diff --git a/modules.json b/modules.json index d9db588..ea627ba 100644 --- a/modules.json +++ b/modules.json @@ -7,28 +7,28 @@ "nf-core": { "fastqc": { "branch": "master", - "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", + "git_sha": "46eca555142d6e597729fcb682adcc791796f514", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "b80f5fd12ff7c43938f424dd76392a2704fa2396", "installed_by": ["modules"] }, "quartonotebook": { "branch": "master", - "git_sha": "93b7e1bf63944488fe77ad490a9de62a73959bed", + "git_sha": "04e1b2340f6cf9cd7b9b06fb7d86da4531714519", "installed_by": ["modules"], "patch": "modules/nf-core/quartonotebook/quartonotebook.diff" }, "spaceranger/count": { "branch": "master", - "git_sha": "2f0ef0cd414ea43e33625023c72b6af936dce63d", + "git_sha": "238b3efbbd113529d19ec866eba545911bc27682", "installed_by": ["modules"] }, "untar": { "branch": "master", - "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", + "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", "installed_by": ["modules"] } } diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test index 70edae4..e9d79a0 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ b/modules/nf-core/fastqc/tests/main.nf.test @@ -23,17 +23,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } + { assert process.success }, + // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. + // looks like this:
Mon 2 Oct 2023
test.gz
+ // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -54,16 +51,14 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -83,13 +78,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -109,13 +102,11 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -138,22 +129,20 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, - { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } + { assert process.success }, + { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, + { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, + { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, + { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, + { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, + { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, + { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, + { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, + { assert path(process.out.html[0][1][0]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][1]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][2]).text.contains("File typeConventional base calls") }, + { assert path(process.out.html[0][1][3]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } @@ -173,21 +162,18 @@ nextflow_process { then { assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } + { assert process.success }, + { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, + { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, + { assert path(process.out.html[0][1]).text.contains("File typeConventional base calls") }, + { assert snapshot(process.out.versions).match() } ) } } test("sarscov2 single-end [fastq] - stub") { - options "-stub" - + options "-stub" when { process { """ @@ -201,12 +187,123 @@ nextflow_process { then { assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } + { assert process.success }, + { assert snapshot(process.out).match() } ) } } + test("sarscov2 paired-end [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [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(process.out).match() } + ) + } + } + + test("sarscov2 interleaved [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [id: 'test', single_end: false], // meta map + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 paired-end [bam] - stub") { + + options "-stub" + when { + 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) + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 multiple [fastq] - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [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), + 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/test2_2.fastq.gz', checkIfExists: true) ] + ]) + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("sarscov2 custom_prefix - stub") { + + options "-stub" + when { + process { + """ + input[0] = Channel.of([ + [ id:'mysample', 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/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap index 86f7c31..d5db309 100644 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ b/modules/nf-core/fastqc/tests/main.nf.test.snap @@ -1,88 +1,392 @@ { - "fastqc_versions_interleaved": { + "sarscov2 custom_prefix": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:07.293713" + "timestamp": "2024-07-22T11:02:16.374038" }, - "fastqc_stub": { + "sarscov2 single-end [fastq] - stub": { "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": true + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": true + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:24.993809" + }, + "sarscov2 custom_prefix - stub": { + "content": [ + { + "0": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "mysample", + "single_end": true + }, + "mysample.