opt-in +modules/nf-core/bedtools/** @edmundmiller +modules/nf-core/dragmap/** @edmundmiller +modules/nf-core/ensemblvep/** @maxulysse +modules/nf-core/gatk4/** @maxulysse +modules/nf-core/homer/** @edmundmiller +modules/nf-core/snpeff/** @maxulysse modules/nf-core/pints/caller/** @edmundmiller -modules/nf-core/pirate/** @rpetit3 -modules/nf-core/plasmidfinder/** @rpetit3 -modules/nf-core/plasmidid/** @joseespinosa @drpatelh -modules/nf-core/platypus/** @kubranarci -modules/nf-core/plink2/extract/** @nebfield -modules/nf-core/plink2/score/** @nebfield -modules/nf-core/plink2/vcf/** @nebfield -modules/nf-core/plink/bcf/** @atrigila -modules/nf-core/plink/exclude/** @atrigila -modules/nf-core/plink/extract/** @nebfield -modules/nf-core/plink/indep/** @atrigila -modules/nf-core/plink/indeppairwise/** @atrigila -modules/nf-core/plink/recode/** @atrigila -modules/nf-core/plink/vcf/** @Mxrcon @abhi18av -modules/nf-core/pmdtools/filter/** @alexandregilardet -modules/nf-core/pneumocat/** @rpetit3 -modules/nf-core/porechop/abi/** @sofstam -modules/nf-core/porechop/porechop/** @ggabernet @jasmezz @d4straub @LaurenceKuhl @SusiJo @jonasscheid @jonoave @GokceOGUZ @jfy133 -modules/nf-core/preseq/ccurve/** @drpatelh @edmundmiller -modules/nf-core/preseq/lcextrap/** @drpatelh @edmundmiller -modules/nf-core/pretextmap/** @marrip @getrudeln -modules/nf-core/pretextsnapshot/** @epaule -modules/nf-core/prinseqplusplus/** @jfy133 -modules/nf-core/prodigal/** @grst -modules/nf-core/prokka/** @rpetit3 -modules/nf-core/propr/logratio/** @suzannejin @oprana22 -modules/nf-core/propr/propd/** @suzannejin -modules/nf-core/proteus/readproteingroups/** @WackerO -modules/nf-core/pureclip/** @charlotteanne @marcjones -modules/nf-core/purecn/coverage/** @aldosr @lbeltrame -modules/nf-core/purecn/intervalfile/** @aldosr @lbeltrame -modules/nf-core/purecn/normaldb/** @aldosr @lbeltrame -modules/nf-core/purecn/run/** @aldosr @lbeltrame -modules/nf-core/purgedups/calcuts/** @mahesh-panchal -modules/nf-core/purgedups/getseqs/** @mahesh-panchal -modules/nf-core/purgedups/histplot/** @mahesh-panchal -modules/nf-core/purgedups/pbcstat/** @mahesh-panchal -modules/nf-core/purgedups/purgedups/** @mahesh-panchal -modules/nf-core/purgedups/splitfa/** @mahesh-panchal -modules/nf-core/pycoqc/** @joseespinosa @drpatelh -modules/nf-core/pydamage/analyze/** @maxibor -modules/nf-core/pydamage/filter/** @maxibor -modules/nf-core/pyrodigal/** @louperelo -modules/nf-core/qcat/** @yuukiiwa @drpatelh -modules/nf-core/qualimap/bamqccram/** @FriederikeHanssen -modules/nf-core/qualimap/bamqc/** @phue -modules/nf-core/qualimap/rnaseq/** @FriederikeHanssen -modules/nf-core/quast/** @drpatelh @kevinmenden -modules/nf-core/quilt/quilt/** @atrigila -modules/nf-core/racon/** @avantonder -modules/nf-core/rapidnj/** @aunderwo @avantonder -modules/nf-core/rasusa/** @thanhleviet -modules/nf-core/raven/** @fmalmeida -modules/nf-core/raxmlng/** @avantonder @aunderwo -modules/nf-core/rgi/main/** @rpetit3 @jfy133 -modules/nf-core/rhocall/annotate/** @ramprasadn -modules/nf-core/rmarkdownnotebook/** @grst -modules/nf-core/roary/** @rpetit3 -modules/nf-core/rsem/calculateexpression/** @drpatelh @kevinmenden -modules/nf-core/rsem/preparereference/** @drpatelh @kevinmenden -modules/nf-core/rseqc/bamstat/** @drpatelh @kevinmenden -modules/nf-core/rseqc/inferexperiment/** @drpatelh @kevinmenden -modules/nf-core/rseqc/innerdistance/** @drpatelh @kevinmenden -modules/nf-core/rseqc/junctionannotation/** @drpatelh @kevinmenden -modules/nf-core/rseqc/junctionsaturation/** @drpatelh @kevinmenden -modules/nf-core/rseqc/readdistribution/** @drpatelh @kevinmenden -modules/nf-core/rseqc/readduplication/** @drpatelh @kevinmenden -modules/nf-core/rseqc/tin/** @drpatelh -modules/nf-core/rtgtools/format/** @nvnieuwk -modules/nf-core/rtgtools/pedfilter/** @nvnieuwk -modules/nf-core/rtgtools/rocplot/** @nvnieuwk -modules/nf-core/rtgtools/vcfeval/** @nvnieuwk -modules/nf-core/salmon/index/** @kevinmenden @drpatelh -modules/nf-core/salmon/quant/** @kevinmenden @drpatelh -modules/nf-core/salsa2/** @scorreard -modules/nf-core/sam2lca/analyze/** @maxibor -modules/nf-core/sambamba/flagstat/** @kubranarci -modules/nf-core/sambamba/markdup/** @BioInf2305 -modules/nf-core/samblaster/** @lescai -modules/nf-core/samtools/ampliconclip/** @bjohnnyd -modules/nf-core/samtools/bam2fq/** @lescai -modules/nf-core/samtools/calmd/** @JackCurragh -modules/nf-core/samtools/cat/** @matthdsm -modules/nf-core/samtools/collatefastq/** @lescai @maxulysse @matthdsm -modules/nf-core/samtools/collate/** @priyanka-surana -modules/nf-core/samtools/convert/** @FriederikeHanssen @maxulysse -modules/nf-core/samtools/coverage/** @LouisLeNezet -modules/nf-core/samtools/depth/** @louperelo @nevinwu -modules/nf-core/samtools/dict/** @muffato -modules/nf-core/samtools/faidx/** @drpatelh @phue -modules/nf-core/samtools/fasta/** @priyanka-surana -modules/nf-core/samtools/fastq/** @priyanka-surana @suzannejin -modules/nf-core/samtools/fixmate/** @sppearce -modules/nf-core/samtools/flagstat/** @drpatelh -modules/nf-core/samtools/getrg/** @matthdsm -modules/nf-core/samtools/idxstats/** @drpatelh -modules/nf-core/samtools/import/** @matthdsm -modules/nf-core/samtools/index/** @drpatelh @maxulysse -modules/nf-core/samtools/markdup/** @priyanka-surana -modules/nf-core/samtools/merge/** @drpatelh @yuukiiwa @maxulysse @FriederikeHanssen @ramprasadn -modules/nf-core/samtools/mpileup/** @drpatelh @joseespinosa -modules/nf-core/samtools/reheader/** @louislenezet -modules/nf-core/samtools/sort/** @drpatelh -modules/nf-core/samtools/stats/** @drpatelh @FriederikeHanssen @ramprasadn -modules/nf-core/samtools/view/** @drpatelh @joseespinosa @FriederikeHanssen @priyanka-surana -modules/nf-core/scimap/mcmicro/** @luiskuhn -modules/nf-core/scoary/** @rpetit3 -modules/nf-core/scramble/clusteranalysis/** @nvnieuwk -modules/nf-core/scramble/clusteridentifier/** @nvnieuwk -modules/nf-core/seacr/callpeak/** @chris-cheshire -modules/nf-core/segemehl/align/** @BarryDigby -modules/nf-core/segemehl/index/** @BarryDigby -modules/nf-core/semibin/singleeasybin/** @BigDataBiology -modules/nf-core/sentieon/** @DonFreed -modules/nf-core/sentieon/applyvarcal/** @assp8200 -modules/nf-core/sentieon/bwaindex/** @drpatelh @maxulysse -modules/nf-core/sentieon/bwamem/** @asp8200 -modules/nf-core/sentieon/datametrics/** @ramprasadn -modules/nf-core/sentieon/dedup/** @asp8200 -modules/nf-core/sentieon/dnamodelapply/** @ramprasadn -modules/nf-core/sentieon/dnascope/** @ramprasadn -modules/nf-core/sentieon/gvcftyper/** @asp8200 -modules/nf-core/sentieon/haplotyper/** @asp8200 -modules/nf-core/sentieon/readwriter/** @ramprasadn -modules/nf-core/sentieon/tnhaplotyper2/** @asp8200 -modules/nf-core/sentieon/tnscope/** @ramprasadn -modules/nf-core/sentieon/varcal/** @asp8200 -modules/nf-core/sentieon/wgsmetrics/** @ramprasadn -modules/nf-core/seqkit/fx2tab/** @heuermh -modules/nf-core/seqkit/grep/** @Joon-Klaps -modules/nf-core/seqkit/pair/** @sateeshperi @mjcipriano @hseabolt -modules/nf-core/seqkit/replace/** @mjcipriano -modules/nf-core/seqkit/sliding/** @DLBPointon -modules/nf-core/seqkit/split2/** @FriederikeHanssen -modules/nf-core/seqkit/stats/** @Midnighter -modules/nf-core/seqkit/tab2fx/** @heuermh -modules/nf-core/seqsero2/** @rpetit3 -modules/nf-core/seqtk/cutn/** @DLBPointon -modules/nf-core/seqtk/mergepe/** @emnilsson -modules/nf-core/seqtk/rename/** @hseabolt @mjcipriano @sateeshperi -modules/nf-core/seqtk/sample/** @kaurravneet4123 @sidorov-si @adamrtalbot -modules/nf-core/seqtk/seq/** @hseabolt @mjcipriano @sateeshperi -modules/nf-core/seqtk/subseq/** @sidorov-si -modules/nf-core/sequencetools/pileupcaller/** @TCLamnidis -modules/nf-core/sequenzautils/bam2seqz/** @kaurravneet4123 -modules/nf-core/sequenzautils/gcwiggle/** @kaurravneet4123 -modules/nf-core/seqwish/induce/** @heuermh -modules/nf-core/seroba/run/** @rpetit3 -modules/nf-core/sexdeterrmine/** @TCLamnidis -modules/nf-core/sgdemux/** @nh13 @sam-white04 -modules/nf-core/shapeit5/ligate/** @louislenezet -modules/nf-core/shapeit5/phasecommon/** @LouisLeNezet -modules/nf-core/shapeit5/phaserare/** @LouisLeNezet -modules/nf-core/shapeit5/switch/** @LouisLeNezet -modules/nf-core/shasta/** @fmalmeida -modules/nf-core/shasum/** @matthdsm -modules/nf-core/shigatyper/** @rpetit3 -modules/nf-core/shigeifinder/** @rpetit3 -modules/nf-core/shinyngs/app/** @pinin4fjords -modules/nf-core/shinyngs/staticdifferential/** @pinin4fjords -modules/nf-core/shinyngs/staticexploratory/** @pinin4fjords -modules/nf-core/shinyngs/validatefomcomponents/** @pinin4fjords -modules/nf-core/shovill/** @rpetit3 -modules/nf-core/sickle/** @BioInf2305 -modules/nf-core/simpleaf/index/** @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords -modules/nf-core/simpleaf/quant/** @fmalmeida @maxulysse @Khajidu @apeltzer @pinin4fjords -modules/nf-core/sistr/** @rpetit3 -modules/nf-core/slimfastq/** @Midnighter -modules/nf-core/smncopynumbercaller/** @peterpru -modules/nf-core/smoothxg/** @heuermh, @subwaystation -modules/nf-core/smoove/call/** @scorreard @nvnieuwk -modules/nf-core/snakemake/** @adamrtalbot -modules/nf-core/snapaligner/align/** @matthdsm -modules/nf-core/snapaligner/index/** @matthdsm -modules/nf-core/sniffles/** @christopher-hakkaart @yuukiiwa -modules/nf-core/snippy/core/** @rpetit3 -modules/nf-core/snippy/run/** @rpetit3 -modules/nf-core/snpdists/** @abhi18av -modules/nf-core/snpeff/download/** @maxulysse -modules/nf-core/snpeff/snpeff/** @maxulysse -modules/nf-core/snpsift/annotate/** @LlaneroHiboreo -modules/nf-core/snpsift/dbnsfp/** @LlaneroHiboreo -modules/nf-core/snpsift/split/** @SusiJo @jonasscheid -modules/nf-core/snpsites/** @avantonder -modules/nf-core/somalier/ancestry/** @atrigila -modules/nf-core/somalier/extract/** @ashotmarg @nvnieuwk -modules/nf-core/somalier/relate/** @ashotmarg @nvnieuwk -modules/nf-core/sortmerna/** @drpatelh @mashehu -modules/nf-core/sourmash/compare/** @taylorreiter -modules/nf-core/sourmash/gather/** @vmikk @taylorreiter -modules/nf-core/sourmash/index/** @emnilsson -modules/nf-core/sourmash/sketch/** @Midnighter -modules/nf-core/sourmash/taxannotate/** @vmikk @taylorreiter -modules/nf-core/spaceranger/count/** @grst -modules/nf-core/spaceranger/mkgtf/** @grst -modules/nf-core/spaceranger/mkref/** @grst -modules/nf-core/spades/** @JoseEspinosa @drpatelh @d4straub -modules/nf-core/spatyper/** @rpetit3 -modules/nf-core/spring/compress/** @xec-cm -modules/nf-core/spring/decompress/** @xec-cm -modules/nf-core/sratools/fasterqdump/** @Midnighter -modules/nf-core/sratools/prefetch/** @Midnighter -modules/nf-core/srst2/srst2/** @jvhagey -modules/nf-core/ssuissero/** @rpetit3 -modules/nf-core/stadeniolib/scramble/** @matthdsm -modules/nf-core/staphopiasccmec/** @rpetit3 -modules/nf-core/star/align/** @kevinmenden @drpatelh @praveenraj2018 -modules/nf-core/star/genomegenerate/** @kevinmenden @drpatelh -modules/nf-core/star/starsolo/** @kevinmenden @ggabernet @grst @fmalmeida @rhreynolds @apeltzer @vivian-chen16 @maxulysse @joaodemeirelles -modules/nf-core/stecfinder/** @rpetit3 -modules/nf-core/stitch/** @saulpierotti -modules/nf-core/stranger/** @ljmesi -modules/nf-core/strelka/germline/** @arontommi -modules/nf-core/strelka/somatic/** @drpatelh -modules/nf-core/stringtie/merge/** @yuukiiwa -modules/nf-core/stringtie/stringtie/** @drpatelh -modules/nf-core/subread/featurecounts/** @ntoda03 -modules/nf-core/survivor/filter/** @LlaneroHiboreo -modules/nf-core/survivor/merge/** @nvnieuwk -modules/nf-core/survivor/simsv/** @nvnieuwk -modules/nf-core/svaba/** @kubranarci -modules/nf-core/svdb/merge/** @ramprasadn -modules/nf-core/svdb/query/** @ramprasadn -modules/nf-core/svtk/baftest/** @nvnieuwk -modules/nf-core/svtk/countsvtypes/** @nvnieuwk -modules/nf-core/svtk/rdtest2vcf/** @nvnieuwk -modules/nf-core/svtk/standardize/** @nvnieuwk -modules/nf-core/svtk/vcf2bed/** @nvnieuwk -modules/nf-core/svtyper/svtyper/** @kubranarci -modules/nf-core/tabix/bgzip/** @joseespinosa @drpatelh @maxulysse @nvnieuwk -modules/nf-core/tabix/bgziptabix/** @maxulysse @DLBPointon -modules/nf-core/tabix/tabix/** @joseespinosa @drpatelh @maxulysse -modules/nf-core/tailfindr/** @lucacozzuto -modules/nf-core/taxpasta/merge/** @sofstam @jfy133 -modules/nf-core/taxpasta/standardise/** @Midnighter -modules/nf-core/tbprofiler/profile/** @rpetit3 -modules/nf-core/tcoffee/align/** @luisas -modules/nf-core/tiara/tiara/** @prototaxites -modules/nf-core/tiddit/cov/** @projectoriented @ramprasadn -modules/nf-core/tiddit/sv/** @maxulysse -modules/nf-core/topas/gencons/** @aidaanva -modules/nf-core/transdecoder/longorf/** @Danilo2771 -modules/nf-core/transdecoder/predict/** @Danilo2771 -modules/nf-core/trimgalore/** @drpatelh @FelixKrueger -modules/nf-core/trimmomatic/** @alyssa-ab -modules/nf-core/trinity/** @timslittle -modules/nf-core/truvari/bench/** @nvnieuwk -modules/nf-core/ucsc/bedclip/** @drpatelh -modules/nf-core/ucsc/bedgraphtobigwig/** @drpatelh -modules/nf-core/ucsc/bedtobigbed/** @drpatelh -modules/nf-core/ucsc/bigwigaverageoverbed/** @jianhong -modules/nf-core/ucsc/gtftogenepred/** @BarryDigby @anoronh4 -modules/nf-core/ucsc/liftover/** @nebfield -modules/nf-core/ucsc/wigtobigwig/** @jianhong @projectoriented -modules/nf-core/ultra/align/** @sguizard -modules/nf-core/ultra/index/** @sguizard -modules/nf-core/ultra/pipeline/** @sguizard @lassefolkersen @ksahlin -modules/nf-core/ultraplex/** @CharlotteAnne @oscarwilkins @chris-cheshire @marc-jones @iraiosub @samirelanduk -modules/nf-core/umicollapse/** @CharlotteAnne @chris-cheshire -modules/nf-core/umitools/dedup/** @drpatelh @grst @klkeys -modules/nf-core/umitools/extract/** @drpatelh @grst -modules/nf-core/umitools/group/** @Joon-Klaps -modules/nf-core/unicycler/** @JoseEspinosa @drpatelh @d4straub -modules/nf-core/universc/** @kbattenb @tomkellygenetics -modules/nf-core/untarfiles/** @joseespinosa @drpatelh @matthdsm @jfy133 @pinin4fjords -modules/nf-core/untar/** @joseespinosa @drpatelh @matthdsm @jfy133 -modules/nf-core/unzipfiles/** @jfy133 @pinin4fjords -modules/nf-core/unzip/** @jfy133 -modules/nf-core/upd/** @hrydbeck -modules/nf-core/vardictjava/** @nvnieuwk -modules/nf-core/variantbam/** @bjohnnyd -modules/nf-core/varlociraptor/callvariants/** @FriederikeHanssen -modules/nf-core/varlociraptor/estimatealignmentproperties/** @FriederikeHanssen -modules/nf-core/varlociraptor/preprocess/** @FriederikeHanssen -modules/nf-core/vcf2db/** @nvnieuwk -modules/nf-core/vcf2maf/** @adamrtalbot -modules/nf-core/vcfanno/** @projectoriented @matthdsm -modules/nf-core/vcflib/vcfbreakmulti/** @lucpen -modules/nf-core/vcflib/vcffilter/** @zachary-foster -modules/nf-core/vcflib/vcfuniq/** @drpatelh -modules/nf-core/vcftools/** @Mark-S-Hill -modules/nf-core/verifybamid/verifybamid2/** @manifestoso -modules/nf-core/verifybamid/verifybamid/** @manifestoso -modules/nf-core/vg/construct/** @nvnieuwk -modules/nf-core/vg/deconstruct/** @heuermh, @subwaystation -modules/nf-core/vg/index/** @nvnieuwk -modules/nf-core/vrhyme/extractunbinned/** @CarsonJM -modules/nf-core/vrhyme/linkbins/** @CarsonJM -modules/nf-core/vrhyme/vrhyme/** @CarsonJM -modules/nf-core/vsearch/cluster/** @mirpedrol -modules/nf-core/vsearch/sintax/** @jtangrot -modules/nf-core/vsearch/sort/** @mirpedrol -modules/nf-core/vsearch/usearchglobal/** @jtangrot -modules/nf-core/vt/decompose/** @nvnieuwk -modules/nf-core/vt/normalize/** @nvnieuwk -modules/nf-core/wfmash/** @subwaystation -modules/nf-core/wgsim/** @priyanka-surana -modules/nf-core/whamg/** @nvnieuwk -modules/nf-core/windowmasker/convert/** @alxndrdiaz -modules/nf-core/windowmasker/mkcounts/** @DLBPointon -modules/nf-core/windowmasker/ustat/** @DLBPointon -modules/nf-core/wisecondorx/convert/** @nvnieuwk -modules/nf-core/wisecondorx/gender/** @nvnieuwk -modules/nf-core/wisecondorx/newref/** @nvnieuwk -modules/nf-core/wisecondorx/predict/** @nvnieuwk -modules/nf-core/yahs/** @ksenia-krasheninnikova -modules/nf-core/yara/index/** @apeltzer -modules/nf-core/yara/mapper/** @apeltzer -modules/nf-core/zip/** @jfy133 @pinin4fjords -subworkflows/nf-core/bam_cnv_wisecondorx/** @nvnieuwk -subworkflows/nf-core/bam_create_som_pon_gatk/** @GCJMackenzie -subworkflows/nf-core/bam_dedup_stats_samtools_umitools/** @drpatelh @KamilMaliszArdigen -subworkflows/nf-core/bam_docounts_contamination_angsd/** @scarlhoff -subworkflows/nf-core/bam_markduplicates_picard/** @dmarron @drpatelh -subworkflows/nf-core/bam_markduplicates_samtools/** @priyanka-surana -subworkflows/nf-core/bam_ngscheckmate/** @SPPearce -subworkflows/nf-core/bam_qc_picard/** @matthdsm -subworkflows/nf-core/bam_rseqc/** @drpatelh @kevinmenden -subworkflows/nf-core/bam_sort_stats_samtools/** @drpatelh -subworkflows/nf-core/bam_split_by_region/** @TCLamnidis -subworkflows/nf-core/bam_stats_samtools/** @drpatelh -subworkflows/nf-core/bam_tumor_normal_somatic_variant_calling_gatk/** @GCJMackenzie -subworkflows/nf-core/bam_tumor_only_somatic_variant_calling_gatk/** @GCJMackenzie -subworkflows/nf-core/bam_variant_calling_sort_freebayes_bcftools/** @priyanka-surana @FriederikeHanssen @ramprasadn -subworkflows/nf-core/bam_variant_demix_boot_freyja/** @Joon-Klaps -subworkflows/nf-core/bcl_demultiplex/** @matthdsm -subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/** @drpatelh @KamilMaliszArdigen -subworkflows/nf-core/bed_scatter_bedtools/** @nvnieuwk -subworkflows/nf-core/fasta_binning_concoct/** @jfy133 -subworkflows/nf-core/fasta_clean_fcs/** @scorreard -subworkflows/nf-core/fasta_index_dna/** @matthdsm @ramprasadn -subworkflows/nf-core/fasta_newick_epang_gappa/** @erikrikarddaniel -subworkflows/nf-core/fastq_align_bamcmp_bwa/** @sppearce -subworkflows/nf-core/fastq_align_bowtie2/** @drpatelh -subworkflows/nf-core/fastq_align_bwaaln/** @jfy133 -subworkflows/nf-core/fastq_align_bwa/** @JoseEspinosa -subworkflows/nf-core/fastq_align_chromap/** @JoseEspinosa -subworkflows/nf-core/fastq_align_dna/** @matthdsm -subworkflows/nf-core/fastq_align_hisat2/** @priyanka-surana -subworkflows/nf-core/fastq_align_star/** @JoseEspinosa -subworkflows/nf-core/fastq_contam_seqtk_kraken/** @apeltzer -subworkflows/nf-core/fastq_create_umi_consensus_fgbio/** @lescai -subworkflows/nf-core/fastq_download_prefetch_fasterqdump_sratools/** @Midnighter @drpatelh -subworkflows/nf-core/fastq_fastqc_umitools_fastp/** @robsyme -subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/** @drpatelh @KamilMaliszArdigen -subworkflows/nf-core/fastq_ngscheckmate/** @SPPearce -subworkflows/nf-core/fastq_subsample_fq_salmon/** @robsyme @drpatelh -subworkflows/nf-core/fastq_trim_fastp_fastqc/** @Joon-Klaps -subworkflows/nf-core/homer/groseq/** @edmundmiller -subworkflows/nf-core/initialise/** @adamrtalbot -subworkflows/nf-core/multiple_impute_glimpse2/** @LouisLeNezet -subworkflows/nf-core/utils_nextflow_pipeline/** @adamrtalbot @drpatelh -subworkflows/nf-core/utils_nf_core_pipeline/** @adamrtalbot @drpatelh -subworkflows/nf-core/utils_nf_validataion_pipeline/** @adamrtalbot @drpatelh -subworkflows/nf-core/vcf_annotate_ensemblvep/** @maxulysse @matthdsm @nvnieuwk -subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** @maxulysse @matthdsm @nvnieuwk -subworkflows/nf-core/vcf_annotate_snpeff/** @maxulysse -subworkflows/nf-core/vcf_extract_relate_somalier/** @nvnieuwk -subworkflows/nf-core/vcf_gather_bcftools/** @nvnieuwk -subworkflows/nf-core/vcf_impute_glimpse/** @LouisLeNezet -subworkflows/nf-core/vcf_phase_shapeit5/** @LouisLeNezet +modules/nf-core/preseq/ccurve/** @edmundmiller +modules/nf-core/preseq/lcextrap/** @edmundmiller +subworkflows/nf-core/homer/** @edmundmiller From 30a97c755895b7dfe40a730b0695c554a10f1cdd Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Mon, 7 Oct 2024 13:50:52 +0200 Subject: [PATCH 120/486] =?UTF-8?q?update=20star=20module=20to=20different?= =?UTF-8?q?iate=20.sortedByCoord.out.bam=20and=20.Align=E2=80=A6=20(#6661)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * update star module to differentiate .sortedByCoord.out.bam and .Aligned.sortedByCoord.out.bam * update star version * prettier * update tests for initial software versions * update test * update meta * fix linting * update snapshots * update nextflow.config * update nextflow.config * update nextflow.config * update nextflow.config * update nextflow.config * add docker config * add docker config * remove local docker config * remove local docker config --- modules/nf-core/star/align/main.nf | 33 +- modules/nf-core/star/align/meta.yml | 26 +- .../star/align/tests/main.nf.test.snap | 324 ++++++++++-------- .../star/align/tests/nextflow.arriba.config | 3 - .../nf-core/star/align/tests/nextflow.config | 3 - .../align/tests/nextflow.starfusion.config | 3 - .../fastq_align_star/tests/main.nf.test.snap | 144 ++++---- 7 files changed, 291 insertions(+), 245 deletions(-) diff --git a/modules/nf-core/star/align/main.nf b/modules/nf-core/star/align/main.nf index ae67e00403f1..b5bc9ddf8efc 100644 --- a/modules/nf-core/star/align/main.nf +++ b/modules/nf-core/star/align/main.nf @@ -21,33 +21,34 @@ process STAR_ALIGN { tuple val(meta), path('*Log.progress.out'), emit: log_progress path "versions.yml" , emit: versions - tuple val(meta), path('*d.out.bam') , optional:true, emit: bam - tuple val(meta), path('*sortedByCoord.out.bam') , optional:true, emit: bam_sorted - tuple val(meta), path('*toTranscriptome.out.bam'), optional:true, emit: bam_transcript - tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted - tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq - tuple val(meta), path('*.tab') , optional:true, emit: tab - tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab - tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab - tuple val(meta), path('*.out.junction') , optional:true, emit: junction - tuple val(meta), path('*.out.sam') , optional:true, emit: sam - tuple val(meta), path('*.wig') , optional:true, emit: wig - tuple val(meta), path('*.bg') , optional:true, emit: bedgraph + tuple val(meta), path('*d.out.bam') , optional:true, emit: bam + tuple val(meta), path("${prefix}.sortedByCoord.out.bam") , optional:true, emit: bam_sorted + tuple val(meta), path("${prefix}.Aligned.sortedByCoord.out.bam") , optional:true, emit: bam_sorted_aligned + tuple val(meta), path('*toTranscriptome.out.bam') , optional:true, emit: bam_transcript + tuple val(meta), path('*Aligned.unsort.out.bam') , optional:true, emit: bam_unsorted + tuple val(meta), path('*fastq.gz') , optional:true, emit: fastq + tuple val(meta), path('*.tab') , optional:true, emit: tab + tuple val(meta), path('*.SJ.out.tab') , optional:true, emit: spl_junc_tab + tuple val(meta), path('*.ReadsPerGene.out.tab') , optional:true, emit: read_per_gene_tab + tuple val(meta), path('*.out.junction') , optional:true, emit: junction + tuple val(meta), path('*.out.sam') , optional:true, emit: sam + tuple val(meta), path('*.wig') , optional:true, emit: wig + tuple val(meta), path('*.bg') , optional:true, emit: bedgraph when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def reads1 = [], reads2 = [] meta.single_end ? [reads].flatten().each{reads1 << it} : reads.eachWithIndex{ v, ix -> ( ix & 1 ? reads2 : reads1) << v } def ignore_gtf = star_ignore_sjdbgtf ? '' : "--sjdbGTFfile $gtf" def seq_platform = seq_platform ? "'PL:$seq_platform'" : "" def seq_center = seq_center ? "'CN:$seq_center'" : "" - def attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" + attrRG = args.contains("--outSAMattrRGline") ? "" : "--outSAMattrRGline 'ID:$prefix' $seq_center 'SM:$prefix' $seq_platform" def out_sam_type = (args.contains('--outSAMtype')) ? '' : '--outSAMtype BAM Unsorted' - def mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' + mv_unsorted_bam = (args.contains('--outSAMtype BAM Unsorted SortedByCoordinate')) ? "mv ${prefix}.Aligned.out.bam ${prefix}.Aligned.unsort.out.bam" : '' """ STAR \\ --genomeDir $index \\ @@ -79,7 +80,7 @@ process STAR_ALIGN { """ stub: - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ echo "" | gzip > ${prefix}.unmapped_1.fastq.gz echo "" | gzip > ${prefix}.unmapped_2.fastq.gz diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index d30556b515a9..d9cba2aa7042 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -100,10 +100,13 @@ output: type: file description: Sorted BAM file of read alignments (optional) pattern: "*sortedByCoord.out.bam" - - "*sortedByCoord.out.bam": + - ${prefix}.sortedByCoord.out.bam: type: file description: Sorted BAM file of read alignments (optional) pattern: "*sortedByCoord.out.bam" + - bam_sorted_aligned: + - meta: {} + - ${prefix}.Aligned.sortedByCoord.out.bam: {} - bam_transcript: - meta: type: file @@ -146,9 +149,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*.SJ.out.tab" - "*.SJ.out.tab": - type: file - description: STAR output splice junction tab file + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.SJ.out.tab" - read_per_gene_tab: - meta: @@ -156,9 +162,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*.ReadsPerGene.out.tab" - "*.ReadsPerGene.out.tab": - type: file - description: STAR output read per gene tab file + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.ReadsPerGene.out.tab" - junction: - meta: @@ -175,9 +184,12 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + pattern: "*.out.sam" - "*.out.sam": - type: file - description: STAR output SAM file + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] pattern: "*.out.sam" - wig: - meta: diff --git a/modules/nf-core/star/align/tests/main.nf.test.snap b/modules/nf-core/star/align/tests/main.nf.test.snap index c814eb56cbfd..0da28d37c6f6 100644 --- a/modules/nf-core/star/align/tests/main.nf.test.snap +++ b/modules/nf-core/star/align/tests/main.nf.test.snap @@ -26,7 +26,11 @@ "id": "test", "single_end": true }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -35,7 +39,7 @@ "id": "test", "single_end": true }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -44,7 +48,7 @@ "id": "test", "single_end": true }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -53,7 +57,7 @@ "id": "test", "single_end": true }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -62,10 +66,19 @@ "id": "test", "single_end": true }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -105,10 +118,7 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -117,7 +127,7 @@ "id": "test", "single_end": true }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -126,7 +136,7 @@ "id": "test", "single_end": true }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -135,10 +145,7 @@ "id": "test", "single_end": true }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -148,9 +155,8 @@ "single_end": true }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -173,10 +179,16 @@ "id": "test", "single_end": true }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": true + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -312,7 +324,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:04.712114" + "timestamp": "2024-10-01T11:39:15.440397" }, "homo_sapiens - paired_end - arriba - stub": { "content": [ @@ -341,7 +353,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -350,7 +366,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -359,7 +375,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -368,7 +384,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -377,10 +393,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -420,10 +445,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -432,7 +454,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -441,7 +463,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -450,10 +472,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -463,9 +482,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -488,10 +506,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -627,7 +651,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:28.874293" + "timestamp": "2024-10-01T11:40:15.472109" }, "homo_sapiens - single_end": { "content": [ @@ -644,13 +668,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": true - }, - "test.Aligned.sortedByCoord.out.bam:md5,c6cfaccaf91bc7fdabed3cfe236d4535" - ] + ], [ @@ -711,7 +729,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T18:02:34.35338" + "timestamp": "2024-10-01T11:23:08.001162" }, "homo_sapiens - paired_end": { "content": [ @@ -728,13 +746,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,b9ee1c607e07323bc1652ef3babb543f" - ] + ], [ @@ -795,7 +807,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T18:03:16.701923" + "timestamp": "2024-10-01T11:24:46.295219" }, "homo_sapiens - paired_end - multiple - stub": { "content": [ @@ -824,7 +836,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -833,7 +849,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -842,7 +858,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -851,7 +867,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -860,10 +876,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -903,10 +928,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -915,7 +937,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -924,7 +946,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -933,10 +955,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -946,9 +965,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -971,10 +989,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1110,7 +1134,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:51.360287" + "timestamp": "2024-10-01T11:41:07.310866" }, "homo_sapiens - paired_end - multiple": { "content": [ @@ -1127,13 +1151,7 @@ ] ], [ - [ - { - "id": "test", - "single_end": false - }, - "test.Aligned.sortedByCoord.out.bam:md5,ab07c21d63ab0a6c07d171d213c81d5a" - ] + ], [ @@ -1194,7 +1212,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:13:28.987438" + "timestamp": "2024-10-01T11:38:46.605044" }, "homo_sapiens - paired_end - stub": { "content": [ @@ -1223,7 +1241,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1232,7 +1254,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1241,7 +1263,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1250,7 +1272,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1259,10 +1281,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1302,10 +1333,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1314,7 +1342,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1323,7 +1351,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1332,10 +1360,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1345,9 +1370,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1370,10 +1394,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1509,7 +1539,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:16.798018" + "timestamp": "2024-10-01T11:39:51.595873" }, "homo_sapiens - paired_end - starfusion": { "content": [ @@ -1584,7 +1614,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:10:55.371956" + "timestamp": "2024-10-01T11:35:43.874508" }, "homo_sapiens - paired_end - arriba": { "content": [ @@ -1653,7 +1683,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T13:05:10.7534" + "timestamp": "2024-10-01T11:28:32.599223" }, "homo_sapiens - paired_end - starfusion - stub": { "content": [ @@ -1682,7 +1712,11 @@ "id": "test", "single_end": false }, - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + [ + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", + "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] ], "11": [ @@ -1691,7 +1725,7 @@ "id": "test", "single_end": false }, - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "12": [ @@ -1700,7 +1734,7 @@ "id": "test", "single_end": false }, - "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "13": [ @@ -1709,7 +1743,7 @@ "id": "test", "single_end": false }, - "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Chimeric.out.junction:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "14": [ @@ -1718,10 +1752,19 @@ "id": "test", "single_end": false }, - "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.out.sam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "15": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Signal.UniqueMultiple.str1.out.wig:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "16": [ [ { "id": "test", @@ -1761,10 +1804,7 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "6": [ @@ -1773,7 +1813,7 @@ "id": "test", "single_end": false }, - "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "7": [ @@ -1782,7 +1822,7 @@ "id": "test", "single_end": false }, - "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.toTranscriptome.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "8": [ @@ -1791,10 +1831,7 @@ "id": "test", "single_end": false }, - [ - "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", - "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" - ] + "test.Aligned.unsort.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "9": [ @@ -1804,9 +1841,8 @@ "single_end": false }, [ - "test.ReadsPerGene.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.SJ.out.tab:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.tab:md5,d41d8cd98f00b204e9800998ecf8427e" + "test.unmapped_1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test.unmapped_2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ] ], @@ -1829,10 +1865,16 @@ "id": "test", "single_end": false }, - [ - "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e", - "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" - ] + "test.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "bam_sorted_aligned": [ + [ + { + "id": "test", + "single_end": false + }, + "test.Aligned.sortedByCoord.out.bam:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "bam_transcript": [ @@ -1968,6 +2010,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.3" }, - "timestamp": "2024-07-22T15:16:40.64399" + "timestamp": "2024-10-01T11:40:42.29249" } } \ No newline at end of file diff --git a/modules/nf-core/star/align/tests/nextflow.arriba.config b/modules/nf-core/star/align/tests/nextflow.arriba.config index 2324b9e58fec..cf09323fc202 100644 --- a/modules/nf-core/star/align/tests/nextflow.arriba.config +++ b/modules/nf-core/star/align/tests/nextflow.arriba.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.config b/modules/nf-core/star/align/tests/nextflow.config index c4ac58088bbd..18bc2ee8a447 100644 --- a/modules/nf-core/star/align/tests/nextflow.config +++ b/modules/nf-core/star/align/tests/nextflow.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/modules/nf-core/star/align/tests/nextflow.starfusion.config b/modules/nf-core/star/align/tests/nextflow.starfusion.config index 467b64977c70..7880bfcf5073 100644 --- a/modules/nf-core/star/align/tests/nextflow.starfusion.config +++ b/modules/nf-core/star/align/tests/nextflow.starfusion.config @@ -9,6 +9,3 @@ process { } } - -// Fix chown issue for the output star folder -docker.runOptions = '--platform=linux/amd64 -u $(id -u):$(id -g)' diff --git a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap index 93a4329a202c..66f709b2060d 100644 --- a/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_align_star/tests/main.nf.test.snap @@ -61,15 +61,15 @@ "id": "test", "single_end": true }, - "test.sorted.bam.stats:md5,8e74b58e799fbf5082c39f98f14c3f46" + "test.sorted.bam.stats:md5,30abf517cda76c6a7468541781c4dd7a" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:58:48.537976" + "timestamp": "2024-10-02T12:47:34.744504" }, "bam_sorted_single_end": { "content": [ @@ -229,15 +229,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,ad0665b0f48b4374f21ca3dd6d3c0d88" + "test.sorted.bam.bai:md5,976fd845b520008692ad34ffad8ee285" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:59:42.224779" + "timestamp": "2024-10-02T12:48:46.014079" }, "stats_paired_end_with_transcriptome": { "content": [ @@ -247,15 +247,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,ba343720cd202366636bdb606c1361b9" + "test.sorted.bam.stats:md5,d7509941ffbfb221115faa2481115f23" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.630724" + "timestamp": "2024-10-02T12:49:58.005177" }, "tab_single_end": { "content": [ @@ -331,15 +331,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,40de55db306ef865530f939bbf9299d5" + "test.sorted.bam:md5,13558b77ef97e9ffb694c89eb3e6c147" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.533399" + "timestamp": "2024-10-02T12:51:14.677514" }, "bai_transcript_paired_end_with_transcriptome": { "content": [ @@ -349,15 +349,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,1dd687a38a2d7fb959272c659678a484" + "test.sorted.bam.bai:md5,db96436abfc1ab7d723717beb0f3df7e" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.813279" + "timestamp": "2024-10-02T12:49:58.119857" }, "bai_paired_end_with_transcriptome": { "content": [ @@ -367,15 +367,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,f4104865dd069f7b0922f94bd7b05b9f" + "test.sorted.bam.bai:md5,19b220e6a7d620f5f38418f82bd037e5" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.552294" + "timestamp": "2024-10-02T12:49:57.943382" }, "idxstats_transcript_paired_end": { "content": [ @@ -415,15 +415,15 @@ "id": "test", "single_end": true }, - "test.sorted.bam:md5,6c4beda83d0372cc3f16864e2f5990de" + "test.sorted.bam:md5,6d4390cf855abab0a98f959b31b78d79" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:58:48.479685" + "timestamp": "2024-10-02T12:47:34.424462" }, "idxstats_single_end": { "content": [ @@ -463,15 +463,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,ba860fb9ece9a136b262d4b7779c6a52" + "test.sorted.bam.stats:md5,10ca84181b17dafd7248296114f05333" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.911706" + "timestamp": "2024-10-02T12:49:58.210566" }, "orig_bam_transcript_paired_end_transcripts_no_transcriptome": { "content": [ @@ -535,15 +535,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,7dccfc9a0e8d530aa222dd8fde13c03e" + "test.sorted.bam:md5,b1a25c0b25f792c2c483c322f85b545d" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.714095" + "timestamp": "2024-10-02T12:49:58.059043" }, "fastq_single_end": { "content": [ @@ -565,15 +565,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,ba343720cd202366636bdb606c1361b9" + "test.sorted.bam.stats:md5,d7509941ffbfb221115faa2481115f23" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:59:42.341245" + "timestamp": "2024-10-02T12:48:46.139348" }, "flagstat_paired_end_with_transcriptome": { "content": [ @@ -619,15 +619,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,318219d2960e6ae1fdde8d3da0d4bb64" + "test.sorted.bam:md5,2b175d7c087679d22be5e4d6722acebd" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:00:38.477259" + "timestamp": "2024-10-02T12:49:57.88028" }, "flagstat_transcript_paired_end_transcripts_no_transcriptome": { "content": [ @@ -709,15 +709,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,ba343720cd202366636bdb606c1361b9" + "test.sorted.bam.stats:md5,d7509941ffbfb221115faa2481115f23" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.477062" + "timestamp": "2024-10-02T12:51:14.61369" }, "bai_transcript_paired_end_transcripts_no_transcriptome": { "content": [ @@ -727,15 +727,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,e6382105b52943a408505f25f27872b0" + "test.sorted.bam.bai:md5,06f3624daa0de1ec71cd3b45ef9e628f" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.58742" + "timestamp": "2024-10-02T12:51:14.73189" }, "orig_bam_single_end": { "content": [ @@ -781,15 +781,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,3758b81996c73509c052aac035530aaf" + "test.sorted.bam:md5,50f3b756671f700c51b584c4565b28e0" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:59:42.104272" + "timestamp": "2024-10-02T12:48:45.895658" }, "bam_paired_end_transcripts_no_transcriptome": { "content": [ @@ -799,15 +799,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam:md5,318219d2960e6ae1fdde8d3da0d4bb64" + "test.sorted.bam:md5,2b175d7c087679d22be5e4d6722acebd" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.363913" + "timestamp": "2024-10-02T12:51:14.499013" }, "stats_transcript_paired_end": { "content": [ @@ -841,15 +841,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.bai:md5,f4104865dd069f7b0922f94bd7b05b9f" + "test.sorted.bam.bai:md5,19b220e6a7d620f5f38418f82bd037e5" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.422582" + "timestamp": "2024-10-02T12:51:14.553177" }, "idxstats_paired_end_with_transcriptome": { "content": [ @@ -931,15 +931,15 @@ "id": "test", "single_end": false }, - "test.sorted.bam.stats:md5,625f0d8e29429337c7383d4d25814c6c" + "test.sorted.bam.stats:md5,10c63f09ff2b849443bafad71a824b0e" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T11:01:40.644021" + "timestamp": "2024-10-02T12:51:14.805201" }, "bam_sorted_paired_end_with_transcriptome": { "content": [ @@ -961,15 +961,15 @@ "id": "test", "single_end": true }, - "test.sorted.bam.bai:md5,73c7f3fe35663c287cb421f1c8b761ae" + "test.sorted.bam.bai:md5,b8c0e9281fa362e0dad93e2cd03445eb" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-01T14:09:07.343206" + "timestamp": "2024-10-02T12:47:34.635359" }, "fastq_paired_end": { "content": [ From b56ac062cb5fa01ef3d76a05f44cc9d6f0234140 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 7 Oct 2024 15:41:08 +0200 Subject: [PATCH 121/486] fix indentation in motus_preplong meta.yml (#6746) --- modules/nf-core/motus/preplong/meta.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/motus/preplong/meta.yml b/modules/nf-core/motus/preplong/meta.yml index 6ef63949a04d..4db88011ea23 100644 --- a/modules/nf-core/motus/preplong/meta.yml +++ b/modules/nf-core/motus/preplong/meta.yml @@ -42,9 +42,9 @@ output: pattern: "*.gz" - versions: - versions.yml: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@sofstam" From b924e697b272ae1b2deff9226dbd05039cad54f1 Mon Sep 17 00:00:00 2001 From: lmfaber <43934950+lmfaber@users.noreply.github.com> Date: Mon, 7 Oct 2024 16:30:35 +0200 Subject: [PATCH 122/486] Add jvarkit/sam2tsv (#6731) * Add jvarkit sam2tsv module * add keyword for searchability * Fix PR suggestions * Validate yaml files, run prettier, make regions file sample-based. * Apply suggestions from code review Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update test snapshot to reflect the whole module output. * Lint meta.yml with nf-core module lint jvarkit/sam2tsv --fix --------- Co-authored-by: Joris van Steenbrugge Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> --- .../nf-core/jvarkit/sam2tsv/environment.yml | 5 ++ modules/nf-core/jvarkit/sam2tsv/main.nf | 53 +++++++++++++ modules/nf-core/jvarkit/sam2tsv/meta.yml | 69 +++++++++++++++++ .../jvarkit/sam2tsv/tests/main.nf.test | 74 +++++++++++++++++++ .../jvarkit/sam2tsv/tests/main.nf.test.snap | 68 +++++++++++++++++ .../nf-core/jvarkit/sam2tsv/tests/tags.yml | 2 + 6 files changed, 271 insertions(+) create mode 100644 modules/nf-core/jvarkit/sam2tsv/environment.yml create mode 100644 modules/nf-core/jvarkit/sam2tsv/main.nf create mode 100644 modules/nf-core/jvarkit/sam2tsv/meta.yml create mode 100644 modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test create mode 100644 modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test.snap create mode 100644 modules/nf-core/jvarkit/sam2tsv/tests/tags.yml diff --git a/modules/nf-core/jvarkit/sam2tsv/environment.yml b/modules/nf-core/jvarkit/sam2tsv/environment.yml new file mode 100644 index 000000000000..013223af092f --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/environment.yml @@ -0,0 +1,5 @@ +channels: + - bioconda + - conda-forge +dependencies: + - "bioconda::jvarkit=2024.08.25" diff --git a/modules/nf-core/jvarkit/sam2tsv/main.nf b/modules/nf-core/jvarkit/sam2tsv/main.nf new file mode 100644 index 000000000000..fdc49cbd8bad --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/main.nf @@ -0,0 +1,53 @@ +process JVARKIT_SAM2TSV { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/jvarkit:2024.08.25--hdfd78af_1': + 'biocontainers/jvarkit:2024.08.25--hdfd78af_1' }" + + input: + tuple val(meta), path(bam), path(bai), path(regions_file) + tuple val(meta2), path(fasta), path(fasta_index), path(fasta_dict) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def regions_file = regions_file ? " --regions" + " '${regions_file}' " : "" + + """ + mkdir -p TMP + + jvarkit -Xmx1g -XX:-UsePerfData -Djava.io.tmpdir=TMP sam2tsv \\ + --reference "${fasta}" \\ + --output "${prefix}.tsv" \\ + ${args} \\ + ${regions_file} \\ + "${bam}" + rm -rf TMP + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch "${prefix}.tsv" + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + jvarkit: \$(jvarkit -v) + END_VERSIONS + """ +} diff --git a/modules/nf-core/jvarkit/sam2tsv/meta.yml b/modules/nf-core/jvarkit/sam2tsv/meta.yml new file mode 100644 index 000000000000..fe9a2b1cfc89 --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/meta.yml @@ -0,0 +1,69 @@ +name: "jvarkit_sam2tsv" +description: Convert sam files to tsv files +keywords: + - sam + - tsv + - jvarkit +tools: + - "jvarkit": + description: "Java utilities for Bioinformatics." + homepage: "https://github.com/lindenb/jvarkit" + documentation: "https://jvarkit.readthedocs.io/" + tool_dev_url: "https://github.com/lindenb/jvarkit" + doi: "10.6084/m9.figshare.1425030" + licence: ["MIT License"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - bam: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - regions_file: + type: file + description: Optional. Restrict to regions listed in a file + pattern: "*.{vcf,bed,gtf,gff,vcf.gz,bed.gz,gtf.gz,gff.gz}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [id: 'reference'] + - fasta: + type: file + description: Reference genome + pattern: "*.{fasta,fa}" + - fasta_index: + type: file + description: Reference genome information for fasta index + pattern: "*.{fasta.fai,fa.fai}" + - fasta_dict: + type: file + description: Reference genome information for fasta dict + pattern: "*.{.dict}" + +output: + - tsv: + - meta: + type: map + description: Groovy Map containing TSV information e.g. [ id:'test' ] + - "*.tsv": + type: file + description: Output file + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lmfaber" +maintainers: + - "@lmfaber" diff --git a/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test b/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test new file mode 100644 index 000000000000..cf1d05549f73 --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test @@ -0,0 +1,74 @@ +nextflow_process { + + name "Test Process JVARKIT_SAM2TSV" + script "../main.nf" + process "JVARKIT_SAM2TSV" + + tag "modules" + tag "modules_nfcore" + tag "jvarkit" + tag "jvarkit/sam2tsv" + + test("sarscov2 - tsv") { + + when { + process { + """ + input[0] =[ + [id:"tsv_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [id:"tsv_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.tsv[0][1]).text.startsWith("#Read-Name Flag")}, + { assert snapshot(process.out).match() + } + ) + } + } + + test("sarscov2 - tsv - stub") { + + options "-stub" + + when { + process { + """ + input[0] =[ + [id:"tsv_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + [] + ] + input[1] = [ + [id:"tsv_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.fai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.dict', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() + } + ) + } + } +} diff --git a/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test.snap b/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test.snap new file mode 100644 index 000000000000..6a13240a570d --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 - tsv": { + "content": [ + { + "0": [ + [ + { + "id": "tsv_test" + }, + "tsv_test.tsv:md5,6218e8d498160c442d2bde239878a4d1" + ] + ], + "1": [ + "versions.yml:md5,c628a51b7377878922ebd473c89ada95" + ], + "tsv": [ + [ + { + "id": "tsv_test" + }, + "tsv_test.tsv:md5,6218e8d498160c442d2bde239878a4d1" + ] + ], + "versions": [ + "versions.yml:md5,c628a51b7377878922ebd473c89ada95" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T13:09:35.31109992" + }, + "sarscov2 - tsv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "tsv_test" + }, + "tsv_test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,c628a51b7377878922ebd473c89ada95" + ], + "tsv": [ + [ + { + "id": "tsv_test" + }, + "tsv_test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,c628a51b7377878922ebd473c89ada95" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T13:09:45.395583956" + } +} \ No newline at end of file diff --git a/modules/nf-core/jvarkit/sam2tsv/tests/tags.yml b/modules/nf-core/jvarkit/sam2tsv/tests/tags.yml new file mode 100644 index 000000000000..c44a7dd33a74 --- /dev/null +++ b/modules/nf-core/jvarkit/sam2tsv/tests/tags.yml @@ -0,0 +1,2 @@ +jvarkit/sam2tsv: + - "modules/nf-core/jvarkit/sam2tsv/**" From f85452fcbebab5dfd77c0752236f6f86e9a03b32 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 7 Oct 2024 16:57:29 +0200 Subject: [PATCH 123/486] Don't use test scripts when the `-fisher` option has been given in vardictjava (#6747) * add option to run --fisher for vardict * use a check for the `-fisher` arg instead --- modules/nf-core/vardictjava/main.nf | 12 +-- .../nf-core/vardictjava/tests/main.nf.test | 77 ++++++++++++++++-- .../vardictjava/tests/main.nf.test.snap | 78 +++++++++++++++++-- .../nf-core/vardictjava/tests/nextflow.config | 3 + 4 files changed, 152 insertions(+), 18 deletions(-) create mode 100644 modules/nf-core/vardictjava/tests/nextflow.config diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 6329391c8376..a2c7666b5203 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -14,7 +14,7 @@ process VARDICTJAVA { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -25,9 +25,12 @@ process VARDICTJAVA { def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + // Don't run test scripts when -fisher has been used by vardictjava + def run_test = !args.contains("-fisher") + def somatic = bams instanceof List && bams.size() == 2 ? true : false def input = somatic ? "-b \"${bams[0]}|${bams[1]}\"" : "-b ${bams}" - def filter = somatic ? "testsomatic.R" : "teststrandbias.R" + def test = run_test ? somatic ? "| testsomatic.R" : "| teststrandbias.R" : "" def convert_to_vcf = somatic ? "var2vcf_paired.pl" : "var2vcf_valid.pl" """ export JAVA_OPTS='"-Xms${task.memory.toMega()/4}m" "-Xmx${task.memory.toGiga()}g" "-Dsamjdk.reference_fasta=${fasta}"' @@ -37,7 +40,7 @@ process VARDICTJAVA { -th ${task.cpus} \\ -G ${fasta} \\ ${bed} \\ - | ${filter} \\ + ${test} \\ | ${convert_to_vcf} \\ ${args2} \\ | bgzip ${args3} --threads ${task.cpus} > ${prefix}.vcf.gz @@ -50,9 +53,6 @@ process VARDICTJAVA { """ stub: - def args = task.ext.args ?: '-c 1 -S 2 -E 3' - def args2 = task.ext.args2 ?: '' - def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ diff --git a/modules/nf-core/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test index 8e5fec102669..31e1058cad8c 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test +++ b/modules/nf-core/vardictjava/tests/main.nf.test @@ -10,9 +10,6 @@ nextflow_process { test("homo_sapiens - [bam, bai, bed] - fasta - fai") { when { - params { - outdir = $outputDir - } process { """ input[0] = Channel.value([ @@ -47,9 +44,6 @@ nextflow_process { test("homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai") { when { - params { - outdir = $outputDir - } process { """ input[0] = Channel.value([ @@ -87,4 +81,75 @@ nextflow_process { } + test("homo_sapiens - [bam, bai, bed] - fasta - fai - fisher") { + + config "./nextflow.config" + when { + process { + """ + input[0] = Channel.value([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + input[1] = [ + [id:"ref"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:"ref"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + + + } + + } + + test("homo_sapiens - [bam, bai, bed] - fasta - fai - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.value([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true) + ]) + input[1] = [ + [id:"ref"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ] + input[2] = [ + [id:"ref"], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + + + } + + } + } diff --git a/modules/nf-core/vardictjava/tests/main.nf.test.snap b/modules/nf-core/vardictjava/tests/main.nf.test.snap index c32a68b74240..35674ed17820 100644 --- a/modules/nf-core/vardictjava/tests/main.nf.test.snap +++ b/modules/nf-core/vardictjava/tests/main.nf.test.snap @@ -27,10 +27,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T19:08:38.328190023" + "timestamp": "2024-10-07T16:05:15.117453312" }, "homo_sapiens - [[bam, bam], [bai, bai], bed] - fasta - fai": { "content": [ @@ -60,9 +60,75 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-04T19:08:54.416661915" + "timestamp": "2024-10-07T16:05:26.932438089" + }, + "homo_sapiens - [bam, bai, bed] - fasta - fai - fisher": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" + ] + ], + "1": [ + "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,e8411ecae49b4f6afa6ea0b681ea506e" + ] + ], + "versions": [ + "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T16:05:38.456816851" + }, + "homo_sapiens - [bam, bai, bed] - fasta - fai - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,6bf7aa0cbaac4a6e2acab2c475ec2389" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T16:05:48.440804849" } } \ No newline at end of file diff --git a/modules/nf-core/vardictjava/tests/nextflow.config b/modules/nf-core/vardictjava/tests/nextflow.config new file mode 100644 index 000000000000..c6e8571bd419 --- /dev/null +++ b/modules/nf-core/vardictjava/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = "-c 1 -S 2 -E 3 -fisher" +} \ No newline at end of file From e069b3a0bd4cd3917ef86053a0f95c76d8962e50 Mon Sep 17 00:00:00 2001 From: Delfina Terradas <155591053+delfiterradas@users.noreply.github.com> Date: Mon, 7 Oct 2024 12:57:35 -0300 Subject: [PATCH 124/486] Add seqkit translate (#6706) * TSeqkit tanslate module addedd * Started test * Add seqkit translate * Added seqkit/translate * Seqkit/translate meta.yml fix * Update modules/nf-core/seqkit/translate/environment.yml Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --------- Co-authored-by: dawn cj Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .../nf-core/seqkit/translate/environment.yml | 5 + modules/nf-core/seqkit/translate/main.nf | 62 ++++++ modules/nf-core/seqkit/translate/meta.yml | 47 ++++ .../seqkit/translate/tests/main.nf.test | 193 +++++++++++++++++ .../seqkit/translate/tests/main.nf.test.snap | 202 ++++++++++++++++++ 5 files changed, 509 insertions(+) create mode 100644 modules/nf-core/seqkit/translate/environment.yml create mode 100644 modules/nf-core/seqkit/translate/main.nf create mode 100644 modules/nf-core/seqkit/translate/meta.yml create mode 100644 modules/nf-core/seqkit/translate/tests/main.nf.test create mode 100644 modules/nf-core/seqkit/translate/tests/main.nf.test.snap diff --git a/modules/nf-core/seqkit/translate/environment.yml b/modules/nf-core/seqkit/translate/environment.yml new file mode 100644 index 000000000000..95584e3c48b0 --- /dev/null +++ b/modules/nf-core/seqkit/translate/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::seqkit=2.8.2" diff --git a/modules/nf-core/seqkit/translate/main.nf b/modules/nf-core/seqkit/translate/main.nf new file mode 100644 index 000000000000..2b6a60634f2d --- /dev/null +++ b/modules/nf-core/seqkit/translate/main.nf @@ -0,0 +1,62 @@ +process SEQKIT_TRANSLATE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqkit:2.8.2--h9ee0642_1': + 'biocontainers/seqkit:2.8.2--h9ee0642_1' }" + + input: + tuple val(meta), path(fastx) + + output: + tuple val(meta), path("${prefix}.*"), emit: fastx + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def extension = "fastq" + if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) { + extension = "fasta" + } + extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension + def call_gzip = extension.endsWith('.gz') ? "| gzip -c $args2" : '' + if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + seqkit \\ + translate \\ + --threads ${task.cpus} \\ + ${args} \\ + ${fastx} \\ + ${call_gzip} \\ + > ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$(seqkit version | cut -d' ' -f2) + END_VERSIONS + """ + + stub: + prefix = task.ext.prefix ?: "${meta.id}" + def extension = "fastq" + if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz|.+\.fsa|.+\.fsa.gz/ ) { + extension = "fasta" + } + extension = fastx.toString().endsWith('.gz') ? "${extension}.gz" : extension + if("${prefix}.${extension}" == "$fastx") error "Input and output names are the same, use \"task.ext.prefix\" to disambiguate!" + """ + touch ${prefix}.${extension} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqkit: \$(seqkit version | cut -d' ' -f2) + END_VERSIONS + """ +} diff --git a/modules/nf-core/seqkit/translate/meta.yml b/modules/nf-core/seqkit/translate/meta.yml new file mode 100644 index 000000000000..19e711bfbaa1 --- /dev/null +++ b/modules/nf-core/seqkit/translate/meta.yml @@ -0,0 +1,47 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "seqkit_translate" +description: Translate DNA/RNA to protein sequence +keywords: + - seqkit + - translate + - protein +tools: + - "seqkit": + description: "A cross-platform and ultrafast toolkit for FASTA/Q file manipulation" + homepage: "https://bioinf.shenwei.me/seqkit/" + documentation: "https://bioinf.shenwei.me/seqkit/usage/" + tool_dev_url: "https://github.com/shenwei356/seqkit" + doi: "10.1371/journal.pone.0163962" + licence: ["MIT"] + identifier: biotools:seqkit + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - fastx: + type: file + description: Input fasta/fastq file + pattern: "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]" +output: + - fastx: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1' ]` + - ${prefix}.*: + type: file + description: Translated fasta/fastq file + pattern: "*.