From 24d45182054e26a0ede6ff5105895fa356fd22ef Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 11 Oct 2024 11:24:30 +0200 Subject: [PATCH 1/3] bump all modules --- modules.json | 74 +++--- modules/nf-core/bcftools/annotate/meta.yml | 91 ++++---- modules/nf-core/bcftools/norm/meta.yml | 102 +++++---- .../nf-core/bcftools/pluginscatter/meta.yml | 127 ++++++----- modules/nf-core/bcftools/query/meta.yml | 82 +++---- modules/nf-core/bcftools/reheader/meta.yml | 91 ++++---- modules/nf-core/bcftools/sort/meta.yml | 71 +++--- modules/nf-core/bcftools/stats/meta.yml | 124 ++++++---- modules/nf-core/bedtools/intersect/meta.yml | 70 +++--- .../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 + modules/nf-core/bedtools/merge/meta.yml | 46 ++-- modules/nf-core/bedtools/split/meta.yml | 48 ++-- .../download/ensemblvep-download.diff | 13 +- modules/nf-core/ensemblvep/download/meta.yml | 56 +++-- .../ensemblvep/vep/ensemblvep-vep.diff | 12 +- .../nf-core/ensemblvep/vep/environment.yml | 1 - modules/nf-core/ensemblvep/vep/meta.yml | 148 ++++++------ .../gatk4/calibratedragstrmodel/meta.yml | 95 ++++---- .../gatk4/composestrtablefile/meta.yml | 45 ++-- .../gatk4/createsequencedictionary/meta.yml | 37 +-- .../nf-core/gatk4/genomicsdbimport/meta.yml | 139 ++++++++---- modules/nf-core/gatk4/genotypegvcfs/meta.yml | 170 +++++++------- modules/nf-core/gatk4/haplotypecaller/main.nf | 1 + .../nf-core/gatk4/haplotypecaller/meta.yml | 178 ++++++++------- modules/nf-core/gawk/meta.yml | 56 +++-- modules/nf-core/mosdepth/meta.yml | 214 ++++++++++++------ modules/nf-core/rtgtools/format/meta.yml | 69 +++--- modules/nf-core/rtgtools/pedfilter/meta.yml | 52 +++-- modules/nf-core/rtgtools/rocplot/meta.yml | 63 +++--- .../rtgtools/rocplot/tests/main.nf.test | 4 +- .../nf-core/samtools/convert/environment.yml | 6 +- modules/nf-core/samtools/convert/main.nf | 4 +- modules/nf-core/samtools/convert/meta.yml | 111 +++++---- .../samtools/convert/tests/main.nf.test.snap | 26 +-- .../nf-core/samtools/faidx/environment.yml | 10 +- modules/nf-core/samtools/faidx/main.nf | 4 +- modules/nf-core/samtools/faidx/meta.yml | 85 ++++--- .../samtools/faidx/tests/main.nf.test.snap | 50 ++-- .../nf-core/samtools/index/environment.yml | 6 +- modules/nf-core/samtools/index/main.nf | 4 +- modules/nf-core/samtools/index/meta.yml | 68 +++--- .../samtools/index/tests/main.nf.test.snap | 46 ++-- .../nf-core/samtools/merge/environment.yml | 6 +- modules/nf-core/samtools/merge/main.nf | 4 +- modules/nf-core/samtools/merge/meta.yml | 117 ++++++---- .../samtools/merge/tests/main.nf.test.snap | 32 +-- modules/nf-core/snpeff/snpeff/meta.yml | 96 +++++--- .../nf-core/snpeff/snpeff/tests/main.nf.test | 4 +- .../snpeff/snpeff/tests/nextflow.config | 3 +- modules/nf-core/somalier/extract/meta.yml | 109 ++++----- modules/nf-core/somalier/relate/meta.yml | 85 ++++--- 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/main.nf | 5 +- modules/nf-core/tabix/bgziptabix/meta.yml | 70 +++--- .../tabix/bgziptabix/tests/main.nf.test | 29 +++ .../tabix/bgziptabix/tests/main.nf.test.snap | 73 ++++-- modules/nf-core/tabix/tabix/environment.yml | 3 - modules/nf-core/tabix/tabix/meta.yml | 55 +++-- modules/nf-core/untar/environment.yml | 2 - modules/nf-core/untar/meta.yml | 43 ++-- modules/nf-core/vardictjava/main.nf | 12 +- modules/nf-core/vardictjava/meta.yml | 98 ++++---- .../nf-core/vardictjava/tests/main.nf.test | 77 ++++++- .../vardictjava/tests/main.nf.test.snap | 78 ++++++- .../nf-core/vardictjava/tests/nextflow.config | 3 + modules/nf-core/vcf2db/meta.yml | 53 +++-- modules/nf-core/vcfanno/meta.yml | 86 +++---- 72 files changed, 2495 insertions(+), 1604 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 create mode 100644 modules/nf-core/vardictjava/tests/nextflow.config diff --git a/modules.json b/modules.json index 82de0068..3b79c49f 100644 --- a/modules.json +++ b/modules.json @@ -7,7 +7,7 @@ "nf-core": { "bcftools/annotate": { "branch": "master", - "git_sha": "88ae68490e8f2478a1e1bbeedac970fd7cc73022", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/bcftools/annotate/bcftools-annotate.diff" }, @@ -23,99 +23,99 @@ }, "bcftools/norm": { "branch": "master", - "git_sha": "f6cc00f107826cfaf1c933297b10ed1757b41479", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/pluginscatter": { "branch": "master", - "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/query": { "branch": "master", - "git_sha": "34ac993e081b32d2170ab790d0386b74122f9d36", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/reheader": { "branch": "master", - "git_sha": "c32611ac6813055b9321d2827678e2f8aebcb394", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bcftools/sort": { "branch": "master", - "git_sha": "cdf83b18471db290a28fe98c2a0852cb05864890", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "bcftools/stats": { "branch": "master", - "git_sha": "a5ba4d59c2b248c0379b0f8aeb4e7e754566cd1f", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/intersect": { "branch": "master", - "git_sha": "06c8865e36741e05ad32ef70ab3fac127486af48", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/merge": { "branch": "master", - "git_sha": "a3d614e4a7b8691a259bcfe33ad80903217d6215", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "bedtools/split": { "branch": "master", - "git_sha": "6dc8a32e32158bb4d3f9af92c802233b5d4f8e4d", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "ensemblvep/download": { "branch": "master", - "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/ensemblvep/download/ensemblvep-download.diff" }, "ensemblvep/vep": { "branch": "master", - "git_sha": "54c183cba37cac58860d9967feaae54acf9cc3e0", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["vcf_annotate_ensemblvep_snpeff"], "patch": "modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff" }, "gatk4/calibratedragstrmodel": { "branch": "master", - "git_sha": "3f42e07a1133064c569b0dbe182979527bca9e59", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gatk4/composestrtablefile": { "branch": "master", - "git_sha": "926e2f394d01c71d3abbdbca9c588630bfe51abf", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gatk4/createsequencedictionary": { "branch": "master", - "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gatk4/genomicsdbimport": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gatk4/genotypegvcfs": { "branch": "master", - "git_sha": "8b74c800af3d91e0d7bfbecb902308dc4369071c", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gatk4/haplotypecaller": { "branch": "master", - "git_sha": "c332ea831f95f750be962c4b5de655f7a1e6e245", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "gawk": { "branch": "master", - "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "mosdepth": { "branch": "master", - "git_sha": "9bfc81874554e87740bcb3e5e07acf0a153c9ecb", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "multiqc": { @@ -125,18 +125,18 @@ }, "rtgtools/format": { "branch": "master", - "git_sha": "e743b2dea725bcfc4b76a209981808987332013a", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "rtgtools/pedfilter": { "branch": "master", - "git_sha": "c1c2a770cfb0bfbf093a2434a27f091ebbc65987", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/rtgtools/pedfilter/rtgtools-pedfilter.diff" }, "rtgtools/rocplot": { "branch": "master", - "git_sha": "64770369d851c45c364e410e052ef9a6c3a7d2bb", + "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd", "installed_by": ["modules"] }, "rtgtools/vcfeval": { @@ -146,73 +146,73 @@ }, "samtools/convert": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "46eca555142d6e597729fcb682adcc791796f514", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "samtools/merge": { "branch": "master", - "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519", + "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208", "installed_by": ["modules"] }, "snpeff/snpeff": { "branch": "master", - "git_sha": "3ad7292d9b8da881386e9d5b58364d7da489b38b", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["vcf_annotate_ensemblvep_snpeff"] }, "somalier/extract": { "branch": "master", - "git_sha": "458c882987320e27fc90723ec96c127a243a5497", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "somalier/relate": { "branch": "master", - "git_sha": "458c882987320e27fc90723ec96c127a243a5497", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"], "patch": "modules/nf-core/somalier/relate/somalier-relate.diff" }, "tabix/bgzip": { "branch": "master", - "git_sha": "b20be35facfc5acdc1259f132ed79339d79e989f", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "tabix/bgziptabix": { "branch": "master", - "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", + "git_sha": "f448e846bdadd80fc8be31fbbc78d9f5b5131a45", "installed_by": ["modules"] }, "tabix/tabix": { "branch": "master", - "git_sha": "0840b387799172e77510393ed09e4d4ec1bc6d7c", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules", "vcf_annotate_ensemblvep_snpeff"] }, "untar": { "branch": "master", - "git_sha": "4e5f4687318f24ba944a13609d3ea6ebd890737d", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "vardictjava": { "branch": "master", - "git_sha": "e61e5a13ef49c5595986bd31efb85c3f0709a282", + "git_sha": "f85452fcbebab5dfd77c0752236f6f86e9a03b32", "installed_by": ["modules"] }, "vcf2db": { "branch": "master", - "git_sha": "730f3aee80d5f8d0b5fc532202ac59361414d006", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] }, "vcfanno": { "branch": "master", - "git_sha": "9a8bba5910982ae637dedb8664e3121db77e173f", + "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", "installed_by": ["modules"] } } diff --git a/modules/nf-core/bcftools/annotate/meta.yml b/modules/nf-core/bcftools/annotate/meta.yml index 248eee0c..5bfccd2b 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/norm/meta.yml b/modules/nf-core/bcftools/norm/meta.yml index a0cdeaf1..b6edeb4a 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/pluginscatter/meta.yml b/modules/nf-core/bcftools/pluginscatter/meta.yml index 71805c03..5a31dacc 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/query/meta.yml b/modules/nf-core/bcftools/query/meta.yml index 303ef610..279b3205 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 d903cc0f..47e5344c 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/sort/meta.yml b/modules/nf-core/bcftools/sort/meta.yml index dfbddcba..f7a6eff1 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/stats/meta.yml b/modules/nf-core/bcftools/stats/meta.yml index 7ea2103e..655a61c5 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/bedtools/intersect/meta.yml b/modules/nf-core/bedtools/intersect/meta.yml index 0939cb54..45ecf377 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/intersect/tests/main.nf.test b/modules/nf-core/bedtools/intersect/tests/main.nf.test new file mode 100644 index 00000000..cd770946 --- /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 00000000..b748dd49 --- /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 00000000..f1f9e693 --- /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 00000000..6219cc40 --- /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/modules/nf-core/bedtools/merge/meta.yml b/modules/nf-core/bedtools/merge/meta.yml index d7463e3d..6da54205 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/split/meta.yml b/modules/nf-core/bedtools/split/meta.yml index 725bb9a2..7e126d22 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/ensemblvep/download/ensemblvep-download.diff b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff index 6d346d7b..71a470ea 100644 --- a/modules/nf-core/ensemblvep/download/ensemblvep-download.diff +++ b/modules/nf-core/ensemblvep/download/ensemblvep-download.diff @@ -14,18 +14,7 @@ Changes in 'ensemblvep/download/main.nf': input: tuple val(meta), val(assembly), val(species), val(cache_version) -Changes in 'ensemblvep/download/environment.yml': ---- modules/nf-core/ensemblvep/download/environment.yml -+++ 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 - +'modules/nf-core/ensemblvep/download/environment.yml' is unchanged 'modules/nf-core/ensemblvep/download/meta.yml' is unchanged 'modules/nf-core/ensemblvep/download/tests/tags.yml' is unchanged 'modules/nf-core/ensemblvep/download/tests/main.nf.test' is unchanged diff --git a/modules/nf-core/ensemblvep/download/meta.yml b/modules/nf-core/ensemblvep/download/meta.yml index a4277ad7..8da9621c 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/vep/ensemblvep-vep.diff b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff index e09aa620..6837716a 100644 --- a/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff +++ b/modules/nf-core/ensemblvep/vep/ensemblvep-vep.diff @@ -14,17 +14,7 @@ Changes in 'ensemblvep/vep/main.nf': input: tuple val(meta), path(vcf), path(custom_extra_files) -Changes in 'ensemblvep/vep/environment.yml': ---- modules/nf-core/ensemblvep/vep/environment.yml -+++ modules/nf-core/ensemblvep/vep/environment.yml -@@ -2,6 +2,5 @@ - channels: - - conda-forge - - bioconda -- - defaults - dependencies: - - bioconda::ensembl-vep=112.0 - +'modules/nf-core/ensemblvep/vep/environment.yml' is unchanged 'modules/nf-core/ensemblvep/vep/meta.yml' is unchanged 'modules/nf-core/ensemblvep/vep/tests/tags.yml' is unchanged 'modules/nf-core/ensemblvep/vep/tests/tab.gz.config' is unchanged diff --git a/modules/nf-core/ensemblvep/vep/environment.yml b/modules/nf-core/ensemblvep/vep/environment.yml index 87b88372..283a45bb 100644 --- a/modules/nf-core/ensemblvep/vep/environment.yml +++ b/modules/nf-core/ensemblvep/vep/environment.yml @@ -1,4 +1,3 @@ -name: ensemblvep_vep channels: - conda-forge - bioconda diff --git a/modules/nf-core/ensemblvep/vep/meta.yml b/modules/nf-core/ensemblvep/vep/meta.yml index d8ff8d14..9288a938 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/gatk4/calibratedragstrmodel/meta.yml b/modules/nf-core/gatk4/calibratedragstrmodel/meta.yml index bf2ca2d7..cc19131b 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/composestrtablefile/meta.yml b/modules/nf-core/gatk4/composestrtablefile/meta.yml index 249aed24..fd56c797 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/createsequencedictionary/meta.yml b/modules/nf-core/gatk4/createsequencedictionary/meta.yml index f9d70be0..7b5156bb 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/genomicsdbimport/meta.yml b/modules/nf-core/gatk4/genomicsdbimport/meta.yml index 11e565b1..174ae2eb 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 eb704364..0c1fe491 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/haplotypecaller/main.nf b/modules/nf-core/gatk4/haplotypecaller/main.nf index 3043ee07..b2aff489 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 \\ diff --git a/modules/nf-core/gatk4/haplotypecaller/meta.yml b/modules/nf-core/gatk4/haplotypecaller/meta.yml index 703b99a0..9d4a05e9 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/gawk/meta.yml b/modules/nf-core/gawk/meta.yml index 2b6033b0..05170082 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/mosdepth/meta.yml b/modules/nf-core/mosdepth/meta.yml index 9caaf2cd..dc783c90 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/rtgtools/format/meta.yml b/modules/nf-core/rtgtools/format/meta.yml index 1991b807..e09aff3a 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 4e90fd7b..c8eee99d 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 2b4d43d7..8fccb318 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/rocplot/tests/main.nf.test b/modules/nf-core/rtgtools/rocplot/tests/main.nf.test index c7c37084..52c5386d 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/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml index da2df5e4..62054fc9 100644 --- a/modules/nf-core/samtools/convert/environment.yml +++ b/modules/nf-core/samtools/convert/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf index 03b7b525..cf9253d1 100644 --- a/modules/nf-core/samtools/convert/main.nf +++ b/modules/nf-core/samtools/convert/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_CONVERT { conda "${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/meta.yml b/modules/nf-core/samtools/convert/meta.yml index 55828971..d5bfa161 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/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap index 51362902..a021254e 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/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml index f8450fa5..62054fc9 100644 --- a/modules/nf-core/samtools/faidx/environment.yml +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -1,10 +1,8 @@ -name: samtools_faidx - +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda - - defaults - dependencies: - - bioconda::htslib=1.20 - - bioconda::samtools=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index bdcdbc95..28c0a81c 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_FAIDX { conda "${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/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index f3c25de2..6721b2cb 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/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap index 3223b72b..1bbb3ec2 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/index/environment.yml b/modules/nf-core/samtools/index/environment.yml index da2df5e4..62054fc9 100644 --- a/modules/nf-core/samtools/index/environment.yml +++ b/modules/nf-core/samtools/index/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index e002585b..31175610 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_INDEX { conda "${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/meta.yml b/modules/nf-core/samtools/index/meta.yml index 01a4ee03..db8df0d5 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/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap index 799d199c..72d65e81 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/merge/environment.yml b/modules/nf-core/samtools/merge/environment.yml index da2df5e4..62054fc9 100644 --- a/modules/nf-core/samtools/merge/environment.yml +++ b/modules/nf-core/samtools/merge/environment.yml @@ -1,6 +1,8 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json channels: - conda-forge - bioconda dependencies: - - bioconda::samtools=1.20 - - bioconda::htslib=1.20 + - bioconda::htslib=1.21 + - bioconda::samtools=1.21 diff --git a/modules/nf-core/samtools/merge/main.nf b/modules/nf-core/samtools/merge/main.nf index 693b1d80..34da4c7c 100644 --- a/modules/nf-core/samtools/merge/main.nf +++ b/modules/nf-core/samtools/merge/main.nf @@ -4,8 +4,8 @@ process SAMTOOLS_MERGE { conda "${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/meta.yml b/modules/nf-core/samtools/merge/meta.yml index 2e8f3dbb..235aa219 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/merge/tests/main.nf.test.snap b/modules/nf-core/samtools/merge/tests/main.nf.test.snap index 17bc846f..0a41e01a 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/snpeff/snpeff/meta.yml b/modules/nf-core/snpeff/snpeff/meta.yml index 7559c3de..ef3d495a 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/snpeff/snpeff/tests/main.nf.test b/modules/nf-core/snpeff/snpeff/tests/main.nf.test index 803ff02c..2be0b7d7 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 d31ebf6b..a950a047 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" } diff --git a/modules/nf-core/somalier/extract/meta.yml b/modules/nf-core/somalier/extract/meta.yml index aabaf5d6..25621667 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 42638f4f..0da72821 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/tabix/bgzip/environment.yml b/modules/nf-core/tabix/bgzip/environment.yml index c863e920..017c259d 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 621d49ea..131e92cf 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 ] + - ${output}.gzi: + type: file + description: Optional gzip index file for compressed inputs + pattern: "*.gzi" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/tabix/bgziptabix/environment.yml b/modules/nf-core/tabix/bgziptabix/environment.yml index c863e920..017c259d 100644 --- a/modules/nf-core/tabix/bgziptabix/environment.yml +++ b/modules/nf-core/tabix/bgziptabix/environment.yml @@ -1,6 +1,7 @@ channels: - conda-forge - bioconda + dependencies: - - bioconda::tabix=1.11 - bioconda::htslib=1.20 + - bioconda::tabix=1.11 diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf index 05041f49..22f37a77 100644 --- a/modules/nf-core/tabix/bgziptabix/main.nf +++ b/modules/nf-core/tabix/bgziptabix/main.nf @@ -34,10 +34,11 @@ process TABIX_BGZIPTABIX { stub: def prefix = task.ext.prefix ?: "${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/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml index 438aba4d..806fbc12 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/bgziptabix/tests/main.nf.test b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test index 1a84d74f..4d4130dc 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 c166ea72..fb87799b 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 diff --git a/modules/nf-core/tabix/tabix/environment.yml b/modules/nf-core/tabix/tabix/environment.yml index 