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:31:01.425198" + "timestamp": "2024-07-22T11:03:10.93942" }, - "fastqc_versions_multiple": { + "sarscov2 interleaved [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:55.797907" + "timestamp": "2024-07-22T11:01:42.355718" }, - "fastqc_versions_bam": { + "sarscov2 paired-end [bam]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:40:26.795862" + "timestamp": "2024-07-22T11:01:53.276274" }, - "fastqc_versions_single": { + "sarscov2 multiple [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:27.043675" + "timestamp": "2024-07-22T11:02:05.527626" }, - "fastqc_versions_paired": { + "sarscov2 paired-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:31.188871" + }, + "sarscov2 paired-end [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:34.273566" + }, + "sarscov2 multiple [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:39:47.584191" + "timestamp": "2024-07-22T11:03:02.304411" }, - "fastqc_versions_custom_prefix": { + "sarscov2 single-end [fastq]": { "content": [ [ "versions.yml:md5,e1cc25ca8af856014824abd842e93978" ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:01:19.095607" + }, + "sarscov2 interleaved [fastq] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-22T11:02:44.640184" + }, + "sarscov2 paired-end [bam] - stub": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "2": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "html": [ + [ + { + "id": "test", + "single_end": false + }, + "test.html:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ], + "versions": [ + "versions.yml:md5,e1cc25ca8af856014824abd842e93978" + ], + "zip": [ + [ + { + "id": "test", + "single_end": false + }, + "test.zip:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.3" }, - "timestamp": "2024-01-31T17:41:14.576531" + "timestamp": "2024-07-22T11:02:53.550742" } } \ No newline at end of file diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml index ca39fb6..2121492 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.23 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352..459dfea 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -3,14 +3,16 @@ process MULTIQC { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.23--pyhdfd78af_0' : + 'biocontainers/multiqc:1.23--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) + path(replace_names) + path(sample_names) output: path "*multiqc_report.html", emit: report @@ -26,6 +28,8 @@ process MULTIQC { def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' + def replace = replace_names ? "--replace-names ${replace_names}" : '' + def samples = sample_names ? "--sample-names ${sample_names}" : '' """ multiqc \\ --force \\ @@ -33,6 +37,8 @@ process MULTIQC { $config \\ $extra_config \\ $logo \\ + $replace \\ + $samples \\ . cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index 45a9bc3..382c08c 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -29,6 +29,19 @@ input: 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 diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test index f1c4242..6aa27f4 100644 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -17,6 +17,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -41,6 +43,8 @@ nextflow_process { input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } @@ -66,6 +70,8 @@ nextflow_process { input[1] = [] input[2] = [] input[3] = [] + input[4] = [] + input[5] = [] """ } } diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap index 7c3ff58..45e95e5 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:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:48:55.657331" + "timestamp": "2024-07-10T12:41:34.562023" }, "multiqc_stub": { "content": [ @@ -17,25 +17,25 @@ "multiqc_report.html", "multiqc_data", "multiqc_plots", - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:49.071937" + "timestamp": "2024-07-10T11:27:11.933869532" }, "multiqc_versions_config": { "content": [ [ - "versions.yml:md5,21f35ee29416b9b3073c28733efe4b7d" + "versions.yml:md5,87904cd321df21fac35d18f0fc01bb19" ] ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.2" }, - "timestamp": "2024-02-29T08:49:25.457567" + "timestamp": "2024-07-10T11:26:56.709849369" } -} +} \ No newline at end of file diff --git a/modules/nf-core/quartonotebook/tests/main.nf.test b/modules/nf-core/quartonotebook/tests/main.nf.test index aeec8b1..4fa0ac2 100644 --- a/modules/nf-core/quartonotebook/tests/main.nf.test +++ b/modules/nf-core/quartonotebook/tests/main.nf.test @@ -17,7 +17,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook + file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook ] input[1] = [:] // Parameters input[2] = [] // Input files @@ -44,7 +44,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook + file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook ] input[1] = [] // Parameters input[2] = [] // Input files @@ -76,10 +76,10 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook + file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook ] input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters - input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files + input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files input[3] = [] // Extensions """ } @@ -103,10 +103,10 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['quarto_python'], checkIfExists: true) // Notebook + file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_python.qmd', checkIfExists: true) // Notebook ] input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters - input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files + input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files input[3] = [] // Extensions """ } @@ -135,10 +135,10 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['rmarkdown'], checkIfExists: true) // notebook + file(params.modules_testdata_base_path + 'generic/notebooks/rmarkdown/rmarkdown_notebook.Rmd', checkIfExists: true) // notebook ] input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters - input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files + input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files input[3] = [] // Extensions """ } @@ -162,10 +162,10 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['ipython_ipynb'], checkIfExists: true) // notebook + file(params.modules_testdata_base_path + 'generic/notebooks/jupyter/ipython_notebook.ipynb', checkIfExists: true) // notebook ] input[1] = [input_filename: "hello.txt", n_iter: 12] // parameters - input[2] = file(params.test_data['generic']['txt']['hello'], checkIfExists: true) // Input files + input[2] = file(params.modules_testdata_base_path + 'generic/txt/hello.txt', checkIfExists: true) // Input files input[3] = [] // Extensions """ } @@ -191,7 +191,7 @@ nextflow_process { """ input[0] = [ [ id:'test' ], // meta map - file(params.test_data['generic']['notebooks']['quarto_r'], checkIfExists: true) // Notebook + file(params.modules_testdata_base_path + 'generic/notebooks/quarto/quarto_r.qmd', checkIfExists: true) // Notebook ] input[1] = [:] // Parameters input[2] = [] // Input files diff --git a/modules/nf-core/spaceranger/count/tests/main.nf.test b/modules/nf-core/spaceranger/count/tests/main.nf.test index 7631d85..2be6525 100644 --- a/modules/nf-core/spaceranger/count/tests/main.nf.test +++ b/modules/nf-core/spaceranger/count/tests/main.nf.test @@ -19,7 +19,7 @@ nextflow_process { script "../../mkgtf/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } } @@ -30,8 +30,8 @@ nextflow_process { script "../../mkref/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = 'homo_sapiens_chr22_reference' """ } @@ -48,10 +48,10 @@ nextflow_process { area: 'D1' ], // Meta map [ - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_fastq_1_gz']), - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_fastq_2_gz']) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz', checkIfExists: true) ], // Reads - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_image']), // Image + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg', checkIfExists: true), // Image [], // Cytaimage [], // Darkimage [], // Colorizedimage @@ -94,7 +94,7 @@ nextflow_process { script "../../mkgtf/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } } @@ -105,8 +105,8 @@ nextflow_process { script "../../mkref/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = 'homo_sapiens_chr22_reference' """ } @@ -125,10 +125,10 @@ nextflow_process { area: 'D1' ], // Meta map [ - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_fastq_1_gz']), - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_fastq_2_gz']) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R1_001.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_S1_L001_R2_001.fastq.gz', checkIfExists: true) ], // Reads - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_v1_image']), // Image + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-ovarian-cancer-1-standard_v1_ffpe/Visium_FFPE_Human_Ovarian_Cancer_image.jpg', checkIfExists: true), // Image [], // Cytaimage [], // Darkimage [], // Colorizedimage @@ -155,7 +155,7 @@ nextflow_process { script "../../mkgtf/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) """ } } @@ -166,8 +166,8 @@ nextflow_process { script "../../mkref/main.nf" process { """ - input[0] = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - input[1] = file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) + input[0] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) + input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) input[2] = 'homo_sapiens_chr22_reference' """ } @@ -184,18 +184,18 @@ nextflow_process { area: 'B1' ], // Meta map [ - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_cytassist_fastq_1_gz']), - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_cytassist_fastq_2_gz']) + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R1_001.