{fna,fsa,fas,fa,fasta,fastq,fq}[.gz]" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@delfiterradas" +maintainers: + - "@delfiterradas" diff --git a/modules/nf-core/seqkit/translate/tests/main.nf.test b/modules/nf-core/seqkit/translate/tests/main.nf.test new file mode 100644 index 000000000000..de1547fbddf7 --- /dev/null +++ b/modules/nf-core/seqkit/translate/tests/main.nf.test @@ -0,0 +1,193 @@ +nextflow_process { + + name "Test Process SEQKIT_TRANSLATE" + script "../main.nf" + process "SEQKIT_TRANSLATE" + + tag "modules" + tag "modules_nfcore" + tag "seqkit" + tag "seqkit/translate" + + test("sarscov2 - genome_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - genome_fasta_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - test_1_fastq_gz") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - transcriptome_fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test'], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/transcriptome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 - bam - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("file_name_conflict-fail_with_error") { + when { + process { + """ + input[0] = [ + [ id:'test_1' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("Input and output names are the same") } + ) + } + + } + + test("sarscov2-genome_fasta-stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + + } + + test("file_name_conflict-fail_with_error-stub") { + + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'genome' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert !process.success }, + { assert process.stdout.toString().contains("Input and output names are the same") } + ) + } + + } + +} diff --git a/modules/nf-core/seqkit/translate/tests/main.nf.test.snap b/modules/nf-core/seqkit/translate/tests/main.nf.test.snap new file mode 100644 index 000000000000..68a27185c5fd --- /dev/null +++ b/modules/nf-core/seqkit/translate/tests/main.nf.test.snap @@ -0,0 +1,202 @@ +{ + "sarscov2 - genome_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fasta:md5,bbd96f0e48a0ef530d8535dd2e9dda2d" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test" + }, + "test.fasta:md5,bbd96f0e48a0ef530d8535dd2e9dda2d" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-27T14:11:33.440888698" + }, + "sarscov2 - bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fastq:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-20T15:24:19.344543763" + }, + "sarscov2-genome_fasta-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test" + }, + "test.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-27T13:58:35.061712261" + }, + "sarscov2 - transcriptome_fasta": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fasta:md5,8ace22c911902152e71043cf62661f1f" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test" + }, + "test.fasta:md5,8ace22c911902152e71043cf62661f1f" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-27T14:12:02.993246822" + }, + "sarscov2 - genome_fasta_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fasta.gz:md5,bbd96f0e48a0ef530d8535dd2e9dda2d" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test" + }, + "test.fasta.gz:md5,bbd96f0e48a0ef530d8535dd2e9dda2d" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-27T14:11:43.884810694" + }, + "sarscov2 - test_1_fastq_gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,c80e171f26a8c1f81c3b3f004d861b7a" + ] + ], + "1": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ], + "fastx": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,c80e171f26a8c1f81c3b3f004d861b7a" + ] + ], + "versions": [ + "versions.yml:md5,bf64d8d652a9b313153c953eab761f33" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-09-27T14:11:53.792592007" + } +} \ No newline at end of file From 58b4d685b1c93429917fec530f5d656aca3f2ef6 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Tue, 8 Oct 2024 06:15:32 +0200 Subject: [PATCH 125/486] Bump all GANON modules to 2.1.0 and fix build module (#6748) * Bump ganon to 2.1.0 and fix build module * Fix missing versions.yml in sanpshot * Fix classify tests --- .../nf-core/ganon/buildcustom/environment.yml | 2 +- modules/nf-core/ganon/buildcustom/main.nf | 33 ++++++++++--------- modules/nf-core/ganon/buildcustom/meta.yml | 7 ++++ .../ganon/buildcustom/tests/main.nf.test | 10 ++++-- .../ganon/buildcustom/tests/main.nf.test.snap | 19 ++++++++--- .../ganon/buildcustom/tests/nextflow.config | 5 +++ .../nf-core/ganon/classify/environment.yml | 2 +- modules/nf-core/ganon/classify/main.nf | 31 +++++++++-------- .../nf-core/ganon/classify/tests/main.nf.test | 18 +++++++--- .../ganon/classify/tests/main.nf.test.snap | 28 +++++++++++++--- .../ganon/classify/tests/nextflow.config | 5 +-- modules/nf-core/ganon/report/environment.yml | 2 +- modules/nf-core/ganon/report/main.nf | 13 ++++---- .../nf-core/ganon/report/tests/main.nf.test | 3 +- .../ganon/report/tests/main.nf.test.snap | 20 +++++++---- .../ganon/report/tests/nextflow.config | 3 ++ modules/nf-core/ganon/table/environment.yml | 2 +- modules/nf-core/ganon/table/main.nf | 13 ++++---- .../nf-core/ganon/table/tests/main.nf.test | 3 +- .../ganon/table/tests/main.nf.test.snap | 20 +++++++---- .../nf-core/ganon/table/tests/nextflow.config | 4 ++- 21 files changed, 159 insertions(+), 84 deletions(-) create mode 100644 modules/nf-core/ganon/buildcustom/tests/nextflow.config diff --git a/modules/nf-core/ganon/buildcustom/environment.yml b/modules/nf-core/ganon/buildcustom/environment.yml index 98f34de89e17..0e073d5ba75f 100644 --- a/modules/nf-core/ganon/buildcustom/environment.yml +++ b/modules/nf-core/ganon/buildcustom/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ganon=2.0.0 + - bioconda::ganon=2.1.0 diff --git a/modules/nf-core/ganon/buildcustom/main.nf b/modules/nf-core/ganon/buildcustom/main.nf index ac1c0eca1141..212e49f7f97d 100644 --- a/modules/nf-core/ganon/buildcustom/main.nf +++ b/modules/nf-core/ganon/buildcustom/main.nf @@ -1,21 +1,21 @@ process GANON_BUILDCUSTOM { - tag "$meta.id" + tag "${meta.id}" label 'process_high' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ganon:2.0.0--py39ha35b9be_0': - 'biocontainers/ganon:2.0.0--py39ha35b9be_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/ganon:2.1.0--py310hab1bfa5_1' + : 'biocontainers/ganon:2.1.0--py310hab1bfa5_1'}" input: tuple val(meta), path(input) + val input_type path taxonomy_files path genome_size_files output: - tuple val(meta), path("*.{hibf,ibf,tax}") , emit: db - tuple val(meta), path("*.info.tsv") , emit: info , optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.{hibf,ibf,tax}"), emit: db + tuple val(meta), path("*.info.tsv"), emit: info, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -23,17 +23,18 @@ process GANON_BUILDCUSTOM { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def taxonomy_args = taxonomy_files ? "--taxonomy-files ${taxonomy_files}" : "" - def genome_size_args = genome_size_files ? "--genome-size-files ${genome_size_files}" : "" + def input_cmd = input_type == 'fasta' ? "--input ${input}" : input_type == 'tsv' ? "--input-file ${input}" : error("Invalid input type: ${input_type}. Options: fasta, tsv") + def taxonomy_args = taxonomy_files ? "--taxonomy-files ${taxonomy_files}" : "" + def genome_size_args = genome_size_files ? "--genome-size-files ${genome_size_files}" : "" """ ganon \\ build-custom \\ --threads ${task.cpus} \\ - --input $input \\ + --input ${input} \\ --db-prefix ${prefix} \\ - $taxonomy_args \\ - $genome_size_args \\ - $args + ${taxonomy_args} \\ + ${genome_size_args} \\ + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -44,8 +45,8 @@ process GANON_BUILDCUSTOM { stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def taxonomy_args = taxonomy_files ? "--taxonomy-files ${taxonomy_files}" : "" - def genome_size_args = genome_size_files ? "--genome-size-files ${genome_size_files}" : "" + def taxonomy_args = taxonomy_files ? "--taxonomy-files ${taxonomy_files}" : "" + def genome_size_args = genome_size_files ? "--genome-size-files ${genome_size_files}" : "" """ touch ${prefix}.hibf touch ${prefix}.tax diff --git a/modules/nf-core/ganon/buildcustom/meta.yml b/modules/nf-core/ganon/buildcustom/meta.yml index 538fd21306d9..39bc07349adc 100644 --- a/modules/nf-core/ganon/buildcustom/meta.yml +++ b/modules/nf-core/ganon/buildcustom/meta.yml @@ -29,6 +29,13 @@ input: List of input FASTA files, or a directory containing input FASTA files. Note you must supply --input-extension via ext.args if FASTA extensions do not end in the default `fna.gz`. pattern: "*" + - - input_type: + type: string + description: | + Specify whether the file(s) given to the input channel are in FASTA format (and will be supplied as --input) + or in TSV format (and will be supplied as --input-file). For TSV format, the 'file' column should be just the + file name so that it's local to the working directory of this process. + pattern: "fasta|tsv" - - taxonomy_files: type: file description: Pre-downloaded taxonomy files of input sequences. See ganon docs diff --git a/modules/nf-core/ganon/buildcustom/tests/main.nf.test b/modules/nf-core/ganon/buildcustom/tests/main.nf.test index 3d97408bbdb4..8fa422780352 100644 --- a/modules/nf-core/ganon/buildcustom/tests/main.nf.test +++ b/modules/nf-core/ganon/buildcustom/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process GANON_BUILDCUSTOM" script "../main.nf" process "GANON_BUILDCUSTOM" + config "./nextflow.config" tag "modules" tag "modules_nfcore" @@ -18,8 +19,9 @@ nextflow_process { [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ] - input[1] = [] + input[1] = 'fasta' input[2] = [] + input[3] = [] """ } } @@ -28,7 +30,8 @@ nextflow_process { assertAll( { assert process.success }, { assert snapshot( - process.out.db.get(0).get(1).findAll { file(it).name != "test.tax" } + process.out.db.get(0).get(1).findAll { file(it).name != "test.tax" }, + process.out.versions ).match() }, { assert file(process.out.db.get(0).get(1).find { file(it).name == "test.tax" }).text.contains("MT192765.1") }, @@ -47,8 +50,9 @@ nextflow_process { [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ] - input[1] = [] + input[1] = 'fasta' input[2] = [] + input[3] = [] """ } } diff --git a/modules/nf-core/ganon/buildcustom/tests/main.nf.test.snap b/modules/nf-core/ganon/buildcustom/tests/main.nf.test.snap index d1d2b18ee6be..2c3243ffbdc4 100644 --- a/modules/nf-core/ganon/buildcustom/tests/main.nf.test.snap +++ b/modules/nf-core/ganon/buildcustom/tests/main.nf.test.snap @@ -22,7 +22,7 @@ ] ], "2": [ - "versions.yml:md5,644b8508be28bf66eb6e66ef12be858c" + "versions.yml:md5,9c73293ae36914c6ce3718ad6728ad9e" ], "db": [ [ @@ -44,18 +44,29 @@ ] ], "versions": [ - "versions.yml:md5,644b8508be28bf66eb6e66ef12be858c" + "versions.yml:md5,9c73293ae36914c6ce3718ad6728ad9e" ] } ], - "timestamp": "2024-01-10T15:15:49.270265503" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T17:00:22.98042261" }, "sarscov2 - genome fasta": { "content": [ [ "test.hibf:md5,d10fe6fc6d198696bc15ca85a1459614" + ], + [ + "versions.yml:md5,9c73293ae36914c6ce3718ad6728ad9e" ] ], - "timestamp": "2024-01-10T15:15:44.000168145" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T19:03:25.060306554" } } \ No newline at end of file diff --git a/modules/nf-core/ganon/buildcustom/tests/nextflow.config b/modules/nf-core/ganon/buildcustom/tests/nextflow.config new file mode 100644 index 000000000000..a12988eee894 --- /dev/null +++ b/modules/nf-core/ganon/buildcustom/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: GANON_BUILDCUSTOM { + ext.args = "--input-target sequence" + } +} diff --git a/modules/nf-core/ganon/classify/environment.yml b/modules/nf-core/ganon/classify/environment.yml index 98f34de89e17..0e073d5ba75f 100644 --- a/modules/nf-core/ganon/classify/environment.yml +++ b/modules/nf-core/ganon/classify/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ganon=2.0.0 + - bioconda::ganon=2.1.0 diff --git a/modules/nf-core/ganon/classify/main.nf b/modules/nf-core/ganon/classify/main.nf index d6db825e9bb5..65ee6765244f 100644 --- a/modules/nf-core/ganon/classify/main.nf +++ b/modules/nf-core/ganon/classify/main.nf @@ -1,24 +1,23 @@ process GANON_CLASSIFY { - tag "$meta.id" + tag "${meta.id}" label 'process_high' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ganon:2.0.0--py39ha35b9be_0': - 'biocontainers/ganon:2.0.0--py39ha35b9be_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/ganon:2.1.0--py310hab1bfa5_1' + : 'biocontainers/ganon:2.1.0--py310hab1bfa5_1'}" input: - tuple val(meta) , path(fastqs) - path(db) + tuple val(meta), path(fastqs) + path db output: tuple val(meta), path("*.tre"), emit: tre tuple val(meta), path("*.rep"), emit: report - tuple val(meta), path("*.one"), emit: one , optional: true - tuple val(meta), path("*.all"), emit: all , optional: true - tuple val(meta), path("*.unc"), emit: unc , optional: true + tuple val(meta), path("*.one"), emit: one, optional: true + tuple val(meta), path("*.all"), emit: all, optional: true + tuple val(meta), path("*.unc"), emit: unc, optional: true tuple val(meta), path("*.log"), emit: log - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -26,17 +25,17 @@ process GANON_CLASSIFY { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}" + def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}" """ dbprefix=\$(find -L . -name '*.*ibf' | sed 's/\\.h\\?ibf\$//') ganon \\ classify \\ --db-prefix \${dbprefix%%.*ibf} \\ - $args \\ - --threads $task.cpus \\ + ${args} \\ + --threads ${task.cpus} \\ --output-prefix ${prefix} \\ - $input \ + ${input} \ 2>&1 | tee ${prefix}.log cat <<-END_VERSIONS > versions.yml @@ -48,7 +47,7 @@ process GANON_CLASSIFY { stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}" + def input = meta.single_end ? "--single-reads ${fastqs}" : "--paired-reads ${fastqs}" """ touch ${prefix}.tre touch ${prefix}.rep diff --git a/modules/nf-core/ganon/classify/tests/main.nf.test b/modules/nf-core/ganon/classify/tests/main.nf.test index e581ca065eb7..40ea069e7821 100644 --- a/modules/nf-core/ganon/classify/tests/main.nf.test +++ b/modules/nf-core/ganon/classify/tests/main.nf.test @@ -20,8 +20,9 @@ nextflow_process { [ id:'test' ], // meta map file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true), ] - input[1] = [] + input[1] = 'fasta' input[2] = [] + input[3] = [] """ } } @@ -46,8 +47,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.tre, - process.out.report).match()}, + { assert snapshot( + process.out.tre, + process.out.report, + process.out.versions + ).match()}, { assert file(process.out.log[0][1]).text.contains("Total elapsed time:") } ) } @@ -74,8 +78,12 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.tre, - process.out.report).match()}, + { assert snapshot( + process.out.tre, + process.out.report, + process.out.versions + ).match() + }, { assert file(process.out.log[0][1]).text.contains("Total elapsed time:") } ) } diff --git a/modules/nf-core/ganon/classify/tests/main.nf.test.snap b/modules/nf-core/ganon/classify/tests/main.nf.test.snap index 40b36b14fcc2..1006fc57e5b5 100644 --- a/modules/nf-core/ganon/classify/tests/main.nf.test.snap +++ b/modules/nf-core/ganon/classify/tests/main.nf.test.snap @@ -57,7 +57,7 @@ ] ], "6": [ - "versions.yml:md5,e13af9e126ff4a9ea7ee4b706fbbc0bb" + "versions.yml:md5,7c113ab3c2c1ea32c9f27ceef48db17a" ], "all": [ [ @@ -114,11 +114,15 @@ ] ], "versions": [ - "versions.yml:md5,e13af9e126ff4a9ea7ee4b706fbbc0bb" + "versions.yml:md5,7c113ab3c2c1ea32c9f27ceef48db17a" ] } ], - "timestamp": "2024-01-06T15:08:06.626813557" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T17:06:22.835846753" }, "sarscov2 paired-end [fastq]": { "content": [ @@ -139,9 +143,16 @@ }, "test.rep:md5,757e5cbf7a978913277401285d743336" ] + ], + [ + "versions.yml:md5,7c113ab3c2c1ea32c9f27ceef48db17a" ] ], - "timestamp": "2024-01-06T15:07:49.528458193" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T19:26:16.339673954" }, "sarscov2 single-end [fastq]": { "content": [ @@ -162,8 +173,15 @@ }, "test.rep:md5,9b5f8051aa459a80a678e36259a15746" ] + ], + [ + "versions.yml:md5,7c113ab3c2c1ea32c9f27ceef48db17a" ] ], - "timestamp": "2024-01-06T15:07:12.092925016" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T19:25:41.074523387" } } \ No newline at end of file diff --git a/modules/nf-core/ganon/classify/tests/nextflow.config b/modules/nf-core/ganon/classify/tests/nextflow.config index 18712875d15f..56bec927bd34 100644 --- a/modules/nf-core/ganon/classify/tests/nextflow.config +++ b/modules/nf-core/ganon/classify/tests/nextflow.config @@ -1,7 +1,8 @@ process { - + withName: GANON_BUILDCUSTOM { + ext.args = "--input-target sequence" + } withName: GANON_CLASSIFY { ext.args = "--output-one --output-all --output-unclassified" } - } diff --git a/modules/nf-core/ganon/report/environment.yml b/modules/nf-core/ganon/report/environment.yml index 98f34de89e17..0e073d5ba75f 100644 --- a/modules/nf-core/ganon/report/environment.yml +++ b/modules/nf-core/ganon/report/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ganon=2.0.0 + - bioconda::ganon=2.1.0 diff --git a/modules/nf-core/ganon/report/main.nf b/modules/nf-core/ganon/report/main.nf index 2b1998f154aa..3f520de0e7bc 100644 --- a/modules/nf-core/ganon/report/main.nf +++ b/modules/nf-core/ganon/report/main.nf @@ -1,11 +1,10 @@ process GANON_REPORT { - tag "$meta.id" + tag "${meta.id}" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ganon:2.0.0--py39ha35b9be_0': - 'biocontainers/ganon:2.0.0--py39ha35b9be_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/ganon:2.1.0--py310hab1bfa5_1' + : 'biocontainers/ganon:2.1.0--py310hab1bfa5_1'}" input: tuple val(meta), path(rep) @@ -13,7 +12,7 @@ process GANON_REPORT { output: tuple val(meta), path("*.tre"), emit: tre - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -30,7 +29,7 @@ process GANON_REPORT { --input ${rep} \\ --output-prefix ${prefix} \\ --db-prefix \${dbprefix%%.*ibf} \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ganon/report/tests/main.nf.test b/modules/nf-core/ganon/report/tests/main.nf.test index d350eed066b9..e6437b498bcb 100644 --- a/modules/nf-core/ganon/report/tests/main.nf.test +++ b/modules/nf-core/ganon/report/tests/main.nf.test @@ -21,8 +21,9 @@ nextflow_process { [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), ] - input[1] = [] + input[1] = 'fasta' input[2] = [] + input[3] = [] """ } } diff --git a/modules/nf-core/ganon/report/tests/main.nf.test.snap b/modules/nf-core/ganon/report/tests/main.nf.test.snap index abad8035e3f3..ee248e7d1737 100644 --- a/modules/nf-core/ganon/report/tests/main.nf.test.snap +++ b/modules/nf-core/ganon/report/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,7219068902254fbc97f84e8e163213d0" + "versions.yml:md5,e405868d6136de433a8ddbd8e6e3333d" ], "tre": [ [ @@ -24,11 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,7219068902254fbc97f84e8e163213d0" + "versions.yml:md5,e405868d6136de433a8ddbd8e6e3333d" ] } ], - "timestamp": "2024-01-06T18:50:07.439069779" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T17:09:42.438141974" }, "sarscov2 single-end [fastq]": { "content": [ @@ -43,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,7219068902254fbc97f84e8e163213d0" + "versions.yml:md5,e405868d6136de433a8ddbd8e6e3333d" ], "tre": [ [ @@ -55,10 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,7219068902254fbc97f84e8e163213d0" + "versions.yml:md5,e405868d6136de433a8ddbd8e6e3333d" ] } ], - "timestamp": "2024-01-06T18:49:52.505817066" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T18:32:50.997968794" } } \ No newline at end of file diff --git a/modules/nf-core/ganon/report/tests/nextflow.config b/modules/nf-core/ganon/report/tests/nextflow.config index e6dd3131e9f2..96982fa83310 100644 --- a/modules/nf-core/ganon/report/tests/nextflow.config +++ b/modules/nf-core/ganon/report/tests/nextflow.config @@ -1,4 +1,7 @@ process { + withName: GANON_BUILDCUSTOM { + ext.args = "--input-target sequence" + } withName: GANON_CLASSIFY { ext.args = "--output-one --output-all --output-unclassified" } diff --git a/modules/nf-core/ganon/table/environment.yml b/modules/nf-core/ganon/table/environment.yml index 98f34de89e17..0e073d5ba75f 100644 --- a/modules/nf-core/ganon/table/environment.yml +++ b/modules/nf-core/ganon/table/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ganon=2.0.0 + - bioconda::ganon=2.1.0 diff --git a/modules/nf-core/ganon/table/main.nf b/modules/nf-core/ganon/table/main.nf index d8f247c151da..1e3fca6b4537 100644 --- a/modules/nf-core/ganon/table/main.nf +++ b/modules/nf-core/ganon/table/main.nf @@ -1,18 +1,17 @@ process GANON_TABLE { - tag "$meta.id" + tag "${meta.id}" label 'process_single' - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ganon:2.0.0--py39ha35b9be_0': - 'biocontainers/ganon:2.0.0--py39ha35b9be_0' }" + container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/ganon:2.1.0--py310hab1bfa5_1' + : 'biocontainers/ganon:2.1.0--py310hab1bfa5_1'}" input: tuple val(meta), path(tre) output: tuple val(meta), path("*.txt"), emit: txt - path "versions.yml" , emit: versions + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when @@ -25,7 +24,7 @@ process GANON_TABLE { table \\ --input ${tre} \\ --output-file ${prefix}.txt \\ - $args + ${args} cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/ganon/table/tests/main.nf.test b/modules/nf-core/ganon/table/tests/main.nf.test index 43b6cf0a1d11..9aae4ead0c5d 100644 --- a/modules/nf-core/ganon/table/tests/main.nf.test +++ b/modules/nf-core/ganon/table/tests/main.nf.test @@ -22,8 +22,9 @@ nextflow_process { [ id:'test' ], // meta map file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), ] - input[1] = [] + input[1] = 'fasta' input[2] = [] + input[3] = [] """ } } diff --git a/modules/nf-core/ganon/table/tests/main.nf.test.snap b/modules/nf-core/ganon/table/tests/main.nf.test.snap index 2c5c312d0c72..2346f7a713c7 100644 --- a/modules/nf-core/ganon/table/tests/main.nf.test.snap +++ b/modules/nf-core/ganon/table/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,1cec68ee4a3dcc057d475497732b72c1" + "versions.yml:md5,6a8b6c7a69b2bdd5490414f3352b5a7d" ], "txt": [ [ @@ -22,11 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,1cec68ee4a3dcc057d475497732b72c1" + "versions.yml:md5,6a8b6c7a69b2bdd5490414f3352b5a7d" ] } ], - "timestamp": "2024-01-07T14:27:58.631022945" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T17:13:04.938896022" }, "sarscov2 single-end [fastq]": { "content": [ @@ -40,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,1cec68ee4a3dcc057d475497732b72c1" + "versions.yml:md5,6a8b6c7a69b2bdd5490414f3352b5a7d" ], "txt": [ [ @@ -51,10 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,1cec68ee4a3dcc057d475497732b72c1" + "versions.yml:md5,6a8b6c7a69b2bdd5490414f3352b5a7d" ] } ], - "timestamp": "2024-01-07T14:27:37.318272937" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-07T18:33:41.271256635" } } \ No newline at end of file diff --git a/modules/nf-core/ganon/table/tests/nextflow.config b/modules/nf-core/ganon/table/tests/nextflow.config index 26114b4cf7bb..e6d793577897 100644 --- a/modules/nf-core/ganon/table/tests/nextflow.config +++ b/modules/nf-core/ganon/table/tests/nextflow.config @@ -1,11 +1,13 @@ process { + withName: GANON_BUILDCUSTOM { + ext.args = "--input-target sequence" + } withName: GANON_CLASSIFY { ext.args = "--output-one --output-all --output-unclassified" } withName: GANON_REPORT { ext.args = "--report-type reads --output-format tsv" } - withName: GANON_TABLE { ext.args = "--output-format tsv --output-value percentages" } From fcbacea597a35899fada99e82170b9a5f8d16faf Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Tue, 8 Oct 2024 08:12:40 +0200 Subject: [PATCH 126/486] Update GitHub Actions (#6750) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/fix-linting.yml | 2 +- .github/workflows/test.yml | 26 +++++++++++++------------- 2 files changed, 14 insertions(+), 14 deletions(-) diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index c0c0e4bd36e8..30bfcffb8ec8 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -14,7 +14,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: token: ${{ secrets.nf_core_bot_auth_token }} diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 8be6d86d95de..a50fd46f895b 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -29,7 +29,7 @@ jobs: pre-commit: runs-on: ubuntu-latest steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 # FIXME Flip this off once we get to less than a couple hundred. Adding @@ -42,7 +42,7 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out repository - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Install NodeJS uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 @@ -58,7 +58,7 @@ jobs: editorconfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - uses: actions/setup-node@0a44ba7841725637a19e28fa30b79a866c81b0a6 # v4 with: @@ -78,7 +78,7 @@ jobs: modules: ${{ steps.tags.outputs.modules }} subworkflows: ${{ steps.tags.outputs.subworkflows }} steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: fetch-depth: 2 # To retrieve the preceding commit. @@ -111,7 +111,7 @@ jobs: # Prod for version bumping steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 with: fetch-depth: 0 @@ -148,14 +148,14 @@ jobs: "${{ fromJson(needs.nf-test-changes.outputs.modules) }}", ] steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.11" - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 id: cache-pip with: path: ~/.cache/pip @@ -194,7 +194,7 @@ jobs: "${{ fromJson(needs.nf-test-changes.outputs.subworkflows) }}", ] steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 @@ -398,14 +398,14 @@ jobs: NXF_ANSI_LOG: false steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - name: Set up Python uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5 with: python-version: "3.11" - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 id: cache-pip-pytest with: path: ~/.cache/pip @@ -472,7 +472,7 @@ jobs: - name: Upload logs on failure if: failure() - uses: actions/upload-artifact@50769540e7f4bd5e21e526ee35c689e35e0d6874 # v4 + uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4 with: name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} path: | @@ -653,7 +653,7 @@ jobs: SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} steps: - - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 + - uses: actions/checkout@eef61447b9ff4aafe5dcd4e0bbf5d482be7e7871 # v4 - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 with: @@ -682,7 +682,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 + - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 id: cache-pip-pdiff with: path: ~/.cache/pip From f85dbddd7a335fc0f5ac331e8d22ca94123b654b Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Tue, 8 Oct 2024 10:03:50 +0200 Subject: [PATCH 127/486] add index to bcftools filter input to enable region filtering (#6751) add index to bcftools filter input --- modules/nf-core/bcftools/filter/main.nf | 2 +- modules/nf-core/bcftools/filter/meta.yml | 4 ++ .../bcftools/filter/tests/main.nf.test | 52 +++++++++++++++---- .../bcftools/filter/tests/main.nf.test.snap | 45 ++++++++++++++++ .../filter/tests/region_filter.config | 4 ++ 5 files changed, 97 insertions(+), 10 deletions(-) create mode 100644 modules/nf-core/bcftools/filter/tests/region_filter.config diff --git a/modules/nf-core/bcftools/filter/main.nf b/modules/nf-core/bcftools/filter/main.nf index 8f92c51a2e29..36cbf8c2be26 100644 --- a/modules/nf-core/bcftools/filter/main.nf +++ b/modules/nf-core/bcftools/filter/main.nf @@ -8,7 +8,7 @@ process BCFTOOLS_FILTER { 'biocontainers/bcftools:1.20--h8b25389_0' }" input: - tuple val(meta), path(vcf) + tuple val(meta), path(vcf), path(tbi) output: tuple val(meta), path("*.${extension}"), emit: vcf diff --git a/modules/nf-core/bcftools/filter/meta.yml b/modules/nf-core/bcftools/filter/meta.yml index 8ac594fc2225..d72f27554e9f 100644 --- a/modules/nf-core/bcftools/filter/meta.yml +++ b/modules/nf-core/bcftools/filter/meta.yml @@ -23,6 +23,10 @@ input: type: file description: VCF input file pattern: "*.{vcf,bcf,vcf.gz,bcf.gz}" + - tbi: + type: file + description: VCF index file + pattern: "*.tbi" output: - vcf: - meta: diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test b/modules/nf-core/bcftools/filter/tests/main.nf.test index 646f37adaec7..fadff0e30e2a 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test @@ -18,7 +18,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -42,7 +43,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -72,7 +74,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -102,7 +105,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -132,7 +136,8 @@ nextflow_process { """ input[0] = [ [id:"bcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -147,6 +152,31 @@ nextflow_process { } + test("sarscov2 - vcf.gz, tbi - region filter") { + + config "./region_filter.config" + + when { + process { + """ + input[0] = [ + [id:"bcf_test"], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match("region filter") } + ) + } + + } + test("sarscov2 - vcf - stub") { config "./nextflow.config" @@ -157,7 +187,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -182,7 +213,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -208,7 +240,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } @@ -234,7 +267,8 @@ nextflow_process { """ input[0] = [ [id:"vcf_test"], - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + [] ] """ } diff --git a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap index 3d7605f2665a..640907e42097 100644 --- a/modules/nf-core/bcftools/filter/tests/main.nf.test.snap +++ b/modules/nf-core/bcftools/filter/tests/main.nf.test.snap @@ -1,4 +1,49 @@ { + "region filter": { + "content": [ + { + "0": [ + [ + { + "id": "bcf_test" + }, + "bcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ], + "csi": [ + + ], + "tbi": [ + + ], + "vcf": [ + [ + { + "id": "bcf_test" + }, + "bcf_test_vcf.vcf.gz:md5,8e722884ffb75155212a3fc053918766" + ] + ], + "versions": [ + "versions.yml:md5,9a336d1ee26b527d7a2bdbeead155f64" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T09:14:47.394005264" + }, "sarscov2 - vcf_gz_index_tbi - stub": { "content": [ { diff --git a/modules/nf-core/bcftools/filter/tests/region_filter.config b/modules/nf-core/bcftools/filter/tests/region_filter.config new file mode 100644 index 000000000000..b18fb4bf0dae --- /dev/null +++ b/modules/nf-core/bcftools/filter/tests/region_filter.config @@ -0,0 +1,4 @@ +process { + ext.prefix = { "${meta.id}_vcf" } + ext.args = "--output-type z -r MT192765.1 --no-version" +} From b7800db9b069ed505db3f9d91b8c72faea9be17b Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 8 Oct 2024 13:22:31 +0200 Subject: [PATCH 128/486] add tests for multiple input files (#6752) * add tests for multiple input files * align * capture header and readsMD5 * no need to capture header/readsMD5 --- modules/nf-core/samtools/sort/main.nf | 10 +- .../nf-core/samtools/sort/tests/main.nf.test | 64 ++++++++++++ .../samtools/sort/tests/main.nf.test.snap | 99 ++++++++++++++++++- 3 files changed, 166 insertions(+), 7 deletions(-) diff --git a/modules/nf-core/samtools/sort/main.nf b/modules/nf-core/samtools/sort/main.nf index acfd9252ce4a..caf3c61a87d0 100644 --- a/modules/nf-core/samtools/sort/main.nf +++ b/modules/nf-core/samtools/sort/main.nf @@ -12,11 +12,11 @@ process SAMTOOLS_SORT { tuple val(meta2), path(fasta) output: - tuple val(meta), path("*.bam"), emit: bam, optional: true - tuple val(meta), path("*.cram"), emit: cram, optional: true - tuple val(meta), path("*.crai"), emit: crai, optional: true - tuple val(meta), path("*.csi"), emit: csi, optional: true - path "versions.yml" , emit: versions + tuple val(meta), path("*.bam"), emit: bam, optional: true + tuple val(meta), path("*.cram"), emit: cram, optional: true + tuple val(meta), path("*.crai"), emit: crai, optional: true + tuple val(meta), path("*.csi"), emit: csi, optional: true + path "versions.yml", emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test b/modules/nf-core/samtools/sort/tests/main.nf.test index c2ea9c72ac18..b05e6691bea5 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test +++ b/modules/nf-core/samtools/sort/tests/main.nf.test @@ -39,6 +39,40 @@ nextflow_process { } } + test("multiple bam") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot( + process.out.bam, + process.out.csi.collect { it.collect { it instanceof Map ? it : file(it).name } }, + process.out.versions + ).match()} + ) + } + } + test("cram") { config "./nextflow_cram.config" @@ -98,6 +132,36 @@ nextflow_process { } } + test("multiple bam - stub") { + + config "./nextflow.config" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test2.paired_end.sorted.bam', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'fasta' ], // meta map + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + test("cram - stub") { options "-stub" diff --git a/modules/nf-core/samtools/sort/tests/main.nf.test.snap b/modules/nf-core/samtools/sort/tests/main.nf.test.snap index 2d6b29004325..469891fe3ead 100644 --- a/modules/nf-core/samtools/sort/tests/main.nf.test.snap +++ b/modules/nf-core/samtools/sort/tests/main.nf.test.snap @@ -159,6 +159,101 @@ }, "timestamp": "2024-09-16T08:50:19.061912443" }, + "multiple bam": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi" + ] + ], + [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:59:55.479443" + }, + "multiple bam - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "1": [ + + ], + "2": [ + + ], + "3": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "4": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam:md5,8a16ba90c7d294cbb4c33ac0f7127a12" + ] + ], + "crai": [ + + ], + "cram": [ + + ], + "csi": [ + [ + { + "id": "test", + "single_end": false + }, + "test.sorted.bam.csi:md5,d185916eaff9afeb4d0aeab3310371f9" + ] + ], + "versions": [ + "versions.yml:md5,2659b187d681241451539d4c53500b9f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.09.0" + }, + "timestamp": "2024-10-08T11:36:13.781404" + }, "bam": { "content": [ [ @@ -185,8 +280,8 @@ ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-09-16T08:49:43.971158333" + "timestamp": "2024-10-08T11:59:46.372244" } } \ No newline at end of file From c57727832a7c4627bcc1d16cb93fd100ec3dc870 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Wed, 9 Oct 2024 09:24:31 +0200 Subject: [PATCH 129/486] Update actions/cache digest to 3624ceb (#6757) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/test.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index a50fd46f895b..e689240e9b77 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -155,7 +155,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 + - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4 id: cache-pip with: path: ~/.cache/pip @@ -405,7 +405,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 + - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4 id: cache-pip-pytest with: path: ~/.cache/pip @@ -682,7 +682,7 @@ jobs: with: python-version: "3.11" - - uses: actions/cache@2cdf405574d6ef1f33a1d12acccd3ae82f47b3f2 # v4 + - uses: actions/cache@3624ceb22c1c5a301c8db4169662070a689d9ea8 # v4 id: cache-pip-pdiff with: path: ~/.cache/pip From 9d05360da397692321d377b6102d2fb22507c6ef Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Wed, 9 Oct 2024 10:25:25 +0200 Subject: [PATCH 130/486] =?UTF-8?q?Fix=20large=20comment=20block=20headers?= =?UTF-8?q?=20so=20they=20don't=20cause=20phantom=20merge=20con=E2=80=A6?= =?UTF-8?q?=20(#6755)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Fix large comment block headers so they don't cause phantom merge conflicts * Apply suggestions from code review * fix color code --------- Co-authored-by: Júlia Mir Pedrol --- .../filtervep/tests/nextflow.config | 10 +- .../ensemblvep/filtervep/tests/tab.gz.config | 8 +- .../ensemblvep/filtervep/tests/vcf.config | 6 +- .../nf-core/utils_nextflow_pipeline/main.nf | 46 ++- .../nf-core/utils_nfcore_pipeline/main.nf | 279 ++++++++++-------- .../nf-core/utils_nfvalidation_plugin/main.nf | 17 +- 6 files changed, 190 insertions(+), 176 deletions(-) diff --git a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config index aee2e62b02f4..16cfe9939994 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/nextflow.config @@ -1,10 +1,10 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ params { - vep_cache_version = "112" - vep_genome = "WBcel235" - vep_species = "caenorhabditis_elegans" + vep_cache_version = "112" + vep_genome = "WBcel235" + vep_species = "caenorhabditis_elegans" } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config index 0aa5ea752287..cdad2d94d35e 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/tab.gz.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ process { @@ -13,12 +13,12 @@ process { } withName: ENSEMBLVEP_VEP { - ext.args = '--tab' + ext.args = '--tab' ext.prefix = { "${meta.id}_vep" } } withName: ENSEMBLVEP_FILTERVEP { - ext.args = '--filter "Feature_type is Transcript"' + ext.args = '--filter "Feature_type is Transcript"' ext.suffix = "tab" } } diff --git a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config index 0b65fe5c4f15..ee2aef5745b4 100644 --- a/modules/nf-core/ensemblvep/filtervep/tests/vcf.config +++ b/modules/nf-core/ensemblvep/filtervep/tests/vcf.config @@ -1,7 +1,7 @@ /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Nextflow config file for running tests -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ process { @@ -13,7 +13,7 @@ process { } withName: ENSEMBLVEP_VEP { - ext.args = '--vcf' + ext.args = '--vcf' ext.prefix = { "${meta.id}_vep" } } diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 28e32b200e40..2b0dc67a6a08 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { - take: print_version // boolean: print version dump_parameters // boolean: dump parameters @@ -22,7 +21,7 @@ workflow UTILS_NEXTFLOW_PIPELINE { // Print workflow version and exit on --version // if (print_version) { - log.info "${workflow.manifest.name} ${getWorkflowVersion()}" + log.info("${workflow.manifest.name} ${getWorkflowVersion()}") System.exit(0) } @@ -45,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -72,11 +71,11 @@ def getWorkflowVersion() { // Dump pipeline parameters to a JSON file // def dumpParametersToJSON(outdir) { - def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') - def filename = "params_${timestamp}.json" - def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") - def jsonStr = groovy.json.JsonOutput.toJson(params) - temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) + def timestamp = new java.util.Date().format('yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = groovy.json.JsonOutput.toJson(params) + temp_pf.text = groovy.json.JsonOutput.prettyPrint(jsonStr) nextflow.extension.FilesEx.copyTo(temp_pf.toPath(), "${outdir}/pipeline_info/params_${timestamp}.json") temp_pf.delete() @@ -91,9 +90,14 @@ def checkCondaChannels() { try { def config = parser.load("conda config --show channels".execute().text) channels = config.channels - } catch(NullPointerException | IOException e) { - log.warn "Could not verify conda channel configuration." - return + } + catch (NullPointerException e) { + log.warn("Could not verify conda channel configuration.") + return null + } + catch (IOException e) { + log.warn("Could not verify conda channel configuration.") + return null } // Check that all channels are present @@ -106,19 +110,13 @@ def checkCondaChannels() { required_channels_in_order.eachWithIndex { channel, index -> if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index+1])) + channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) } } if (channels_missing | channel_priority_violation) { - log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + - " There is a problem with your Conda configuration!\n\n" + - " You will need to set-up the conda-forge and bioconda channels correctly.\n" + - " Please refer to https://bioconda.github.io/\n" + - " The observed channel order is \n" + - " ${channels}\n" + - " but the following channel order is required:\n" + - " ${required_channels_in_order}\n" + - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + log.warn( + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + ) } } diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index cbd8495bb606..8cda47bcff39 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,13 +3,12 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { - take: nextflow_cli_args @@ -22,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // @@ -33,12 +32,9 @@ workflow UTILS_NFCORE_PIPELINE { def checkConfigProvided() { def valid_config = true as Boolean if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { - log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + - "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + - " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + - " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + - " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + - "Please refer to the quick start section and usage docs for the pipeline.\n " + log.warn( + "[${workflow.manifest.name}] You are attempting to run the pipeline without any custom configuration!\n\n" + "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + "Please refer to the quick start section and usage docs for the pipeline.\n " + ) valid_config = false } return valid_config @@ -49,12 +45,14 @@ def checkConfigProvided() { // def checkProfileProvided(nextflow_cli_args) { if (workflow.profile.endsWith(',')) { - error "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + error( + "The `-profile` option cannot end with a trailing comma, please remove it and re-run the pipeline!\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } if (nextflow_cli_args[0]) { - log.warn "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + - "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + log.warn( + "nf-core pipelines do not accept positional arguments. The positional argument `${nextflow_cli_args[0]}` has been detected.\n" + "HINT: A common mistake is to provide multiple values separated by spaces e.g. `-profile test, docker`.\n" + ) } } @@ -70,13 +68,7 @@ def workflowCitation() { manifest_doi.each { doi_ref -> temp_doi_ref += " https://doi.org/${doi_ref.replace('https://doi.org/', '').replace(' ', '')}\n" } - return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + - "* The pipeline\n" + - temp_doi_ref + "\n" + - "* The nf-core framework\n" + - " https://doi.org/10.1038/s41587-020-0439-x\n\n" + - "* Software dependencies\n" + - " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" + return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + "* The pipeline\n" + temp_doi_ref + "\n" + "* The nf-core framework\n" + " https://doi.org/10.1038/s41587-020-0439-x\n\n" + "* Software dependencies\n" + " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" } // @@ -102,7 +94,7 @@ def getWorkflowVersion() { // def processVersionsFromYAML(yaml_file) { def yaml = new org.yaml.snakeyaml.Yaml() - def versions = yaml.load(yaml_file).collectEntries { k, v -> [ k.tokenize(':')[-1], v ] } + def versions = yaml.load(yaml_file).collectEntries { k, v -> [k.tokenize(':')[-1], v] } return yaml.dumpAsMap(versions).trim() } @@ -112,8 +104,8 @@ def processVersionsFromYAML(yaml_file) { def workflowVersionToYAML() { return """ Workflow: - $workflow.manifest.name: ${getWorkflowVersion()} - Nextflow: $workflow.nextflow.version + ${workflow.manifest.name}: ${getWorkflowVersion()} + Nextflow: ${workflow.nextflow.version} """.stripIndent().trim() } @@ -121,11 +113,7 @@ def workflowVersionToYAML() { // Get channel of software versions used in pipeline in YAML format // def softwareVersionsToYAML(ch_versions) { - return ch_versions - .unique() - .map { version -> processVersionsFromYAML(version) } - .unique() - .mix(Channel.of(workflowVersionToYAML())) + return ch_versions.unique().map { version -> processVersionsFromYAML(version) }.unique().mix(Channel.of(workflowVersionToYAML())) } // @@ -133,25 +121,31 @@ def softwareVersionsToYAML(ch_versions) { // def paramsSummaryMultiqc(summary_params) { def summary_section = '' - summary_params.keySet().each { group -> - def group_params = summary_params.get(group) // This gets the parameters of that particular group - if (group_params) { - summary_section += "

$group

\n" - summary_section += "
\n" - group_params.keySet().sort().each { param -> - summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" + summary_params + .keySet() + .each { group -> + def group_params = summary_params.get(group) + // This gets the parameters of that particular group + if (group_params) { + summary_section += "

${group}

\n" + summary_section += "
\n" + group_params + .keySet() + .sort() + .each { param -> + summary_section += "
${param}
${group_params.get(param) ?: 'N/A'}
\n" + } + summary_section += "
\n" } - summary_section += "
\n" } - } - def yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" as String - yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" - yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" - yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" - yaml_file_text += "plot_type: 'html'\n" - yaml_file_text += "data: |\n" - yaml_file_text += "${summary_section}" + def yaml_file_text = "id: '${workflow.manifest.name.replace('/', '-')}-summary'\n" as String + yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" + yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" + yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" + yaml_file_text += "plot_type: 'html'\n" + yaml_file_text += "data: |\n" + yaml_file_text += "${summary_section}" return yaml_file_text } @@ -199,54 +193,54 @@ def logColours(monochrome_logs=true) { colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" // Regular Colors - colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" - colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" - colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" - colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" - colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" - colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" - colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" - colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" // Bold - colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" - colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" - colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" - colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" - colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" - colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" - colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" - colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" // Underline - colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" - colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" - colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" - colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" - colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" - colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" - colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" - colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" // High Intensity - colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" - colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" - colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" - colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" - colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" - colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" - colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" - colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" // Bold High Intensity - colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" - colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" - colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" - colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" - colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" - colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" - colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" - colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" return colorcodes } @@ -261,14 +255,15 @@ def attachMultiqcReport(multiqc_report) { mqc_report = multiqc_report.getVal() if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { if (mqc_report.size() > 1) { - log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" + log.warn("[${workflow.manifest.name}] Found multiple reports from process 'MULTIQC', will use only one") } mqc_report = mqc_report[0] } } - } catch (all) { + } + catch (Exception all) { if (multiqc_report) { - log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" + log.warn("[${workflow.manifest.name}] Could not attach MultiQC report to summary email") } } return mqc_report @@ -280,26 +275,35 @@ def attachMultiqcReport(multiqc_report) { def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdir, monochrome_logs=true, multiqc_report=null) { // Set up the e-mail variables - def subject = "[$workflow.manifest.name] Successful: $workflow.runName" + def subject = "[${workflow.manifest.name}] Successful: ${workflow.runName}" if (!workflow.success) { - subject = "[$workflow.manifest.name] FAILED: $workflow.runName" + subject = "[${workflow.manifest.name}] FAILED: ${workflow.runName}" } def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] misc_fields['Date Started'] = workflow.start misc_fields['Date Completed'] = workflow.complete misc_fields['Pipeline script file path'] = workflow.scriptFile misc_fields['Pipeline script hash ID'] = workflow.scriptId - if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository - if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId - if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision - misc_fields['Nextflow Version'] = workflow.nextflow.version - misc_fields['Nextflow Build'] = workflow.nextflow.build + if (workflow.repository) { + misc_fields['Pipeline repository Git URL'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['Pipeline repository Git Commit'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['Pipeline Git branch/tag'] = workflow.revision + } + misc_fields['Nextflow Version'] = workflow.nextflow.version + misc_fields['Nextflow Build'] = workflow.nextflow.build misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp def email_fields = [:] @@ -337,7 +341,7 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi // Render the sendmail template def max_multiqc_email_size = (params.containsKey('max_multiqc_email_size') ? params.max_multiqc_email_size : 0) as nextflow.util.MemoryUnit - def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] + def smail_fields = [email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "${workflow.projectDir}", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes()] def sf = new File("${workflow.projectDir}/assets/sendmail_template.txt") def sendmail_template = engine.createTemplate(sf).make(smail_fields) def sendmail_html = sendmail_template.toString() @@ -346,30 +350,32 @@ def completionEmail(summary_params, email, email_on_fail, plaintext_email, outdi def colors = logColours(monochrome_logs) as Map if (email_address) { try { - if (plaintext_email) { throw new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } + if (plaintext_email) { +new org.codehaus.groovy.GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") sendmail_tf.withWriter { w -> w << sendmail_html } - [ 'sendmail', '-t' ].execute() << sendmail_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" - } catch (all) { + ['sendmail', '-t'].execute() << sendmail_html + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (sendmail)-") + } + catch (Exception all) { // Catch failures and try with plaintext - def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] + def mail_cmd = ['mail', '-s', subject, '--content-type=text/html', email_address] mail_cmd.execute() << email_html - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Sent summary e-mail to ${email_address} (mail)-") } } // Write summary e-mail HTML to a file def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html"); + nextflow.extension.FilesEx.copyTo(output_hf.toPath(), "${outdir}/pipeline_info/pipeline_report.html") output_hf.delete() // Write summary e-mail TXT to a file def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } - nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt"); + nextflow.extension.FilesEx.copyTo(output_tf.toPath(), "${outdir}/pipeline_info/pipeline_report.txt") output_tf.delete() } @@ -380,12 +386,14 @@ def completionSummary(monochrome_logs=true) { def colors = logColours(monochrome_logs) as Map if (workflow.success) { if (workflow.stats.ignoredCount == 0) { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.green} Pipeline completed successfully${colors.reset}-") + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-") } - } else { - log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" + } + else { + log.info("-${colors.purple}[${workflow.manifest.name}]${colors.red} Pipeline completed with errors${colors.reset}-") } } @@ -394,21 +402,30 @@ def completionSummary(monochrome_logs=true) { // def imNotification(summary_params, hook_url) { def summary = [:] - summary_params.keySet().sort().each { group -> - summary << summary_params[group] - } + summary_params + .keySet() + .sort() + .each { group -> + summary << summary_params[group] + } def misc_fields = [:] - misc_fields['start'] = workflow.start - misc_fields['complete'] = workflow.complete - misc_fields['scriptfile'] = workflow.scriptFile - misc_fields['scriptid'] = workflow.scriptId - if (workflow.repository) misc_fields['repository'] = workflow.repository - if (workflow.commitId) misc_fields['commitid'] = workflow.commitId - if (workflow.revision) misc_fields['revision'] = workflow.revision - misc_fields['nxf_version'] = workflow.nextflow.version - misc_fields['nxf_build'] = workflow.nextflow.build - misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp + misc_fields['start'] = workflow.start + misc_fields['complete'] = workflow.complete + misc_fields['scriptfile'] = workflow.scriptFile + misc_fields['scriptid'] = workflow.scriptId + if (workflow.repository) { + misc_fields['repository'] = workflow.repository + } + if (workflow.commitId) { + misc_fields['commitid'] = workflow.commitId + } + if (workflow.revision) { + misc_fields['revision'] = workflow.revision + } + misc_fields['nxf_version'] = workflow.nextflow.version + misc_fields['nxf_build'] = workflow.nextflow.build + misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp def msg_fields = [:] msg_fields['version'] = getWorkflowVersion() @@ -433,13 +450,13 @@ def imNotification(summary_params, hook_url) { def json_message = json_template.toString() // POST - def post = new URL(hook_url).openConnection(); + def post = new URL(hook_url).openConnection() post.setRequestMethod("POST") post.setDoOutput(true) post.setRequestProperty("Content-Type", "application/json") - post.getOutputStream().write(json_message.getBytes("UTF-8")); - def postRC = post.getResponseCode(); - if (! postRC.equals(200)) { - log.warn(post.getErrorStream().getText()); + post.getOutputStream().write(json_message.getBytes("UTF-8")) + def postRC = post.getResponseCode() + if (!postRC.equals(200)) { + log.warn(post.getErrorStream().getText()) } } diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf index 2585b65d1b0d..e50a5e35ab5b 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -3,9 +3,9 @@ // /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-VALIDATION PLUGIN -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { paramsHelp } from 'plugin/nf-validation' @@ -13,13 +13,12 @@ include { paramsSummaryLog } from 'plugin/nf-validation' include { validateParameters } from 'plugin/nf-validation' /* -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -======================================================================================== +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFVALIDATION_PLUGIN { - take: print_help // boolean: print help workflow_command // string: default commmand used to run pipeline @@ -30,7 +29,7 @@ workflow UTILS_NFVALIDATION_PLUGIN { main: - log.debug "Using schema file: ${schema_filename}" + log.debug("Using schema file: ${schema_filename}") // Default values for strings pre_help_text = pre_help_text ?: '' @@ -41,19 +40,19 @@ workflow UTILS_NFVALIDATION_PLUGIN { // Print help message if needed // if (print_help) { - log.info pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text + log.info(pre_help_text + paramsHelp(workflow_command, parameters_schema: schema_filename) + post_help_text) System.exit(0) } // // Print parameter summary to stdout // - log.info pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text + log.info(pre_help_text + paramsSummaryLog(workflow, parameters_schema: schema_filename) + post_help_text) // // Validate parameters relative to the parameter JSON schema // - if (validate_params){ + if (validate_params) { validateParameters(parameters_schema: schema_filename) } From 772684d9d66f37b650c8ba5146ac1ee3ecba2acb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Wed, 9 Oct 2024 11:52:23 +0200 Subject: [PATCH 131/486] skip nested double quotes (#6758) --- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 8cda47bcff39..b78273ca4c1d 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -128,12 +128,12 @@ def paramsSummaryMultiqc(summary_params) { // This gets the parameters of that particular group if (group_params) { summary_section += "

${group}

\n" - summary_section += "
\n" + summary_section += "
\n" group_params .keySet() .sort() .each { param -> - summary_section += "
${param}
${group_params.get(param) ?: 'N/A'}
\n" + summary_section += "
${param}
${group_params.get(param) ?: 'N/A'}
\n" } summary_section += "