4d1f9dd4..017c259d 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/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml index ae5b4f43..7864832d 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/untar/environment.yml b/modules/nf-core/untar/environment.yml index 4f498244..c7794856 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/untar/meta.yml b/modules/nf-core/untar/meta.yml index a9a2110f..290346b3 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 ] + - $prefix: + type: directory + description: Directory containing contents of archive + pattern: "*/" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions.yml: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@joseespinosa" - "@drpatelh" diff --git a/modules/nf-core/vardictjava/main.nf b/modules/nf-core/vardictjava/main.nf index 6329391c..a2c7666b 100644 --- a/modules/nf-core/vardictjava/main.nf +++ b/modules/nf-core/vardictjava/main.nf @@ -14,7 +14,7 @@ process VARDICTJAVA { output: tuple val(meta), path("*.vcf.gz"), emit: vcf - path "versions.yml" , emit: versions + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when @@ -25,9 +25,12 @@ process VARDICTJAVA { def args3 = task.ext.args3 ?: '' def prefix = task.ext.prefix ?: "${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/meta.yml b/modules/nf-core/vardictjava/meta.yml index 5c2fc921..801db6fa 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/vardictjava/tests/main.nf.test b/modules/nf-core/vardictjava/tests/main.nf.test index 8e5fec10..31e1058c 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 c32a68b7..35674ed1 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 00000000..c6e8571b --- /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 diff --git a/modules/nf-core/vcf2db/meta.yml b/modules/nf-core/vcf2db/meta.yml index b6529a6a..48795c21 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/vcfanno/meta.yml b/modules/nf-core/vcfanno/meta.yml index 89c781ad..18d27127 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" From 411a6bbe892684f11a5222b9930f39f9023217bc Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 11 Oct 2024 11:37:41 +0200 Subject: [PATCH 2/3] make linting happy --- .nf-core.yml | 2 ++ conf/base.config | 1 - nextflow.config | 5 +++-- 3 files changed, 5 insertions(+), 3 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 4f491e32..ad9a71ec 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -25,6 +25,8 @@ lint: - custom_config - manifest.name - manifest.homePage + - validation.help.afterText + - validation.summary.afterText nf_core_version: 3.0.1 repository_type: pipeline template: diff --git a/conf/base.config b/conf/base.config index 1240cc86..6ed8a916 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { 1 * task.attempt } memory = { 8.GB * task.attempt } time = { 4.h * task.attempt } diff --git a/nextflow.config b/nextflow.config index be6dfaf1..0ce19e52 100644 --- a/nextflow.config +++ b/nextflow.config @@ -235,8 +235,6 @@ profiles { includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load nf-cmgg/germline custom profiles from different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/germline.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled @@ -323,6 +321,9 @@ validation { -\033[2m----------------------------------------------------\033[0m- """ } + summary { + beforeText = validation.help.beforeText + } } // Load modules.config for DSL2 module specific options From 43c27bfd69c5b834d9e92ce5bedd99cd6407917d Mon Sep 17 00:00:00 2001 From: Nicolas Vannieuwkerke Date: Fri, 11 Oct 2024 11:39:09 +0200 Subject: [PATCH 3/3] fix template comment ci action --- .github/workflows/template_version_comment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/template_version_comment.yml b/.github/workflows/template_version_comment.yml index 9dea41f0..d01fb43f 100644 --- a/.github/workflows/template_version_comment.yml +++ b/.github/workflows/template_version_comment.yml @@ -12,7 +12,7 @@ jobs: uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4 - name: Read template version from .nf-core.yml - uses: pietrobolcato/action-read-yaml@1.0.0 + uses: pietrobolcato/action-read-yaml@1.1.0 id: read_yml with: config: ${{ github.workspace }}/.nf-core.yml