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_2_S1_L001_R2_001.fastq.gz', checkIfExists: true) ], // Reads [], // Image - file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_cytassist_image']), // Cytaimage + file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_image.tif', checkIfExists: true), // Cytaimage [], // Darkimage [], // Colorizedimage [], // Manual alignment (default: automatic alignment) file('https://s3.us-west-2.amazonaws.com/10x.spatial-slides/gpr/V52Y10/V52Y10-317.gpr') // Slide specification (default: automatic download) ] input[1] = SPACERANGER_MKREF.out.reference // Reference - input[2] = file(params.test_data['homo_sapiens']['10xgenomics']['spaceranger']['test_10x_ffpe_cytassist_probeset']) // Probeset (default: use the one included with Space Ranger) + input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/10xgenomics/spaceranger/human-brain-cancer-11-mm-capture-area-ffpe-2-standard_v2_ffpe_cytassist/CytAssist_11mm_FFPE_Human_Glioblastoma_probe_set.csv', checkIfExists: true) // Probeset (default: use the one included with Space Ranger) """ } } diff --git a/modules/nf-core/untar/environment.yml b/modules/nf-core/untar/environment.yml index 0c9cbb1..4f49824 100644 --- a/modules/nf-core/untar/environment.yml +++ b/modules/nf-core/untar/environment.yml @@ -1,11 +1,9 @@ name: untar - channels: - conda-forge - bioconda - defaults - dependencies: - conda-forge::grep=3.11 - - conda-forge::sed=4.7 + - conda-forge::sed=4.8 - conda-forge::tar=1.34 diff --git a/modules/nf-core/untar/main.nf b/modules/nf-core/untar/main.nf index 8a75bb9..9bd8f55 100644 --- a/modules/nf-core/untar/main.nf +++ b/modules/nf-core/untar/main.nf @@ -4,8 +4,8 @@ process UNTAR { conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : - 'nf-core/ubuntu:20.04' }" + 'https://depot.galaxyproject.org/singularity/ubuntu:22.04' : + 'nf-core/ubuntu:22.04' }" input: tuple val(meta), path(archive) @@ -52,8 +52,29 @@ process UNTAR { stub: prefix = task.ext.prefix ?: ( meta.id ? "${meta.id}" : archive.toString().replaceFirst(/\.[^\.]+(.gz)?$/, "")) """ - mkdir $prefix - touch ${prefix}/file.txt + mkdir ${prefix} + ## Dry-run untaring the archive to get the files and place all in prefix + if [[ \$(tar -taf ${archive} | grep -o -P "^.*?\\/" | uniq | wc -l) -eq 1 ]]; then + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch \${i} + else + mkdir -p \${i} + fi + done + else + for i in `tar -tf ${archive}`; + do + if [[ \$(echo "\${i}" | grep -E "/\$") == "" ]]; + then + touch ${prefix}/\${i} + else + mkdir -p ${prefix}/\${i} + fi + done + fi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/untar/tests/main.nf.test b/modules/nf-core/untar/tests/main.nf.test index 2a7c97b..c957517 100644 --- a/modules/nf-core/untar/tests/main.nf.test +++ b/modules/nf-core/untar/tests/main.nf.test @@ -6,6 +6,7 @@ nextflow_process { tag "modules" tag "modules_nfcore" tag "untar" + test("test_untar") { when { @@ -19,10 +20,9 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar") }, + { assert snapshot(process.out).match() }, ) } - } test("test_untar_onlyfiles") { @@ -38,10 +38,48 @@ nextflow_process { then { assertAll ( { assert process.success }, - { assert snapshot(process.out.untar).match("test_untar_onlyfiles") }, + { assert snapshot(process.out).match() }, ) } + } + + test("test_untar - stub") { + + options "-stub" + when { + process { + """ + input[0] = [ [], 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_untar_onlyfiles - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ [], file(params.modules_testdata_base_path + 'generic/tar/hello.tar.gz', checkIfExists: true) ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out).match() }, + ) + } + } } diff --git a/modules/nf-core/untar/tests/main.nf.test.snap b/modules/nf-core/untar/tests/main.nf.test.snap index 6455029..ceb91b7 100644 --- a/modules/nf-core/untar/tests/main.nf.test.snap +++ b/modules/nf-core/untar/tests/main.nf.test.snap @@ -1,42 +1,158 @@ { "test_untar_onlyfiles": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:28.231047" + }, + "test_untar_onlyfiles - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hello.txt:md5,e59ff97941044f85df5297e1c302d260" + [ + + ], + [ + "hello.txt:md5,d41d8cd98f00b204e9800998ecf8427e" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:41.320643" + "timestamp": "2024-07-10T12:04:45.773103" + }, + "test_untar - stub": { + "content": [ + { + "0": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ + [ + [ + + ], + [ + "hash.