\n" } From f533459a222ac53eb4c6bb7a5f574e4069197cdb Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 9 Oct 2024 14:43:39 +0200 Subject: [PATCH 132/486] remove extra ~~~~~~ (#6760) --- subworkflows/nf-core/utils_nextflow_pipeline/main.nf | 8 ++++---- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 8 ++++---- subworkflows/nf-core/utils_nfvalidation_plugin/main.nf | 8 ++++---- 3 files changed, 12 insertions(+), 12 deletions(-) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 2b0dc67a6a08..4d7f09c04ddd 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NEXTFLOW_PIPELINE { @@ -44,9 +44,9 @@ workflow UTILS_NEXTFLOW_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index b78273ca4c1d..805dcc424cf1 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFCORE_PIPELINE { @@ -21,9 +21,9 @@ workflow UTILS_NFCORE_PIPELINE { } /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ FUNCTIONS -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ // diff --git a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf index e50a5e35ab5b..2398c620c5f3 100644 --- a/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf +++ b/subworkflows/nf-core/utils_nfvalidation_plugin/main.nf @@ -3,9 +3,9 @@ // /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ IMPORT NF-VALIDATION PLUGIN -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ include { paramsHelp } from 'plugin/nf-validation' @@ -13,9 +13,9 @@ include { paramsSummaryLog } from 'plugin/nf-validation' include { validateParameters } from 'plugin/nf-validation' /* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ SUBWORKFLOW DEFINITION -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ workflow UTILS_NFVALIDATION_PLUGIN { From 53fcc37e256ea30818fb793bbe98b63e4a40deb8 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Wed, 9 Oct 2024 19:57:02 +0200 Subject: [PATCH 133/486] FIX: fastq_fastqc_umitools_trimgalore - update snapshot (#6761) fix snapshot --- .../tests/main.nf.test.snap | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index b37a75c9bbc9..264ffb2225ea 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -377,14 +377,14 @@ ], [ - + null ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.09.0" }, - "timestamp": "2024-07-22T17:05:49.455992" + "timestamp": "2024-10-09T19:19:22.192915" }, "test single end read with UMI - stub": { "content": [ From d7462e71f9129083ce10c3fe953ed401781e0ebd Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Wed, 9 Oct 2024 22:26:31 +0200 Subject: [PATCH 134/486] Add stubs to spring module (#6756) * update module * remove pytest --------- Co-authored-by: Carson J Miller <68351153+CarsonJM@users.noreply.github.com> --- modules/nf-core/spring/compress/main.nf | 13 ++ .../spring/compress/tests/main.nf.test | 58 +++++++ .../spring/compress/tests/main.nf.test.snap | 26 ++++ modules/nf-core/spring/decompress/main.nf | 13 ++ .../spring/decompress/test/main.nf.test | 77 ++++++++++ .../spring/decompress/test/main.nf.test.snap | 144 ++++++++++++++++++ tests/config/pytest_modules.yml | 3 - 7 files changed, 331 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/spring/compress/main.nf b/modules/nf-core/spring/compress/main.nf index 2b096216e2cb..5f8ceb374efc 100644 --- a/modules/nf-core/spring/compress/main.nf +++ b/modules/nf-core/spring/compress/main.nf @@ -37,4 +37,17 @@ process SPRING_COMPRESS { spring: ${VERSION} END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + """ + touch ${prefix}.spring + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + spring: ${VERSION} + END_VERSIONS + """ + } diff --git a/modules/nf-core/spring/compress/tests/main.nf.test b/modules/nf-core/spring/compress/tests/main.nf.test index 45690c34fd65..ead6e028335f 100644 --- a/modules/nf-core/spring/compress/tests/main.nf.test +++ b/modules/nf-core/spring/compress/tests/main.nf.test @@ -64,4 +64,62 @@ nextflow_process { } } + test("test-spring-compress-single-end-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.spring[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + + test("test-spring-compress-paired-end-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + ] + + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.spring[0][1]).name, + process.out.versions + ).match() + } + ) + } + } + } diff --git a/modules/nf-core/spring/compress/tests/main.nf.test.snap b/modules/nf-core/spring/compress/tests/main.nf.test.snap index c3a8912b2ee8..957e1ed42008 100644 --- a/modules/nf-core/spring/compress/tests/main.nf.test.snap +++ b/modules/nf-core/spring/compress/tests/main.nf.test.snap @@ -1,4 +1,30 @@ { + "test-spring-compress-single-end-stub": { + "content": [ + "test.spring", + [ + "versions.yml:md5,2882bc3a3593cb048417c38e7452a788" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T09:56:05.145653656" + }, + "test-spring-compress-paired-end-stub": { + "content": [ + "test.spring", + [ + "versions.yml:md5,2882bc3a3593cb048417c38e7452a788" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T09:56:11.592113469" + }, "test-spring-compress-single-end": { "content": [ "test.spring", diff --git a/modules/nf-core/spring/decompress/main.nf b/modules/nf-core/spring/decompress/main.nf index 4cf78299178a..86ced26906fa 100644 --- a/modules/nf-core/spring/decompress/main.nf +++ b/modules/nf-core/spring/decompress/main.nf @@ -38,4 +38,17 @@ process SPRING_DECOMPRESS { spring: ${VERSION} END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def VERSION = '1.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def output = write_one_fastq_gz ? "echo '' | gzip > ${prefix}.fastq.gz" : "echo '' | gzip > ${prefix}_R1.fastq.gz; echo '' | gzip > ${prefix}_R2.fastq.gz" + """ + ${output} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + spring: ${VERSION} + END_VERSIONS + """ } diff --git a/modules/nf-core/spring/decompress/test/main.nf.test b/modules/nf-core/spring/decompress/test/main.nf.test index 550c6746b82f..9428a86bcff0 100644 --- a/modules/nf-core/spring/decompress/test/main.nf.test +++ b/modules/nf-core/spring/decompress/test/main.nf.test @@ -8,6 +8,8 @@ nextflow_process { script "../main.nf" process "SPRING_DECOMPRESS" + + test("Write-One-File") { setup { @@ -75,4 +77,79 @@ nextflow_process { ) } } + + test("Write-One-File-stub") { + + options "-stub" + + setup { + run("SPRING_COMPRESS") { + options "-stub" + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + [] + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = true // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Write-Two-Files-stub") { + + options "-stub" + + setup { + run("SPRING_COMPRESS") { + options "-stub" + script "../../compress/main.nf" + process { + """ + input[0] = [ + [ id:'test2' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + ] + """ + } + } + } + + when { + process { + """ + input[0] = SPRING_COMPRESS.out.spring + input[1] = false // write_one_fastq_gz + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + } \ No newline at end of file diff --git a/modules/nf-core/spring/decompress/test/main.nf.test.snap b/modules/nf-core/spring/decompress/test/main.nf.test.snap index 14a11d2c41df..7dcadbab61d4 100644 --- a/modules/nf-core/spring/decompress/test/main.nf.test.snap +++ b/modules/nf-core/spring/decompress/test/main.nf.test.snap @@ -1,4 +1,76 @@ { + "Write-One-File stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test" + }, + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/2a6cfab794852e23e6324eb4955668b2/work/42/aee6c82c1ca502c3b02339f597188b/test.fastq.gz" + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T10:03:50.626223289" + }, + "Write-Two-Files stub": { + "content": [ + { + "0": [ + [ + { + "id": "test2" + }, + [ + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" + ] + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test2" + }, + [ + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R1.fastq.gz", + "/home/ramprasad.neethiraj/nextflow/modules/.nf-test/tests/528557b5a81e4bffb57c38b19c7aa351/work/74/fc5d116d011bcd47d6f7de8d42ac34/test2_R2.fastq.gz" + ] + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T10:03:57.417015606" + }, "Write-Two-Files": { "content": [ { @@ -70,5 +142,77 @@ "nextflow": "24.04.2" }, "timestamp": "2024-06-21T13:02:07.466039653" + }, + "Write-One-File-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test" + }, + "test.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T13:55:53.594615215" + }, + "Write-Two-Files-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test2_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "1": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ], + "fastq": [ + [ + { + "id": "test2" + }, + [ + "test2_R1.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940", + "test2_R2.fastq.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ] + ], + "versions": [ + "versions.yml:md5,4711df5941f1464e3693d24dd29c705b" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T13:56:01.212228909" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 2d544dfd48c0..5d8a9be3c4fb 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -636,9 +636,6 @@ sourmash/taxannotate: spatyper: - modules/nf-core/spatyper/** - tests/modules/nf-core/spatyper/** -spring/decompress: - - modules/nf-core/spring/decompress/** - - tests/modules/nf-core/spring/decompress/** srst2/srst2: - modules/nf-core/srst2/srst2/** - tests/modules/nf-core/srst2/srst2/** From aef0e7467478130e861365232c3c4cc3247938ec Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Thu, 10 Oct 2024 10:25:46 +0100 Subject: [PATCH 135/486] Fix badly named variable (#6763) --- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 4ed073efcfb7..c655af41588b 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -20,7 +20,7 @@ def calculateStrandedness(forwardFragments, reverseFragments, unstrandedFragment def totalFragments = forwardFragments + reverseFragments + unstrandedFragments def totalStrandedFragments = forwardFragments + reverseFragments - def library_strandedness = 'undetermined' + def strandedness = 'undetermined' if (totalStrandedFragments > 0) { def forwardProportion = forwardFragments / (totalStrandedFragments as double) def reverseProportion = reverseFragments / (totalStrandedFragments as double) From 1b6b9a3338d011367137808b49b923515080e3ba Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Thu, 10 Oct 2024 12:25:01 +0200 Subject: [PATCH 136/486] remove for loop (#6707) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * remove for loop * Update subworkflows/nf-core/utils_nfcore_pipeline/main.nf Co-authored-by: Matthias Hörtenhuber --------- Co-authored-by: Matthias Hörtenhuber --- subworkflows/nf-core/utils_nextflow_pipeline/main.nf | 8 +------- subworkflows/nf-core/utils_nfcore_pipeline/main.nf | 2 +- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index 4d7f09c04ddd..b17b8774516c 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -106,13 +106,7 @@ def checkCondaChannels() { def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean // Check that they are in the right order - def channel_priority_violation = false - - required_channels_in_order.eachWithIndex { channel, index -> - if (index < required_channels_in_order.size() - 1) { - channel_priority_violation |= !(channels.indexOf(channel) < channels.indexOf(required_channels_in_order[index + 1])) - } - } + def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { log.warn( diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf index 805dcc424cf1..5cb7bafef38e 100644 --- a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf @@ -62,7 +62,7 @@ def checkProfileProvided(nextflow_cli_args) { def workflowCitation() { def temp_doi_ref = "" def manifest_doi = workflow.manifest.doi.tokenize(",") - // Using a loop to handle multiple DOIs + // Handling multiple DOIs // Removing `https://doi.org/` to handle pipelines using DOIs vs DOI resolvers // Removing ` ` since the manifest.doi is a string and not a proper list manifest_doi.each { doi_ref -> From 27443372c48c53f277b9066d10f6bf0a0215a990 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 10 Oct 2024 17:35:39 +0200 Subject: [PATCH 137/486] =?UTF-8?q?Change=20centrifuge=20build=20to=20expo?= =?UTF-8?q?rt=20a=20directory=20of=20all=20the=20files=20(like=20=E2=80=A6?= =?UTF-8?q?=20(#6767)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Change centrifuge build to export a directory of all the files (like other reference building/database building modules) * Fix meta.yaml linting --- modules/nf-core/centrifuge/build/main.nf | 19 +++++++++++-------- modules/nf-core/centrifuge/build/meta.yml | 11 +++++++---- 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/modules/nf-core/centrifuge/build/main.nf b/modules/nf-core/centrifuge/build/main.nf index c741e537c5a2..b767040de7f0 100644 --- a/modules/nf-core/centrifuge/build/main.nf +++ b/modules/nf-core/centrifuge/build/main.nf @@ -15,7 +15,7 @@ process CENTRIFUGE_BUILD { path size_table output: - tuple val(meta), path("*.cf") , emit: cf + tuple val(meta), path("${prefix}/") , emit: cf path "versions.yml" , emit: versions when: @@ -23,13 +23,15 @@ process CENTRIFUGE_BUILD { script: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" def size_table_cmd = size_table ? "--size_table ${size_table}" : "" """ + mkdir ${prefix} + centrifuge-build \\ -p $task.cpus \\ $fasta \\ - ${prefix} \\ + ${prefix}/${prefix} \\ --conversion-table $conversion_table \\ --taxonomy-tree $taxonomy_tree \\ --name-table $name_table \\ @@ -43,12 +45,13 @@ process CENTRIFUGE_BUILD { stub: def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.1.cf - touch ${prefix}.2.cf - touch ${prefix}.3.cf - touch ${prefix}.4.cf + mkdir -p ${prefix}/ + touch ${prefix}/${prefix}.1.cf + touch ${prefix}/${prefix}.2.cf + touch ${prefix}/${prefix}.3.cf + touch ${prefix}/${prefix}.4.cf cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/centrifuge/build/meta.yml b/modules/nf-core/centrifuge/build/meta.yml index 65a34f6d7b07..85299fc4d496 100644 --- a/modules/nf-core/centrifuge/build/meta.yml +++ b/modules/nf-core/centrifuge/build/meta.yml @@ -52,10 +52,13 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - "*.cf": - type: file - description: Index files for the centrifuge database - pattern: "*.{cf}" + pattern: "${prefix}/" + - "${prefix}/": + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + pattern: "${prefix}/" - versions: - versions.yml: type: file From 963235f9dde9625282554d2d371260718fa0a775 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 11 Oct 2024 11:18:52 +0200 Subject: [PATCH 138/486] Update actions/upload-artifact digest to b4b15b8 (#6769) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .github/workflows/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index e689240e9b77..4be8bbe5c924 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -472,7 +472,7 @@ jobs: - name: Upload logs on failure if: failure() - uses: actions/upload-artifact@604373da6381bf24206979c74d06a550515601b9 # v4 + uses: actions/upload-artifact@b4b15b8c7c6ac21ea08fcf65892d2ee8f75cf882 # v4 with: name: logs-${{ matrix.profile }}-${{ steps.parsed.outputs.result }} path: | From 3aa0aec1d52d492fe241919f0c6100ebf0074082 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=BAlia=20Mir=20Pedrol?= Date: Fri, 11 Oct 2024 11:57:36 +0200 Subject: [PATCH 139/486] use multi-line string for warning (#6770) * use multi-line string for warning * fix star/align meta.yml information --- modules/nf-core/star/align/meta.yml | 111 ++++++++++-------- .../nf-core/utils_nextflow_pipeline/main.nf | 14 ++- 2 files changed, 72 insertions(+), 53 deletions(-) diff --git a/modules/nf-core/star/align/meta.yml b/modules/nf-core/star/align/meta.yml index d9cba2aa7042..5cfe763e369e 100644 --- a/modules/nf-core/star/align/meta.yml +++ b/modules/nf-core/star/align/meta.yml @@ -56,27 +56,30 @@ input: output: - log_final: - meta: - type: file - description: STAR final log file - pattern: "*Log.final.out" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*Log.final.out": type: file description: STAR final log file pattern: "*Log.final.out" - log_out: - meta: - type: file - description: STAR lot out file - pattern: "*Log.out" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*Log.out": type: file description: STAR lot out file pattern: "*Log.out" - log_progress: - meta: - type: file - description: STAR log progress file - pattern: "*Log.progress.out" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*Log.progress.out": type: file description: STAR log progress file @@ -88,57 +91,70 @@ output: pattern: "versions.yml" - bam: - meta: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*d.out.bam": type: file description: Output BAM file containing read alignments pattern: "*.{bam}" - bam_sorted: - meta: - type: file - description: Sorted BAM file of read alignments (optional) - pattern: "*sortedByCoord.out.bam" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - ${prefix}.sortedByCoord.out.bam: type: file description: Sorted BAM file of read alignments (optional) pattern: "*sortedByCoord.out.bam" - bam_sorted_aligned: - - meta: {} - - ${prefix}.Aligned.sortedByCoord.out.bam: {} - - bam_transcript: - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.Aligned.sortedByCoord.out.bam: type: file - description: Output BAM file of transcriptome alignment (optional) - pattern: "*toTranscriptome.out.bam" + description: Sorted BAM file of read alignments (optional) + pattern: "*.Aligned.sortedByCoord.out.bam" + - bam_transcript: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*toTranscriptome.out.bam": type: file description: Output BAM file of transcriptome alignment (optional) pattern: "*toTranscriptome.out.bam" - bam_unsorted: - meta: - type: file - description: Unsorted BAM file of read alignments (optional) - pattern: "*Aligned.unsort.out.bam" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*Aligned.unsort.out.bam": type: file description: Unsorted BAM file of read alignments (optional) pattern: "*Aligned.unsort.out.bam" - fastq: - meta: - type: file - description: Unmapped FastQ files (optional) - pattern: "*fastq.gz" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*fastq.gz": type: file description: Unmapped FastQ files (optional) pattern: "*fastq.gz" - tab: - meta: - type: file - description: STAR output tab file(s) (optional) - pattern: "*.tab" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*.tab": type: file description: STAR output tab file(s) (optional) @@ -149,12 +165,9 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.SJ.out.tab" - "*.SJ.out.tab": - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + type: file + description: STAR output splice junction tab file pattern: "*.SJ.out.tab" - read_per_gene_tab: - meta: @@ -162,18 +175,16 @@ output: description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.ReadsPerGene.out.tab" - "*.ReadsPerGene.out.tab": + type: file + description: STAR output read per gene tab file + pattern: "*.ReadsPerGene.out.tab" + - junction: + - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.ReadsPerGene.out.tab" - - junction: - - meta: - type: file - description: STAR chimeric junction output file (optional) - pattern: "*.out.junction" - "*.out.junction": type: file description: STAR chimeric junction output file (optional) @@ -186,25 +197,25 @@ output: e.g. [ id:'test', single_end:false ] pattern: "*.out.sam" - "*.out.sam": + type: file + description: STAR output SAM file(s) (optional) + pattern: "*.out.sam" + - wig: + - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - pattern: "*.out.sam" - - wig: - - meta: - type: file - description: STAR output wiggle format file(s) (optional) - pattern: "*.wig" - "*.wig": type: file description: STAR output wiggle format file(s) (optional) pattern: "*.wig" - bedgraph: - meta: - type: file - description: STAR output bedGraph format file(s) (optional) - pattern: "*.bg" + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - "*.bg": type: file description: STAR output bedGraph format file(s) (optional) diff --git a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf index b17b8774516c..0fcbf7b3f23a 100644 --- a/subworkflows/nf-core/utils_nextflow_pipeline/main.nf +++ b/subworkflows/nf-core/utils_nextflow_pipeline/main.nf @@ -109,8 +109,16 @@ def checkCondaChannels() { def channel_priority_violation = required_channels_in_order != channels.findAll { ch -> ch in required_channels_in_order } if (channels_missing | channel_priority_violation) { - log.warn( - "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + " There is a problem with your Conda configuration!\n\n" + " You will need to set-up the conda-forge and bioconda channels correctly.\n" + " Please refer to https://bioconda.github.io/\n" + " The observed channel order is \n" + " ${channels}\n" + " but the following channel order is required:\n" + " ${required_channels_in_order}\n" + "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" - ) + log.warn """\ + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + There is a problem with your Conda configuration! + You will need to set-up the conda-forge and bioconda channels correctly. + Please refer to https://bioconda.github.io/ + The observed channel order is + ${channels} + but the following channel order is required: + ${required_channels_in_order} + ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" + """.stripIndent(true) } } From cf17ca47590cc578dfb47db1c2a44ef86f89976d Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Fri, 11 Oct 2024 11:58:31 +0200 Subject: [PATCH 140/486] multiqc_plots is a folder not a file (#6762) --- modules/nf-core/multiqc/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 9724d2f34efa..cc0643e1d586 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -52,7 +52,7 @@ process MULTIQC { stub: """ mkdir multiqc_data - touch multiqc_plots + mkdir multiqc_plots touch multiqc_report.html cat <<-END_VERSIONS > versions.yml From 573ba82ecf1505775d1a4332bc3cf55cacc3d094 Mon Sep 17 00:00:00 2001 From: Jonas Scheid <43858870+jonasscheid@users.noreply.github.com> Date: Fri, 11 Oct 2024 16:57:19 +0200 Subject: [PATCH 141/486] Bump openms tools to version 3.2.0 (#6754) * update container version-tag * update snapshots * bump conda versions --- .../openms/decoydatabase/environment.yml | 2 +- modules/nf-core/openms/decoydatabase/main.nf | 4 +-- .../decoydatabase/tests/main.nf.test.snap | 10 +++---- .../nf-core/openms/idfilter/environment.yml | 2 +- modules/nf-core/openms/idfilter/main.nf | 6 ++-- .../openms/idfilter/tests/main.nf.test.snap | 24 ++++++++-------- .../openms/idmassaccuracy/environment.yml | 2 +- modules/nf-core/openms/idmassaccuracy/main.nf | 4 +-- .../idmassaccuracy/tests/main.nf.test.snap | 12 ++++---- .../nf-core/openms/idmerger/environment.yml | 2 +- modules/nf-core/openms/idmerger/main.nf | 4 +-- .../openms/idmerger/tests/main.nf.test.snap | 18 ++++++------ .../nf-core/openms/idripper/environment.yml | 2 +- modules/nf-core/openms/idripper/main.nf | 4 +-- .../openms/idripper/tests/main.nf.test.snap | 28 ++++++++++++------- .../openms/idscoreswitcher/environment.yml | 2 +- .../nf-core/openms/idscoreswitcher/main.nf | 4 +-- .../idscoreswitcher/tests/main.nf.test.snap | 24 ++++++++++------ .../openms/peakpickerhires/environment.yml | 2 +- .../nf-core/openms/peakpickerhires/main.nf | 4 +-- .../peakpickerhires/tests/main.nf.test.snap | 18 ++++++------ .../openms/peptideindexer/environment.yml | 2 +- modules/nf-core/openms/peptideindexer/main.nf | 4 +-- .../peptideindexer/tests/main.nf.test.snap | 24 ++++++++-------- .../cometadapter/environment.yml | 2 +- .../openmsthirdparty/cometadapter/main.nf | 4 +-- .../openmsthirdparty/cometadapter/meta.yml | 2 +- .../cometadapter/tests/main.nf.test.snap | 4 +-- 28 files changed, 118 insertions(+), 102 deletions(-) diff --git a/modules/nf-core/openms/decoydatabase/environment.yml b/modules/nf-core/openms/decoydatabase/environment.yml index 3391b183243c..31614292dbe7 100644 --- a/modules/nf-core/openms/decoydatabase/environment.yml +++ b/modules/nf-core/openms/decoydatabase/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::openms=3.1.0 + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/decoydatabase/main.nf b/modules/nf-core/openms/decoydatabase/main.nf index cfac99c36238..5c3a55ce341b 100644 --- a/modules/nf-core/openms/decoydatabase/main.nf +++ b/modules/nf-core/openms/decoydatabase/main.nf @@ -4,8 +4,8 @@ process OPENMS_DECOYDATABASE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' : - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' : + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap b/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap index 1206179a894a..699b8c2d8ef2 100644 --- a/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap +++ b/modules/nf-core/openms/decoydatabase/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,29955625bab2d7680a741faab680f3a6" + "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426" ], "decoy_fasta": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,29955625bab2d7680a741faab680f3a6" + "versions.yml:md5,6c32e4ec0949f616baefa1b17efbe426" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-12T16:26:35.886966049" + "timestamp": "2024-10-08T11:22:32.701406062" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idfilter/environment.yml b/modules/nf-core/openms/idfilter/environment.yml index 5793e993cc53..5ec74436391a 100644 --- a/modules/nf-core/openms/idfilter/environment.yml +++ b/modules/nf-core/openms/idfilter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/idfilter/main.nf b/modules/nf-core/openms/idfilter/main.nf index 6c8d5bbdb615..763c2bf955d4 100644 --- a/modules/nf-core/openms/idfilter/main.nf +++ b/modules/nf-core/openms/idfilter/main.nf @@ -2,10 +2,10 @@ process OPENMS_IDFILTER { tag "$meta.id" label 'process_single' - conda "bioconda::openms=3.1.0" + conda "bioconda::openms=3.2.0" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' : - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' : + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(id_file), path(filter_file) diff --git a/modules/nf-core/openms/idfilter/tests/main.nf.test.snap b/modules/nf-core/openms/idfilter/tests/main.nf.test.snap index 21d221158a8e..0b74a186c17b 100644 --- a/modules/nf-core/openms/idfilter/tests/main.nf.test.snap +++ b/modules/nf-core/openms/idfilter/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b" + "versions.yml:md5,8a95c69294e90ae931b766218dc87dec" ], "filtered": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b" + "versions.yml:md5,8a95c69294e90ae931b766218dc87dec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T12:24:23.590979361" + "timestamp": "2024-10-08T11:45:00.758602574" }, "proteomics - filter - idxml": { "content": [ @@ -40,29 +40,29 @@ { "id": "test" }, - "test.idXML:md5,9efbb130c9a34807a4db1be64a7d395f" + "test.idXML:md5,59b0c4592ee45e1d2158b399ba838002" ] ], "1": [ - "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b" + "versions.yml:md5,8a95c69294e90ae931b766218dc87dec" ], "filtered": [ [ { "id": "test" }, - "test.idXML:md5,9efbb130c9a34807a4db1be64a7d395f" + "test.idXML:md5,59b0c4592ee45e1d2158b399ba838002" ] ], "versions": [ - "versions.yml:md5,180b8b0b5aa3a0439c4695e8c2a20c7b" + "versions.yml:md5,8a95c69294e90ae931b766218dc87dec" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-18T12:24:09.504917196" + "timestamp": "2024-10-08T11:44:53.291545021" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idmassaccuracy/environment.yml b/modules/nf-core/openms/idmassaccuracy/environment.yml index 5793e993cc53..5ec74436391a 100644 --- a/modules/nf-core/openms/idmassaccuracy/environment.yml +++ b/modules/nf-core/openms/idmassaccuracy/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/idmassaccuracy/main.nf b/modules/nf-core/openms/idmassaccuracy/main.nf index 9759ad40919a..b1e8deac16b1 100644 --- a/modules/nf-core/openms/idmassaccuracy/main.nf +++ b/modules/nf-core/openms/idmassaccuracy/main.nf @@ -4,8 +4,8 @@ process OPENMS_IDMASSACCURACY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h191ead1_4' : - 'biocontainers/openms:3.1.0--h191ead1_4' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' : + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(mzmls), path(idxmls) diff --git a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap index 9accf9a2accf..c9f056e174f7 100644 --- a/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap +++ b/modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + "versions.yml:md5,9bf83a6db02732d209de6819818aed26" ], "frag_err": [ [ @@ -38,7 +38,7 @@ ] ], "versions": [ - "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + "versions.yml:md5,9bf83a6db02732d209de6819818aed26" ] } ], @@ -46,7 +46,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T05:12:06.655389198" + "timestamp": "2024-10-08T11:26:08.231171982" }, "proteomics - openms - mass_error": { "content": [ @@ -63,7 +63,7 @@ ], "2": [ - "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + "versions.yml:md5,9bf83a6db02732d209de6819818aed26" ], "frag_err": [ [ @@ -77,7 +77,7 @@ ], "versions": [ - "versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7" + "versions.yml:md5,9bf83a6db02732d209de6819818aed26" ] } ], @@ -85,6 +85,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T05:11:55.087464408" + "timestamp": "2024-10-08T11:25:57.38948188" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idmerger/environment.yml b/modules/nf-core/openms/idmerger/environment.yml index 3391b183243c..31614292dbe7 100644 --- a/modules/nf-core/openms/idmerger/environment.yml +++ b/modules/nf-core/openms/idmerger/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::openms=3.1.0 + - bioconda::openms=3.2.0 diff --git a/modules/nf-core/openms/idmerger/main.nf b/modules/nf-core/openms/idmerger/main.nf index 99ffdafa9128..62a7a5062379 100644 --- a/modules/nf-core/openms/idmerger/main.nf +++ b/modules/nf-core/openms/idmerger/main.nf @@ -4,8 +4,8 @@ process OPENMS_IDMERGER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' : - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' : + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(idxmls) diff --git a/modules/nf-core/openms/idmerger/tests/main.nf.test.snap b/modules/nf-core/openms/idmerger/tests/main.nf.test.snap index 6603da98f0b9..fa034582afba 100644 --- a/modules/nf-core/openms/idmerger/tests/main.nf.test.snap +++ b/modules/nf-core/openms/idmerger/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "proteomics - openms - idxml": { "content": [ [ - "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9" + "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-12T17:33:25.047982404" + "timestamp": "2024-10-08T12:02:35.595648853" }, "proteomics - openms - idxml - stub": { "content": [ @@ -23,7 +23,7 @@ ] ], "1": [ - "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9" + "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3" ], "idxml": [ [ @@ -34,14 +34,14 @@ ] ], "versions": [ - "versions.yml:md5,09d83e713284f55e18cebcc20eda07b9" + "versions.yml:md5,8051ce1c0fe4404798507d607ebf52a3" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-12T17:33:34.498327729" + "timestamp": "2024-10-08T12:02:42.76246364" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idripper/environment.yml b/modules/nf-core/openms/idripper/environment.yml index 5793e993cc53..5ec74436391a 100644 --- a/modules/nf-core/openms/idripper/environment.yml +++ b/modules/nf-core/openms/idripper/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/idripper/main.nf b/modules/nf-core/openms/idripper/main.nf index 7350af4253ef..463afa257733 100644 --- a/modules/nf-core/openms/idripper/main.nf +++ b/modules/nf-core/openms/idripper/main.nf @@ -4,8 +4,8 @@ process OPENMS_IDRIPPER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3': - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4': + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(merged_idxml) diff --git a/modules/nf-core/openms/idripper/tests/main.nf.test.snap b/modules/nf-core/openms/idripper/tests/main.nf.test.snap index 2b58f423925d..2851a262ca88 100644 --- a/modules/nf-core/openms/idripper/tests/main.nf.test.snap +++ b/modules/nf-core/openms/idripper/tests/main.nf.test.snap @@ -8,13 +8,13 @@ "id": "test" }, [ - "HepG2_rep1_small.idXML:md5,ca1c4549a42e0b0c0be8345cf5062dfd", - "HepG2_rep2_small.idXML:md5,14a4e9a7dca3c62db38b6345a63d80d5" + "HepG2_rep1_small.idXML:md5,0124479eaf5bba215a801aff613f08d6", + "HepG2_rep2_small.idXML:md5,4b26909ad111957d4bbfa9981c80e92d" ] ] ], "1": [ - "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0" + "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948" ], "idxmls": [ [ @@ -22,17 +22,21 @@ "id": "test" }, [ - "HepG2_rep1_small.idXML:md5,ca1c4549a42e0b0c0be8345cf5062dfd", - "HepG2_rep2_small.idXML:md5,14a4e9a7dca3c62db38b6345a63d80d5" + "HepG2_rep1_small.idXML:md5,0124479eaf5bba215a801aff613f08d6", + "HepG2_rep2_small.idXML:md5,4b26909ad111957d4bbfa9981c80e92d" ] ] ], "versions": [ - "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0" + "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948" ] } ], - "timestamp": "2024-01-05T10:53:57.761966016" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T12:02:51.318615048" }, "proteomics - split - idxml - stub": { "content": [ @@ -49,7 +53,7 @@ ] ], "1": [ - "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0" + "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948" ], "idxmls": [ [ @@ -63,10 +67,14 @@ ] ], "versions": [ - "versions.yml:md5,7a7ebf177e4987780b6371dab640e6c0" + "versions.yml:md5,e016c1da0449e1d29d4c34198ff1a948" ] } ], - "timestamp": "2024-01-05T10:54:05.672792514" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T12:02:59.481185212" } } \ No newline at end of file diff --git a/modules/nf-core/openms/idscoreswitcher/environment.yml b/modules/nf-core/openms/idscoreswitcher/environment.yml index 5793e993cc53..5ec74436391a 100644 --- a/modules/nf-core/openms/idscoreswitcher/environment.yml +++ b/modules/nf-core/openms/idscoreswitcher/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/idscoreswitcher/main.nf b/modules/nf-core/openms/idscoreswitcher/main.nf index e24211760458..41ecb2df7fb3 100644 --- a/modules/nf-core/openms/idscoreswitcher/main.nf +++ b/modules/nf-core/openms/idscoreswitcher/main.nf @@ -4,8 +4,8 @@ process OPENMS_IDSCORESWITCHER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3': - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4': + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(idxml) diff --git a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap index 3d9d95a45b6f..287209db1455 100644 --- a/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap +++ b/modules/nf-core/openms/idscoreswitcher/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fc26aec256a1ab21dd6eec546146e7f5" + "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32" ], "idxml": [ [ @@ -22,11 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,fc26aec256a1ab21dd6eec546146e7f5" + "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32" ] } ], - "timestamp": "2024-01-05T15:38:28.11227936" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T12:08:26.611231415" }, "proteomics - switch_score - idxml": { "content": [ @@ -36,25 +40,29 @@ { "id": "test" }, - "test.idXML:md5,c9cb1593610b60cc1d9ca2c4defab690" + "test.idXML:md5,51e9c25b89ab47dab73d947e43f0633b" ] ], "1": [ - "versions.yml:md5,fc26aec256a1ab21dd6eec546146e7f5" + "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32" ], "idxml": [ [ { "id": "test" }, - "test.idXML:md5,c9cb1593610b60cc1d9ca2c4defab690" + "test.idXML:md5,51e9c25b89ab47dab73d947e43f0633b" ] ], "versions": [ - "versions.yml:md5,fc26aec256a1ab21dd6eec546146e7f5" + "versions.yml:md5,6ba0a7c237c0553ecaa343d7d0638e32" ] } ], - "timestamp": "2024-01-05T15:38:21.402742579" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T12:08:17.9635299" } } \ No newline at end of file diff --git a/modules/nf-core/openms/peakpickerhires/environment.yml b/modules/nf-core/openms/peakpickerhires/environment.yml index 456a019bf148..d4d40e896b1f 100644 --- a/modules/nf-core/openms/peakpickerhires/environment.yml +++ b/modules/nf-core/openms/peakpickerhires/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/peakpickerhires/main.nf b/modules/nf-core/openms/peakpickerhires/main.nf index f4f621aed1f8..153cab4f91a8 100644 --- a/modules/nf-core/openms/peakpickerhires/main.nf +++ b/modules/nf-core/openms/peakpickerhires/main.nf @@ -4,8 +4,8 @@ process OPENMS_PEAKPICKERHIRES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3' : - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4' : + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(mzml) diff --git a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap index 0f056d2cdd91..c99a542ed53f 100644 --- a/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap +++ b/modules/nf-core/openms/peakpickerhires/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "proteomics - mzML": { "content": [ [ - "versions.yml:md5,b4ddcc39c47d566b91e172fcf25e8b80" + "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-12T17:29:48.256324624" + "timestamp": "2024-10-08T12:13:25.732124582" }, "proteomics - mzML - stub": { "content": [ @@ -23,7 +23,7 @@ ] ], "1": [ - "versions.yml:md5,b4ddcc39c47d566b91e172fcf25e8b80" + "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e" ], "mzml": [ [ @@ -34,14 +34,14 @@ ] ], "versions": [ - "versions.yml:md5,b4ddcc39c47d566b91e172fcf25e8b80" + "versions.yml:md5,3db8a4b45ffebff2eac6118cbca4bb4e" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-12T17:29:57.976530253" + "timestamp": "2024-10-08T12:13:32.716358119" } } \ No newline at end of file diff --git a/modules/nf-core/openms/peptideindexer/environment.yml b/modules/nf-core/openms/peptideindexer/environment.yml index e4ec4037ee8a..d6e51812af34 100644 --- a/modules/nf-core/openms/peptideindexer/environment.yml +++ b/modules/nf-core/openms/peptideindexer/environment.yml @@ -3,4 +3,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms=3.1.0" + - "bioconda::openms=3.2.0" diff --git a/modules/nf-core/openms/peptideindexer/main.nf b/modules/nf-core/openms/peptideindexer/main.nf index ae7c245a547d..2bf824c39318 100644 --- a/modules/nf-core/openms/peptideindexer/main.nf +++ b/modules/nf-core/openms/peptideindexer/main.nf @@ -4,8 +4,8 @@ process OPENMS_PEPTIDEINDEXER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms:3.1.0--h8964181_3': - 'biocontainers/openms:3.1.0--h8964181_3' }" + 'https://depot.galaxyproject.org/singularity/openms:3.2.0--haddbca4_4': + 'biocontainers/openms:3.2.0--haddbca4_4' }" input: tuple val(meta), path(id_file) diff --git a/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap b/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap index 433905ac1e71..bc41f96655ef 100644 --- a/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap +++ b/modules/nf-core/openms/peptideindexer/tests/main.nf.test.snap @@ -7,30 +7,30 @@ { "id": "test" }, - "test_pi.idXML:md5,39d2a1b6f504ef50d9e682045aa8aed3" + "test_pi.idXML:md5,f18620bed99c99f292b4e1804c3a47ad" ] ], "1": [ - "versions.yml:md5,04d2b88660370f1cdfb1fc68cb3caf80" + "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42" ], "id_file_pi": [ [ { "id": "test" }, - "test_pi.idXML:md5,39d2a1b6f504ef50d9e682045aa8aed3" + "test_pi.idXML:md5,f18620bed99c99f292b4e1804c3a47ad" ] ], "versions": [ - "versions.yml:md5,04d2b88660370f1cdfb1fc68cb3caf80" + "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-20T15:04:51.120367545" + "timestamp": "2024-10-08T11:26:20.161342857" }, "proteomics - refresh_idxml - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,04d2b88660370f1cdfb1fc68cb3caf80" + "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42" ], "id_file_pi": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,04d2b88660370f1cdfb1fc68cb3caf80" + "versions.yml:md5,01ee06728114ec0a7b0980ad83eedd42" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-03-20T12:38:05.159279937" + "timestamp": "2024-10-08T11:26:28.558838022" } } \ No newline at end of file diff --git a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml index 3c2729e75f1b..dfc106036087 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/environment.yml +++ b/modules/nf-core/openmsthirdparty/cometadapter/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - "bioconda::openms-thirdparty=3.1.0" + - "bioconda::openms-thirdparty=3.2.0" diff --git a/modules/nf-core/openmsthirdparty/cometadapter/main.nf b/modules/nf-core/openmsthirdparty/cometadapter/main.nf index b193974ae866..15a28391d56b 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/main.nf +++ b/modules/nf-core/openmsthirdparty/cometadapter/main.nf @@ -4,8 +4,8 @@ process OPENMSTHIRDPARTY_COMETADAPTER { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.1.0--h9ee0642_4' : - 'biocontainers/openms-thirdparty:3.1.0--h9ee0642_4' }" + 'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.2.0--h9ee0642_4' : + 'biocontainers/openms-thirdparty:3.2.0--h9ee0642_4' }" input: tuple val(meta), path(mzml), path(fasta) diff --git a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml index fc7e688102d4..453781fb3bfe 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/meta.yml +++ b/modules/nf-core/openmsthirdparty/cometadapter/meta.yml @@ -13,7 +13,7 @@ tools: homepage: "https://openms.de" documentation: "https://openms.readthedocs.io/en/latest/index.html" tool_dev_url: "https://github.com/OpenMS/OpenMS" - doi: "10.1038/nmeth.3959" + doi: "10.1038/s41592-024-02197-7" licence: ["BSD"] identifier: "" diff --git a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap index 9eb65951ab52..939aa4151ec2 100644 --- a/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap +++ b/modules/nf-core/openmsthirdparty/cometadapter/tests/main.nf.test.snap @@ -45,7 +45,7 @@ "content": [ { "OPENMSTHIRDPARTY_COMETADAPTER": { - "CometAdapter": "3.1.0", + "CometAdapter": "3.2.0", "Comet": "2023.01 rev. 2" } } @@ -54,6 +54,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-13T13:57:35.577894316" + "timestamp": "2024-10-08T11:29:53.094774827" } } \ No newline at end of file From 55554aef178ebe6cb1d8224c4617f568ed7bba5d Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Sat, 12 Oct 2024 06:19:04 +0200 Subject: [PATCH 142/486] Update pre-commit hook python-jsonschema/check-jsonschema to v0.29.4 (#6773) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index d195d3d90444..c5c1c433593d 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -6,7 +6,7 @@ repos: additional_dependencies: - prettier@3.2.5 - repo: https://github.com/python-jsonschema/check-jsonschema - rev: 0.29.3 + rev: 0.29.4 hooks: - id: check-jsonschema # match meta.ymls in one of the subdirectories of modules/nf-core From 7fd374ec22647b9aac628095498313661701b6a1 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Sat, 12 Oct 2024 13:25:41 +0200 Subject: [PATCH 143/486] Add TAR module (#6772) * start filling in mneta * Fix linting * Replace switch with ifelse * Fix ype in in if else --- modules/nf-core/tar/environment.yml | 12 ++ modules/nf-core/tar/main.nf | 74 +++++++ modules/nf-core/tar/meta.yml | 67 +++++++ modules/nf-core/tar/tests/main.nf.test | 210 ++++++++++++++++++++ modules/nf-core/tar/tests/main.nf.test.snap | 126 ++++++++++++ 5 files changed, 489 insertions(+) create mode 100644 modules/nf-core/tar/environment.yml create mode 100644 modules/nf-core/tar/main.nf create mode 100644 modules/nf-core/tar/meta.yml create mode 100644 modules/nf-core/tar/tests/main.nf.test create mode 100644 modules/nf-core/tar/tests/main.nf.test.snap diff --git a/modules/nf-core/tar/environment.yml b/modules/nf-core/tar/environment.yml new file mode 100644 index 000000000000..1decc62432db --- /dev/null +++ b/modules/nf-core/tar/environment.yml @@ -0,0 +1,12 @@ +channels: + - conda-forge + - bioconda + +dependencies: + - conda-forge::bzip2=1.0.8 + - conda-forge::gzip=1.13 + - conda-forge::lzip=1.21 + - conda-forge::lzop=1.04 + - conda-forge::tar=1.34 + - conda-forge::xz=5.2.6 + - conda-forge::zstd=1.5.6 diff --git a/modules/nf-core/tar/main.nf b/modules/nf-core/tar/main.nf new file mode 100644 index 000000000000..60f828101b9d --- /dev/null +++ b/modules/nf-core/tar/main.nf @@ -0,0 +1,74 @@ +process TAR { + tag "${meta.id}" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/98/98946ea8217c35441352a94f3e0cd1dfa24137c323e8b0f5dfcb3123b465d0b1/data': + 'community.wave.seqera.io/library/bzip2_gzip_lzip_lzop_pruned:5a822ddcf829e7af' }" + + input: + tuple val(meta), path(input) + val compress_type + + output: + tuple val(meta), path("*.tar${compress_type}"), emit: archive + path "versions.yml", emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + valid_compress_types = ['.bz2', '.xz', '.lz', '.lzma', '.lzo', '.zst', '.gz', ''] + if (!compress_type in valid_compress_types) { + error("ERROR: Invalid compress_type: ${compress_type} for TAR. Set as empty string for no compression. Compression options: ${valid_compress_types.join(", ")}") + } + + if (compress_type == '.bz2') { + compress_flag = '--bzip2' + } else if (compress_type == '.xz') { + compress_flag = '--xz' + } else if (compress_type == '.lz') { + compress_flag = '--lzip' + } else if (compress_type == '.lzma') { + compress_flag = '--lzma' + } else if (compress_type == '.lzo') { + compress_flag = '--lzop' + } else if (compress_type == '.zst') { + compress_flag = '--zstd' + } else if (compress_type == '.gz') { + compress_flag = '--gzip' + } else if (compress_type == '') { + compress_flag = '' + } else { + error("ERROR: Invalid compress_type: ${compress_type} for TAR. Set as empty string for no compression. Compression options: ${valid_compress_types.join(", ")}") + } + + """ + tar \\ + -c \\ + ${compress_flag} \\ + ${args} \\ + -f ${prefix}.tar${compress_type} \\ + ${input} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tar: \$(tar --version | grep tar | sed 's/.*) //g') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + echo "" | gzip -c > ${prefix}.tar.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tar: \$(tar --version | grep tar | sed 's/.*) //g') + END_VERSIONS + """ +} diff --git a/modules/nf-core/tar/meta.yml b/modules/nf-core/tar/meta.yml new file mode 100644 index 000000000000..9a3cbde631b8 --- /dev/null +++ b/modules/nf-core/tar/meta.yml @@ -0,0 +1,67 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "tar" +description: Compress directories into tarballs with various compression options +keywords: + - untar + - tar + - tarball + - compression + - archive + - gzip + - targz +tools: + - "tar": + description: "GNU Tar provides the ability to create tar archives, as well as + various other kinds of manipulation." + homepage: "https://www.gnu.org/software/tar/" + documentation: "https://www.gnu.org/software/tar/manual/" + licence: ["GPLv3"] + identifier: "" + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - input: + type: directory + description: A file or directory to be archived + pattern: "*/" + ontologies: + - edam: "http://edamontology.org/data_1049" + - - compress_type: + type: string + description: | + A string defining which type of (optional) compression to apply to the archive. + Provide an empty string in quotes for no compression + pattern: ".bz2|.xz|.lz|.lzma|.lzo|.zst|.gz" +output: + - archive: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}" + ontologies: &id001 + - edam: "http://edamontology.org/format_25722" + - edam: "http://edamontology.org/format_2573" + - edam: "http://edamontology.org/format_3462" + + - "*.tar${compress_type}": + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.tar{.bz2,.xz,.lz,.lzma,.lzo,.zst,.gz,}" + ontologies: *id001 + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jfy133" +maintainers: + - "@jfy133" diff --git a/modules/nf-core/tar/tests/main.nf.test b/modules/nf-core/tar/tests/main.nf.test new file mode 100644 index 000000000000..0c8dc4793b32 --- /dev/null +++ b/modules/nf-core/tar/tests/main.nf.test @@ -0,0 +1,210 @@ +// nf-core modules test tar +nextflow_process { + + name "Test Process TAR" + script "../main.nf" + process "TAR" + + tag "modules" + tag "modules_nfcore" + tag "tar" + tag "untar" + + setup { + run("UNTAR") { + script "../../untar/main.nf" + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kraken2.tar.gz', checkIfExists: true) + ] + """ + } + } + } + + test("sarscov2 - genome - db - kraken2 - none") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .gz") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.gz' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .bz2") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.bz2' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .lzip") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.lz' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .lzma") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.lzma' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .lzo") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.lzo' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - .zst") { + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.zst' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.archive[0][1]).name, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - genome - db - kraken2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = UNTAR.out.untar + input[1] = '.gz' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/tar/tests/main.nf.test.snap b/modules/nf-core/tar/tests/main.nf.test.snap new file mode 100644 index 000000000000..9881e7ee714f --- /dev/null +++ b/modules/nf-core/tar/tests/main.nf.test.snap @@ -0,0 +1,126 @@ +{ + "sarscov2 - genome - db - kraken2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ], + "archive": [ + [ + { + "id": "test" + }, + "test.tar.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T17:39:29.878210779" + }, + "sarscov2 - genome - db - kraken2 - .bz2": { + "content": [ + "test.tar.bz2", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:04:03.312488057" + }, + "sarscov2 - genome - db - kraken2 - .zst": { + "content": [ + "test.tar.zst", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:04:42.327014114" + }, + "sarscov2 - genome - db - kraken2 - .lzip": { + "content": [ + "test.tar.lz", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:04:12.94431061" + }, + "sarscov2 - genome - db - kraken2 - .lzo": { + "content": [ + "test.tar.lzo", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:04:32.489438637" + }, + "sarscov2 - genome - db - kraken2 - .lzma": { + "content": [ + "test.tar.lzma", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:04:22.523407809" + }, + "sarscov2 - genome - db - kraken2 - .gz": { + "content": [ + "test.tar.gz", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T19:03:54.163215135" + }, + "sarscov2 - genome - db - kraken2 - none": { + "content": [ + "test.tar", + [ + "versions.yml:md5,5244284efaeb7329ac2e3a8c72432461" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T18:56:50.875583591" + } +} \ No newline at end of file From 283613159e079152f1336cef0db1c836086206e0 Mon Sep 17 00:00:00 2001 From: Daniel Straub <42973691+d4straub@users.noreply.github.com> Date: Mon, 14 Oct 2024 11:47:35 +0200 Subject: [PATCH 144/486] Update MaxBin2: allow multiple abund files (#6776) * allow multiple abund files * Apply suggestions from code review Co-authored-by: James A. Fellows Yates * Update modules/nf-core/maxbin2/main.nf Co-authored-by: James A. Fellows Yates --------- Co-authored-by: James A. Fellows Yates --- modules/nf-core/maxbin2/main.nf | 12 +++++++++++- modules/nf-core/maxbin2/meta.yml | 15 +++++++++++++-- 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/modules/nf-core/maxbin2/main.nf b/modules/nf-core/maxbin2/main.nf index 9b7a0fd41c2e..845c8e4ed918 100644 --- a/modules/nf-core/maxbin2/main.nf +++ b/modules/nf-core/maxbin2/main.nf @@ -13,6 +13,7 @@ process MAXBIN2 { output: tuple val(meta), path("*.fasta.gz") , emit: binned_fastas tuple val(meta), path("*.summary") , emit: summary + tuple val(meta), path("*.abundance") , emit: abundance , optional: true tuple val(meta), path("*.log.gz") , emit: log tuple val(meta), path("*.marker.gz") , emit: marker_counts tuple val(meta), path("*.noclass.gz") , emit: unbinned_fasta @@ -27,7 +28,16 @@ process MAXBIN2 { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def associate_files = reads ? "-reads $reads" : "-abund $abund" + if (reads && abund) { error("ERROR: MaxBin2 can only accept one of `reads` or `abund`, no both. Check input.") } + def associate_files = "" + if ( reads ) { + associate_files = "-reads $reads" + } else if ( abund instanceof List ) { + associate_files = "-abund ${abund[0]}" + for (i in 2..abund.size()) { associate_files += " -abund$i ${abund[i-1]}" } + } else { + associate_files = "-abund $abund" + } """ mkdir input/ && mv $contigs input/ run_MaxBin.pl \\ diff --git a/modules/nf-core/maxbin2/meta.yml b/modules/nf-core/maxbin2/meta.yml index 538ba07f3fd3..9546afb1aaa1 100644 --- a/modules/nf-core/maxbin2/meta.yml +++ b/modules/nf-core/maxbin2/meta.yml @@ -35,8 +35,8 @@ input: supply at the same time as abundance files. pattern: "*.fasta" - abund: - type: file - description: Contig abundance files, i.e. reads against each contig. See MaxBin2 + type: list + description: One or more contig abundance files, i.e. average depth of reads against each contig. See MaxBin2 README for details. Do not supply at the same time as read files. output: - binned_fastas: @@ -60,6 +60,17 @@ output: description: Summary file describing which contigs are being classified into which bin pattern: "*.summary" + - abundance: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.abundance": + type: file + description: Abundance of each bin if multiple abundance files were supplied + which bin + pattern: "*.abundance" - log: - meta: type: map From a4835a6fa6e0b9d8ed2459dba29915bf9847c719 Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Mon, 14 Oct 2024 16:11:14 +0200 Subject: [PATCH 145/486] Fix tar to always follow symlinks due to nxf staging in work dirs (#6778) --- modules/nf-core/tar/main.nf | 1 + 1 file changed, 1 insertion(+) diff --git a/modules/nf-core/tar/main.nf b/modules/nf-core/tar/main.nf index 60f828101b9d..4b49fe8ff32f 100644 --- a/modules/nf-core/tar/main.nf +++ b/modules/nf-core/tar/main.nf @@ -49,6 +49,7 @@ process TAR { """ tar \\ -c \\ + -h \\ ${compress_flag} \\ ${args} \\ -f ${prefix}.tar${compress_type} \\ From 4026bab16a91b1b0b18d80ff465819ca725f33fd Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Oct 2024 12:14:02 +0100 Subject: [PATCH 146/486] Fix usage of empty versions channel from trimming (#6781) * Fix usage of empty versions channel from trimming * Fix snap --- subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf | 2 +- subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf | 2 +- .../fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap | 4 ++-- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf index ab6cbb320c59..9c355a5e328f 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_fastp/main.nf @@ -160,5 +160,5 @@ workflow FASTQ_FASTQC_UMITOOLS_FASTP { fastqc_trim_html // channel: [ val(meta), [ html ] ] fastqc_trim_zip // channel: [ val(meta), [ zip ] ] - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf index db2e5b329ca9..4ffc3698478d 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/main.nf @@ -119,5 +119,5 @@ workflow FASTQ_FASTQC_UMITOOLS_TRIMGALORE { trim_log // channel: [ val(meta), [ txt ] ] trim_read_count // channel: [ val(meta), val(count) ] - versions = ch_versions.ifEmpty(null) // channel: [ versions.yml ] + versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 264ffb2225ea..46bf3acf29ee 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -377,7 +377,7 @@ ], [ - null + ] ], "meta": { @@ -521,4 +521,4 @@ }, "timestamp": "2024-07-22T17:06:09.844235" } -} \ No newline at end of file +} diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index c655af41588b..05078d23dcbf 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -139,7 +139,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! // - if (trimmer == 'trimgalore') { + if (trimmer == 'trimgalore' && !skip_trimming) { FASTQ_FASTQC_UMITOOLS_TRIMGALORE ( ch_filtered_reads, skip_fastqc, @@ -162,7 +162,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp // - if (trimmer == 'fastp') { + if (trimmer == 'fastp' && !skip_trimming) { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc, From 0755c617637d21b2c290b26d225debe3070aa109 Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Tue, 15 Oct 2024 19:06:13 +0530 Subject: [PATCH 147/486] update bismark apps (#6774) * update bismark v0.24.2, rm input stageAs, add stub, update tests+snap * udpate bismark/genomepreparation tests * update bismark/align main to take separate fasta and update tests+snap * update bismark/methylationextractor main, tests+snap * update bismark/coverage2cytosine main, tests+snap * update bismark/deduplicate main, tests+snap * typo fix * bismark/report/ update main, stub tests+snap * bismark/summary update ver, +stub, tests+snap --- modules/nf-core/bismark/align/environment.yml | 2 +- modules/nf-core/bismark/align/main.nf | 25 +- modules/nf-core/bismark/align/meta.yml | 17 +- .../nf-core/bismark/align/tests/main.nf.test | 237 ++++++------------ .../bismark/align/tests/main.nf.test.snap | 63 ++--- modules/nf-core/bismark/align/tests/tags.yml | 2 - .../bismark/coverage2cytosine/environment.yml | 2 +- .../nf-core/bismark/coverage2cytosine/main.nf | 26 +- .../bismark/coverage2cytosine/meta.yml | 17 +- .../coverage2cytosine/tests/main.nf.test | 15 +- .../coverage2cytosine/tests/main.nf.test.snap | 10 +- .../bismark/coverage2cytosine/tests/tags.yml | 2 - .../bismark/deduplicate/environment.yml | 2 +- modules/nf-core/bismark/deduplicate/main.nf | 23 +- modules/nf-core/bismark/deduplicate/meta.yml | 1 + .../bismark/deduplicate/tests/main.nf.test | 10 +- .../deduplicate/tests/main.nf.test.snap | 10 +- .../bismark/deduplicate/tests/tags.yml | 2 - .../bismark/genomepreparation/environment.yml | 2 +- .../nf-core/bismark/genomepreparation/main.nf | 27 +- .../bismark/genomepreparation/meta.yml | 13 +- .../genomepreparation/tests/main.nf.test | 41 ++- .../genomepreparation/tests/main.nf.test.snap | 129 +++++++--- .../bismark/genomepreparation/tests/tags.yml | 2 - .../methylationextractor/environment.yml | 2 +- .../bismark/methylationextractor/main.nf | 22 +- .../bismark/methylationextractor/meta.yml | 8 +- .../methylationextractor/tests/main.nf.test | 12 +- .../tests/main.nf.test.snap | 38 +-- .../methylationextractor/tests/tags.yml | 2 - .../nf-core/bismark/report/environment.yml | 2 +- modules/nf-core/bismark/report/main.nf | 17 +- modules/nf-core/bismark/report/meta.yml | 1 + .../nf-core/bismark/report/tests/main.nf.test | 38 ++- .../bismark/report/tests/main.nf.test.snap | 13 +- modules/nf-core/bismark/report/tests/tags.yml | 2 - .../nf-core/bismark/summary/environment.yml | 2 +- modules/nf-core/bismark/summary/main.nf | 21 +- modules/nf-core/bismark/summary/meta.yml | 3 +- .../bismark/summary/tests/main.nf.test | 25 +- .../bismark/summary/tests/main.nf.test.snap | 8 +- .../nf-core/bismark/summary/tests/tags.yml | 2 - 42 files changed, 520 insertions(+), 378 deletions(-) delete mode 100644 modules/nf-core/bismark/align/tests/tags.yml delete mode 100644 modules/nf-core/bismark/coverage2cytosine/tests/tags.yml delete mode 100644 modules/nf-core/bismark/deduplicate/tests/tags.yml delete mode 100644 modules/nf-core/bismark/genomepreparation/tests/tags.yml delete mode 100644 modules/nf-core/bismark/methylationextractor/tests/tags.yml delete mode 100644 modules/nf-core/bismark/report/tests/tags.yml delete mode 100644 modules/nf-core/bismark/summary/tests/tags.yml diff --git a/modules/nf-core/bismark/align/environment.yml b/modules/nf-core/bismark/align/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/align/environment.yml +++ b/modules/nf-core/bismark/align/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/align/main.nf b/modules/nf-core/bismark/align/main.nf index 3487979ec95f..f6f04b936954 100644 --- a/modules/nf-core/bismark/align/main.nf +++ b/modules/nf-core/bismark/align/main.nf @@ -4,17 +4,18 @@ process BISMARK_ALIGN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: tuple val(meta), path("*bam") , emit: bam tuple val(meta), path("*report.txt"), emit: report - tuple val(meta), path("*fq.gz") , optional:true, emit: unmapped + tuple val(meta), path("*fq.gz") , emit: unmapped, optional: true path "versions.yml" , emit: versions when: @@ -54,8 +55,9 @@ process BISMARK_ALIGN { args += " --multicore ${ccore}" } } - """ + mv $fasta $index/ + bismark \\ $fastq \\ --genome $index \\ @@ -67,4 +69,17 @@ process BISMARK_ALIGN { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bam + touch ${prefix}.report.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/align/meta.yml b/modules/nf-core/bismark/align/meta.yml index e0a979b39e1c..fa794b79303c 100644 --- a/modules/nf-core/bismark/align/meta.yml +++ b/modules/nf-core/bismark/align/meta.yml @@ -31,7 +31,21 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - - index: + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference genome FASTA file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: type: directory description: Bismark genome index directory pattern: "BismarkIndex" @@ -75,3 +89,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/align/tests/main.nf.test b/modules/nf-core/bismark/align/tests/main.nf.test index d6fac9f88212..2ee01b84ef40 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test +++ b/modules/nf-core/bismark/align/tests/main.nf.test @@ -3,264 +3,181 @@ nextflow_process { name "Test Process BISMARK_ALIGN" script "../main.nf" process "BISMARK_ALIGN" + tag "modules" tag "modules_nfcore" tag "bismark" tag "bismark/align" tag "bismark/genomepreparation" - test("Should run bismark/align (bowtie2 single end) without failures") { - config './nextflow_bowtie2.config' - - setup { - run("BISMARK_GENOMEPREPARATION") { - script "../../genomepreparation/main.nf" - process { - """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - """ - } + setup { + run("BISMARK_GENOMEPREPARATION") { + script "../../genomepreparation/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ } } + } + + test("bowtie2 single-end / sarscov2 genome [fasta]") { + config './nextflow_bowtie2.config' when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } then { assertAll( - { assert process.success }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith("bt2_SE_report.txt") - assert path(get(1)).readLines().last().contains("Bismark completed in") - } + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() } - }, - { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.unmapped, - process.out.versions - ).match() - } ) } } - test("Should run bismark/align (bowtie2 paired end) without failures") { + test("bowtie2 paired-end / sarscov2 genome [fasta]") { config './nextflow_bowtie2.config' - setup { - run("BISMARK_GENOMEPREPARATION") { - script "../../genomepreparation/main.nf" - process { - """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - """ - } - } - } when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ - [ id:'test', single_end:false ], + input[0] = Channel.of([ + [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } then { assertAll( - { assert process.success }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith("_bt2_PE_report.txt") - assert path(get(1)).readLines().last().contains("Bismark completed in") - } + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, + file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() } - }, - { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.unmapped, - process.out.versions - ).match() - } ) } } - test("Should run bismark/align (hisat2 single end) without failures") { + test("hisat2 single-end / sarscov2 genome [fasta]") { config './nextflow_hisat2.config' - setup { - run("BISMARK_GENOMEPREPARATION") { - script "../../genomepreparation/main.nf" - process { - """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - """ - } - } - } - when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } then { assertAll( - { assert process.success }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith("hisat2_SE_report.txt") - assert path(get(1)).readLines().last().contains("Bismark completed in") - } + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() } - }, - { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.unmapped, - process.out.versions - ).match() - } ) } } - test("Should run bismark/align (hisat2 paired end) without failures") { + test("hisat2 paired-end / sarscov2 genome [fasta]") { config './nextflow_hisat2.config' - setup { - run("BISMARK_GENOMEPREPARATION") { - script "../../genomepreparation/main.nf" - process { - """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - """ - } - } - } - when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ - [ id:'test', single_end:false ], + input[0] = Channel.of([ + [ id:'test', single_end:true ], [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) ] - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } then { assertAll( - { assert process.success }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith("hisat2_PE_report.txt") - assert path(get(1)).readLines().last().contains("Bismark completed in") - } + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1][0]).getReadsMD5() }, + file(process.out.report[0][1][0]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5009"), + process.out.unmapped, + process.out.versions + ).match() } - }, - { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.unmapped, - process.out.versions - ).match() - } ) } } - test("Should run bismark/align (minimap2 single end) without failures") { + test("minimap2 single-end / sarscov2 genome [fasta]") { config './nextflow_minimap2.config' - setup { - run("BISMARK_GENOMEPREPARATION") { - script "../../genomepreparation/main.nf" - process { - """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - """ - } - } - } - when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:true ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } then { assertAll( - { assert process.success }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith("mm2_SE_report.txt") - assert path(get(1)).readLines().last().contains("Bismark completed in") - } + { assert process.success }, + { assert snapshot( + process.out.bam.collect { bam(it[1]).getReadsMD5() }, + file(process.out.report[0][1]).readLines().contains("Number of alignments with a unique best hit from the different alignments:\t5047"), + process.out.unmapped, + process.out.versions + ).match() } - }, - { assert snapshot( - process.out.bam.collect { bam(it[1]).getReadsMD5() }, - process.out.unmapped, - process.out.versions - ).match() - } ) } } + } diff --git a/modules/nf-core/bismark/align/tests/main.nf.test.snap b/modules/nf-core/bismark/align/tests/main.nf.test.snap index 66b89918bf8a..3842cd6d91db 100644 --- a/modules/nf-core/bismark/align/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/align/tests/main.nf.test.snap @@ -1,92 +1,97 @@ { - "Should run bismark/align (hisat2 paired end) without failures": { + "bowtie2 paired-end / sarscov2 genome [fasta]": { "content": [ [ - "fb9d284aec4b2c727af3c5ffd77c6381" + "936c0d5ce713130113e99e09a5b53afd" ], + true, [ ], [ - "versions.yml:md5,908dc37f43469e417f419f1173047da5" + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:23:02.893088" + "timestamp": "2024-10-13T17:35:23.192447327" }, - "Should run bismark/align (bowtie2 paired end) without failures": { + "hisat2 paired-end / sarscov2 genome [fasta]": { "content": [ [ - "458c5350c3f96a8dde710985bfb62827" + "936c0d5ce713130113e99e09a5b53afd" ], + true, [ ], [ - "versions.yml:md5,908dc37f43469e417f419f1173047da5" + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:22:24.892023" + "timestamp": "2024-10-13T17:36:10.145541495" }, - "Should run bismark/align (hisat2 single end) without failures": { + "minimap2 single-end / sarscov2 genome [fasta]": { "content": [ [ - "936c0d5ce713130113e99e09a5b53afd" + "d354e6c6d6a06e36630590de8f27031a" ], + true, [ ], [ - "versions.yml:md5,908dc37f43469e417f419f1173047da5" + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:22:43.401686" + "timestamp": "2024-10-13T17:36:32.094369612" }, - "Should run bismark/align (minimap2 single end) without failures": { + "bowtie2 single-end / sarscov2 genome [fasta]": { "content": [ [ - "d354e6c6d6a06e36630590de8f27031a" + "936c0d5ce713130113e99e09a5b53afd" ], + true, [ ], [ - "versions.yml:md5,908dc37f43469e417f419f1173047da5" + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:23:20.046695" + "timestamp": "2024-10-13T17:34:58.431003479" }, - "Should run bismark/align (bowtie2 single end) without failures": { + "hisat2 single-end / sarscov2 genome [fasta]": { "content": [ [ "936c0d5ce713130113e99e09a5b53afd" ], + true, [ ], [ - "versions.yml:md5,908dc37f43469e417f419f1173047da5" + "versions.yml:md5,50c4bb6313fda6a7c6212ceb5dd638f5" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:22:05.435199" + "timestamp": "2024-10-13T17:35:45.557280528" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/align/tests/tags.yml b/modules/nf-core/bismark/align/tests/tags.yml deleted file mode 100644 index dd99d8190f5d..000000000000 --- a/modules/nf-core/bismark/align/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/align: - - modules/nf-core/bismark/align/** diff --git a/modules/nf-core/bismark/coverage2cytosine/environment.yml b/modules/nf-core/bismark/coverage2cytosine/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/coverage2cytosine/environment.yml +++ b/modules/nf-core/bismark/coverage2cytosine/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/coverage2cytosine/main.nf b/modules/nf-core/bismark/coverage2cytosine/main.nf index 0ad2d434bca7..37ce2e5c5187 100644 --- a/modules/nf-core/bismark/coverage2cytosine/main.nf +++ b/modules/nf-core/bismark/coverage2cytosine/main.nf @@ -4,15 +4,16 @@ process BISMARK_COVERAGE2CYTOSINE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(coverage_file) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: - tuple val(meta), path("*.cov.gz"), optional: true , emit: coverage + tuple val(meta), path("*.cov.gz") , emit: coverage, optional: true tuple val(meta), path("*report.txt.gz") , emit: report tuple val(meta), path("*cytosine_context_summary.txt") , emit: summary path "versions.yml" , emit: versions @@ -23,8 +24,9 @@ process BISMARK_COVERAGE2CYTOSINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - """ + mv $fasta $index/ + coverage2cytosine \\ $coverage_file \\ --genome $index \\ @@ -37,4 +39,18 @@ process BISMARK_COVERAGE2CYTOSINE { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.cov.gz + touch ${prefix}.report.txt.gz + touch ${prefix}.cytosine_context_summary.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/coverage2cytosine/meta.yml b/modules/nf-core/bismark/coverage2cytosine/meta.yml index f35117f4f27e..705b57f51b97 100644 --- a/modules/nf-core/bismark/coverage2cytosine/meta.yml +++ b/modules/nf-core/bismark/coverage2cytosine/meta.yml @@ -31,7 +31,21 @@ input: type: file description: | A file containing methylation calls per position, in the format produced by bismark_methylation_extractor. - - - index: + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: | + Reference genome FASTA file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: type: directory description: Bismark genome index directory pattern: "BismarkIndex" @@ -75,3 +89,4 @@ authors: - "@ewels" maintainers: - "@ewels" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test index 3ed5c0d2d37c..ac4f7ae265db 100644 --- a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test +++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process BISMARK_COVERAGE2CYTOSINE" script "../main.nf" process "BISMARK_COVERAGE2CYTOSINE" + tag "modules" tag "modules_nfcore" tag "bismark" @@ -10,14 +11,17 @@ nextflow_process { tag "bismark/methylationextractor" tag "bismark/genomepreparation" - test("Should run bismark/coverage2cytosine without failures") { + test("sarscov2 genome [fasta] | sarscov2 paired-end methylated [bam]") { setup { run("BISMARK_GENOMEPREPARATION") { script "../../genomepreparation/main.nf" process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -26,10 +30,10 @@ nextflow_process { script "../../methylationextractor/main.nf" process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) - ] + ]) input[1] = BISMARK_GENOMEPREPARATION.out.index """ } @@ -40,7 +44,8 @@ nextflow_process { process { """ input[0] = BISMARK_METHYLATIONEXTRACTOR.out.coverage - input[1] = BISMARK_GENOMEPREPARATION.out.index + input[1] = input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap index e7d2c195d1ec..58c029867dd9 100644 --- a/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/coverage2cytosine/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run bismark/coverage2cytosine without failures": { + "sarscov2 genome [fasta] | sarscov2 paired-end methylated [bam]": { "content": [ { "0": [ @@ -24,7 +24,7 @@ ] ], "3": [ - "versions.yml:md5,9ad535f8f13a38c9bc3f0975fbfee39c" + "versions.yml:md5,d68e9a778e9c156a80869e880c0518c8" ], "coverage": [ @@ -48,14 +48,14 @@ ] ], "versions": [ - "versions.yml:md5,9ad535f8f13a38c9bc3f0975fbfee39c" + "versions.yml:md5,d68e9a778e9c156a80869e880c0518c8" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.4" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-02T10:10:27.945147685" + "timestamp": "2024-10-13T18:20:45.406703493" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/coverage2cytosine/tests/tags.yml b/modules/nf-core/bismark/coverage2cytosine/tests/tags.yml deleted file mode 100644 index aec54b6754db..000000000000 --- a/modules/nf-core/bismark/coverage2cytosine/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/coverage2cytosine: - - modules/nf-core/bismark/coverage2cytosine/** diff --git a/modules/nf-core/bismark/deduplicate/environment.yml b/modules/nf-core/bismark/deduplicate/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/deduplicate/environment.yml +++ b/modules/nf-core/bismark/deduplicate/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/deduplicate/main.nf b/modules/nf-core/bismark/deduplicate/main.nf index e41b601ba9fd..2da9312c9d92 100644 --- a/modules/nf-core/bismark/deduplicate/main.nf +++ b/modules/nf-core/bismark/deduplicate/main.nf @@ -4,8 +4,8 @@ process BISMARK_DEDUPLICATE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(bam) @@ -19,9 +19,9 @@ process BISMARK_DEDUPLICATE { task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - def seqtype = meta.single_end ? '-s' : '-p' + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def seqtype = meta.single_end ? '-s' : '-p' """ deduplicate_bismark \\ $args \\ @@ -33,4 +33,17 @@ process BISMARK_DEDUPLICATE { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.deduplicated.bam + touch ${prefix}.deduplication_report.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/deduplicate/meta.yml b/modules/nf-core/bismark/deduplicate/meta.yml index 31ffeb945b16..5de7c2102a6a 100644 --- a/modules/nf-core/bismark/deduplicate/meta.yml +++ b/modules/nf-core/bismark/deduplicate/meta.yml @@ -62,3 +62,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/deduplicate/tests/main.nf.test b/modules/nf-core/bismark/deduplicate/tests/main.nf.test index 1f67b7d25852..a82b4b73f7c2 100644 --- a/modules/nf-core/bismark/deduplicate/tests/main.nf.test +++ b/modules/nf-core/bismark/deduplicate/tests/main.nf.test @@ -3,23 +3,21 @@ nextflow_process { name "Test Process BISMARK_DEDUPLICATE" script "../main.nf" process "BISMARK_DEDUPLICATE" + tag "bismark" tag "bismark/deduplicate" tag "modules" tag "modules_nfcore" - test("Should run bismark/deduplicate without failures") { + test("sarscov2 paired-end methylated [bam]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) - ] + ]) """ } } diff --git a/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap index 7e4aea389909..98e72559b968 100644 --- a/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/deduplicate/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run bismark/deduplicate without failures": { + "sarscov2 paired-end methylated [bam]": { "content": [ [ "8036b4b920354438ddd1871c88f5088" @@ -14,13 +14,13 @@ ] ], [ - "versions.yml:md5,1859cf7d4e598dec0678f073c9e2f539" + "versions.yml:md5,80ac07cad7c9ea075ffd7b75d74c39cd" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-08-03T19:28:29.457009" + "timestamp": "2024-10-13T18:31:09.804719461" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/deduplicate/tests/tags.yml b/modules/nf-core/bismark/deduplicate/tests/tags.yml deleted file mode 100644 index 35ac35059274..000000000000 --- a/modules/nf-core/bismark/deduplicate/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/deduplicate: - - modules/nf-core/bismark/deduplicate/** diff --git a/modules/nf-core/bismark/genomepreparation/environment.yml b/modules/nf-core/bismark/genomepreparation/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/genomepreparation/environment.yml +++ b/modules/nf-core/bismark/genomepreparation/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/genomepreparation/main.nf b/modules/nf-core/bismark/genomepreparation/main.nf index 7f5a2eeedfb3..e8b9fedae201 100644 --- a/modules/nf-core/bismark/genomepreparation/main.nf +++ b/modules/nf-core/bismark/genomepreparation/main.nf @@ -4,15 +4,15 @@ process BISMARK_GENOMEPREPARATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: - path fasta, stageAs: "BismarkIndex/*" + tuple val(meta), path(fasta) output: - path "BismarkIndex" , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("BismarkIndex"), emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,10 +20,27 @@ process BISMARK_GENOMEPREPARATION { script: def args = task.ext.args ?: '' """ + mkdir BismarkIndex + mv $fasta BismarkIndex/ + bismark_genome_preparation \\ $args \\ BismarkIndex + rm BismarkIndex/$fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + """ + mkdir BismarkIndex + touch BismarkIndex/$fasta + cat <<-END_VERSIONS > versions.yml "${task.process}": bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') diff --git a/modules/nf-core/bismark/genomepreparation/meta.yml b/modules/nf-core/bismark/genomepreparation/meta.yml index 18ca34a9f8dc..c1880271b154 100644 --- a/modules/nf-core/bismark/genomepreparation/meta.yml +++ b/modules/nf-core/bismark/genomepreparation/meta.yml @@ -23,11 +23,21 @@ tools: licence: ["GPL-3.0-or-later"] identifier: biotools:bismark input: - - - fasta: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: type: file description: Input genome fasta file output: - index: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - BismarkIndex: type: directory description: Bismark genome index directory @@ -41,3 +51,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test index bd9b95e38fe7..3ba997227834 100644 --- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test @@ -3,31 +3,54 @@ nextflow_process { name "Test Process BISMARK_GENOMEPREPARATION" script "../main.nf" process "BISMARK_GENOMEPREPARATION" - tag "bismark" - tag "bismark/genomepreparation" + tag "modules" + tag "bismark/genomepreparation" + tag "bismark" tag "modules_nfcore" - test("Should run bismark/genomepreparation without failures") { + test("sarscov2 genome [fasta]") { when { - params { - outdir = "$outputDir" - } process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } then { assertAll( - { assert process.success }, - { assert snapshot(process.out).match() } + { assert process.success }, + { assert snapshot(process.out).match() } ) } + } + + test("sarscov2 genome [fasta] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } } diff --git a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap index a343efad4c4e..caf8afc8891d 100644 --- a/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/genomepreparation/tests/main.nf.test.snap @@ -1,65 +1,114 @@ { - "Should run bismark/genomepreparation without failures": { + "sarscov2 genome [fasta] - stub": { "content": [ { "0": [ [ + { + "id": "test" + }, + [ + "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ], + "index": [ + [ + { + "id": "test" + }, + [ + "genome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T08:26:30.051110425" + }, + "sarscov2 genome [fasta]": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, [ [ - "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", - "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", - "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", - "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", - "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", - "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" - ], - [ - "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", - "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", - "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", - "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", - "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", - "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + [ + "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", + "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", + "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", + "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", + "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", + "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" + ], + [ + "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", + "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", + "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", + "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", + "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", + "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + ] ] - ], - "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6" + ] ] ], "1": [ - "versions.yml:md5,92d3bda85e8d9517fce396c615141003" + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" ], "index": [ [ + { + "id": "test" + }, [ [ - "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", - "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", - "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", - "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", - "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", - "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" - ], - [ - "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", - "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", - "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", - "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", - "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", - "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", - "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + [ + "BS_CT.1.bt2:md5,10a8854e5eeb95629f46d24b0d8da70c", + "BS_CT.2.bt2:md5,bc5d407e6fce3e1cdb4b23ab2a20f707", + "BS_CT.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_CT.4.bt2:md5,6c4f549575e5882ff3a97ae10ae2e7be", + "BS_CT.rev.1.bt2:md5,d37d586b41b6a36efb25839961d242cb", + "BS_CT.rev.2.bt2:md5,48bf400de85cd7324fbf6bf38fe2dc95", + "genome_mfa.CT_conversion.fa:md5,903b9f357eea4a5f36e21e78e0fe1dfa" + ], + [ + "BS_GA.1.bt2:md5,a6fa4068ed10872568f32568c66cb600", + "BS_GA.2.bt2:md5,fc5b634e2f5137801e3801d62ad05f74", + "BS_GA.3.bt2:md5,4ed93abba181d8dfab2e303e33114777", + "BS_GA.4.bt2:md5,b1e855685ed634daa7df8e180c9b2fc4", + "BS_GA.rev.1.bt2:md5,17f51e65f44477962226a83b369b2bc4", + "BS_GA.rev.2.bt2:md5,d36044c5dfe37af0411f60d446585bc6", + "genome_mfa.GA_conversion.fa:md5,e529375ec2039112161465b5169fcd59" + ] ] - ], - "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6" + ] ] ], "versions": [ - "versions.yml:md5,92d3bda85e8d9517fce396c615141003" + "versions.yml:md5,4d9a42530334575b18a6bde4ae72f7d6" ] } ], - "timestamp": "2023-10-17T16:14:41.509500586" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-13T08:26:20.352083082" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/genomepreparation/tests/tags.yml b/modules/nf-core/bismark/genomepreparation/tests/tags.yml deleted file mode 100644 index 279f91bba2df..000000000000 --- a/modules/nf-core/bismark/genomepreparation/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/genomepreparation: - - modules/nf-core/bismark/genomepreparation/** diff --git a/modules/nf-core/bismark/methylationextractor/environment.yml b/modules/nf-core/bismark/methylationextractor/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/methylationextractor/environment.yml +++ b/modules/nf-core/bismark/methylationextractor/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/methylationextractor/main.nf b/modules/nf-core/bismark/methylationextractor/main.nf index 44395155492f..3a71d35deeda 100644 --- a/modules/nf-core/bismark/methylationextractor/main.nf +++ b/modules/nf-core/bismark/methylationextractor/main.nf @@ -4,12 +4,12 @@ process BISMARK_METHYLATIONEXTRACTOR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(bam) - path index + tuple val(meta2), path(index) output: tuple val(meta), path("*.bedGraph.gz") , emit: bedgraph @@ -49,4 +49,20 @@ process BISMARK_METHYLATIONEXTRACTOR { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bedGraph.gz + touch ${prefix}.txt.gz + touch ${prefix}.cov.gz + touch ${prefix}_splitting_report.txt + touch ${prefix}.M-bias.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/methylationextractor/meta.yml b/modules/nf-core/bismark/methylationextractor/meta.yml index 673cb1ca557e..2aaefdfab16e 100644 --- a/modules/nf-core/bismark/methylationextractor/meta.yml +++ b/modules/nf-core/bismark/methylationextractor/meta.yml @@ -31,7 +31,12 @@ input: type: file description: BAM file containing read alignments pattern: "*.{bam}" - - - index: + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: type: directory description: Bismark genome index directory pattern: "BismarkIndex" @@ -95,3 +100,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test index dea2c1fed8ca..fce2e35be5a4 100644 --- a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test +++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test @@ -3,20 +3,24 @@ nextflow_process { name "Test Process BISMARK_METHYLATIONEXTRACTOR" script "../main.nf" process "BISMARK_METHYLATIONEXTRACTOR" + tag "modules" tag "modules_nfcore" tag "bismark" tag "bismark/methylationextractor" tag "bismark/genomepreparation" - test("Should run bismark/methylationextractor without failures") { + test("sarscov2 paired-end methylated [bam] / sarscov2 genome [fasta]") { setup { run("BISMARK_GENOMEPREPARATION") { script "../../genomepreparation/main.nf" process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -25,10 +29,10 @@ nextflow_process { when { process { """ - input[0] = [ + input[0] = Channel.of([ [ id:'test', single_end:false ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.methylated.bam', checkIfExists: true) - ] + ]) input[1] = BISMARK_GENOMEPREPARATION.out.index """ } diff --git a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap index 52c26306a1ca..dd83c755fa82 100644 --- a/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/methylationextractor/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "Should run bismark/methylationextractor without failures": { + "sarscov2 paired-end methylated [bam] / sarscov2 genome [fasta]": { "content": [ { "0": [ @@ -18,12 +18,12 @@ "single_end": false }, [ - "CHG_OB_test.paired_end.methylated.txt.gz:md5,2dcbf53d334758bc8ea8e7f7a9482f0b", - "CHG_OT_test.paired_end.methylated.txt.gz:md5,08bf48d70cf160f03f16106246c042a3", - "CHH_OB_test.paired_end.methylated.txt.gz:md5,3d9a2ed915593c69551cdf825d92e595", - "CHH_OT_test.paired_end.methylated.txt.gz:md5,979b5e8e8e9b8b7de556383be736cf20", - "CpG_OB_test.paired_end.methylated.txt.gz:md5,4ee4561c082c6659fa245a27d6ac9744", - "CpG_OT_test.paired_end.methylated.txt.gz:md5,63c7462425494fab87c10babebab49bb" + "CHG_OB_test.paired_end.methylated.txt.gz:md5,de98c596d927732d0a5a4cf4b3b9e7ae", + "CHG_OT_test.paired_end.methylated.txt.gz:md5,64ea7598db55ae810bc6846afe1941b8", + "CHH_OB_test.paired_end.methylated.txt.gz:md5,fac33b1186436430913d844662862972", + "CHH_OT_test.paired_end.methylated.txt.gz:md5,2a1509bd87032f9ae2c7ca5d0d728b3a", + "CpG_OB_test.paired_end.methylated.txt.gz:md5,dfecc0ceaca41ac848ff7d6e990a3f17", + "CpG_OT_test.paired_end.methylated.txt.gz:md5,5280f3ea983ee0f33b7c467f63f6c6d1" ] ] ], @@ -42,7 +42,7 @@ "id": "test", "single_end": false }, - "test.paired_end.methylated_splitting_report.txt:md5,4ebaa7ff42aad09b4c7edd38150fef12" + "test.paired_end.methylated_splitting_report.txt:md5,25f4f2fbf35cc9d7dc9e21209c40ca07" ] ], "4": [ @@ -55,7 +55,7 @@ ] ], "5": [ - "versions.yml:md5,b2efe40312b4b8fcd8276d788f89c1da" + "versions.yml:md5,c01f97c8def49098023fded456717776" ], "bedgraph": [ [ @@ -91,12 +91,12 @@ "single_end": false }, [ - "CHG_OB_test.paired_end.methylated.txt.gz:md5,2dcbf53d334758bc8ea8e7f7a9482f0b", - "CHG_OT_test.paired_end.methylated.txt.gz:md5,08bf48d70cf160f03f16106246c042a3", - "CHH_OB_test.paired_end.methylated.txt.gz:md5,3d9a2ed915593c69551cdf825d92e595", - "CHH_OT_test.paired_end.methylated.txt.gz:md5,979b5e8e8e9b8b7de556383be736cf20", - "CpG_OB_test.paired_end.methylated.txt.gz:md5,4ee4561c082c6659fa245a27d6ac9744", - "CpG_OT_test.paired_end.methylated.txt.gz:md5,63c7462425494fab87c10babebab49bb" + "CHG_OB_test.paired_end.methylated.txt.gz:md5,de98c596d927732d0a5a4cf4b3b9e7ae", + "CHG_OT_test.paired_end.methylated.txt.gz:md5,64ea7598db55ae810bc6846afe1941b8", + "CHH_OB_test.paired_end.methylated.txt.gz:md5,fac33b1186436430913d844662862972", + "CHH_OT_test.paired_end.methylated.txt.gz:md5,2a1509bd87032f9ae2c7ca5d0d728b3a", + "CpG_OB_test.paired_end.methylated.txt.gz:md5,dfecc0ceaca41ac848ff7d6e990a3f17", + "CpG_OT_test.paired_end.methylated.txt.gz:md5,5280f3ea983ee0f33b7c467f63f6c6d1" ] ] ], @@ -106,18 +106,18 @@ "id": "test", "single_end": false }, - "test.paired_end.methylated_splitting_report.txt:md5,4ebaa7ff42aad09b4c7edd38150fef12" + "test.paired_end.methylated_splitting_report.txt:md5,25f4f2fbf35cc9d7dc9e21209c40ca07" ] ], "versions": [ - "versions.yml:md5,b2efe40312b4b8fcd8276d788f89c1da" + "versions.yml:md5,c01f97c8def49098023fded456717776" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "23.10.4" + "nextflow": "24.04.4" }, - "timestamp": "2024-08-02T08:07:52.585249564" + "timestamp": "2024-10-13T18:09:13.593807534" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/methylationextractor/tests/tags.yml b/modules/nf-core/bismark/methylationextractor/tests/tags.yml deleted file mode 100644 index 272e4df1f435..000000000000 --- a/modules/nf-core/bismark/methylationextractor/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/methylationextractor: - - modules/nf-core/bismark/methylationextractor/** diff --git a/modules/nf-core/bismark/report/environment.yml b/modules/nf-core/bismark/report/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/report/environment.yml +++ b/modules/nf-core/bismark/report/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/report/main.nf b/modules/nf-core/bismark/report/main.nf index 6570f098c54b..e68ee8e56ea6 100644 --- a/modules/nf-core/bismark/report/main.nf +++ b/modules/nf-core/bismark/report/main.nf @@ -4,8 +4,8 @@ process BISMARK_REPORT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: tuple val(meta), path(align_report), path(dedup_report), path(splitting_report), path(mbias) @@ -27,4 +27,17 @@ process BISMARK_REPORT { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.report.txt + touch ${prefix}.report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/report/meta.yml b/modules/nf-core/bismark/report/meta.yml index 52fece5aeeb0..c1191e9b46dc 100644 --- a/modules/nf-core/bismark/report/meta.yml +++ b/modules/nf-core/bismark/report/meta.yml @@ -61,3 +61,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/report/tests/main.nf.test b/modules/nf-core/bismark/report/tests/main.nf.test index aa373e9aa04b..9082bbde836e 100644 --- a/modules/nf-core/bismark/report/tests/main.nf.test +++ b/modules/nf-core/bismark/report/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process BISMARK_REPORT" script "../main.nf" process "BISMARK_REPORT" + tag "modules" tag "modules_nfcore" tag "bismark" @@ -12,14 +13,17 @@ nextflow_process { tag "bismark/methylationextractor" tag "bismark/genomepreparation" - test("Should run bismark/report without failures") { + test("sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]") { setup { run("BISMARK_GENOMEPREPARATION") { script "../../genomepreparation/main.nf" process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -28,14 +32,12 @@ nextflow_process { script "../../align/main.nf" process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } @@ -61,9 +63,6 @@ nextflow_process { } when { - params { - outdir = "$outputDir" - } process { """ input[0] = BISMARK_ALIGN.out.report @@ -77,15 +76,10 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out.versions).match("versions") }, - { - with(process.out.report) { - with(get(0)) { - assert get(1).endsWith('_PE_report.html') - assert path(get(1)).readLines().last().contains('') - } - } - } + { assert snapshot( + file(process.out.report[0][1]).name, + process.out.versions + ).match() }, ) } diff --git a/modules/nf-core/bismark/report/tests/main.nf.test.snap b/modules/nf-core/bismark/report/tests/main.nf.test.snap index dc05e6551389..e1ebf0223d92 100644 --- a/modules/nf-core/bismark/report/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/report/tests/main.nf.test.snap @@ -1,10 +1,15 @@ { - "versions": { + "sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]": { "content": [ + "test.methylated_1_bismark_bt2_SE_report.html", [ - "versions.yml:md5,c2e2c0bd500e9ce95ae7ab82f667270b" + "versions.yml:md5,12d0b9440211d6540bbdc42e14fa18e6" ] ], - "timestamp": "2023-10-17T16:13:42.879192383" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T18:47:46.955822618" } -} \ No newline at end of file +} diff --git a/modules/nf-core/bismark/report/tests/tags.yml b/modules/nf-core/bismark/report/tests/tags.yml deleted file mode 100644 index c72a1f94fec4..000000000000 --- a/modules/nf-core/bismark/report/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/report: - - modules/nf-core/bismark/report/** diff --git a/modules/nf-core/bismark/summary/environment.yml b/modules/nf-core/bismark/summary/environment.yml index fbc3fdf202c8..9bc4753bdabb 100644 --- a/modules/nf-core/bismark/summary/environment.yml +++ b/modules/nf-core/bismark/summary/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::bismark=0.24.0 + - bioconda::bismark=0.24.2 diff --git a/modules/nf-core/bismark/summary/main.nf b/modules/nf-core/bismark/summary/main.nf index 34cebffbfb3d..2aadfc03c947 100644 --- a/modules/nf-core/bismark/summary/main.nf +++ b/modules/nf-core/bismark/summary/main.nf @@ -3,8 +3,8 @@ process BISMARK_SUMMARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bismark:0.24.0--hdfd78af_0' : - 'biocontainers/bismark:0.24.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bismark:0.24.2--hdfd78af_0' : + 'biocontainers/bismark:0.24.2--hdfd78af_0' }" input: val(bam) @@ -14,8 +14,8 @@ process BISMARK_SUMMARY { path(mbias) output: - path "*report.{html,txt}", emit: summary - path "versions.yml" , emit: versions + path("*report.{html,txt}"), emit: summary + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -30,4 +30,17 @@ process BISMARK_SUMMARY { bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') END_VERSIONS """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.report.txt + touch ${prefix}.report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bismark: \$(echo \$(bismark -v 2>&1) | sed 's/^.*Bismark Version: v//; s/Copyright.*\$//') + END_VERSIONS + """ } diff --git a/modules/nf-core/bismark/summary/meta.yml b/modules/nf-core/bismark/summary/meta.yml index 907a2d706b6f..da18a5c8817c 100644 --- a/modules/nf-core/bismark/summary/meta.yml +++ b/modules/nf-core/bismark/summary/meta.yml @@ -45,7 +45,7 @@ input: pattern: "*.txt" output: - summary: - - "*report.{html": + - "*report.{html,txt}": type: file description: Bismark summary pattern: "*.{html,txt}" @@ -58,3 +58,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bismark/summary/tests/main.nf.test b/modules/nf-core/bismark/summary/tests/main.nf.test index 2621fc582f2f..046a59592b54 100644 --- a/modules/nf-core/bismark/summary/tests/main.nf.test +++ b/modules/nf-core/bismark/summary/tests/main.nf.test @@ -3,6 +3,7 @@ nextflow_process { name "Test Process BISMARK_SUMMARY" script "../main.nf" process "BISMARK_SUMMARY" + tag "modules" tag "modules_nfcore" tag "bismark" @@ -12,14 +13,17 @@ nextflow_process { tag "bismark/genomepreparation" tag "bismark/methylationextractor" - test("Should run bismark/summary without failures") { + test("sarscov2 genome [fasta] | sarscov2 single-end methylated [fastq]") { setup { run("BISMARK_GENOMEPREPARATION") { script "../../genomepreparation/main.nf" process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -28,14 +32,12 @@ nextflow_process { script "../../align/main.nf" process { """ - input[0] = [ - [ id:'test', single_end:false ], - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BISMARK_GENOMEPREPARATION.out.index + input[0] = Channel.of([ + [ id:'test', single_end:true ], + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ [ id:'sarscov2'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ]) + input[2] = BISMARK_GENOMEPREPARATION.out.index """ } } @@ -61,9 +63,6 @@ nextflow_process { } when { - params { - outdir = "$outputDir" - } process { """ input[0] = BISMARK_ALIGN.out.bam.collect { meta, bam -> bam } diff --git a/modules/nf-core/bismark/summary/tests/main.nf.test.snap b/modules/nf-core/bismark/summary/tests/main.nf.test.snap index acb445c1cc23..d9d0209ec545 100644 --- a/modules/nf-core/bismark/summary/tests/main.nf.test.snap +++ b/modules/nf-core/bismark/summary/tests/main.nf.test.snap @@ -2,9 +2,13 @@ "versions": { "content": [ [ - "versions.yml:md5,22bb5a457e4eef7ab3556e464263ce04" + "versions.yml:md5,daa43bc3da654ba5a8acbc9d272a9e90" ] ], - "timestamp": "2023-10-17T15:12:35.102032381" + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T18:31:02.192850471" } } \ No newline at end of file diff --git a/modules/nf-core/bismark/summary/tests/tags.yml b/modules/nf-core/bismark/summary/tests/tags.yml deleted file mode 100644 index 3d7ee0379bc0..000000000000 --- a/modules/nf-core/bismark/summary/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -bismark/summary: - - modules/nf-core/bismark/summary/** From 2f9a5431355897e299cb41928c45f51ea8410c42 Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Tue, 15 Oct 2024 16:04:22 +0200 Subject: [PATCH 148/486] New module: deepvariant/vcfstatsreport (#6777) * New module: deepvariant/vcfstatsreport * Add stub tests * exclude conda tests * Update main.nf Single thread. --- .github/workflows/test.yml | 2 + .../deepvariant/vcfstatsreport/main.nf | 59 ++++ .../deepvariant/vcfstatsreport/meta.yml | 47 ++++ .../vcfstatsreport/tests/main.nf.test | 183 ++++++++++++ .../vcfstatsreport/tests/main.nf.test.snap | 266 ++++++++++++++++++ .../deepvariant/vcfstatsreport/tests/tags.yml | 2 + 6 files changed, 559 insertions(+) create mode 100644 modules/nf-core/deepvariant/vcfstatsreport/main.nf create mode 100644 modules/nf-core/deepvariant/vcfstatsreport/meta.yml create mode 100644 modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test create mode 100644 modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap create mode 100644 modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml index 4be8bbe5c924..96851ec4a8d3 100644 --- a/.github/workflows/test.yml +++ b/.github/workflows/test.yml @@ -548,6 +548,8 @@ jobs: path: modules/nf-core/deepvariant/postprocessvariants - profile: conda path: modules/nf-core/deepvariant/rundeepvariant + - profile: conda + path: modules/nf-core/deepvariant/vcfstatsreport - profile: conda path: modules/nf-core/ensemblvep/vep - profile: conda diff --git a/modules/nf-core/deepvariant/vcfstatsreport/main.nf b/modules/nf-core/deepvariant/vcfstatsreport/main.nf new file mode 100644 index 000000000000..5bbf06b633f4 --- /dev/null +++ b/modules/nf-core/deepvariant/vcfstatsreport/main.nf @@ -0,0 +1,59 @@ +process DEEPVARIANT_VCFSTATSREPORT { + tag "$meta.id" + label 'process_single' + + // FIXME Conda is not supported at the moment + // BUG https://github.com/nf-core/modules/issues/1754 + // BUG https://github.com/bioconda/bioconda-recipes/issues/30310 + container "nf-core/deepvariant:1.6.1" + + input: + tuple val(meta), path(vcf) + + output: + tuple val(meta), path("${prefix}.visual_report.html"), emit: report + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 + // FIXME Revert this on next version bump + def VERSION = '1.6.1' + + """ + /opt/deepvariant/bin/vcf_stats_report \\ + --input_vcf=${vcf} \\ + --outfile_base ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant: $VERSION + END_VERSIONS + """ + + stub: + // Exit if running this module with -profile conda / -profile mamba + if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { + error "DEEPVARIANT module does not support Conda. Please use Docker / Singularity / Podman instead." + } + prefix = task.ext.prefix ?: "${meta.id}" + // WARN https://github.com/nf-core/modules/pull/5801#issuecomment-2194293755 + // FIXME Revert this on next version bump + def VERSION = '1.6.1' + """ + touch ${prefix}.visual_report.html + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deepvariant: $VERSION + END_VERSIONS + """ +} diff --git a/modules/nf-core/deepvariant/vcfstatsreport/meta.yml b/modules/nf-core/deepvariant/vcfstatsreport/meta.yml new file mode 100644 index 000000000000..c882a1b1249e --- /dev/null +++ b/modules/nf-core/deepvariant/vcfstatsreport/meta.yml @@ -0,0 +1,47 @@ +name: deepvariant_vcfstatsreport +description: DeepVariant is an analysis pipeline that uses a deep neural network to + call genetic variants from next-generation DNA sequencing data +keywords: + - variant calling + - machine learning + - neural network +tools: + - deepvariant: + description: DeepVariant is an analysis pipeline that uses a deep neural network + to call genetic variants from next-generation DNA sequencing data + homepage: https://github.com/google/deepvariant + documentation: https://github.com/google/deepvariant + tool_dev_url: https://github.com/google/deepvariant + doi: "10.1038/nbt.4235" + licence: ["BSD-3-clause"] + identifier: biotools:deepvariant +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "{*.vcf,vcf.gz,bcf,bcf.gz}" +output: + - report: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - ${prefix}.visual_report.html: + type: file + description: Visual report in HTML format + pattern: "*.html" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@fellen31" +maintainers: + - "@fellen31" diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test new file mode 100644 index 000000000000..bec946efd8cc --- /dev/null +++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test @@ -0,0 +1,183 @@ +nextflow_process { + + name "Test Process DEEPVARIANT_VCFSTATSREPORT" + script "../main.nf" + process "DEEPVARIANT_VCFSTATSREPORT" + + tag "deepvariant/vcfstatsreport" + tag "deepvariant" + tag "modules" + tag "modules_nfcore" + + test("vcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("vcf.gz") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bcf") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bcf.gz") { + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("vcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("vcf.gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bcf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("bcf.gz - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + '/genomics/sarscov2/illumina/vcf/test.bcf.gz', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap new file mode 100644 index 000000000000..9a9ac3cef600 --- /dev/null +++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/main.nf.test.snap @@ -0,0 +1,266 @@ +{ + "bcf.gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T08:19:35.672028563" + }, + "bcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T07:47:10.485269156" + }, + "vcf.gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T08:34:50.411910578" + }, + "vcf.gz": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T07:47:00.438649988" + }, + "vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,28e2e19d97cdeddf25813534384ae9ca" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-11T07:44:07.427456921" + }, + "bcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T08:35:03.341417618" + }, + "bcf.gz - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T08:35:13.52398762" + }, + "vcf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ], + "report": [ + [ + { + "id": "test" + }, + "test.visual_report.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,3378d1cbd4b3ba7579dcd6c47266f996" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-14T08:34:35.977457571" + } +} \ No newline at end of file diff --git a/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml b/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml new file mode 100644 index 000000000000..3b1f592291ce --- /dev/null +++ b/modules/nf-core/deepvariant/vcfstatsreport/tests/tags.yml @@ -0,0 +1,2 @@ +deepvariant/vcfstatsreport: + - modules/nf-core/deepvariant/vcfstatsreport/** From 9082d6440bdffbb4f5d9bd9d753361933b3febcb Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Tue, 15 Oct 2024 19:40:03 +0100 Subject: [PATCH 149/486] Don't skip whole trimming workflows (#6785) --- .../nf-core/fastq_qc_trim_filter_setstrandedness/main.nf | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf index 05078d23dcbf..c655af41588b 100644 --- a/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf +++ b/subworkflows/nf-core/fastq_qc_trim_filter_setstrandedness/main.nf @@ -139,7 +139,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with TrimGalore! // - if (trimmer == 'trimgalore' && !skip_trimming) { + if (trimmer == 'trimgalore') { FASTQ_FASTQC_UMITOOLS_TRIMGALORE ( ch_filtered_reads, skip_fastqc, @@ -162,7 +162,7 @@ workflow FASTQ_QC_TRIM_FILTER_SETSTRANDEDNESS { // // SUBWORKFLOW: Read QC, extract UMI and trim adapters with fastp // - if (trimmer == 'fastp' && !skip_trimming) { + if (trimmer == 'fastp') { FASTQ_FASTQC_UMITOOLS_FASTP ( ch_filtered_reads, skip_fastqc, From 847683c1bb3a94d846e18916f14c2bc60a447041 Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Wed, 16 Oct 2024 13:26:57 +0200 Subject: [PATCH 150/486] Fix SVDB/merge stubs (#6787) --- modules/nf-core/svdb/merge/main.nf | 7 +- modules/nf-core/svdb/merge/tests/main.nf.test | 52 ++++++++++++++ .../svdb/merge/tests/main.nf.test.snap | 68 +++++++++++++++++++ 3 files changed, 125 insertions(+), 2 deletions(-) create mode 100644 modules/nf-core/svdb/merge/tests/main.nf.test.snap diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index c24a9a7c388e..afc34bb4bcdf 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -36,7 +36,10 @@ process SVDB_MERGE { $prio \\ --vcf $input \\ > ${prefix}.vcf - bgzip ${prefix}.vcf + + bgzip \\ + --threads ${task.cpus} \\ + ${prefix}.vcf cat <<-END_VERSIONS > versions.yml "${task.process}": @@ -48,7 +51,7 @@ process SVDB_MERGE { stub: def prefix = task.ext.prefix ?: "${meta.id}" """ - touch ${prefix}.vcf.gz + echo | gzip > ${prefix}.vcf.gz cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test index 42f7c5706777..b0743a699f0b 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test +++ b/modules/nf-core/svdb/merge/tests/main.nf.test @@ -56,4 +56,56 @@ nextflow_process { } + test("test_svdb_merge - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + ]) + input[1] = [ 'tiddit', 'cnvnator'] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test_svdb_merge_noprio - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + ]) + input[1] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + } diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test.snap b/modules/nf-core/svdb/merge/tests/main.nf.test.snap new file mode 100644 index 000000000000..e79b2583b38b --- /dev/null +++ b/modules/nf-core/svdb/merge/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "test_svdb_merge - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T09:00:41.058996433" + }, + "test_svdb_merge_noprio - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ], + "vcf": [ + [ + { + "id": "test" + }, + "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T09:00:49.58223306" + } +} \ No newline at end of file From aa2f43221437b20cd204fb7ddbc7302fe859780f Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Wed, 16 Oct 2024 18:38:11 +0530 Subject: [PATCH 151/486] rm fasta from bwameth index folder to be handled separately (#6780) * rm fasta from bwameth index folder to be handled separately + update test + snaps * provide fasta separtely to index folder * add stub test --- modules/nf-core/bwameth/align/main.nf | 10 +-- modules/nf-core/bwameth/align/meta.yml | 15 +++- .../nf-core/bwameth/align/tests/main.nf.test | 69 +++++++++++-------- .../bwameth/align/tests/main.nf.test.snap | 32 ++++----- modules/nf-core/bwameth/index/main.nf | 25 +++++-- modules/nf-core/bwameth/index/meta.yml | 14 +++- .../nf-core/bwameth/index/tests/main.nf.test | 11 +-- .../bwameth/index/tests/main.nf.test.snap | 42 ++++++----- 8 files changed, 139 insertions(+), 79 deletions(-) diff --git a/modules/nf-core/bwameth/align/main.nf b/modules/nf-core/bwameth/align/main.nf index 476463ae0df2..8ce2ee322990 100644 --- a/modules/nf-core/bwameth/align/main.nf +++ b/modules/nf-core/bwameth/align/main.nf @@ -9,7 +9,8 @@ process BWAMETH_ALIGN { input: tuple val(meta), path(reads) - path index + tuple val(meta2), path(fasta) + tuple val(meta3), path(index) output: tuple val(meta), path("*.bam"), emit: bam @@ -24,17 +25,16 @@ process BWAMETH_ALIGN { def prefix = task.ext.prefix ?: "${meta.id}" def read_group = meta.read_group ? "-R ${meta.read_group}" : "" """ - INDEX=`find -L ${index} -name "*.bwameth.c2t" | sed 's/\\.bwameth.c2t\$//'` - # Modify the timestamps so that bwameth doesn't complain about building the index # See https://github.com/nf-core/methylseq/pull/217 - touch -c -- * + touch -c $index/* + mv $fasta $index/ bwameth.py \\ $args \\ $read_group \\ -t $task.cpus \\ - --reference \$INDEX \\ + --reference $index/$fasta \\ $reads \\ | samtools view $args2 -@ $task.cpus -bhS -o ${prefix}.bam - diff --git a/modules/nf-core/bwameth/align/meta.yml b/modules/nf-core/bwameth/align/meta.yml index 6cd78268d11f..593d17304fcf 100644 --- a/modules/nf-core/bwameth/align/meta.yml +++ b/modules/nf-core/bwameth/align/meta.yml @@ -33,7 +33,20 @@ input: description: | List of input FastQ files of size 1 and 2 for single-end and paired-end data, respectively. - - - index: + - - meta2: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + - - meta3: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - index: type: directory description: Directory containing bwameth genome index output: diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test b/modules/nf-core/bwameth/align/tests/main.nf.test index 94b1f56fde6d..211e09562677 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test +++ b/modules/nf-core/bwameth/align/tests/main.nf.test @@ -16,26 +16,29 @@ nextflow_process { script "../../../bwameth/index/main.nf" process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) - + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } } - test("test-bwameth-align-single-end") { + test("sarscov2 methylated single_end [fastq]") { when { process { """ - input[0] = [ - [ id:'test', single_end:true ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BWAMETH_INDEX.out.index - + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true) + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index """ } } @@ -52,20 +55,23 @@ nextflow_process { } } - test("test-bwameth-align-paired-end") { + test("sarscov2 methylated paired_end [fastq]") { when { process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BWAMETH_INDEX.out.index - + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index """ } } @@ -88,15 +94,18 @@ nextflow_process { when { process { """ - input[0] = [ - [ id:'test', single_end:false ], // meta map - [ - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) - ] - ] - input[1] = BWAMETH_INDEX.out.index - + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test.methylated_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) + input[2] = BWAMETH_INDEX.out.index """ } } diff --git a/modules/nf-core/bwameth/align/tests/main.nf.test.snap b/modules/nf-core/bwameth/align/tests/main.nf.test.snap index 2c8c120f3513..a90108105f10 100644 --- a/modules/nf-core/bwameth/align/tests/main.nf.test.snap +++ b/modules/nf-core/bwameth/align/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "test-bwameth-align-single-end": { + "sarscov2 methylated single_end [fastq]": { "content": [ "5fdda0ada69daa3956c65a24c9d1c1e0", [ @@ -10,20 +10,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T20:43:02.509483" - }, - "test-bwameth-align-paired-end": { - "content": [ - "cbd5cfa8b446e26987898a45a94770ba", - [ - "versions.yml:md5,c00660f78aeab4fabe00092c70656098" - ] - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-04T20:43:10.963043" + "timestamp": "2024-10-16T07:50:08.241201566" }, "test-bwameth-align-paired-end-stub": { "content": [ @@ -58,6 +45,19 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-04T20:43:17.04632" + "timestamp": "2024-10-16T08:00:51.770330645" + }, + "sarscov2 methylated paired_end [fastq]": { + "content": [ + "cbd5cfa8b446e26987898a45a94770ba", + [ + "versions.yml:md5,c00660f78aeab4fabe00092c70656098" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T07:50:20.75109829" } } \ No newline at end of file diff --git a/modules/nf-core/bwameth/index/main.nf b/modules/nf-core/bwameth/index/main.nf index 33c83d907913..5059f134fb67 100644 --- a/modules/nf-core/bwameth/index/main.nf +++ b/modules/nf-core/bwameth/index/main.nf @@ -8,11 +8,11 @@ process BWAMETH_INDEX { 'biocontainers/bwameth:0.2.7--pyh7cba7a3_0' }" input: - path fasta, stageAs: "bwameth/*" + tuple val(meta), path(fasta) output: - path "bwameth" , emit: index - path "versions.yml" , emit: versions + tuple val(meta), path("BwamethIndex"), emit: index + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,7 +20,24 @@ process BWAMETH_INDEX { script: def args = task.ext.args ?: '' """ - bwameth.py index $fasta + mkdir BwamethIndex + mv $fasta BwamethIndex/ + + bwameth.py index BwamethIndex/$fasta + + rm BwamethIndex/$fasta + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bwameth: \$(bwameth.py --version | cut -f2 -d" ") + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + """ + mkdir BwamethIndex + touch BwamethIndex/$fasta cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/bwameth/index/meta.yml b/modules/nf-core/bwameth/index/meta.yml index d92273c4d7e0..2194e2258045 100644 --- a/modules/nf-core/bwameth/index/meta.yml +++ b/modules/nf-core/bwameth/index/meta.yml @@ -19,12 +19,21 @@ tools: licence: ["MIT"] identifier: "" input: - - - fasta: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: type: file description: Input genome fasta file output: - index: - - bwameth: + - meta: + type: directory + description: Directory containing bwameth genome index + pattern: "index" + - BwamethIndex: type: directory description: Directory containing bwameth genome index pattern: "index" @@ -37,3 +46,4 @@ authors: - "@phue" maintainers: - "@phue" + - "@sateeshperi" diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test b/modules/nf-core/bwameth/index/tests/main.nf.test index a314788ab00f..152c8366881e 100644 --- a/modules/nf-core/bwameth/index/tests/main.nf.test +++ b/modules/nf-core/bwameth/index/tests/main.nf.test @@ -10,12 +10,15 @@ nextflow_process { tag "bwameth" tag "bwameth/index" - test("test-bwameth-index") { - + test("sarscov2 genome [fasta]") { + when { process { """ - input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[0] = Channel.of([ + [ id:'test' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ]) """ } } @@ -27,5 +30,5 @@ nextflow_process { ) } } - + } diff --git a/modules/nf-core/bwameth/index/tests/main.nf.test.snap b/modules/nf-core/bwameth/index/tests/main.nf.test.snap index 27f07221db3c..fb427880686f 100644 --- a/modules/nf-core/bwameth/index/tests/main.nf.test.snap +++ b/modules/nf-core/bwameth/index/tests/main.nf.test.snap @@ -1,16 +1,20 @@ { - "test-bwameth-index": { + "sarscov2 genome [fasta]": { "content": [ { "0": [ [ - "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6", - "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", - "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", - "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", - "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", - "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", - "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + { + "id": "test" + }, + [ + "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", + "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", + "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", + "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", + "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", + "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + ] ] ], "1": [ @@ -18,13 +22,17 @@ ], "index": [ [ - "genome.fasta:md5,6e9fe4042a72f2345f644f239272b7e6", - "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", - "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", - "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", - "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", - "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", - "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + { + "id": "test" + }, + [ + "genome.fasta.bwameth.c2t:md5,98039984526a41d04d6bd92fcc040c62", + "genome.fasta.bwameth.c2t.amb:md5,249a4195069071ce47cd0bae68abe376", + "genome.fasta.bwameth.c2t.ann:md5,46524d4359dcdfb203a235ab3b930dbb", + "genome.fasta.bwameth.c2t.bwt:md5,84f65df7d42dbe84c9ccfaddfdd5ea6b", + "genome.fasta.bwameth.c2t.pac:md5,4d8e51cb0bbdeaf24576bdf0264d8653", + "genome.fasta.bwameth.c2t.sa:md5,d25f6486f5134f57ed5b258f6fbb8673" + ] ] ], "versions": [ @@ -33,9 +41,9 @@ } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-28T13:57:11.602104" + "timestamp": "2024-10-14T20:32:13.750317299" } } \ No newline at end of file From eaeecb111aa52667b1a43eaf11cdd016f01faf78 Mon Sep 17 00:00:00 2001 From: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Date: Wed, 16 Oct 2024 15:59:20 +0100 Subject: [PATCH 152/486] proovframe map init push (#6790) * proovframe map init push * stub test renamed properly * text contains test instead, because conda was failing (produces 0s column isntead of a values column) * meta spacing fixed --- .../nf-core/proovframe/map/environment.yml | 7 +++ modules/nf-core/proovframe/map/main.nf | 48 +++++++++++++++ modules/nf-core/proovframe/map/meta.yml | 56 ++++++++++++++++++ .../nf-core/proovframe/map/tests/main.nf.test | 59 +++++++++++++++++++ .../proovframe/map/tests/main.nf.test.snap | 49 +++++++++++++++ 5 files changed, 219 insertions(+) create mode 100644 modules/nf-core/proovframe/map/environment.yml create mode 100644 modules/nf-core/proovframe/map/main.nf create mode 100644 modules/nf-core/proovframe/map/meta.yml create mode 100644 modules/nf-core/proovframe/map/tests/main.nf.test create mode 100644 modules/nf-core/proovframe/map/tests/main.nf.test.snap diff --git a/modules/nf-core/proovframe/map/environment.yml b/modules/nf-core/proovframe/map/environment.yml new file mode 100644 index 000000000000..a1a698f477be --- /dev/null +++ b/modules/nf-core/proovframe/map/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::proovframe=0.9.7" diff --git a/modules/nf-core/proovframe/map/main.nf b/modules/nf-core/proovframe/map/main.nf new file mode 100644 index 000000000000..75eb835ca264 --- /dev/null +++ b/modules/nf-core/proovframe/map/main.nf @@ -0,0 +1,48 @@ +process PROOVFRAME_MAP { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/proovframe:0.9.7--hdfd78af_1': + 'biocontainers/proovframe:0.9.7--hdfd78af_1' }" + + input: + tuple val(meta), path(faa), path(fasta) + + output: + tuple val(meta), path("*.tsv"), emit: tsv + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + proovframe \\ + map \\ + ${args} \\ + -a ${faa} \\ + -o ${prefix}.tsv \\ + ${fasta} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + proovframe: 0.9.7 + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.tsv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + proovframe: 0.9.7 + END_VERSIONS + """ +} diff --git a/modules/nf-core/proovframe/map/meta.yml b/modules/nf-core/proovframe/map/meta.yml new file mode 100644 index 000000000000..5c9388640553 --- /dev/null +++ b/modules/nf-core/proovframe/map/meta.yml @@ -0,0 +1,56 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "proovframe_map" +description: frame-shift correction for long read (meta)genomics - maps proteins to reads +keywords: + - frame-shift correction + - long-read sequencing + - sequence analysis +tools: + - "proovframe": + description: "frame-shift correction for long read (meta)genomics" + homepage: "https://github.com/thackl/proovframe" + documentation: "https://github.com/thackl/proovframe" + tool_dev_url: "https://github.com/thackl/proovframe" + doi: "10.1101/2021.08.23.457338" + licence: ["MIT"] + identifier: biotools:proovframe + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - faa: + type: file + description: A FASTA file containing a database of guide protein sequences + pattern: "*.{faa,fasta,fa}" + - fasta: + type: file + description: A FASTA file containing raw read nucleotide sequences + pattern: "*.{fasta,fa}" + +output: + - tsv: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.tsv": + type: file + description: Output TSV file with the frameshift-aware protein to read alignments + pattern: "*.tsv" + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@manuelcarbajo" + - "@MGS-sails" + - "@vagkaratzas" +maintainers: + - "@vagkaratzas" diff --git a/modules/nf-core/proovframe/map/tests/main.nf.test b/modules/nf-core/proovframe/map/tests/main.nf.test new file mode 100644 index 000000000000..3a3068ffc18c --- /dev/null +++ b/modules/nf-core/proovframe/map/tests/main.nf.test @@ -0,0 +1,59 @@ +nextflow_process { + + name "Test Process PROOVFRAME_MAP" + script "../main.nf" + process "PROOVFRAME_MAP" + + tag "modules" + tag "modules_nfcore" + tag "proovframe" + tag "proovframe/map" + + test("sarscov2 - tsv") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert path(process.out.tsv[0][1]).text.contains('MT192765.1 ENSSASP00005000002.1 100.0 7096 1 0 259 21545 1') }, + { assert snapshot(process.out.versions).match() } + ) + } + + } + + test("sarscov2 - tsv - stub") { + options '-stub' + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/proovframe/map/tests/main.nf.test.snap b/modules/nf-core/proovframe/map/tests/main.nf.test.snap new file mode 100644 index 000000000000..b0224d1728ea --- /dev/null +++ b/modules/nf-core/proovframe/map/tests/main.nf.test.snap @@ -0,0 +1,49 @@ +{ + "sarscov2 - tsv": { + "content": [ + [ + "versions.yml:md5,f49f29b8134fdb539364ee46855eb313" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.04.5" + }, + "timestamp": "2024-10-16T15:02:00.599243234" + }, + "sarscov2 - tsv - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,f49f29b8134fdb539364ee46855eb313" + ], + "tsv": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,f49f29b8134fdb539364ee46855eb313" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.04.5" + }, + "timestamp": "2024-10-16T15:02:21.855444606" + } +} \ No newline at end of file From 3c464e75051db485c1b37ab9f1ea2182fb3d3533 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Nicol=C3=A1s=20Schcolnicov?= <90359308+nschcolnicov@users.noreply.github.com> Date: Wed, 16 Oct 2024 14:09:03 -0300 Subject: [PATCH 153/486] Added samshee (#6749) * Added samshee * Fix pre-commit * Fix linting * Add more options * Remove nextflow.config * Addressing PR comments * Add python version * Add file schema testing and missing arg * Fixing test * Fix test * fix tests conda * Fix conda env.yml --------- Co-authored-by: zxBIB Schcolnicov --- modules/nf-core/samshee/environment.yml | 6 + modules/nf-core/samshee/main.nf | 47 ++++++++ modules/nf-core/samshee/meta.yml | 47 ++++++++ modules/nf-core/samshee/tests/main.nf.test | 85 ++++++++++++++ .../nf-core/samshee/tests/main.nf.test.snap | 107 ++++++++++++++++++ modules/nf-core/samshee/tests/nextflow.config | 9 ++ 6 files changed, 301 insertions(+) create mode 100644 modules/nf-core/samshee/environment.yml create mode 100644 modules/nf-core/samshee/main.nf create mode 100644 modules/nf-core/samshee/meta.yml create mode 100644 modules/nf-core/samshee/tests/main.nf.test create mode 100644 modules/nf-core/samshee/tests/main.nf.test.snap create mode 100644 modules/nf-core/samshee/tests/nextflow.config diff --git a/modules/nf-core/samshee/environment.yml b/modules/nf-core/samshee/environment.yml new file mode 100644 index 000000000000..35a8e2e78523 --- /dev/null +++ b/modules/nf-core/samshee/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::samshee=0.2.1 + - python=3.13.0 diff --git a/modules/nf-core/samshee/main.nf b/modules/nf-core/samshee/main.nf new file mode 100644 index 000000000000..6d7ba2e60179 --- /dev/null +++ b/modules/nf-core/samshee/main.nf @@ -0,0 +1,47 @@ +process SAMSHEE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/65/659cdc3068a6fbce17ccb199bb3afc8600c65940743c1a0214b3bf0eed4df1a3/data' : + 'community.wave.seqera.io/library/pip_samshee:9b655e3c18eee356' }" + + input: + tuple val(meta), path(samplesheet) + path(file_schema_validator) + + output: + tuple val(meta), path("*_formatted.csv"), emit: samplesheet + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def arg_file_schema_validator = file_schema_validator ? "--schema '{\"\$ref\": \"file:${file_schema_validator}\"}'" : "" + def args = task.ext.args ?: "" + """ + # Run validation command and capture output + python -m samshee $samplesheet \ + $args \ + $arg_file_schema_validator \ + > ${samplesheet.baseName}_formatted.csv + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" ) + python: \$( python --version | sed -e "s/Python //g" ) + END_VERSIONS + """ + + stub: + """ + touch ${samplesheet.baseName}_formatted.csv + cat <<-END_VERSIONS > versions.yml + "${task.process}": + samshee: \$( python -m pip show --version samshee | grep "Version" | sed -e "s/Version: //g" ) + python: \$( python --version | sed -e "s/Python //g" ) + END_VERSIONS + """ +} diff --git a/modules/nf-core/samshee/meta.yml b/modules/nf-core/samshee/meta.yml new file mode 100644 index 000000000000..50789dfbaef4 --- /dev/null +++ b/modules/nf-core/samshee/meta.yml @@ -0,0 +1,47 @@ +name: samshee +description: Module to validate illumina® Sample Sheet v2 files. +keywords: + - samplesheet + - illumina + - bclconvert + - bcl2fastq +tools: + - samshee: + description: A schema-agnostic parser and writer for illumina® sample sheets v2 and similar documents. + homepage: https://github.com/lit-regensburg/samshee + documentation: https://github.com/lit-regensburg/samshee/blob/main/README.md + tool_dev_url: https://github.com/lit-regensburg/samshee + licence: [MIT license] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', lane:1 ] + - samplesheet: + type: file + description: "illumina v2 samplesheet" + pattern: "*.{csv}" + - - file_schema_validator: + type: string + description: "Optional JSON file used additional samplesheet validation settings" +output: + - samplesheet: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', lane:1 ] + - "*_formatted.csv": + type: file + description: "illumina v2 samplesheet" + - versions: + - versions.yml: + type: file + description: File containing software version + pattern: "versions.yml" +authors: + - "@nschcolnicov" +maintainers: + - "@nschcolnicov" diff --git a/modules/nf-core/samshee/tests/main.nf.test b/modules/nf-core/samshee/tests/main.nf.test new file mode 100644 index 000000000000..5bec682f18fc --- /dev/null +++ b/modules/nf-core/samshee/tests/main.nf.test @@ -0,0 +1,85 @@ +nextflow_process { + + name "Test Process samshee" + script "../main.nf" + process "SAMSHEE" + config "./nextflow.config" + tag "modules" + tag "modules_nfcore" + tag "samshee" + + test("test samplesheet_v1") { + + when { + params { + v1_schema = true + json_schema_validator = '{"required": ["Data"]}' + name_schema_validator = null + } + process { + """ + input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/miseq_35147139/miseq_35147139_samplesheet.csv", checkIfExists: true) ] + input[1] = file("schema.json") + new File("schema.json").text = '''{ + "\$schema": "https://json-schema.org/draft/2020-12/schema", + "required": ["Settings"] + }''' + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + test("test samplesheet_v2") { + + when { + params { + v1_schema = null + json_schema_validator = null + name_schema_validator = '{"$ref": "urn:samshee:illuminav2/v1"}' + } + process { + """ + input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ] + input[1] = [] + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + + test("stub") { + + options "-stub" + + when { + params { + v1_schema = null + json_schema_validator = null + name_schema_validator = null + } + process { + """ + input[0] = [ [ id: 'test', lane:1 ], file("https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NextSeq2000/SampleSheet.csv", checkIfExists: true) ] + input[1] = [] + """ + } + } + + then { + assert process.success + assert snapshot(process.out).match() + } + + } + +} diff --git a/modules/nf-core/samshee/tests/main.nf.test.snap b/modules/nf-core/samshee/tests/main.nf.test.snap new file mode 100644 index 000000000000..b3729eba261f --- /dev/null +++ b/modules/nf-core/samshee/tests/main.nf.test.snap @@ -0,0 +1,107 @@ +{ + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "lane": 1 + }, + "SampleSheet_formatted.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ], + "samplesheet": [ + [ + { + "id": "test", + "lane": 1 + }, + "SampleSheet_formatted.csv:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T15:25:40.722007136" + }, + "test samplesheet_v1": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "lane": 1 + }, + "miseq_35147139_samplesheet_formatted.csv:md5,2a6ee5b13242aeefdeeaa98671f1ee26" + ] + ], + "1": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ], + "samplesheet": [ + [ + { + "id": "test", + "lane": 1 + }, + "miseq_35147139_samplesheet_formatted.csv:md5,2a6ee5b13242aeefdeeaa98671f1ee26" + ] + ], + "versions": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T15:25:02.353128191" + }, + "test samplesheet_v2": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "lane": 1 + }, + "SampleSheet_formatted.csv:md5,9a1cac9e958256a17c7f43a8e15cb697" + ] + ], + "1": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ], + "samplesheet": [ + [ + { + "id": "test", + "lane": 1 + }, + "SampleSheet_formatted.csv:md5,9a1cac9e958256a17c7f43a8e15cb697" + ] + ], + "versions": [ + "versions.yml:md5,77af0194d386117bf52aaabdf350a976" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-16T15:25:24.540910786" + } +} \ No newline at end of file diff --git a/modules/nf-core/samshee/tests/nextflow.config b/modules/nf-core/samshee/tests/nextflow.config new file mode 100644 index 000000000000..ecf1ff663e4a --- /dev/null +++ b/modules/nf-core/samshee/tests/nextflow.config @@ -0,0 +1,9 @@ +process { + withName: SAMSHEE { + ext.args = [ + params.json_schema_validator ? "--schema '${params.json_schema_validator}'" : "", + params.name_schema_validator ? "--schema '${params.name_schema_validator}'" : "", + params.v1_schema ? "--output-format sectioned" : "", + ].join(" ").trim() + } +} From 7741dfc830e77a8ead2fcb50b01461ee09d0cdfe Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 17 Oct 2024 10:26:08 +0200 Subject: [PATCH 154/486] Arriba download update (#6745) * add specific files created * typo * add from nf-test template * remove from pytest_modules * update environement file * update arriba * add tests * use latest conda build * arriba conda env * update environement * update meta * update tags in test * move arriba test to stubs as timeout for merge queue --- modules/nf-core/arriba/arriba/environment.yml | 3 + modules/nf-core/arriba/arriba/main.nf | 17 ++- modules/nf-core/arriba/arriba/meta.yml | 39 +------ .../nf-core/arriba/arriba/tests/main.nf.test | 107 ++++++++++++++++++ .../arriba/arriba/tests/main.nf.test.snap | 55 +++++++++ .../arriba/arriba/tests}/nextflow.config | 5 - modules/nf-core/arriba/download/main.nf | 9 +- modules/nf-core/arriba/download/meta.yml | 32 +++++- .../arriba/download/tests/main.nf.test | 29 +++-- .../arriba/download/tests/main.nf.test.snap | 62 +++++----- .../nf-core/arriba/download/tests/tags.yml | 2 + tests/config/pytest_modules.yml | 15 ++- tests/modules/nf-core/arriba/arriba/main.nf | 61 ---------- tests/modules/nf-core/arriba/arriba/test.yml | 87 -------------- 14 files changed, 281 insertions(+), 242 deletions(-) create mode 100644 modules/nf-core/arriba/arriba/tests/main.nf.test create mode 100644 modules/nf-core/arriba/arriba/tests/main.nf.test.snap rename {tests/modules/nf-core/arriba/arriba => modules/nf-core/arriba/arriba/tests}/nextflow.config (84%) create mode 100644 modules/nf-core/arriba/download/tests/tags.yml delete mode 100644 tests/modules/nf-core/arriba/arriba/main.nf delete mode 100644 tests/modules/nf-core/arriba/arriba/test.yml diff --git a/modules/nf-core/arriba/arriba/environment.yml b/modules/nf-core/arriba/arriba/environment.yml index d0883a0d2059..c3a88ffbdf8f 100644 --- a/modules/nf-core/arriba/arriba/environment.yml +++ b/modules/nf-core/arriba/arriba/environment.yml @@ -1,5 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda + dependencies: - bioconda::arriba=2.4.0 diff --git a/modules/nf-core/arriba/arriba/main.nf b/modules/nf-core/arriba/arriba/main.nf index 761d0bf35879..75dbf93ad9fc 100644 --- a/modules/nf-core/arriba/arriba/main.nf +++ b/modules/nf-core/arriba/arriba/main.nf @@ -8,14 +8,13 @@ process ARRIBA_ARRIBA { 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: - tuple val(meta), path(bam) + tuple val(meta), path(bam) tuple val(meta2), path(fasta) tuple val(meta3), path(gtf) - tuple val(meta4), path(blacklist) - tuple val(meta5), path(known_fusions) - tuple val(meta6), path(structural_variants) - tuple val(meta7), path(tags) - tuple val(meta8), path(protein_domains) + path(blacklist) + path(known_fusions) + path(cytobands) + path(protein_domains) output: tuple val(meta), path("*.fusions.tsv") , emit: fusions @@ -30,8 +29,7 @@ process ARRIBA_ARRIBA { def prefix = task.ext.prefix ?: "${meta.id}" def blacklist = blacklist ? "-b $blacklist" : "-f blacklist" def known_fusions = known_fusions ? "-k $known_fusions" : "" - def structural_variants = structural_variants ? "-d $structual_variants" : "" - def tags = tags ? "-t $tags" : "" + def cytobands = cytobands ? "-d $cytobands" : "" def protein_domains = protein_domains ? "-p $protein_domains" : "" """ @@ -43,8 +41,7 @@ process ARRIBA_ARRIBA { -O ${prefix}.fusions.discarded.tsv \\ $blacklist \\ $known_fusions \\ - $structural_variants \\ - $tags \\ + $cytobands \\ $protein_domains \\ $args diff --git a/modules/nf-core/arriba/arriba/meta.yml b/modules/nf-core/arriba/arriba/meta.yml index f230dda1fbe3..91ba21039611 100644 --- a/modules/nf-core/arriba/arriba/meta.yml +++ b/modules/nf-core/arriba/arriba/meta.yml @@ -43,48 +43,19 @@ input: type: file description: Annotation GTF file pattern: "*.{gtf}" - - - meta4: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - blacklist: + - - blacklist: type: file description: Blacklist file pattern: "*.{tsv}" - - - meta5: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - known_fusions: + - - known_fusions: type: file description: Known fusions file pattern: "*.{tsv}" - - - meta6: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - structural_variants: - type: file - description: Structural variants file - pattern: "*.{tsv}" - - - meta7: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - tags: + - - cytobands: type: file - description: Tags file + description: Cytobands file pattern: "*.{tsv}" - - - meta8: - type: map - description: | - Groovy Map containing reference information - e.g. [ id:'test' ] - - protein_domains: + - - protein_domains: type: file description: Protein domains file pattern: "*.{gff3}" diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test b/modules/nf-core/arriba/arriba/tests/main.nf.test new file mode 100644 index 000000000000..4cff86e50ef2 --- /dev/null +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test @@ -0,0 +1,107 @@ + +nextflow_process { + + name "Test Process ARRIBA_ARRIBA" + script "../main.nf" + process "ARRIBA_ARRIBA" + + tag "modules" + tag "modules_nfcore" + tag "arriba" + tag "arriba/arriba" + tag "arriba/download" + tag "star/genomegenerate" + tag "star/align" + + setup { + config "./nextflow.config" + options "-stub" + run("ARRIBA_DOWNLOAD") { + script "../../../arriba/download/main.nf" + process { + """ + input[0] = 'GRCh38' + """ + } + } + run("STAR_GENOMEGENERATE") { + script "../../../star/genomegenerate/main.nf" + options "-stub" + process { + """ + input[0] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + run("STAR_ALIGN") { + script "../../../star/align/main.nf" + options "-stub" + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) + ] + ]) + input[1] = STAR_GENOMEGENERATE.out.index + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = false + input[4] = 'illumina' + input[5] = false + """ + } + } + } + + test("homo_sapiens - paired_end - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true) ] + ]) + input[1] = Channel.of([ + [ id:'test_fasta' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] + ]) + input[2] = Channel.of([ + [ id:'test_gtf' ], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] + ]) + input[3] = [] + + input[4] = [] + + input[5] = [] + + input[6] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/arriba/arriba/tests/main.nf.test.snap b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap new file mode 100644 index 000000000000..14d46f6b87a1 --- /dev/null +++ b/modules/nf-core/arriba/arriba/tests/main.nf.test.snap @@ -0,0 +1,55 @@ +{ + "homo_sapiens - paired_end - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "2": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ], + "fusions": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "fusions_fail": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" + ] + ], + "versions": [ + "versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-08T15:41:23.945072" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/arriba/arriba/nextflow.config b/modules/nf-core/arriba/arriba/tests/nextflow.config similarity index 84% rename from tests/modules/nf-core/arriba/arriba/nextflow.config rename to modules/nf-core/arriba/arriba/tests/nextflow.config index 1b66d8dfa7fe..d3d5b00f6657 100644 --- a/tests/modules/nf-core/arriba/arriba/nextflow.config +++ b/modules/nf-core/arriba/arriba/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: STAR_GENOMEGENERATE { ext.args = '--genomeSAindexNbases 11' } - withName: STAR_ALIGN { ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' } - } diff --git a/modules/nf-core/arriba/download/main.nf b/modules/nf-core/arriba/download/main.nf index 96a4e33628f7..2e63b2d0b179 100644 --- a/modules/nf-core/arriba/download/main.nf +++ b/modules/nf-core/arriba/download/main.nf @@ -8,10 +8,14 @@ process ARRIBA_DOWNLOAD { 'biocontainers/arriba:2.4.0--h0033a41_2' }" input: + val(genome) output: - path "*" , emit: reference - path "versions.yml" , emit: versions + path "blacklist*${genome}*.tsv.gz" , emit: blacklist + path "cytobands*${genome}*.tsv" , emit: cytobands + path "protein_domains*${genome}*.gff3" , emit: protein_domains + path "known_fusions*${genome}*.tsv.gz" , emit: known_fusions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -36,7 +40,6 @@ process ARRIBA_DOWNLOAD { touch protein_domains_hg38_GRCh38_v2.4.0.gff3 touch cytobands_hg38_GRCh38_v2.4.0.tsv touch known_fusions_hg38_GRCh38_v2.4.0.tsv.gz - touch protein_domains_hg38_GRCh38_v2.4.0.gff3 cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/arriba/download/meta.yml b/modules/nf-core/arriba/download/meta.yml index 531c66c2f776..892b7ac9b78e 100644 --- a/modules/nf-core/arriba/download/meta.yml +++ b/modules/nf-core/arriba/download/meta.yml @@ -15,12 +15,34 @@ tools: licence: ["MIT"] identifier: biotools:Arriba +input: + - - genome: + type: string + description: hg38, hg19, GRCh38, GRCh37 for humans are accepted output: - - reference: - - "*": - type: directory - description: Folder with arriba references - pattern: "*" + - blacklist: + - blacklist*${genome}*.tsv.gz: + type: str + description: The blacklist removes recurrent alignment artifacts and transcripts + which are present in healthy tissue + pattern: ".tsv.gz" + - cytobands: + - cytobands*${genome}*.tsv: + type: file + description: Coordinates of the Giemsa staining bands. This information is used + to draw ideograms + pattern: ".tsv" + - protein_domains: + - protein_domains*${genome}*.gff3: + type: file + description: Protein domain annotations + patter: "*.gff3" + - known_fusions: + - known_fusions*${genome}*.tsv.gz: + type: file + description: Arriba is more sensitive to those fusions to improve the detection + rate of expected or highly relevant events, such as recurrent fusions + patter: "*.tsv.gz" - versions: - versions.yml: type: file diff --git a/modules/nf-core/arriba/download/tests/main.nf.test b/modules/nf-core/arriba/download/tests/main.nf.test index cccc95db2c02..2c32c7a0f3ad 100644 --- a/modules/nf-core/arriba/download/tests/main.nf.test +++ b/modules/nf-core/arriba/download/tests/main.nf.test @@ -11,11 +11,10 @@ nextflow_process { tag "arriba/download" test("test-arriba-download") { - when { process { """ - + input[0] = 'GRCh38' """ } } @@ -23,11 +22,27 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot( - process.out.reference[0].collect { file(it).name }.toSorted(), - process.out.versions - ).match() - } + { assert snapshot(process.out).match() } + ) + } + + } + + test("download - stub") { + + options "-stub" + + when { + process { + """ + input[0] = 'GRCh38' + """ + } + } + + then { + assertAll( + { assert process.success } ) } } diff --git a/modules/nf-core/arriba/download/tests/main.nf.test.snap b/modules/nf-core/arriba/download/tests/main.nf.test.snap index eda3f7066400..fe9b18b94835 100644 --- a/modules/nf-core/arriba/download/tests/main.nf.test.snap +++ b/modules/nf-core/arriba/download/tests/main.nf.test.snap @@ -1,35 +1,43 @@ { - "test-arriba-download": { + "download": { "content": [ - [ - "CREDITS", - "RefSeq_viral_genomes_v2.4.0.fa.gz", - "blacklist_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz", - "blacklist_hg38_GRCh38_v2.4.0.tsv.gz", - "blacklist_mm10_GRCm38_v2.4.0.tsv.gz", - "blacklist_mm39_GRCm39_v2.4.0.tsv.gz", - "cytobands_hg19_hs37d5_GRCh37_v2.4.0.tsv", - "cytobands_hg38_GRCh38_v2.4.0.tsv", - "cytobands_mm10_GRCm38_v2.4.0.tsv", - "cytobands_mm39_GRCm39_v2.4.0.tsv", - "known_fusions_hg19_hs37d5_GRCh37_v2.4.0.tsv.gz", - "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz", - "known_fusions_mm10_GRCm38_v2.4.0.tsv.gz", - "known_fusions_mm39_GRCm39_v2.4.0.tsv.gz", - "protein_domains_hg19_hs37d5_GRCh37_v2.4.0.gff3", - "protein_domains_hg38_GRCh38_v2.4.0.gff3", - "protein_domains_mm10_GRCm38_v2.4.0.gff3", - "protein_domains_mm39_GRCm39_v2.4.0.gff3", - "versions.yml" - ], - [ - "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" - ] + { + "0": [ + "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318" + ], + "1": [ + "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c" + ], + "2": [ + "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978" + ], + "3": [ + "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c" + ], + "4": [ + "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" + ], + "blacklist": [ + "blacklist_hg38_GRCh38_v2.4.0.tsv.gz:md5,e3098a4be51aece78aede64b55c39318" + ], + "cytobands": [ + "cytobands_hg38_GRCh38_v2.4.0.tsv:md5,7bd504feefb33fcfc9be0517439a423c" + ], + "known_fusions": [ + "known_fusions_hg38_GRCh38_v2.4.0.tsv.gz:md5,4f00f81ccb5f4db283f1a22b8b0da67c" + ], + "protein_domains": [ + "protein_domains_hg38_GRCh38_v2.4.0.gff3:md5,43c387a784ebeed71b4147076cebf978" + ], + "versions": [ + "versions.yml:md5,98c69df5eaea5caf0b4af7b8d7af4893" + ] + } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:00:38.086459" + "timestamp": "2024-10-08T11:12:17.010496" } } \ No newline at end of file diff --git a/modules/nf-core/arriba/download/tests/tags.yml b/modules/nf-core/arriba/download/tests/tags.yml new file mode 100644 index 000000000000..f510bbf1a142 --- /dev/null +++ b/modules/nf-core/arriba/download/tests/tags.yml @@ -0,0 +1,2 @@ +arriba/download: + - "modules/nf-core/arriba/download/**" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 5d8a9be3c4fb..584db480a14f 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1,9 +1,18 @@ amps: - modules/nf-core/amps/** - tests/modules/nf-core/amps/** -arriba/arriba: - - modules/nf-core/arriba/arriba/** - - tests/modules/nf-core/arriba/arriba/** +angsd/contamination: + - modules/nf-core/angsd/contamination/** + - tests/modules/nf-core/angsd/contamination/** +angsd/docounts: + - modules/nf-core/angsd/docounts/** + - tests/modules/nf-core/angsd/docounts/** +arcashla/extract: + - modules/nf-core/arcashla/extract/** + - tests/modules/nf-core/arcashla/extract/** +ariba/getref: + - modules/nf-core/ariba/getref/** + - tests/modules/nf-core/ariba/getref/** artic/guppyplex: - modules/nf-core/artic/guppyplex/** - tests/modules/nf-core/artic/guppyplex/** diff --git a/tests/modules/nf-core/arriba/arriba/main.nf b/tests/modules/nf-core/arriba/arriba/main.nf deleted file mode 100644 index 2d5b9a3ce713..000000000000 --- a/tests/modules/nf-core/arriba/arriba/main.nf +++ /dev/null @@ -1,61 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { STAR_GENOMEGENERATE } from '../../../../../modules/nf-core/star/genomegenerate/main.nf' -include { STAR_ALIGN } from '../../../../../modules/nf-core/star/align/main.nf' -include { ARRIBA_ARRIBA } from '../../../../../modules/nf-core/arriba/arriba/main.nf' - -workflow test_arriba_single_end { - - input = [ [ id:'test', single_end:true ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - ] - ] - fasta = [ - [ id:'test_fasta' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - ] - fai = [ - [ id:'test_fai' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - ] - gtf = [ - [ id:'test_fasta_gtf' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) ] - ] - star_ignore_sjdbgtf = false - seq_platform = 'illumina' - seq_center = false - - STAR_GENOMEGENERATE ( fasta, gtf ) - STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - ARRIBA_ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) -} - -workflow test_arriba_paired_end { - - input = [ [ id:'test', single_end:false ], // meta map - [ file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_1_fastq_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_2_fastq_gz'], checkIfExists: true) ] - ] - fasta = [ - [ id:'test_fasta' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] - ] - fai = [ - [ id:'test_gtf' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) ] - ] - gtf = [ - [ id:'test_fasta_fai' ], // meta map - [ file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) ] - ] - star_ignore_sjdbgtf = false - seq_platform = 'illumina' - seq_center = false - - STAR_GENOMEGENERATE ( fasta, gtf ) - STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center ) - ARRIBA_ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [[],[]], [[],[]], [[],[]], [[],[]], [[],[]]) -} diff --git a/tests/modules/nf-core/arriba/arriba/test.yml b/tests/modules/nf-core/arriba/arriba/test.yml deleted file mode 100644 index 19db9f0d6b64..000000000000 --- a/tests/modules/nf-core/arriba/arriba/test.yml +++ /dev/null @@ -1,87 +0,0 @@ -- name: arriba arriba test_arriba_single_end - command: nextflow run ./tests/modules/nf-core/arriba/arriba -entry test_arriba_single_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/arriba/nextflow.config - tags: - - arriba - - arriba/arriba - files: - - path: output/arriba/test.fusions.discarded.tsv - - path: output/arriba/test.fusions.tsv - md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70 - - path: output/star/star/Genome - md5sum: a654229fbca6071dcb6b01ce7df704da - - path: output/star/star/Log.out - - path: output/star/star/SA - md5sum: 8c3edc46697b72c9e92440d4cf43506c - - path: output/star/star/SAindex - md5sum: 9f085c626553b1c52f2827421972ac10 - - path: output/star/star/chrLength.txt - md5sum: c81f40f27e72606d7d07097c1d56a5b5 - - path: output/star/star/chrName.txt - md5sum: 5ae68a67b70976ee95342a7451cb5af1 - - path: output/star/star/chrNameLength.txt - md5sum: b190587cae0531f3cf25552d8aa674db - - path: output/star/star/chrStart.txt - md5sum: 8d3291e6bcdbe9902fbd7c887494173f - - path: output/star/star/exonInfo.tab - md5sum: 0d560290fab688b7268d88d5494bf9fe - - path: output/star/star/geneInfo.tab - md5sum: 8b608537307443ffaee4927d2b428805 - - path: output/star/star/genomeParameters.txt - md5sum: 9e42067b1ec70b773257529230dd7b3a - - path: output/star/star/sjdbInfo.txt - md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: 8760c33e966dad0b39f440301ebbdee4 - - path: output/star/star/sjdbList.out.tab - md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 - - path: output/star/star/transcriptInfo.tab - md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - - path: output/star/test.Aligned.out.bam - - path: output/star/test.Log.final.out - - path: output/star/test.Log.out - - path: output/star/test.Log.progress.out - - path: output/star/test.SJ.out.tab - -- name: arriba arriba test_arriba_paired_end - command: nextflow run ./tests/modules/nf-core/arriba/arriba -entry test_arriba_paired_end -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/arriba/arriba/nextflow.config - tags: - - arriba - - arriba/arriba - files: - - path: output/arriba/test.fusions.discarded.tsv - - path: output/arriba/test.fusions.tsv - md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70 - - path: output/star/star/Genome - md5sum: a654229fbca6071dcb6b01ce7df704da - - path: output/star/star/Log.out - - path: output/star/star/SA - md5sum: 8c3edc46697b72c9e92440d4cf43506c - - path: output/star/star/SAindex - md5sum: 9f085c626553b1c52f2827421972ac10 - - path: output/star/star/chrLength.txt - md5sum: c81f40f27e72606d7d07097c1d56a5b5 - - path: output/star/star/chrName.txt - md5sum: 5ae68a67b70976ee95342a7451cb5af1 - - path: output/star/star/chrNameLength.txt - md5sum: b190587cae0531f3cf25552d8aa674db - - path: output/star/star/chrStart.txt - md5sum: 8d3291e6bcdbe9902fbd7c887494173f - - path: output/star/star/exonInfo.tab - md5sum: 0d560290fab688b7268d88d5494bf9fe - - path: output/star/star/geneInfo.tab - md5sum: 8b608537307443ffaee4927d2b428805 - - path: output/star/star/genomeParameters.txt - md5sum: 9e42067b1ec70b773257529230dd7b3a - - path: output/star/star/sjdbInfo.txt - md5sum: 5690ea9d9f09f7ff85b7fd47bd234903 - - path: output/star/star/sjdbList.fromGTF.out.tab - md5sum: 8760c33e966dad0b39f440301ebbdee4 - - path: output/star/star/sjdbList.out.tab - md5sum: 9e4f991abbbfeb3935a2bb21b9e258f1 - - path: output/star/star/transcriptInfo.tab - md5sum: 0c3a5adb49d15e5feff81db8e29f2e36 - - path: output/star/test.Aligned.out.bam - - path: output/star/test.Log.final.out - - path: output/star/test.Log.out - - path: output/star/test.Log.progress.out - - path: output/star/test.SJ.out.tab From 84b38813467877822f33a76a2f997bc40325331b Mon Sep 17 00:00:00 2001 From: Annick Renevey <47788523+rannick@users.noreply.github.com> Date: Thu, 17 Oct 2024 11:03:47 +0200 Subject: [PATCH 155/486] Update arriba no check (#6765) * add specific files created * typo * add from nf-test template * remove from pytest_modules * update environement file * update arriba * add tests * use latest conda build * arriba conda env * update environement * update meta * update tags in test * remove ssl check --- modules/nf-core/arriba/download/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-core/arriba/download/main.nf b/modules/nf-core/arriba/download/main.nf index 2e63b2d0b179..c45120adb5d5 100644 --- a/modules/nf-core/arriba/download/main.nf +++ b/modules/nf-core/arriba/download/main.nf @@ -22,7 +22,7 @@ process ARRIBA_DOWNLOAD { script: """ - wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz + wget https://github.com/suhrig/arriba/releases/download/v2.4.0/arriba_v2.4.0.tar.gz -O arriba_v2.4.0.tar.gz --no-check-certificate tar -xzvf arriba_v2.4.0.tar.gz rm arriba_v2.4.0.tar.gz mv arriba_v2.4.0/database/* . From a1a55bca58e86c0b89d48de9d7a39d4dba34d504 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 09:23:16 +0200 Subject: [PATCH 156/486] Update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 (#6682) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index c5c1c433593d..351a51a9b3ad 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -23,7 +23,7 @@ repos: - id: renovate-config-validator # use ruff for python files - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.6 + rev: v0.7.0 hooks: - id: ruff files: \.py$ From b80931c5be241910c62795bbf70534df18b3905f Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Fri, 18 Oct 2024 09:26:54 +0200 Subject: [PATCH 157/486] Allow sorting inputs to SVDB (#6794) * Sort input files order * Allow sorted inputs to SVDB * update tests * Update meta --- modules/nf-core/svdb/merge/main.nf | 35 ++- modules/nf-core/svdb/merge/meta.yml | 16 +- modules/nf-core/svdb/merge/tests/main.nf.test | 291 +++++++++++++++++- .../svdb/merge/tests/main.nf.test.snap | 194 +++++++++++- .../nf-core/svdb/merge/tests/nextflow.config | 5 + 5 files changed, 507 insertions(+), 34 deletions(-) create mode 100644 modules/nf-core/svdb/merge/tests/nextflow.config diff --git a/modules/nf-core/svdb/merge/main.nf b/modules/nf-core/svdb/merge/main.nf index afc34bb4bcdf..d28f2a97cffd 100644 --- a/modules/nf-core/svdb/merge/main.nf +++ b/modules/nf-core/svdb/merge/main.nf @@ -8,11 +8,12 @@ process SVDB_MERGE { input: tuple val(meta), path(vcfs) - val (priority) + val(priority) + val(sort_inputs) output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -20,15 +21,37 @@ process SVDB_MERGE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def input = "${vcfs.join(" ")}" - def prio = "" + + // Ensure priority list matches the number of VCFs if priority is provided + if (priority && vcfs.collect().size() != priority.collect().size()) { + error "If priority is used, one tag per VCF is needed" + } + + if (sort_inputs && vcfs.collect().size() > 1) { + if (priority) { + // make vcf-prioprity pairs and sort on VCF name, so priority is also sorted the same + def pairs = vcfs.indices.collect { [vcfs[it], priority[it]] } + pairs = pairs.sort { a, b -> a[0].name <=> b[0].name } + vcfs = pairs.collect { it[0] } + priority = pairs.collect { it[1] } + } else { + // if there's no priority input just sort the vcfs by name + vcfs = vcfs.sort { it.name } + } + } + + // If there's only one input VCF the code above is not executed, and that VCF becomes the input + input = vcfs + + def prio = "" if(priority) { prio = "--priority ${priority.join(',')}" input = "" - for (int index = 0; index < vcfs.size(); index++) { - input += " ${vcfs[index]}:${priority[index]}" + for (int index = 0; index < vcfs.collect().size(); index++) { + input += "${vcfs[index]}:${priority[index]} " } } + """ svdb \\ --merge \\ diff --git a/modules/nf-core/svdb/merge/meta.yml b/modules/nf-core/svdb/merge/meta.yml index 7dc7c67588ad..d6cc17580f11 100644 --- a/modules/nf-core/svdb/merge/meta.yml +++ b/modules/nf-core/svdb/merge/meta.yml @@ -19,12 +19,22 @@ input: e.g. [ id:'test' ] - vcfs: type: list - description: Two or more VCF files. Order of files should correspond to the - order of tags used for priority. + description: | + One or more VCF files. The order and number of files should correspond to + the order and number of tags in the `priority` input channel. pattern: "*.{vcf,vcf.gz}" - - priority: type: list - description: prioritise the input vcf files according to this list, e.g ['tiddit','cnvnator'] + description: | + Prioritize the input VCF files according to this list, + e.g ['tiddit','cnvnator']. The order and number of tags should correspond to + the order and number of VCFs in the `vcfs` input channel. + - - sort_inputs: + type: boolean + description: | + Should the input files be sorted by name. The priority tag will be sorted + together with it's corresponding VCF file. + output: - vcf: - meta: diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test b/modules/nf-core/svdb/merge/tests/main.nf.test index b0743a699f0b..0dddffa3e73a 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test +++ b/modules/nf-core/svdb/merge/tests/main.nf.test @@ -2,23 +2,86 @@ nextflow_process { name "Test Process SVDB_MERGE" script "modules/nf-core/svdb/merge/main.nf" + config "./nextflow.config" process "SVDB_MERGE" tag "modules" tag "modules_nfcore" tag "svdb" tag "svdb/merge" - test("test_svdb_merge") { + test("1 sample, [], []") { when { process { """ input[0] = Channel.of([ [ id:'test' ], // meta map - [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] ]) - input[1] = [ 'tiddit', 'cnvnator'] + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } + } + + test("1 sample, [], true") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } + } + + test("1 sample, ['tiddit'], []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit'] + input[2] = [] """ } } @@ -26,23 +89,122 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") } + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:tiddit") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } ) } + } + + test("1 sample, ['tiddit'], true") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit'] + input[2] = true + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:tiddit") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } + } + test("2 samples, [], []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = [] + input[2] = [] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test2.vcf test.vcf") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } } - test("test_svdb_merge_noprio") { + test("2 samples, [], true") { when { process { """ input[0] = Channel.of([ [ id:'test' ], // meta map - [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] ]) input[1] = [] + input[2] = true + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf test2.vcf") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } + } + + test("2 samples, ['tiddit', 'cnvnator'], []") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit', 'cnvnator'] + input[2] = [] """ } } @@ -50,13 +212,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert path(process.out.vcf.get(0).get(1)).linesGzip.contains("##fileformat=VCFv4.1") } + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test2.vcf:tiddit test.vcf:cnvnator") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } ) } + } + + test("2 samples, ['tiddit', 'cnvnator'], true") { + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit', 'cnvnator'] + input[2] = true + """ + } + } + then { + assertAll ( + { assert process.success }, + { assert path(process.out.vcf.get(0).get(1)).linesGzip[2].contains("--vcf test.vcf:cnvnator test2.vcf:tiddit") }, // SVDB command line + { assert snapshot( + path(process.out.vcf.get(0).get(1)).vcf.summary, + path(process.out.vcf.get(0).get(1)).vcf.variantsMD5, + process.out.versions + ).match() } + ) + } } - test("test_svdb_merge - stub") { + test("2 samples, [], [] - stub") { options "-stub" @@ -65,10 +262,13 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test' ], // meta map - [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] ]) - input[1] = [ 'tiddit', 'cnvnator'] + input[1] = [] + input[2] = [] """ } } @@ -79,10 +279,9 @@ nextflow_process { { assert snapshot(process.out).match() } ) } - } - test("test_svdb_merge_noprio - stub") { + test("2 samples, [], true - stub") { options "-stub" @@ -91,10 +290,41 @@ nextflow_process { """ input[0] = Channel.of([ [ id:'test' ], // meta map - [file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true) ] + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] ]) input[1] = [] + input[2] = true + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("2 samples, ['tiddit', 'cnvnator'], [] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit', 'cnvnator'] + input[2] = [] """ } } @@ -105,7 +335,34 @@ nextflow_process { { assert snapshot(process.out).match() } ) } + } + + test("2 samples, ['tiddit', 'cnvnator'], true - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([ + [ id:'test' ], // meta map + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + ]) + input[1] = ['tiddit', 'cnvnator'] + input[2] = true + """ + } + } + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } } } diff --git a/modules/nf-core/svdb/merge/tests/main.nf.test.snap b/modules/nf-core/svdb/merge/tests/main.nf.test.snap index e79b2583b38b..a5daf368604f 100644 --- a/modules/nf-core/svdb/merge/tests/main.nf.test.snap +++ b/modules/nf-core/svdb/merge/tests/main.nf.test.snap @@ -1,5 +1,183 @@ { - "test_svdb_merge - stub": { + "1 sample, [], []": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", + "60fb4cab2aa891bebef8ffdbd0e41bc3", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:30:08.029708713" + }, + "2 samples, ['tiddit', 'cnvnator'], true - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ], + "vcf": [ + [ + { + "id": "test" + }, + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:32:10.741546957" + }, + "2 samples, ['tiddit', 'cnvnator'], []": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", + "254e56e4fc8356d68424828438da66e3", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:31:15.105041662" + }, + "2 samples, [], []": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", + "7ad648266e57d405b5b01aaea4613d1c", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:41:54.793936976" + }, + "2 samples, ['tiddit', 'cnvnator'], true": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", + "74ed58e115db54f30036bfd68a7dc432", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:31:29.320496992" + }, + "1 sample, ['tiddit'], []": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", + "9dd588cd870672b78192f48ad440b5d", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:30:30.590239659" + }, + "1 sample, [], true": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", + "60fb4cab2aa891bebef8ffdbd0e41bc3", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:30:22.670145479" + }, + "1 sample, ['tiddit'], true": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=1, variantCount=9, phased=false, phasedAutodetect=false]", + "9dd588cd870672b78192f48ad440b5d", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:30:40.958649472" + }, + "2 samples, [], true": { + "content": [ + "VcfFile [chromosomes=[MT192765.1], sampleCount=2, variantCount=9, phased=false, phasedAutodetect=false]", + "de0a3b56cdee89e4c9cd4fbb4ad3391d", + [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:31:01.933044815" + }, + "2 samples, ['tiddit', 'cnvnator'], [] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "1": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ], + "vcf": [ + [ + { + "id": "test" + }, + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + ] + ], + "versions": [ + "versions.yml:md5,772f39343052d54d9bcb21d4892da203" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-17T08:31:59.830493054" + }, + "2 samples, [], [] - stub": { "content": [ { "0": [ @@ -7,7 +185,7 @@ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -18,7 +196,7 @@ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ @@ -30,9 +208,9 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-16T09:00:41.058996433" + "timestamp": "2024-10-17T08:41:07.289491939" }, - "test_svdb_merge_noprio - stub": { + "2 samples, [], true - stub": { "content": [ { "0": [ @@ -40,7 +218,7 @@ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "1": [ @@ -51,7 +229,7 @@ { "id": "test" }, - "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" + "merged.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" ] ], "versions": [ @@ -63,6 +241,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-10-16T09:00:49.58223306" + "timestamp": "2024-10-17T08:31:48.40721064" } } \ No newline at end of file diff --git a/modules/nf-core/svdb/merge/tests/nextflow.config b/modules/nf-core/svdb/merge/tests/nextflow.config new file mode 100644 index 000000000000..25f38031feff --- /dev/null +++ b/modules/nf-core/svdb/merge/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: 'SVDB_MERGE' { + ext.prefix = "merged" + } +} From c466a8278f6a495eb97421c453fa8706f14cc459 Mon Sep 17 00:00:00 2001 From: lmfaber <43934950+lmfaber@users.noreply.github.com> Date: Fri, 18 Oct 2024 10:23:45 +0200 Subject: [PATCH 158/486] new module: bedtools/nuc (#6797) * new module: bedtools/nuc * new module: bedtools/nuc Add stub test * new module: bedtools/nuc Change input name from bed to intervals --- modules/nf-core/bedtools/nuc/environment.yml | 5 + modules/nf-core/bedtools/nuc/main.nf | 48 +++++++ modules/nf-core/bedtools/nuc/meta.yml | 57 ++++++++ .../nf-core/bedtools/nuc/tests/main.nf.test | 102 +++++++++++++ .../bedtools/nuc/tests/main.nf.test.snap | 134 ++++++++++++++++++ 5 files changed, 346 insertions(+) create mode 100644 modules/nf-core/bedtools/nuc/environment.yml create mode 100644 modules/nf-core/bedtools/nuc/main.nf create mode 100644 modules/nf-core/bedtools/nuc/meta.yml create mode 100644 modules/nf-core/bedtools/nuc/tests/main.nf.test create mode 100644 modules/nf-core/bedtools/nuc/tests/main.nf.test.snap diff --git a/modules/nf-core/bedtools/nuc/environment.yml b/modules/nf-core/bedtools/nuc/environment.yml new file mode 100644 index 000000000000..5683bc05f230 --- /dev/null +++ b/modules/nf-core/bedtools/nuc/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::bedtools=2.31.1 diff --git a/modules/nf-core/bedtools/nuc/main.nf b/modules/nf-core/bedtools/nuc/main.nf new file mode 100644 index 000000000000..afeb4af00271 --- /dev/null +++ b/modules/nf-core/bedtools/nuc/main.nf @@ -0,0 +1,48 @@ +process BEDTOOLS_NUC { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/bedtools:2.31.1--hf5e1c6e_0' : + 'biocontainers/bedtools:2.31.1--hf5e1c6e_0' }" + + input: + tuple val(meta), path(fasta), path(intervals) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + if ("${intervals}" == "${prefix}.bed") error "Input and output names are the same, set prefix in module configuration to disambiguate!" + """ + bedtools \\ + nuc \\ + -fi ${fasta} \\ + -bed ${intervals} \\ + ${args} \\ + > ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.bed + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bedtools: \$(bedtools --version | sed -e "s/bedtools v//g") + END_VERSIONS + """ +} diff --git a/modules/nf-core/bedtools/nuc/meta.yml b/modules/nf-core/bedtools/nuc/meta.yml new file mode 100644 index 000000000000..ef203d26a47e --- /dev/null +++ b/modules/nf-core/bedtools/nuc/meta.yml @@ -0,0 +1,57 @@ +name: bedtools_nuc +description: Profiles the nucleotide content of intervals in a fasta file. +keywords: + - bed + - nucBed + - bedtools + - GC content + - AT content + - nucleotide content + - intervals +tools: + - bedtools: + description: A set of tools for genomic analysis tasks, specifically enabling + genome arithmetic (merge, count, complement) on various file types. + homepage: https://bedtools.readthedocs.io + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/nuc.html + doi: "10.1093/bioinformatics/btq033" + licence: ["MIT"] + identifier: biotools:bedtools +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Genome reference + pattern: "*.{fa,fasta}" + - intervals: + type: file + description: BED/GFF/VCF file of ranges to extract from -fi + pattern: "*.{bed,gff,vcf}" +output: + - bed: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - "*.bed": + type: file + description: "The following information will be reported after each BED entry: %AT content, %GC content, + Number of As observed, Number of Cs observed, Number of Gs observed, Number of Ts observed, + Number of Ns observed, Number of other bases observed, The length of the explored sequence/interval, + The seq. extracted from the FASTA file. (opt., if -seq is used), + The number of times a user's pattern was observed. (opt., if -pattern is used.)" + pattern: "*.bed" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@lmfaber" +maintainers: + - "@lmfaber" diff --git a/modules/nf-core/bedtools/nuc/tests/main.nf.test b/modules/nf-core/bedtools/nuc/tests/main.nf.test new file mode 100644 index 000000000000..f3a5c901cbd1 --- /dev/null +++ b/modules/nf-core/bedtools/nuc/tests/main.nf.test @@ -0,0 +1,102 @@ +nextflow_process { + + name "Test Process BEDTOOLS_NUC" + script "../main.nf" + process "BEDTOOLS_NUC" + + tag "modules" + tag "modules_nfcore" + tag "bedtools" + tag "bedtools/nuc" + + test("test-bedtools-nuc-bed") { + + when { + process { + """ + input[0] = [ + [ id:'test_bed'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-nuc-gff3") { + + when { + process { + """ + input[0] = [ + [ id:'test_gff3'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-nuc-vcf") { + + when { + process { + """ + input[0] = [ + [ id:'test_vcf'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test-bedtools-nuc-bed-stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test_bed'], + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true) + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/bedtools/nuc/tests/main.nf.test.snap b/modules/nf-core/bedtools/nuc/tests/main.nf.test.snap new file mode 100644 index 000000000000..56f6738594c5 --- /dev/null +++ b/modules/nf-core/bedtools/nuc/tests/main.nf.test.snap @@ -0,0 +1,134 @@ +{ + "test-bedtools-nuc-bed": { + "content": [ + { + "0": [ + [ + { + "id": "test_bed" + }, + "test_bed.bed:md5,f34ec56b3186b9c074356b896d34d44e" + ] + ], + "1": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ], + "bed": [ + [ + { + "id": "test_bed" + }, + "test_bed.bed:md5,f34ec56b3186b9c074356b896d34d44e" + ] + ], + "versions": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-15T14:32:40.394499729" + }, + "test-bedtools-nuc-gff3": { + "content": [ + { + "0": [ + [ + { + "id": "test_gff3" + }, + "test_gff3.bed:md5,2866b82a11e5fc2e54a5438136eb4c59" + ] + ], + "1": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ], + "bed": [ + [ + { + "id": "test_gff3" + }, + "test_gff3.bed:md5,2866b82a11e5fc2e54a5438136eb4c59" + ] + ], + "versions": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-15T14:32:48.012672011" + }, + "test-bedtools-nuc-bed-stub": { + "content": [ + { + "0": [ + [ + { + "id": "test_bed" + }, + "test_bed.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ], + "bed": [ + [ + { + "id": "test_bed" + }, + "test_bed.bed:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T09:25:16.512687469" + }, + "test-bedtools-nuc-vcf": { + "content": [ + { + "0": [ + [ + { + "id": "test_vcf" + }, + "test_vcf.bed:md5,35427609e3c2a0e2ead5850c22843ff3" + ] + ], + "1": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ], + "bed": [ + [ + { + "id": "test_vcf" + }, + "test_vcf.bed:md5,35427609e3c2a0e2ead5850c22843ff3" + ] + ], + "versions": [ + "versions.yml:md5,2dc7899a3701ac995280a885eb1898b6" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-15T14:32:55.968243738" + } +} \ No newline at end of file From cb08035150685b11d890d90c9534d4f16869eaec Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Fri, 18 Oct 2024 11:30:58 +0200 Subject: [PATCH 159/486] Some syntax updates (#6801) * some syntax updates * eclint --- modules/nf-core/bcftools/annotate/main.nf | 10 +++++----- modules/nf-core/bedtools/split/main.nf | 6 +++--- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/modules/nf-core/bcftools/annotate/main.nf b/modules/nf-core/bcftools/annotate/main.nf index c3b8b19652c0..9ffdfdf0a490 100644 --- a/modules/nf-core/bcftools/annotate/main.nf +++ b/modules/nf-core/bcftools/annotate/main.nf @@ -59,12 +59,12 @@ process BCFTOOLS_ANNOTATE { args.contains("--output-type z") || args.contains("-Oz") ? "vcf.gz" : args.contains("--output-type v") || args.contains("-Ov") ? "vcf" : "vcf" - def index = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : - args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : - args.contains("--write-index") || args.contains("-W") ? "csi" : - "" + def index_extension = args.contains("--write-index=tbi") || args.contains("-W=tbi") ? "tbi" : + args.contains("--write-index=csi") || args.contains("-W=csi") ? "csi" : + args.contains("--write-index") || args.contains("-W") ? "csi" : + "" def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch" - def create_index = extension.endsWith(".gz") && index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index}" : "" + def create_index = extension.endsWith(".gz") && index_extension.matches("csi|tbi") ? "touch ${prefix}.${extension}.${index_extension}" : "" """ ${create_cmd} ${prefix}.${extension} diff --git a/modules/nf-core/bedtools/split/main.nf b/modules/nf-core/bedtools/split/main.nf index b555024cde28..2b3af64f6b9d 100644 --- a/modules/nf-core/bedtools/split/main.nf +++ b/modules/nf-core/bedtools/split/main.nf @@ -38,9 +38,9 @@ process BEDTOOLS_SPLIT { stub: def prefix = task.ext.prefix ?: "${meta.id}" - create_beds = (1..count).collect { - number = "0".multiply(4 - it.toString().size()) + "${it}" - " touch ${prefix}.${number}.bed" + def create_beds = (1..count).collect { number -> + def numberString = "0".multiply(4 - number.toString().size()) + "${number}" + " touch ${prefix}.${numberString}.bed" }.join("\n") """ From a591752e1c323547d107a408ee1cbbd2c270f0c8 Mon Sep 17 00:00:00 2001 From: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Date: Fri, 18 Oct 2024 12:53:51 +0100 Subject: [PATCH 160/486] proovframe/fix module (#6800) * proovframe/fix module * proovframe version automatic extraction, both for fix and map modules --- .../nf-core/proovframe/fix/environment.yml | 7 ++ modules/nf-core/proovframe/fix/main.nf | 49 ++++++++++++ modules/nf-core/proovframe/fix/meta.yml | 61 +++++++++++++++ .../nf-core/proovframe/fix/tests/main.nf.test | 76 +++++++++++++++++++ .../proovframe/fix/tests/main.nf.test.snap | 72 ++++++++++++++++++ modules/nf-core/proovframe/map/main.nf | 4 +- .../proovframe/map/tests/main.nf.test.snap | 4 +- 7 files changed, 269 insertions(+), 4 deletions(-) create mode 100644 modules/nf-core/proovframe/fix/environment.yml create mode 100644 modules/nf-core/proovframe/fix/main.nf create mode 100644 modules/nf-core/proovframe/fix/meta.yml create mode 100644 modules/nf-core/proovframe/fix/tests/main.nf.test create mode 100644 modules/nf-core/proovframe/fix/tests/main.nf.test.snap diff --git a/modules/nf-core/proovframe/fix/environment.yml b/modules/nf-core/proovframe/fix/environment.yml new file mode 100644 index 000000000000..a1a698f477be --- /dev/null +++ b/modules/nf-core/proovframe/fix/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::proovframe=0.9.7" diff --git a/modules/nf-core/proovframe/fix/main.nf b/modules/nf-core/proovframe/fix/main.nf new file mode 100644 index 000000000000..cf9d7b2385e1 --- /dev/null +++ b/modules/nf-core/proovframe/fix/main.nf @@ -0,0 +1,49 @@ +process PROOVFRAME_FIX { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/proovframe:0.9.7--hdfd78af_1': + 'biocontainers/proovframe:0.9.7--hdfd78af_1' }" + + input: + tuple val(meta) , path(fa) + tuple val(meta2), path(tsv) + + output: + tuple val(meta), path("*.fa"), emit: out_fa + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + proovframe \\ + fix \\ + ${args} \\ + -o ${prefix}.fa \\ + ${fa} \\ + ${tsv} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.fa + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*') + END_VERSIONS + """ +} diff --git a/modules/nf-core/proovframe/fix/meta.yml b/modules/nf-core/proovframe/fix/meta.yml new file mode 100644 index 000000000000..b8df94cc9297 --- /dev/null +++ b/modules/nf-core/proovframe/fix/meta.yml @@ -0,0 +1,61 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "proovframe_fix" +description: frame-shift correction for long read (meta)genomics - fix frameshifts + in reads +keywords: + - frame-shift correction + - long-read sequencing + - sequence analysis +tools: + - "proovframe": + description: "frame-shift correction for long read (meta)genomics" + homepage: "https://github.com/thackl/proovframe" + documentation: "https://github.com/thackl/proovframe" + tool_dev_url: "https://github.com/thackl/proovframe" + doi: "10.1101/2021.08.23.457338" + licence: ["MIT"] + identifier: biotools:proovframe + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fa: + type: file + description: "A FASTA file containing a database of guide protein sequences" + pattern: "*.{faa,fasta,fa}" + - - meta2: + type: map + description: | + Groovy Map containing reference information + e.g. [ id:'test' ] + - tsv: + type: file + description: "Output TSV file from proovframe/map with the frameshift-aware protein to read alignments\ + \ from proovframe/map" + pattern: "*.{tsv}" + +output: + - out_fa: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - "*.fa": + type: file + description: "Result FASTA with fixed frameshift reads" + pattern: "*.{fa}" + - versions: + - "versions.yml": + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@mcarbajo" + - "@vagkaratzas" +maintainers: + - "@vagkaratzas" diff --git a/modules/nf-core/proovframe/fix/tests/main.nf.test b/modules/nf-core/proovframe/fix/tests/main.nf.test new file mode 100644 index 000000000000..1e57fa920c7f --- /dev/null +++ b/modules/nf-core/proovframe/fix/tests/main.nf.test @@ -0,0 +1,76 @@ +nextflow_process { + + name "Test Process PROOVFRAME_FIX" + script "../main.nf" + process "PROOVFRAME_FIX" + + tag "modules" + tag "modules_nfcore" + tag "proovframe" + tag "proovframe/map" + tag "proovframe/fix" + + setup { + run("PROOVFRAME_MAP") { + script "../../map/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + """ + } + } + } + + test("test - fa_tsv") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = PROOVFRAME_MAP.out.tsv + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("test - faa_fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + ] + input[1] = PROOVFRAME_MAP.out.tsv + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} diff --git a/modules/nf-core/proovframe/fix/tests/main.nf.test.snap b/modules/nf-core/proovframe/fix/tests/main.nf.test.snap new file mode 100644 index 000000000000..840ac48434e5 --- /dev/null +++ b/modules/nf-core/proovframe/fix/tests/main.nf.test.snap @@ -0,0 +1,72 @@ +{ + "test - fa_tsv": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,83eccce28287b72c524ea022996d465f" + ] + ], + "1": [ + "versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4" + ], + "out_fa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,83eccce28287b72c524ea022996d465f" + ] + ], + "versions": [ + "versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.04.5" + }, + "timestamp": "2024-10-18T12:17:51.685565164" + }, + "test - faa_fasta - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4" + ], + "out_fa": [ + [ + { + "id": "test", + "single_end": false + }, + "test.fa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,285ddd6be0ed62527fe62fde1df82bf4" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "23.04.5" + }, + "timestamp": "2024-10-18T12:17:57.181403559" + } +} \ No newline at end of file diff --git a/modules/nf-core/proovframe/map/main.nf b/modules/nf-core/proovframe/map/main.nf index 75eb835ca264..7f318d4708e7 100644 --- a/modules/nf-core/proovframe/map/main.nf +++ b/modules/nf-core/proovframe/map/main.nf @@ -30,7 +30,7 @@ process PROOVFRAME_MAP { cat <<-END_VERSIONS > versions.yml "${task.process}": - proovframe: 0.9.7 + proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*') END_VERSIONS """ @@ -42,7 +42,7 @@ process PROOVFRAME_MAP { cat <<-END_VERSIONS > versions.yml "${task.process}": - proovframe: 0.9.7 + proovframe: \$(proovframe 2>&1 | grep -o 'proovframe-v[0-9]*\\.[0-9]*\\.[0-9]*' | grep -o '[0-9]*\\.[0-9]*\\.[0-9]*') END_VERSIONS """ } diff --git a/modules/nf-core/proovframe/map/tests/main.nf.test.snap b/modules/nf-core/proovframe/map/tests/main.nf.test.snap index b0224d1728ea..a499560e2a63 100644 --- a/modules/nf-core/proovframe/map/tests/main.nf.test.snap +++ b/modules/nf-core/proovframe/map/tests/main.nf.test.snap @@ -9,7 +9,7 @@ "nf-test": "0.9.0", "nextflow": "23.04.5" }, - "timestamp": "2024-10-16T15:02:00.599243234" + "timestamp": "2024-10-18T12:19:19.854923441" }, "sarscov2 - tsv - stub": { "content": [ @@ -44,6 +44,6 @@ "nf-test": "0.9.0", "nextflow": "23.04.5" }, - "timestamp": "2024-10-16T15:02:21.855444606" + "timestamp": "2024-10-18T12:19:25.120972507" } } \ No newline at end of file From 9530ba667bb6c809d998fb9bd567bb9514cb23e5 Mon Sep 17 00:00:00 2001 From: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> Date: Fri, 18 Oct 2024 17:40:11 +0530 Subject: [PATCH 161/486] pangolin - use seqera containers + nf-test; rm pytests (#6740) * use seqera containers + nf-test; rm pytests * Update modules/nf-core/pangolin/main.nf Co-authored-by: Joon Klaps * update snapshots * fix home path sing & update conda env * Fixing the meta.yml and pining pangolin-data --------- Co-authored-by: Joon Klaps --- modules/nf-core/pangolin/environment.yml | 4 +- modules/nf-core/pangolin/main.nf | 6 +- modules/nf-core/pangolin/meta.yml | 8 +-- modules/nf-core/pangolin/tests/main.nf.test | 57 ++++++++++++++++ .../nf-core/pangolin/tests/main.nf.test.snap | 68 +++++++++++++++++++ tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/pangolin/main.nf | 12 ---- .../modules/nf-core/pangolin/nextflow.config | 5 -- tests/modules/nf-core/pangolin/test.yml | 7 -- 9 files changed, 136 insertions(+), 34 deletions(-) create mode 100644 modules/nf-core/pangolin/tests/main.nf.test create mode 100644 modules/nf-core/pangolin/tests/main.nf.test.snap delete mode 100644 tests/modules/nf-core/pangolin/main.nf delete mode 100644 tests/modules/nf-core/pangolin/nextflow.config delete mode 100644 tests/modules/nf-core/pangolin/test.yml diff --git a/modules/nf-core/pangolin/environment.yml b/modules/nf-core/pangolin/environment.yml index 4fcf2f1f85a2..d4379368c851 100644 --- a/modules/nf-core/pangolin/environment.yml +++ b/modules/nf-core/pangolin/environment.yml @@ -2,4 +2,6 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::pangolin=4.2 + - bioconda::pangolin-data=1.30 + - bioconda::pangolin=4.3 + - bioconda::snakemake=7.30.1 diff --git a/modules/nf-core/pangolin/main.nf b/modules/nf-core/pangolin/main.nf index 00cf42909d1c..08200de2ceae 100644 --- a/modules/nf-core/pangolin/main.nf +++ b/modules/nf-core/pangolin/main.nf @@ -4,8 +4,8 @@ process PANGOLIN { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pangolin:4.2--pyhdfd78af_1' : - 'biocontainers/pangolin:4.2--pyhdfd78af_1' }" + 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/bb/bb7bac48e43a9cd6274e1f99c761a5785b74f6d8a55313ee634aaffbe87c1869/data' : + 'community.wave.seqera.io/library/pangolin-data_pangolin_snakemake:5bbc297f7502ff33' }" input: tuple val(meta), path(fasta) @@ -21,6 +21,8 @@ process PANGOLIN { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ + export XDG_CACHE_HOME=/tmp/.cache + pangolin \\ $fasta\\ --outfile ${prefix}.pangolin.csv \\ diff --git a/modules/nf-core/pangolin/meta.yml b/modules/nf-core/pangolin/meta.yml index 9220aefc1453..78713c132215 100644 --- a/modules/nf-core/pangolin/meta.yml +++ b/modules/nf-core/pangolin/meta.yml @@ -5,7 +5,7 @@ keywords: - pangolin - lineage tools: - - star: + - pangolin: description: | Phylogenetic Assignment of Named Global Outbreak LINeages homepage: https://github.com/cov-lineages/pangolin#pangolearn-description @@ -24,9 +24,9 @@ input: output: - report: - meta: - type: file - description: Pangolin lineage report - pattern: "*.{csv}" + type: map + description: | + Groovy Map containing sample information - "*.csv": type: file description: Pangolin lineage report diff --git a/modules/nf-core/pangolin/tests/main.nf.test b/modules/nf-core/pangolin/tests/main.nf.test new file mode 100644 index 000000000000..1ee097e3c746 --- /dev/null +++ b/modules/nf-core/pangolin/tests/main.nf.test @@ -0,0 +1,57 @@ +nextflow_process { + + name "Test Process PANGOLIN" + script "../main.nf" + process "PANGOLIN" + + tag "modules" + tag "modules_nfcore" + tag "pangolin" + + test("sarscov2 genome [fasta]") { + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + + test("sarscov2 genome [fasta] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) ] + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + + } + +} \ No newline at end of file diff --git a/modules/nf-core/pangolin/tests/main.nf.test.snap b/modules/nf-core/pangolin/tests/main.nf.test.snap new file mode 100644 index 000000000000..681a4783686f --- /dev/null +++ b/modules/nf-core/pangolin/tests/main.nf.test.snap @@ -0,0 +1,68 @@ +{ + "sarscov2 genome [fasta] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4" + ] + ], + "1": [ + "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a" + ], + "report": [ + [ + { + "id": "test" + }, + "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4" + ] + ], + "versions": [ + "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:33:48.797026222" + }, + "sarscov2 genome [fasta]": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4" + ] + ], + "1": [ + "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a" + ], + "report": [ + [ + { + "id": "test" + }, + "test.pangolin.csv:md5,2cc701567cf37bad5c6574c29aa595d4" + ] + ], + "versions": [ + "versions.yml:md5,65ec45a19faa92a922073b9b08d90a8a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T10:33:17.535254436" + } +} \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 584db480a14f..e40cb75442fb 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -476,9 +476,6 @@ nucmer: oncocnv: - modules/nf-core/oncocnv/** - tests/modules/nf-core/oncocnv/** -pangolin: - - modules/nf-core/pangolin/** - - tests/modules/nf-core/pangolin/** parabricks/applybqsr: - modules/nf-core/parabricks/applybqsr/** - tests/modules/nf-core/parabricks/applybqsr/** diff --git a/tests/modules/nf-core/pangolin/main.nf b/tests/modules/nf-core/pangolin/main.nf deleted file mode 100644 index 6bed60ae0d76..000000000000 --- a/tests/modules/nf-core/pangolin/main.nf +++ /dev/null @@ -1,12 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PANGOLIN } from '../../../../modules/nf-core/pangolin/main.nf' - -workflow test_pangolin { - input = [ [ id:'test' ], // meta map - [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] ] - - PANGOLIN ( input ) -} diff --git a/tests/modules/nf-core/pangolin/nextflow.config b/tests/modules/nf-core/pangolin/nextflow.config deleted file mode 100644 index 8730f1c4b930..000000000000 --- a/tests/modules/nf-core/pangolin/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - -} diff --git a/tests/modules/nf-core/pangolin/test.yml b/tests/modules/nf-core/pangolin/test.yml deleted file mode 100644 index 2b24c99d430b..000000000000 --- a/tests/modules/nf-core/pangolin/test.yml +++ /dev/null @@ -1,7 +0,0 @@ -- name: pangolin - command: nextflow run ./tests/modules/nf-core/pangolin -entry test_pangolin -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/pangolin/nextflow.config - tags: - - pangolin - files: - - path: ./output/pangolin/test.pangolin.csv - md5sum: 5913b1fc7645798ab7be31e9029c5f7e From 74ac5351a11a184171489dee73652e8b69ba9d22 Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Fri, 18 Oct 2024 15:20:44 +0200 Subject: [PATCH 162/486] new module elprep/fastatoelfasta (#6804) new modules elprep/fastatoelfasta --- .../elprep/fastatoelfasta/environment.yml | 7 ++ modules/nf-core/elprep/fastatoelfasta/main.nf | 50 ++++++++++++++ .../nf-core/elprep/fastatoelfasta/meta.yml | 55 ++++++++++++++++ .../elprep/fastatoelfasta/tests/main.nf.test | 66 +++++++++++++++++++ .../fastatoelfasta/tests/main.nf.test.snap | 62 +++++++++++++++++ 5 files changed, 240 insertions(+) create mode 100644 modules/nf-core/elprep/fastatoelfasta/environment.yml create mode 100644 modules/nf-core/elprep/fastatoelfasta/main.nf create mode 100644 modules/nf-core/elprep/fastatoelfasta/meta.yml create mode 100644 modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test create mode 100644 modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test.snap diff --git a/modules/nf-core/elprep/fastatoelfasta/environment.yml b/modules/nf-core/elprep/fastatoelfasta/environment.yml new file mode 100644 index 000000000000..6ab3f8fc5d71 --- /dev/null +++ b/modules/nf-core/elprep/fastatoelfasta/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::elprep=5.1.3" diff --git a/modules/nf-core/elprep/fastatoelfasta/main.nf b/modules/nf-core/elprep/fastatoelfasta/main.nf new file mode 100644 index 000000000000..861350bf5006 --- /dev/null +++ b/modules/nf-core/elprep/fastatoelfasta/main.nf @@ -0,0 +1,50 @@ +process ELPREP_FASTATOELFASTA { + tag "$meta.id" + label 'process_low' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/elprep:5.1.3--he881be0_1': + 'biocontainers/elprep:5.1.3--he881be0_1' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.elfasta") , emit: elfasta + tuple val(meta), path("logs/elprep/elprep*"), emit: log + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + elprep fasta-to-elfasta \\ + $fasta \\ + ${prefix}.elfasta \\ + --log-path ./ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//') + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def timestamp = "${java.time.OffsetDateTime.now().format(java.time.format.DateTimeFormatter.ISO_DATE_TIME)}" + + """ + mkdir -p logs/elprep + + touch ${prefix}.elfasta + touch logs/elprep/elprep-${timestamp}.log + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//') + END_VERSIONS + """ +} diff --git a/modules/nf-core/elprep/fastatoelfasta/meta.yml b/modules/nf-core/elprep/fastatoelfasta/meta.yml new file mode 100644 index 000000000000..41a8be31af50 --- /dev/null +++ b/modules/nf-core/elprep/fastatoelfasta/meta.yml @@ -0,0 +1,55 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "elprep_fastatoelfasta" +description: Convert a file in FASTA format to the ELFASTA format +keywords: + - fasta + - elfasta + - elprep +tools: + - "elprep": + description: "elPrep is a high-performance tool for preparing .sam/.bam files + for variant calling in sequencing pipelines. It can be used as a drop-in replacement + for SAMtools/Picard/GATK4." + homepage: "https://github.com/ExaScience/elprep" + documentation: "https://github.com/ExaScience/elprep" + tool_dev_url: "https://github.com/ExaScience/elprep" + doi: "10.1371/journal.pone.0244471" + licence: ["AGPL v3"] + identifier: biotools:elprep + +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - fasta: + type: file + description: FASTA file + pattern: "*.{fasta,fa,fna}" +output: + - elfasta: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.elfasta" + - "*.elfasta": + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.elfasta" + - log: + - meta: {} + - logs/elprep/elprep*: {} + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test b/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test new file mode 100644 index 000000000000..d22f6d9d2820 --- /dev/null +++ b/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test @@ -0,0 +1,66 @@ +nextflow_process { + + name "Test Process ELPREP_FASTATOELFASTA" + script "../main.nf" + process "ELPREP_FASTATOELFASTA" + + tag "modules" + tag "modules_nfcore" + tag "elprep" + tag "elprep/fastatoelfasta" + + test("sarscov2 - fasta") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.elfasta, + process.out.log.collect { [it[0], file(it[1]).exists()] }, + process.out.versions + ).match() } + ) + } + + } + + test("sarscov2 - fasta - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true), + ] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.elfasta, + process.out.log.collect { [it[0], file(it[1]).exists()] }, + process.out.versions + ).match() } + ) + } + + } + +} diff --git a/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test.snap b/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test.snap new file mode 100644 index 000000000000..799bb0fb7c45 --- /dev/null +++ b/modules/nf-core/elprep/fastatoelfasta/tests/main.nf.test.snap @@ -0,0 +1,62 @@ +{ + "sarscov2 - fasta - stub": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.elfasta:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + true + ] + ], + [ + "versions.yml:md5,bf313ed1289a8969464c5593b0ff67be" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T14:29:50.861439255" + }, + "sarscov2 - fasta": { + "content": [ + [ + [ + { + "id": "test", + "single_end": false + }, + "test.elfasta:md5,09a6f76bed84ee211ef0d962e26c77f1" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + true + ] + ], + [ + "versions.yml:md5,bf313ed1289a8969464c5593b0ff67be" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T14:25:24.238816922" + } +} \ No newline at end of file From 66b22564bc1bc0db7292f2073cdef954ead773e7 Mon Sep 17 00:00:00 2001 From: Luisa Santus Date: Fri, 18 Oct 2024 16:49:38 +0200 Subject: [PATCH 163/486] add regressive, fix tcoffee and consensus (#6802) * add regressive, fix tcoffee and consensus * fix meta * fix equal sign alignment * fix --- modules/nf-core/tcoffee/align/main.nf | 8 - modules/nf-core/tcoffee/consensus/main.nf | 10 +- modules/nf-core/tcoffee/consensus/meta.yml | 17 ++- .../tcoffee/consensus/tests/eval.config | 6 + .../tcoffee/consensus/tests/main.nf.test | 29 +++- .../tcoffee/consensus/tests/main.nf.test.snap | 29 ++-- .../tcoffee/consensus/tests/sequence.config | 5 - .../tcoffee/regressive/environment.yml | 6 + modules/nf-core/tcoffee/regressive/main.nf | 64 ++++++++ modules/nf-core/tcoffee/regressive/meta.yml | 80 ++++++++++ .../tcoffee/regressive/tests/main.nf.test | 137 ++++++++++++++++++ .../regressive/tests/main.nf.test.snap | 42 ++++++ .../tcoffee/regressive/tests/sequence.config | 3 + .../tcoffee/regressive/tests/tree.config | 5 + 14 files changed, 403 insertions(+), 38 deletions(-) create mode 100644 modules/nf-core/tcoffee/consensus/tests/eval.config create mode 100644 modules/nf-core/tcoffee/regressive/environment.yml create mode 100644 modules/nf-core/tcoffee/regressive/main.nf create mode 100644 modules/nf-core/tcoffee/regressive/meta.yml create mode 100644 modules/nf-core/tcoffee/regressive/tests/main.nf.test create mode 100644 modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap create mode 100644 modules/nf-core/tcoffee/regressive/tests/sequence.config create mode 100644 modules/nf-core/tcoffee/regressive/tests/tree.config diff --git a/modules/nf-core/tcoffee/align/main.nf b/modules/nf-core/tcoffee/align/main.nf index 45be6226cb2a..09bb879deedf 100644 --- a/modules/nf-core/tcoffee/align/main.nf +++ b/modules/nf-core/tcoffee/align/main.nf @@ -39,14 +39,6 @@ process TCOFFEE_ALIGN { -outfile $outfile \ $write_output - # If stdout file exist and compress is true, then compress the file - # This is a patch for the current behaviour of the regressive algorithm - # that does not support the stdout redirection - if [ -f stdout ] && [ "$compress" = true ]; then - pigz -cp ${task.cpus} < stdout > ${prefix}.aln.gz - rm stdout - fi - cat <<-END_VERSIONS > versions.yml "${task.process}": tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}') diff --git a/modules/nf-core/tcoffee/consensus/main.nf b/modules/nf-core/tcoffee/consensus/main.nf index 666c1ee0f7f0..6f06c6965695 100644 --- a/modules/nf-core/tcoffee/consensus/main.nf +++ b/modules/nf-core/tcoffee/consensus/main.nf @@ -14,8 +14,9 @@ process TCOFFEE_CONSENSUS { val(compress) output: - tuple val(meta), path("*.{aln,aln.gz}"), emit: alignment - path "versions.yml" , emit: versions + tuple val(meta), path("*.{aln,aln.gz}") , emit: alignment + tuple val(meta), path("*.{html,sp_ascii}") , emit: eval, optional: true + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -35,11 +36,6 @@ process TCOFFEE_CONSENSUS { -outfile $outfile \ $write_output - if [ -f stdout ] && [ "$compress" = true ]; then - pigz -cp ${task.cpus} < stdout > ${prefix}.aln.gz - rm stdout - fi - cat <<-END_VERSIONS > versions.yml "${task.process}": tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}') diff --git a/modules/nf-core/tcoffee/consensus/meta.yml b/modules/nf-core/tcoffee/consensus/meta.yml index c485e06a41d3..ba6f0da2e5b0 100644 --- a/modules/nf-core/tcoffee/consensus/meta.yml +++ b/modules/nf-core/tcoffee/consensus/meta.yml @@ -18,7 +18,6 @@ tools: description: "Parallel implementation of the gzip algorithm." homepage: "https://zlib.net/pigz/" documentation: "https://zlib.net/pigz/pigz.pdf" - identifier: "" input: - - meta: @@ -52,10 +51,22 @@ output: description: | Groovy Map containing sample information e.g. `[ id:'sample1' ]` + pattern: "*.{fa,fasta,aln}" - "*.{aln,aln.gz}": type: file - description: Consensus alignment in FASTA format - pattern: "*.{fa,fasta,aln}" + description: Alignment file in FASTA format. May be gzipped. + pattern: "*.aln{.gz,}" + - eval: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + pattern: "*.{html, score_ascii}" + - "*.{html,sp_ascii}": + type: file + description: Consensus evaluation file. + pattern: "*.{html, score_ascii}" - versions: - versions.yml: type: file diff --git a/modules/nf-core/tcoffee/consensus/tests/eval.config b/modules/nf-core/tcoffee/consensus/tests/eval.config new file mode 100644 index 000000000000..c31be4d6e8cf --- /dev/null +++ b/modules/nf-core/tcoffee/consensus/tests/eval.config @@ -0,0 +1,6 @@ +process { + withName: "TCOFFEE_CONSENSUS"{ + ext.args = { "-output fasta_aln, score_html, sp_ascii" } + ext.prefix = "consensus" + } +} diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test b/modules/nf-core/tcoffee/consensus/tests/main.nf.test index 5f013e3f9e7f..8b115825cd6f 100644 --- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test +++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test @@ -13,8 +13,6 @@ nextflow_process { tag "clustalo/guidetree" tag "famsa/align" - config "./sequence.config" - setup { run("CLUSTALO_GUIDETREE") { script "../../../clustalo/guidetree/main.nf" @@ -55,6 +53,30 @@ nextflow_process { } test("consensus - no tree - uncompressed - seatoxin ") { + config "./sequence.config" + + when { + process { + """ + msas = FAMSA_ALIGN.out.alignment.mix(MAGUS_ALIGN.out.alignment).groupTuple() + input[0] = msas + input[1] = [[:],[]] + input[2] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") } + ) + } + } + + test("consensus_evaluation - no tree - uncompressed - seatoxin ") { + config "./eval.config" when { process { @@ -77,6 +99,8 @@ nextflow_process { } test("consensus - tree - compressed- seatoxin") { + config "./sequence.config" + when { process { """ @@ -97,6 +121,7 @@ nextflow_process { } test("consensus - stub") { + config "./sequence.config" options "-stub" diff --git a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap index ed50562d0e63..4af4326217ff 100644 --- a/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap +++ b/modules/nf-core/tcoffee/consensus/tests/main.nf.test.snap @@ -6,10 +6,6 @@ "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, "timestamp": "2024-09-18T13:54:43.924522245" }, "consensus - stub": { @@ -30,6 +26,9 @@ ] ], "1": [ + + ], + "2": [ "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ], @@ -46,6 +45,9 @@ }, "consensus.aln:md5,d41d8cd98f00b204e9800998ecf8427e" ] + ], + "eval": [ + ], "versions": [ "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", @@ -53,11 +55,7 @@ ] } ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-09-18T13:55:25.155000209" + "timestamp": "2024-10-18T11:41:11.216683" }, "consensus - tree - compressed- seatoxin": { "content": [ @@ -66,10 +64,15 @@ "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" ] ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, "timestamp": "2024-09-18T13:55:03.627733582" + }, + "consensus_evaluation - no tree - uncompressed - seatoxin ": { + "content": [ + [ + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1", + "versions.yml:md5,79d4f7ac70fab29f8cd0a18a4d3f76d1" + ] + ], + "timestamp": "2024-10-18T11:43:51.839734" } } \ No newline at end of file diff --git a/modules/nf-core/tcoffee/consensus/tests/sequence.config b/modules/nf-core/tcoffee/consensus/tests/sequence.config index b23494c3cfe5..cef48803415b 100644 --- a/modules/nf-core/tcoffee/consensus/tests/sequence.config +++ b/modules/nf-core/tcoffee/consensus/tests/sequence.config @@ -1,9 +1,4 @@ process { - - withName: "TCOFFEE_ALIGN"{ - ext.prefix = "tcoffee_test" - ext.args = { "-output fasta_aln" } - } withName: "TCOFFEE_CONSENSUS"{ ext.args = { "-output fasta_aln" } ext.prefix = "consensus" diff --git a/modules/nf-core/tcoffee/regressive/environment.yml b/modules/nf-core/tcoffee/regressive/environment.yml new file mode 100644 index 000000000000..26a17e709832 --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/environment.yml @@ -0,0 +1,6 @@ +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::t-coffee=13.46.0.919e8c6b + - conda-forge::pigz=2.8 diff --git a/modules/nf-core/tcoffee/regressive/main.nf b/modules/nf-core/tcoffee/regressive/main.nf new file mode 100644 index 000000000000..baf825681b5c --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/main.nf @@ -0,0 +1,64 @@ +process TCOFFEE_REGRESSIVE { + tag "$meta.id" + label 'process_medium' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0': + 'biocontainers/mulled-v2-a76a981c07359a31ff55b9dc13bd3da5ce1909c1:84c8f17f1259b49e2f7783b95b7a89c6f2cb199e-0' }" + + input: + tuple val(meta) , path(fasta) + tuple val(meta2), path(tree) + tuple val(meta3), path(template), path(accessory_informations) + val(compress) + + output: + tuple val(meta), path("*.aln{.gz,}"), emit: alignment + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def tree_args = tree ? "-regtree $tree" : "" + def template_args = template ? "-template_file $template" : "" + def outfile = compress ? "stdout" : "${prefix}.aln" + """ + export TEMP='./' + t_coffee -reg \ + -seq ${fasta} \ + $tree_args \ + $template_args \ + $args \ + -reg_thread ${task.cpus} \ + -outfile $outfile + + if [ "$compress" = true ]; then + pigz -cp ${task.cpus} < stdout > ${prefix}.aln.gz + rm stdout + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}') + pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + # Otherwise, tcoffee will crash when calling its version + export TEMP='./' + touch ${prefix}.aln${compress ? '.gz':''} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + tcoffee: \$( t_coffee -version | awk '{gsub("Version_", ""); print \$3}') + pigz: \$(echo \$(pigz --version 2>&1) | sed 's/^.*pigz\\w*//' )) + END_VERSIONS + """ +} diff --git a/modules/nf-core/tcoffee/regressive/meta.yml b/modules/nf-core/tcoffee/regressive/meta.yml new file mode 100644 index 000000000000..9f9c896744aa --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/meta.yml @@ -0,0 +1,80 @@ +name: "tcoffee_regressive" +description: Aligns sequences using the regressive algorithm as implemented in the T_COFFEE package +keywords: + - alignment + - MSA + - genomics +tools: + - "tcoffee": + description: "A collection of tools for Computing, Evaluating and Manipulating + Multiple Alignments of DNA, RNA, Protein Sequences and Structures." + homepage: "http://www.tcoffee.org/Projects/tcoffee/" + documentation: "https://tcoffee.readthedocs.io/en/latest/tcoffee_main_documentation.html" + tool_dev_url: "https://github.com/cbcrg/tcoffee" + doi: "10.1038/s41587-019-0333-6" + licence: ["GPL v3"] + identifier: "" + - "pigz": + description: "Parallel implementation of the gzip algorithm." + homepage: "https://zlib.net/pigz/" + documentation: "https://zlib.net/pigz/pigz.pdf" + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - fasta: + type: file + description: Input sequences in FASTA format + pattern: "*.{fa,fasta}" + - - meta2: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_tree']` + - tree: + type: file + description: Input guide tree in Newick format + pattern: "*.{dnd}" + - - meta3: + type: map + description: | + Groovy Map containing tree information + e.g. `[ id:'test_infos']` + - template: + type: file + description: T_coffee template file that maps sequences to the accessory information + files to be used. + pattern: "*" + - accessory_informations: + type: file + description: Accessory files to be used in the alignment. For example, it could + be protein structures or secondary structures. + pattern: "*" + - - compress: + type: boolean + description: Flag representing whether the output MSA should be compressed. + Set to true to enable/false to disable compression. Compression is done using + pigz, and is multithreaded. +output: + - alignment: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test']` + - "*.aln{.gz,}": + type: file + description: Alignment file in FASTA format. May be gzipped. + pattern: "*.aln{.gz,}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@luisas" +maintainers: + - "@luisas" diff --git a/modules/nf-core/tcoffee/regressive/tests/main.nf.test b/modules/nf-core/tcoffee/regressive/tests/main.nf.test new file mode 100644 index 000000000000..c4f013e483d7 --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/tests/main.nf.test @@ -0,0 +1,137 @@ +nextflow_process { + + name "Test Process TCOFFEE_REGRESSIVE" + script "../main.nf" + process "TCOFFEE_REGRESSIVE" + + tag "modules" + tag "modules_nfcore" + tag "tcoffee" + tag "tcoffee/regressive" + tag "famsa/guidetree" + tag "untar" + + test("align_sequence - compressed - seatoxin") { + + config "./sequence.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[],[]] + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }, + ) + } + } + + test("align_sequence - uncompressed - seatoxin") { + + config "./sequence.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[],[]] + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getText().contains("1ahl") }, + ) + } + } + + test("align_with_guide_tree - uncompressed - seatoxin") { + + config "./tree.config" + + setup { + + run("FAMSA_GUIDETREE") { + script "../../../famsa/guidetree//main.nf" + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + + """ + } + } + } + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = FAMSA_GUIDETREE.out.tree.collect{ meta, tree -> tree }.map{ tree -> [[ id: 'test'], tree]} + input[2] = [ [:], [], [] ] + input[3] = true + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.versions).match()}, + { assert path(process.out.alignment.get(0).get(1)).getTextGzip().contains("1ahl") }, + ) + } + + } + + test("align_sequence - uncompressed - seatoxin - stub") { + options "-stub" + config "./sequence.config" + + when { + process { + """ + input[0] = [ [ id:'test' ], + file(params.modules_testdata_base_path + "../../multiplesequencealign/testdata/setoxin-ref.fa", checkIfExists: true) + ] + input[1] = [[:],[]] + input[2] = [[:],[],[]] + input[3] = false + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.alignment, + process.out.versions + ).match() + } + ) + } + } + +} \ No newline at end of file diff --git a/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap b/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap new file mode 100644 index 000000000000..2445b0986d53 --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/tests/main.nf.test.snap @@ -0,0 +1,42 @@ +{ + "align_sequence - uncompressed - seatoxin": { + "content": [ + [ + "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af" + ] + ], + "timestamp": "2024-10-18T11:10:07.232451" + }, + "align_sequence - compressed - seatoxin": { + "content": [ + [ + "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af" + ] + ], + "timestamp": "2024-10-18T11:32:03.211575" + }, + "align_with_guide_tree - uncompressed - seatoxin": { + "content": [ + [ + "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af" + ] + ], + "timestamp": "2024-10-18T11:32:23.841131" + }, + "align_sequence - uncompressed - seatoxin - stub": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.aln:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + [ + "versions.yml:md5,044bf3966a378112bdfad5ad4fce13af" + ] + ], + "timestamp": "2024-10-18T11:10:21.369064" + } +} \ No newline at end of file diff --git a/modules/nf-core/tcoffee/regressive/tests/sequence.config b/modules/nf-core/tcoffee/regressive/tests/sequence.config new file mode 100644 index 000000000000..69c6fc17c9c7 --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/tests/sequence.config @@ -0,0 +1,3 @@ +process { + ext.args = { "-output fasta_aln" } +} diff --git a/modules/nf-core/tcoffee/regressive/tests/tree.config b/modules/nf-core/tcoffee/regressive/tests/tree.config new file mode 100644 index 000000000000..d426ed454ab2 --- /dev/null +++ b/modules/nf-core/tcoffee/regressive/tests/tree.config @@ -0,0 +1,5 @@ +process { + withName: "TCOFFEE_ALIGN"{ + ext.args = { "-output fasta_aln" } + } +} From 49f4e50534fe4b64101e62ea41d5dc43b1324358 Mon Sep 17 00:00:00 2001 From: Jonathan Manning Date: Sat, 19 Oct 2024 17:44:36 +0100 Subject: [PATCH 164/486] Update some module versions (#6798) * Update modules for versions with ARM builds * update picard containers * Fix containers for getchromsizes * Pick python version with ARM conda builds and biocontainer * Fix other containers * Remove quay.io * Bump bedgraphtobigwig * First batch of nf-test updates * Second batch of nf-test updates * Update thests for liftovervcf * One more nf-test update * Last update: trimgalore * match conda cutadapt to trimgalore container * change r-base for picard * [skip ci] nf-test migration for picard/collectrnaseqmetrics * nf-test migration for picard/filtersamreads * Factor out setup * Move bam checking to nft-bam * Add missing tags --- .../custom/getchromsizes/environment.yml | 4 +- modules/nf-core/custom/getchromsizes/main.nf | 4 +- .../getchromsizes/tests/main.nf.test.snap | 40 +++--- .../nf-core/custom/tx2gene/environment.yml | 2 +- modules/nf-core/custom/tx2gene/main.nf | 4 +- .../custom/tx2gene/tests/main.nf.test.snap | 20 +-- .../addorreplacereadgroups/environment.yml | 2 +- .../picard/addorreplacereadgroups/main.nf | 4 +- .../tests/main.nf.test.snap | 26 ++-- .../picard/bedtointervallist/environment.yml | 2 +- .../nf-core/picard/bedtointervallist/main.nf | 4 +- .../bedtointervallist/tests/main.nf.test.snap | 8 +- .../nf-core/picard/cleansam/environment.yml | 2 +- modules/nf-core/picard/cleansam/main.nf | 4 +- .../picard/cleansam/tests/main.nf.test.snap | 6 +- .../picard/collecthsmetrics/environment.yml | 2 +- .../nf-core/picard/collecthsmetrics/main.nf | 4 +- .../collecthsmetrics/tests/main.nf.test.snap | 40 +++--- .../collectinsertsizemetrics/environment.yml | 2 +- .../picard/collectinsertsizemetrics/main.nf | 4 +- .../tests/main.nf.test.snap | 14 +- .../collectmultiplemetrics/environment.yml | 2 +- .../picard/collectmultiplemetrics/main.nf | 4 +- .../tests/main.nf.test.snap | 18 +-- .../collectrnaseqmetrics/environment.yml | 2 +- .../picard/collectrnaseqmetrics/main.nf | 4 +- .../collectrnaseqmetrics/tests/main.nf.test | 81 ++++++++++++ .../tests/main.nf.test.snap | 60 +++++++++ .../tests}/nextflow.config | 6 - .../picard/collectwgsmetrics/environment.yml | 4 +- .../nf-core/picard/collectwgsmetrics/main.nf | 4 +- .../collectwgsmetrics/tests/main.nf.test.snap | 12 +- .../createsequencedictionary/environment.yml | 2 +- .../picard/createsequencedictionary/main.nf | 4 +- .../tests/main.nf.test.snap | 10 +- .../crosscheckfingerprints/environment.yml | 2 +- .../picard/crosscheckfingerprints/main.nf | 4 +- .../tests/main.nf.test.snap | 16 +-- .../picard/extractfingerprint/environment.yml | 2 +- .../nf-core/picard/extractfingerprint/main.nf | 4 +- .../tests/main.nf.test.snap | 8 +- .../nf-core/picard/fastqtosam/environment.yml | 2 +- modules/nf-core/picard/fastqtosam/main.nf | 4 +- .../picard/fastqtosam/tests/main.nf.test.snap | 18 +-- .../picard/filtersamreads/environment.yml | 2 +- modules/nf-core/picard/filtersamreads/main.nf | 4 +- .../picard/filtersamreads/tests/main.nf.test | 122 ++++++++++++++++++ .../filtersamreads/tests/main.nf.test.snap | 102 +++++++++++++++ .../filtersamreads/tests}/nextflow.config | 5 - .../picard/fixmateinformation/environment.yml | 2 +- .../nf-core/picard/fixmateinformation/main.nf | 4 +- .../tests/main.nf.test.snap | 6 +- .../picard/liftovervcf/environment.yml | 2 +- modules/nf-core/picard/liftovervcf/main.nf | 4 +- .../liftovervcf/tests/main.nf.test.snap | 12 +- .../picard/markduplicates/environment.yml | 2 +- modules/nf-core/picard/markduplicates/main.nf | 4 +- .../markduplicates/tests/main.nf.test.snap | 48 +++---- .../picard/mergesamfiles/environment.yml | 2 +- modules/nf-core/picard/mergesamfiles/main.nf | 4 +- .../mergesamfiles/tests/main.nf.test.snap | 6 +- .../picard/renamesampleinvcf/environment.yml | 2 +- .../nf-core/picard/renamesampleinvcf/main.nf | 4 +- .../renamesampleinvcf/tests/main.nf.test.snap | 6 +- .../scatterintervalsbyns/environment.yml | 2 +- .../picard/scatterintervalsbyns/main.nf | 4 +- .../tests/main.nf.test.snap | 16 +-- .../nf-core/picard/sortsam/environment.yml | 2 +- modules/nf-core/picard/sortsam/main.nf | 4 +- .../picard/sortsam/tests/main.nf.test.snap | 6 +- .../nf-core/picard/sortvcf/environment.yml | 2 +- modules/nf-core/picard/sortvcf/main.nf | 4 +- .../picard/sortvcf/tests/main.nf.test.snap | 6 +- modules/nf-core/salmon/index/environment.yml | 2 +- modules/nf-core/salmon/index/main.nf | 4 +- .../salmon/index/tests/main.nf.test.snap | 16 +-- modules/nf-core/salmon/quant/environment.yml | 2 +- modules/nf-core/salmon/quant/main.nf | 4 +- .../salmon/quant/tests/main.nf.test.snap | 64 ++++----- .../stringtie/stringtie/environment.yml | 2 +- modules/nf-core/stringtie/stringtie/main.nf | 4 +- .../stringtie/tests/main.nf.test.snap | 64 ++++----- .../subread/featurecounts/environment.yml | 2 +- modules/nf-core/subread/featurecounts/main.nf | 4 +- .../featurecounts/tests/main.nf.test.snap | 78 +++++------ modules/nf-core/trimgalore/environment.yml | 4 +- modules/nf-core/trimgalore/main.nf | 4 +- .../trimgalore/tests/main.nf.test.snap | 36 +++--- .../ucsc/bedgraphtobigwig/environment.yml | 2 +- modules/nf-core/ucsc/bedgraphtobigwig/main.nf | 8 +- .../bedgraphtobigwig/tests/main.nf.test.snap | 16 +-- .../tests/main.nf.test.snap | 26 ++-- .../bam_qc_picard/tests/main.nf.test.snap | 20 +-- .../tests/main.nf.test.snap | 20 +-- .../tests/main.nf.test.snap | 44 +++---- .../tests/main.nf.test.snap | 18 +-- .../tests/main.nf.test.snap | 42 +++--- tests/config/pytest_modules.yml | 6 - .../picard/collectrnaseqmetrics/main.nf | 32 ----- .../picard/collectrnaseqmetrics/test.yml | 15 --- .../nf-core/picard/filtersamreads/main.nf | 32 ----- .../nf-core/picard/filtersamreads/test.yml | 30 ----- 102 files changed, 850 insertions(+), 611 deletions(-) create mode 100644 modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test create mode 100644 modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap rename {tests/modules/nf-core/picard/collectrnaseqmetrics => modules/nf-core/picard/collectrnaseqmetrics/tests}/nextflow.config (81%) create mode 100644 modules/nf-core/picard/filtersamreads/tests/main.nf.test create mode 100644 modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap rename {tests/modules/nf-core/picard/filtersamreads => modules/nf-core/picard/filtersamreads/tests}/nextflow.config (62%) delete mode 100644 tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf delete mode 100644 tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml delete mode 100644 tests/modules/nf-core/picard/filtersamreads/main.nf delete mode 100644 tests/modules/nf-core/picard/filtersamreads/test.yml diff --git a/modules/nf-core/custom/getchromsizes/environment.yml b/modules/nf-core/custom/getchromsizes/environment.yml index b98cbb99092d..2bcd47ee161b 100644 --- a/modules/nf-core/custom/getchromsizes/environment.yml +++ b/modules/nf-core/custom/getchromsizes/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/custom/getchromsizes/main.nf b/modules/nf-core/custom/getchromsizes/main.nf index 3edf7c221aa3..d8c7405c6e45 100644 --- a/modules/nf-core/custom/getchromsizes/main.nf +++ b/modules/nf-core/custom/getchromsizes/main.nf @@ -4,8 +4,8 @@ process CUSTOM_GETCHROMSIZES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' : - 'biocontainers/samtools:1.20--h50ea8bc_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' : + 'biocontainers/samtools:1.21--h50ea8bc_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap index c37b284d761c..d2072e22c62d 100644 --- a/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap +++ b/modules/nf-core/custom/getchromsizes/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:38:36.927106" + "timestamp": "2024-10-18T10:11:37.459094476" }, "test_custom_getchromsizes": { "content": [ @@ -87,7 +87,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -109,15 +109,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:22:34.14237" + "timestamp": "2024-10-18T10:11:01.526301351" }, "test_custom_getchromsizes_bgzip": { "content": [ @@ -147,7 +147,7 @@ ] ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -174,15 +174,15 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-20T13:23:06.241379" + "timestamp": "2024-10-18T10:11:14.32456385" }, "test_custom_getchromsizes - stub": { "content": [ @@ -207,7 +207,7 @@ ], "3": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ], "fai": [ [ @@ -229,14 +229,14 @@ ] ], "versions": [ - "versions.yml:md5,0d5a7c33bddcb1edad6bf0705b258e6f" + "versions.yml:md5,f68edc4d5999d8cb07147b9be115d60b" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T12:24:05.697845" + "timestamp": "2024-10-18T10:11:26.505487624" } } \ No newline at end of file diff --git a/modules/nf-core/custom/tx2gene/environment.yml b/modules/nf-core/custom/tx2gene/environment.yml index 9f5f9fb9b470..9824d0c277a4 100644 --- a/modules/nf-core/custom/tx2gene/environment.yml +++ b/modules/nf-core/custom/tx2gene/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - python=3.9.5 + - python=3.10.4 diff --git a/modules/nf-core/custom/tx2gene/main.nf b/modules/nf-core/custom/tx2gene/main.nf index 99c00aa06923..eed5e97b1cc8 100644 --- a/modules/nf-core/custom/tx2gene/main.nf +++ b/modules/nf-core/custom/tx2gene/main.nf @@ -4,8 +4,8 @@ process CUSTOM_TX2GENE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.9--1' : - 'biocontainers/python:3.9--1' }" + 'https://depot.galaxyproject.org/singularity/python:3.10.4' : + 'biocontainers/python:3.10.4' }" input: tuple val(meta), path(gtf) diff --git a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap index c19f10f71628..2be5fe547d18 100644 --- a/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap +++ b/modules/nf-core/custom/tx2gene/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ], "tx2gene": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,fb8145d7fbc6043ba031249b23ecda50" + "versions.yml:md5,e504b95d76ef4cf65ba0b38cddce2840" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-05T13:13:11.305047" + "timestamp": "2024-10-18T10:24:12.19104487" }, "saccharomyces_cerevisiae - gtf - stub": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ], "tx2gene": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,5613eefbca41377128f1d8dc09b9fb60" + "versions.yml:md5,48194bffef8cb833e82e31166f3d486c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T15:15:34.064489" + "timestamp": "2024-10-18T10:24:24.729694098" } } \ No newline at end of file diff --git a/modules/nf-core/picard/addorreplacereadgroups/environment.yml b/modules/nf-core/picard/addorreplacereadgroups/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/environment.yml +++ b/modules/nf-core/picard/addorreplacereadgroups/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/addorreplacereadgroups/main.nf b/modules/nf-core/picard/addorreplacereadgroups/main.nf index 3f03c6808a50..5a71e085afe3 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/main.nf +++ b/modules/nf-core/picard/addorreplacereadgroups/main.nf @@ -4,8 +4,8 @@ process PICARD_ADDORREPLACEREADGROUPS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap index f823197d2849..3ae6b917141d 100644 --- a/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap +++ b/modules/nf-core/picard/addorreplacereadgroups/tests/main.nf.test.snap @@ -3,14 +3,14 @@ "content": [ "test.replaced.cram", [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:54:40.471730168" + "timestamp": "2024-10-18T10:13:23.115450366" }, "sarscov2 - bam - stub": { "content": [ @@ -30,7 +30,7 @@ ], "3": [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ], "bai": [ @@ -47,28 +47,28 @@ ], "versions": [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:55:08.402649243" + "timestamp": "2024-10-18T10:13:47.23694937" }, "sarscov2 - bam": { "content": [ "null.replaced.bam", "null.replaced.bai", [ - "versions.yml:md5,7ec6e56d1d70ed028928dc82b32b27cd" + "versions.yml:md5,e82588e0fecbeafdff36e3b3001b3bca" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:54:22.239968953" + "timestamp": "2024-10-18T10:12:53.083677142" } } \ No newline at end of file diff --git a/modules/nf-core/picard/bedtointervallist/environment.yml b/modules/nf-core/picard/bedtointervallist/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/bedtointervallist/environment.yml +++ b/modules/nf-core/picard/bedtointervallist/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/bedtointervallist/main.nf b/modules/nf-core/picard/bedtointervallist/main.nf index 2cc6cbd2f0fc..c8eddb1a12e7 100644 --- a/modules/nf-core/picard/bedtointervallist/main.nf +++ b/modules/nf-core/picard/bedtointervallist/main.nf @@ -4,8 +4,8 @@ process PICARD_BEDTOINTERVALLIST { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta) , path(bed) diff --git a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap index 6abbf0e92f9e..7382eafc8519 100644 --- a/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap +++ b/modules/nf-core/picard/bedtointervallist/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8" ], "interval_list": [ [ @@ -22,14 +22,14 @@ ] ], "versions": [ - "versions.yml:md5,8d0ce8ecdf3bc716de22d75e61aaaf65" + "versions.yml:md5,33540ea0c31ded2c1db95f82406034f8" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:39:08.82372" + "timestamp": "2024-10-18T10:17:35.308452582" } } \ No newline at end of file diff --git a/modules/nf-core/picard/cleansam/environment.yml b/modules/nf-core/picard/cleansam/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/cleansam/environment.yml +++ b/modules/nf-core/picard/cleansam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/cleansam/main.nf b/modules/nf-core/picard/cleansam/main.nf index 7b95cebdc0f0..f2ab79bd53bd 100644 --- a/modules/nf-core/picard/cleansam/main.nf +++ b/modules/nf-core/picard/cleansam/main.nf @@ -4,8 +4,8 @@ process PICARD_CLEANSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap index 63e2927e57a2..efecdb5efe31 100644 --- a/modules/nf-core/picard/cleansam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/cleansam/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "798439cbd7fd81cbcc5078022dc5479d", [ - "versions.yml:md5,f99b648dc3d150a0561094e3a142ee22" + "versions.yml:md5,412651954aecab12c868ee78cf9fa724" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:36:05.525364" + "timestamp": "2024-10-18T10:46:32.969920917" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collecthsmetrics/environment.yml b/modules/nf-core/picard/collecthsmetrics/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/collecthsmetrics/environment.yml +++ b/modules/nf-core/picard/collecthsmetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collecthsmetrics/main.nf b/modules/nf-core/picard/collecthsmetrics/main.nf index a9cbafd44f24..1d017ef8db20 100644 --- a/modules/nf-core/picard/collecthsmetrics/main.nf +++ b/modules/nf-core/picard/collecthsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTHSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai), path(bait_intervals, stageAs: "baits/*"), path(target_intervals, stageAs: 'targets/*') diff --git a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap index 53855d13b689..4d21710a0623 100644 --- a/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collecthsmetrics/tests/main.nf.test.snap @@ -106,26 +106,26 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:45:46.991614248" + "timestamp": "2024-10-18T10:51:55.291163084" }, "versions": { "content": [ [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:36:50.350567213" + "timestamp": "2024-10-18T10:51:30.748857589" }, "sarscov2 - bam - samebed": { "content": [ @@ -234,14 +234,14 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:46:33.770516478" + "timestamp": "2024-10-18T10:52:43.803456585" }, "sarscov2 - bam": { "content": [ @@ -350,14 +350,14 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:45:16.117386245" + "timestamp": "2024-10-18T10:51:01.881343611" }, "sarscov2 - bam - bed": { "content": [ @@ -466,13 +466,13 @@ "89\t0\t0" ], [ - "versions.yml:md5,e390b048af294086f56621c38ebde05a" + "versions.yml:md5,bdfc7b655683e7b66f68e894c999805e" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:46:13.489487836" + "timestamp": "2024-10-18T10:52:22.830749735" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/environment.yml +++ b/modules/nf-core/picard/collectinsertsizemetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectinsertsizemetrics/main.nf b/modules/nf-core/picard/collectinsertsizemetrics/main.nf index 1a49a7f0af2b..c3014d806c94 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/main.nf +++ b/modules/nf-core/picard/collectinsertsizemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTINSERTSIZEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap index bcb5b4557b76..cbe9329d0524 100644 --- a/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectinsertsizemetrics/tests/main.nf.test.snap @@ -9,14 +9,14 @@ ], "test.pdf", [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T12:23:29.392944" + "timestamp": "2024-10-18T10:55:45.769771444" }, "test-picard-collectinsertsizemetrics-stub": { "content": [ @@ -40,7 +40,7 @@ ] ], "2": [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ], "histogram": [ [ @@ -61,14 +61,14 @@ ] ], "versions": [ - "versions.yml:md5,4423bfe2194f61d919c382d2225b0835" + "versions.yml:md5,38d39e9882afe7ac015213c286745056" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-30T12:20:03.841884" + "timestamp": "2024-10-18T10:56:09.914953495" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectmultiplemetrics/environment.yml b/modules/nf-core/picard/collectmultiplemetrics/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/environment.yml +++ b/modules/nf-core/picard/collectmultiplemetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectmultiplemetrics/main.nf b/modules/nf-core/picard/collectmultiplemetrics/main.nf index c5555871dc39..cf1af40af3c2 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/main.nf +++ b/modules/nf-core/picard/collectmultiplemetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTMULTIPLEMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta) , path(bam), path(bai) diff --git a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap index 1859541b6dd0..a76a3237577c 100644 --- a/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectmultiplemetrics/tests/main.nf.test.snap @@ -16,14 +16,14 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:03:36.631174" + "timestamp": "2024-10-18T11:05:12.591021247" }, "test-picard-collectmultiplemetrics-cram": { "content": [ @@ -42,14 +42,14 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:04:13.955902" + "timestamp": "2024-10-18T11:06:08.499320579" }, "test-picard-collectmultiplemetrics-nofasta": { "content": [ @@ -68,13 +68,13 @@ "test.CollectMultipleMetrics.read_length_histogram.pdf" ], [ - "versions.yml:md5,b68b83e8dd0f9360453213acad639338" + "versions.yml:md5,791db2719d57a997f8253b3ba97d62d7" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:03:54.707587" + "timestamp": "2024-10-18T11:05:42.117033611" } } \ No newline at end of file diff --git a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/environment.yml +++ b/modules/nf-core/picard/collectrnaseqmetrics/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/modules/nf-core/picard/collectrnaseqmetrics/main.nf index 0c8f2cfa2c1c..eb80fdc70c25 100644 --- a/modules/nf-core/picard/collectrnaseqmetrics/main.nf +++ b/modules/nf-core/picard/collectrnaseqmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTRNASEQMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test new file mode 100644 index 000000000000..9ab1855217af --- /dev/null +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test @@ -0,0 +1,81 @@ +nextflow_process { + + name "Test Process PICARD_COLLECTRNASEQMETRICS" + script "../main.nf" + process "PICARD_COLLECTRNASEQMETRICS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/collectrnaseqmetrics" + tag "ucsc/gtftogenepred" + + setup { + run("UCSC_GTFTOGENEPRED") { + script "../../../ucsc/gtftogenepred/main.nf" + process { + """ + input[0] = Channel.of([ + [ id:'test' ], + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gtf', checkIfExists: true) ] + ]) + """ + } + } + } + + test("sarscov2 - fasta - gtf") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] } + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert file(process.out.metrics[0][1]).text.contains('CollectRnaSeqMetrics') }, + { assert snapshot( + process.out.versions, + process.out.pdf + ).match() } + ) + } + } + + test("sarscov2 - fasta - gtf - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) + ] + input[1] = UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] } + input[2] = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true) + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap new file mode 100644 index 000000000000..ad6503afdfb9 --- /dev/null +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/main.nf.test.snap @@ -0,0 +1,60 @@ +{ + "sarscov2 - fasta - gtf": { + "content": [ + [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ], + [ + + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:10:39.199344417" + }, + "sarscov2 - fasta - gtf - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.rna_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ], + "metrics": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.rna_metrics:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "pdf": [ + + ], + "versions": [ + "versions.yml:md5,8d0867f89947c081711de09338138c2e" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:10:57.248132065" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config similarity index 81% rename from tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config rename to modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config index 9bdb2070dbc5..bc82e10c1b52 100644 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config +++ b/modules/nf-core/picard/collectrnaseqmetrics/tests/nextflow.config @@ -1,11 +1,7 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName:UCSC_GTFTOGENEPRED { ext.args = "-genePredExt -geneNameAsName2 -ignoreGroupsWithoutExons" } - withName:PICARD_COLLECTRNASEQMETRICS { ext.args = { ( meta.strandedness == "forward" || meta.single_end ) ? "--STRAND_SPECIFICITY FIRST_READ_TRANSCRIPTION_STRAND" : @@ -13,7 +9,5 @@ process { "--STRAND_SPECIFICITY SECOND_READ_TRANSCRIPTION_STRAND" : "--STRAND_SPECIFICITY NONE" } - } - } diff --git a/modules/nf-core/picard/collectwgsmetrics/environment.yml b/modules/nf-core/picard/collectwgsmetrics/environment.yml index 58d525818627..13265842fcfe 100644 --- a/modules/nf-core/picard/collectwgsmetrics/environment.yml +++ b/modules/nf-core/picard/collectwgsmetrics/environment.yml @@ -2,5 +2,5 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 - - r::r-base + - bioconda::picard=3.3.0 + - conda-forge::r-base=4.4.1 diff --git a/modules/nf-core/picard/collectwgsmetrics/main.nf b/modules/nf-core/picard/collectwgsmetrics/main.nf index 6002a7ca95c8..39cf7d2b7d11 100644 --- a/modules/nf-core/picard/collectwgsmetrics/main.nf +++ b/modules/nf-core/picard/collectwgsmetrics/main.nf @@ -4,8 +4,8 @@ process PICARD_COLLECTWGSMETRICS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap index f188382b038f..1958fcdebe2b 100644 --- a/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap +++ b/modules/nf-core/picard/collectwgsmetrics/tests/main.nf.test.snap @@ -3,26 +3,26 @@ "content": [ true, [ - "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe" + "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:02:46.301176" + "timestamp": "2024-10-18T10:15:18.13771243" }, "test-picard-collectwgsmetrics": { "content": [ true, [ - "versions.yml:md5,06b5898fb06823b736c90e1dcebe75fe" + "versions.yml:md5,9927db69fdd55176be5cdbd427d000c2" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T11:02:25.132069" + "timestamp": "2024-10-18T10:14:57.786056996" } } \ No newline at end of file diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/createsequencedictionary/environment.yml +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index 4630a0d51e2b..49637d1840cf 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -4,8 +4,8 @@ process PICARD_CREATESEQUENCEDICTIONARY { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap index 3f3f8c8ec90a..8142f2af32f9 100644 --- a/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap +++ b/modules/nf-core/picard/createsequencedictionary/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ], "reference_dict": [ [ @@ -22,7 +22,7 @@ ] ], "versions": [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ] } ], @@ -30,19 +30,19 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-19T07:02:59.686224426" + "timestamp": "2024-10-18T10:49:55.602683425" }, "sarscov2 - fasta": { "content": [ "test.dict", [ - "versions.yml:md5,fdb110d8c303ffa0615bb200f9a2c999" + "versions.yml:md5,3ed186b70c3df55fd4965f48485a01cb" ] ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-16T14:31:34.330709472" + "timestamp": "2024-10-18T10:49:40.396060224" } } \ No newline at end of file diff --git a/modules/nf-core/picard/crosscheckfingerprints/environment.yml b/modules/nf-core/picard/crosscheckfingerprints/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/environment.yml +++ b/modules/nf-core/picard/crosscheckfingerprints/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/crosscheckfingerprints/main.nf b/modules/nf-core/picard/crosscheckfingerprints/main.nf index f6df55ade7b9..61afa6615050 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/main.nf +++ b/modules/nf-core/picard/crosscheckfingerprints/main.nf @@ -4,8 +4,8 @@ process PICARD_CROSSCHECKFINGERPRINTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(input1), path(input1_index), path(input2), path(input2_index), path(haplotype_map) diff --git a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap index f283f13305fe..f9e6963a445e 100644 --- a/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap +++ b/modules/nf-core/picard/crosscheckfingerprints/tests/main.nf.test.snap @@ -22,25 +22,25 @@ "Crosscheck versions stub": { "content": [ [ - "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" + "versions.yml:md5,baa5c1b1dc10b95cb42ea1b3d66a294f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:57:33.939689662" + "timestamp": "2024-10-18T11:02:39.2311109" }, "Crosscheck versions - bam": { "content": [ [ - "versions.yml:md5,4c5a7212fc3d33ef2693462e3b792b89" + "versions.yml:md5,baa5c1b1dc10b95cb42ea1b3d66a294f" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:57:08.745266455" + "timestamp": "2024-10-18T11:02:13.953034883" } } \ No newline at end of file diff --git a/modules/nf-core/picard/extractfingerprint/environment.yml b/modules/nf-core/picard/extractfingerprint/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/extractfingerprint/environment.yml +++ b/modules/nf-core/picard/extractfingerprint/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/extractfingerprint/main.nf b/modules/nf-core/picard/extractfingerprint/main.nf index 68b532330457..79b71f58ebbe 100644 --- a/modules/nf-core/picard/extractfingerprint/main.nf +++ b/modules/nf-core/picard/extractfingerprint/main.nf @@ -4,8 +4,8 @@ process PICARD_EXTRACTFINGERPRINT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(bai) diff --git a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap index a754ef93e28a..4b71c2f07bc3 100644 --- a/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap +++ b/modules/nf-core/picard/extractfingerprint/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "versions": { "content": [ [ - "versions.yml:md5,cbf898a998bb9b90d2e4110ee343d674" + "versions.yml:md5,5dd134f2a6a47c9592e2d77e007194db" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:53:08.359314244" + "timestamp": "2024-10-18T11:01:27.275230101" }, "extract_fingerprint": { "content": [ diff --git a/modules/nf-core/picard/fastqtosam/environment.yml b/modules/nf-core/picard/fastqtosam/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/fastqtosam/environment.yml +++ b/modules/nf-core/picard/fastqtosam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/fastqtosam/main.nf b/modules/nf-core/picard/fastqtosam/main.nf index dedd70a0318e..f44aa16c78a2 100644 --- a/modules/nf-core/picard/fastqtosam/main.nf +++ b/modules/nf-core/picard/fastqtosam/main.nf @@ -4,8 +4,8 @@ process PICARD_FASTQTOSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap index 2f999dcc9c9c..69e952739ca0 100644 --- a/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/fastqtosam/tests/main.nf.test.snap @@ -3,39 +3,39 @@ "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:50:01.762254" + "timestamp": "2024-10-18T11:04:07.175501513" }, "test-picard-fastqtosam-single": { "content": [ "e6a4aa204d980e177a0458596f0a70ac", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:49:32.460549" + "timestamp": "2024-10-18T11:03:34.501608306" }, "test-picard-fastqtosam-paired": { "content": [ "e3cfa46b13cc4fc425cccae944f43b10", [ - "versions.yml:md5,24527dfda806cbcfd1609c4734f973f1" + "versions.yml:md5,6a1888e4186ca3d82bd4d74ee677094c" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:49:47.018269" + "timestamp": "2024-10-18T11:03:53.864451058" } } \ No newline at end of file diff --git a/modules/nf-core/picard/filtersamreads/environment.yml b/modules/nf-core/picard/filtersamreads/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/filtersamreads/environment.yml +++ b/modules/nf-core/picard/filtersamreads/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/filtersamreads/main.nf b/modules/nf-core/picard/filtersamreads/main.nf index 32977bdc306f..7d0147e5c932 100644 --- a/modules/nf-core/picard/filtersamreads/main.nf +++ b/modules/nf-core/picard/filtersamreads/main.nf @@ -4,8 +4,8 @@ process PICARD_FILTERSAMREADS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam), path(readlist) diff --git a/modules/nf-core/picard/filtersamreads/tests/main.nf.test b/modules/nf-core/picard/filtersamreads/tests/main.nf.test new file mode 100644 index 000000000000..3cdde655c89a --- /dev/null +++ b/modules/nf-core/picard/filtersamreads/tests/main.nf.test @@ -0,0 +1,122 @@ +nextflow_process { + + name "Test Process PICARD_FILTERSAMREADS" + script "../main.nf" + process "PICARD_FILTERSAMREADS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "picard" + tag "picard/filtersamreads" + tag "picard/sortsam" + + setup { + run("PICARD_SORTSAM") { + script "../../../picard/sortsam/main.nf" + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true) + ] + input[1] = 'queryname' + """ + } + } + } + + test("sarscov2 - bam") { + + when { + process { + """ + input[0] = PICARD_SORTSAM.out.bam.map{[ it[0], it[1], [] ]} + input[1] = 'includeAligned' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 - stub") { + + options "-stub" + + when { + process { + """ + input[0] = PICARD_SORTSAM.out.bam.map{[ it[0], it[1], [] ]} + input[1] = 'includeAligned' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 - bam - readlist") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt', checkIfExists: true) + ] + input[1] = 'includeReadList' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + bam(process.out.bam[0][1]).getReadsMD5(), + process.out.versions + ).match() } + ) + } + } + + test("sarscov2 - bam - readlist - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false, strandedness:'forward' ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.single_end.sorted.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/picard/test.single_end.bam.readlist.txt', checkIfExists: true) + ] + input[1] = 'includeReadList' + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap b/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap new file mode 100644 index 000000000000..437239dedc5a --- /dev/null +++ b/modules/nf-core/picard/filtersamreads/tests/main.nf.test.snap @@ -0,0 +1,102 @@ +{ + "sarscov2 - bam - readlist - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:57:21.286660977" + }, + "sarscov2 - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ], + "bam": [ + [ + { + "id": "test", + "single_end": false, + "strandedness": "forward" + }, + "test.filtered.bam:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:56:49.461946443" + }, + "sarscov2 - bam - readlist": { + "content": [ + "3c2a0fcd376bd70060073cb361fe91c1", + [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:57:05.707924464" + }, + "sarscov2 - bam": { + "content": [ + "b9847fed94d2b7286e18caaa099658ce", + [ + "versions.yml:md5,0685c8c10a1531ea249eca9030e8ec3a" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T16:56:32.776141481" + } +} \ No newline at end of file diff --git a/tests/modules/nf-core/picard/filtersamreads/nextflow.config b/modules/nf-core/picard/filtersamreads/tests/nextflow.config similarity index 62% rename from tests/modules/nf-core/picard/filtersamreads/nextflow.config rename to modules/nf-core/picard/filtersamreads/tests/nextflow.config index 653e96332916..27844058124e 100644 --- a/tests/modules/nf-core/picard/filtersamreads/nextflow.config +++ b/modules/nf-core/picard/filtersamreads/tests/nextflow.config @@ -1,13 +1,8 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: PICARD_SORTSAM { ext.prefix = { "${meta.id}.sorted" } } - withName: PICARD_FILTERSAMREADS { ext.prefix = { "${meta.id}.filtered" } } - } diff --git a/modules/nf-core/picard/fixmateinformation/environment.yml b/modules/nf-core/picard/fixmateinformation/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/fixmateinformation/environment.yml +++ b/modules/nf-core/picard/fixmateinformation/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/fixmateinformation/main.nf b/modules/nf-core/picard/fixmateinformation/main.nf index bf29e24cc07c..2c075b8c69b2 100644 --- a/modules/nf-core/picard/fixmateinformation/main.nf +++ b/modules/nf-core/picard/fixmateinformation/main.nf @@ -4,8 +4,8 @@ process PICARD_FIXMATEINFORMATION { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap index 799173a6f929..fb9e08afcd38 100644 --- a/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap +++ b/modules/nf-core/picard/fixmateinformation/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "ddd0dc8f0cf1996d19dae51681187114", [ - "versions.yml:md5,36a59533c3e8578b046c4c2ec9caa8d4" + "versions.yml:md5,309cc65dc7918a6f1d81f5e0cf9455e4" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:45:26.092108" + "timestamp": "2024-10-18T10:23:11.403813574" } } \ No newline at end of file diff --git a/modules/nf-core/picard/liftovervcf/environment.yml b/modules/nf-core/picard/liftovervcf/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/liftovervcf/environment.yml +++ b/modules/nf-core/picard/liftovervcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/liftovervcf/main.nf b/modules/nf-core/picard/liftovervcf/main.nf index a4b27c88e5fe..69feb624ac06 100644 --- a/modules/nf-core/picard/liftovervcf/main.nf +++ b/modules/nf-core/picard/liftovervcf/main.nf @@ -4,8 +4,8 @@ process PICARD_LIFTOVERVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(input_vcf) diff --git a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap index 585ea369e8b0..e88aa9706dcf 100644 --- a/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/liftovervcf/tests/main.nf.test.snap @@ -4,27 +4,27 @@ "test.lifted.vcf.gz", "test.unlifted.vcf.gz", [ - "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:38:05.840798" + "timestamp": "2024-10-18T12:08:23.913395641" }, "test-picard-liftovervcf": { "content": [ "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]", "39a9de5185d94289283bd27cfcdeba97", [ - "versions.yml:md5,e1aaacb3c05a0d822f7abdcf3a55fa91" + "versions.yml:md5,af33ca5d76aec86863614805fbb4fafb" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:41:33.022998" + "timestamp": "2024-10-18T12:08:12.803193917" } } \ No newline at end of file diff --git a/modules/nf-core/picard/markduplicates/environment.yml b/modules/nf-core/picard/markduplicates/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/markduplicates/environment.yml +++ b/modules/nf-core/picard/markduplicates/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/markduplicates/main.nf b/modules/nf-core/picard/markduplicates/main.nf index cf18ac35ca99..8a2ed64e6a67 100644 --- a/modules/nf-core/picard/markduplicates/main.nf +++ b/modules/nf-core/picard/markduplicates/main.nf @@ -4,8 +4,8 @@ process PICARD_MARKDUPLICATES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap index 8b37e65b1bcc..13770a8e2e16 100644 --- a/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap +++ b/modules/nf-core/picard/markduplicates/tests/main.nf.test.snap @@ -27,7 +27,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -54,15 +54,15 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:32.025869" + "timestamp": "2024-10-18T10:58:50.046420643" }, "sarscov2 [unsorted bam] - stub": { "content": [ @@ -92,7 +92,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -119,69 +119,69 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:20.497105" + "timestamp": "2024-10-18T10:58:36.738907079" }, "sarscov2 [unsorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:50:14.881666" + "timestamp": "2024-10-18T10:57:16.683233382" }, "sarscov2 [sorted bam]": { "content": [ "test.marked.bam", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.bam --OUTPUT test.marked.bam --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:52:03.11428" + "timestamp": "2024-10-18T10:57:47.416956759" }, "homo_sapiens [cram]": { "content": [ "test.marked.cram", [ "## htsjdk.samtools.metrics.StringHeader", - "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --USE_END_IN_UNPAIRED_READS false --USE_UNPAIRED_CLIPPED_END false --UNPAIRED_END_UNCERTAINTY 0 --UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", + "# MarkDuplicates --INPUT test.paired_end.sorted.cram --OUTPUT test.marked.cram --METRICS_FILE test.marked.MarkDuplicates.metrics.txt --ASSUME_SORT_ORDER queryname --REFERENCE_SEQUENCE genome.fasta --MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP 50000 --MAX_FILE_HANDLES_FOR_READ_ENDS_MAP 8000 --SORTING_COLLECTION_SIZE_RATIO 0.25 --TAG_DUPLICATE_SET_MEMBERS false --REMOVE_SEQUENCING_DUPLICATES false --TAGGING_POLICY DontTag --CLEAR_DT true --DUPLEX_UMI false --FLOW_MODE false --FLOW_DUP_STRATEGY FLOW_QUALITY_SUM_STRATEGY --FLOW_USE_END_IN_UNPAIRED_READS false --FLOW_USE_UNPAIRED_CLIPPED_END false --FLOW_UNPAIRED_END_UNCERTAINTY 0 --FLOW_UNPAIRED_START_UNCERTAINTY 0 --FLOW_SKIP_FIRST_N_FLOWS 0 --FLOW_Q_IS_KNOWN_END false --FLOW_EFFECTIVE_QUALITY_THRESHOLD 15 --ADD_PG_TAG_TO_READS true --REMOVE_DUPLICATES false --ASSUME_SORTED false --DUPLICATE_SCORING_STRATEGY SUM_OF_BASE_QUALITIES --PROGRAM_RECORD_ID MarkDuplicates --PROGRAM_GROUP_NAME MarkDuplicates --READ_NAME_REGEX --OPTICAL_DUPLICATE_PIXEL_DISTANCE 100 --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --VALIDATION_STRINGENCY STRICT --COMPRESSION_LEVEL 5 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false", "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:53:05.403139" + "timestamp": "2024-10-18T10:58:15.143314223" }, "homo_sapiens [cram] - stub": { "content": [ @@ -211,7 +211,7 @@ ] ], "4": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ], "bai": [ @@ -238,14 +238,14 @@ ] ], "versions": [ - "versions.yml:md5,33dd4b32140e801e0d2e50aeefd0788d" + "versions.yml:md5,88717faa02b215b99eef3d05214a6fea" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T11:56:43.438188" + "timestamp": "2024-10-18T10:59:03.402916523" } } \ No newline at end of file diff --git a/modules/nf-core/picard/mergesamfiles/environment.yml b/modules/nf-core/picard/mergesamfiles/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/mergesamfiles/environment.yml +++ b/modules/nf-core/picard/mergesamfiles/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/mergesamfiles/main.nf b/modules/nf-core/picard/mergesamfiles/main.nf index 1e6e2274b9f5..435339c63c9b 100644 --- a/modules/nf-core/picard/mergesamfiles/main.nf +++ b/modules/nf-core/picard/mergesamfiles/main.nf @@ -4,8 +4,8 @@ process PICARD_MERGESAMFILES { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap index 22d2331e46a8..fe6213003291 100644 --- a/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap +++ b/modules/nf-core/picard/mergesamfiles/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "730da54c088350ff625d34b95e623dca", [ - "versions.yml:md5,3b5243ec10606330dd11a38fa7c7fa1f" + "versions.yml:md5,ba6df729752dd204080f8580ea5420c5" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T10:50:00.555746" + "timestamp": "2024-10-18T10:18:37.724686799" } } \ No newline at end of file diff --git a/modules/nf-core/picard/renamesampleinvcf/environment.yml b/modules/nf-core/picard/renamesampleinvcf/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/renamesampleinvcf/environment.yml +++ b/modules/nf-core/picard/renamesampleinvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/renamesampleinvcf/main.nf b/modules/nf-core/picard/renamesampleinvcf/main.nf index 3e4f38caa3c5..9e5e2e2dc601 100644 --- a/modules/nf-core/picard/renamesampleinvcf/main.nf +++ b/modules/nf-core/picard/renamesampleinvcf/main.nf @@ -5,8 +5,8 @@ process PICARD_RENAMESAMPLEINVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap index a9bf7b7bf04a..6a21666ad2d3 100644 --- a/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/renamesampleinvcf/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "e21a2349f41663d1fc38f47fbe65a6d5", [ - "versions.yml:md5,d4de734264e0c3b33d23e4a40de26a5f" + "versions.yml:md5,89be4b901aa05e78d449d11b00eff5e9" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:32:02.18878" + "timestamp": "2024-10-18T09:53:47.55538945" } } \ No newline at end of file diff --git a/modules/nf-core/picard/scatterintervalsbyns/environment.yml b/modules/nf-core/picard/scatterintervalsbyns/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/environment.yml +++ b/modules/nf-core/picard/scatterintervalsbyns/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/scatterintervalsbyns/main.nf b/modules/nf-core/picard/scatterintervalsbyns/main.nf index 344284804a1c..fa5c7b145ffb 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/main.nf +++ b/modules/nf-core/picard/scatterintervalsbyns/main.nf @@ -4,8 +4,8 @@ process PICARD_SCATTERINTERVALSBYNS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap index e08dff683341..68393dfefac1 100644 --- a/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap +++ b/modules/nf-core/picard/scatterintervalsbyns/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ], "intervals": [ [ @@ -24,15 +24,15 @@ ] ], "versions": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-27T10:31:47.186455" + "timestamp": "2024-10-18T11:09:20.872478896" }, "test-picard-scatterintervalsbyns": { "content": [ @@ -47,7 +47,7 @@ ] ], "1": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ], "intervals": [ [ @@ -59,14 +59,14 @@ ] ], "versions": [ - "versions.yml:md5,f92227dd1ef9396cd9ee2be53eb80459" + "versions.yml:md5,7d9c51e1cb3e2998ce5802e2a8a50728" ] } ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:25:45.447792" + "timestamp": "2024-10-18T11:08:57.399354562" } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortsam/environment.yml b/modules/nf-core/picard/sortsam/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/sortsam/environment.yml +++ b/modules/nf-core/picard/sortsam/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/sortsam/main.nf b/modules/nf-core/picard/sortsam/main.nf index af23e294bede..e3f4945d5b52 100644 --- a/modules/nf-core/picard/sortsam/main.nf +++ b/modules/nf-core/picard/sortsam/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTSAM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap index bf447b8d1352..22728f45d551 100644 --- a/modules/nf-core/picard/sortsam/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortsam/tests/main.nf.test.snap @@ -3,13 +3,13 @@ "content": [ "b9847fed94d2b7286e18caaa099658ce", [ - "versions.yml:md5,f53876b7c58b5aa1564606f3c9c34108" + "versions.yml:md5,b1d858b31471d4a0ce2407c491b6e299" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:23:48.485054" + "timestamp": "2024-10-18T10:09:43.110521445" } } \ No newline at end of file diff --git a/modules/nf-core/picard/sortvcf/environment.yml b/modules/nf-core/picard/sortvcf/environment.yml index ff4a85edb5f1..1d715d564e99 100644 --- a/modules/nf-core/picard/sortvcf/environment.yml +++ b/modules/nf-core/picard/sortvcf/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::picard=3.2.0 + - bioconda::picard=3.3.0 diff --git a/modules/nf-core/picard/sortvcf/main.nf b/modules/nf-core/picard/sortvcf/main.nf index 7133c13ae0c1..a094e6bfae75 100644 --- a/modules/nf-core/picard/sortvcf/main.nf +++ b/modules/nf-core/picard/sortvcf/main.nf @@ -4,8 +4,8 @@ process PICARD_SORTVCF { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.2.0--hdfd78af_0' : - 'biocontainers/picard:3.2.0--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/picard:3.3.0--hdfd78af_0' : + 'biocontainers/picard:3.3.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) diff --git a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap index db80323bfe56..e4a02c4f3e23 100644 --- a/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap +++ b/modules/nf-core/picard/sortvcf/tests/main.nf.test.snap @@ -9,13 +9,13 @@ "##INFO=" ], [ - "versions.yml:md5,11949a1af95080dcc5bd1c75d68dee71" + "versions.yml:md5,e6e6356d3b5b1b8e8cfd5d4958c694e6" ] ], "meta": { - "nf-test": "0.8.4", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T09:20:13.124551" + "timestamp": "2024-10-18T10:45:30.685264704" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/index/environment.yml b/modules/nf-core/salmon/index/environment.yml index 471164faadc5..b3f75777e46c 100644 --- a/modules/nf-core/salmon/index/environment.yml +++ b/modules/nf-core/salmon/index/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/index/main.nf b/modules/nf-core/salmon/index/main.nf index e755d9a344f6..3d653c0d08e4 100644 --- a/modules/nf-core/salmon/index/main.nf +++ b/modules/nf-core/salmon/index/main.nf @@ -4,8 +4,8 @@ process SALMON_INDEX { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: path genome_fasta diff --git a/modules/nf-core/salmon/index/tests/main.nf.test.snap b/modules/nf-core/salmon/index/tests/main.nf.test.snap index 703e455c574e..e5899b51151e 100644 --- a/modules/nf-core/salmon/index/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/index/tests/main.nf.test.snap @@ -2,25 +2,25 @@ "versions": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-22T14:26:33.32036" + "timestamp": "2024-10-18T10:00:47.087293189" }, "versions stub": { "content": [ [ - "versions.yml:md5,563eeafb4577be0b13801d7021c0bf42" + "versions.yml:md5,85337fa0a286ea35073ee5260974e307" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-04-23T09:47:58.828124" + "timestamp": "2024-10-18T10:01:03.89824494" } } \ No newline at end of file diff --git a/modules/nf-core/salmon/quant/environment.yml b/modules/nf-core/salmon/quant/environment.yml index 471164faadc5..b3f75777e46c 100644 --- a/modules/nf-core/salmon/quant/environment.yml +++ b/modules/nf-core/salmon/quant/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::salmon=1.10.1 + - bioconda::salmon=1.10.3 diff --git a/modules/nf-core/salmon/quant/main.nf b/modules/nf-core/salmon/quant/main.nf index 6c528b240914..f1e3b5cda31d 100644 --- a/modules/nf-core/salmon/quant/main.nf +++ b/modules/nf-core/salmon/quant/main.nf @@ -4,8 +4,8 @@ process SALMON_QUANT { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/salmon:1.10.1--h7e5ed60_0' : - 'biocontainers/salmon:1.10.1--h7e5ed60_0' }" + 'https://depot.galaxyproject.org/singularity/salmon:1.10.3--h6dccd9a_2' : + 'biocontainers/salmon:1.10.3--h6dccd9a_2' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/salmon/quant/tests/main.nf.test.snap b/modules/nf-core/salmon/quant/tests/main.nf.test.snap index 547ce2de1e03..ea22a80ce984 100644 --- a/modules/nf-core/salmon/quant/tests/main.nf.test.snap +++ b/modules/nf-core/salmon/quant/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "sarscov2 - single_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -15,15 +15,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:22.424672" + "timestamp": "2024-10-18T10:01:16.989080539" }, "sarscov2 - single_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -36,15 +36,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:32.292277" + "timestamp": "2024-10-18T10:01:29.340996235" }, "sarscov2 - single_end lib type A": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -57,15 +57,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:42.656382" + "timestamp": "2024-10-18T10:01:43.056167576" }, "sarscov2 - pair_end multiple": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -78,15 +78,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:33.03647" + "timestamp": "2024-10-18T10:03:05.500792631" }, "sarscov2 - pair_end multiple stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -99,15 +99,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:43.388379" + "timestamp": "2024-10-18T10:03:26.428959203" }, "sarscov2 - single_end lib type A stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -120,15 +120,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:51:52.612664" + "timestamp": "2024-10-18T10:02:03.420850208" }, "sarscov2 - pair_end": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -141,15 +141,15 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:05.577881" + "timestamp": "2024-10-18T10:02:16.130074696" }, "sarscov2 - pair_end stub": { "content": [ [ - "versions.yml:md5,80eb3d2ad36960c7e9263f81ede9d263" + "versions.yml:md5,0d510d5db6398e2c8ca9443330740607" ], [ [ @@ -162,9 +162,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-14T09:52:15.286461" + "timestamp": "2024-10-18T10:02:39.470004547" } } \ No newline at end of file diff --git a/modules/nf-core/stringtie/stringtie/environment.yml b/modules/nf-core/stringtie/stringtie/environment.yml index 0556de41a75a..906b7486c0e8 100644 --- a/modules/nf-core/stringtie/stringtie/environment.yml +++ b/modules/nf-core/stringtie/stringtie/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::stringtie=2.2.1 + - bioconda::stringtie=2.2.3 diff --git a/modules/nf-core/stringtie/stringtie/main.nf b/modules/nf-core/stringtie/stringtie/main.nf index 6e25ba27d54c..4635c8c5b13d 100644 --- a/modules/nf-core/stringtie/stringtie/main.nf +++ b/modules/nf-core/stringtie/stringtie/main.nf @@ -4,8 +4,8 @@ process STRINGTIE_STRINGTIE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/stringtie:2.2.1--hecb563c_2' : - 'biocontainers/stringtie:2.2.1--hecb563c_2' }" + 'https://depot.galaxyproject.org/singularity/stringtie:2.2.3--h43eeafb_0' : + 'biocontainers/stringtie:2.2.3--h43eeafb_0' }" input: tuple val(meta), path(bam) diff --git a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap index 124dd4cbe1c1..d4645de3ee25 100644 --- a/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap +++ b/modules/nf-core/stringtie/stringtie/tests/main.nf.test.snap @@ -31,18 +31,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,f56cf8aba2c4a5673bc7963ba5f12d04" + "test.transcripts.gtf:md5,37154e7bda96544f24506ee902bb561d" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:44.299962" + "timestamp": "2024-10-18T09:56:50.294157199" }, "sarscov2 [bam] - forward strandedness": { "content": [ @@ -61,18 +61,18 @@ "id": "test", "strandedness": "forward" }, - "test.transcripts.gtf:md5,569137af5be452413086b50653a97203" + "test.transcripts.gtf:md5,6087dfc9700a52d9e4a1ae3fcd1d1dfd" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:35.177738" + "timestamp": "2024-10-18T09:56:39.4249133" }, "sarscov2 [bam] - forward strandedness - stub": { "content": [ @@ -114,7 +114,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -153,15 +153,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:32.885078" + "timestamp": "2024-10-18T09:57:23.008470065" }, "sarscov2 [bam] - forward strandedness + reference annotation - stub": { "content": [ @@ -203,7 +203,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -242,15 +242,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:43.325777" + "timestamp": "2024-10-18T09:57:33.622824981" }, "sarscov2 [bam] - reverse strandedness + reference annotation - stub": { "content": [ @@ -292,7 +292,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -331,15 +331,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:37:06.085936" + "timestamp": "2024-10-18T09:57:55.803421433" }, "sarscov2 [bam] - reverse strandedness - stub": { "content": [ @@ -381,7 +381,7 @@ ] ], "4": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ], "abundance": [ [ @@ -420,15 +420,15 @@ ] ], "versions": [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:36:53.837578" + "timestamp": "2024-10-18T09:57:44.825389635" }, "sarscov2 [bam] - reverse strandedness + reference annotation": { "content": [ @@ -462,18 +462,18 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,bb346053a8c156b803b055133376c7fa" + "test.transcripts.gtf:md5,fbabb4e3888bbede67f11f692e484880" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:34:03.114695" + "timestamp": "2024-10-18T09:57:11.793664242" }, "sarscov2 [bam] - reverse strandedness": { "content": [ @@ -492,17 +492,17 @@ "id": "test", "strandedness": "reverse" }, - "test.transcripts.gtf:md5,31c34aec2bf36bb0ea3c16c2afeeeb1f" + "test.transcripts.gtf:md5,01d6da00a3c458420841e57427297183" ] ], [ - "versions.yml:md5,3410e8ac349d18c85ddee89337851d38" + "versions.yml:md5,06593ea00cc35bf06f2de2753e0c3913" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:33:52.874479" + "timestamp": "2024-10-18T09:57:01.166309777" } } \ No newline at end of file diff --git a/modules/nf-core/subread/featurecounts/environment.yml b/modules/nf-core/subread/featurecounts/environment.yml index 7e919aa31774..fdb575020094 100644 --- a/modules/nf-core/subread/featurecounts/environment.yml +++ b/modules/nf-core/subread/featurecounts/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::subread=2.0.1 + - bioconda::subread=2.0.6 diff --git a/modules/nf-core/subread/featurecounts/main.nf b/modules/nf-core/subread/featurecounts/main.nf index 471bd16fd8de..d51de1e0b66a 100644 --- a/modules/nf-core/subread/featurecounts/main.nf +++ b/modules/nf-core/subread/featurecounts/main.nf @@ -4,8 +4,8 @@ process SUBREAD_FEATURECOUNTS { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/subread:2.0.1--hed695b0_0' : - 'biocontainers/subread:2.0.1--hed695b0_0' }" + 'https://depot.galaxyproject.org/singularity/subread:2.0.6--he4a0461_2' : + 'biocontainers/subread:2.0.6--he4a0461_2' }" input: tuple val(meta), path(bams), path(annotation) diff --git a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap index 72e8dcddfdf3..5a743f0ce3aa 100644 --- a/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap +++ b/modules/nf-core/subread/featurecounts/tests/main.nf.test.snap @@ -8,15 +8,15 @@ "single_end": true, "strandedness": "forward" }, - "test.featureCounts.txt:md5,0012df4c0a0e47eec1440017ab34f75f" + "test.featureCounts.txt:md5,4cf89f0e702ba9abef3fa571e68fe8f0" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.685863663" + "timestamp": "2024-10-18T10:19:47.695388295" }, "unstranded_counts": { "content": [ @@ -27,15 +27,15 @@ "single_end": true, "strandedness": "unstranded" }, - "test.featureCounts.txt:md5,3307d31b44a5d6bb3389786bb8f4e91f" + "test.featureCounts.txt:md5,c4ef2c2a80547fbb3074331bc0a1bda3" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.67903701" + "timestamp": "2024-10-18T10:21:03.208334705" }, "reverse_summary": { "content": [ @@ -80,7 +80,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -103,15 +103,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:22.628032" + "timestamp": "2024-10-18T10:20:10.040191252" }, "sarscov2 [bam] - reverse - stub": { "content": [ @@ -137,7 +137,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -160,15 +160,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:04:52.371212" + "timestamp": "2024-10-18T10:20:42.708101743" }, "reverse_counts": { "content": [ @@ -179,15 +179,15 @@ "single_end": true, "strandedness": "reverse" }, - "test.featureCounts.txt:md5,8175816b8260ed444d59232bd7e7120b" + "test.featureCounts.txt:md5,a7d8843ebc12d855c2e68d3e2e137582" ] ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.160010804" + "timestamp": "2024-10-18T10:20:24.490755916" }, "sarscov2 [bam] - unstranded - stub": { "content": [ @@ -213,7 +213,7 @@ ] ], "2": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ], "counts": [ [ @@ -236,15 +236,15 @@ ] ], "versions": [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:05:25.058902" + "timestamp": "2024-10-18T10:21:19.244837771" }, "forward_summary": { "content": [ @@ -268,14 +268,14 @@ "forward_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:10.704797013" + "timestamp": "2024-10-18T10:19:48.001158764" }, "unstranded_summary": { "content": [ @@ -299,25 +299,25 @@ "reverse_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:25.175265594" + "timestamp": "2024-10-18T10:20:24.551053149" }, "unstranded_versions": { "content": [ [ - "versions.yml:md5,c2c0903b93c93d9afd2667052b9ee726" + "versions.yml:md5,956ebb9da6a1747fc47d393fb5931fc2" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-23T15:50:38.69390501" + "timestamp": "2024-10-18T10:21:03.25895568" } } \ No newline at end of file diff --git a/modules/nf-core/trimgalore/environment.yml b/modules/nf-core/trimgalore/environment.yml index f172c1b39e9b..910ffa882f54 100644 --- a/modules/nf-core/trimgalore/environment.yml +++ b/modules/nf-core/trimgalore/environment.yml @@ -3,5 +3,5 @@ channels: - bioconda dependencies: - - bioconda::cutadapt=3.4 - - bioconda::trim-galore=0.6.7 + - bioconda::cutadapt=4.2 + - bioconda::trim-galore=0.6.10 diff --git a/modules/nf-core/trimgalore/main.nf b/modules/nf-core/trimgalore/main.nf index 0e2f32902bc4..30d17edc1769 100644 --- a/modules/nf-core/trimgalore/main.nf +++ b/modules/nf-core/trimgalore/main.nf @@ -4,8 +4,8 @@ process TRIMGALORE { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.7--hdfd78af_0' : - 'biocontainers/trim-galore:0.6.7--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/trim-galore:0.6.10--hdfd78af_0' : + 'biocontainers/trim-galore:0.6.10--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/trimgalore/tests/main.nf.test.snap b/modules/nf-core/trimgalore/tests/main.nf.test.snap index 6cb31c9f9d2c..61b3504a9911 100644 --- a/modules/nf-core/trimgalore/tests/main.nf.test.snap +++ b/modules/nf-core/trimgalore/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "test_trimgalore_single_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:20.401347" + "timestamp": "2024-10-18T12:50:36.440264431" }, "test_trimgalore_single_end - stub": { "content": [ @@ -42,7 +42,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -69,7 +69,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -77,10 +77,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:27:44.964166" + "timestamp": "2024-10-18T12:50:51.25902234" }, "test_trimgalore_paired_end - stub": { "content": [ @@ -119,7 +119,7 @@ ], "5": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "html": [ @@ -152,7 +152,7 @@ ], "versions": [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ], "zip": [ @@ -160,21 +160,21 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-21T10:28:07.611496" + "timestamp": "2024-10-18T12:51:19.024228479" }, "test_trimgalore_paired_end": { "content": [ [ - "versions.yml:md5,47d966cbb31c80eb8f7fe860d55659b7" + "versions.yml:md5,0376fafd6096035de5c7ca6cb4e5e119" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.01.0" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-02-29T16:33:28.960497" + "timestamp": "2024-10-18T12:51:02.471703095" } } \ No newline at end of file diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml index a54fb8f1654b..27868a444c52 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml +++ b/modules/nf-core/ucsc/bedgraphtobigwig/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::ucsc-bedgraphtobigwig=445 + - bioconda::ucsc-bedgraphtobigwig=469 diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf index bff0b00a93aa..81cdee95326d 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/main.nf +++ b/modules/nf-core/ucsc/bedgraphtobigwig/main.nf @@ -5,8 +5,8 @@ process UCSC_BEDGRAPHTOBIGWIG { // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions. conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:445--h954228d_0' : - 'biocontainers/ucsc-bedgraphtobigwig:445--h954228d_0' }" + 'https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:469--h9b8f530_0' : + 'biocontainers/ucsc-bedgraphtobigwig:469--h9b8f530_0' }" input: tuple val(meta), path(bedgraph) @@ -22,7 +22,7 @@ process UCSC_BEDGRAPHTOBIGWIG { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ bedGraphToBigWig \\ $bedgraph \\ @@ -37,7 +37,7 @@ process UCSC_BEDGRAPHTOBIGWIG { stub: def prefix = task.ext.prefix ?: "${meta.id}" - def VERSION = '445' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. + def VERSION = '469' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. """ touch ${prefix}.bigWig diff --git a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap index 7b0181583131..7c731f651023 100644 --- a/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap +++ b/modules/nf-core/ucsc/bedgraphtobigwig/tests/main.nf.test.snap @@ -11,7 +11,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -22,15 +22,15 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:06:05.176746" + "timestamp": "2024-10-18T10:47:58.558813949" }, "Should run without failures": { "content": [ @@ -44,7 +44,7 @@ ] ], "1": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ], "bigwig": [ [ @@ -55,14 +55,14 @@ ] ], "versions": [ - "versions.yml:md5,93b027527145a243903a3c687c3453b8" + "versions.yml:md5,db26514184acfdf220bb2f061382cf8c" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T12:05:56.658148" + "timestamp": "2024-10-18T10:47:36.476844229" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap index 093d9c8c3967..50ecf675d12c 100644 --- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "homo_sapiens - cram": { "content": [ "test.cram", - "test.cram.crai:md5,cb5268070f99cdd0d86f43613e5fc7db", + "test.cram.crai:md5,9a74bf028b7146d8ef285442a14bbc8f", "test.flagstat:md5,93b0ef463df947ede1f42ff60396c34d", "test.idxstats:md5,e179601fa7b8ebce81ac3765206f6c15", "test.stats:md5,1a4569080c6f73546a863b0c3bc72c49", @@ -10,7 +10,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -18,7 +18,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:04.991702832" + "timestamp": "2024-10-18T10:59:53.440891602" }, "sarscov2 - bam - stub": { "content": [ @@ -90,7 +90,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -160,7 +160,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -169,7 +169,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:20.672273462" + "timestamp": "2024-10-18T11:00:20.860494683" }, "homo_sapiens - cram - stub": { "content": [ @@ -235,7 +235,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ], "bai": [ @@ -299,7 +299,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] } @@ -308,12 +308,12 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:06:36.739909544" + "timestamp": "2024-10-18T11:00:42.042387118" }, "sarscov2 - bam": { "content": [ - "test.bam:md5,d1a53820e4a6e42ca8aceab51d74cf57", - "test.bam.bai:md5,be9485a644813773fb893a0a6b9b977c", + "test.bam:md5,c8a3a56d56bf2c87f09e143ed2f78a7d", + "test.bam.bai:md5,7d205e4e0b3d98887b1eafb5c50a3363", "test.flagstat:md5,4f7ffd1e6a5e85524d443209ac97d783", "test.idxstats:md5,df60a8c8d6621100d05178c93fb053a2", "test.stats:md5,ba007b13981dad548358c7c957d41e12", @@ -321,7 +321,7 @@ "versions.yml:md5,39f93ad916207c307cdb142959a19e95", "versions.yml:md5,5a97b3ae2f98b3fd84c475f26a7e01b7", "versions.yml:md5,6f95a91fadb30bd32b77143d18f2e1f9", - "versions.yml:md5,adb00ecc904d3a27f552c360ac35a8a9", + "versions.yml:md5,a54e44823e415885a18a6b62e3087fca", "versions.yml:md5,b867241d6184a7ff9312f6f493f1b49c" ] ], @@ -329,6 +329,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-09-16T08:05:46.507645441" + "timestamp": "2024-10-18T10:59:22.840531827" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap index f02de25e29c1..d3e8656a46a0 100644 --- a/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bam_qc_picard/tests/main.nf.test.snap @@ -57,15 +57,15 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,d61a29a9b3d8c60ed90b068df8032979", - "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d" + "versions.yml:md5,92450dccc1a141f405d689d7f07480c0", + "versions.yml:md5,df149b65b51dcad73b8914e6ce30fadf" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:38:29.298437201" + "timestamp": "2024-10-18T10:16:09.107786306" }, "sascov2_wgs - [bam,bai]": { "content": [ @@ -114,14 +114,14 @@ "## htsjdk.samtools.metrics.StringHeader" ], [ - "versions.yml:md5,e71b3af11ad159b26b503337cd90ee3d", - "versions.yml:md5,ebe92bff64a6e7b1a0aa741674d24893" + "versions.yml:md5,21d43bb86ef743e75e729dfa77ba8f91", + "versions.yml:md5,92450dccc1a141f405d689d7f07480c0" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-10T09:38:09.338919835" + "timestamp": "2024-10-18T10:15:48.344077986" } } \ No newline at end of file diff --git a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap index 26ed39c00a71..7bbcf72b7cba 100644 --- a/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap +++ b/subworkflows/nf-core/bedgraph_bedclip_bedgraphtobigwig/tests/main.nf.test.snap @@ -21,7 +21,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -43,16 +43,16 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2023-11-26T01:55:31.016058335" + "timestamp": "2024-10-18T10:48:23.095911334" }, "sarscov2 [bedgraph] [genome_sizes] - stub": { "content": [ @@ -76,7 +76,7 @@ ] ], "2": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ], "bedgraph": [ @@ -98,15 +98,15 @@ ] ], "versions": [ - "versions.yml:md5,21c57fc724b374139b11f88017251733", + "versions.yml:md5,1202cdc73b5829361d5b150dcf7fe865", "versions.yml:md5,72a7b07bc0e796ff6805c57f7340337f" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T12:22:51.388076" + "timestamp": "2024-10-18T10:48:45.587883209" } } \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap index 46bf3acf29ee..f8a746aa6b5e 100644 --- a/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_fastqc_umitools_trimgalore/tests/main.nf.test.snap @@ -60,8 +60,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -122,17 +122,17 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:34.919444" + "timestamp": "2024-10-18T12:18:56.222595833" }, "test paired end read without UMI - stub": { "content": [ @@ -192,7 +192,7 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -250,16 +250,16 @@ ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:51.765414" + "timestamp": "2024-10-18T12:19:07.775855857" }, "test paired end read without UMI": { "content": [ @@ -288,15 +288,15 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:37.366404" + "timestamp": "2024-10-18T12:18:19.621101515" }, "test single end read with UMI": { "content": [ @@ -322,16 +322,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:04:53.072227" + "timestamp": "2024-10-18T12:17:51.049984482" }, "test paired end read with UMI": { "content": [ @@ -357,16 +357,16 @@ ], [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:05:16.709704" + "timestamp": "2024-10-18T12:18:07.106739839" }, "test skip all steps": { "content": [ @@ -447,8 +447,8 @@ ] ], "9": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ], "fastqc_html": [ @@ -509,16 +509,16 @@ ] ], "versions": [ - "versions.yml:md5,0a5b8fa83ba29cf645bf9e9471cca150", "versions.yml:md5,3e4b7f058c0aa96ba41c3e4d6df6e839", + "versions.yml:md5,71a31a3f411d571b513308e3ca93deb0", "versions.yml:md5,7e740129a23c5ac21c27476e30f8a6d2" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.3" + "nextflow": "24.04.4" }, - "timestamp": "2024-07-22T17:06:09.844235" + "timestamp": "2024-10-18T12:18:42.513733457" } -} +} \ No newline at end of file diff --git a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap index e0c944f3157d..f7e64e1f3625 100644 --- a/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap +++ b/subworkflows/nf-core/fastq_subsample_fq_salmon/tests/main.nf.test.snap @@ -30,14 +30,14 @@ ], [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:35.832206" + "timestamp": "2024-10-18T10:04:10.67385556" }, "homo_sapiens paired-end [fastq] - stub": { "content": [ @@ -104,7 +104,7 @@ ], "5": [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ], "index": [ [ @@ -168,14 +168,14 @@ ], "versions": [ "versions.yml:md5,12c0d1f67c2afb97470ae0974e5e01bb", - "versions.yml:md5,885fde9e7beac002b3a17b66b92db4bd" + "versions.yml:md5,acbe540e7ede18f7999975729fde869c" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:08:56.819" + "timestamp": "2024-10-18T10:04:26.972793491" } } \ No newline at end of file diff --git a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap index 4db35cced7f2..9c49c1513751 100644 --- a/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap +++ b/subworkflows/nf-core/quantify_pseudo_alignment/tests/main.nf.test.snap @@ -54,17 +54,17 @@ ] ], [ - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:19.861809" + "timestamp": "2024-10-18T10:06:55.431718491" }, "salmon - stub": { "content": [ @@ -122,9 +122,9 @@ ] ], "14": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ], "2": [ @@ -308,18 +308,18 @@ ] ], "versions": [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:36:55.281379" + "timestamp": "2024-10-18T10:07:30.425544183" }, "kallisto - stub": { "content": [ @@ -375,7 +375,7 @@ ] ], "14": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" @@ -559,7 +559,7 @@ ] ], "versions": [ - "versions.yml:md5,7afb76ee798ceb1e5dff5879d28ef85a", + "versions.yml:md5,c10c51dad5b22c80ebacb805645137ad", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed", "versions.yml:md5,ea39658f8685118d81d42acd451e66ea" @@ -567,10 +567,10 @@ } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:37:29.239014" + "timestamp": "2024-10-18T10:08:20.127524239" }, "salmon": { "content": [ @@ -629,16 +629,16 @@ ] ], [ - "versions.yml:md5,4c3564e1ba17d8ce2b0ee784251ddd87", - "versions.yml:md5,b44caeec65491d47e098c7ddaf024b96", + "versions.yml:md5,be28c034506b52fd01f9b2fb0fc678e3", "versions.yml:md5,d5243289a32cde9e90e20f1a202bb566", + "versions.yml:md5,df9cd6573913e1c58ebc6714e6318432", "versions.yml:md5,e9e7d18c3de83f1113fb1ff0c55d35ed" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-03T15:35:48.954002" + "timestamp": "2024-10-18T10:06:18.517305145" } } \ No newline at end of file diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index e40cb75442fb..596b04c8d8c8 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -512,12 +512,6 @@ paragraph/multigrmpy: phyloflash: - modules/nf-core/phyloflash/** - tests/modules/nf-core/phyloflash/** -picard/collectrnaseqmetrics: - - modules/nf-core/picard/collectrnaseqmetrics/** - - tests/modules/nf-core/picard/collectrnaseqmetrics/** -picard/filtersamreads: - - modules/nf-core/picard/filtersamreads/** - - tests/modules/nf-core/picard/filtersamreads/** plink/exclude: - modules/nf-core/plink/exclude/** - tests/modules/nf-core/plink/exclude/** diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf b/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf deleted file mode 100644 index a53d7bbeecbf..000000000000 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { UCSC_GTFTOGENEPRED } from '../../../../../modules/nf-core/ucsc/gtftogenepred/main.nf' -include { PICARD_COLLECTRNASEQMETRICS } from '../../../../../modules/nf-core/picard/collectrnaseqmetrics/main.nf' - -workflow test_picard_collectrnaseqmetrics { - - fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - gtf = file(params.test_data['sarscov2']['genome']['genome_gtf'], checkIfExists: true) - - input_gtftogenepred = [ - [ id:'test'], - gtf - ] - - UCSC_GTFTOGENEPRED(input_gtftogenepred) - - input_collectrnaseqmetrics = [ - [ id:'test', single_end:false, strandedness:'forward' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) - ] - - PICARD_COLLECTRNASEQMETRICS( - input_collectrnaseqmetrics, - UCSC_GTFTOGENEPRED.out.refflat.map{ it[1] }, - fasta, - [] - ) - -} diff --git a/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml b/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml deleted file mode 100644 index 01289cb93a14..000000000000 --- a/tests/modules/nf-core/picard/collectrnaseqmetrics/test.yml +++ /dev/null @@ -1,15 +0,0 @@ -- name: picard collectrnaseqmetrics test_picard_collectrnaseqmetrics - command: nextflow run ./tests/modules/nf-core/picard/collectrnaseqmetrics -entry test_picard_collectrnaseqmetrics -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/collectrnaseqmetrics/nextflow.config - tags: - - picard - - picard/collectrnaseqmetrics - files: - - path: output/picard/test.rna_metrics - contains: - - "CollectRnaSeqMetrics" - - path: output/picard/versions.yml - - path: output/ucsc/test.genepred - md5sum: 779e4749efaf38da3443ddfde30cc76c - - path: output/ucsc/test.refflat - md5sum: 4101802f41d4cf7ee2667587da11bf42 - - path: output/ucsc/versions.yml diff --git a/tests/modules/nf-core/picard/filtersamreads/main.nf b/tests/modules/nf-core/picard/filtersamreads/main.nf deleted file mode 100644 index 3687bbfb19bb..000000000000 --- a/tests/modules/nf-core/picard/filtersamreads/main.nf +++ /dev/null @@ -1,32 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { PICARD_SORTSAM } from '../../../../../modules/nf-core/picard/sortsam/main.nf' -include { PICARD_FILTERSAMREADS } from '../../../../../modules/nf-core/picard/filtersamreads/main.nf' - -workflow test_picard_filtersamreads { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true) ] - sort_order = 'queryname' - filter = 'includeAligned' - - PICARD_SORTSAM ( input, sort_order ) - PICARD_SORTSAM.out.bam - .map { - [ it[0], it[1], [] ] - } - .set{ ch_sorted_for_filtersamreads } - PICARD_FILTERSAMREADS ( ch_sorted_for_filtersamreads, filter ) -} - -workflow test_picard_filtersamreads_readlist { - - input = [ [ id:'test', single_end:false ], // meta map - file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_single_end_bam_readlist_txt'], checkIfExists: true) ] - filter = 'includeReadList' - - PICARD_FILTERSAMREADS ( input, filter ) -} diff --git a/tests/modules/nf-core/picard/filtersamreads/test.yml b/tests/modules/nf-core/picard/filtersamreads/test.yml deleted file mode 100644 index 1404960b6651..000000000000 --- a/tests/modules/nf-core/picard/filtersamreads/test.yml +++ /dev/null @@ -1,30 +0,0 @@ -- name: picard filtersamreads test_picard_filtersamreads - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - path: output/picard/test.sorted.bam - md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - path: output/picard/versions.yml - -- name: picard filtersamreads test_picard_filtersamreads_readlist - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - md5sum: 1e86b738b56f2c2b09f4cab52baf05c7 - - path: output/picard/versions.yml - -- name: picard filtersamreads test_picard_filtersamreads_readlist stub - command: nextflow run ./tests/modules/nf-core/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/nf-core/picard/filtersamreads/nextflow.config -stub-run - tags: - - picard - - picard/filtersamreads - files: - - path: output/picard/test.filtered.bam - - path: output/picard/versions.yml From 97321eded31a12598837a476d3615300af413bb7 Mon Sep 17 00:00:00 2001 From: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com> Date: Sun, 20 Oct 2024 11:55:55 +0200 Subject: [PATCH 165/486] Add gzip support and multiple files for gawk (#6810) * Update gawk * Update test * Update documentation --- modules/nf-core/gawk/main.nf | 12 ++- modules/nf-core/gawk/meta.yml | 3 +- modules/nf-core/gawk/tests/main.nf.test | 52 ++++++++++++- modules/nf-core/gawk/tests/main.nf.test.snap | 80 ++++++++++++++++++-- 4 files changed, 133 insertions(+), 14 deletions(-) diff --git a/modules/nf-core/gawk/main.nf b/modules/nf-core/gawk/main.nf index ca4689297c93..7514246eeb8b 100644 --- a/modules/nf-core/gawk/main.nf +++ b/modules/nf-core/gawk/main.nf @@ -8,7 +8,7 @@ process GAWK { 'biocontainers/gawk:5.3.0' }" input: - tuple val(meta), path(input) + tuple val(meta), path(input, arity: '0..*') path(program_file) output: @@ -22,15 +22,19 @@ process GAWK { def args = task.ext.args ?: '' // args is used for the main arguments of the tool def args2 = task.ext.args2 ?: '' // args2 is used to specify a program when no program file has been given prefix = task.ext.prefix ?: "${meta.id}" - suffix = task.ext.suffix ?: "${input.getExtension()}" + suffix = task.ext.suffix ?: "${input.collect{ it.getExtension()}.get(0)}" // use the first extension of the input files - program = program_file ? "-f ${program_file}" : "${args2}" + program = program_file ? "-f ${program_file}" : "${args2}" + lst_gz = input.collect{ it.getExtension().endsWith("gz") } + unzip = lst_gz.contains(false) ? "" : "find ${input} -exec zcat {} \\; | \\" + input_cmd = unzip ? "" : "${input}" """ + ${unzip} awk \\ ${args} \\ ${program} \\ - ${input} \\ + ${input_cmd} \\ > ${prefix}.${suffix} cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 051700820dee..2da41405de7b 100644 --- a/modules/nf-core/gawk/meta.yml +++ b/modules/nf-core/gawk/meta.yml @@ -26,7 +26,8 @@ input: - input: type: file description: The input file - Specify the logic that needs to be executed on - this file on the `ext.args2` or in the program file + this file on the `ext.args2` or in the program file. + If the files have a `.gz` extension, they will be unzipped using `zcat`. pattern: "*" - - program_file: type: file diff --git a/modules/nf-core/gawk/tests/main.nf.test b/modules/nf-core/gawk/tests/main.nf.test index fce82ca95adf..5952e9a2935d 100644 --- a/modules/nf-core/gawk/tests/main.nf.test +++ b/modules/nf-core/gawk/tests/main.nf.test @@ -8,7 +8,7 @@ nextflow_process { tag "modules_nfcore" tag "gawk" - test("convert fasta to bed") { + test("Convert fasta to bed") { config "./nextflow.config" when { @@ -31,7 +31,7 @@ nextflow_process { } } - test("convert fasta to bed with program file") { + test("Convert fasta to bed with program file") { config "./nextflow_with_program_file.config" when { @@ -53,4 +53,52 @@ nextflow_process { ) } } + + test("Extract first column from multiple files") { + config "./nextflow_with_program_file.config" + tag "test" + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true), + file(params.modules_testdata_base_path + 'generic/txt/species_names.txt', checkIfExists: true)] + ] + input[1] = Channel.of('BEGIN {FS=" "}; {print \$1}').collectFile(name:"program.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("Unzip files before processing") { + config "./nextflow_with_program_file.config" + + when { + process { + """ + input[0] = [ + [ id:'test' ], // meta map + [file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/vcf/NA24385_sv.vcf.gz', checkIfExists: true)] + ] + input[1] = Channel.of('/^#CHROM/ { print \$1, \$10 }').collectFile(name:"column_header.txt") + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } } \ No newline at end of file diff --git a/modules/nf-core/gawk/tests/main.nf.test.snap b/modules/nf-core/gawk/tests/main.nf.test.snap index 4f3a759c628d..d396f738b6ab 100644 --- a/modules/nf-core/gawk/tests/main.nf.test.snap +++ b/modules/nf-core/gawk/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "convert fasta to bed with program file": { + "Convert fasta to bed": { "content": [ { "0": [ @@ -28,11 +28,11 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T15:20:02.495430346" + "timestamp": "2024-10-19T13:14:02.347809811" }, - "convert fasta to bed": { + "Convert fasta to bed with program file": { "content": [ { "0": [ @@ -61,8 +61,74 @@ ], "meta": { "nf-test": "0.8.4", - "nextflow": "24.03.0" + "nextflow": "24.04.4" }, - "timestamp": "2024-05-17T15:19:53.291809648" + "timestamp": "2024-10-19T13:14:11.894616209" + }, + "Extract first column from multiple files": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,566c51674bd643227bb2d83e0963376d" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:04:47.729300129" + }, + "Unzip files before processing": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "1": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ], + "output": [ + [ + { + "id": "test" + }, + "test.bed:md5,1e31ebd4a060aab5433bbbd9ab24e403" + ] + ], + "versions": [ + "versions.yml:md5,842acc9870dc8ac280954047cb2aa23a" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-19T22:08:19.533527657" } -} \ No newline at end of file +} From 3a6dd1a94fbc3ad0d0f77ebfea2f507fe0dc5814 Mon Sep 17 00:00:00 2001 From: Daniel Schmitz Date: Sun, 20 Oct 2024 12:36:37 +0200 Subject: [PATCH 166/486] Update Hifiasm to 0.19.9 (#6796) * Bumped version to 0.19.9 * Added tests * Updated test snapshots * Checking explicitly for empty maternal haplotypes * Changed Test names * Removed Optional outputs expected to be empty * Added assertions for unstable outputs * Removed pytest * Removed hifiasm from pytest modules * Added stub test * Updated snapshots * Added f0 argument to prevent runner from being killed * Actually using the config now. --- modules/nf-core/hifiasm/environment.yml | 2 +- modules/nf-core/hifiasm/main.nf | 4 +- modules/nf-core/hifiasm/tests/main.nf.test | 195 +++++++++++ .../nf-core/hifiasm/tests/main.nf.test.snap | 319 ++++++++++++++++++ modules/nf-core/hifiasm/tests/nextflow.config | 3 + tests/config/pytest_modules.yml | 3 - tests/modules/nf-core/hifiasm/main.nf | 46 --- tests/modules/nf-core/hifiasm/nextflow.config | 9 - tests/modules/nf-core/hifiasm/test.yml | 53 --- 9 files changed, 520 insertions(+), 114 deletions(-) create mode 100644 modules/nf-core/hifiasm/tests/main.nf.test create mode 100644 modules/nf-core/hifiasm/tests/main.nf.test.snap create mode 100644 modules/nf-core/hifiasm/tests/nextflow.config delete mode 100644 tests/modules/nf-core/hifiasm/main.nf delete mode 100644 tests/modules/nf-core/hifiasm/nextflow.config delete mode 100644 tests/modules/nf-core/hifiasm/test.yml diff --git a/modules/nf-core/hifiasm/environment.yml b/modules/nf-core/hifiasm/environment.yml index d3bd7d0cea29..80293d119873 100644 --- a/modules/nf-core/hifiasm/environment.yml +++ b/modules/nf-core/hifiasm/environment.yml @@ -2,4 +2,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::hifiasm=0.19.8 + - bioconda::hifiasm=0.19.9 diff --git a/modules/nf-core/hifiasm/main.nf b/modules/nf-core/hifiasm/main.nf index 36169f85968e..0f9b074b3c31 100644 --- a/modules/nf-core/hifiasm/main.nf +++ b/modules/nf-core/hifiasm/main.nf @@ -4,8 +4,8 @@ process HIFIASM { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/hifiasm:0.19.8--h43eeafb_0' : - 'biocontainers/hifiasm:0.19.8--h43eeafb_0' }" + 'https://depot.galaxyproject.org/singularity/hifiasm:0.19.9--h43eeafb_0' : + 'biocontainers/hifiasm:0.19.9--h43eeafb_0' }" input: tuple val(meta), path(reads) diff --git a/modules/nf-core/hifiasm/tests/main.nf.test b/modules/nf-core/hifiasm/tests/main.nf.test new file mode 100644 index 000000000000..07e9ce89c3cf --- /dev/null +++ b/modules/nf-core/hifiasm/tests/main.nf.test @@ -0,0 +1,195 @@ +nextflow_process { + + name "Test Process HifiAsm" + script "../main.nf" + process "HIFIASM" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "hifiasm" + + test("homo_sapiens pacbio hifi [fastq, , , , ]") { + when { + process { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert file(process.out.corrected_reads.get(0).get(1)).exists() }, + { assert file(process.out.source_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.log.get(0).get(1)).exists() }, + { assert snapshot( + process.out.raw_unitigs, + process.out.processed_contigs, + process.out.processed_unitigs, + process.out.paternal_contigs, + process.out.maternal_contigs, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, yak, yak, , ]") { + when { + process { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test2.yak', checkIfExists: true) + input[3] = [] + input[4] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert file(process.out.corrected_reads.get(0).get(1)).exists() }, + { assert file(process.out.source_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.log.get(0).get(1)).exists() }, + { assert file(process.out.maternal_contigs.get(0).get(1)).length() == 0}, + { assert snapshot( + process.out.raw_unitigs, + process.out.processed_unitigs, + process.out.paternal_contigs, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, , , fastq, fastq]") { + when { + process { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = [] + input[2] = [] + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz', checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + """ + } + } + then { + assertAll( + { assert process.success }, + { assert file(process.out.corrected_reads.get(0).get(1)).exists() }, + { assert file(process.out.source_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.reverse_overlaps.get(0).get(1)).exists() }, + { assert file(process.out.log.get(0).get(1)).exists() }, + { assert file(process.out.maternal_contigs.get(0).get(1)).length() == 0}, + { assert snapshot( + process.out.raw_unitigs, + process.out.processed_unitigs, + process.out.paternal_contigs, + process.out.versions + ).match() } + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, yak, yak, fastq, fastq]") { + when { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test2.yak', checkIfExists: true) + input[3] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz, checkIfExists: true) + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz, checkIfExists: true) + """ + } + then { + assertAll( + { assert !process.success} + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, yak, , , ]") { + when { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/yak/test.yak', checkIfExists: true) + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + then { + assertAll( + { assert !process.success} + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, , , , fastq]") { + when { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz', checkIfExists: true) + """ + } + then { + assertAll( + { assert !process.success} + ) + } + } + + test("homo_sapiens pacbio hifi [fastq, , , , ] - stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id : 'test'], + [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/pacbio/fastq/test_hifi.fastq.gz', checkIfExists: true)] + ] + input[1] = [] + input[2] = [] + input[3] = [] + input[4] = [] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match()} + ) + } + } +} \ No newline at end of file diff --git a/modules/nf-core/hifiasm/tests/main.nf.test.snap b/modules/nf-core/hifiasm/tests/main.nf.test.snap new file mode 100644 index 000000000000..932fce839dca --- /dev/null +++ b/modules/nf-core/hifiasm/tests/main.nf.test.snap @@ -0,0 +1,319 @@ +{ + "homo_sapiens pacbio hifi [fastq, , , , ] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.asm.r_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test" + }, + "test.asm.ec.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "10": [ + [ + { + "id": "test" + }, + "test.stderr.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "11": [ + "versions.yml:md5,981b5ef63d639c5f0fae9846b07c6d53" + ], + "2": [ + [ + { + "id": "test" + }, + "test.asm.ovlp.source.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "3": [ + [ + { + "id": "test" + }, + "test.asm.ovlp.reverse.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "4": [ + [ + { + "id": "test" + }, + "test.asm.bp.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "5": [ + [ + { + "id": "test" + }, + "test.asm.p_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "6": [ + [ + { + "id": "test" + }, + "test.asm.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "7": [ + [ + { + "id": "test" + }, + "test.asm.a_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "8": [ + [ + { + "id": "test" + }, + "test.asm.hap1.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "9": [ + [ + { + "id": "test" + }, + "test.asm.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "alternate_contigs": [ + [ + { + "id": "test" + }, + "test.asm.a_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "corrected_reads": [ + [ + { + "id": "test" + }, + "test.asm.ec.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "log": [ + [ + { + "id": "test" + }, + "test.stderr.log:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "maternal_contigs": [ + [ + { + "id": "test" + }, + "test.asm.hap2.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "paternal_contigs": [ + [ + { + "id": "test" + }, + "test.asm.hap1.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "primary_contigs": [ + [ + { + "id": "test" + }, + "test.asm.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "processed_contigs": [ + [ + { + "id": "test" + }, + "test.asm.bp.p_ctg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "processed_unitigs": [ + [ + { + "id": "test" + }, + "test.asm.p_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "raw_unitigs": [ + [ + { + "id": "test" + }, + "test.asm.r_utg.gfa:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "reverse_overlaps": [ + [ + { + "id": "test" + }, + "test.asm.ovlp.reverse.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "source_overlaps": [ + [ + { + "id": "test" + }, + "test.asm.ovlp.source.bin:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,981b5ef63d639c5f0fae9846b07c6d53" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T09:26:14.077804563" + }, + "homo_sapiens pacbio hifi [fastq, , , fastq, fastq]": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.asm.hic.r_utg.gfa:md5,9cb983397b093bcf9ef5a01c5aa52c6c" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.hic.p_utg.gfa:md5,3e2b4815145b06bb74f1b74876e767dc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.hic.hap1.p_ctg.gfa:md5,467a7f7d6dd15b773f15ccce84e0f28d" + ] + ], + [ + "versions.yml:md5,981b5ef63d639c5f0fae9846b07c6d53" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T09:03:04.159625282" + }, + "homo_sapiens pacbio hifi [fastq, , , , ]": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.asm.bp.r_utg.gfa:md5,9cb983397b093bcf9ef5a01c5aa52c6c" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.bp.p_ctg.gfa:md5,c83aba621a6ae5a5b5b39dbdc1a0ba9d" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.bp.p_utg.gfa:md5,3e2b4815145b06bb74f1b74876e767dc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.bp.hap1.p_ctg.gfa:md5,1206beee1cda7b39e48e0a080fde0801" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.bp.hap2.p_ctg.gfa:md5,765b53fbf44b43826174585438a3578e" + ] + ], + [ + "versions.yml:md5,981b5ef63d639c5f0fae9846b07c6d53" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T09:02:09.113570192" + }, + "homo_sapiens pacbio hifi [fastq, yak, yak, , ]": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.asm.dip.r_utg.gfa:md5,9cb983397b093bcf9ef5a01c5aa52c6c" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.dip.p_utg.gfa:md5,3e2b4815145b06bb74f1b74876e767dc" + ] + ], + [ + [ + { + "id": "test" + }, + "test.asm.dip.hap1.p_ctg.gfa:md5,9d4d20104ef4bc3d2896ae25c6b35c06" + ] + ], + [ + "versions.yml:md5,981b5ef63d639c5f0fae9846b07c6d53" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T09:02:35.562018153" + } +} \ No newline at end of file diff --git a/modules/nf-core/hifiasm/tests/nextflow.config b/modules/nf-core/hifiasm/tests/nextflow.config new file mode 100644 index 000000000000..8dc2ae48a298 --- /dev/null +++ b/modules/nf-core/hifiasm/tests/nextflow.config @@ -0,0 +1,3 @@ +process { + ext.args = "-f0" +} diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 596b04c8d8c8..27bfefee6f1a 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -296,9 +296,6 @@ gunc/run: hicexplorer/hicpca: - modules/nf-core/hicexplorer/hicpca/** - tests/modules/nf-core/hicexplorer/hicpca/** -hifiasm: - - modules/nf-core/hifiasm/** - - tests/modules/nf-core/hifiasm/** hlala/preparegraph: - modules/nf-core/hlala/preparegraph/** - tests/modules/nf-core/hlala/preparegraph/** diff --git a/tests/modules/nf-core/hifiasm/main.nf b/tests/modules/nf-core/hifiasm/main.nf deleted file mode 100644 index 0c62af0d0ee9..000000000000 --- a/tests/modules/nf-core/hifiasm/main.nf +++ /dev/null @@ -1,46 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { HIFIASM } from '../../../../modules/nf-core/hifiasm/main.nf' - -/* - * Test with long reads only - */ -workflow test_hifiasm_hifi_only { - input = [ - [ id:'test' ], // meta map - [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ] - ] - - HIFIASM ( input, [], [], [], [] ) -} - -/* - * Test with parental reads for phasing - */ -workflow test_hifiasm_with_parental_reads { - input = [ - [ id:'test' ], // meta map - [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ] - ] - paternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test_yak'], checkIfExists: true) - maternal_kmer_dump = file(params.test_data['homo_sapiens']['illumina']['test2_yak'], checkIfExists: true) - - HIFIASM ( input, paternal_kmer_dump, maternal_kmer_dump, [], [] ) -} - -/* - * Test with parental reads for phasing - */ -workflow test_hifiasm_with_hic { - input = [ - [ id:'test' ], // meta map - [ file(params.test_data['homo_sapiens']['pacbio']['hifi'], checkIfExists: true) ] - ] - hic_reads1 = file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true) - hic_reads2 = file(params.test_data['homo_sapiens']['illumina']['test_2_fastq_gz'], checkIfExists: true) - - HIFIASM ( input, [], [], hic_reads1, hic_reads2 ) -} - diff --git a/tests/modules/nf-core/hifiasm/nextflow.config b/tests/modules/nf-core/hifiasm/nextflow.config deleted file mode 100644 index 0994c9014604..000000000000 --- a/tests/modules/nf-core/hifiasm/nextflow.config +++ /dev/null @@ -1,9 +0,0 @@ -process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - - withName: HIFIASM { - ext.args = '-f0' - } - -} diff --git a/tests/modules/nf-core/hifiasm/test.yml b/tests/modules/nf-core/hifiasm/test.yml deleted file mode 100644 index 1a305d3a1edf..000000000000 --- a/tests/modules/nf-core/hifiasm/test.yml +++ /dev/null @@ -1,53 +0,0 @@ -- name: hifiasm test_hifiasm_hifi_only - command: nextflow run ./tests/modules/nf-core/hifiasm -entry test_hifiasm_hifi_only -c ./tests/config/nextflow.config - tags: - - hifiasm - files: - - path: output/hifiasm/test.asm.bp.hap1.p_ctg.gfa - md5sum: 1206beee1cda7b39e48e0a080fde0801 - - path: output/hifiasm/test.asm.bp.hap2.p_ctg.gfa - md5sum: 765b53fbf44b43826174585438a3578e - - path: output/hifiasm/test.asm.bp.p_ctg.gfa - md5sum: c83aba621a6ae5a5b5b39dbdc1a0ba9d - - path: output/hifiasm/test.asm.bp.p_utg.gfa - md5sum: 3e2b4815145b06bb74f1b74876e767dc - - path: output/hifiasm/test.asm.bp.r_utg.gfa - md5sum: 9cb983397b093bcf9ef5a01c5aa52c6c - - path: output/hifiasm/test.asm.ec.bin - - path: output/hifiasm/test.asm.ovlp.reverse.bin - - path: output/hifiasm/test.asm.ovlp.source.bin - - path: output/hifiasm/versions.yml - -- name: hifiasm test_hifiasm_with_parental_reads - command: nextflow run ./tests/modules/nf-core/hifiasm -entry test_hifiasm_with_parental_reads -c ./tests/config/nextflow.config - tags: - - hifiasm - files: - - path: output/hifiasm/test.asm.dip.hap1.p_ctg.gfa - md5sum: 9d4d20104ef4bc3d2896ae25c6b35c06 - - path: output/hifiasm/test.asm.dip.hap2.p_ctg.gfa - - path: output/hifiasm/test.asm.dip.p_utg.gfa - md5sum: 3e2b4815145b06bb74f1b74876e767dc - - path: output/hifiasm/test.asm.dip.r_utg.gfa - md5sum: 9cb983397b093bcf9ef5a01c5aa52c6c - - path: output/hifiasm/test.asm.ec.bin - - path: output/hifiasm/test.asm.ovlp.reverse.bin - - path: output/hifiasm/test.asm.ovlp.source.bin - - path: output/hifiasm/versions.yml - -- name: hifiasm test_hifiasm_with_hic - command: nextflow run ./tests/modules/nf-core/hifiasm -entry test_hifiasm_with_hic -c ./tests/config/nextflow.config - tags: - - hifiasm - files: - - path: output/hifiasm/test.asm.ec.bin - - path: output/hifiasm/test.asm.hic.hap1.p_ctg.gfa - md5sum: 467a7f7d6dd15b773f15ccce84e0f28d - - path: output/hifiasm/test.asm.hic.hap2.p_ctg.gfa - - path: output/hifiasm/test.asm.hic.p_utg.gfa - md5sum: 3e2b4815145b06bb74f1b74876e767dc - - path: output/hifiasm/test.asm.hic.r_utg.gfa - md5sum: 9cb983397b093bcf9ef5a01c5aa52c6c - - path: output/hifiasm/test.asm.ovlp.reverse.bin - - path: output/hifiasm/test.asm.ovlp.source.bin - - path: output/hifiasm/versions.yml From 6d5d163242f4bad63b81c41aeaf0d7bbeb8e2431 Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Mon, 21 Oct 2024 09:31:13 +0200 Subject: [PATCH 167/486] Pypgx/preparedepthofcoverage (#6729) * Support nft-compress in nf-test.config (#6727) * Load nft-compress for nf-test support for compressed files in nf-test * alphabetic order * pypgx/preparedepthofcoverage * removed debug lines * only storing zipped md5sums rather than plain text * removed tags.yml --------- Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com> Co-authored-by: Sateesh_Peri <33637490+sateeshperi@users.noreply.github.com> --- .../preparedepthofcoverage/environment.yml | 7 ++ .../pypgx/preparedepthofcoverage/main.nf | 53 +++++++++++++++ .../pypgx/preparedepthofcoverage/meta.yml | 61 +++++++++++++++++ .../preparedepthofcoverage/tests/main.nf.test | 65 +++++++++++++++++++ .../tests/main.nf.test.snap | 46 +++++++++++++ 5 files changed, 232 insertions(+) create mode 100644 modules/nf-core/pypgx/preparedepthofcoverage/environment.yml create mode 100644 modules/nf-core/pypgx/preparedepthofcoverage/main.nf create mode 100644 modules/nf-core/pypgx/preparedepthofcoverage/meta.yml create mode 100644 modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test create mode 100644 modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test.snap diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml b/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml new file mode 100644 index 000000000000..d18360bed974 --- /dev/null +++ b/modules/nf-core/pypgx/preparedepthofcoverage/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - "bioconda::pypgx=0.25.0" diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/main.nf b/modules/nf-core/pypgx/preparedepthofcoverage/main.nf new file mode 100644 index 000000000000..1682eae234ba --- /dev/null +++ b/modules/nf-core/pypgx/preparedepthofcoverage/main.nf @@ -0,0 +1,53 @@ +process PYPGX_PREPAREDEPTHOFCOVERAGE { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0': + 'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }" + + input: + tuple val(meta), path(bam), path(bai) + val(pgx_genes) + val(assembly_version) + + output: + tuple val(meta), path('*.zip'), emit: coverage + path("versions.yml"), emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def genes = "--genes ${pgx_genes.join(' ')}" ?: '' + def assembly = assembly_version ?: "GRCh38" + + """ + pypgx prepare-depth-of-coverage \\ + ${args} \\ + ${genes} \\ + --assembly ${assembly} \\ + ${prefix}.zip \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + python -c 'import zipfile; zipfile.ZipFile("${prefix}.zip", "w").close()' + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/meta.yml b/modules/nf-core/pypgx/preparedepthofcoverage/meta.yml new file mode 100644 index 000000000000..71fe4de093be --- /dev/null +++ b/modules/nf-core/pypgx/preparedepthofcoverage/meta.yml @@ -0,0 +1,61 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pypgx_preparedepthofcoverage" +description: Prepare a depth of coverage file for all target genes with SV from BAM + files. +keywords: + - Pharmacogenetics + - pypgx + - SV +tools: + - "pypgx": + description: "A Python package for pharmacogenomics research" + homepage: "https://pypgx.readthedocs.io/en/latest/" + documentation: "https://pypgx.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/sbslee/pypgx" + doi: "10.1371/journal.pone.0272129" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - bai: + type: file + description: Input BAM index file + pattern: "*.{bam.bai}" + - - pgx_genes: + type: list + description: List of PGx genes supported by PyPGx to include in variant calling. + - - assembly_version: + type: string + description: Genome assembly version to use. + pattern: "{GRCh37,GRCh38}" +output: + - coverage: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.{zip}" + - "*.zip": + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.{zip}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jorivansteenbrugge" +maintainers: + - "@jorivansteenbrugge" diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test b/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test new file mode 100644 index 000000000000..43d768d31ed9 --- /dev/null +++ b/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test @@ -0,0 +1,65 @@ +// nf-core modules test pypgx/preparedepthofcoverage +nextflow_process { + + name "Test Process PYPGX_PREPAREDEPTHOFCOVERAGE" + script "../main.nf" + process "PYPGX_PREPAREDEPTHOFCOVERAGE" + + tag "modules" + tag "modules_nfcore" + tag "pypgx" + tag "pypgx/preparedepthofcoverage" + + test("human paired end bam CYP2D6 locus - GRCh37") { + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam.bai', checkIfExists: true) + ] + input[1] = ["CYP2D6"] + input[2] = "GRCh37" + """ + } + } + then { + def zipFile = path(process.out.coverage[0][1]).zip + def paths = zipFile.extractAll() + def metaFile = paths.find { it.getFileName().toString() == 'metadata.txt' } + def dataFile = paths.find { it.getFileName().toString() == 'data.tsv' } + + assertAll( + {assert process.success}, + {assert zipFile.isValid()}, + {assert snapshot( + metaFile, + dataFile).match()} + ) + } + } + + test("stub") { + options "-stub" + when { + process { + """ + input[0] = [ + [ id:'test' ], + [], + [] + ] + input[1] = [] + input[2] = "" + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test.snap b/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test.snap new file mode 100644 index 000000000000..ab6ae57d57b5 --- /dev/null +++ b/modules/nf-core/pypgx/preparedepthofcoverage/tests/main.nf.test.snap @@ -0,0 +1,46 @@ +{ + "human paired end bam CYP2D6 locus - GRCh37": { + "content": [ + "metadata.txt:md5,36e844724abd194e915ca0a9793cddc8", + "data.tsv:md5,4291d10aa774208ba97a9b753face059" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-04T08:27:28.096562" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c" + ] + ], + "1": [ + "versions.yml:md5,245a2588c91875e1fe561955c4a0ad27" + ], + "coverage": [ + [ + { + "id": "test" + }, + "test.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c" + ] + ], + "versions": [ + "versions.yml:md5,245a2588c91875e1fe561955c4a0ad27" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-04T08:27:34.813018" + } +} \ No newline at end of file From 04fe0472ff86b3bb065be3be0db0ff4a07d73a4a Mon Sep 17 00:00:00 2001 From: Joris van Steenbrugge Date: Mon, 21 Oct 2024 09:32:22 +0200 Subject: [PATCH 168/486] Pypgx/computecontrolstatistics (#6728) * pypgx/computecontrolstatistics * working tests & linting * fixed nf-test * only storing zipped md5sums rather than plain text * removed tags.yml --------- Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com> --- .../computecontrolstatistics/environment.yml | 7 ++ .../pypgx/computecontrolstatistics/main.nf | 54 +++++++++++++++ .../pypgx/computecontrolstatistics/meta.yml | 61 +++++++++++++++++ .../tests/main.nf.test | 67 +++++++++++++++++++ .../tests/main.nf.test.snap | 46 +++++++++++++ 5 files changed, 235 insertions(+) create mode 100644 modules/nf-core/pypgx/computecontrolstatistics/environment.yml create mode 100644 modules/nf-core/pypgx/computecontrolstatistics/main.nf create mode 100644 modules/nf-core/pypgx/computecontrolstatistics/meta.yml create mode 100644 modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test create mode 100644 modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test.snap diff --git a/modules/nf-core/pypgx/computecontrolstatistics/environment.yml b/modules/nf-core/pypgx/computecontrolstatistics/environment.yml new file mode 100644 index 000000000000..36c4150bd259 --- /dev/null +++ b/modules/nf-core/pypgx/computecontrolstatistics/environment.yml @@ -0,0 +1,7 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json +channels: + - conda-forge + - bioconda +dependencies: + - bioconda::pypgx=0.25.0 diff --git a/modules/nf-core/pypgx/computecontrolstatistics/main.nf b/modules/nf-core/pypgx/computecontrolstatistics/main.nf new file mode 100644 index 000000000000..54397240b3db --- /dev/null +++ b/modules/nf-core/pypgx/computecontrolstatistics/main.nf @@ -0,0 +1,54 @@ +process PYPGX_COMPUTECONTROLSTATISTICS { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pypgx:0.25.0--pyh7e72e81_0': + 'biocontainers/pypgx:0.25.0--pyh7e72e81_0' }" + + input: + tuple val(meta), path(bam), path(bai) + val(control_gene) + val(assembly_version) + + output: + tuple val(meta), path('*.zip'), emit: control_stats + path("versions.yml"), emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def control = "${control_gene}" ?: "VDR" + def assembly = "${assembly_version}" ?: "GRCh38" + + """ + pypgx compute-control-statistics \\ + ${args} \\ + --assembly ${assembly} \\ + ${control} \\ + ${prefix}_${control}.zip \\ + $bam + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ + + stub: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def control = "${control_gene}" ?: "VDR" + """ + # zip program unavailable in container + python -c 'import zipfile; zipfile.ZipFile("${prefix}_${control}.zip", "w").close()' + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pypgx: \$(echo \$(pypgx -v 2>&1) | sed 's/.* //') + END_VERSIONS + """ +} diff --git a/modules/nf-core/pypgx/computecontrolstatistics/meta.yml b/modules/nf-core/pypgx/computecontrolstatistics/meta.yml new file mode 100644 index 000000000000..011c80b6ec4b --- /dev/null +++ b/modules/nf-core/pypgx/computecontrolstatistics/meta.yml @@ -0,0 +1,61 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "pypgx_computecontrolstatistics" +description: Compute summary statistics for control gene from BAM files. +keywords: + - pypgx + - pharmacogenetics + - controlstatistics +tools: + - "pypgx": + description: "A Python package for pharmacogenomics research" + homepage: "https://pypgx.readthedocs.io/en/latest/" + documentation: "https://pypgx.readthedocs.io/en/latest/" + tool_dev_url: "https://github.com/sbslee/pypgx" + doi: "10.1371/journal.pone.0272129" + licence: ["MIT"] + identifier: "" +input: + - - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + - bam: + type: file + description: Sorted BAM file + pattern: "*.{bam}" + - bai: + type: file + description: BAM index file + pattern: "*.{bai}" + - - control_gene: + type: string + description: Gene to use as control gene + pattern: "{VDR,EGFR,RYR1}" + - - assembly_version: + type: string + description: Genome assembly version to use. + pattern: "{GRCh37,GRCh38}" +output: + - control_stats: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.{zip}" + - "*.zip": + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + pattern: "*.{zip}" + - versions: + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@jorivansteenbrugge" +maintainers: + - "@jorivansteenbrugge" diff --git a/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test b/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test new file mode 100644 index 000000000000..8caccda33ee0 --- /dev/null +++ b/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test @@ -0,0 +1,67 @@ +nextflow_process { + name "Test Process PYPGX_COMPUTECONTROLSTATISTICS" + script "../main.nf" + process "PYPGX_COMPUTECONTROLSTATISTICS" + + tag "modules" + tag "modules_nfcore" + tag "pypgx" + tag "pypgx/computecontrolstatistics" + + test("human paired end bam CYP2D6 locus - GRCh37 - VDR control gene") { + when { + process { + """ + input[0] = [ + [id: 'test'], + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.PGx.CYP2D6.bam.bai', checkIfExists: true) + ] + input[1] = "VDR" + input[2] = "GRCh37" + """ + } + } + then { + def zipFile = path(process.out.control_stats[0][1]).zip + def paths = zipFile.extractAll() + def metaFile = paths.find { it.getFileName().toString() == 'metadata.txt' } + def dataFile = paths.find { it.getFileName().toString() == 'data.tsv' } + + assertAll( + {assert process.success}, + {assert zipFile.isValid()}, + {assert snapshot( + metaFile, + dataFile).match()} + ) + } + } + + + test("stub") { + options "-stub" + + when { + process { + """ + input[0] = [ + [id: 'test'], + [], + [] + ] + input[1] = "" + input[2] = "" + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + +} diff --git a/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test.snap b/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test.snap new file mode 100644 index 000000000000..c43874686229 --- /dev/null +++ b/modules/nf-core/pypgx/computecontrolstatistics/tests/main.nf.test.snap @@ -0,0 +1,46 @@ +{ + "human paired end bam CYP2D6 locus - GRCh37 - VDR control gene": { + "content": [ + "metadata.txt:md5,175f4a9b9ec25f71cf06a712e9eb8646", + "data.tsv:md5,6d417ea67384d7d534f14b0bf7b292e3" + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-04T08:34:05.001792" + }, + "stub": { + "content": [ + { + "0": [ + [ + { + "id": "test" + }, + "test_VDR.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c" + ] + ], + "1": [ + "versions.yml:md5,5e02770f9a0c92d5ea726fe7668e33e1" + ], + "control_stats": [ + [ + { + "id": "test" + }, + "test_VDR.zip:md5,76cdb2bad9582d23c1f6f4d868218d6c" + ] + ], + "versions": [ + "versions.yml:md5,5e02770f9a0c92d5ea726fe7668e33e1" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-10-04T08:34:11.905783" + } +} \ No newline at end of file From 1b2fdf082b2ea7976b112e149a474d816094724c Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke <101190534+nvnieuwk@users.noreply.github.com> Date: Mon, 21 Oct 2024 10:50:04 +0200 Subject: [PATCH 169/486] Add nf-test to vcf_annotation_ensemblvep_snpeff + some general fixes (#6779) * update annotations subwf * finish the subwf * fix tests * update test files (gotta update snapshot tomorrow too) * finish update * Update subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf Co-authored-by: Maxime U Garcia * Update subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf Co-authored-by: Maxime U Garcia * fix new_meta not defined --------- Co-authored-by: Maxime U Garcia --- .../vcf_annotate_ensemblvep_snpeff/main.nf | 56 ++- .../vcf_annotate_ensemblvep_snpeff/meta.yml | 24 +- .../tests/main.nf.test | 332 +++++++++++++++ .../tests/main.nf.test.snap | 338 +++++++++++++++ .../tests}/nextflow.config | 7 +- tests/config/pytest_modules.yml | 3 - .../vcf_annotate_ensemblvep_snpeff/main.nf | 202 --------- .../vcf_annotate_ensemblvep_snpeff/test.yml | 384 ------------------ 8 files changed, 726 insertions(+), 620 deletions(-) create mode 100644 subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test create mode 100644 subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap rename {tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff => subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests}/nextflow.config (79%) delete mode 100644 tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf delete mode 100644 tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf index 91cace4d1d9f..9829b319f96d 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf @@ -5,6 +5,7 @@ include { ENSEMBLVEP_VEP } from '../../../modules/nf-core/ensemblvep/vep/main' include { SNPEFF_SNPEFF } from '../../../modules/nf-core/snpeff/snpeff/main' include { TABIX_TABIX } from '../../../modules/nf-core/tabix/tabix/main' +include { TABIX_BGZIP } from '../../../modules/nf-core/tabix/bgzip/main' include { BCFTOOLS_PLUGINSCATTER } from '../../../modules/nf-core/bcftools/pluginscatter/main' include { BCFTOOLS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main' include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main' @@ -24,7 +25,9 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { val_sites_per_chunk // value: the amount of variants per scattered VCF main: - ch_versions = Channel.empty() + def ch_versions = Channel.empty() + def ch_vep_input = Channel.empty() + def ch_scatter = Channel.empty() // Check if val_sites_per_chunk is set and scatter if it is if(val_sites_per_chunk) { @@ -32,7 +35,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { // Prepare the input VCF channel for scattering (split VCFs from custom files) // - ch_input = ch_vcf + def ch_input = ch_vcf .multiMap { meta, vcf, tbi, custom_files -> vcf: [ meta, vcf, tbi ] custom: [ meta, custom_files ] @@ -63,7 +66,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { // If multiple files are created, a list will be made as output of the process // So if the output isn't a list, there is always one file and if there is a list, // the amount of files in the list gets counted by .size() - is_list = vcfs instanceof ArrayList + def is_list = vcfs instanceof ArrayList count = is_list ? vcfs.size() : 1 [ meta, is_list ? vcfs : [vcfs], count ] // Channel containing the list of VCFs and the size of this list @@ -72,21 +75,22 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { .combine(ch_input.custom, by: 0) // Re-add the sample specific custom files .multiMap { meta, vcf, count, custom_files -> // Define the new ID. The `_annotated` is to disambiguate the VEP output with its input - new_id = "${meta.id}${vcf.name.replace(meta.id,"").tokenize(".")[0]}_annotated" as String - new_meta = meta + [id:new_id] + def new_id = "${meta.id}${vcf.name.replace(meta.id,"").tokenize(".")[0]}_annotated" as String // Create channels: one with the VEP input and one with the original ID and count of scattered VCFs - input: [ new_meta, vcf, custom_files ] - count: [ new_meta, meta.id, count ] + input: [ meta + [id:new_id], vcf, custom_files ] + count: [ meta + [id:new_id], meta.id, count ] } ch_vep_input = ch_scatter.input } else { // Use the normal input when no scattering has to be performed - ch_vep_input = ch_vcf.map { meta, vcf, tbi, files -> [ meta, vcf, files ] } + ch_vep_input = ch_vcf.map { meta, vcf, _tbi, files -> [ meta, vcf, files ] } } // Annotate with ensemblvep if it's part of the requested tools + def ch_vep_output = Channel.empty() + def ch_vep_reports = Channel.empty() if("ensemblvep" in val_tools_to_use){ ENSEMBLVEP_VEP( ch_vep_input, @@ -102,11 +106,14 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { ch_vep_output = ENSEMBLVEP_VEP.out.vcf ch_vep_reports = ENSEMBLVEP_VEP.out.report } else { - ch_vep_output = ch_vep_input.map { meta, vcf, files -> [ meta, vcf ] } - ch_vep_reports = Channel.empty() + ch_vep_output = ch_vep_input.map { meta, vcf, _files -> [ meta, vcf ] } } // Annotate with snpeff if it's part of the requested tools + def ch_snpeff_output = Channel.empty() + def ch_snpeff_reports = Channel.empty() + def ch_snpeff_html = Channel.empty() + def ch_snpeff_genes = Channel.empty() if("snpeff" in val_tools_to_use){ SNPEFF_SNPEFF( ch_vep_output, @@ -115,31 +122,36 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { ) ch_versions = ch_versions.mix(SNPEFF_SNPEFF.out.versions.first()) - ch_snpeff_output = SNPEFF_SNPEFF.out.vcf ch_snpeff_reports = SNPEFF_SNPEFF.out.report ch_snpeff_html = SNPEFF_SNPEFF.out.summary_html ch_snpeff_genes = SNPEFF_SNPEFF.out.genes_txt + + TABIX_BGZIP( + SNPEFF_SNPEFF.out.vcf + ) + ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first()) + ch_snpeff_output = TABIX_BGZIP.out.output } else { ch_snpeff_output = ch_vep_output - ch_snpeff_reports = Channel.empty() - ch_snpeff_html = Channel.empty() - ch_snpeff_genes = Channel.empty() } // Gather the files back together if they were scattered + def ch_ready_vcfs = Channel.empty() if(val_sites_per_chunk) { // // Concatenate the VCFs back together with bcftools concat // - ch_concat_input = ch_snpeff_output + def ch_concat_input = ch_snpeff_output .join(ch_scatter.count, failOnDuplicate:true, failOnMismatch:true) .map { meta, vcf, id, count -> - new_meta = meta + [id:id] + def new_meta = meta + [id:id] [ groupKey(new_meta, count), vcf ] } .groupTuple() // Group the VCFs which need to be concatenated - .map { it + [[]] } + .map { meta, vcf -> + [ meta, vcf, [] ] + } BCFTOOLS_CONCAT( ch_concat_input @@ -164,7 +176,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { // Index the resulting bgzipped VCFs // - ch_tabix_input = ch_ready_vcfs + def ch_tabix_input = ch_ready_vcfs .branch { meta, vcf -> // Split the bgzipped VCFs from the unzipped VCFs (only bgzipped VCFs should be indexed) bgzip: vcf.extension == "gz" @@ -177,15 +189,15 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF { ) ch_versions = ch_versions.mix(TABIX_TABIX.out.versions) - ch_vcf_tbi = ch_tabix_input.bgzip + def ch_vcf_tbi = ch_tabix_input.bgzip .join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true) .mix(ch_tabix_input.unzip) emit: vcf_tbi = ch_vcf_tbi // channel: [ val(meta), path(vcf), path(tbi) ] vep_reports = ch_vep_reports // channel: [ path(html) ] - snpeff_reports = ch_snpeff_reports // channel: [ path(csv) ] - snpeff_html = ch_snpeff_html // channel: [ path(html) ] - snpeff_genes = ch_snpeff_genes // channel: [ path(genes) ] + snpeff_reports = ch_snpeff_reports // channel: [ val(meta), path(csv) ] + snpeff_html = ch_snpeff_html // channel: [ val(meta), path(html) ] + snpeff_genes = ch_snpeff_genes // channel: [ val(meta), path(genes) ] versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml index 6fe096c078be..b0541d66e60d 100644 --- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/meta.yml @@ -8,9 +8,12 @@ keywords: - ensemblvep - snpeff components: + - ensemblvep/download - ensemblvep/vep + - snpeff/download - snpeff/snpeff - tabix/tabix + - tabix/bgzip - bcftools/pluginscatter - bcftools/concat - bcftools/sort @@ -42,7 +45,9 @@ input: Structure: [ path(file1), path(file2)... ] - val_snpeff_db: type: string - description: database to use for snpeff + description: | + database to use for snpeff, usually consists of the genome and the database version + e.g. WBcel235.105 - ch_snpeff_cache: description: | the root cache folder for snpeff (optional) @@ -60,10 +65,23 @@ output: description: | Compressed vcf file + tabix index Structure: [ val(meta), path(vcf), path(tbi) ] - - reports: + - vep_reports: type: file - description: html reports + description: html reports generated by Ensembl VEP pattern: "*.html" + - snpeff_reports: + description: | + csv reports generated by snpeff + Structure: [ val(meta), path(csv) ] + - snpeff_html: + description: | + html reports generated by snpeff + Structure: [ val(meta), path(html) ] + - snpeff_genes: + description: | + txt (tab separated) file having counts of the number of variants + affecting each transcript and gene + Structure: [ val(meta), path(txt) ] - versions: type: file description: File containing software versions diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test new file mode 100644 index 000000000000..e6d851e68f16 --- /dev/null +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test @@ -0,0 +1,332 @@ +nextflow_workflow { + + name "Test Subworkflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF" + script "../main.nf" + workflow "VCF_ANNOTATE_ENSEMBLVEP_SNPEFF" + + tag "subworkflows" + tag "subworkflows_nfcore" + tag "subworkflows/vcf_annotate_ensemblvep_snpeff" + tag "ensemblvep/download" + tag "ensemblvep/vep" + tag "snpeff/download" + tag "snpeff/snpeff" + tag "tabix/tabix" + tag "tabix/bgzip" + tag "bcftools/pluginscatter" + tag "bcftools/concat" + tag "bcftools/sort" + + config "./nextflow.config" + + test("sarscov2 - ensemblvep") { + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../../../modules/nf-core/ensemblvep/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235", + "caenorhabditis_elegans", + "110" + ] + """ + } + } + } + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'custom_test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true) + ] + ]) + input[1] = [[],[]] + input[2] = "WBcel235" + input[3] = "caenorhabditis_elegans" + input[4] = "110" + input[5] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } + input[6] = [] + input[7] = [] + input[8] = [] + input[9] = ["ensemblvep"] + input[10] = 5 + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.vcf_tbi.collect { [it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name] }, + workflow.out.vep_reports.collect { it instanceof String ? file(it).name : it }, + workflow.out.snpeff_reports.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_html.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_genes.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.versions.collect { it instanceof String ? file(it).name : it } + ).match()} + ) + } + } + + test("sarscov2 - snpeff") { + + setup { + run("SNPEFF_DOWNLOAD") { + script "../../../../modules/nf-core/snpeff/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235.105" + ] + """ + } + } + } + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true), + [] + ], + [ + [ id:'custom_test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true) + ] + ]) + input[1] = [[],[]] + input[2] = "WBcel235" + input[3] = "caenorhabditis_elegans" + input[4] = "110" + input[5] = [] + input[6] = [] + input[7] = "WBcel235.105" + input[8] = SNPEFF_DOWNLOAD.out.cache + input[9] = ["snpeff"] + input[10] = 5 + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.vcf_tbi.collect { [it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name] }, + workflow.out.vep_reports.collect { it instanceof String ? file(it).name : it }, + workflow.out.snpeff_reports.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_html.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_genes.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.versions.collect { it instanceof String ? file(it).name : it } + ).match()} + ) + } + } + + test("sarscov2 - snpeff + ensemblvep") { + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../../../modules/nf-core/ensemblvep/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235", + "caenorhabditis_elegans", + "110" + ] + """ + } + } + + run("SNPEFF_DOWNLOAD") { + script "../../../../modules/nf-core/snpeff/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235.105" + ] + """ + } + } + } + + when { + workflow { + """ + input[0] = Channel.of( [ + [ id:'custom_test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true) + ] + ]) + input[1] = [[],[]] + input[2] = "WBcel235" + input[3] = "caenorhabditis_elegans" + input[4] = "110" + input[5] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } + input[6] = [] + input[7] = "WBcel235.105" + input[8] = SNPEFF_DOWNLOAD.out.cache + input[9] = ["snpeff", "ensemblvep"] + input[10] = 5 + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.vcf_tbi.collect { [it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name] }, + workflow.out.vep_reports.collect { it instanceof String ? file(it).name : it }, + workflow.out.snpeff_reports.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_html.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_genes.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.versions.collect { it instanceof String ? file(it).name : it } + ).match()} + ) + } + } + + test("sarscov2 - ensemblvep - large chunks") { + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../../../modules/nf-core/ensemblvep/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235", + "caenorhabditis_elegans", + "110" + ] + """ + } + } + } + + when { + workflow { + """ + input[0] = Channel.of( [ + [ id:'custom_test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true) + ] + ]) + input[1] = [[],[]] + input[2] = "WBcel235" + input[3] = "caenorhabditis_elegans" + input[4] = "110" + input[5] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } + input[6] = [] + input[7] = [] + input[8] = [] + input[9] = ["ensemblvep"] + input[10] = 100 + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.vcf_tbi.collect { [it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name] }, + workflow.out.vep_reports.collect { it instanceof String ? file(it).name : it }, + workflow.out.snpeff_reports.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_html.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_genes.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.versions.collect { it instanceof String ? file(it).name : it } + ).match()} + ) + } + } + + test("sarscov2 - ensemblvep - no scatter") { + + setup { + run("ENSEMBLVEP_DOWNLOAD") { + script "../../../../modules/nf-core/ensemblvep/download" + process { + """ + input[0] = [ + [id:"reference"], + "WBcel235", + "caenorhabditis_elegans", + "110" + ] + """ + } + } + } + + when { + workflow { + """ + input[0] = Channel.of([ + [ id:'custom_test', single_end:false ], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test2.vcf.gz.tbi', checkIfExists: true), + [ + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test3.vcf.gz.tbi', checkIfExists: true) + ] + ]) + input[1] = [[],[]] + input[2] = "WBcel235" + input[3] = "caenorhabditis_elegans" + input[4] = "110" + input[5] = ENSEMBLVEP_DOWNLOAD.out.cache.map { meta, cache -> cache } + input[6] = [] + input[7] = [] + input[8] = [] + input[9] = ["ensemblvep"] + input[10] = [] + """ + } + } + + then { + assertAll( + { assert workflow.success}, + { assert snapshot( + workflow.out.vcf_tbi.collect { [it[0], "${file(it[1]).name},variantsMD5:${path(it[1]).vcf.variantsMD5}", file(it[2]).name] }, + workflow.out.vep_reports.collect { it instanceof String ? file(it).name : it }, + workflow.out.snpeff_reports.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_html.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.snpeff_genes.collect { it.collect { it instanceof String ? file(it).name : it } }, + workflow.out.versions.collect { it instanceof String ? file(it).name : it } + ).match()} + ) + } + } +} diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap new file mode 100644 index 000000000000..dcca7b566cde --- /dev/null +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap @@ -0,0 +1,338 @@ +{ + "sarscov2 - snpeff": { + "content": [ + [ + [ + { + "groupSize": 2, + "groupTarget": { + "id": "custom_test", + "single_end": false + } + }, + "custom_test.vcf.gz,variantsMD5:e9323877c6352459351537ac6539914a", + "custom_test.vcf.gz.tbi" + ], + [ + { + "groupSize": 2, + "groupTarget": { + "id": "test", + "single_end": false + } + }, + "test.vcf.gz,variantsMD5:e9323877c6352459351537ac6539914a", + "test.vcf.gz.tbi" + ] + ], + [ + + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "custom_test0_annotated.csv" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "custom_test1_annotated.csv" + ], + [ + { + "id": "test0_annotated", + "single_end": false + }, + "test0_annotated.csv" + ], + [ + { + "id": "test1_annotated", + "single_end": false + }, + "test1_annotated.csv" + ] + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "snpEff_summary.html" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "snpEff_summary.html" + ], + [ + { + "id": "test0_annotated", + "single_end": false + }, + "snpEff_summary.html" + ], + [ + { + "id": "test1_annotated", + "single_end": false + }, + "snpEff_summary.html" + ] + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "custom_test0_annotated.genes.txt" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "custom_test1_annotated.genes.txt" + ], + [ + { + "id": "test0_annotated", + "single_end": false + }, + "test0_annotated.genes.txt" + ], + [ + { + "id": "test1_annotated", + "single_end": false + }, + "test1_annotated.genes.txt" + ] + ], + [ + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T07:57:12.127577423" + }, + "sarscov2 - ensemblvep - large chunks": { + "content": [ + [ + [ + { + "groupSize": 1, + "groupTarget": { + "id": "custom_test", + "single_end": false + } + }, + "custom_test.vcf.gz,variantsMD5:370b92bc4c236a7b4c6d152319447af3", + "custom_test.vcf.gz.tbi" + ] + ], + [ + "custom_test0_annotated.vep.vcf.gz_summary.html" + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T08:30:06.857146079" + }, + "sarscov2 - snpeff + ensemblvep": { + "content": [ + [ + [ + { + "groupSize": 2, + "groupTarget": { + "id": "custom_test", + "single_end": false + } + }, + "custom_test.vcf.gz,variantsMD5:69492a5e9f3bf9d36aad9c14783c849d", + "custom_test.vcf.gz.tbi" + ] + ], + [ + "custom_test0_annotated.vep.vcf.gz_summary.html", + "custom_test1_annotated.vep.vcf.gz_summary.html" + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "custom_test0_annotated.csv" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "custom_test1_annotated.csv" + ] + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "snpEff_summary.html" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "snpEff_summary.html" + ] + ], + [ + [ + { + "id": "custom_test0_annotated", + "single_end": false + }, + "custom_test0_annotated.genes.txt" + ], + [ + { + "id": "custom_test1_annotated", + "single_end": false + }, + "custom_test1_annotated.genes.txt" + ] + ], + [ + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T08:29:31.390244289" + }, + "sarscov2 - ensemblvep - no scatter": { + "content": [ + [ + [ + { + "id": "custom_test", + "single_end": false + }, + "custom_test.vep.vcf.gz,variantsMD5:370b92bc4c236a7b4c6d152319447af3", + "custom_test.vep.vcf.gz.tbi" + ] + ], + [ + "custom_test.vep.vcf.gz_summary.html" + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml", + "versions.yml" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T08:30:32.047882286" + }, + "sarscov2 - ensemblvep": { + "content": [ + [ + [ + { + "groupSize": 2, + "groupTarget": { + "id": "custom_test", + "single_end": false + } + }, + "custom_test.vcf.gz,variantsMD5:370b92bc4c236a7b4c6d152319447af3", + "custom_test.vcf.gz.tbi" + ] + ], + [ + "custom_test0_annotated.vep.vcf.gz_summary.html", + "custom_test1_annotated.vep.vcf.gz_summary.html" + ], + [ + + ], + [ + + ], + [ + + ], + [ + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml", + "versions.yml" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-18T08:26:42.202930396" + } +} \ No newline at end of file diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/nextflow.config similarity index 79% rename from tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config rename to subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/nextflow.config index fa4f5b43091c..634ec18a79fb 100644 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/nextflow.config +++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/nextflow.config @@ -1,20 +1,15 @@ process { - - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: BCFTOOLS_CONCAT { ext.prefix = { "${meta.id}_concat" } } - withName: ENSEMBLVEP_DOWNLOAD { ext.args = '--AUTO c --CONVERT --NO_BIOPERL --NO_HTSLIB --NO_TEST --NO_UPDATE' } - withName: ENSEMBLVEP_VEP { + ext.prefix = { "${meta.id}.vep" } ext.args = {[ "--vcf --offline", meta.id.startsWith("custom_test") ? "--custom test3.vcf.gz,,vcf,exact,0,TOPMED" : "" ].join(" ")} } - } diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 27bfefee6f1a..babb50ac4c97 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -714,9 +714,6 @@ subworkflows/utils_nfcore_pipeline: subworkflows/vcf_annotate_ensemblvep: - subworkflows/nf-core/vcf_annotate_ensemblvep/** - tests/subworkflows/nf-core/vcf_annotate_ensemblvep/** -subworkflows/vcf_annotate_ensemblvep_snpeff: - - subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** - - tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/** subworkflows/vcf_annotate_snpeff: - subworkflows/nf-core/vcf_annotate_snpeff/** - tests/subworkflows/nf-core/vcf_annotate_snpeff/** diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf deleted file mode 100644 index ce160e4756b4..000000000000 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf +++ /dev/null @@ -1,202 +0,0 @@ -#!/usr/bin/env nextflow - -nextflow.enable.dsl = 2 - -include { ENSEMBLVEP_DOWNLOAD } from '../../../../modules/nf-core/ensemblvep/download/main' -include { SNPEFF_DOWNLOAD } from '../../../../modules/nf-core/snpeff/download/main' -include { VCF_ANNOTATE_ENSEMBLVEP_SNPEFF } from '../../../../subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main' - -snpeff_cache_version = "105" -snpeff_genome = "WBcel235" -snpeff_cache_input = Channel.of([[id:"${snpeff_genome}.${snpeff_cache_version}"], snpeff_genome, snpeff_cache_version]) -vep_cache_version = "110" -vep_genome = "WBcel235" -vep_species = "caenorhabditis_elegans" -vep_cache_input = Channel.of([[id:"${vep_cache_version}_${vep_genome}"], vep_genome, vep_species, vep_cache_version]) - -workflow vcf_annotate_ensemblvep_snpeff_vep { - input = Channel.of([ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - [] - ],[ - [ id:'custom_test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [ - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) - ] - ]) - - ENSEMBLVEP_DOWNLOAD(vep_cache_input) - - vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first() - - VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( - input, - [[],[]], - vep_genome, - vep_species, - vep_cache_version, - vep_cache, - [], - [], - [], - ["ensemblvep"], - 5 - ) -} - -workflow vcf_annotate_ensemblvep_snpeff_snpeff { - input = Channel.of([ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - [] - ],[ - [ id:'custom_test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [ - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) - ] - ]) - - SNPEFF_DOWNLOAD(snpeff_cache_input) - - snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() - - VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( - input, - [[],[]], - [], - [], - [], - [], - [], - "${snpeff_genome}.${snpeff_cache_version}", - snpeff_cache, - ["snpeff"], - 5 - ) -} - -workflow vcf_annotate_ensemblvep_snpeff_both { - input = Channel.of([ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - [] - ],[ - [ id:'custom_test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [ - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) - ] - ]) - - ENSEMBLVEP_DOWNLOAD(vep_cache_input) - SNPEFF_DOWNLOAD(snpeff_cache_input) - - snpeff_cache = SNPEFF_DOWNLOAD.out.cache.first() - vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first() - - VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( - input, - [[],[]], - vep_genome, - vep_species, - vep_cache_version, - vep_cache, - [], - "${snpeff_genome}.${snpeff_cache_version}", - snpeff_cache, - ["ensemblvep", "snpeff"], - 5 - ) -} - -workflow vcf_annotate_ensemblvep_snpeff_large_chunks { - input = Channel.of([ - [ id:'test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - [] - ],[ - [ id:'custom_test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [ - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) - ] - ]) - - fasta = Channel.value([ - [id:"fasta"], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ]) - - ENSEMBLVEP_DOWNLOAD(vep_cache_input) - - vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first() - - VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( - input, - fasta, - vep_genome, - vep_species, - vep_cache_version, - vep_cache, - [], - [], - [], - ["ensemblvep"], - 100 - ) -} - -workflow vcf_annotate_ensemblvep_snpeff_no_scatter { - input = Channel.of([ - [ id:'test1' ], // meta map - file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true), - [] - ],[ - [ id:'custom_test' ], // meta map - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test2_vcf_gz_tbi'], checkIfExists: true), - [ - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz'], checkIfExists: true), - file(params.test_data['sarscov2']['illumina']['test3_vcf_gz_tbi'], checkIfExists: true) - ] - ]) - - fasta = Channel.value([ - [id:"fasta"], - file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) - ]) - - ENSEMBLVEP_DOWNLOAD(vep_cache_input) - - vep_cache = ENSEMBLVEP_DOWNLOAD.out.cache.map{ meta, cache -> [cache] }.first() - - VCF_ANNOTATE_ENSEMBLVEP_SNPEFF ( - input, - fasta, - vep_genome, - vep_species, - vep_cache_version, - vep_cache, - [], - [], - [], - ["ensemblvep"], - [] - ) -} diff --git a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml b/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml deleted file mode 100644 index 92fa202cb90d..000000000000 --- a/tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/test.yml +++ /dev/null @@ -1,384 +0,0 @@ -- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_vep - command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_vep -c ./tests/config/nextflow.config - tags: - - bcftools - - bcftools/concat - - bcftools/pluginscatter - - bcftools/sort - - ensemblvep - - ensemblvep/vep - - snpeff - - snpeff/snpeff - - subworkflows - - subworkflows/vcf_annotate_ensemblvep_snpeff - - tabix - - tabix/tabix - files: - - path: output/bcftools/custom_test.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test0.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test1.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test_concat.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test0.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test1.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test_concat.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/ensemblvep/custom_test0_annotated.summary.html - contains: - - "" - - "" - - path: output/ensemblvep/custom_test0_annotated.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/ensemblvep/custom_test1_annotated.summary.html - contains: - - "" - - "" - - path: output/ensemblvep/custom_test1_annotated.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/ensemblvep/test0_annotated.summary.html - contains: - - "" - - "" - - path: output/ensemblvep/test0_annotated.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/ensemblvep/test1_annotated.summary.html - contains: - - "" - - "" - - path: output/ensemblvep/test1_annotated.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/tabix/custom_test.vcf.gz.tbi - - path: output/tabix/test.vcf.gz.tbi -- name: vcf_annotate_ensemblvep_snpeff vcf_annotate_ensemblvep_snpeff_snpeff - command: nextflow run ./tests/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff -entry vcf_annotate_ensemblvep_snpeff_snpeff -c ./tests/config/nextflow.config - tags: - - bcftools - - bcftools/concat - - bcftools/pluginscatter - - bcftools/sort - - ensemblvep - - ensemblvep/vep - - snpeff - - snpeff/snpeff - - subworkflows - - subworkflows/vcf_annotate_ensemblvep_snpeff - - tabix - - tabix/tabix - files: - - path: output/bcftools/custom_test.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test0.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test1.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/custom_test_concat.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test0.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test1.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/bcftools/test_concat.vcf.gz - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/snpeff/custom_test0_annotated.ann.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/snpeff/custom_test0_annotated.csv - contains: - - "# Summary table" - - path: output/snpeff/custom_test0_annotated.genes.txt - md5sum: 130536bf0237d7f3f746d32aaa32840a - - path: output/snpeff/custom_test1_annotated.ann.vcf - contains: - - "##fileformat=VCFv4.2" - - '##FILTER=' - - path: output/snpeff/custom_test1_annotated.csv - contains: - - "# Summary table" - - path: output/snpeff/custom_test1_annotated.genes.txt - md5sum: 130536bf0237d7f3f746d32aaa32840a - - path: output/snpeff/snpEff_summary.html - contains: - - '