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "opts.k2d:md5,d41d8cd98f00b204e9800998ecf8427e", + "taxo.k2d:md5,d41d8cd98f00b204e9800998ecf8427e" + ] + ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ] + } + ], + "meta": { + "nf-test": "0.8.4", + "nextflow": "24.04.3" + }, + "timestamp": "2024-07-10T12:04:36.777441" }, "test_untar": { "content": [ - [ - [ + { + "0": [ [ - - ], + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] + ] + ], + "1": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" + ], + "untar": [ [ - "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", - "opts.k2d:md5,a033d00cf6759407010b21700938f543", - "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + [ + + ], + [ + "hash.k2d:md5,8b8598468f54a7087c203ad0190555d9", + "opts.k2d:md5,a033d00cf6759407010b21700938f543", + "taxo.k2d:md5,094d5891cdccf2f1468088855c214b2c" + ] ] + ], + "versions": [ + "versions.yml:md5,6063247258c56fd271d076bb04dd7536" ] - ] + } ], "meta": { "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nextflow": "24.04.3" }, - "timestamp": "2024-02-28T11:49:33.795172" + "timestamp": "2024-07-10T12:04:19.377674" } } \ No newline at end of file diff --git a/tests/pipeline/test_downstream.nf.test.snap b/tests/pipeline/test_downstream.nf.test.snap index 8e1a3d2..b99dead 100644 --- a/tests/pipeline/test_downstream.nf.test.snap +++ b/tests/pipeline/test_downstream.nf.test.snap @@ -1,7 +1,7 @@ { "nf_core_pipeline_software_mqc_versions.yml": { "content": [ - "{CLUSTERING={quarto=1.3.450, papermill=null}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_DOWNSTREAM_INPUT={untar=1.3}, Workflow={nf-core/spatialvi=v1.0dev}}" + "{CLUSTERING={quarto=1.3.450, papermill=null}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_UNTAR_REFERENCE={untar=1.34}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_DOWNSTREAM_INPUT={untar=1.34}, Workflow={nf-core/spatialvi=v1.0dev}}" ], "meta": { "nf-test": "0.8.4", @@ -9,4 +9,4 @@ }, "timestamp": "2024-03-19T18:46:59.035976" } -} \ No newline at end of file +} diff --git a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap index bc10f4c..7b91971 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v1.nf.test.snap @@ -1,7 +1,7 @@ { "software_versions": { "content": [ - "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.30}, CLUSTERING={quarto=1.3.302, scanpy=1.9.3}, QUALITY_CONTROLS={quarto=1.3.302, scanpy=1.9.3}, READ_DATA={scanpy=1.7.2}, SPATIAL_DE={SpatialDE=1.1.3, leidenalg=0.9.1, quarto=1.3.302, scanpy=1.9.3}, Workflow={nf-core/spatialvi=1.0dev}}" + "{CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, FASTQC={fastqc=0.12.1}, SPACERANGER_COUNT={spaceranger=2.1.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.34}, CLUSTERING={quarto=1.3.302, scanpy=1.9.3}, QUALITY_CONTROLS={quarto=1.3.302, scanpy=1.9.3}, READ_DATA={scanpy=1.7.2}, SPATIAL_DE={SpatialDE=1.1.3, leidenalg=0.9.1, quarto=1.3.302, scanpy=1.9.3}, Workflow={nf-core/spatialvi=1.0dev}}" ], "meta": { "nf-test": "0.8.4", @@ -11,7 +11,7 @@ }, "nf_core_pipeline_software_mqc_versions.yml": { "content": [ - "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialvi=v1.0dev}}" + "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.34}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.34}, Workflow={nf-core/spatialvi=v1.0dev}}" ], "meta": { "nf-test": "0.8.4", diff --git a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap index 8a82bd8..a245c7f 100644 --- a/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap +++ b/tests/pipeline/test_spaceranger_ffpe_v2_cytassist.nf.test.snap @@ -1,7 +1,7 @@ { "nf_core_pipeline_software_mqc_versions.yml": { "content": [ - "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.3}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.3}, Workflow={nf-core/spatialvi=v1.0dev}}" + "{CLUSTERING={quarto=1.3.450, papermill=null}, FASTQC={fastqc=0.12.1}, QUALITY_CONTROLS={quarto=1.3.450, papermill=null}, READ_DATA={spatialdata_io=0.1.2}, SPACERANGER_COUNT={spaceranger=3.0.0}, SPACERANGER_UNTAR_REFERENCE={untar=1.34}, SPATIALLY_VARIABLE_GENES={quarto=1.3.450, papermill=null}, UNTAR_SPACERANGER_INPUT={untar=1.34}, Workflow={nf-core/spatialvi=v1.0dev}}" ], "meta": { "nf-test": "0.8.4", @@ -9,4 +9,4 @@ }, "timestamp": "2024-04-04T10:42:54.76102" } -} \ No newline at end of file +} diff --git a/workflows/spatialvi.nf b/workflows/spatialvi.nf index cc2c4cd..7f611fe 100644 --- a/workflows/spatialvi.nf +++ b/workflows/spatialvi.nf @@ -130,7 +130,9 @@ workflow SPATIALVI { ch_multiqc_files.collect(), ch_multiqc_config.toList(), ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() + ch_multiqc_logo.toList(), + [], + [], ) emit: