diff --git a/.github/workflows/code-linting.yml b/.github/workflows/code-linting.yml index d15c4af6..145dd5d9 100644 --- a/.github/workflows/code-linting.yml +++ b/.github/workflows/code-linting.yml @@ -12,9 +12,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: "10" + - uses: actions/setup-node@v2 - name: Install markdownlint run: npm install -g markdownlint-cli @@ -27,9 +25,7 @@ jobs: steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v1 - with: - node-version: "10" + - uses: actions/setup-node@v2 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -44,9 +40,7 @@ jobs: uses: actions/checkout@v2 - name: Install NodeJS - uses: actions/setup-node@v1 - with: - node-version: "10" + uses: actions/setup-node@v2 - name: Install yaml-lint run: npm install -g yaml-lint diff --git a/.gitpod.yml b/.gitpod.yml index 289c86e5..25078360 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,14 +1,14 @@ image: nfcore/gitpod:latest vscode: - extensions: # based on nf-core.nf-core-extensionpack + extensions: # based on nf-core.nf-core-extensionpack - codezombiech.gitignore # Language support for .gitignore files - # - cssho.vscode-svgviewer # SVG viewer + # - cssho.vscode-svgviewer # SVG viewer - davidanson.vscode-markdownlint # Markdown/CommonMark linting and style checking for Visual Studio Code - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar - mechatroner.rainbow-csv # Highlight columns in csv files in different colors - # - nextflow.nextflow # Nextflow syntax highlighting + # - nextflow.nextflow # Nextflow syntax highlighting - oderwat.indent-rainbow # Highlight indentation level - streetsidesoftware.code-spell-checker # Spelling checker for source code diff --git a/.markdownlint.yml b/.markdownlint.yml index 9b72da3c..7890d0f2 100644 --- a/.markdownlint.yml +++ b/.markdownlint.yml @@ -8,4 +8,4 @@ header-increment: false no-duplicate-header: siblings_only: true ul-indent: - indent: 4 + indent: 4 diff --git a/.yamllint.yml b/.yamllint.yml new file mode 100644 index 00000000..6889fa34 --- /dev/null +++ b/.yamllint.yml @@ -0,0 +1,5 @@ +extends: default + +rules: + document-start: disable + line-length: disable diff --git a/modules/abacas/meta.yml b/modules/abacas/meta.yml index 039fb0be..c685e650 100644 --- a/modules/abacas/meta.yml +++ b/modules/abacas/meta.yml @@ -14,7 +14,7 @@ tools: documentation: http://abacas.sourceforge.net/documentation.html tool_dev_url: None doi: "10.1093/bioinformatics/btp347" - licence: ['GPL v2-or-later'] + licence: ["GPL v2-or-later"] input: - meta: diff --git a/modules/adapterremoval/meta.yml b/modules/adapterremoval/meta.yml index 05386fd8..4923fa42 100644 --- a/modules/adapterremoval/meta.yml +++ b/modules/adapterremoval/meta.yml @@ -1,50 +1,50 @@ name: adapterremoval description: Trim sequencing adapters and collapse overlapping reads keywords: - - trimming - - adapters - - merging - - fastq + - trimming + - adapters + - merging + - fastq tools: - - adapterremoval: - description: The AdapterRemoval v2 tool for merging and clipping reads. - homepage: https://github.com/MikkelSchubert/adapterremoval - documentation: https://adapterremoval.readthedocs.io - licence: ['GPL v3'] + - adapterremoval: + description: The AdapterRemoval v2 tool for merging and clipping reads. + homepage: https://github.com/MikkelSchubert/adapterremoval + documentation: https://adapterremoval.readthedocs.io + licence: ["GPL v3"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - pattern: "*.{fq,fastq,fg.gz,fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + pattern: "*.{fq,fastq,fg.gz,fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 or 2 for - single-end or collapsed data and paired-end data, respectively. - pattern: "*.{fastq.gz}" - - log: - type: file - description: AdapterRemoval log file - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input adapter trimmed FastQ files of size 1 or 2 for + single-end or collapsed data and paired-end data, respectively. + pattern: "*.{fastq.gz}" + - log: + type: file + description: AdapterRemoval log file + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxibor" + - "@maxibor" diff --git a/modules/agrvate/meta.yml b/modules/agrvate/meta.yml index a8ab5816..bcaa6c0b 100644 --- a/modules/agrvate/meta.yml +++ b/modules/agrvate/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/VishnuRaghuram94/AgrVATE tool_dev_url: https://github.com/VishnuRaghuram94/AgrVATE doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/amps/meta.yml b/modules/amps/meta.yml index 43d68599..34f825af 100644 --- a/modules/amps/meta.yml +++ b/modules/amps/meta.yml @@ -24,7 +24,7 @@ tools: documentation: "https://github.com/keyfm/amps" tool_dev_url: "https://github.com/keyfm/amps" doi: "10.1186/s13059-019-1903-0" - licence: ['GPL >=3'] + licence: ["GPL >=3"] input: - maltextract_results: diff --git a/modules/arriba/meta.yml b/modules/arriba/meta.yml index 6ca16dab..4bde2f08 100644 --- a/modules/arriba/meta.yml +++ b/modules/arriba/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://arriba.readthedocs.io/en/latest/ tool_dev_url: https://github.com/suhrig/arriba doi: "10.1101/gr.257246.119" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/artic/guppyplex/meta.yml b/modules/artic/guppyplex/meta.yml index 5056f908..fe288289 100644 --- a/modules/artic/guppyplex/meta.yml +++ b/modules/artic/guppyplex/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/artic/minion/meta.yml b/modules/artic/minion/meta.yml index 464e1dc7..5ef55673 100644 --- a/modules/artic/minion/meta.yml +++ b/modules/artic/minion/meta.yml @@ -1,6 +1,6 @@ name: artic_minion description: | - Run the alignment/variant-call/consensus logic of the artic pipeline + Run the alignment/variant-call/consensus logic of the artic pipeline keywords: - artic - aggregate @@ -12,7 +12,7 @@ tools: documentation: https://artic.readthedocs.io/en/latest/ tool_dev_url: https://github.com/artic-network/fieldbioinformatics doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map @@ -21,11 +21,11 @@ input: e.g. [ id:'test', single_end:false ] - fastq: type: file - description: FastQ file containing reads + description: FastQ file containing reads pattern: "*.{fastq.gz}" - fast5_dir: type: directory - description: Directory containing MinION FAST5 files + description: Directory containing MinION FAST5 files pattern: "*" - sequencing_summary: type: file diff --git a/modules/assemblyscan/meta.yml b/modules/assemblyscan/meta.yml index 40ea98b9..7b0b67fa 100644 --- a/modules/assemblyscan/meta.yml +++ b/modules/assemblyscan/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/rpetit3/assembly-scan tool_dev_url: https://github.com/rpetit3/assembly-scan doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/ataqv/ataqv/meta.yml b/modules/ataqv/ataqv/meta.yml index 760bf95f..a25272da 100644 --- a/modules/ataqv/ataqv/meta.yml +++ b/modules/ataqv/ataqv/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/ParkerLab/ataqv/blob/master/README.rst tool_dev_url: https://github.com/ParkerLab/ataqv doi: "https://doi.org/10.1016/j.cels.2020.02.009" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/bakta/main.nf b/modules/bakta/main.nf index 95e87899..a7f971ef 100644 --- a/modules/bakta/main.nf +++ b/modules/bakta/main.nf @@ -2,10 +2,10 @@ process BAKTA { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::bakta=1.2.2" : null) + conda (params.enable_conda ? "bioconda::bakta=1.3.1" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/bakta:1.2.2--pyhdfd78af_0' : - 'quay.io/biocontainers/bakta:1.2.2--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/bakta:1.3.1--pyhdfd78af_0' : + 'quay.io/biocontainers/bakta:1.3.1--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) @@ -23,6 +23,7 @@ process BAKTA { tuple val(meta), path("${prefix}.hypotheticals.tsv"), emit: hypotheticals_tsv tuple val(meta), path("${prefix}.hypotheticals.faa"), emit: hypotheticals_faa tuple val(meta), path("${prefix}.tsv") , emit: tsv + tuple val(meta), path("${prefix}.txt") , emit: txt path "versions.yml" , emit: versions when: @@ -61,6 +62,7 @@ process BAKTA { touch ${prefix}.hypotheticals.tsv touch ${prefix}.hypotheticals.faa touch ${prefix}.tsv + touch ${prefix}.txt cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/bakta/meta.yml b/modules/bakta/meta.yml index 29e6edbe..2514a996 100644 --- a/modules/bakta/meta.yml +++ b/modules/bakta/meta.yml @@ -1,17 +1,17 @@ name: bakta -description: Rapid annotation of bacterial genomes & plasmids. +description: Annotation of bacterial genomes (isolates, MAGs) and plasmids keywords: - annotation - fasta - - prokaryote + - bacteria tools: - bakta: - description: Rapid & standardized annotation of bacterial genomes & plasmids. + description: Rapid & standardized annotation of bacterial genomes, MAGs & plasmids. homepage: https://github.com/oschwengers/bakta documentation: https://github.com/oschwengers/bakta tool_dev_url: https://github.com/oschwengers/bakta doi: "10.1099/mgen.0.000685" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -29,7 +29,7 @@ input: Path to the Bakta database - proteins: type: file - description: FASTA file of trusted proteins to first annotate from (optional) + description: FASTA/GenBank file of trusted proteins to first annotate from (optional) - prodigal_tf: type: file description: Training file to use for Prodigal (optional) @@ -44,6 +44,10 @@ output: type: file description: File containing software versions pattern: "versions.yml" + - txt: + type: file + description: genome statistics and annotation summary + pattern: "*.txt" - tsv: type: file description: annotations as simple human readble tab separated values @@ -83,3 +87,4 @@ output: authors: - "@rpetit3" + - "@oschwengers" diff --git a/modules/bamaligncleaner/meta.yml b/modules/bamaligncleaner/meta.yml index d1e171f7..f248c1ad 100644 --- a/modules/bamaligncleaner/meta.yml +++ b/modules/bamaligncleaner/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://github.com/maxibor/bamAlignCleaner documentation: https://github.com/maxibor/bamAlignCleaner tool_dev_url: https://github.com/maxibor/bamAlignCleaner - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/bamcmp/meta.yml b/modules/bamcmp/meta.yml index 480d8609..36a5ff1b 100644 --- a/modules/bamcmp/meta.yml +++ b/modules/bamcmp/meta.yml @@ -10,14 +10,15 @@ keywords: tools: - bamcmp: - description: Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, - sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else - reads which multimap to the contamination genome will be spuriously kept. + description: + Bamcmp is a tool for deconvolving host and graft reads, using two bam files. Reads should be mapped to two genomes, and the mapped, + sorted bam files supplied to the tool. It is highly recommended to use the "-s as" option not the "-s mapq" option, else + reads which multimap to the contamination genome will be spuriously kept. homepage: https://github.com/CRUKMI-ComputationalBiology/bamcmp documentation: https://github.com/CRUKMI-ComputationalBiology/bamcmp tool_dev_url: https://github.com/CRUKMI-ComputationalBiology/bamcmp doi: "10.1158/1541-7786.MCR-16-0431" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/bamtools/convert/meta.yml b/modules/bamtools/convert/meta.yml index acc7e4df..5796a4ab 100644 --- a/modules/bamtools/convert/meta.yml +++ b/modules/bamtools/convert/meta.yml @@ -19,7 +19,7 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/bamtools/split/meta.yml b/modules/bamtools/split/meta.yml index b9b52f59..0e848212 100644 --- a/modules/bamtools/split/meta.yml +++ b/modules/bamtools/split/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/pezmaster31/bamtools/wiki tool_dev_url: http://github.com/pezmaster31/bamtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/bamutil/trimbam/meta.yml b/modules/bamutil/trimbam/meta.yml index a91ba0e1..29f8c951 100644 --- a/modules/bamutil/trimbam/meta.yml +++ b/modules/bamutil/trimbam/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://genome.sph.umich.edu/wiki/BamUtil:_trimBam tool_dev_url: https://github.com/statgen/bamUtil doi: "10.1101/gr.176552.114" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/bandage/image/meta.yml b/modules/bandage/image/meta.yml index 1c2b9840..1e824c4f 100644 --- a/modules/bandage/image/meta.yml +++ b/modules/bandage/image/meta.yml @@ -1,44 +1,44 @@ name: bandage_image description: Render an assembly graph in GFA 1.0 format to PNG and SVG image formats keywords: - - gfa - - graph - - assembly - - visualisation + - gfa + - graph + - assembly + - visualisation tools: - - bandage: - description: | - Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily - homepage: https://github.com/rrwick/Bandage - documentation: https://github.com/rrwick/Bandage - licence: ['GPL-3.0-or-later'] + - bandage: + description: | + Bandage - a Bioinformatics Application for Navigating De novo Assembly Graphs Easily + homepage: https://github.com/rrwick/Bandage + documentation: https://github.com/rrwick/Bandage + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly graph in GFA 1.0 format - pattern: "*.gfa" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly graph in GFA 1.0 format + pattern: "*.gfa" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - png: - type: file - description: Bandage image in PNG format - pattern: "*.png" - - svg: - type: file - description: Bandage image in SVG format - pattern: "*.svg" - - 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 ] + - png: + type: file + description: Bandage image in PNG format + pattern: "*.png" + - svg: + type: file + description: Bandage image in SVG format + pattern: "*.svg" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/bbmap/align/meta.yml b/modules/bbmap/align/meta.yml index fe4d4334..a4682aee 100644 --- a/modules/bbmap/align/meta.yml +++ b/modules/bbmap/align/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" - licence: ['UC-LBL license (see package)'] + licence: ["UC-LBL license (see package)"] input: - meta: @@ -24,14 +24,14 @@ input: - fastq: type: file description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. - ref: type: file description: | - Either "ref" a directory containing an index, the name of another directory - with a "ref" subdirectory containing an index or the name of a fasta formatted - nucleotide file containg the reference to map to. + Either "ref" a directory containing an index, the name of another directory + with a "ref" subdirectory containing an index or the name of a fasta formatted + nucleotide file containg the reference to map to. output: - meta: diff --git a/modules/bbmap/bbduk/meta.yml b/modules/bbmap/bbduk/meta.yml index 50ab6ed4..6abd3d97 100644 --- a/modules/bbmap/bbduk/meta.yml +++ b/modules/bbmap/bbduk/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" - licence: ['UC-LBL license (see package)'] + licence: ["UC-LBL license (see package)"] input: - meta: @@ -20,14 +20,14 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. - contaminants: - type: file - description: | - Reference files containing adapter and/or contaminant sequences for sequence kmer matching + type: file + description: | + Reference files containing adapter and/or contaminant sequences for sequence kmer matching output: - meta: diff --git a/modules/bbmap/bbsplit/meta.yml b/modules/bbmap/bbsplit/meta.yml index 2e3d07c0..9d9f10da 100644 --- a/modules/bbmap/bbsplit/meta.yml +++ b/modules/bbmap/bbsplit/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" - licence: ['UC-LBL license (see package)'] + licence: ["UC-LBL license (see package)"] input: - meta: diff --git a/modules/bbmap/index/meta.yml b/modules/bbmap/index/meta.yml index 0b3e5778..e8b455ed 100644 --- a/modules/bbmap/index/meta.yml +++ b/modules/bbmap/index/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/ tool_dev_url: None doi: "" - licence: ['UC-LBL license (see package)'] + licence: ["UC-LBL license (see package)"] input: - fasta: diff --git a/modules/bcftools/concat/meta.yml b/modules/bcftools/concat/meta.yml index b2848595..3984276f 100644 --- a/modules/bcftools/concat/meta.yml +++ b/modules/bcftools/concat/meta.yml @@ -1,43 +1,43 @@ name: bcftools_concat description: Concatenate VCF files keywords: - - variant calling - - concat - - bcftools - - VCF + - variant calling + - concat + - bcftools + - VCF tools: - - concat: - description: | - Concatenate VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - concat: + description: | + Concatenate VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: files - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: files + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF concatenated output file - pattern: "*.{vcf.gz}" - - 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 ] + - vcf: + type: file + description: VCF concatenated output file + pattern: "*.{vcf.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" diff --git a/modules/bcftools/consensus/meta.yml b/modules/bcftools/consensus/meta.yml index 761115a6..05a93a56 100644 --- a/modules/bcftools/consensus/meta.yml +++ b/modules/bcftools/consensus/meta.yml @@ -1,49 +1,49 @@ name: bcftools_consensus description: Compresses VCF files keywords: - - variant calling - - consensus - - VCF + - variant calling + - consensus + - VCF tools: - - consensus: - description: | - Create consensus sequence by applying VCF variants to a reference fasta file. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - consensus: + description: | + Create consensus sequence by applying VCF variants to a reference fasta file. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF file - pattern: "*.{vcf}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF file + pattern: "*.{vcf}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA reference consensus file - pattern: "*.{fasta,fa}" - - 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 ] + - fasta: + type: file + description: FASTA reference consensus file + pattern: "*.{fasta,fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/filter/meta.yml b/modules/bcftools/filter/meta.yml index 72d28bf0..05a6d828 100644 --- a/modules/bcftools/filter/meta.yml +++ b/modules/bcftools/filter/meta.yml @@ -1,41 +1,41 @@ name: bcftools_filter description: Filters VCF files keywords: - - variant calling - - filtering - - VCF + - variant calling + - filtering + - VCF tools: - - filter: - description: | - Apply fixed-threshold filters to VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - filter: + description: | + Apply fixed-threshold filters to VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF filtered output file - pattern: "*.{vcf}" - - 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 ] + - vcf: + type: file + description: VCF filtered output file + pattern: "*.{vcf}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/index/meta.yml b/modules/bcftools/index/meta.yml index 0d5dd3ef..b883fa5f 100644 --- a/modules/bcftools/index/meta.yml +++ b/modules/bcftools/index/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://samtools.github.io/bcftools/howtos/index.html tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/gigascience/giab008" - licence: ['MIT', 'GPL-3.0-or-later'] + licence: ["MIT", "GPL-3.0-or-later"] input: - meta: diff --git a/modules/bcftools/isec/meta.yml b/modules/bcftools/isec/meta.yml index d0be6dce..d9554bcc 100644 --- a/modules/bcftools/isec/meta.yml +++ b/modules/bcftools/isec/meta.yml @@ -1,49 +1,49 @@ name: bcftools_isec description: Apply set operations to VCF files keywords: - - variant calling - - intersect - - union - - complement - - VCF + - variant calling + - intersect + - union + - complement + - VCF tools: - - isec: - description: | - Computes intersections, unions and complements of VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - isec: + description: | + Computes intersections, unions and complements of VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: files - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbis: - type: files - description: | - List containing the tbi index files corresponding to the vcfs input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: files + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: files + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - results: - type: directory - description: Folder containing the set operations results perform on the vcf files - pattern: "${prefix}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results: + type: directory + description: Folder containing the set operations results perform on the vcf files + pattern: "${prefix}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/merge/meta.yml b/modules/bcftools/merge/meta.yml index c7e3a280..4223fd54 100644 --- a/modules/bcftools/merge/meta.yml +++ b/modules/bcftools/merge/meta.yml @@ -1,47 +1,47 @@ name: bcftools_merge description: Merge VCF files keywords: - - variant calling - - merge - - VCF + - variant calling + - merge + - VCF tools: - - merge: - description: | - Merge VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - merge: + description: | + Merge VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcfs: - type: files - description: | - List containing 2 or more vcf files - e.g. [ 'file1.vcf', 'file2.vcf' ] - - tbis: - type: files - description: | - List containing the tbi index files corresponding to the vcfs input files - e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcfs: + type: files + description: | + List containing 2 or more vcf files + e.g. [ 'file1.vcf', 'file2.vcf' ] + - tbis: + type: files + description: | + List containing the tbi index files corresponding to the vcfs input files + e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ] output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF merged output file - pattern: "*.{vcf.gz}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF merged output file + pattern: "*.{vcf.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/mpileup/meta.yml b/modules/bcftools/mpileup/meta.yml index 483d0e71..d10dac14 100644 --- a/modules/bcftools/mpileup/meta.yml +++ b/modules/bcftools/mpileup/meta.yml @@ -1,57 +1,57 @@ name: bcftools_mpileup description: Compresses VCF files keywords: - - variant calling - - mpileup - - VCF + - variant calling + - mpileup + - VCF tools: - - mpileup: - description: | - Generates genotype likelihoods at each genomic position with coverage. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - mpileup: + description: | + Generates genotype likelihoods at each genomic position with coverage. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" - - save_mpileup: - type: boolean - description: Save mpileup file generated by bcftools mpileup - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" + - save_mpileup: + type: boolean + description: Save mpileup file generated by bcftools mpileup + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF gzipped output file - pattern: "*.{vcf.gz}" - - tbi: - type: file - description: tabix index file - pattern: "*.{tbi}" - - stats: - type: file - description: Text output file containing stats - pattern: "*{stats.txt}" - - 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 ] + - vcf: + type: file + description: VCF gzipped output file + pattern: "*.{vcf.gz}" + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - stats: + type: file + description: Text output file containing stats + pattern: "*{stats.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/norm/meta.yml b/modules/bcftools/norm/meta.yml index 27978a53..ce4aee85 100644 --- a/modules/bcftools/norm/meta.yml +++ b/modules/bcftools/norm/meta.yml @@ -6,41 +6,41 @@ keywords: - variant calling - VCF tools: - - norm: - description: | - Normalize VCF files. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - norm: + description: | + Normalize VCF files. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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' - - 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' + - 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: VCF normalized output file - pattern: "*.{vcf.gz}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" + - "@abhi18av" diff --git a/modules/bcftools/query/meta.yml b/modules/bcftools/query/meta.yml index e49f13c8..fd4fd473 100644 --- a/modules/bcftools/query/meta.yml +++ b/modules/bcftools/query/meta.yml @@ -6,56 +6,56 @@ keywords: - bcftools - VCF tools: - - query: - description: | - Extracts fields from VCF or BCF files and outputs them in user-defined format. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - query: + description: | + Extracts fields from VCF or BCF files and outputs them in user-defined format. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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 ] - - txt: - type: file - description: BCFTools query output file - pattern: "*.txt" - - 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 ] + - txt: + type: file + description: BCFTools query output file + pattern: "*.txt" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@abhi18av" - "@drpatelh" diff --git a/modules/bcftools/reheader/meta.yml b/modules/bcftools/reheader/meta.yml index ee8cba32..eaf44927 100644 --- a/modules/bcftools/reheader/meta.yml +++ b/modules/bcftools/reheader/meta.yml @@ -11,7 +11,7 @@ tools: homepage: http://samtools.github.io/bcftools/bcftools.html documentation: http://samtools.github.io/bcftools/bcftools.html#reheader doi: 10.1093/gigascience/giab008 - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/bcftools/sort/meta.yml b/modules/bcftools/sort/meta.yml index af894e82..0c244a48 100644 --- a/modules/bcftools/sort/meta.yml +++ b/modules/bcftools/sort/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://www.htslib.org/doc/bcftools.html tool_dev_url: https://github.com/samtools/bcftools doi: "10.1093/bioinformatics/btp352" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/bcftools/stats/meta.yml b/modules/bcftools/stats/meta.yml index 505bf729..304b88ec 100644 --- a/modules/bcftools/stats/meta.yml +++ b/modules/bcftools/stats/meta.yml @@ -1,42 +1,42 @@ name: bcftools_stats description: Generates stats from VCF files keywords: - - variant calling - - stats - - VCF + - variant calling + - stats + - VCF tools: - - stats: - description: | - Parses VCF or BCF and produces text file stats which is suitable for - machine processing and can be plotted using plot-vcfstats. - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - stats: + description: | + Parses VCF or BCF and produces text file stats which is suitable for + machine processing and can be plotted using plot-vcfstats. + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF input file - pattern: "*.{vcf}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: VCF input file + pattern: "*.{vcf}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: Text output file containing stats - pattern: "*_{stats.txt}" - - 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 ] + - stats: + type: file + description: Text output file containing stats + pattern: "*_{stats.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bcftools/view/meta.yml b/modules/bcftools/view/meta.yml index df5b0f8f..326fd1fa 100644 --- a/modules/bcftools/view/meta.yml +++ b/modules/bcftools/view/meta.yml @@ -1,63 +1,63 @@ name: bcftools_view description: View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF keywords: - - variant calling - - view - - bcftools - - VCF + - variant calling + - view + - bcftools + - VCF tools: - - view: - description: | - View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF - homepage: http://samtools.github.io/bcftools/bcftools.html - documentation: http://www.htslib.org/doc/bcftools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - view: + description: | + View, subset and filter VCF or BCF files by position and filtering expression. Convert between VCF and BCF + homepage: http://samtools.github.io/bcftools/bcftools.html + documentation: http://www.htslib.org/doc/bcftools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - The vcf file to be inspected. - e.g. 'file.vcf' - - index: - type: file - description: | - The tab index for the VCF file to be inspected. - e.g. 'file.tbi' - - regions: - type: file - description: | - Optionally, restrict the operation to regions listed in this file. - e.g. 'file.vcf' - - targets: - type: file - description: | - Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) - e.g. 'file.vcf' - - samples: - type: file - description: | - Optional, file of sample names to be included or excluded. - e.g. 'file.tsv' + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - vcf: + type: file + description: | + The vcf file to be inspected. + e.g. 'file.vcf' + - index: + type: file + description: | + The tab index for the VCF file to be inspected. + e.g. 'file.tbi' + - regions: + type: file + description: | + Optionally, restrict the operation to regions listed in this file. + e.g. 'file.vcf' + - targets: + type: file + description: | + Optionally, restrict the operation to regions listed in this file (doesn't rely upon index files) + e.g. 'file.vcf' + - samples: + type: file + description: | + Optional, file of sample names to be included or excluded. + e.g. 'file.tsv' output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: VCF normalized output file - pattern: "*.{vcf.gz}" - - 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 ] + - vcf: + type: file + description: VCF normalized output file + pattern: "*.{vcf.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" + - "@abhi18av" diff --git a/modules/bedtools/bamtobed/meta.yml b/modules/bedtools/bamtobed/meta.yml index e8c67047..5a4ff73a 100644 --- a/modules/bedtools/bamtobed/meta.yml +++ b/modules/bedtools/bamtobed/meta.yml @@ -1,38 +1,38 @@ name: bedtools_bamtobed description: Converts a bam file to a bed12 file. keywords: - - bam - - bed + - bam + - bed tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Input BAM file - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Input BAM file + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed file containing genomic intervals. - pattern: "*.{bed}" - - 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 ] + - bed: + type: file + description: Bed file containing genomic intervals. + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" - - "@drpatelh" + - "@yuukiiwa" + - "@drpatelh" diff --git a/modules/bedtools/complement/meta.yml b/modules/bedtools/complement/meta.yml index 2ad8749c..708a2161 100644 --- a/modules/bedtools/complement/meta.yml +++ b/modules/bedtools/complement/meta.yml @@ -1,43 +1,43 @@ name: bedtools_complement description: Returns all intervals in a genome that are not covered by at least one interval in the input BED/GFF/VCF file. keywords: - - bed - - complement + - bed + - complement tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/complement.html + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Input BED file - pattern: "*.{bed}" - - sizes: - type: file - description: File which defines the chromosome lengths for a given genome - pattern: "*.{sizes}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" + - sizes: + type: file + description: File which defines the chromosome lengths for a given genome + pattern: "*.{sizes}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed file with all genomic intervals that are not covered by at least one record from the input file. - pattern: "*.{bed}" - - 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 ] + - bed: + type: file + description: Bed file with all genomic intervals that are not covered by at least one record from the input file. + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/bedtools/genomecov/meta.yml b/modules/bedtools/genomecov/meta.yml index 0713e95b..83bfab98 100644 --- a/modules/bedtools/genomecov/meta.yml +++ b/modules/bedtools/genomecov/meta.yml @@ -1,51 +1,51 @@ name: bedtools_genomecov description: Computes histograms (default), per-base reports (-d) and BEDGRAPH (-bg) summaries of feature coverage (e.g., aligned sequences) for a given genome. keywords: - - bed - - bam - - genomecov + - bed + - bam + - genomecov tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BAM/BED/GFF/VCF - pattern: "*.{bam|bed|gff|vcf}" - - scale: - type: value - description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch - - sizes: - type: file - description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BAM/BED/GFF/VCF + pattern: "*.{bam|bed|gff|vcf}" + - scale: + type: value + description: Number containing the scale factor for the output. Set to 1 to disable. Setting to a value other than 1 will also get the -bg bedgraph output format as this is required for this command switch + - sizes: + type: file + description: Tab-delimited table of chromosome names in the first column and chromosome sizes in the second column + - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - genomecov: - type: file - description: Computed genome coverage file - pattern: "*.${extension}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - genomecov: + type: file + description: Computed genome coverage file + pattern: "*.${extension}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" - - "@sidorov-si" - - "@chris-cheshire" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" + - "@sidorov-si" + - "@chris-cheshire" diff --git a/modules/bedtools/getfasta/meta.yml b/modules/bedtools/getfasta/meta.yml index 38715c3d..11335100 100644 --- a/modules/bedtools/getfasta/meta.yml +++ b/modules/bedtools/getfasta/meta.yml @@ -1,34 +1,34 @@ name: bedtools_getfasta description: extract sequences in a FASTA file based on intervals defined in a feature file. keywords: - - bed - - fasta - - getfasta + - bed + - fasta + - getfasta tools: - - bedtools: - description: | - 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'] + - bedtools: + description: | + 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"] input: - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - fasta: - type: file - description: Output fasta file with extracted sequences - pattern: "*.{fa}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - fasta: + type: file + description: Output fasta file with extracted sequences + pattern: "*.{fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bedtools/intersect/meta.yml b/modules/bedtools/intersect/meta.yml index 3bcb6ece..6e21e928 100644 --- a/modules/bedtools/intersect/meta.yml +++ b/modules/bedtools/intersect/meta.yml @@ -1,47 +1,47 @@ name: bedtools_intersect description: Allows one to screen for overlaps between two sets of genomic features. keywords: - - bed - - intersect + - bed + - intersect tools: - - bedtools: - description: | - 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'] + - bedtools: + description: | + 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"] 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}" - - extension: - type: value - description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.). + - 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}" + - extension: + type: value + description: Extension of the output file. It is set by the user and corresponds to the file format which depends on arguments (e. g., ".bed", ".bam", ".txt", etc.). 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: "*.${extension}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intersect: + type: file + description: File containing the description of overlaps found between the two features + pattern: "*.${extension}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" - - "@sidorov-si" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" + - "@sidorov-si" diff --git a/modules/bedtools/makewindows/meta.yml b/modules/bedtools/makewindows/meta.yml index a536d75f..9de31f43 100644 --- a/modules/bedtools/makewindows/meta.yml +++ b/modules/bedtools/makewindows/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://bedtools.readthedocs.io/en/latest/content/tools/makewindows.html tool_dev_url: None doi: "10.1093/bioinformatics/btq033" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/bedtools/maskfasta/meta.yml b/modules/bedtools/maskfasta/meta.yml index 0b7aa3ed..cc33df3e 100644 --- a/modules/bedtools/maskfasta/meta.yml +++ b/modules/bedtools/maskfasta/meta.yml @@ -1,44 +1,44 @@ name: bedtools_maskfasta description: masks sequences in a FASTA file based on intervals defined in a feature file. keywords: - - bed - - fasta - - maskfasta + - bed + - fasta + - maskfasta tools: - - bedtools: - description: | - 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'] + - bedtools: + description: | + 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"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed feature file - pattern: "*.{bed}" - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Bed feature file + pattern: "*.{bed}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Output masked fasta file - pattern: "*.{fa}" - - 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 ] + - fasta: + type: file + description: Output masked fasta file + pattern: "*.{fa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bedtools/merge/meta.yml b/modules/bedtools/merge/meta.yml index 40a42b7b..76743679 100644 --- a/modules/bedtools/merge/meta.yml +++ b/modules/bedtools/merge/meta.yml @@ -1,39 +1,39 @@ 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. keywords: - - bed - - merge + - bed + - merge tools: - - bedtools: - description: | - 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'] + - bedtools: + description: | + 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"] 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}" - - 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 ] + - bed: + type: file + description: Overlapped bed file with combined features + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/bedtools/slop/meta.yml b/modules/bedtools/slop/meta.yml index a4713936..4835b71b 100644 --- a/modules/bedtools/slop/meta.yml +++ b/modules/bedtools/slop/meta.yml @@ -1,39 +1,39 @@ name: bedtools_slop description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) keywords: - - bed - - slopBed + - bed + - slopBed tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html + licence: ["MIT"] 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: Slopped BED file - pattern: "*.{bed}" - - 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 ] + - bed: + type: file + description: Slopped BED file + pattern: "*.{bed}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/modules/bedtools/sort/meta.yml b/modules/bedtools/sort/meta.yml index c7b1b098..369e51ff 100644 --- a/modules/bedtools/sort/meta.yml +++ b/modules/bedtools/sort/meta.yml @@ -1,46 +1,46 @@ name: bedtools_sort description: Sorts a feature file by chromosome and other criteria. keywords: - - bed - - sort + - bed + - sort tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/sort.html + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - intervals: - type: file - description: BED/BEDGRAPH - pattern: "*.{bed|bedGraph}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - intervals: + type: file + description: BED/BEDGRAPH + pattern: "*.{bed|bedGraph}" - - extension: - type: string - description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. + - extension: + type: string + description: Extension of the output file (e. g., ".bg", ".bedgraph", ".txt", ".tab", etc.) It is set arbitrarily by the user and corresponds to the file format which depends on arguments. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - - sorted: - type: file - description: Sorted output file - pattern: "*.${extension}" + - sorted: + type: file + description: Sorted output file + pattern: "*.${extension}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@Emiller88" - - "@sruthipsuresh" - - "@drpatelh" - - "@chris-cheshire" + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" + - "@chris-cheshire" diff --git a/modules/bedtools/subtract/meta.yml b/modules/bedtools/subtract/meta.yml index b9245a55..19978f74 100644 --- a/modules/bedtools/subtract/meta.yml +++ b/modules/bedtools/subtract/meta.yml @@ -1,16 +1,16 @@ name: bedtools_subtract description: Finds overlaps between two sets of regions (A and B), removes the overlaps from A and reports the remaining portion of A. keywords: - - bed - - gff - - vcf - - subtract + - bed + - gff + - vcf + - subtract tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html - licence: ['MIT'] + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/subtract.html + licence: ["MIT"] input: - meta: diff --git a/modules/biobambam/bammarkduplicates2/main.nf b/modules/biobambam/bammarkduplicates2/main.nf new file mode 100644 index 00000000..a93e55b5 --- /dev/null +++ b/modules/biobambam/bammarkduplicates2/main.nf @@ -0,0 +1,38 @@ +process BIOBAMBAM_BAMMARKDUPLICATES2 { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::biobambam=2.0.182" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/biobambam:2.0.182--h7d875b9_0': + 'quay.io/biocontainers/biobambam:2.0.182--h7d875b9_0' }" + + input: + tuple val(meta), path(bam) + + output: + tuple val(meta), path("*.bam") , emit: bam + tuple val(meta), path("*.metrics.txt"), emit: metrics + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + bammarkduplicates2 \\ + $args \\ + I=$bam \\ + O=${prefix}.bam \\ + M=${prefix}.metrics.txt \\ + tmpfile=$prefix \\ + markthreads=$task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + bammarkduplicates2: \$(echo \$(bammarkduplicates2 --version 2>&1) | sed 's/^This is biobambam2 version //; s/..biobambam2 is .*\$//' ) + END_VERSIONS + """ +} diff --git a/modules/biobambam/bammarkduplicates2/meta.yml b/modules/biobambam/bammarkduplicates2/meta.yml new file mode 100644 index 00000000..52e2eb75 --- /dev/null +++ b/modules/biobambam/bammarkduplicates2/meta.yml @@ -0,0 +1,44 @@ +name: biobambam_bammarkduplicates2 +description: Locate and tag duplicate reads in a BAM file +keywords: + - markduplicates + - bam + - cram +tools: + - biobambam: + description: | + biobambam is a set of tools for early stage alignment file processing. + homepage: https://gitlab.com/german.tischler/biobambam2 + documentation: https://gitlab.com/german.tischler/biobambam2/-/blob/master/README.md + doi: 10.1186/1751-0473-9-13 + licence: ["GPL v3"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file with duplicate reads marked/removed + pattern: "*.{bam}" + - metrics: + type: file + description: Duplicate metrics file generated by biobambam + pattern: "*.{metrics.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@muffato" diff --git a/modules/bismark/align/meta.yml b/modules/bismark/align/meta.yml index 79948e1c..f780c959 100644 --- a/modules/bismark/align/meta.yml +++ b/modules/bismark/align/meta.yml @@ -1,59 +1,59 @@ name: bismark_align description: Performs alignment of BS-Seq reads using bismark keywords: - - bismark - - 3-letter genome - - map - - methylation - - 5mC - - methylseq - - bisulphite - - bam + - bismark + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bam tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: dir + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - unmapped: - type: file - description: Output FastQ file(s) containing unmapped reads - pattern: "*.{fq.gz}" - - report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - 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 ] + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - unmapped: + type: file + description: Output FastQ file(s) containing unmapped reads + pattern: "*.{fq.gz}" + - report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bismark/deduplicate/meta.yml b/modules/bismark/deduplicate/meta.yml index 9e28cd22..2b89e520 100644 --- a/modules/bismark/deduplicate/meta.yml +++ b/modules/bismark/deduplicate/meta.yml @@ -1,52 +1,52 @@ name: bismark_deduplicate description: | - Removes alignments to the same position in the genome - from the Bismark mapping output. + Removes alignments to the same position in the genome + from the Bismark mapping output. keywords: - - bismark - - 3-letter genome - - map - - methylation - - 5mC - - methylseq - - bisulphite - - bam + - bismark + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bam tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Deduplicated output BAM file containing read alignments - pattern: "*.{deduplicated.bam}" - - report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - 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 ] + - bam: + type: file + description: Deduplicated output BAM file containing read alignments + pattern: "*.{deduplicated.bam}" + - report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bismark/genomepreparation/meta.yml b/modules/bismark/genomepreparation/meta.yml index 2a17f1fb..b30ff651 100644 --- a/modules/bismark/genomepreparation/meta.yml +++ b/modules/bismark/genomepreparation/meta.yml @@ -1,37 +1,37 @@ name: bismark_genomepreparation description: | - Converts a specified reference genome into two different bisulfite - converted versions and indexes them for alignments. + Converts a specified reference genome into two different bisulfite + converted versions and indexes them for alignments. keywords: - - bismark - - 3-letter genome - - index - - methylation - - 5mC - - methylseq - - bisulphite - - fasta + - bismark + - 3-letter genome + - index + - methylation + - 5mC + - methylseq + - bisulphite + - fasta tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: dir + description: Bismark genome index directory + pattern: "BismarkIndex" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bismark/methylationextractor/meta.yml b/modules/bismark/methylationextractor/meta.yml index 602fc06d..407cefca 100644 --- a/modules/bismark/methylationextractor/meta.yml +++ b/modules/bismark/methylationextractor/meta.yml @@ -1,67 +1,67 @@ name: bismark_methylationextractor description: Extracts methylation information for individual cytosines from alignments. keywords: - - bismark - - consensus - - map - - methylation - - 5mC - - methylseq - - bisulphite - - bam - - bedGraph + - bismark + - consensus + - map + - methylation + - 5mC + - methylseq + - bisulphite + - bam + - bedGraph tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file containing read alignments - pattern: "*.{bam}" - - index: - type: dir - description: Bismark genome index directory - pattern: "BismarkIndex" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file containing read alignments + pattern: "*.{bam}" + - index: + type: dir + description: Bismark genome index directory + pattern: "BismarkIndex" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: Bismark output file containing coverage and methylation metrics - pattern: "*.{bedGraph.gz}" - - methylation_calls: - type: file - description: Bismark output file containing strand-specific methylation calls - pattern: "*.{txt.gz}" - - coverage: - type: file - description: Bismark output file containing coverage metrics - pattern: "*.{cov.gz}" - - report: - type: file - description: Bismark splitting reports - pattern: "*_{splitting_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{M-bias.txt}" - - 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 ] + - bedgraph: + type: file + description: Bismark output file containing coverage and methylation metrics + pattern: "*.{bedGraph.gz}" + - methylation_calls: + type: file + description: Bismark output file containing strand-specific methylation calls + pattern: "*.{txt.gz}" + - coverage: + type: file + description: Bismark output file containing coverage metrics + pattern: "*.{cov.gz}" + - report: + type: file + description: Bismark splitting reports + pattern: "*_{splitting_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{M-bias.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bismark/report/meta.yml b/modules/bismark/report/meta.yml index e849e109..002aeb34 100644 --- a/modules/bismark/report/meta.yml +++ b/modules/bismark/report/meta.yml @@ -1,60 +1,60 @@ name: bismark_report description: Collects bismark alignment reports keywords: - - bismark - - qc - - methylation - - 5mC - - methylseq - - bisulphite - - report + - bismark + - qc + - methylation + - 5mC + - methylseq + - bisulphite + - report tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - align_report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*{splitting_report.txt}" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{txt}" - - fasta: - type: file - description: Input genome fasta file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - align_report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*{splitting_report.txt}" + - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{txt}" + - fasta: + type: file + description: Input genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - report: - type: file - description: Bismark reports - pattern: "*.{html,txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - report: + type: file + description: Bismark reports + pattern: "*.{html,txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bismark/summary/meta.yml b/modules/bismark/summary/meta.yml index 0494bb8e..5c8e8b6a 100644 --- a/modules/bismark/summary/meta.yml +++ b/modules/bismark/summary/meta.yml @@ -1,54 +1,54 @@ name: bismark_summary description: | - Uses Bismark report files of several samples in a run folder - to generate a graphical summary HTML report. + Uses Bismark report files of several samples in a run folder + to generate a graphical summary HTML report. keywords: - - bismark - - qc - - methylation - - 5mC - - methylseq - - bisulphite - - report - - summary + - bismark + - qc + - methylation + - 5mC + - methylseq + - bisulphite + - report + - summary tools: - - bismark: - description: | - Bismark is a tool to map bisulfite treated sequencing reads - and perform methylation calling in a quick and easy-to-use fashion. - homepage: https://github.com/FelixKrueger/Bismark - documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs - doi: 10.1093/bioinformatics/btr167 - licence: ['GPL-3.0-or-later'] + - bismark: + description: | + Bismark is a tool to map bisulfite treated sequencing reads + and perform methylation calling in a quick and easy-to-use fashion. + homepage: https://github.com/FelixKrueger/Bismark + documentation: https://github.com/FelixKrueger/Bismark/tree/master/Docs + doi: 10.1093/bioinformatics/btr167 + licence: ["GPL-3.0-or-later"] input: - - bam: - type: file - description: Bismark alignment - pattern: "*.{bam}" - - align_report: - type: file - description: Bismark alignment reports - pattern: "*{report.txt}" - - dedup_report: - type: file - description: Bismark deduplication reports - pattern: "*.{deduplication_report.txt}" - - splitting_report: - type: file - description: Bismark splitting reports - pattern: "*{splitting_report.txt}" - - mbias: - type: file - description: Text file containing methylation bias information - pattern: "*.{txt}" + - bam: + type: file + description: Bismark alignment + pattern: "*.{bam}" + - align_report: + type: file + description: Bismark alignment reports + pattern: "*{report.txt}" + - dedup_report: + type: file + description: Bismark deduplication reports + pattern: "*.{deduplication_report.txt}" + - splitting_report: + type: file + description: Bismark splitting reports + pattern: "*{splitting_report.txt}" + - mbias: + type: file + description: Text file containing methylation bias information + pattern: "*.{txt}" output: - - summary: - type: file - description: Bismark summary - pattern: "*.{html,txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - summary: + type: file + description: Bismark summary + pattern: "*.{html,txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/blast/blastn/meta.yml b/modules/blast/blastn/meta.yml index 39acb663..2742278d 100644 --- a/modules/blast/blastn/meta.yml +++ b/modules/blast/blastn/meta.yml @@ -1,41 +1,41 @@ name: blast_blastn description: Queries a BLAST DNA database keywords: - - fasta - - blast - - blastn - - DNA sequence + - fasta + - blast + - blastn + - DNA sequence tools: - - blast: - description: | - BLAST finds regions of similarity between biological sequences. - homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi - documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs - doi: 10.1016/S0022-2836(05)80360-2 - licence: ['US-Government-Work'] + - blast: + description: | + BLAST finds regions of similarity between biological sequences. + homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi + documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs + doi: 10.1016/S0022-2836(05)80360-2 + licence: ["US-Government-Work"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing queries sequences - pattern: "*.{fa,fasta}" - - db: - type: directory - description: Directory containing blast database - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing queries sequences + pattern: "*.{fa,fasta}" + - db: + type: directory + description: Directory containing blast database + pattern: "*" output: - - txt: - type: file - description: File containing blastn hits - pattern: "*.{blastn.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - txt: + type: file + description: File containing blastn hits + pattern: "*.{blastn.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/blast/makeblastdb/meta.yml b/modules/blast/makeblastdb/meta.yml index c9d18cba..83c4b292 100644 --- a/modules/blast/makeblastdb/meta.yml +++ b/modules/blast/makeblastdb/meta.yml @@ -1,31 +1,31 @@ name: blast_makeblastdb description: Builds a BLAST database keywords: - - fasta - - blast - - database + - fasta + - blast + - database tools: - - blast: - description: | - BLAST finds regions of similarity between biological sequences. - homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi - documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs - doi: 10.1016/S0022-2836(05)80360-2 - licence: ['US-Government-Work'] + - blast: + description: | + BLAST finds regions of similarity between biological sequences. + homepage: https://blast.ncbi.nlm.nih.gov/Blast.cgi + documentation: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=Blastdocs + doi: 10.1016/S0022-2836(05)80360-2 + licence: ["US-Government-Work"] input: - - fasta: - type: file - description: Input fasta file - pattern: "*.{fa,fasta}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fa,fasta}" output: - - db: - type: directory - description: Output directory containing blast database files - pattern: "*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - db: + type: directory + description: Output directory containing blast database files + pattern: "*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bowtie/align/meta.yml b/modules/bowtie/align/meta.yml index 07d480be..f5145b5a 100644 --- a/modules/bowtie/align/meta.yml +++ b/modules/bowtie/align/meta.yml @@ -1,46 +1,46 @@ name: bowtie_align description: Align reads to a reference genome using bowtie keywords: - - align - - fasta - - genome - - reference + - align + - fasta + - genome + - reference tools: - - bowtie: - description: | - bowtie is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bowtie-bio.sourceforge.net/index.shtml - documentation: http://bowtie-bio.sourceforge.net/manual.shtml - arxiv: arXiv:1303.3997 - licence: ['Artistic-2.0'] + - bowtie: + description: | + bowtie is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bowtie-bio.sourceforge.net/index.shtml + documentation: http://bowtie-bio.sourceforge.net/manual.shtml + arxiv: arXiv:1303.3997 + licence: ["Artistic-2.0"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: Bowtie genome index files - pattern: "*.ebwt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: Bowtie genome index files + pattern: "*.ebwt" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" authors: - - "@kevinmenden" + - "@kevinmenden" diff --git a/modules/bowtie/build/meta.yml b/modules/bowtie/build/meta.yml index 016adcfe..0c41bbac 100644 --- a/modules/bowtie/build/meta.yml +++ b/modules/bowtie/build/meta.yml @@ -1,32 +1,32 @@ name: bowtie_build description: Create bowtie index for reference genome keywords: - - index - - fasta - - genome - - reference + - index + - fasta + - genome + - reference tools: - - bowtie: - description: | - bowtie is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bowtie-bio.sourceforge.net/index.shtml - documentation: http://bowtie-bio.sourceforge.net/manual.shtml - arxiv: arXiv:1303.3997 - licence: ['Artistic-2.0'] + - bowtie: + description: | + bowtie is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bowtie-bio.sourceforge.net/index.shtml + documentation: http://bowtie-bio.sourceforge.net/manual.shtml + arxiv: arXiv:1303.3997 + licence: ["Artistic-2.0"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: file - description: Bowtie genome index files - pattern: "*.ebwt" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: file + description: Bowtie genome index files + pattern: "*.ebwt" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@kevinmenden" - - "@drpatelh" + - "@kevinmenden" + - "@drpatelh" diff --git a/modules/bowtie2/align/meta.yml b/modules/bowtie2/align/meta.yml index 77c9e397..f80421ec 100644 --- a/modules/bowtie2/align/meta.yml +++ b/modules/bowtie2/align/meta.yml @@ -1,51 +1,51 @@ name: bowtie2_align description: Align reads to a reference genome using bowtie2 keywords: - - align - - fasta - - genome - - reference + - align + - fasta + - genome + - reference tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ['GPL-3.0-or-later'] + - bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.ebwt" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.ebwt" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - - log: - type: file - description: Aligment log - pattern: "*.log" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - log: + type: file + description: Aligment log + pattern: "*.log" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bowtie2/build/meta.yml b/modules/bowtie2/build/meta.yml index ecc54e9b..2da9a217 100644 --- a/modules/bowtie2/build/meta.yml +++ b/modules/bowtie2/build/meta.yml @@ -1,33 +1,33 @@ name: bowtie2_build description: Builds bowtie index for reference genome keywords: - - build - - index - - fasta - - genome - - reference + - build + - index + - fasta + - genome + - reference tools: - - bowtie2: - description: | - Bowtie 2 is an ultrafast and memory-efficient tool for aligning - sequencing reads to long reference sequences. - homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml - documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml - doi: 10.1038/nmeth.1923 - licence: ['GPL-3.0-or-later'] + - bowtie2: + description: | + Bowtie 2 is an ultrafast and memory-efficient tool for aligning + sequencing reads to long reference sequences. + homepage: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml + documentation: http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml + doi: 10.1038/nmeth.1923 + licence: ["GPL-3.0-or-later"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: file - description: Bowtie2 genome index files - pattern: "*.bt2" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: file + description: Bowtie2 genome index files + pattern: "*.bt2" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/bwa/aln/meta.yml b/modules/bwa/aln/meta.yml index d2424a5f..a8b74b8b 100644 --- a/modules/bwa/aln/meta.yml +++ b/modules/bwa/aln/meta.yml @@ -10,30 +10,30 @@ keywords: - map - fastq tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://bio-bwa.sourceforge.net/ - doi: "10.1093/bioinformatics/btp324" - licence: ['GPL-3.0-or-later'] + - bwa: + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: http://bio-bwa.sourceforge.net/ + doi: "10.1093/bioinformatics/btp324" + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" output: - meta: diff --git a/modules/bwa/index/meta.yml b/modules/bwa/index/meta.yml index 11d62df3..2bbd81d9 100644 --- a/modules/bwa/index/meta.yml +++ b/modules/bwa/index/meta.yml @@ -1,32 +1,32 @@ name: bwa_index description: Create BWA index for reference genome keywords: - - index - - fasta - - genome - - reference + - index + - fasta + - genome + - reference tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://www.htslib.org/doc/samtools.html - arxiv: arXiv:1303.3997 - licence: ['GPL-3.0-or-later'] + - bwa: + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: http://www.htslib.org/doc/samtools.html + arxiv: arXiv:1303.3997 + licence: ["GPL-3.0-or-later"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: file - description: BWA genome index files - pattern: "*.{amb,ann,bwt,pac,sa}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: file + description: BWA genome index files + pattern: "*.{amb,ann,bwt,pac,sa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@maxulysse" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/bwa/mem/meta.yml b/modules/bwa/mem/meta.yml index c7c28f19..f84c5227 100644 --- a/modules/bwa/mem/meta.yml +++ b/modules/bwa/mem/meta.yml @@ -1,50 +1,50 @@ name: bwa_mem description: Performs fastq alignment to a fasta reference using BWA keywords: - - mem - - bwa - - alignment - - map - - fastq - - bam - - sam + - mem + - bwa + - alignment + - map + - fastq + - bam + - sam tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://www.htslib.org/doc/samtools.html - arxiv: arXiv:1303.3997 - licence: ['GPL-3.0-or-later'] + - bwa: + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: http://www.htslib.org/doc/samtools.html + arxiv: arXiv:1303.3997 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{amb,ann,bwt,pac,sa}" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@jeremy1805" + - "@drpatelh" + - "@jeremy1805" diff --git a/modules/bwa/sampe/meta.yml b/modules/bwa/sampe/meta.yml index 7b530a03..5920dc32 100644 --- a/modules/bwa/sampe/meta.yml +++ b/modules/bwa/sampe/meta.yml @@ -11,14 +11,14 @@ keywords: - sam - bam tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://bio-bwa.sourceforge.net/ - doi: "10.1093/bioinformatics/btp324" - licence: ['GPL-3.0-or-later'] + - bwa: + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: http://bio-bwa.sourceforge.net/ + doi: "10.1093/bioinformatics/btp324" + licence: ["GPL-3.0-or-later"] input: - meta: @@ -35,9 +35,9 @@ input: description: SAI file specified alongside meta and reads in input channel. pattern: "*.sai" - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX + pattern: "bwa/" output: - meta: diff --git a/modules/bwa/samse/meta.yml b/modules/bwa/samse/meta.yml index 9a9ecb39..9524a4c8 100644 --- a/modules/bwa/samse/meta.yml +++ b/modules/bwa/samse/meta.yml @@ -12,14 +12,14 @@ keywords: - bam tools: - - bwa: - description: | - BWA is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: http://bio-bwa.sourceforge.net/ - documentation: http://bio-bwa.sourceforge.net/ - doi: "10.1093/bioinformatics/btp324" - licence: ['GPL-3.0-or-later'] + - bwa: + description: | + BWA is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: http://bio-bwa.sourceforge.net/ + documentation: http://bio-bwa.sourceforge.net/ + doi: "10.1093/bioinformatics/btp324" + licence: ["GPL-3.0-or-later"] input: - meta: @@ -36,9 +36,9 @@ input: description: SAI file specified alongside meta and reads in input channel. pattern: "*.sai" - index: - type: directory - description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX - pattern: "bwa/" + type: directory + description: Directory containing BWA index files (amb,ann,bwt,pac,sa) from BWA_INDEX + pattern: "bwa/" output: - meta: diff --git a/modules/bwamem2/index/meta.yml b/modules/bwamem2/index/meta.yml index e0f6014c..1b52448d 100644 --- a/modules/bwamem2/index/meta.yml +++ b/modules/bwamem2/index/meta.yml @@ -1,30 +1,30 @@ name: bwamem2_index description: Create BWA-mem2 index for reference genome keywords: - - index - - fasta - - genome - - reference + - index + - fasta + - genome + - reference tools: - - bwa: - description: | - BWA-mem2 is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: https://github.com/bwa-mem2/bwa-mem2 - documentation: https://github.com/bwa-mem2/bwa-mem2#usage - licence: ['MIT'] + - bwa: + description: | + BWA-mem2 is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: https://github.com/bwa-mem2/bwa-mem2 + documentation: https://github.com/bwa-mem2/bwa-mem2#usage + licence: ["MIT"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: file - description: BWA genome index files - pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: file + description: BWA genome index files + pattern: "*.{0132,amb,ann,bwt.2bit.64,pac}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/bwamem2/mem/meta.yml b/modules/bwamem2/mem/meta.yml index 71e83759..25c97f91 100644 --- a/modules/bwamem2/mem/meta.yml +++ b/modules/bwamem2/mem/meta.yml @@ -1,49 +1,49 @@ name: bwamem2_mem description: Performs fastq alignment to a fasta reference using BWA keywords: - - mem - - bwa - - alignment - - map - - fastq - - bam - - sam + - mem + - bwa + - alignment + - map + - fastq + - bam + - sam tools: - - bwa: - description: | - BWA-mem2 is a software package for mapping DNA sequences against - a large reference genome, such as the human genome. - homepage: https://github.com/bwa-mem2/bwa-mem2 - documentation: http://www.htslib.org/doc/samtools.html - arxiv: arXiv:1303.3997 - licence: ['MIT'] + - bwa: + description: | + BWA-mem2 is a software package for mapping DNA sequences against + a large reference genome, such as the human genome. + homepage: https://github.com/bwa-mem2/bwa-mem2 + documentation: http://www.htslib.org/doc/samtools.html + arxiv: arXiv:1303.3997 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: file - description: BWA genome index files - pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" - - sort_bam: - type: boolean - description: use samtools sort (true) or samtools view (false) - pattern: "true or false" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: file + description: BWA genome index files + pattern: "Directory containing BWA index *.{0132,amb,ann,bwt.2bit.64,pac}" + - sort_bam: + type: boolean + description: use samtools sort (true) or samtools view (false) + pattern: "true or false" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/bwameth/align/meta.yml b/modules/bwameth/align/meta.yml index 1cd66237..1db8210e 100644 --- a/modules/bwameth/align/meta.yml +++ b/modules/bwameth/align/meta.yml @@ -1,52 +1,52 @@ name: bwameth_align description: Performs alignment of BS-Seq reads using bwameth keywords: - - bwameth - - alignment - - 3-letter genome - - map - - methylation - - 5mC - - methylseq - - bisulphite - - fastq - - bam + - bwameth + - alignment + - 3-letter genome + - map + - methylation + - 5mC + - methylseq + - bisulphite + - fastq + - bam tools: - - bwameth: - description: | - Fast and accurate alignment of BS-Seq reads - using bwa-mem and a 3-letter genome. - homepage: https://github.com/brentp/bwa-meth - documentation: https://github.com/brentp/bwa-meth - arxiv: arXiv:1401.1129 - licence: ['MIT'] + - bwameth: + description: | + Fast and accurate alignment of BS-Seq reads + using bwa-mem and a 3-letter genome. + homepage: https://github.com/brentp/bwa-meth + documentation: https://github.com/brentp/bwa-meth + arxiv: arXiv:1401.1129 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - index: - type: dir - description: Directory containing bwameth genome index + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - index: + type: dir + description: Directory containing bwameth genome index output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - 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 ] + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/bwameth/index/meta.yml b/modules/bwameth/index/meta.yml index 352dfd0f..8c116b6e 100644 --- a/modules/bwameth/index/meta.yml +++ b/modules/bwameth/index/meta.yml @@ -1,33 +1,33 @@ name: bwameth_index description: Performs indexing of c2t converted reference genome keywords: - - bwameth - - 3-letter genome - - index - - methylseq - - bisulphite - - fasta + - bwameth + - 3-letter genome + - index + - methylseq + - bisulphite + - fasta tools: - - bwameth: - description: | - Fast and accurate alignment of BS-Seq reads - using bwa-mem and a 3-letter genome. - homepage: https://github.com/brentp/bwa-meth - documentation: https://github.com/brentp/bwa-meth - arxiv: arXiv:1401.1129 - licence: ['MIT'] + - bwameth: + description: | + Fast and accurate alignment of BS-Seq reads + using bwa-mem and a 3-letter genome. + homepage: https://github.com/brentp/bwa-meth + documentation: https://github.com/brentp/bwa-meth + arxiv: arXiv:1401.1129 + licence: ["MIT"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - index: - type: dir - description: Directory containing bwameth genome index - pattern: "index" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - index: + type: dir + description: Directory containing bwameth genome index + pattern: "index" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/cat/cat/meta.yml b/modules/cat/cat/meta.yml index b3f370ee..e0a6361d 100644 --- a/modules/cat/cat/meta.yml +++ b/modules/cat/cat/meta.yml @@ -10,7 +10,7 @@ tools: homepage: None documentation: https://man7.org/linux/man-pages/man1/cat.1.html tool_dev_url: None - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - files_in: type: file diff --git a/modules/cat/fastq/meta.yml b/modules/cat/fastq/meta.yml index 1992fa34..c836598e 100644 --- a/modules/cat/fastq/meta.yml +++ b/modules/cat/fastq/meta.yml @@ -1,39 +1,39 @@ name: cat_fastq description: Concatenates fastq files keywords: - - fastq - - concatenate + - fastq + - concatenate tools: - - cat: - description: | - The cat utility reads files sequentially, writing them to the standard output. - documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html - licence: ['GPL-3.0-or-later'] + - cat: + description: | + The cat utility reads files sequentially, writing them to the standard output. + documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FastQ files to be concatenated. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FastQ files to be concatenated. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Merged fastq file - pattern: "*.{merged.fastq.gz}" - - 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 ] + - reads: + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/cellranger/count/meta.yml b/modules/cellranger/count/meta.yml index e4647c98..c7c65751 100644 --- a/modules/cellranger/count/meta.yml +++ b/modules/cellranger/count/meta.yml @@ -1,40 +1,40 @@ name: cellranger_count description: Module to use Cell Ranger's pipelines analyze sequencing data produced from Chromium Single Cell Gene Expression. keywords: - - align - - count - - reference + - align + - count + - reference tools: - - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. - homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger - documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - doi: "" - licence: 10x Genomics EULA + - cellranger: + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger + documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" + licence: 10x Genomics EULA input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - reference: - type: folder - description: Folder containing all the reference indices needed by Cell Ranger + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - reference: + type: folder + description: Folder containing all the reference indices needed by Cell Ranger output: - - outs: - type: file - description: Files containing the outputs of Cell Ranger - pattern: "sample-${meta.gem}/outs/*" - - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - outs: + type: file + description: Files containing the outputs of Cell Ranger + pattern: "sample-${meta.gem}/outs/*" + - versions: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@Emiller88" diff --git a/modules/cellranger/mkfastq/meta.yml b/modules/cellranger/mkfastq/meta.yml index e288fb8c..1aff3064 100644 --- a/modules/cellranger/mkfastq/meta.yml +++ b/modules/cellranger/mkfastq/meta.yml @@ -7,31 +7,31 @@ keywords: - illumina - bcl2fastq tools: - - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. - homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger - documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - doi: "" - licence: 10x Genomics EULA + - cellranger: + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger + documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" + licence: 10x Genomics EULA input: - - bcl: - type: file - description: Base call files - pattern: "*.bcl.bgzf" - - csv: - type: file - description: Sample sheet - pattern: "*.csv" + - bcl: + type: file + description: Base call files + pattern: "*.bcl.bgzf" + - csv: + type: file + description: Sample sheet + pattern: "*.csv" output: - - fastq: - type: file - description: Unaligned FastQ files - pattern: "*.fastq.gz" - - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - fastq: + type: file + description: Unaligned FastQ files + pattern: "*.fastq.gz" + - versions: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@Emiller88" diff --git a/modules/cellranger/mkgtf/meta.yml b/modules/cellranger/mkgtf/meta.yml index c160072f..2136ef4e 100644 --- a/modules/cellranger/mkgtf/meta.yml +++ b/modules/cellranger/mkgtf/meta.yml @@ -1,31 +1,31 @@ name: cellranger_mkgtf description: Module to build a filtered gtf needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkgtf command. keywords: - - reference - - mkref - - index + - reference + - mkref + - index tools: - - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. - homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger - documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - doi: "" - licence: 10x Genomics EULA + - cellranger: + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger + documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" + licence: 10x Genomics EULA input: - - gtf: - type: file - description: - pattern: "*.gtf" + - gtf: + type: file + description: + pattern: "*.gtf" output: - - gtf: - type: folder - description: gtf transcriptome file - pattern: "*.filtered.gtf" - - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - gtf: + type: folder + description: gtf transcriptome file + pattern: "*.filtered.gtf" + - versions: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" - "@Emiller88" diff --git a/modules/cellranger/mkref/meta.yml b/modules/cellranger/mkref/meta.yml index 06bf5b93..171f6d08 100644 --- a/modules/cellranger/mkref/meta.yml +++ b/modules/cellranger/mkref/meta.yml @@ -1,37 +1,37 @@ name: cellranger_mkref description: Module to build the reference needed by the 10x Genomics Cell Ranger tool. Uses the cellranger mkref command. keywords: - - reference - - mkref - - index + - reference + - mkref + - index tools: - - cellranger: - description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. - homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger - documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov - doi: "" - licence: 10x Genomics EULA + - cellranger: + description: Cell Ranger by 10x Genomics is a set of analysis pipelines that process Chromium single-cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis, and more. + homepage: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger + documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + tool_dev_url: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ov + doi: "" + licence: 10x Genomics EULA input: - - fasta: - type: file - description: fasta genome file - pattern: "*.{fasta,fa}" - - gtf: - type: file - description: gtf transcriptome file - pattern: "*.gtf" - - reference_name: - type: val - description: name to give the reference folder - pattern: str + - fasta: + type: file + description: fasta genome file + pattern: "*.{fasta,fa}" + - gtf: + type: file + description: gtf transcriptome file + pattern: "*.gtf" + - reference_name: + type: val + description: name to give the reference folder + pattern: str output: - - reference: - type: folder - description: Folder containing all the reference indices needed by Cell Ranger - - versions: - type: file - description: File containing software version - pattern: "versions.yml" + - reference: + type: folder + description: Folder containing all the reference indices needed by Cell Ranger + - versions: + type: file + description: File containing software version + pattern: "versions.yml" authors: - "@ggabernet" diff --git a/modules/checkm/lineagewf/meta.yml b/modules/checkm/lineagewf/meta.yml index 29c6096e..bcdb472f 100644 --- a/modules/checkm/lineagewf/meta.yml +++ b/modules/checkm/lineagewf/meta.yml @@ -19,7 +19,7 @@ tools: documentation: https://github.com/Ecogenomics/CheckM/wiki tool_dev_url: https://github.com/Ecogenomics/CheckM doi: "10.1101/gr.186072.114" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/chromap/chromap/meta.yml b/modules/chromap/chromap/meta.yml index 57936c67..a86fddc9 100644 --- a/modules/chromap/chromap/meta.yml +++ b/modules/chromap/chromap/meta.yml @@ -1,19 +1,19 @@ name: chromap_chromap description: | - Performs preprocessing and alignment of chromatin fastq files to - fasta reference files using chromap. + Performs preprocessing and alignment of chromatin fastq files to + fasta reference files using chromap. keywords: - - chromap - - alignment - - map - - fastq - - bam - - sam - - hi-c - - atac-seq - - chip-seq - - trimming - - duplicate removal + - chromap + - alignment + - map + - fastq + - bam + - sam + - hi-c + - atac-seq + - chip-seq + - trimming + - duplicate removal tools: - chromap: description: Fast alignment and preprocessing of chromatin profiles @@ -21,7 +21,7 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: type: map diff --git a/modules/chromap/index/meta.yml b/modules/chromap/index/meta.yml index a6a18fe9..6659221f 100644 --- a/modules/chromap/index/meta.yml +++ b/modules/chromap/index/meta.yml @@ -1,10 +1,10 @@ name: chromap_index description: Indexes a fasta reference genome ready for chromatin profiling. keywords: - - index - - fasta - - genome - - reference + - index + - fasta + - genome + - reference tools: - chromap: description: Fast alignment and preprocessing of chromatin profiles @@ -12,7 +12,7 @@ tools: documentation: https://github.com/haowenz/chromap tool_dev_url: https://github.com/haowenz/chromap doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - fasta: diff --git a/modules/clonalframeml/meta.yml b/modules/clonalframeml/meta.yml index 874a04be..af5cf91b 100644 --- a/modules/clonalframeml/meta.yml +++ b/modules/clonalframeml/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/xavierdidelot/clonalframeml/wiki tool_dev_url: https://github.com/xavierdidelot/ClonalFrameML doi: "10.1371/journal.pcbi.1004041" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/cmseq/polymut/meta.yml b/modules/cmseq/polymut/meta.yml index 49e6b519..56a65cd9 100644 --- a/modules/cmseq/polymut/meta.yml +++ b/modules/cmseq/polymut/meta.yml @@ -17,7 +17,7 @@ tools: homepage: https://github.com/SegataLab/cmseq documentation: https://github.com/SegataLab/cmseq tool_dev_url: https://github.com/SegataLab/cmseq - licence: ['MIT License'] + licence: ["MIT License"] input: - meta: diff --git a/modules/cnvkit/batch/meta.yml b/modules/cnvkit/batch/meta.yml index 0d263041..474c55f2 100644 --- a/modules/cnvkit/batch/meta.yml +++ b/modules/cnvkit/batch/meta.yml @@ -10,7 +10,7 @@ tools: CNVkit is a Python library and command-line software toolkit to infer and visualize copy number from high-throughput DNA sequencing data. It is designed for use with hybrid capture, including both whole-exome and custom target panels, and short-read sequencing platforms such as Illumina and Ion Torrent. homepage: https://cnvkit.readthedocs.io/en/stable/index.html documentation: https://cnvkit.readthedocs.io/en/stable/index.html - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] params: - outdir: type: string @@ -85,9 +85,9 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@kaurravneet4123" - - "@KevinMenden" - - "@MaxUlysse" - - "@drpatelh" - - "@fbdtemme" - - "@lassefolkersen" + - "@kaurravneet4123" + - "@KevinMenden" + - "@MaxUlysse" + - "@drpatelh" + - "@fbdtemme" + - "@lassefolkersen" diff --git a/modules/cooler/cload/meta.yml b/modules/cooler/cload/meta.yml index 8ac75911..ddb0443b 100644 --- a/modules/cooler/cload/meta.yml +++ b/modules/cooler/cload/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/cooler/digest/meta.yml b/modules/cooler/digest/meta.yml index 6ce95ad7..56e2c08c 100644 --- a/modules/cooler/digest/meta.yml +++ b/modules/cooler/digest/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - fasta: diff --git a/modules/cooler/dump/meta.yml b/modules/cooler/dump/meta.yml index a9d1afd5..fc12cdf3 100644 --- a/modules/cooler/dump/meta.yml +++ b/modules/cooler/dump/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - meta: diff --git a/modules/cooler/merge/meta.yml b/modules/cooler/merge/meta.yml index f5c0a733..2688dc96 100644 --- a/modules/cooler/merge/meta.yml +++ b/modules/cooler/merge/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/cooler/zoomify/meta.yml b/modules/cooler/zoomify/meta.yml index 74bdbf44..d9e12b05 100644 --- a/modules/cooler/zoomify/meta.yml +++ b/modules/cooler/zoomify/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://cooler.readthedocs.io/en/latest/index.html tool_dev_url: https://github.com/open2c/cooler doi: "10.1093/bioinformatics/btz540" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/csvtk/concat/meta.yml b/modules/csvtk/concat/meta.yml index 6c7f9f10..2d2f856d 100644 --- a/modules/csvtk/concat/meta.yml +++ b/modules/csvtk/concat/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://bioinf.shenwei.me/csvtk tool_dev_url: https://github.com/shenwei356/csvtk doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/csvtk/split/meta.yml b/modules/csvtk/split/meta.yml index 45b71d14..334cc6ac 100644 --- a/modules/csvtk/split/meta.yml +++ b/modules/csvtk/split/meta.yml @@ -7,13 +7,13 @@ keywords: tools: - csvtk: description: - CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit - that allows rapid data investigation and manipulation. + CSVTK is a cross-platform, efficient and practical CSV/TSV toolkit + that allows rapid data investigation and manipulation. homepage: https://bioinf.shenwei.me/csvtk/ documentation: https://bioinf.shenwei.me/csvtk/ tool_dev_url: https://github.com/shenwei356/csvtk doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/custom/dumpsoftwareversions/meta.yml b/modules/custom/dumpsoftwareversions/meta.yml index 5b5b8a60..60b546a0 100644 --- a/modules/custom/dumpsoftwareversions/meta.yml +++ b/modules/custom/dumpsoftwareversions/meta.yml @@ -8,7 +8,7 @@ tools: description: Custom module used to dump software versions within the nf-core pipeline template homepage: https://github.com/nf-core/tools documentation: https://github.com/nf-core/tools - licence: ['MIT'] + licence: ["MIT"] input: - versions: type: file diff --git a/modules/custom/getchromsizes/meta.yml b/modules/custom/getchromsizes/meta.yml index eb1db4bb..ee6c2571 100644 --- a/modules/custom/getchromsizes/meta.yml +++ b/modules/custom/getchromsizes/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://www.htslib.org/doc/samtools.html tool_dev_url: https://github.com/samtools/samtools doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + licence: ["MIT"] input: - fasta: @@ -33,7 +33,6 @@ output: description: File containing software version pattern: "versions.yml" - authors: - "@tamara-hodgetts" - "@chris-cheshire" diff --git a/modules/cutadapt/meta.yml b/modules/cutadapt/meta.yml index b4e6f6e7..bcfe291c 100644 --- a/modules/cutadapt/meta.yml +++ b/modules/cutadapt/meta.yml @@ -11,7 +11,7 @@ tools: Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. documentation: https://cutadapt.readthedocs.io/en/stable/index.html doi: DOI:10.14806/ej.17.1.200 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/damageprofiler/meta.yml b/modules/damageprofiler/meta.yml index 19ba908f..b41aeb8d 100644 --- a/modules/damageprofiler/meta.yml +++ b/modules/damageprofiler/meta.yml @@ -18,7 +18,7 @@ tools: documentation: https://damageprofiler.readthedocs.io/ tool_dev_url: https://github.com/Integrative-Transcriptomics/DamageProfiler doi: "10.1093/bioinformatics/btab190" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/dastool/dastool/meta.yml b/modules/dastool/dastool/meta.yml index 12d31e9f..a77df9bd 100644 --- a/modules/dastool/dastool/meta.yml +++ b/modules/dastool/dastool/meta.yml @@ -20,7 +20,7 @@ tools: documentation: https://github.com/cmks/DAS_Tool tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" - licence: ['BSD'] + licence: ["BSD"] input: - meta: @@ -47,7 +47,6 @@ input: type: val description: Engine used for single copy gene identification. USEARCH is not supported due to it being proprietary [blast/diamond] - output: - meta: type: map @@ -84,7 +83,7 @@ output: pattern: "*.proteins.faa" - fasta_archaea_scg: type: file - description: Results of archaeal single-copy-gene prediction + description: Results of archaeal single-copy-gene prediction pattern: "*.archaea.scg" - fasta_bacteria_scg: type: file diff --git a/modules/dastool/scaffolds2bin/meta.yml b/modules/dastool/scaffolds2bin/meta.yml index f41a3cf2..0bf8618d 100644 --- a/modules/dastool/scaffolds2bin/meta.yml +++ b/modules/dastool/scaffolds2bin/meta.yml @@ -20,7 +20,7 @@ tools: documentation: https://github.com/cmks/DAS_Tool tool_dev_url: https://github.com/cmks/DAS_Tool doi: "10.1038/s41564-018-0171-1" - licence: ['BSD'] + licence: ["BSD"] input: - meta: diff --git a/modules/dedup/meta.yml b/modules/dedup/meta.yml index 0ddd648f..17cf4e26 100644 --- a/modules/dedup/meta.yml +++ b/modules/dedup/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://dedup.readthedocs.io/en/latest/ tool_dev_url: https://github.com/apeltzer/DeDup doi: "10.1186/s13059-016-0918-z" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -54,7 +54,5 @@ output: description: Dedup log information pattern: "*log" - - authors: - "@jfy133" diff --git a/modules/deeparg/downloaddata/meta.yml b/modules/deeparg/downloaddata/meta.yml index 6cfa192e..352999e2 100644 --- a/modules/deeparg/downloaddata/meta.yml +++ b/modules/deeparg/downloaddata/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ doi: "10.1186/s40168-018-0401-z" - licence: ['MIT'] + licence: ["MIT"] input: - none: There is no input. This module downloads a pre-built database for use with deepARG. diff --git a/modules/deeparg/predict/meta.yml b/modules/deeparg/predict/meta.yml index 244b9df7..fa50c70e 100644 --- a/modules/deeparg/predict/meta.yml +++ b/modules/deeparg/predict/meta.yml @@ -16,7 +16,7 @@ tools: documentation: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ tool_dev_url: https://bitbucket.org/gusphdproj/deeparg-ss/src/master/ doi: "10.1186/s40168-018-0401-z" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/deeptools/bamcoverage/main.nf b/modules/deeptools/bamcoverage/main.nf new file mode 100644 index 00000000..83e3ffeb --- /dev/null +++ b/modules/deeptools/bamcoverage/main.nf @@ -0,0 +1,37 @@ +process DEEPTOOLS_BAMCOVERAGE { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0': + 'quay.io/biocontainers/deeptools:3.5.1--py_0' }" + + input: + tuple val(meta), path(input), path(input_index) + + output: + tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true + tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}.bigWig" + + """ + bamCoverage \ + --bam $input \ + $args \ + --numberOfProcessors ${task.cpus} \ + --outFileName ${prefix} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g") + END_VERSIONS + """ +} diff --git a/modules/deeptools/bamcoverage/meta.yml b/modules/deeptools/bamcoverage/meta.yml new file mode 100644 index 00000000..d0590b2a --- /dev/null +++ b/modules/deeptools/bamcoverage/meta.yml @@ -0,0 +1,49 @@ +name: deeptools_bamcoverage +description: This tool takes an alignment of reads or fragments as input (BAM file) and generates a coverage track (bigWig or bedGraph) as output. +keywords: + - sort +tools: + - deeptools: + description: A set of user-friendly tools for normalization and visualzation of deep-sequencing data + homepage: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html + documentation: https://deeptools.readthedocs.io/en/develop/content/tools/bamCoverage.html + tool_dev_url: https://github.com/deeptools/deepTools/ + doi: "https://doi.org/10.1093/nar/gkw257" + licence: ['GPL v3'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - bigWig: + type: file + description: BigWig file + pattern: "*.bigWig" + - bedgraph: + type: file + description: Bedgraph file + pattern: "*.bedgraph" + +authors: + - "@FriederikeHanssen" diff --git a/modules/deeptools/computematrix/meta.yml b/modules/deeptools/computematrix/meta.yml index 584fade1..eaa990dd 100644 --- a/modules/deeptools/computematrix/meta.yml +++ b/modules/deeptools/computematrix/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/deeptools/plotfingerprint/meta.yml b/modules/deeptools/plotfingerprint/meta.yml index 3acd1471..07c25748 100644 --- a/modules/deeptools/plotfingerprint/meta.yml +++ b/modules/deeptools/plotfingerprint/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/deeptools/plotheatmap/meta.yml b/modules/deeptools/plotheatmap/meta.yml index 34f2865b..ea206fb6 100644 --- a/modules/deeptools/plotheatmap/meta.yml +++ b/modules/deeptools/plotheatmap/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/deeptools/plotprofile/meta.yml b/modules/deeptools/plotprofile/meta.yml index 5b61aed4..795fda44 100644 --- a/modules/deeptools/plotprofile/meta.yml +++ b/modules/deeptools/plotprofile/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://deeptools.readthedocs.io/en/develop/index.html tool_dev_url: https://github.com/deeptools/deepTools doi: "10.1093/nar/gku365" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/deepvariant/meta.yml b/modules/deepvariant/meta.yml index d4423d69..b2d480a3 100644 --- a/modules/deepvariant/meta.yml +++ b/modules/deepvariant/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/google/deepvariant tool_dev_url: https://github.com/google/deepvariant doi: "https://doi.org/10.1038/nbt.4235" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/delly/call/meta.yml b/modules/delly/call/meta.yml index 56539188..642e095d 100644 --- a/modules/delly/call/meta.yml +++ b/modules/delly/call/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/dellytools/delly/blob/master/README.md tool_dev_url: None doi: "DOI:10.1093/bioinformatics/bts378" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - meta: diff --git a/modules/diamond/blastp/meta.yml b/modules/diamond/blastp/meta.yml index 228c1a22..8ac1d371 100644 --- a/modules/diamond/blastp/meta.yml +++ b/modules/diamond/blastp/meta.yml @@ -12,32 +12,32 @@ tools: documentation: https://github.com/bbuchfink/diamond/wiki tool_dev_url: https://github.com/bbuchfink/diamond doi: "doi:10.1038/s41592-021-01101-x" - licence: ['GPL v3.0'] + licence: ["GPL v3.0"] input: - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta}" + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta}" - db: - type: directory - description: Directory containing the protein blast database - pattern: "*" + type: directory + description: Directory containing the protein blast database + pattern: "*" output: - txt: - type: file - description: File containing blastp hits - pattern: "*.{blastp.txt}" + type: file + description: File containing blastp hits + pattern: "*.{blastp.txt}" - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" diff --git a/modules/diamond/blastx/meta.yml b/modules/diamond/blastx/meta.yml index 4a3ab9b6..7eb3d7b4 100644 --- a/modules/diamond/blastx/meta.yml +++ b/modules/diamond/blastx/meta.yml @@ -12,32 +12,32 @@ tools: documentation: https://github.com/bbuchfink/diamond/wiki tool_dev_url: https://github.com/bbuchfink/diamond doi: "doi:10.1038/s41592-021-01101-x" - licence: ['GPL v3.0'] + licence: ["GPL v3.0"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input fasta file containing query sequences - pattern: "*.{fa,fasta}" - - db: - type: directory - description: Directory containing the nucelotide blast database - pattern: "*" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input fasta file containing query sequences + pattern: "*.{fa,fasta}" + - db: + type: directory + description: Directory containing the nucelotide blast database + pattern: "*" output: - - txt: - type: file - description: File containing blastx hits - pattern: "*.{blastx.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - txt: + type: file + description: File containing blastx hits + pattern: "*.{blastx.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@spficklin" diff --git a/modules/diamond/makedb/meta.yml b/modules/diamond/makedb/meta.yml index e378be7e..5db193ee 100644 --- a/modules/diamond/makedb/meta.yml +++ b/modules/diamond/makedb/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/bbuchfink/diamond/wiki tool_dev_url: https://github.com/bbuchfink/diamond doi: "doi:10.1038/s41592-021-01101-x" - licence: ['GPL v3.0'] + licence: ["GPL v3.0"] input: - fasta: diff --git a/modules/dragmap/align/meta.yml b/modules/dragmap/align/meta.yml index e943ccf8..dcce34fb 100644 --- a/modules/dragmap/align/meta.yml +++ b/modules/dragmap/align/meta.yml @@ -1,42 +1,42 @@ name: dragmap_align description: Performs fastq alignment to a reference using DRAGMAP keywords: - - alignment - - map - - fastq - - bam - - sam + - alignment + - map + - fastq + - bam + - sam tools: - - dragmap: - description: Dragmap is the Dragen mapper/aligner Open Source Software. - homepage: https://github.com/Illumina/dragmap - documentation: https://github.com/Illumina/dragmap - tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage - doi: "" - licence: ['GPL v3'] + - dragmap: + description: Dragmap is the Dragen mapper/aligner Open Source Software. + homepage: https://github.com/Illumina/dragmap + documentation: https://github.com/Illumina/dragmap + tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage + doi: "" + licence: ["GPL v3"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. - - hashmap: - type: file - description: DRAGMAP hash table - pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. + - hashmap: + type: file + description: DRAGMAP hash table + pattern: "Directory containing DRAGMAP hash table *.{cmp,.bin,.txt}" output: - - bam: - type: file - description: Output BAM file containing read alignments - pattern: "*.{bam}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - bam: + type: file + description: Output BAM file containing read alignments + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Emiller88" diff --git a/modules/dragmap/hashtable/meta.yml b/modules/dragmap/hashtable/meta.yml index 86e58789..f86a5dbb 100644 --- a/modules/dragmap/hashtable/meta.yml +++ b/modules/dragmap/hashtable/meta.yml @@ -1,30 +1,30 @@ name: dragmap_hashtable description: Create DRAGEN hashtable for reference genome keywords: - - index - - fasta - - genome - - reference + - index + - fasta + - genome + - reference tools: - - dragmap: - description: Dragmap is the Dragen mapper/aligner Open Source Software. - homepage: https://github.com/Illumina/dragmap - documentation: https://github.com/Illumina/dragmap - tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage - doi: "" - licence: ['GPL v3'] + - dragmap: + description: Dragmap is the Dragen mapper/aligner Open Source Software. + homepage: https://github.com/Illumina/dragmap + documentation: https://github.com/Illumina/dragmap + tool_dev_url: https://github.com/Illumina/dragmap#basic-command-line-usage + doi: "" + licence: ["GPL v3"] input: - - fasta: - type: file - description: Input genome fasta file + - fasta: + type: file + description: Input genome fasta file output: - - hashmap: - type: file - description: DRAGMAP hash table - pattern: "*.{cmp,.bin,.txt}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - hashmap: + type: file + description: DRAGMAP hash table + pattern: "*.{cmp,.bin,.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@Emiller88" diff --git a/modules/dragonflye/meta.yml b/modules/dragonflye/meta.yml index 773795db..3260a205 100644 --- a/modules/dragonflye/meta.yml +++ b/modules/dragonflye/meta.yml @@ -10,7 +10,7 @@ tools: description: Microbial assembly pipeline for Nanopore reads homepage: https://github.com/rpetit3/dragonflye documentation: https://github.com/rpetit3/dragonflye/blob/main/README.md - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: @@ -19,9 +19,9 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: file - description: Input Nanopore FASTQ file - pattern: "*.fastq.gz" + type: file + description: Input Nanopore FASTQ file + pattern: "*.fastq.gz" output: - meta: type: map diff --git a/modules/dshbio/exportsegments/meta.yml b/modules/dshbio/exportsegments/meta.yml index eddb6d09..5dcb1364 100644 --- a/modules/dshbio/exportsegments/meta.yml +++ b/modules/dshbio/exportsegments/meta.yml @@ -1,41 +1,41 @@ name: dshbio_exportsegments description: Export assembly segment sequences in GFA 1.0 format to FASTA format keywords: - - gfa - - assembly - - segment + - gfa + - assembly + - segment tools: - - dshbio: - description: | - Reads, features, variants, assemblies, alignments, genomic range trees, pangenome - graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 - or later. - homepage: https://github.com/heuermh/dishevelled-bio - documentation: https://github.com/heuermh/dishevelled-bio - licence: ['LGPL-3.0-or-later'] + - dshbio: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio + licence: ["LGPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Assembly segments in uncompressed or compressed GFA 1.0 format - pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gfa: + type: file + description: Assembly segments in uncompressed or compressed GFA 1.0 format + pattern: "*.{gfa|gfa.bgz|gfa.gz|gfa.zst}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Assembly segment sequences in gzipped FASTA format - pattern: "*.{fa.gz}" - - 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 ] + - fasta: + type: file + description: Assembly segment sequences in gzipped FASTA format + pattern: "*.{fa.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/dshbio/filterbed/meta.yml b/modules/dshbio/filterbed/meta.yml index 77054be4..4547349e 100644 --- a/modules/dshbio/filterbed/meta.yml +++ b/modules/dshbio/filterbed/meta.yml @@ -1,39 +1,39 @@ name: dshbio_filterbed description: Filter features in gzipped BED format keywords: - - bed + - bed tools: - - dshbio: - description: | - Reads, features, variants, assemblies, alignments, genomic range trees, pangenome - graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 - or later. - homepage: https://github.com/heuermh/dishevelled-bio - documentation: https://github.com/heuermh/dishevelled-bio - licence: ['LGPL-3.0-or-later'] + - dshbio: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio + licence: ["LGPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format - pattern: "*.{bed.gz}" - - 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 ] + - bed: + type: file + description: Features in gzipped BED format + pattern: "*.{bed.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/dshbio/filtergff3/meta.yml b/modules/dshbio/filtergff3/meta.yml index aa1bce43..b7de7939 100644 --- a/modules/dshbio/filtergff3/meta.yml +++ b/modules/dshbio/filtergff3/meta.yml @@ -1,39 +1,39 @@ name: dshbio_filtergff3 description: Filter features in gzipped GFF3 format keywords: - - gff3 + - gff3 tools: - - dshbio: - description: | - Reads, features, variants, assemblies, alignments, genomic range trees, pangenome - graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 - or later. - homepage: https://github.com/heuermh/dishevelled-bio - documentation: https://github.com/heuermh/dishevelled-bio - licence: ['LGPL-3.0-or-later'] + - dshbio: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio + licence: ["LGPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format - pattern: "*.{gff3.gz}" - - 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 ] + - gff3: + type: file + description: Features in gzipped GFF3 format + pattern: "*.{gff3.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/dshbio/splitbed/meta.yml b/modules/dshbio/splitbed/meta.yml index a35ea25f..8e8c473f 100644 --- a/modules/dshbio/splitbed/meta.yml +++ b/modules/dshbio/splitbed/meta.yml @@ -1,39 +1,39 @@ name: dshbio_splitbed description: Split features in gzipped BED format keywords: - - bed + - bed tools: - - dshbio: - description: | - Reads, features, variants, assemblies, alignments, genomic range trees, pangenome - graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 - or later. - homepage: https://github.com/heuermh/dishevelled-bio - documentation: https://github.com/heuermh/dishevelled-bio - licence: ['LGPL-3.0-or-later'] + - dshbio: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio + licence: ["LGPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in gzipped BED format to split - pattern: "*.{bed.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Features in gzipped BED format to split + pattern: "*.{bed.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Features in split gzipped BED formatted files - pattern: "*.{bed.gz}" - - 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 ] + - bed: + type: file + description: Features in split gzipped BED formatted files + pattern: "*.{bed.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/dshbio/splitgff3/meta.yml b/modules/dshbio/splitgff3/meta.yml index fdbbe16a..d23f2a15 100644 --- a/modules/dshbio/splitgff3/meta.yml +++ b/modules/dshbio/splitgff3/meta.yml @@ -1,39 +1,39 @@ name: dshbio_splitgff3 description: Split features in gzipped GFF3 format keywords: - - gff3 + - gff3 tools: - - dshbio: - description: | - Reads, features, variants, assemblies, alignments, genomic range trees, pangenome - graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 - or later. - homepage: https://github.com/heuermh/dishevelled-bio - documentation: https://github.com/heuermh/dishevelled-bio - licence: ['LGPL-3.0-or-later'] + - dshbio: + description: | + Reads, features, variants, assemblies, alignments, genomic range trees, pangenome + graphs, and a bunch of random command line tools for bioinformatics. LGPL version 3 + or later. + homepage: https://github.com/heuermh/dishevelled-bio + documentation: https://github.com/heuermh/dishevelled-bio + licence: ["LGPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in gzipped GFF3 format to split - pattern: "*.{gff3.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - gff3: + type: file + description: Features in gzipped GFF3 format to split + pattern: "*.{gff3.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gff3: - type: file - description: Features in split gzipped GFF3 formatted files - pattern: "*.{gff3.gz}" - - 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 ] + - gff3: + type: file + description: Features in split gzipped GFF3 formatted files + pattern: "*.{gff3.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/ectyper/meta.yml b/modules/ectyper/meta.yml index a6beca29..233290e7 100644 --- a/modules/ectyper/meta.yml +++ b/modules/ectyper/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/phac-nml/ecoli_serotyping tool_dev_url: https://github.com/phac-nml/ecoli_serotyping doi: "" - licence: ['Apache 2'] + licence: ["Apache 2"] input: - meta: diff --git a/modules/emmtyper/meta.yml b/modules/emmtyper/meta.yml index 019a8e4c..a63c40b6 100644 --- a/modules/emmtyper/meta.yml +++ b/modules/emmtyper/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/MDU-PHL/emmtyper tool_dev_url: https://github.com/MDU-PHL/emmtyper doi: "" - licence: ['GNU General Public v3 (GPL v3)'] + licence: ["GNU General Public v3 (GPL v3)"] input: - meta: diff --git a/modules/ensemblvep/meta.yml b/modules/ensemblvep/meta.yml index 1b819227..cd9c8905 100644 --- a/modules/ensemblvep/meta.yml +++ b/modules/ensemblvep/meta.yml @@ -1,65 +1,65 @@ name: ENSEMBLVEP description: Ensembl Variant Effect Predictor (VEP) keywords: - - annotation + - annotation tools: - - ensemblvep: - description: | - VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs - or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. - 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'] + - ensemblvep: + description: | + VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs + or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. + 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"] params: - - use_cache: - type: boolean - description: | - Enable the usage of containers with cache - Does not work with conda - - vep_tag: - type: value - description: | - Specify the tag for the container - https://hub.docker.com/r/nfcore/vep/tags + - use_cache: + type: boolean + description: | + Enable the usage of containers with cache + Does not work with conda + - vep_tag: + type: value + description: | + Specify the tag for the container + https://hub.docker.com/r/nfcore/vep/tags input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: | - vcf to annotate - - genome: - type: value - description: | - which genome to annotate with - - species: - type: value - description: | - which species to annotate with - - cache_version: - type: value - description: | - which version of the cache to annotate with - - cache: - type: file - description: | - path to VEP 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 + - genome: + type: value + description: | + which genome to annotate with + - species: + type: value + description: | + which species to annotate with + - cache_version: + type: value + description: | + which version of the cache to annotate with + - cache: + type: file + description: | + path to VEP cache (optional) output: - - vcf: - type: file - description: | - annotated vcf - pattern: "*.ann.vcf" - - report: - type: file - description: VEP report file - pattern: "*.html" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - vcf: + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" + - report: + type: file + description: VEP report file + pattern: "*.html" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/expansionhunter/meta.yml b/modules/expansionhunter/meta.yml index 17d72bb4..3483c0db 100644 --- a/modules/expansionhunter/meta.yml +++ b/modules/expansionhunter/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/Illumina/ExpansionHunter/blob/master/docs/01_Introduction.md tool_dev_url: None doi: "10.1093/bioinformatics/btz431" - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/fargene/meta.yml b/modules/fargene/meta.yml index 35e98008..785b4cc3 100644 --- a/modules/fargene/meta.yml +++ b/modules/fargene/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/fannyhb/fargene tool_dev_url: https://github.com/fannyhb/fargene doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -96,6 +96,5 @@ output: description: The from FASTQ to FASTA converted input files and their translated input sequences. Are only saved if option --store-peptides is used. pattern: "*.{fasta}" - authors: - "@louperelo" diff --git a/modules/fastani/meta.yml b/modules/fastani/meta.yml index dc62d485..2a997716 100644 --- a/modules/fastani/meta.yml +++ b/modules/fastani/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/ParBLiSS/FastANI tool_dev_url: https://github.com/ParBLiSS/FastANI doi: 10.1038/s41467-018-07641-9 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/fastp/meta.yml b/modules/fastp/meta.yml index a1875faf..f53bb09f 100644 --- a/modules/fastp/meta.yml +++ b/modules/fastp/meta.yml @@ -10,7 +10,7 @@ tools: A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. documentation: https://github.com/OpenGene/fastp doi: https://doi.org/10.1093/bioinformatics/bty560 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/fastqc/meta.yml b/modules/fastqc/meta.yml index b09553a3..4da5bb5a 100644 --- a/modules/fastqc/meta.yml +++ b/modules/fastqc/meta.yml @@ -1,52 +1,52 @@ name: fastqc description: Run FastQC on sequenced reads keywords: - - quality control - - qc - - adapters - - fastq + - quality control + - qc + - adapters + - fastq tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ['GPL-2.0-only'] + - fastqc: + description: | + FastQC gives general quality metrics about your reads. + It provides information about the quality score distribution + across your reads, the per base sequence content (%A/C/G/T). + You get information about adapter contamination and other + overrepresented sequences. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ + documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - 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 ] + - html: + type: file + description: FastQC report + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive + pattern: "*_{fastqc.zip}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@grst" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/fastqscan/meta.yml b/modules/fastqscan/meta.yml index 99538b5a..909a964f 100644 --- a/modules/fastqscan/meta.yml +++ b/modules/fastqscan/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/rpetit3/fastq-scan tool_dev_url: https://github.com/rpetit3/fastq-scan doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/fasttree/meta.yml b/modules/fasttree/meta.yml index 5906675b..c90e8d7c 100644 --- a/modules/fasttree/meta.yml +++ b/modules/fasttree/meta.yml @@ -10,7 +10,7 @@ tools: documentation: http://www.microbesonline.org/fasttree/#Usage tool_dev_url: None doi: "" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - alignment: diff --git a/modules/fgbio/callmolecularconsensusreads/meta.yml b/modules/fgbio/callmolecularconsensusreads/meta.yml index 523f3214..37182512 100644 --- a/modules/fgbio/callmolecularconsensusreads/meta.yml +++ b/modules/fgbio/callmolecularconsensusreads/meta.yml @@ -2,44 +2,44 @@ name: fgbio_callmolecularconsensusreads description: Calls consensus sequences from reads with the same unique molecular tag. keywords: - - UMIs - - consensus sequence - - bam - - sam + - UMIs + - consensus sequence + - bam + - sam tools: - - fgbio: - description: Tools for working with genomic and high throughput sequencing data. - homepage: https://github.com/fulcrumgenomics/fgbio - documentation: http://fulcrumgenomics.github.io/fgbio/ - licence: ['MIT'] + - fgbio: + description: Tools for working with genomic and high throughput sequencing data. + homepage: https://github.com/fulcrumgenomics/fgbio + documentation: http://fulcrumgenomics.github.io/fgbio/ + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - bam: - type: file - description: | - The input SAM or BAM file. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - bam: + type: file + description: | + The input SAM or BAM file. + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Output SAM or BAM file to write consensus reads. - pattern: "*.{bam,sam}" - - 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 ] + - bam: + type: file + description: | + Output SAM or BAM file to write consensus reads. + pattern: "*.{bam,sam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@sruthipsuresh" + - "@sruthipsuresh" diff --git a/modules/fgbio/fastqtobam/meta.yml b/modules/fgbio/fastqtobam/meta.yml index e356d315..3081cafc 100644 --- a/modules/fgbio/fastqtobam/meta.yml +++ b/modules/fgbio/fastqtobam/meta.yml @@ -1,6 +1,6 @@ name: fgbio_fastqtobam description: | - Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file + Using the FGBIO tools, converts FASTQ files sequenced with UMIs into BAM files, moving the UMI barcode into the RX field of the BAM file keywords: - fastqtobam - fgbio @@ -11,7 +11,7 @@ tools: documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - reads: @@ -22,11 +22,11 @@ input: - read_structure: type: string description: | - A read structure should always be provided for each of the fastq files. - If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string - will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T"). - If the read does not contain any UMI, the structure will be +T (i.e. only template of any length). - https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures + A read structure should always be provided for each of the fastq files. + If single end, the string will contain only one structure (i.e. "2M11S+T"), if paired-end the string + will contain two structures separated by a blank space (i.e. "2M11S+T 2M11S+T"). + If the read does not contain any UMI, the structure will be +T (i.e. only template of any length). + https://github.com/fulcrumgenomics/fgbio/wiki/Read-Structures output: - meta: diff --git a/modules/fgbio/groupreadsbyumi/meta.yml b/modules/fgbio/groupreadsbyumi/meta.yml index 18ce149e..c544040b 100644 --- a/modules/fgbio/groupreadsbyumi/meta.yml +++ b/modules/fgbio/groupreadsbyumi/meta.yml @@ -1,11 +1,11 @@ name: fgbio_groupreadsbyumi description: | - Groups reads together that appear to have come from the same original molecule. - Reads are grouped by template, and then templates are sorted by the 5’ mapping positions - of the reads from the template, used from earliest mapping position to latest. - Reads that have the same end positions are then sub-grouped by UMI sequence. - (!) Note: the MQ tag is required on reads with mapped mates (!) - This can be added using samblaster with the optional argument --addMateTags. + Groups reads together that appear to have come from the same original molecule. + Reads are grouped by template, and then templates are sorted by the 5’ mapping positions + of the reads from the template, used from earliest mapping position to latest. + Reads that have the same end positions are then sub-grouped by UMI sequence. + (!) Note: the MQ tag is required on reads with mapped mates (!) + This can be added using samblaster with the optional argument --addMateTags. keywords: - UMI - groupreads @@ -17,7 +17,7 @@ tools: documentation: http://fulcrumgenomics.github.io/fgbio/tools/latest/ tool_dev_url: https://github.com/fulcrumgenomics/fgbio doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/fgbio/sortbam/meta.yml b/modules/fgbio/sortbam/meta.yml index b8040dab..465b9606 100644 --- a/modules/fgbio/sortbam/meta.yml +++ b/modules/fgbio/sortbam/meta.yml @@ -1,43 +1,43 @@ name: fgbio_sortbam description: Sorts a SAM or BAM file. Several sort orders are available, including coordinate, queryname, random, and randomquery. keywords: - - sort - - bam - - sam + - sort + - bam + - sam tools: - - fgbio: - description: Tools for working with genomic and high throughput sequencing data. - homepage: https://github.com/fulcrumgenomics/fgbio - documentation: http://fulcrumgenomics.github.io/fgbio/ - licence: ['MIT'] + - fgbio: + description: Tools for working with genomic and high throughput sequencing data. + homepage: https://github.com/fulcrumgenomics/fgbio + documentation: http://fulcrumgenomics.github.io/fgbio/ + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false, collapse:false ] - - bam: - type: file - description: | - The input SAM or BAM file to be sorted. - pattern: "*.{bam,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false, collapse:false ] + - bam: + type: file + description: | + The input SAM or BAM file to be sorted. + pattern: "*.{bam,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Output SAM or BAM file. - pattern: "*.{bam,sam}" - - 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 ] + - bam: + type: file + description: | + Output SAM or BAM file. + pattern: "*.{bam,sam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@sruthipsuresh" + - "@sruthipsuresh" diff --git a/modules/filtlong/meta.yml b/modules/filtlong/meta.yml index 7616a176..b3626e62 100644 --- a/modules/filtlong/meta.yml +++ b/modules/filtlong/meta.yml @@ -14,7 +14,7 @@ tools: documentation: None tool_dev_url: https://github.com/rrwick/Filtlong doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/flash/meta.yml b/modules/flash/meta.yml index 06807523..e5a783f5 100644 --- a/modules/flash/meta.yml +++ b/modules/flash/meta.yml @@ -11,7 +11,7 @@ tools: homepage: https://ccb.jhu.edu/software/FLASH/ documentation: {} doi: 10.1093/bioinformatics/btr507 - licence: ['GPL v3+'] + licence: ["GPL v3+"] input: - meta: diff --git a/modules/freebayes/main.nf b/modules/freebayes/main.nf index e67e4c72..73b1da96 100644 --- a/modules/freebayes/main.nf +++ b/modules/freebayes/main.nf @@ -8,10 +8,9 @@ process FREEBAYES { 'quay.io/biocontainers/freebayes:1.3.5--py38ha193a2f_3' }" input: - tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index) + tuple val(meta), path(input_1), path(input_1_index), path(input_2), path(input_2_index), path(target_bed) path fasta path fasta_fai - path targets path samples path populations path cnv @@ -27,7 +26,7 @@ process FREEBAYES { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" def input = input_2 ? "${input_1} ${input_2}" : "${input_1}" - def targets_file = targets ? "--target ${targets}" : "" + def targets_file = target_bed ? "--target ${target_bed}" : "" def samples_file = samples ? "--samples ${samples}" : "" def populations_file = populations ? "--populations ${populations}" : "" def cnv_file = cnv ? "--cnv-map ${cnv}" : "" diff --git a/modules/freebayes/meta.yml b/modules/freebayes/meta.yml index abba1daa..cbbd297e 100644 --- a/modules/freebayes/meta.yml +++ b/modules/freebayes/meta.yml @@ -16,7 +16,7 @@ tools: documentation: https://github.com/freebayes/freebayes tool_dev_url: https://github.com/freebayes/freebayes doi: "arXiv:1207.3907" - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -31,7 +31,11 @@ input: - input_index: type: file description: BAM/CRAM/SAM index file - pattern: "*.bam.bai" + pattern: "*.{bai,crai}" + - target_bed: + type: file + description: Optional - Limit analysis to targets listed in this BED-format FILE. + pattern: "*.bed" - fasta: type: file description: reference fasta file @@ -40,10 +44,6 @@ input: type: file description: reference fasta file index pattern: "*.{fa,fasta}.fai" - - targets: - type: file - description: Optional - Limit analysis to targets listed in this BED-format FILE. - pattern: "*.bed" - samples: type: file description: Optional - Limit analysis to samples listed (one per line) in the FILE. @@ -55,10 +55,10 @@ input: - cnv: type: file description: | - A copy number map BED file, which has either a sample-level ploidy: - sample_name copy_number - or a region-specific format: - seq_name start end sample_name copy_number + A copy number map BED file, which has either a sample-level ploidy: + sample_name copy_number + or a region-specific format: + seq_name start end sample_name copy_number pattern: "*.bed" output: diff --git a/modules/gatk4/applybqsr/main.nf b/modules/gatk4/applybqsr/main.nf index 672e93e0..851afc04 100644 --- a/modules/gatk4/applybqsr/main.nf +++ b/modules/gatk4/applybqsr/main.nf @@ -2,10 +2,10 @@ process GATK4_APPLYBQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(bqsr_table), path(intervals) diff --git a/modules/gatk4/applybqsr/meta.yml b/modules/gatk4/applybqsr/meta.yml index ad1f82a1..82d3cbf3 100644 --- a/modules/gatk4/applybqsr/meta.yml +++ b/modules/gatk4/applybqsr/meta.yml @@ -6,13 +6,13 @@ keywords: tools: - gatk4: description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: @@ -47,7 +47,6 @@ input: description: GATK sequence dictionary pattern: "*.dict" - output: - meta: type: map diff --git a/modules/gatk4/applyvqsr/main.nf b/modules/gatk4/applyvqsr/main.nf index 006840b3..3049aa79 100644 --- a/modules/gatk4/applyvqsr/main.nf +++ b/modules/gatk4/applyvqsr/main.nf @@ -2,19 +2,16 @@ process GATK4_APPLYVQSR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(recal), path(recalidx), path(tranches) path fasta path fai path dict - val allelespecific - val truthsensitivity - val mode output: tuple val(meta), path("*.vcf.gz") , emit: vcf @@ -28,9 +25,6 @@ process GATK4_APPLYVQSR { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" refCommand = fasta ? "-R ${fasta} " : '' - alleleSpecificCommand = allelespecific ? '-AS' : '' - truthSensitivityCommand = truthsensitivity ? "--truth-sensitivity-filter-level ${truthsensitivity}" : '' - modeCommand = mode ? "--mode ${mode} " : 'SNP' def avail_mem = 3 if (!task.memory) { @@ -43,11 +37,8 @@ process GATK4_APPLYVQSR { ${refCommand} \\ -V ${vcf} \\ -O ${prefix}.vcf.gz \\ - ${alleleSpecificCommand} \\ - ${truthSensitivityCommand} \\ --tranches-file $tranches \\ --recal-file $recal \\ - ${modeCommand} \\ $args cat <<-END_VERSIONS > versions.yml diff --git a/modules/gatk4/applyvqsr/meta.yml b/modules/gatk4/applyvqsr/meta.yml index b757f3e9..4a99db45 100644 --- a/modules/gatk4/applyvqsr/meta.yml +++ b/modules/gatk4/applyvqsr/meta.yml @@ -17,7 +17,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: @@ -57,18 +57,6 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" - - allelespecific: - type: boolean - description: Whether or not to run ApplyVQSR in allele specific mode, this should be kept the same as the stage 1 VariantRecalibrator run. - pattern: "{true,false}" - - truthsensitivity: - type: double - description: Value to be used as the truth sensitivity cutoff score. - pattern: "99.0" - - mode: - type: String - description: Specifies which recalibration mode to employ, should be the same as the stage 1 VariantRecalibrator run. (SNP is default, BOTH is intended for testing only) - pattern: "{SNP,INDEL,BOTH}" output: - vcf: diff --git a/modules/gatk4/baserecalibrator/main.nf b/modules/gatk4/baserecalibrator/main.nf index 48c127f0..ecb41d9b 100644 --- a/modules/gatk4/baserecalibrator/main.nf +++ b/modules/gatk4/baserecalibrator/main.nf @@ -2,10 +2,10 @@ process GATK4_BASERECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/gatk4/baserecalibrator/meta.yml b/modules/gatk4/baserecalibrator/meta.yml index 641a50df..2e52b8ab 100644 --- a/modules/gatk4/baserecalibrator/meta.yml +++ b/modules/gatk4/baserecalibrator/meta.yml @@ -5,14 +5,13 @@ keywords: tools: - gatk4: description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] - + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/bedtointervallist/main.nf b/modules/gatk4/bedtointervallist/main.nf index 9f2b2dfe..74256dd1 100644 --- a/modules/gatk4/bedtointervallist/main.nf +++ b/modules/gatk4/bedtointervallist/main.nf @@ -2,10 +2,10 @@ process GATK4_BEDTOINTERVALLIST { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bed) diff --git a/modules/gatk4/bedtointervallist/meta.yml b/modules/gatk4/bedtointervallist/meta.yml index 910f9552..986f1592 100644 --- a/modules/gatk4/bedtointervallist/meta.yml +++ b/modules/gatk4/bedtointervallist/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/calculatecontamination/main.nf b/modules/gatk4/calculatecontamination/main.nf index 177f4878..298739ab 100644 --- a/modules/gatk4/calculatecontamination/main.nf +++ b/modules/gatk4/calculatecontamination/main.nf @@ -2,10 +2,10 @@ process GATK4_CALCULATECONTAMINATION { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(pileup), path(matched) diff --git a/modules/gatk4/calculatecontamination/meta.yml b/modules/gatk4/calculatecontamination/meta.yml index 8c843732..e5e870dc 100644 --- a/modules/gatk4/calculatecontamination/meta.yml +++ b/modules/gatk4/calculatecontamination/meta.yml @@ -16,7 +16,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/createsequencedictionary/main.nf b/modules/gatk4/createsequencedictionary/main.nf index 714843c2..87d52a59 100644 --- a/modules/gatk4/createsequencedictionary/main.nf +++ b/modules/gatk4/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESEQUENCEDICTIONARY { tag "$fasta" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: path fasta diff --git a/modules/gatk4/createsequencedictionary/meta.yml b/modules/gatk4/createsequencedictionary/meta.yml index 54f479b3..bd247888 100644 --- a/modules/gatk4/createsequencedictionary/meta.yml +++ b/modules/gatk4/createsequencedictionary/meta.yml @@ -1,32 +1,32 @@ name: gatk4_createsequencedictionary description: Creates a sequence dictionary for a reference sequence keywords: - - dictionary - - fasta + - dictionary + - fasta tools: - - gatk: - description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. - homepage: https://gatk.broadinstitute.org/hc/en-us - documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s - doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + - gatk: + description: | + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + doi: 10.1158/1538-7445.AM2017-3590 + licence: ["Apache-2.0"] input: - - fasta: - type: file - description: Input fasta file - pattern: "*.{fasta,fa}" + - fasta: + type: file + description: Input fasta file + pattern: "*.{fasta,fa}" output: - - dict: - type: file - description: gatk dictionary file - pattern: "*.{dict}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - dict: + type: file + description: gatk dictionary file + pattern: "*.{dict}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/gatk4/createsomaticpanelofnormals/main.nf b/modules/gatk4/createsomaticpanelofnormals/main.nf index a82c24d8..c030f4e3 100644 --- a/modules/gatk4/createsomaticpanelofnormals/main.nf +++ b/modules/gatk4/createsomaticpanelofnormals/main.nf @@ -2,10 +2,10 @@ process GATK4_CREATESOMATICPANELOFNORMALS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(genomicsdb) diff --git a/modules/gatk4/estimatelibrarycomplexity/main.nf b/modules/gatk4/estimatelibrarycomplexity/main.nf index 2894e305..ba68bf70 100644 --- a/modules/gatk4/estimatelibrarycomplexity/main.nf +++ b/modules/gatk4/estimatelibrarycomplexity/main.nf @@ -2,10 +2,10 @@ process GATK4_ESTIMATELIBRARYCOMPLEXITY { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(cram) diff --git a/modules/gatk4/estimatelibrarycomplexity/meta.yml b/modules/gatk4/estimatelibrarycomplexity/meta.yml index 94c1817d..9f2dee60 100644 --- a/modules/gatk4/estimatelibrarycomplexity/meta.yml +++ b/modules/gatk4/estimatelibrarycomplexity/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/fastqtosam/main.nf b/modules/gatk4/fastqtosam/main.nf index 631c0394..0c85a74f 100644 --- a/modules/gatk4/fastqtosam/main.nf +++ b/modules/gatk4/fastqtosam/main.nf @@ -2,10 +2,10 @@ process GATK4_FASTQTOSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(reads) diff --git a/modules/gatk4/fastqtosam/meta.yml b/modules/gatk4/fastqtosam/meta.yml index 8bd9eed5..0b173274 100644 --- a/modules/gatk4/fastqtosam/meta.yml +++ b/modules/gatk4/fastqtosam/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -24,8 +24,9 @@ input: e.g. [ id:'test', single_end:false ] - reads: type: file - description: List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + description: + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. pattern: "*.fastq.gz" output: diff --git a/modules/gatk4/filtermutectcalls/main.nf b/modules/gatk4/filtermutectcalls/main.nf index a7dd9a61..77175c7d 100644 --- a/modules/gatk4/filtermutectcalls/main.nf +++ b/modules/gatk4/filtermutectcalls/main.nf @@ -2,10 +2,10 @@ process GATK4_FILTERMUTECTCALLS { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(stats), path(orientationbias), path(segmentation), path(contaminationfile), val(contaminationest) diff --git a/modules/gatk4/filtermutectcalls/meta.yml b/modules/gatk4/filtermutectcalls/meta.yml index 7d85e2b9..5182c89f 100644 --- a/modules/gatk4/filtermutectcalls/meta.yml +++ b/modules/gatk4/filtermutectcalls/meta.yml @@ -1,6 +1,6 @@ name: gatk4_filtermutectcalls description: | - Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering. + Filters the raw output of mutect2, can optionally use outputs of calculatecontamination and learnreadorientationmodel to improve filtering. keywords: - filtermutectcalls - mutect2 diff --git a/modules/gatk4/gatherbqsrreports/main.nf b/modules/gatk4/gatherbqsrreports/main.nf index f8d91a92..279f1ac8 100644 --- a/modules/gatk4/gatherbqsrreports/main.nf +++ b/modules/gatk4/gatherbqsrreports/main.nf @@ -2,10 +2,10 @@ process GATK4_GATHERBQSRREPORTS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(recal_table) diff --git a/modules/gatk4/gatherbqsrreports/meta.yml b/modules/gatk4/gatherbqsrreports/meta.yml index f71afd69..62d008d2 100644 --- a/modules/gatk4/gatherbqsrreports/meta.yml +++ b/modules/gatk4/gatherbqsrreports/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/gatk4/gatherpileupsummaries/main.nf b/modules/gatk4/gatherpileupsummaries/main.nf new file mode 100644 index 00000000..52e57127 --- /dev/null +++ b/modules/gatk4/gatherpileupsummaries/main.nf @@ -0,0 +1,45 @@ +process GATK4_GATHERPILEUPSUMMARIES { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + + + input: + tuple val(meta), path(pileup) + path dict + + output: + tuple val(meta), path("*.pileupsummaries.table"), emit: table + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def input = pileup.collect{ "-I ${it} " }.join(' ') + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK GatherPileupSummaries] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" \ + GatherPileupSummaries \ + --sequence-dictionary ${dict} \ + ${input} \ + -O ${prefix}.pileupsummaries.table + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/gatherpileupsummaries/meta.yml b/modules/gatk4/gatherpileupsummaries/meta.yml new file mode 100644 index 00000000..7885a930 --- /dev/null +++ b/modules/gatk4/gatherpileupsummaries/meta.yml @@ -0,0 +1,41 @@ +name: gatk4_gatherpileupsummaries +description: write your description here +keywords: + - sort +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ['BSD-3-clause'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - pileup: + type: (list of) file(s) + description: Pileup files from gatk4/getpileupsummaries + pattern: "*.pileups.table" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - table: + type: file + description: Pileup file + pattern: "*.pileups.table" + +authors: + - "@FriederikeHanssen" diff --git a/modules/gatk4/genomicsdbimport/main.nf b/modules/gatk4/genomicsdbimport/main.nf index e88471e1..d2d89ccc 100644 --- a/modules/gatk4/genomicsdbimport/main.nf +++ b/modules/gatk4/genomicsdbimport/main.nf @@ -2,10 +2,10 @@ process GATK4_GENOMICSDBIMPORT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(tbi), path(intervalfile), val(intervalval), path(wspace) diff --git a/modules/gatk4/genotypegvcfs/main.nf b/modules/gatk4/genotypegvcfs/main.nf index c3e41229..b596e005 100644 --- a/modules/gatk4/genotypegvcfs/main.nf +++ b/modules/gatk4/genotypegvcfs/main.nf @@ -2,13 +2,13 @@ process GATK4_GENOTYPEGVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: - tuple val(meta), path(gvcf), path(gvcf_index), path(intervals) + tuple val(meta), path(gvcf), path(gvcf_index), path(intervals), path(intervals_index) path fasta path fasta_index path fasta_dict diff --git a/modules/gatk4/genotypegvcfs/meta.yml b/modules/gatk4/genotypegvcfs/meta.yml index 2c9767b2..f465f835 100644 --- a/modules/gatk4/genotypegvcfs/meta.yml +++ b/modules/gatk4/genotypegvcfs/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: @@ -27,7 +27,10 @@ input: pattern: ["*.{vcf,vcf.gz}", "*.{idx,tbi}"] - intervals: type: file - description: Bed file with the genomic regions included in the library (optional) + description: Interval file with the genomic regions included in the library (optional) + - intervals_index: + type: file + description: Interval index file (optional) - fasta: type: file description: Reference fasta file diff --git a/modules/gatk4/getpileupsummaries/main.nf b/modules/gatk4/getpileupsummaries/main.nf index 3667a210..5395c068 100644 --- a/modules/gatk4/getpileupsummaries/main.nf +++ b/modules/gatk4/getpileupsummaries/main.nf @@ -2,16 +2,18 @@ process GATK4_GETPILEUPSUMMARIES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: - tuple val(meta), path(bam), path(bai) + tuple val(meta), path(input), path(index), path(intervals) + path fasta + path fai + path dict path variants path variants_tbi - path sites output: tuple val(meta), path('*.pileups.table'), emit: table @@ -23,9 +25,8 @@ process GATK4_GETPILEUPSUMMARIES { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def sitesCommand = '' - - sitesCommand = sites ? " -L ${sites} " : " -L ${variants} " + def sitesCommand = intervals ? " -L ${intervals} " : " -L ${variants} " + def reference = fasta ? " -R ${fasta}" :"" def avail_mem = 3 if (!task.memory) { @@ -35,9 +36,10 @@ process GATK4_GETPILEUPSUMMARIES { } """ gatk --java-options "-Xmx${avail_mem}g" GetPileupSummaries \\ - -I $bam \\ + -I $input \\ -V $variants \\ $sitesCommand \\ + ${reference} \\ -O ${prefix}.pileups.table \\ $args diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml index 0add299b..a70cf1e5 100644 --- a/modules/gatk4/getpileupsummaries/meta.yml +++ b/modules/gatk4/getpileupsummaries/meta.yml @@ -15,7 +15,7 @@ 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 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: @@ -23,14 +23,30 @@ input: description: | Groovy Map containing sample information e.g. [ id:'test' ] - - bam: + - input: type: file - description: BAM file to be summarised. - pattern: "*.bam" - - bai: + description: BAM/CRAM file to be summarised. + pattern: "*.{bam,cram}" + - input_index: type: file - description: BAM file index. - pattern: "*.bam.bai" + description: BAM/CRAM file index. + pattern: "*.{bai,crai}" + - intervals: + type: file + description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. + pattern: "*.interval_list" + - fasta: + type: file + description: The reference fasta file + pattern: "*.fasta" + - fai: + type: file + description: Index of reference fasta file + pattern: "*.fasta.fai" + - dict: + type: file + description: GATK sequence dictionary + pattern: "*.dict" - variants: type: file description: Population vcf of germline sequencing, containing allele fractions. Is also used as sites file if no separate sites file is specified. @@ -39,10 +55,7 @@ input: type: file description: Index file for the germline resource. pattern: "*.vcf.gz.tbi" - - sites: - type: file - description: File containing specified sites to be used for the summary. If this option is not specified, variants file is used instead automatically. - pattern: "*.interval_list" + output: - pileup: diff --git a/modules/gatk4/haplotypecaller/main.nf b/modules/gatk4/haplotypecaller/main.nf index 6f03ffd2..33871fcf 100644 --- a/modules/gatk4/haplotypecaller/main.nf +++ b/modules/gatk4/haplotypecaller/main.nf @@ -2,10 +2,10 @@ process GATK4_HAPLOTYPECALLER { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(input), path(input_index), path(intervals) diff --git a/modules/gatk4/haplotypecaller/meta.yml b/modules/gatk4/haplotypecaller/meta.yml index 869bd1d2..81851a96 100644 --- a/modules/gatk4/haplotypecaller/meta.yml +++ b/modules/gatk4/haplotypecaller/meta.yml @@ -7,13 +7,13 @@ keywords: tools: - gatk4: description: | - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + with a primary focus on variant discovery and genotyping. Its powerful processing engine + and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/indexfeaturefile/main.nf b/modules/gatk4/indexfeaturefile/main.nf index b5add0e0..275e51f5 100644 --- a/modules/gatk4/indexfeaturefile/main.nf +++ b/modules/gatk4/indexfeaturefile/main.nf @@ -2,10 +2,10 @@ process GATK4_INDEXFEATUREFILE { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(feature_file) diff --git a/modules/gatk4/indexfeaturefile/meta.yml b/modules/gatk4/indexfeaturefile/meta.yml index eebe6b85..721350a9 100644 --- a/modules/gatk4/indexfeaturefile/meta.yml +++ b/modules/gatk4/indexfeaturefile/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s tool_dev_url: https://github.com/broadinstitute/gatk doi: "10.1158/1538-7445.AM2017-3590" - licence: ['BSD-3-clause'] + licence: ["BSD-3-clause"] input: - meta: diff --git a/modules/gatk4/intervallisttobed/main.nf b/modules/gatk4/intervallisttobed/main.nf new file mode 100644 index 00000000..24d20be1 --- /dev/null +++ b/modules/gatk4/intervallisttobed/main.nf @@ -0,0 +1,41 @@ +process GATK4_INTERVALLISTTOBED { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + + input: + tuple val(meta), path(interval) + + output: + tuple val(meta), path("*.bed"), emit: bed + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK IntervalListToBed] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" IntervalListToBed \\ + --INPUT ${interval} \\ + --OUTPUT ${prefix}.bed \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/intervallisttobed/meta.yml b/modules/gatk4/intervallisttobed/meta.yml new file mode 100644 index 00000000..90b78c05 --- /dev/null +++ b/modules/gatk4/intervallisttobed/meta.yml @@ -0,0 +1,41 @@ +name: gatk4_intervallisttobed +keywords: + - interval + - bed +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - interval: + type: file + description: Interval list + pattern: "*.{interval,interval_list}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: BED file + pattern: "*.bed" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@FriederikeHanssen" diff --git a/modules/gatk4/intervallisttools/main.nf b/modules/gatk4/intervallisttools/main.nf index 40c7fb19..352a3240 100644 --- a/modules/gatk4/intervallisttools/main.nf +++ b/modules/gatk4/intervallisttools/main.nf @@ -2,10 +2,10 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(interval_list) diff --git a/modules/gatk4/intervallisttools/meta.yml b/modules/gatk4/intervallisttools/meta.yml index 9e2d994f..804645f3 100644 --- a/modules/gatk4/intervallisttools/meta.yml +++ b/modules/gatk4/intervallisttools/meta.yml @@ -14,7 +14,7 @@ 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 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/learnreadorientationmodel/main.nf b/modules/gatk4/learnreadorientationmodel/main.nf index 7d96c27e..4771a158 100644 --- a/modules/gatk4/learnreadorientationmodel/main.nf +++ b/modules/gatk4/learnreadorientationmodel/main.nf @@ -2,10 +2,10 @@ process GATK4_LEARNREADORIENTATIONMODEL { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(f1r2) diff --git a/modules/gatk4/learnreadorientationmodel/meta.yml b/modules/gatk4/learnreadorientationmodel/meta.yml index 4eff6939..b2dd9612 100644 --- a/modules/gatk4/learnreadorientationmodel/meta.yml +++ b/modules/gatk4/learnreadorientationmodel/meta.yml @@ -15,7 +15,7 @@ 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 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/gatk4/markduplicates/main.nf b/modules/gatk4/markduplicates/main.nf index 735b093e..6b150655 100644 --- a/modules/gatk4/markduplicates/main.nf +++ b/modules/gatk4/markduplicates/main.nf @@ -2,10 +2,10 @@ process GATK4_MARKDUPLICATES { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bams) diff --git a/modules/gatk4/markduplicates/meta.yml b/modules/gatk4/markduplicates/meta.yml index 5777067a..a7dbe8ec 100644 --- a/modules/gatk4/markduplicates/meta.yml +++ b/modules/gatk4/markduplicates/meta.yml @@ -6,14 +6,15 @@ keywords: - sort tools: - gatk4: - description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools + description: + Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037052812-MarkDuplicates-Picard- tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/gatk4/mergebamalignment/main.nf b/modules/gatk4/mergebamalignment/main.nf index e636e1cd..cfeb23dd 100644 --- a/modules/gatk4/mergebamalignment/main.nf +++ b/modules/gatk4/mergebamalignment/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEBAMALIGNMENT { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(aligned), path(unmapped) diff --git a/modules/gatk4/mergebamalignment/meta.yml b/modules/gatk4/mergebamalignment/meta.yml index c66c78db..b4bff490 100644 --- a/modules/gatk4/mergebamalignment/meta.yml +++ b/modules/gatk4/mergebamalignment/meta.yml @@ -12,7 +12,7 @@ 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 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/mergemutectstats/main.nf b/modules/gatk4/mergemutectstats/main.nf new file mode 100644 index 00000000..bb9f91fb --- /dev/null +++ b/modules/gatk4/mergemutectstats/main.nf @@ -0,0 +1,41 @@ +process GATK4_MERGEMUTECTSTATS { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" + + input: + tuple val(meta), path(stats) + output: + tuple val(meta), path("*.vcf.gz.stats"), emit: stats + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def input = stats.collect{ " -stats ${it} "}.join() + + def avail_mem = 3 + if (!task.memory) { + log.info '[GATK MergeMutectStats] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.' + } else { + avail_mem = task.memory.giga + } + """ + gatk --java-options "-Xmx${avail_mem}g" MergeMutectStats \\ + ${input} \\ + -output ${meta.id}.vcf.gz.stats \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/gatk4/mergemutectstats/meta.yml b/modules/gatk4/mergemutectstats/meta.yml new file mode 100644 index 00000000..c9950e14 --- /dev/null +++ b/modules/gatk4/mergemutectstats/meta.yml @@ -0,0 +1,42 @@ +name: gatk4_mergemutectstats +description: Merges mutect2 stats generated on different intervals/regions +keywords: + - mutectstats + - merge +tools: + - gatk4: + description: Genome Analysis Toolkit (GATK4) + homepage: https://gatk.broadinstitute.org/hc/en-us + documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s + tool_dev_url: https://github.com/broadinstitute/gatk + doi: "10.1158/1538-7445.AM2017-3590" + licence: ["BSD-3-clause"] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - stats: + type: (list of) file(s) + description: Stats file + pattern: "*.{stats}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - stats: + type: file + description: Stats file + pattern: "*.vcf.gz.stats" + +authors: + - "@FriederikeHanssen" diff --git a/modules/gatk4/mergevcfs/main.nf b/modules/gatk4/mergevcfs/main.nf index 3e9973e7..54e38667 100644 --- a/modules/gatk4/mergevcfs/main.nf +++ b/modules/gatk4/mergevcfs/main.nf @@ -2,10 +2,10 @@ process GATK4_MERGEVCFS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcfs) diff --git a/modules/gatk4/mergevcfs/meta.yml b/modules/gatk4/mergevcfs/meta.yml index 597f9ec6..8d4123d9 100644 --- a/modules/gatk4/mergevcfs/meta.yml +++ b/modules/gatk4/mergevcfs/meta.yml @@ -12,7 +12,7 @@ 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 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/mutect2/main.nf b/modules/gatk4/mutect2/main.nf index 1c8c3993..568d3393 100644 --- a/modules/gatk4/mutect2/main.nf +++ b/modules/gatk4/mutect2/main.nf @@ -2,17 +2,16 @@ process GATK4_MUTECT2 { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: - tuple val(meta) , path(input) , path(input_index) , val(which_norm) + tuple val(meta) , path(input) , path(input_index) , path(intervals), val(which_norm) val run_single val run_pon val run_mito - val interval_label path fasta path fai path dict @@ -38,6 +37,7 @@ process GATK4_MUTECT2 { def normals_command = '' def inputs_command = '-I ' + input.join( ' -I ') + def interval = intervals ? "-L ${intervals}" : "" if(run_pon) { panels_command = '' @@ -48,7 +48,7 @@ process GATK4_MUTECT2 { normals_command = '' } else if(run_mito){ - panels_command = "-L ${interval_label} --mitochondria-mode" + panels_command = "-L ${intervals} --mitochondria-mode" normals_command = '' } else { @@ -68,6 +68,7 @@ process GATK4_MUTECT2 { ${inputs_command} \\ ${normals_command} \\ ${panels_command} \\ + ${interval} \\ -O ${prefix}.vcf.gz \\ $args diff --git a/modules/gatk4/mutect2/meta.yml b/modules/gatk4/mutect2/meta.yml index 83f6cb7c..69a4acfe 100644 --- a/modules/gatk4/mutect2/meta.yml +++ b/modules/gatk4/mutect2/meta.yml @@ -1,5 +1,5 @@ name: gatk4_mutect2 -description: Call somatic SNVs and indels via local assembly of haplotypes. +description: Call somatic SNVs and indels via local assembly of haplotypes. keywords: - gatk4 - mutect2 @@ -14,7 +14,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: @@ -30,6 +30,10 @@ input: type: list description: list of BAM file indexes, also able to take CRAM indexes as an input pattern: "*.{bam.bai/cram.crai}" + - intervals: + type: File/string + description: Specify region the tools is run on. + pattern: ".{bed,interval_list}/chrM" - which_norm: type: list description: optional list of sample headers contained in the normal sample bam files (these are required for tumor_normal_pair mode) @@ -46,10 +50,6 @@ input: type: boolean description: Specify whether or not to run in mitochondria-mode instead of tumor_normal_pair mode pattern: "true/false" - - interval_label: - type: string - description: Specify the label used for mitochondrial chromosome when mutect2 is run in mitochondria mode. - pattern: "chrM" - fasta: type: file description: The reference fasta file diff --git a/modules/gatk4/revertsam/main.nf b/modules/gatk4/revertsam/main.nf index 23f99ab4..b3bf9f95 100644 --- a/modules/gatk4/revertsam/main.nf +++ b/modules/gatk4/revertsam/main.nf @@ -2,10 +2,10 @@ process GATK4_REVERTSAM { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/revertsam/meta.yml b/modules/gatk4/revertsam/meta.yml index b52dcb36..6cc97d86 100644 --- a/modules/gatk4/revertsam/meta.yml +++ b/modules/gatk4/revertsam/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/samtofastq/main.nf b/modules/gatk4/samtofastq/main.nf index 2da40b6c..53e5013f 100644 --- a/modules/gatk4/samtofastq/main.nf +++ b/modules/gatk4/samtofastq/main.nf @@ -2,10 +2,10 @@ process GATK4_SAMTOFASTQ { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/samtofastq/meta.yml b/modules/gatk4/samtofastq/meta.yml index de4624b5..60ca6aee 100644 --- a/modules/gatk4/samtofastq/meta.yml +++ b/modules/gatk4/samtofastq/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/splitncigarreads/main.nf b/modules/gatk4/splitncigarreads/main.nf index 6d0a35fd..fdd1d974 100644 --- a/modules/gatk4/splitncigarreads/main.nf +++ b/modules/gatk4/splitncigarreads/main.nf @@ -2,10 +2,10 @@ process GATK4_SPLITNCIGARREADS { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(bam) diff --git a/modules/gatk4/splitncigarreads/meta.yml b/modules/gatk4/splitncigarreads/meta.yml index fd6edda0..407e80bd 100644 --- a/modules/gatk4/splitncigarreads/meta.yml +++ b/modules/gatk4/splitncigarreads/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/variantfiltration/main.nf b/modules/gatk4/variantfiltration/main.nf index 3a41d20c..68f3d636 100644 --- a/modules/gatk4/variantfiltration/main.nf +++ b/modules/gatk4/variantfiltration/main.nf @@ -2,10 +2,10 @@ process GATK4_VARIANTFILTRATION { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf), path(vcf_tbi) diff --git a/modules/gatk4/variantfiltration/meta.yml b/modules/gatk4/variantfiltration/meta.yml index 71f0b8b2..04b1c086 100644 --- a/modules/gatk4/variantfiltration/meta.yml +++ b/modules/gatk4/variantfiltration/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: type: map diff --git a/modules/gatk4/variantrecalibrator/main.nf b/modules/gatk4/variantrecalibrator/main.nf index df8a9599..31c9efbd 100644 --- a/modules/gatk4/variantrecalibrator/main.nf +++ b/modules/gatk4/variantrecalibrator/main.nf @@ -2,21 +2,17 @@ process GATK4_VARIANTRECALIBRATOR { tag "$meta.id" label 'process_low' - conda (params.enable_conda ? "bioconda::gatk4=4.2.4.1" : null) + conda (params.enable_conda ? "bioconda::gatk4=4.2.5.0" : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/gatk4:4.2.4.1--hdfd78af_0' : - 'quay.io/biocontainers/gatk4:4.2.4.1--hdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/gatk4:4.2.5.0--hdfd78af_0' : + 'quay.io/biocontainers/gatk4:4.2.5.0--hdfd78af_0' }" input: tuple val(meta), path(vcf) , path(tbi) path fasta path fai path dict - val allelespecific tuple path(resvcfs), path(restbis), val(reslabels) - val annotation - val mode - val create_rscript output: tuple val(meta), path("*.recal") , emit: recal @@ -32,11 +28,7 @@ process GATK4_VARIANTRECALIBRATOR { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" refCommand = fasta ? "-R ${fasta} " : '' - alleleSpecificCommand = allelespecific ? '-AS' : '' resourceCommand = '--resource:' + reslabels.join( ' --resource:') - annotationCommand = '-an ' + annotation.join( ' -an ') - modeCommand = mode ? "--mode ${mode} " : 'SNP' - rscriptCommand = create_rscript ? "--rscript-file ${prefix}.plots.R" : '' def avail_mem = 3 if (!task.memory) { @@ -48,13 +40,9 @@ process GATK4_VARIANTRECALIBRATOR { gatk --java-options "-Xmx${avail_mem}g" VariantRecalibrator \\ ${refCommand} \\ -V ${vcf} \\ - ${alleleSpecificCommand} \\ - ${resourceCommand} \\ - ${annotationCommand} \\ - ${modeCommand} \\ -O ${prefix}.recal \\ --tranches-file ${prefix}.tranches \\ - ${rscriptCommand}\\ + ${resourceCommand} \\ $args cat <<-END_VERSIONS > versions.yml diff --git a/modules/genmap/index/meta.yml b/modules/genmap/index/meta.yml index 2ab0910d..73563c1d 100644 --- a/modules/genmap/index/meta.yml +++ b/modules/genmap/index/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - fasta: diff --git a/modules/genmap/mappability/meta.yml b/modules/genmap/mappability/meta.yml index d2835d92..5469cef5 100644 --- a/modules/genmap/mappability/meta.yml +++ b/modules/genmap/mappability/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/cpockrandt/genmap tool_dev_url: https://github.com/cpockrandt/genmap doi: "10.1093/bioinformatics/btaa222" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - fasta: diff --git a/modules/genrich/meta.yml b/modules/genrich/meta.yml index 37184190..343c25d7 100644 --- a/modules/genrich/meta.yml +++ b/modules/genrich/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://github.com/jsh58/Genrich#readme tool_dev_url: https://github.com/jsh58/Genrich doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map @@ -77,4 +77,3 @@ output: pattern: "*.{version.txt}" authors: - "@JoseEspinosa" - diff --git a/modules/gffread/meta.yml b/modules/gffread/meta.yml index bf1a15cb..20335747 100644 --- a/modules/gffread/meta.yml +++ b/modules/gffread/meta.yml @@ -11,13 +11,13 @@ tools: documentation: http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread tool_dev_url: https://github.com/gpertea/gffread doi: 10.12688/f1000research.23297.1 - licence: ['MIT'] + licence: ["MIT"] input: - gff: - type: file - description: A reference file in either the GFF3, GFF2 or GTF format. - pattern: "*.{gff, gtf}" + type: file + description: A reference file in either the GFF3, GFF2 or GTF format. + pattern: "*.{gff, gtf}" output: - gtf: diff --git a/modules/glnexus/meta.yml b/modules/glnexus/meta.yml index 5ba17cae..0fc19452 100644 --- a/modules/glnexus/meta.yml +++ b/modules/glnexus/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/dnanexus-rnd/GLnexus/wiki/Getting-Started tool_dev_url: None doi: https://doi.org/10.1101/343970 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/graphmap2/align/meta.yml b/modules/graphmap2/align/meta.yml index 9fb1507a..d498069b 100644 --- a/modules/graphmap2/align/meta.yml +++ b/modules/graphmap2/align/meta.yml @@ -1,51 +1,51 @@ name: graphmap2_align description: A versatile pairwise aligner for genomic and spliced nucleotide sequences keywords: - - align - - fasta - - fastq - - genome - - reference + - align + - fasta + - fastq + - genome + - reference tools: - - graphmap2: - description: | - A versatile pairwise aligner for genomic and spliced nucleotide sequences. - homepage: https://github.com/lbcb-sci/graphmap2 - documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads - licence: ['MIT'] + - graphmap2: + description: | + A versatile pairwise aligner for genomic and spliced nucleotide sequences. + homepage: https://github.com/lbcb-sci/graphmap2 + documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input FASTQ files - and paired-end data, respectively. - - fasta: - type: file - description: | - Reference database in FASTA format. - - index: - type: file - description: | - FASTA index in gmidx. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input FASTQ files + and paired-end data, respectively. + - fasta: + type: file + description: | + Reference database in FASTA format. + - index: + type: file + description: | + FASTA index in gmidx. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - sam: - type: file - description: Alignment in SAM format - pattern: "*.sam" - - 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 ] + - sam: + type: file + description: Alignment in SAM format + pattern: "*.sam" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" - - "@drpatelh" + - "@yuukiiwa" + - "@drpatelh" diff --git a/modules/graphmap2/index/meta.yml b/modules/graphmap2/index/meta.yml index 92a0a3d7..8e9d2c1c 100644 --- a/modules/graphmap2/index/meta.yml +++ b/modules/graphmap2/index/meta.yml @@ -1,30 +1,30 @@ name: graphmap2_index description: A versatile pairwise aligner for genomic and spliced nucleotide sequences keywords: - - index - - fasta - - reference + - index + - fasta + - reference tools: - - graphmap2: - description: | - A versatile pairwise aligner for genomic and spliced nucleotide sequences. - homepage: https://github.com/lbcb-sci/graphmap2 - documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads - licence: ['MIT'] + - graphmap2: + description: | + A versatile pairwise aligner for genomic and spliced nucleotide sequences. + homepage: https://github.com/lbcb-sci/graphmap2 + documentation: https://github.com/lbcb-sci/graphmap2#graphmap2---a-highly-sensitive-and-accurate-mapper-for-long-error-prone-reads + licence: ["MIT"] input: - - fasta: - type: file - description: | - Reference database in FASTA format. + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - gmidx: - type: file - description: Graphmap2 fasta index in gmidx format - pattern: "*.gmidx" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - gmidx: + type: file + description: Graphmap2 fasta index in gmidx format + pattern: "*.gmidx" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" - - "@drpatelh" + - "@yuukiiwa" + - "@drpatelh" diff --git a/modules/gstama/merge/meta.yml b/modules/gstama/merge/meta.yml index 1351b864..2f91a56d 100644 --- a/modules/gstama/merge/meta.yml +++ b/modules/gstama/merge/meta.yml @@ -16,7 +16,7 @@ tools: documentation: https://github.com/GenomeRIK/tama/wiki tool_dev_url: https://github.com/sguizard/gs-tama doi: "https://doi.org/10.1186/s12864-020-07123-7" - licence: ['GPL v3 License'] + licence: ["GPL v3 License"] input: - meta: diff --git a/modules/gtdbtk/classifywf/meta.yml b/modules/gtdbtk/classifywf/meta.yml index d70de362..86301035 100644 --- a/modules/gtdbtk/classifywf/meta.yml +++ b/modules/gtdbtk/classifywf/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://ecogenomics.github.io/GTDBTk/ tool_dev_url: https://github.com/Ecogenomics/GTDBTk doi: "10.1093/bioinformatics/btz848" - licence: ['GNU General Public v3 (GPL v3)'] + licence: ["GNU General Public v3 (GPL v3)"] input: - meta: diff --git a/modules/gubbins/meta.yml b/modules/gubbins/meta.yml index f73e2bb0..785366ad 100644 --- a/modules/gubbins/meta.yml +++ b/modules/gubbins/meta.yml @@ -1,8 +1,9 @@ name: gubbins -description: Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies - loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the - putative point mutations outside of these regions. -licence: ['GPL-2.0-only'] +description: + Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies + loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the + putative point mutations outside of these regions. +licence: ["GPL-2.0-only"] keywords: - recombination - alignment @@ -59,4 +60,3 @@ output: pattern: "*.{node_labelled.final_tree.tre}" authors: - "@avantonder" - diff --git a/modules/gunc/downloaddb/meta.yml b/modules/gunc/downloaddb/meta.yml index cb486da0..c36ff3f3 100644 --- a/modules/gunc/downloaddb/meta.yml +++ b/modules/gunc/downloaddb/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" - licence: ['GNU General Public v3 or later (GPL v3+)'] + licence: ["GNU General Public v3 or later (GPL v3+)"] input: - db_name: diff --git a/modules/gunc/run/meta.yml b/modules/gunc/run/meta.yml index 1dd4a8ae..3a85e1fb 100644 --- a/modules/gunc/run/meta.yml +++ b/modules/gunc/run/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://grp-bork.embl-community.io/gunc/ tool_dev_url: https://github.com/grp-bork/gunc doi: "10.1186/s13059-021-02393-0" - licence: ['GNU General Public v3 or later (GPL v3+)'] + licence: ["GNU General Public v3 or later (GPL v3+)"] input: - meta: diff --git a/modules/gunzip/meta.yml b/modules/gunzip/meta.yml index ea1f1546..4d2ebc84 100644 --- a/modules/gunzip/meta.yml +++ b/modules/gunzip/meta.yml @@ -1,34 +1,34 @@ name: gunzip description: Compresses and decompresses files. keywords: - - gunzip - - compression + - gunzip + - compression tools: - - gunzip: - description: | - gzip is a file format and a software application used for file compression and decompression. - documentation: https://www.gnu.org/software/gzip/manual/gzip.html - licence: ['GPL-3.0-or-later'] + - gunzip: + description: | + gzip is a file format and a software application used for file compression and decompression. + documentation: https://www.gnu.org/software/gzip/manual/gzip.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Optional groovy Map containing meta information - e.g. [ id:'test', single_end:false ] - - archive: - type: file - description: File to be compressed/uncompressed - pattern: "*.*" + - meta: + type: map + description: | + Optional groovy Map containing meta information + e.g. [ id:'test', single_end:false ] + - archive: + type: file + description: File to be compressed/uncompressed + pattern: "*.*" output: - - gunzip: - type: file - description: Compressed/uncompressed file - pattern: "*.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - gunzip: + type: file + description: Compressed/uncompressed file + pattern: "*.*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@jfy133" + - "@joseespinosa" + - "@drpatelh" + - "@jfy133" diff --git a/modules/hicap/meta.yml b/modules/hicap/meta.yml index 275df665..a027c050 100644 --- a/modules/hicap/meta.yml +++ b/modules/hicap/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/scwatts/hicap tool_dev_url: https://github.com/scwatts/hicap doi: "https://doi.org/10.1128/JCM.00190-19" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/hisat2/align/meta.yml b/modules/hisat2/align/meta.yml index 6011cc34..7550aefa 100644 --- a/modules/hisat2/align/meta.yml +++ b/modules/hisat2/align/meta.yml @@ -1,10 +1,10 @@ name: hisat2_align description: Align RNA-Seq reads to a reference with HISAT2 keywords: - - align - - fasta - - genome - - reference + - align + - fasta + - genome + - reference tools: - hisat2: @@ -12,19 +12,19 @@ tools: homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - reads: type: file description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. - index: type: file description: HISAT2 genome index file @@ -38,8 +38,8 @@ output: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - bam: type: file description: Output BAM file containing read alignments diff --git a/modules/hisat2/build/meta.yml b/modules/hisat2/build/meta.yml index c08b296d..a2e1fd67 100644 --- a/modules/hisat2/build/meta.yml +++ b/modules/hisat2/build/meta.yml @@ -1,18 +1,18 @@ name: hisat2_build description: Builds HISAT2 index for reference genome keywords: - - build - - index - - fasta - - genome - - reference + - build + - index + - fasta + - genome + - reference tools: - hisat2: description: HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes as well as to a single reference genome. homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" - licence: ['MIT'] + licence: ["MIT"] input: - fasta: diff --git a/modules/hisat2/extractsplicesites/meta.yml b/modules/hisat2/extractsplicesites/meta.yml index 97227faf..7dc1bac8 100644 --- a/modules/hisat2/extractsplicesites/meta.yml +++ b/modules/hisat2/extractsplicesites/meta.yml @@ -1,10 +1,10 @@ name: hisat2_extractsplicesites description: Extracts splicing sites from a gtf files keywords: - - splicing - - gtf - - genome - - reference + - splicing + - gtf + - genome + - reference tools: - hisat2: @@ -12,7 +12,7 @@ tools: homepage: https://daehwankimlab.github.io/hisat2/ documentation: https://daehwankimlab.github.io/hisat2/manual/ doi: "10.1038/s41587-019-0201-4" - licence: ['MIT'] + licence: ["MIT"] input: - gtf: diff --git a/modules/hmmcopy/gccounter/meta.yml b/modules/hmmcopy/gccounter/meta.yml index 71727af2..ab101df6 100644 --- a/modules/hmmcopy/gccounter/meta.yml +++ b/modules/hmmcopy/gccounter/meta.yml @@ -11,14 +11,13 @@ tools: documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - fasta: type: file description: Input genome fasta file - output: - versions: type: file diff --git a/modules/hmmcopy/generatemap/meta.yml b/modules/hmmcopy/generatemap/meta.yml index ca43c6ce..7c345843 100644 --- a/modules/hmmcopy/generatemap/meta.yml +++ b/modules/hmmcopy/generatemap/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - fasta: diff --git a/modules/hmmcopy/mapcounter/meta.yml b/modules/hmmcopy/mapcounter/meta.yml index 8f8b9aae..969a027d 100644 --- a/modules/hmmcopy/mapcounter/meta.yml +++ b/modules/hmmcopy/mapcounter/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - bigwig: diff --git a/modules/hmmcopy/readcounter/meta.yml b/modules/hmmcopy/readcounter/meta.yml index 9b09a55c..81020ed9 100644 --- a/modules/hmmcopy/readcounter/meta.yml +++ b/modules/hmmcopy/readcounter/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/shahcompbio/hmmcopy_utils tool_dev_url: https://github.com/shahcompbio/hmmcopy_utils doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/hmmer/hmmalign/meta.yml b/modules/hmmer/hmmalign/meta.yml index 58dc6b92..296826d4 100644 --- a/modules/hmmer/hmmalign/meta.yml +++ b/modules/hmmer/hmmalign/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://hmmer.org/documentation.html tool_dev_url: None doi: "http://dx.doi.org/10.1371/journal.pcbi.1002195" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - meta: diff --git a/modules/homer/annotatepeaks/meta.yml b/modules/homer/annotatepeaks/meta.yml index c3ab9460..b815e975 100644 --- a/modules/homer/annotatepeaks/meta.yml +++ b/modules/homer/annotatepeaks/meta.yml @@ -10,7 +10,7 @@ tools: HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/homer/findpeaks/meta.yml b/modules/homer/findpeaks/meta.yml index 2aa8db26..e7cef0cd 100644 --- a/modules/homer/findpeaks/meta.yml +++ b/modules/homer/findpeaks/meta.yml @@ -9,7 +9,7 @@ tools: HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/homer/maketagdirectory/meta.yml b/modules/homer/maketagdirectory/meta.yml index 802320f9..2472e0f0 100644 --- a/modules/homer/maketagdirectory/meta.yml +++ b/modules/homer/maketagdirectory/meta.yml @@ -9,7 +9,7 @@ tools: HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/homer/makeucscfile/meta.yml b/modules/homer/makeucscfile/meta.yml index 68d5fcd4..273f456e 100644 --- a/modules/homer/makeucscfile/meta.yml +++ b/modules/homer/makeucscfile/meta.yml @@ -10,7 +10,7 @@ tools: HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. documentation: http://homer.ucsd.edu/homer/ doi: 10.1016/j.molcel.2010.05.004. - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/ichorcna/createpon/main.nf b/modules/ichorcna/createpon/main.nf new file mode 100644 index 00000000..6b249b32 --- /dev/null +++ b/modules/ichorcna/createpon/main.nf @@ -0,0 +1,48 @@ +def VERSION = '0.3.2' // Version information not provided by tool on CLI + +process ICHORCNA_CREATEPON { + label 'process_low' + + conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : + 'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }" + + input: + path wigs + path gc_wig + path map_wig + path centromere + + output: + path "*.rds" , emit: rds + path "*.txt" , emit: txt + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def centro = centromere ? "--centromere ${centromere}" : '' + def prefix = task.ext.prefix ?: "PoN" + + """ + echo ${wigs} | tr " " "\\n" > wig_files.txt + + createPanelOfNormals.R \\ + --filelist wig_files.txt \\ + --gcWig ${gc_wig} \\ + --mapWig ${map_wig} \\ + ${centro} \\ + ${args} \\ + --outfile ${prefix} + + rm wig_files.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ichorcna: $VERSION + END_VERSIONS + """ +} diff --git a/modules/ichorcna/createpon/meta.yml b/modules/ichorcna/createpon/meta.yml new file mode 100644 index 00000000..ce1eca0a --- /dev/null +++ b/modules/ichorcna/createpon/meta.yml @@ -0,0 +1,57 @@ +name: ichorcna_createpon +description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA. This module generates a panel of normals +keywords: + - ichorcna + - cnv + - cna + - cfDNA + - wgs + - panel_of_normals +tools: + - ichorcna: + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + homepage: https://github.com/broadinstitute/ichorCNA + documentation: https://github.com/broadinstitute/ichorCNA/wiki + tool_dev_url: https://github.com/broadinstitute/ichorCNA + doi: "10.1038/s41467-017-00965-y" + licence: ['GPL v3'] + +input: + - wigs: + type: file + description: Any number of hmmcopy/readCounter processed .wig files giving the number of reads in the sample, in each genomic window. These will be averaged over to generate the panel of normals. + pattern: "*.{wig}" + + - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window + pattern: "*.{wig}" + + - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window + pattern: "*.{wig}" + + - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude these windows + pattern: "*.{txt}" + +output: + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + + - rds: + type: file + description: R data file (.rds) containing panel of normals data, medians of each bin. + pattern: "*.rds" + + - txt: + type: file + description: Text file containing panel of normals data, medians of each bin. + pattern: "*.txt" + +authors: + - "@sppearce" diff --git a/modules/ichorcna/run/main.nf b/modules/ichorcna/run/main.nf new file mode 100644 index 00000000..cc72adc9 --- /dev/null +++ b/modules/ichorcna/run/main.nf @@ -0,0 +1,50 @@ +def VERSION = '0.3.2' // Version information not provided by tool on CLI + +process ICHORCNA_RUN { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::r-ichorcna=0.3.2" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/r-ichorcna:0.3.2--r41hdfd78af_0' : + 'quay.io/biocontainers/r-ichorcna:0.3.2--r41hdfd78af_0' }" + + input: + tuple val(meta), path(wig) + path gc_wig + path map_wig + path panel_of_normals + path centromere + + output: + tuple val(meta), path("*.cna.seg") , emit: cna_seg + tuple val(meta), path("*.params.txt") , emit: ichorcna_params + path "**/*genomeWide.pdf" , emit: genome_plot + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def pon = panel_of_normals ? "--normalPanel ${panel_of_normals}" : '' + def centro = centromere ? "--centromere ${centromere}" : '' + + """ + runIchorCNA.R --id ${prefix} \\ + $args \\ + --WIG ${wig} \\ + --id ${meta.id} \\ + --gcWig ${gc_wig} \\ + --mapWig ${map_wig} \\ + ${pon} \\ + ${centro} \\ + --outDir . + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + ichorcna: $VERSION + END_VERSIONS + """ +} diff --git a/modules/ichorcna/run/meta.yml b/modules/ichorcna/run/meta.yml new file mode 100644 index 00000000..f0febddf --- /dev/null +++ b/modules/ichorcna/run/meta.yml @@ -0,0 +1,72 @@ +name: ichorcna_run +description: ichorCNA is an R package for calculating copy number alteration from (low-pass) whole genome sequencing, particularly for use in cell-free DNA +keywords: + - ichorcna + - cnv + - cna + - cfDNA + - wgs +tools: + - ichorcna: + description: Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing. + homepage: https://github.com/broadinstitute/ichorCNA + documentation: https://github.com/broadinstitute/ichorCNA/wiki + tool_dev_url: https://github.com/broadinstitute/ichorCNA + doi: "10.1038/s41467-017-00965-y" + licence: ['GPL v3'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - wig: + type: file + description: hmmcopy/readCounter processed .wig file giving the number of reads in the sample, in each genomic window + pattern: "*.{wig}" + + - gc_wig: + type: file + description: hmmcopy/gcCounter processed .wig file giving the gc content in the reference fasta, in each genomic window + pattern: "*.{wig}" + + - map_wig: + type: file + description: hmmcopy/mapCounter processed .wig file giving the mapability in the reference fasta, in each genomic window + pattern: "*.{wig}" + + - panel_of_normals: + type: file + description: Panel of normals data, generated by calling ichorCNA on a set of normal samples with the same window size etc. + pattern: "*.{rds}" + + - centromere: + type: file + description: Text file giving centromere locations of each genome, to exclude these windows + pattern: "*.{txt}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test'] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - cna_seg: + type: file + description: Predicted copy number variation per segment + pattern: "*.{cng.seg}" + - ichorcna_params: + type: file + description: A text file showing the values that ichorCNA has estimated for tumour fraction, ploidy etc + pattern: "*.{params.txt}" + - genome_plot: + type: file + description: A plot with the best-fit genome-wide CNV data + pattern: "*.{genomeWide.pdf}" +authors: + - "@sppearce" diff --git a/modules/idr/meta.yml b/modules/idr/meta.yml index c89e72a4..7442c25a 100644 --- a/modules/idr/meta.yml +++ b/modules/idr/meta.yml @@ -17,7 +17,7 @@ tools: documentation: None tool_dev_url: https://github.com/kundajelab/idr doi: "" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - peaks: type: tuple of two files diff --git a/modules/iqtree/meta.yml b/modules/iqtree/meta.yml index 0a3b4e4c..2c34a3da 100644 --- a/modules/iqtree/meta.yml +++ b/modules/iqtree/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://www.iqtree.org/doc tool_dev_url: https://github.com/iqtree/iqtree2 doi: doi.org/10.1093/molbev/msaa015 - licence: ['GPL v2-or-later'] + licence: ["GPL v2-or-later"] input: - alignment: diff --git a/modules/ismapper/meta.yml b/modules/ismapper/meta.yml index 810c1674..5b0be8d3 100644 --- a/modules/ismapper/meta.yml +++ b/modules/ismapper/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/jhawkey/IS_mapper tool_dev_url: https://github.com/jhawkey/IS_mapper doi: "https://doi.org/10.1186/s12864-015-1860-2" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - meta: diff --git a/modules/isoseq3/cluster/meta.yml b/modules/isoseq3/cluster/meta.yml index 4086ab05..84631978 100644 --- a/modules/isoseq3/cluster/meta.yml +++ b/modules/isoseq3/cluster/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md doi: "" - licence: ['BSD-3-Clause-Clear'] + licence: ["BSD-3-Clause-Clear"] input: - meta: diff --git a/modules/isoseq3/refine/meta.yml b/modules/isoseq3/refine/meta.yml index eefd015b..2e9e4092 100644 --- a/modules/isoseq3/refine/meta.yml +++ b/modules/isoseq3/refine/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md tool_dev_url: https://github.com/PacificBiosciences/IsoSeq/blob/master/isoseq-clustering.md doi: "" - licence: ['BSD-3-Clause-Clear'] + licence: ["BSD-3-Clause-Clear"] input: - meta: diff --git a/modules/ivar/consensus/meta.yml b/modules/ivar/consensus/meta.yml index aa08ad98..fb562603 100644 --- a/modules/ivar/consensus/meta.yml +++ b/modules/ivar/consensus/meta.yml @@ -1,56 +1,56 @@ name: ivar_consensus description: Generate a consensus sequence from a BAM file using iVar keywords: - - amplicon sequencing - - consensus - - fasta + - amplicon sequencing + - consensus + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar consensus - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file + pattern: "*.bam" + - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM file + pattern: "*.fa" + - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar consensus + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: iVar generated consensus sequence - pattern: "*.fa" - - qual: - type: file - description: iVar generated quality file - pattern: "*.qual.txt" - - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" - - 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 ] + - fasta: + type: file + description: iVar generated consensus sequence + pattern: "*.fa" + - qual: + type: file + description: iVar generated quality file + pattern: "*.qual.txt" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/ivar/trim/meta.yml b/modules/ivar/trim/meta.yml index 44bc742e..d01dd1a2 100644 --- a/modules/ivar/trim/meta.yml +++ b/modules/ivar/trim/meta.yml @@ -1,52 +1,52 @@ name: ivar_trim description: Trim primer sequences rom a BAM file with iVar keywords: - - amplicon sequencing - - trimming - - fasta + - amplicon sequencing + - trimming + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Co-ordinate sorted BAM file - pattern: "*.bam" - - bai: - type: file - description: Index file for co-ordinate sorted BAM file - pattern: "*.bai" - - bed: - type: file - description: BED file with primer labels and positions - pattern: "*.bed" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: Co-ordinate sorted BAM file + pattern: "*.bam" + - bai: + type: file + description: Index file for co-ordinate sorted BAM file + pattern: "*.bai" + - bed: + type: file + description: BED file with primer labels and positions + pattern: "*.bed" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: iVar generated trimmed bam file (unsorted) - pattern: "*.bam" - - log: - type: file - description: Log file generated by iVar for use with MultiQC - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: iVar generated trimmed bam file (unsorted) + pattern: "*.bam" + - log: + type: file + description: Log file generated by iVar for use with MultiQC + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/ivar/variants/meta.yml b/modules/ivar/variants/meta.yml index 29cbd958..6677ffb2 100644 --- a/modules/ivar/variants/meta.yml +++ b/modules/ivar/variants/meta.yml @@ -1,56 +1,56 @@ name: ivar_variants description: Call variants from a BAM file using iVar keywords: - - amplicon sequencing - - variants - - fasta + - amplicon sequencing + - variants + - fasta tools: - - ivar: - description: | - iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. - homepage: https://github.com/andersen-lab/ivar - documentation: https://andersen-lab.github.io/ivar/html/manualpage.html - licence: ['GPL-3.0-or-later'] + - ivar: + description: | + iVar - a computational package that contains functions broadly useful for viral amplicon-based sequencing. + homepage: https://github.com/andersen-lab/ivar + documentation: https://andersen-lab.github.io/ivar/html/manualpage.html + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file - pattern: "*.bam" - - fasta: - type: file - description: The reference sequence used for mapping and generating the BAM file - pattern: "*.fa" - - gff: - type: file - description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. - patter: "*.gff" - - save_mpileup: - type: boolean - description: Save mpileup file generated by ivar variants - patter: "*.mpileup" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: A sorted (with samtools sort) and trimmed (with iVar trim) bam file + pattern: "*.bam" + - fasta: + type: file + description: The reference sequence used for mapping and generating the BAM file + pattern: "*.fa" + - gff: + type: file + description: A GFF file in the GFF3 format can be supplied to specify coordinates of open reading frames (ORFs). In absence of GFF file, amino acid translation will not be done. + patter: "*.gff" + - save_mpileup: + type: boolean + description: Save mpileup file generated by ivar variants + patter: "*.mpileup" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - tsv: - type: file - description: iVar generated TSV file with the variants - pattern: "*.tsv" - - mpileup: - type: file - description: mpileup output from samtools mpileup [OPTIONAL] - pattern: "*.mpileup" - - 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 ] + - tsv: + type: file + description: iVar generated TSV file with the variants + pattern: "*.tsv" + - mpileup: + type: file + description: mpileup output from samtools mpileup [OPTIONAL] + pattern: "*.mpileup" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@andersgs" - - "@drpatelh" + - "@andersgs" + - "@drpatelh" diff --git a/modules/kallisto/index/meta.yml b/modules/kallisto/index/meta.yml index dd952e33..307650b2 100644 --- a/modules/kallisto/index/meta.yml +++ b/modules/kallisto/index/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://pachterlab.github.io/kallisto/manual tool_dev_url: https://github.com/pachterlab/kallisto doi: "" - licence: ['BSD-2-Clause'] + licence: ["BSD-2-Clause"] input: - fasta: diff --git a/modules/khmer/normalizebymedian/meta.yml b/modules/khmer/normalizebymedian/meta.yml index 2227750f..5bd2b205 100644 --- a/modules/khmer/normalizebymedian/meta.yml +++ b/modules/khmer/normalizebymedian/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://khmer.readthedocs.io/en/latest/ tool_dev_url: https://github.com/dib-lab/khmer doi: "https://doi.org/10.12688/f1000research.6924.1" - licence: ['BSD License'] + licence: ["BSD License"] input: - pe_reads: diff --git a/modules/kleborate/meta.yml b/modules/kleborate/meta.yml index eaf837e7..92ab08c8 100644 --- a/modules/kleborate/meta.yml +++ b/modules/kleborate/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/katholt/Kleborate/wiki tool_dev_url: https://github.com/katholt/Kleborate doi: 10.1038/s41467-021-24448-3 - licence: ['GPL v3 or later (GPL v3+)'] + licence: ["GPL v3 or later (GPL v3+)"] input: - meta: diff --git a/modules/kraken2/kraken2/meta.yml b/modules/kraken2/kraken2/meta.yml index 4b894705..9d6a3855 100644 --- a/modules/kraken2/kraken2/meta.yml +++ b/modules/kraken2/kraken2/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://ccb.jhu.edu/software/kraken2/ documentation: https://github.com/DerrickWood/kraken2/wiki/Manual doi: 10.1186/s13059-019-1891-0 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/last/dotplot/meta.yml b/modules/last/dotplot/meta.yml index 2ec94f58..3f718179 100644 --- a/modules/last/dotplot/meta.yml +++ b/modules/last/dotplot/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-dotplot.rst tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: diff --git a/modules/last/lastal/meta.yml b/modules/last/lastal/meta.yml index 94e76878..60d3a746 100644 --- a/modules/last/lastal/meta.yml +++ b/modules/last/lastal/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL v3-or-later'] + licence: ["GPL v3-or-later"] input: - index: diff --git a/modules/last/lastdb/meta.yml b/modules/last/lastdb/meta.yml index e576fa18..53842b0a 100644 --- a/modules/last/lastdb/meta.yml +++ b/modules/last/lastdb/meta.yml @@ -12,19 +12,19 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/lastdb.rst tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - fastx: type: file description: > - Sequence file in FASTA or FASTQ format. - May be compressed with gzip. + Sequence file in FASTA or FASTQ format. + May be compressed with gzip. pattern: "*.{fasta,fasta.gz,fastq,fastq.gz}" output: diff --git a/modules/last/mafconvert/meta.yml b/modules/last/mafconvert/meta.yml index 3336f315..f41506d4 100644 --- a/modules/last/mafconvert/meta.yml +++ b/modules/last/mafconvert/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/ tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL v3-or-later'] + licence: ["GPL v3-or-later"] input: - meta: diff --git a/modules/last/mafswap/meta.yml b/modules/last/mafswap/meta.yml index ce97fe97..1abfbfc5 100644 --- a/modules/last/mafswap/meta.yml +++ b/modules/last/mafswap/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/ tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: diff --git a/modules/last/postmask/meta.yml b/modules/last/postmask/meta.yml index 02e602f6..eacc96d8 100644 --- a/modules/last/postmask/meta.yml +++ b/modules/last/postmask/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-postmask.rst tool_dev_url: https://gitlab.com/mcfrith/last doi: "10.1371/journal.pone.0028819" - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: diff --git a/modules/last/split/meta.yml b/modules/last/split/meta.yml index bc16fe9a..490e0bb5 100644 --- a/modules/last/split/meta.yml +++ b/modules/last/split/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/ tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL v3-or-later'] + licence: ["GPL v3-or-later"] input: - meta: diff --git a/modules/last/train/meta.yml b/modules/last/train/meta.yml index 20c5780d..d564ec4b 100644 --- a/modules/last/train/meta.yml +++ b/modules/last/train/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://gitlab.com/mcfrith/last/-/blob/main/doc/last-train.rst tool_dev_url: https://gitlab.com/mcfrith/last doi: "" - licence: ['GPL v3-or-later'] + licence: ["GPL v3-or-later"] input: - index: diff --git a/modules/leehom/meta.yml b/modules/leehom/meta.yml index b0d6092a..658db227 100644 --- a/modules/leehom/meta.yml +++ b/modules/leehom/meta.yml @@ -16,7 +16,7 @@ tools: documentation: "https://github.com/grenaud/leeHom" tool_dev_url: "https://github.com/grenaud/leeHom" doi: "10.1093/nar/gku699" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -72,6 +72,5 @@ output: description: Log file of command pattern: "*.log" - authors: - "@jfy133" diff --git a/modules/lima/meta.yml b/modules/lima/meta.yml index 567632df..18770ef4 100644 --- a/modules/lima/meta.yml +++ b/modules/lima/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://lima.how/ tool_dev_url: https://github.com/pacificbiosciences/barcoding/ doi: "" - licence: ['BSD-3-Clause-Clear'] + licence: ["BSD-3-Clause-Clear"] input: - meta: diff --git a/modules/lissero/meta.yml b/modules/lissero/meta.yml index d4fb38df..990e2587 100644 --- a/modules/lissero/meta.yml +++ b/modules/lissero/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/MDU-PHL/LisSero/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/lissero doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -41,4 +41,3 @@ output: authors: - "@rpetit3" - diff --git a/modules/lofreq/call/meta.yml b/modules/lofreq/call/meta.yml index 97607663..972e286e 100644 --- a/modules/lofreq/call/meta.yml +++ b/modules/lofreq/call/meta.yml @@ -11,7 +11,7 @@ tools: homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/lofreq/callparallel/meta.yml b/modules/lofreq/callparallel/meta.yml index a7dbd637..cd9d9fa6 100644 --- a/modules/lofreq/callparallel/meta.yml +++ b/modules/lofreq/callparallel/meta.yml @@ -9,7 +9,7 @@ tools: homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/lofreq/filter/meta.yml b/modules/lofreq/filter/meta.yml index fceee6f5..c530a092 100644 --- a/modules/lofreq/filter/meta.yml +++ b/modules/lofreq/filter/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://csb5.github.io/lofreq/ documentation: https://csb5.github.io/lofreq/commands/ doi: "10.1093/nar/gks918 " - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/lofreq/indelqual/meta.yml b/modules/lofreq/indelqual/meta.yml index a6ec7dc2..b98bf2c4 100644 --- a/modules/lofreq/indelqual/meta.yml +++ b/modules/lofreq/indelqual/meta.yml @@ -9,7 +9,7 @@ tools: description: Lofreq is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It's indelqual programme inserts indel qualities in a BAM file homepage: https://csb5.github.io/lofreq/ doi: "10.1093/nar/gks918" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/macrel/contigs/meta.yml b/modules/macrel/contigs/meta.yml index e0b2fabd..25473470 100644 --- a/modules/macrel/contigs/meta.yml +++ b/modules/macrel/contigs/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://macrel.readthedocs.io/en/latest/ tool_dev_url: https://github.com/BigDataBiology/macrel doi: "10.7717/peerj.10555" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/macs2/callpeak/meta.yml b/modules/macs2/callpeak/meta.yml index afb949ec..974ea33a 100644 --- a/modules/macs2/callpeak/meta.yml +++ b/modules/macs2/callpeak/meta.yml @@ -1,10 +1,10 @@ name: macs2_callpeak description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments keywords: - - alignment - - atac-seq - - chip-seq - - peak-calling + - alignment + - atac-seq + - chip-seq + - peak-calling tools: - macs2: description: Model Based Analysis for ChIP-Seq data @@ -12,7 +12,7 @@ tools: documentation: https://docs.csc.fi/apps/macs2/ tool_dev_url: https://github.com/macs3-project/MACS doi: "https://doi.org/10.1101/496521" - licence: ['BSD'] + licence: ["BSD"] input: - meta: @@ -28,7 +28,8 @@ input: description: The control file - macs2_gsize: type: string - description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), + description: + Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9), 'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8) output: diff --git a/modules/malt/build/meta.yml b/modules/malt/build/meta.yml index 9985d834..c8fe06f6 100644 --- a/modules/malt/build/meta.yml +++ b/modules/malt/build/meta.yml @@ -17,7 +17,7 @@ tools: documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf tool_dev_url: None doi: "10.1038/s41559-017-0446-6" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - fastas: diff --git a/modules/malt/run/meta.yml b/modules/malt/run/meta.yml index 740ab8a5..7bd79290 100644 --- a/modules/malt/run/meta.yml +++ b/modules/malt/run/meta.yml @@ -16,7 +16,7 @@ tools: documentation: https://software-ab.informatik.uni-tuebingen.de/download/malt/manual.pdf tool_dev_url: None doi: "10.1038/s41559-017-0446-6" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - fastqs: @@ -26,11 +26,11 @@ input: - mode: type: string description: Program mode - pattern: 'Unknown|BlastN|BlastP|BlastX|Classifier' + pattern: "Unknown|BlastN|BlastP|BlastX|Classifier" - index: type: directory description: Index/database directory from malt-build - pattern: '*/' + pattern: "*/" output: - versions: type: file diff --git a/modules/maltextract/meta.yml b/modules/maltextract/meta.yml index 8f257100..843c1555 100644 --- a/modules/maltextract/meta.yml +++ b/modules/maltextract/meta.yml @@ -21,7 +21,7 @@ tools: documentation: https://github.com/rhuebler/hops tool_dev_url: https://github.com/rhuebler/hops doi: "https://doi.org/10.1186/s13059-019-1903-0" - licence: ['GPL 3'] + licence: ["GPL 3"] input: - rma6: diff --git a/modules/manta/germline/main.nf b/modules/manta/germline/main.nf index fab789ec..5ddba51b 100644 --- a/modules/manta/germline/main.nf +++ b/modules/manta/germline/main.nf @@ -8,11 +8,11 @@ process MANTA_GERMLINE { 'quay.io/biocontainers/manta:1.6.0--h9ee0642_1' }" input: - tuple val(meta), path(input), path(input_index) + tuple val(meta), path(input), path(index) path fasta - path fai - path target_bed - path target_bed_tbi + path fasta_fai + tuple path(target_bed), path(target_bed_tbi) + output: tuple val(meta), path("*candidate_small_indels.vcf.gz") , emit: candidate_small_indels_vcf @@ -29,13 +29,15 @@ process MANTA_GERMLINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def options_manta = target_bed ? "--exome --callRegions $target_bed" : "" + def input_files = input.collect{"--bam ${it}"}.join(' ') + def options_manta = target_bed ? "--callRegions $target_bed" : "" """ configManta.py \ - --bam $input \ + ${input_files} \ --reference $fasta \ + --runDir manta \ $options_manta \ - --runDir manta + $args python manta/runWorkflow.py -m local -j $task.cpus @@ -57,4 +59,20 @@ process MANTA_GERMLINE { manta: \$( configManta.py --version ) END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.candidate_small_indels.vcf.gz + touch ${prefix}.candidate_small_indels.vcf.gz.tbi + touch ${prefix}.candidate_sv.vcf.gz + touch ${prefix}.candidate_sv.vcf.gz.tbi + touch ${prefix}.diploid_sv.vcf.gz + touch ${prefix}.diploid_sv.vcf.gz.tbi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + manta: \$( configManta.py --version ) + END_VERSIONS + """ } diff --git a/modules/manta/germline/meta.yml b/modules/manta/germline/meta.yml index 3bdb8264..d6297ead 100644 --- a/modules/manta/germline/meta.yml +++ b/modules/manta/germline/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -25,17 +25,17 @@ input: e.g. [ id:'test', single_end:false ] - input: type: file - description: BAM/CRAM/SAM file + description: BAM/CRAM/SAM file. For joint calling use a list of files. pattern: "*.{bam,cram,sam}" - - input_index: + - index: type: file - description: BAM/CRAM/SAM index file + description: BAM/CRAM/SAM index file. For joint calling use a list of files. pattern: "*.{bai,crai,sai}" - fasta: type: file description: Genome reference FASTA file pattern: "*.{fa,fasta}" - - fai: + - fasta_fai: type: file description: Genome reference FASTA index file pattern: "*.{fa.fai,fasta.fai}" @@ -85,3 +85,4 @@ output: authors: - "@maxulysse" + - "@ramprasadn" diff --git a/modules/manta/somatic/meta.yml b/modules/manta/somatic/meta.yml index ddd0eafe..ec9cc869 100644 --- a/modules/manta/somatic/meta.yml +++ b/modules/manta/somatic/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/manta/tumoronly/meta.yml b/modules/manta/tumoronly/meta.yml index 86d1c6c0..f902bc77 100644 --- a/modules/manta/tumoronly/meta.yml +++ b/modules/manta/tumoronly/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://github.com/Illumina/manta/blob/v1.6.0/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/manta doi: "10.1093/bioinformatics/btv710" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/mapdamage2/meta.yml b/modules/mapdamage2/meta.yml index e511a0a6..561a3960 100644 --- a/modules/mapdamage2/meta.yml +++ b/modules/mapdamage2/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://ginolhac.github.io/mapDamage/ tool_dev_url: https://github.com/ginolhac/mapDamage doi: "10.1093/bioinformatics/btt193" - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -30,85 +30,85 @@ input: pattern: "*.{fasta}" output: - - meta: - type: map - description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - - runtime_log: - type: file - description: Log file with a summary of command lines used and timestamps. - pattern: "Runtime_log.txt" - - fragmisincorporation_plot: - type: file - description: A pdf file that displays both fragmentation and misincorporation patterns. - pattern: "Fragmisincorporation_plot.pdf" - - length_plot: - type: file - description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. - pattern: "Length_plot.pdf" - - misincorporation: - type: file - description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. - pattern: "misincorporation.txt" - - pctot_freq: - type: file - description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. - pattern: "5pCtoT_freq.txt" - - pgtoa_freq: - type: file - description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. - pattern: "3pGtoA_freq.txt" - - dnacomp: - type: file - description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. - pattern: "dnacomp.txt" - - lgdistribution: - type: file - description: Contains a table with read length distributions per strand. - pattern: "lgdistribution.txt" - - stats_out_mcmc_hist: - type: file - description: A MCMC histogram for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_hist.pdf" - - stats_out_mcmc_iter: - type: file - description: Values for the damage parameters and log likelihood in each MCMC iteration. - pattern: "Stats_out_MCMC_iter.csv" - - stats_out_mcmc_trace: - type: file - description: A MCMC trace plot for the damage parameters and log likelihood. - pattern: "Stats_out_MCMC_trace.pdf" - - stats_out_mcmc_iter_summ_stat: - type: file - description: Summary statistics for the damage parameters estimated posterior distributions. - pattern: "Stats_out_MCMC_iter_summ_stat.csv" - - stats_out_mcmc_post_pred: - type: file - description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. - pattern: "Stats_out_MCMC_post_pred.pdf" - - stats_out_mcmc_correct_prob: - type: file - description: Position specific probability of a C->T and G->A misincorporation is due to damage. - pattern: "Stats_out_MCMC_correct_prob.csv" - - dnacomp_genome: - type: file - description: Contains the global reference genome base composition (computed by seqtk). - pattern: "dnacomp_genome.csv" - - rescaled: - type: file - description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. - pattern: "*.{bam}" - - fasta: - type: file - description: Allignments in a FASTA file, only if flagged by -d. - pattern: "*.{fasta}" - - folder: - type: folder - description: Folder created when --plot-only, --rescale and --stats-only flags are passed. - pattern: "*/" + - meta: + type: map + description: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - runtime_log: + type: file + description: Log file with a summary of command lines used and timestamps. + pattern: "Runtime_log.txt" + - fragmisincorporation_plot: + type: file + description: A pdf file that displays both fragmentation and misincorporation patterns. + pattern: "Fragmisincorporation_plot.pdf" + - length_plot: + type: file + description: A pdf file that displays length distribution of singleton reads per strand and cumulative frequencies of C->T at 5'-end and G->A at 3'-end are also displayed per strand. + pattern: "Length_plot.pdf" + - misincorporation: + type: file + description: Contains a table with occurrences for each type of mutations and relative positions from the reads ends. + pattern: "misincorporation.txt" + - pctot_freq: + type: file + description: Contains frequencies of Cytosine to Thymine mutations per position from the 5'-ends. + pattern: "5pCtoT_freq.txt" + - pgtoa_freq: + type: file + description: Contains frequencies of Guanine to Adenine mutations per position from the 3'-ends. + pattern: "3pGtoA_freq.txt" + - dnacomp: + type: file + description: Contains a table of the reference genome base composition per position, inside reads and adjacent regions. + pattern: "dnacomp.txt" + - lgdistribution: + type: file + description: Contains a table with read length distributions per strand. + pattern: "lgdistribution.txt" + - stats_out_mcmc_hist: + type: file + description: A MCMC histogram for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_hist.pdf" + - stats_out_mcmc_iter: + type: file + description: Values for the damage parameters and log likelihood in each MCMC iteration. + pattern: "Stats_out_MCMC_iter.csv" + - stats_out_mcmc_trace: + type: file + description: A MCMC trace plot for the damage parameters and log likelihood. + pattern: "Stats_out_MCMC_trace.pdf" + - stats_out_mcmc_iter_summ_stat: + type: file + description: Summary statistics for the damage parameters estimated posterior distributions. + pattern: "Stats_out_MCMC_iter_summ_stat.csv" + - stats_out_mcmc_post_pred: + type: file + description: Empirical misincorporation frequency and posterior predictive intervals from the fitted model. + pattern: "Stats_out_MCMC_post_pred.pdf" + - stats_out_mcmc_correct_prob: + type: file + description: Position specific probability of a C->T and G->A misincorporation is due to damage. + pattern: "Stats_out_MCMC_correct_prob.csv" + - dnacomp_genome: + type: file + description: Contains the global reference genome base composition (computed by seqtk). + pattern: "dnacomp_genome.csv" + - rescaled: + type: file + description: Rescaled BAM file, where likely post-mortem damaged bases have downscaled quality scores. + pattern: "*.{bam}" + - fasta: + type: file + description: Allignments in a FASTA file, only if flagged by -d. + pattern: "*.{fasta}" + - folder: + type: folder + description: Folder created when --plot-only, --rescale and --stats-only flags are passed. + pattern: "*/" authors: -- "@darcy220606" + - "@darcy220606" diff --git a/modules/mash/dist/meta.yml b/modules/mash/dist/meta.yml index 8cbaa63c..5ca9373e 100644 --- a/modules/mash/dist/meta.yml +++ b/modules/mash/dist/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://mash.readthedocs.io/en/latest/sketches.html tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" - licence: ['https://github.com/marbl/Mash/blob/master/LICENSE.txt'] + licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] input: - meta: diff --git a/modules/mash/sketch/meta.yml b/modules/mash/sketch/meta.yml index fba0e000..d5c0f3a1 100644 --- a/modules/mash/sketch/meta.yml +++ b/modules/mash/sketch/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://mash.readthedocs.io/en/latest/sketches.html tool_dev_url: https://github.com/marbl/Mash doi: "10.1186/s13059-016-0997-x" - licence: ['https://github.com/marbl/Mash/blob/master/LICENSE.txt'] + licence: ["https://github.com/marbl/Mash/blob/master/LICENSE.txt"] input: - meta: diff --git a/modules/mashtree/meta.yml b/modules/mashtree/meta.yml index 3cf74772..ec5ea338 100644 --- a/modules/mashtree/meta.yml +++ b/modules/mashtree/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/lskatz/mashtree tool_dev_url: https://github.com/lskatz/mashtree doi: "https://doi.org/10.21105/joss.01762" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/maxbin2/meta.yml b/modules/maxbin2/meta.yml index 358f8323..7971d481 100644 --- a/modules/maxbin2/meta.yml +++ b/modules/maxbin2/meta.yml @@ -16,7 +16,7 @@ tools: documentation: https://sourceforge.net/projects/maxbin/ tool_dev_url: https://sourceforge.net/projects/maxbin/ doi: "10.1093/bioinformatics/btv638" - licence: ['BSD 3-clause'] + licence: ["BSD 3-clause"] input: - meta: diff --git a/modules/medaka/meta.yml b/modules/medaka/meta.yml index d194464f..66557460 100644 --- a/modules/medaka/meta.yml +++ b/modules/medaka/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://nanoporetech.github.io/medaka/index.html tool_dev_url: https://github.com/nanoporetech/medaka doi: "" - licence: ['Mozilla Public License 2.0'] + licence: ["Mozilla Public License 2.0"] input: - meta: diff --git a/modules/megahit/meta.yml b/modules/megahit/meta.yml index e4b2181b..f9572ab4 100644 --- a/modules/megahit/meta.yml +++ b/modules/megahit/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/voutcn/megahit tool_dev_url: https://github.com/voutcn/megahit doi: "10.1093/bioinformatics/btv033" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: @@ -24,8 +24,8 @@ input: - reads: type: file description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively in gzipped or uncompressed FASTQ or FASTA format. + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively in gzipped or uncompressed FASTQ or FASTA format. output: - meta: diff --git a/modules/meningotype/meta.yml b/modules/meningotype/meta.yml index 07c2ff5e..fdef2836 100644 --- a/modules/meningotype/meta.yml +++ b/modules/meningotype/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/MDU-PHL/meningotype tool_dev_url: https://github.com/MDU-PHL/meningotype doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/metabat2/jgisummarizebamcontigdepths/meta.yml b/modules/metabat2/jgisummarizebamcontigdepths/meta.yml index 351a4701..ff0ab40e 100644 --- a/modules/metabat2/jgisummarizebamcontigdepths/meta.yml +++ b/modules/metabat2/jgisummarizebamcontigdepths/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://bitbucket.org/berkeleylab/metabat/src/master/ tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" - licence: ['BSD-3-clause-LBNL'] + licence: ["BSD-3-clause-LBNL"] input: - meta: diff --git a/modules/metabat2/metabat2/meta.yml b/modules/metabat2/metabat2/meta.yml index 0ec07b02..04b8df4f 100644 --- a/modules/metabat2/metabat2/meta.yml +++ b/modules/metabat2/metabat2/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://bitbucket.org/berkeleylab/metabat/src/master/ tool_dev_url: https://bitbucket.org/berkeleylab/metabat/src/master/ doi: "10.7717/peerj.7359" - licence: ['BSD-3-clause-LBNL'] + licence: ["BSD-3-clause-LBNL"] input: - meta: @@ -28,8 +28,8 @@ input: - depth: type: file description: | - Optional text file listing the coverage per contig pre-generated - by metabat2_jgisummarizebamcontigdepths + Optional text file listing the coverage per contig pre-generated + by metabat2_jgisummarizebamcontigdepths pattern: "*.txt" output: @@ -63,7 +63,6 @@ output: description: cluster memberships as a matrix format. pattern: "*.tsv.gz" - authors: - "@maxibor" - "@jfy133" diff --git a/modules/metaphlan3/meta.yml b/modules/metaphlan3/meta.yml index 0d3c6f85..d10a27d7 100644 --- a/modules/metaphlan3/meta.yml +++ b/modules/metaphlan3/meta.yml @@ -8,11 +8,11 @@ keywords: - fasta tools: - metaphlan3: - description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance + description: Identify clades (phyla to species) present in the metagenome obtained from a microbiome sample and their relative abundance homepage: https://huttenhower.sph.harvard.edu/metaphlan/ documentation: https://github.com/biobakery/MetaPhlAn doi: "10.7554/eLife.65088" - licence: ['MIT License'] + licence: ["MIT License"] input: - meta: diff --git a/modules/methyldackel/extract/meta.yml b/modules/methyldackel/extract/meta.yml index 3c1dfb2a..810f2456 100644 --- a/modules/methyldackel/extract/meta.yml +++ b/modules/methyldackel/extract/meta.yml @@ -1,58 +1,58 @@ name: methyldackel_extract description: Extracts per-base methylation metrics from alignments keywords: - - methylation - - 5mC - - methylseq - - bisulphite - - consensus - - bedGraph - - bam - - cram + - methylation + - 5mC + - methylseq + - bisulphite + - consensus + - bedGraph + - bam + - cram tools: - - methyldackel: - description: | - A (mostly) universal methylation extractor - for BS-seq experiments. - homepage: https://github.com/brentp/bwa-meth - documentation: https://github.com/brentp/bwa-meth - arxiv: arXiv:1401.1129 - licence: ['MIT'] + - methyldackel: + description: | + A (mostly) universal methylation extractor + for BS-seq experiments. + homepage: https://github.com/brentp/bwa-meth + documentation: https://github.com/brentp/bwa-meth + arxiv: arXiv:1401.1129 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: bedGraph file containing per-base methylation metrics - pattern: "*.{bedGraph}" - - 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 ] + - bedgraph: + type: file + description: bedGraph file containing per-base methylation metrics + pattern: "*.{bedGraph}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/methyldackel/mbias/meta.yml b/modules/methyldackel/mbias/meta.yml index e66cde50..a83ca106 100644 --- a/modules/methyldackel/mbias/meta.yml +++ b/modules/methyldackel/mbias/meta.yml @@ -1,59 +1,59 @@ name: methyldackel_mbias description: Generates methylation bias plots from alignments keywords: - - methylation - - 5mC - - methylseq - - bisulphite - - methylation bias - - mbias - - qc - - bam - - cram + - methylation + - 5mC + - methylseq + - bisulphite + - methylation bias + - mbias + - qc + - bam + - cram tools: - - methyldackel: - description: | - A (mostly) universal methylation extractor - for BS-seq experiments. - homepage: https://github.com/brentp/bwa-meth - documentation: https://github.com/brentp/bwa-meth - arxiv: arXiv:1401.1129 - licence: ['MIT'] + - methyldackel: + description: | + A (mostly) universal methylation extractor + for BS-seq experiments. + homepage: https://github.com/brentp/bwa-meth + documentation: https://github.com/brentp/bwa-meth + arxiv: arXiv:1401.1129 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input genome fasta file - pattern: "*.{fasta,fa}" - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - bam: - type: file - description: BAM/CRAM file - pattern: "*.{bam,cram}" - - bai: - type: file - description: BAM/CRAM index file - pattern: "*.{bai,crai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Input genome fasta file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - bam: + type: file + description: BAM/CRAM file + pattern: "*.{bam,cram}" + - bai: + type: file + description: BAM/CRAM index file + pattern: "*.{bai,crai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - txt: - type: file - description: Text file containing methylation bias - pattern: "*.{txt}" - - 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 ] + - txt: + type: file + description: Text file containing methylation bias + pattern: "*.{txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/minia/meta.yml b/modules/minia/meta.yml index 397a1d49..ae86f75c 100644 --- a/modules/minia/meta.yml +++ b/modules/minia/meta.yml @@ -9,7 +9,7 @@ tools: a human genome on a desktop computer in a day. The output of Minia is a set of contigs. homepage: https://github.com/GATB/minia documentation: https://github.com/GATB/minia - licence: ['AGPL-3.0-or-later'] + licence: ["AGPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/miniasm/meta.yml b/modules/miniasm/meta.yml index e8aedb9a..59865945 100644 --- a/modules/miniasm/meta.yml +++ b/modules/miniasm/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/lh3/miniasm tool_dev_url: https://github.com/lh3/miniasm doi: "10.1093/bioinformatics/btw152" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/minimap2/align/meta.yml b/modules/minimap2/align/meta.yml index 9994fb05..89e24283 100644 --- a/modules/minimap2/align/meta.yml +++ b/modules/minimap2/align/meta.yml @@ -1,47 +1,47 @@ name: minimap2_align description: A versatile pairwise aligner for genomic and spliced nucleotide sequences keywords: - - align - - fasta - - fastq - - genome - - paf - - reference + - align + - fasta + - fastq + - genome + - paf + - reference tools: - - minimap2: - description: | - A versatile pairwise aligner for genomic and spliced nucleotide sequences. - homepage: https://github.com/lh3/minimap2 - documentation: https://github.com/lh3/minimap2#uguide - licence: ['MIT'] + - minimap2: + description: | + A versatile pairwise aligner for genomic and spliced nucleotide sequences. + homepage: https://github.com/lh3/minimap2 + documentation: https://github.com/lh3/minimap2#uguide + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FASTA or FASTQ files of size 1 and 2 for single-end - and paired-end data, respectively. - - reference: - type: file - description: | - Reference database in FASTA format. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FASTA or FASTQ files of size 1 and 2 for single-end + and paired-end data, respectively. + - reference: + type: file + description: | + Reference database in FASTA format. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf: - type: file - description: Alignment in PAF format - pattern: "*.paf" - - 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 ] + - paf: + type: file + description: Alignment in PAF format + pattern: "*.paf" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/minimap2/index/meta.yml b/modules/minimap2/index/meta.yml index 78a39bdd..3bf9f043 100644 --- a/modules/minimap2/index/meta.yml +++ b/modules/minimap2/index/meta.yml @@ -1,30 +1,30 @@ name: minimap2_index description: Provides fasta index required by minimap2 alignment. keywords: - - index - - fasta - - reference + - index + - fasta + - reference tools: - - minimap2: - description: | - A versatile pairwise aligner for genomic and spliced nucleotide sequences. - homepage: https://github.com/lh3/minimap2 - documentation: https://github.com/lh3/minimap2#uguide - licence: ['MIT'] + - minimap2: + description: | + A versatile pairwise aligner for genomic and spliced nucleotide sequences. + homepage: https://github.com/lh3/minimap2 + documentation: https://github.com/lh3/minimap2#uguide + licence: ["MIT"] input: - - fasta: - type: file - description: | - Reference database in FASTA format. + - fasta: + type: file + description: | + Reference database in FASTA format. output: - - mmi: - type: file - description: Minimap2 fasta index. - pattern: "*.mmi" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - mmi: + type: file + description: Minimap2 fasta index. + pattern: "*.mmi" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" - - "@drpatelh" + - "@yuukiiwa" + - "@drpatelh" diff --git a/modules/mlst/meta.yml b/modules/mlst/meta.yml index e9d2a09f..63667f96 100644 --- a/modules/mlst/meta.yml +++ b/modules/mlst/meta.yml @@ -9,7 +9,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index cc7bc86b..ff91e06f 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -2,10 +2,10 @@ process MOSDEPTH { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::mosdepth=0.3.2' : null) + conda (params.enable_conda ? 'bioconda::mosdepth=0.3.3' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.2--h01d7912_0' : - 'quay.io/biocontainers/mosdepth:0.3.2--h01d7912_0' }" + 'https://depot.galaxyproject.org/singularity/mosdepth:0.3.3--hdfd78af_1' : + 'quay.io/biocontainers/mosdepth:0.3.3--hdfd78af_1'}" input: tuple val(meta), path(bam), path(bai) @@ -14,12 +14,13 @@ process MOSDEPTH { output: tuple val(meta), path('*.global.dist.txt') , emit: global_txt - tuple val(meta), path('*.region.dist.txt') , emit: regions_txt + tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed - tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi - tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed - tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi + tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true + tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true + tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true + tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true + tuple val(meta), path('*.regions.bed.gz.csi') , emit: regions_csi , optional:true path "versions.yml" , emit: versions when: @@ -28,7 +29,13 @@ process MOSDEPTH { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def interval = window_size ? "--by ${window_size}" : "--by ${bed}" + if (window_size) { + interval = "--by ${window_size}" + } else if ( bed ) { + interval = "--by ${bed}" + } else { + interval = "" + } """ mosdepth \\ $interval \\ @@ -40,4 +47,22 @@ process MOSDEPTH { mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.global.dist.txt + touch ${prefix}.region.dist.txt + touch ${prefix}.summary.txt + touch ${prefix}.per-base.d4 + touch ${prefix}.per-base.bed.gz + touch ${prefix}.per-base.bed.gz.csi + touch ${prefix}.regions.bed.gz + touch ${prefix}.regions.bed.gz.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ } diff --git a/modules/mosdepth/meta.yml b/modules/mosdepth/meta.yml index be568aa6..636e966b 100644 --- a/modules/mosdepth/meta.yml +++ b/modules/mosdepth/meta.yml @@ -11,7 +11,7 @@ tools: Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing. documentation: https://github.com/brentp/mosdepth doi: 10.1093/bioinformatics/btx699 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map @@ -73,5 +73,6 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" + - "@ramprasadn" diff --git a/modules/msisensor/msi/meta.yml b/modules/msisensor/msi/meta.yml index e3f13e2e..5f291994 100644 --- a/modules/msisensor/msi/meta.yml +++ b/modules/msisensor/msi/meta.yml @@ -10,7 +10,7 @@ tools: documentation: None tool_dev_url: None doi: "10.1093/bioinformatics/btt755" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/msisensor/scan/meta.yml b/modules/msisensor/scan/meta.yml index 4900f8cc..5976166d 100644 --- a/modules/msisensor/scan/meta.yml +++ b/modules/msisensor/scan/meta.yml @@ -10,7 +10,7 @@ tools: documentation: None tool_dev_url: None doi: "10.1093/bioinformatics/btt755" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/msisensorpro/msi_somatic/main.nf b/modules/msisensorpro/msi_somatic/main.nf new file mode 100644 index 00000000..e2da70de --- /dev/null +++ b/modules/msisensorpro/msi_somatic/main.nf @@ -0,0 +1,47 @@ +process MSISENSORPRO_MSI_SOMATIC { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : + 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" + + input: + tuple val(meta), path(normal), path(normal_index), path(tumor), path(tumor_index), path(intervals) + path (fasta) + path (msisensor_scan) + + output: + tuple val(meta), path("${prefix}") , emit: output_report + tuple val(meta), path("${prefix}_dis") , emit: output_dis + tuple val(meta), path("${prefix}_germline"), emit: output_germline + tuple val(meta), path("${prefix}_somatic") , emit: output_somatic + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + def fasta = fasta ? "-g ${fasta}" : "" + def intervals = intervals ? " -e ${intervals} " : "" + """ + msisensor-pro \\ + msi \\ + -d ${msisensor_scan} \\ + -n ${normal} \\ + -t ${tumor} \\ + ${fasta} \\ + -o $prefix \\ + -b ${task.cpus} \\ + ${intervals} \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') + END_VERSIONS + """ +} diff --git a/modules/msisensorpro/msi_somatic/meta.yml b/modules/msisensorpro/msi_somatic/meta.yml new file mode 100644 index 00000000..09bc0e73 --- /dev/null +++ b/modules/msisensorpro/msi_somatic/meta.yml @@ -0,0 +1,80 @@ +name: msisensorpro_msi_somatic +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +keywords: + - micro-satellite-scan + - msisensor-pro + - msi + - somatic +tools: + - msisensorpro: + description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + homepage: https://github.com/xjtu-omics/msisensor-pro + documentation: https://github.com/xjtu-omics/msisensor-pro/wiki + tool_dev_url: https://github.com/xjtu-omics/msisensor-pro + doi: "doi.org/10.1016/j.gpb.2020.02.001" + licence: ['Custom Licence'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - normal: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - normal_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - tumor: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - tumor_index: + type: file + description: BAM/CRAM/SAM index file + pattern: "*.{bai,crai,sai}" + - intervals: + type: file + description: bed file containing interval information, optional + pattern: "*.{bed}" + - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" + - msisensor_scan: + type: file + description: Output from msisensor-pro/scan, conaining list of msi regions + pattern: "*.list" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - output_report: + type: file + description: File containing final report with all detected microsatellites, unstable somatic microsatellites, msi score + - output_dis: + type: file + description: File containing distribution results + - output_germline: + type: file + description: File containing germline results + - output_somatic: + type: file + description: File containing somatic results + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - list: + type: file + description: File containing microsatellite list + pattern: "*.{list}" + +authors: + - "@FriederikeHanssen" diff --git a/modules/msisensorpro/scan/main.nf b/modules/msisensorpro/scan/main.nf new file mode 100644 index 00000000..752606d6 --- /dev/null +++ b/modules/msisensorpro/scan/main.nf @@ -0,0 +1,35 @@ +process MSISENSORPRO_SCAN { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::msisensor-pro=1.2.0" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/msisensor-pro:1.2.0--hfc31af2_0' : + 'quay.io/biocontainers/msisensor-pro:1.2.0--hfc31af2_0' }" + + input: + tuple val(meta), path(fasta) + + output: + tuple val(meta), path("*.list"), emit: list + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + """ + msisensor-pro \\ + scan \\ + -d $fasta \\ + -o ${prefix}.msisensor_scan.list \\ + $args + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + msisensor-pro: \$(msisensor-pro 2>&1 | sed -nE 's/Version:\\sv([0-9]\\.[0-9])/\\1/ p') + END_VERSIONS + """ +} diff --git a/modules/msisensorpro/scan/meta.yml b/modules/msisensorpro/scan/meta.yml new file mode 100644 index 00000000..72c1b84b --- /dev/null +++ b/modules/msisensorpro/scan/meta.yml @@ -0,0 +1,43 @@ +name: msisensorpro_scan +description: MSIsensor-pro evaluates Microsatellite Instability (MSI) for cancer patients with next generation sequencing data. It accepts the whole genome sequencing, whole exome sequencing and target region (panel) sequencing data as input +keywords: + - micro-satellite-scan + - msisensor-pro + - scan +tools: + - msisensorpro: + description: Microsatellite Instability (MSI) detection using high-throughput sequencing data. + homepage: https://github.com/xjtu-omics/msisensor-pro + documentation: https://github.com/xjtu-omics/msisensor-pro/wiki + tool_dev_url: https://github.com/xjtu-omics/msisensor-pro + doi: "doi.org/10.1016/j.gpb.2020.02.001" + licence: ['Custom Licence'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: Reference genome + pattern: "*.{fasta}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - list: + type: file + description: File containing microsatellite list + pattern: "*.{list}" + +authors: + - "@FriederikeHanssen" diff --git a/modules/mtnucratio/meta.yml b/modules/mtnucratio/meta.yml index 824af397..b8cdef36 100644 --- a/modules/mtnucratio/meta.yml +++ b/modules/mtnucratio/meta.yml @@ -15,7 +15,7 @@ tools: documentation: https://github.com/apeltzer/MTNucRatioCalculator tool_dev_url: https://github.com/apeltzer/MTNucRatioCalculator doi: "10.1186/s13059-016-0918-z" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/multiqc/main.nf b/modules/multiqc/main.nf index 0ff7cac1..1264aac1 100644 --- a/modules/multiqc/main.nf +++ b/modules/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_medium' - conda (params.enable_conda ? 'bioconda::multiqc=1.11' : null) + conda (params.enable_conda ? 'bioconda::multiqc=1.12' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.11--pyhdfd78af_0' : - 'quay.io/biocontainers/multiqc:1.11--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.12--pyhdfd78af_0' : + 'quay.io/biocontainers/multiqc:1.12--pyhdfd78af_0' }" input: path multiqc_files diff --git a/modules/multiqc/meta.yml b/modules/multiqc/meta.yml index 63c75a45..6fa891ef 100644 --- a/modules/multiqc/meta.yml +++ b/modules/multiqc/meta.yml @@ -1,40 +1,40 @@ name: MultiQC description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report + - QC + - bioinformatics tools + - Beautiful stand-alone HTML report tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ['GPL-3.0-or-later'] + - multiqc: + description: | + MultiQC searches a given directory for analysis logs and compiles a HTML report. + It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. + homepage: https://multiqc.info/ + documentation: https://multiqc.info/docs/ + licence: ["GPL-3.0-or-later"] input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC + - multiqc_files: + type: file + description: | + List of reports / files recognised by MultiQC, for example the html and zip output of FastQC output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: dir - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: MultiQC report file + pattern: "multiqc_report.html" + - data: + type: dir + description: MultiQC data dir + pattern: "multiqc_data" + - plots: + type: file + description: Plots created by MultiQC + pattern: "*_data" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" + - "@abhi18av" + - "@bunop" + - "@drpatelh" diff --git a/modules/mummer/meta.yml b/modules/mummer/meta.yml index 5f7a983c..ec4f0c86 100644 --- a/modules/mummer/meta.yml +++ b/modules/mummer/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://mummer.sourceforge.net/ tool_dev_url: http://mummer.sourceforge.net/ doi: https://doi.org/10.1186/gb-2004-5-2-r12 - licence: ['The Artistic License'] + licence: ["The Artistic License"] input: - meta: diff --git a/modules/muscle/meta.yml b/modules/muscle/meta.yml index d28afa72..274cc68d 100644 --- a/modules/muscle/meta.yml +++ b/modules/muscle/meta.yml @@ -1,15 +1,15 @@ name: muscle description: MUSCLE is a program for creating multiple alignments of amino acid or nucleotide sequences. A range of options are provided that give you the choice of optimizing accuracy, speed, or some compromise between the two keywords: - - msa - - multiple sequence alignment + - msa + - multiple sequence alignment tools: - muscle: - description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput - homepage: https://www.drive5.com/muscle - documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840 - doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/" - licence: ['http://www.drive5.com/muscle/manual/license.html'] + description: MUSCLE is a multiple sequence alignment tool with high accuracy and throughput + homepage: https://www.drive5.com/muscle + documentation: http://www.drive5.com/muscle/muscle.html#_Toc81224840 + doi: "https://pubmed.ncbi.nlm.nih.gov/15034147/" + licence: ["http://www.drive5.com/muscle/manual/license.html"] input: - fasta: type: file diff --git a/modules/nanolyse/meta.yml b/modules/nanolyse/meta.yml index 326fc221..c5562a04 100644 --- a/modules/nanolyse/meta.yml +++ b/modules/nanolyse/meta.yml @@ -1,47 +1,47 @@ name: nanolyse description: DNA contaminant removal using NanoLyse keywords: - - contaminant_removal + - contaminant_removal tools: - - nanolyse: - description: | - DNA contaminant removal using NanoLyse - homepage: https://github.com/wdecoster/nanolyse - documentation: https://github.com/wdecoster/nanolyse#nanolyse - licence: ['GPL-3.0-or-later'] + - nanolyse: + description: | + DNA contaminant removal using NanoLyse + homepage: https://github.com/wdecoster/nanolyse + documentation: https://github.com/wdecoster/nanolyse#nanolyse + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - Basecalled reads in FASTQ.GZ format - pattern: "*.fastq.gz" - - fasta: - type: file - description: | - A reference fasta file against which to filter. - pattern: "*.fasta" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + Basecalled reads in FASTQ.GZ format + pattern: "*.fastq.gz" + - fasta: + type: file + description: | + A reference fasta file against which to filter. + pattern: "*.fasta" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: Reads with contaminants removed in FASTQ format - pattern: "*.fastq.gz" - - log: - type: file - description: Log of the Nanolyse run. - pattern: "*.log" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: Reads with contaminants removed in FASTQ format + pattern: "*.fastq.gz" + - log: + type: file + description: Log of the Nanolyse run. + pattern: "*.log" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" + - "@yuukiiwa" diff --git a/modules/nanoplot/meta.yml b/modules/nanoplot/meta.yml index 52ebb622..28c8c2d3 100644 --- a/modules/nanoplot/meta.yml +++ b/modules/nanoplot/meta.yml @@ -1,59 +1,59 @@ name: nanoplot description: Run NanoPlot on nanopore-sequenced reads keywords: - - quality control - - qc - - fastq - - sequencing summary - - nanopore + - quality control + - qc + - fastq + - sequencing summary + - nanopore tools: - - nanoplot: - description: | - NanoPlot is a tool for ploting long-read sequencing data and - alignment. - homepage: http://nanoplot.bioinf.be - documentation: https://github.com/wdecoster/NanoPlot - licence: ['GPL-3.0-or-later'] + - nanoplot: + description: | + NanoPlot is a tool for ploting long-read sequencing data and + alignment. + homepage: http://nanoplot.bioinf.be + documentation: https://github.com/wdecoster/NanoPlot + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fastq: - type: file - description: | - List of input basecalled-FastQ files. - - summary_txt: - type: file - description: | - List of sequencing_summary.txt files from running basecalling. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: | + List of input basecalled-FastQ files. + - summary_txt: + type: file + description: | + List of sequencing_summary.txt files from running basecalling. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: NanoPlot report - pattern: "*{.html}" - - png: - type: file - description: Plots generated by NanoPlot - pattern: "*{.png}" - - txt: - type: file - description: Stats from NanoPlot - pattern: "*{.txt}" - - log: - type: file - description: log file of NanoPlot run - pattern: "*{.log}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - html: + type: file + description: NanoPlot report + pattern: "*{.html}" + - png: + type: file + description: Plots generated by NanoPlot + pattern: "*{.png}" + - txt: + type: file + description: Stats from NanoPlot + pattern: "*{.txt}" + - log: + type: file + description: log file of NanoPlot run + pattern: "*{.log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@yuukiiwa" + - "@drpatelh" + - "@yuukiiwa" diff --git a/modules/ncbigenomedownload/meta.yml b/modules/ncbigenomedownload/meta.yml index fd9e0a45..b4ff842a 100644 --- a/modules/ncbigenomedownload/meta.yml +++ b/modules/ncbigenomedownload/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/kblin/ncbi-genome-download tool_dev_url: https://github.com/kblin/ncbi-genome-download doi: "" - licence: ['Apache Software License'] + licence: ["Apache Software License"] input: - meta: diff --git a/modules/nextclade/datasetget/meta.yml b/modules/nextclade/datasetget/meta.yml index 1246d918..d5f65cda 100644 --- a/modules/nextclade/datasetget/meta.yml +++ b/modules/nextclade/datasetget/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - dataset: diff --git a/modules/nextclade/run/meta.yml b/modules/nextclade/run/meta.yml index 40a863e6..d8f1eb37 100644 --- a/modules/nextclade/run/meta.yml +++ b/modules/nextclade/run/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/nextstrain/nextclade tool_dev_url: https://github.com/nextstrain/nextclade doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/ngmaster/meta.yml b/modules/ngmaster/meta.yml index 1dbb02a0..ec796965 100644 --- a/modules/ngmaster/meta.yml +++ b/modules/ngmaster/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/MDU-PHL/ngmaster/blob/master/README.md tool_dev_url: https://github.com/MDU-PHL/ngmaster doi: "10.1099/mgen.0.000076" - licence: ['GPL v3 only'] + licence: ["GPL v3 only"] input: - meta: diff --git a/modules/nucmer/meta.yml b/modules/nucmer/meta.yml index cccf723f..e9108ef2 100644 --- a/modules/nucmer/meta.yml +++ b/modules/nucmer/meta.yml @@ -10,7 +10,7 @@ tools: documentation: http://mummer.sourceforge.net/ tool_dev_url: http://mummer.sourceforge.net/ doi: "https://doi.org/10.1186/gb-2004-5-2-r12" - licence: ['The Artistic License'] + licence: ["The Artistic License"] input: - meta: diff --git a/modules/optitype/meta.yml b/modules/optitype/meta.yml index 37654463..4cacadda 100644 --- a/modules/optitype/meta.yml +++ b/modules/optitype/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/FRED-2/OptiType documentation: https://github.com/FRED-2/OptiType doi: "10.1093/bioinformatics/btu548" - licence: ['BSD-3-Clause'] + licence: ["BSD-3-Clause"] input: - meta: diff --git a/modules/pairix/meta.yml b/modules/pairix/meta.yml index 45577065..05f03f01 100644 --- a/modules/pairix/meta.yml +++ b/modules/pairix/meta.yml @@ -1,7 +1,7 @@ name: pairix description: | - a tool for indexing and querying on a block-compressed text file - containing pairs of genomic coordinates + a tool for indexing and querying on a block-compressed text file + containing pairs of genomic coordinates keywords: - index tools: @@ -11,7 +11,7 @@ tools: documentation: "https://github.com/4dn-dcic/pairix" tool_dev_url: "https://github.com/4dn-dcic/pairix" doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/dedup/meta.yml b/modules/pairtools/dedup/meta.yml index 288b421e..00b0393c 100644 --- a/modules/pairtools/dedup/meta.yml +++ b/modules/pairtools/dedup/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/flip/meta.yml b/modules/pairtools/flip/meta.yml index 0d7aa082..2fe584e6 100644 --- a/modules/pairtools/flip/meta.yml +++ b/modules/pairtools/flip/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/parse/meta.yml b/modules/pairtools/parse/meta.yml index 8c9c30dc..c2f7691d 100644 --- a/modules/pairtools/parse/meta.yml +++ b/modules/pairtools/parse/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/restrict/meta.yml b/modules/pairtools/restrict/meta.yml index 0ab3b420..6b82f033 100644 --- a/modules/pairtools/restrict/meta.yml +++ b/modules/pairtools/restrict/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/select/meta.yml b/modules/pairtools/select/meta.yml index 5e45129b..667c6d0d 100644 --- a/modules/pairtools/select/meta.yml +++ b/modules/pairtools/select/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pairtools/sort/meta.yml b/modules/pairtools/sort/meta.yml index 6db2f9e2..f439c2ac 100644 --- a/modules/pairtools/sort/meta.yml +++ b/modules/pairtools/sort/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://pairtools.readthedocs.io/ tool_dev_url: https://github.com/mirnylab/pairtools doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/pangolin/main.nf b/modules/pangolin/main.nf index 9fbc69b8..5af557ac 100644 --- a/modules/pangolin/main.nf +++ b/modules/pangolin/main.nf @@ -2,10 +2,10 @@ process PANGOLIN { tag "$meta.id" label 'process_medium' - conda (params.enable_conda ? 'bioconda::pangolin=3.1.19' : null) + conda (params.enable_conda ? 'bioconda::pangolin=3.1.20' : null) container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/pangolin:3.1.19--pyhdfd78af_0' : - 'quay.io/biocontainers/pangolin:3.1.19--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/pangolin:3.1.20--pyhdfd78af_0' : + 'quay.io/biocontainers/pangolin:3.1.20--pyhdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/pangolin/meta.yml b/modules/pangolin/meta.yml index a2c0979a..93c25a75 100644 --- a/modules/pangolin/meta.yml +++ b/modules/pangolin/meta.yml @@ -1,34 +1,34 @@ name: pangolin description: Phylogenetic Assignment of Named Global Outbreak LINeages keywords: - - covid - - pangolin - - lineage + - covid + - pangolin + - lineage tools: - - star: - description: | - Phylogenetic Assignment of Named Global Outbreak LINeages - homepage: https://github.com/cov-lineages/pangolin#pangolearn-description - manual: https://github.com/cov-lineages/pangolin#pangolearn-description - licence: ['GPL-3.0-or-later'] + - star: + description: | + Phylogenetic Assignment of Named Global Outbreak LINeages + homepage: https://github.com/cov-lineages/pangolin#pangolearn-description + manual: https://github.com/cov-lineages/pangolin#pangolearn-description + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - - fasta: - type: file - description: | - The genome assembly to be evaluated + - meta: + type: map + description: | + Groovy Map containing sample information + - fasta: + type: file + description: | + The genome assembly to be evaluated output: - - report: - type: file - description: Pangolin lineage report - pattern: "*.{csv}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - report: + type: file + description: Pangolin lineage report + pattern: "*.{csv}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@kevinmenden" - - "@drpatelh" + - "@kevinmenden" + - "@drpatelh" diff --git a/modules/paraclu/meta.yml b/modules/paraclu/meta.yml index a3424c57..38043742 100644 --- a/modules/paraclu/meta.yml +++ b/modules/paraclu/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://gitlab.com/mcfrith/paraclu tool_dev_url: https://gitlab.com/mcfrith/paraclu doi: "" - licence: ['GPL v3-or-later'] + licence: ["GPL v3-or-later"] input: - meta: diff --git a/modules/pbbam/pbmerge/meta.yml b/modules/pbbam/pbmerge/meta.yml index 7042d86b..64b8d641 100644 --- a/modules/pbbam/pbmerge/meta.yml +++ b/modules/pbbam/pbmerge/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://pbbam.readthedocs.io/en/latest/tools/pbmerge.html tool_dev_url: https://github.com/pacificbiosciences/pbbam/ doi: "" - licence: ['BSD-3-Clause-Clear'] + licence: ["BSD-3-Clause-Clear"] input: - meta: diff --git a/modules/pbccs/meta.yml b/modules/pbccs/meta.yml index f55c0d71..5f3e1777 100644 --- a/modules/pbccs/meta.yml +++ b/modules/pbccs/meta.yml @@ -9,7 +9,7 @@ tools: documentation: https://ccs.how/ tool_dev_url: https://github.com/PacificBiosciences/ccs doi: "" - licence: ['BSD-3-Clause-Clear'] + licence: ["BSD-3-Clause-Clear"] input: - meta: diff --git a/modules/peddy/meta.yml b/modules/peddy/meta.yml index 7c3fcf45..b3f40bb5 100644 --- a/modules/peddy/meta.yml +++ b/modules/peddy/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://peddy.readthedocs.io/en/latest/ tool_dev_url: https://github.com/brentp/peddy doi: "https://doi.org/10.1016/j.ajhg.2017.01.017" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/phyloflash/meta.yml b/modules/phyloflash/meta.yml index 3ed7a9fa..d44001da 100644 --- a/modules/phyloflash/meta.yml +++ b/modules/phyloflash/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://hrgv.github.io/phyloFlash/usage.html tool_dev_url: https://github.com/HRGV/phyloFlash doi: "10.1128/mSystems.00920-20" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/picard/collectmultiplemetrics/meta.yml b/modules/picard/collectmultiplemetrics/meta.yml index 613afc62..68b5c65e 100644 --- a/modules/picard/collectmultiplemetrics/meta.yml +++ b/modules/picard/collectmultiplemetrics/meta.yml @@ -1,50 +1,50 @@ name: picard_collectmultiplemetrics description: Collect multiple metrics from a BAM file keywords: - - alignment - - metrics - - statistics - - insert - - quality - - bam + - alignment + - metrics + - statistics + - insert + - quality + - bam tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Genome fasta file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - - pdf: - type: file - description: PDF plots of metrics - pattern: "*.{pdf}" - - 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 ] + - metrics: + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" + - pdf: + type: file + description: PDF plots of metrics + pattern: "*.{pdf}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/picard/collectwgsmetrics/meta.yml b/modules/picard/collectwgsmetrics/meta.yml index 5b4d8139..d6c3d012 100644 --- a/modules/picard/collectwgsmetrics/meta.yml +++ b/modules/picard/collectwgsmetrics/meta.yml @@ -1,47 +1,47 @@ name: picard_collectwgsmetrics description: Collect metrics about coverage and performance of whole genome sequencing (WGS) experiments. keywords: - - alignment - - metrics - - statistics - - quality - - bam + - alignment + - metrics + - statistics + - quality + - bam tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - fasta: - type: file - description: Genome fasta file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - fasta: + type: file + description: Genome fasta file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - metrics: - type: file - description: Alignment metrics files generated by picard - pattern: "*_{metrics}" - - 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 ] + - metrics: + type: file + description: Alignment metrics files generated by picard + pattern: "*_{metrics}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@flowuenne" - - "@lassefolkersen" + - "@drpatelh" + - "@flowuenne" + - "@lassefolkersen" diff --git a/modules/picard/filtersamreads/meta.yml b/modules/picard/filtersamreads/meta.yml index d63ebcf0..4a8bec5c 100644 --- a/modules/picard/filtersamreads/meta.yml +++ b/modules/picard/filtersamreads/meta.yml @@ -6,46 +6,46 @@ keywords: tools: - picard: description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ tool_dev_url: https://github.com/broadinstitute/picard doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam - pattern: "*.{bam}" - - filter: - type: value - description: Picard filter type - pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" - - readlist: - type: file - description: Optional text file containing reads IDs to include or exclude + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM files. If filtering without read list must be sorted by queryname with picard sortsam + pattern: "*.{bam}" + - filter: + type: value + description: Picard filter type + pattern: "includeAligned|excludeAligned|includeReadList|excludeReadList" + - readlist: + type: file + description: Optional text file containing reads IDs to include or exclude output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Filtered BAM file - pattern: "*.{bam}" - - 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 ] + - bam: + type: file + description: Filtered BAM file + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@jfy133" diff --git a/modules/picard/markduplicates/meta.yml b/modules/picard/markduplicates/meta.yml index c9a08b36..842817bc 100644 --- a/modules/picard/markduplicates/meta.yml +++ b/modules/picard/markduplicates/meta.yml @@ -14,7 +14,7 @@ tools: data and formats such as SAM/BAM/CRAM and VCF. homepage: https://broadinstitute.github.io/picard/ documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/picard/mergesamfiles/meta.yml b/modules/picard/mergesamfiles/meta.yml index 3d010c3c..5f07ecd0 100644 --- a/modules/picard/mergesamfiles/meta.yml +++ b/modules/picard/mergesamfiles/meta.yml @@ -1,41 +1,41 @@ name: picard_mergesamfiles description: Merges multiple BAM files into a single file keywords: - - merge - - alignment - - bam - - sam + - merge + - alignment + - bam + - sam tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: List of BAM files - pattern: "*.{bam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: List of BAM files + pattern: "*.{bam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Merged BAM file - pattern: "*.{bam}" - - 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 ] + - bam: + type: file + description: Merged BAM file + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/picard/sortsam/meta.yml b/modules/picard/sortsam/meta.yml index aa90e456..3e34225d 100644 --- a/modules/picard/sortsam/meta.yml +++ b/modules/picard/sortsam/meta.yml @@ -1,17 +1,17 @@ name: picard_sortsam description: Sorts BAM/SAM files based on a variety of picard specific criteria keywords: - - sort - - bam - - sam + - sort + - bam + - sam tools: - - picard: - description: | - A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) - data and formats such as SAM/BAM/CRAM and VCF. - homepage: https://broadinstitute.github.io/picard/ - documentation: https://broadinstitute.github.io/picard/ - licence: ['MIT'] + - picard: + description: | + A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) + data and formats such as SAM/BAM/CRAM and VCF. + homepage: https://broadinstitute.github.io/picard/ + documentation: https://broadinstitute.github.io/picard/ + licence: ["MIT"] input: - meta: @@ -43,6 +43,5 @@ output: description: Sorted BAM/CRAM/SAM file pattern: "*.{bam}" - authors: - "@jfy133" diff --git a/modules/pirate/meta.yml b/modules/pirate/meta.yml index 296dd11d..d67a91e9 100644 --- a/modules/pirate/meta.yml +++ b/modules/pirate/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/SionBayliss/PIRATE/wiki tool_dev_url: https://github.com/SionBayliss/PIRATE doi: "https://doi.org/10.1093/gigascience/giz119" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/plasmidid/meta.yml b/modules/plasmidid/meta.yml index 8cde23c5..4887cb9a 100644 --- a/modules/plasmidid/meta.yml +++ b/modules/plasmidid/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/BU-ISCIII/plasmidID#readme tool_dev_url: https://github.com/BU-ISCIII/plasmidID doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/plink/extract/meta.yml b/modules/plink/extract/meta.yml index 3978fbb4..7fc2d116 100644 --- a/modules/plink/extract/meta.yml +++ b/modules/plink/extract/meta.yml @@ -10,7 +10,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['GPL'] + licence: ["GPL"] input: - meta: diff --git a/modules/plink/vcf/meta.yml b/modules/plink/vcf/meta.yml index d39892b7..bd8ab133 100644 --- a/modules/plink/vcf/meta.yml +++ b/modules/plink/vcf/meta.yml @@ -12,7 +12,7 @@ tools: documentation: None tool_dev_url: "https://www.cog-genomics.org/plink/1.9/dev" doi: "" - licence: ['GPL'] + licence: ["GPL"] input: - meta: diff --git a/modules/plink2/extract/meta.yml b/modules/plink2/extract/meta.yml index 2323dbc7..07c13ebc 100644 --- a/modules/plink2/extract/meta.yml +++ b/modules/plink2/extract/meta.yml @@ -6,13 +6,13 @@ keywords: tools: - plink2: description: | - Whole genome association analysis toolset, designed to perform a range - of basic, large-scale analyses in a computationally efficient manner + Whole genome association analysis toolset, designed to perform a range + of basic, large-scale analyses in a computationally efficient manner homepage: http://www.cog-genomics.org/plink/2.0/ documentation: http://www.cog-genomics.org/plink/2.0/general_usage tool_dev_url: None doi: "10.1186/s13742-015-0047-8" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/plink2/vcf/meta.yml b/modules/plink2/vcf/meta.yml index 1b2f3a9b..5697ebef 100644 --- a/modules/plink2/vcf/meta.yml +++ b/modules/plink2/vcf/meta.yml @@ -6,13 +6,13 @@ keywords: tools: - plink2: description: | - Whole genome association analysis toolset, designed to perform a range - of basic, large-scale analyses in a computationally efficient manner + Whole genome association analysis toolset, designed to perform a range + of basic, large-scale analyses in a computationally efficient manner homepage: http://www.cog-genomics.org/plink/2.0/ documentation: http://www.cog-genomics.org/plink/2.0/general_usage tool_dev_url: None doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/pmdtools/filter/meta.yml b/modules/pmdtools/filter/meta.yml index 72abbfdc..58d562bf 100644 --- a/modules/pmdtools/filter/meta.yml +++ b/modules/pmdtools/filter/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/pontussk/PMDtools tool_dev_url: https://github.com/pontussk/PMDtools doi: "10.1073/pnas.1318934111" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/preseq/lcextrap/meta.yml b/modules/preseq/lcextrap/meta.yml index bdc61228..0e33df25 100755 --- a/modules/preseq/lcextrap/meta.yml +++ b/modules/preseq/lcextrap/meta.yml @@ -11,7 +11,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['GPL'] + licence: ["GPL"] input: - meta: diff --git a/modules/prokka/meta.yml b/modules/prokka/meta.yml index 87446694..7fc9e185 100644 --- a/modules/prokka/meta.yml +++ b/modules/prokka/meta.yml @@ -9,7 +9,7 @@ tools: description: Rapid annotation of prokaryotic genomes homepage: https://github.com/tseemann/prokka doi: "10.1093/bioinformatics/btu153" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: diff --git a/modules/pycoqc/meta.yml b/modules/pycoqc/meta.yml index 33bd6b07..83748855 100644 --- a/modules/pycoqc/meta.yml +++ b/modules/pycoqc/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://tleonardi.github.io/pycoQC/ tool_dev_url: https://github.com/tleonardi/pycoQC doi: "10.21105/joss.01236" - licence: ['GNU General Public v3 (GPL v3)'] + licence: ["GNU General Public v3 (GPL v3)"] input: - meta: diff --git a/modules/pydamage/analyze/meta.yml b/modules/pydamage/analyze/meta.yml index 918fbce9..09dd25eb 100644 --- a/modules/pydamage/analyze/meta.yml +++ b/modules/pydamage/analyze/meta.yml @@ -19,7 +19,7 @@ tools: homepage: https://github.com/maxibor/pydamage documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/pydamage/filter/meta.yml b/modules/pydamage/filter/meta.yml index 706e38b0..c732ab9b 100644 --- a/modules/pydamage/filter/meta.yml +++ b/modules/pydamage/filter/meta.yml @@ -19,7 +19,7 @@ tools: homepage: https://github.com/maxibor/pydamage documentation: https://pydamage.readthedocs.io/ tool_dev_url: https://github.com/maxibor/pydamage - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/qcat/meta.yml b/modules/qcat/meta.yml index e0ab6a0f..97b9b884 100644 --- a/modules/qcat/meta.yml +++ b/modules/qcat/meta.yml @@ -1,40 +1,40 @@ name: qcat description: Demultiplexer for Nanopore samples keywords: - - demultiplex + - demultiplex tools: - - qcat: - description: | - A demultiplexer for Nanopore samples - homepage: https://github.com/nanoporetech/qcat - documentation: https://github.com/nanoporetech/qcat#qcat - licence: ['MPL-2.0'] + - qcat: + description: | + A demultiplexer for Nanopore samples + homepage: https://github.com/nanoporetech/qcat + documentation: https://github.com/nanoporetech/qcat#qcat + licence: ["MPL-2.0"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - Non-demultiplexed fastq files + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + Non-demultiplexed fastq files output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Demultiplexed fastq samples - pattern: "*.fastq.gz" - - 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 ] + - reads: + type: file + description: Demultiplexed fastq samples + pattern: "*.fastq.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" - - "@drpatelh" + - "@yuukiiwa" + - "@drpatelh" diff --git a/modules/qualimap/bamqc/main.nf b/modules/qualimap/bamqc/main.nf index 4bff0254..92f38f8c 100644 --- a/modules/qualimap/bamqc/main.nf +++ b/modules/qualimap/bamqc/main.nf @@ -10,7 +10,6 @@ process QUALIMAP_BAMQC { input: tuple val(meta), path(bam) path gff - val use_gff output: tuple val(meta), path("${prefix}"), emit: results @@ -25,7 +24,7 @@ process QUALIMAP_BAMQC { def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' def memory = task.memory.toGiga() + "G" - def regions = use_gff ? "--gff $gff" : '' + def regions = gff ? "--gff $gff" : '' def strandedness = 'non-strand-specific' if (meta.strandedness == 'forward') { diff --git a/modules/qualimap/bamqc/meta.yml b/modules/qualimap/bamqc/meta.yml index 6888d30e..303532eb 100644 --- a/modules/qualimap/bamqc/meta.yml +++ b/modules/qualimap/bamqc/meta.yml @@ -1,50 +1,47 @@ name: qualimap_bamqc description: Evaluate alignment data keywords: - - quality control - - qc - - bam + - quality control + - qc + - bam tools: - - qualimap: - description: | - Qualimap 2 is a platform-independent application written in - Java and R that provides both a Graphical User Interface and - a command-line interface to facilitate the quality control of - alignment sequencing data and its derivatives like feature counts. - homepage: http://qualimap.bioinfo.cipf.es/ - documentation: http://qualimap.conesalab.org/doc_html/index.html - doi: 10.1093/bioinformatics/bts503 - licence: ['GPL-2.0-only'] + - qualimap: + description: | + Qualimap 2 is a platform-independent application written in + Java and R that provides both a Graphical User Interface and + a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts. + homepage: http://qualimap.bioinfo.cipf.es/ + documentation: http://qualimap.conesalab.org/doc_html/index.html + doi: 10.1093/bioinformatics/bts503 + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file - pattern: "*.{bam}" - - gff: - type: file - description: Feature file with regions of interest - pattern: "*.{gff,gtf,bed}" - - use_gff: - type: boolean - description: Specifies if feature file should be used or not + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM file + pattern: "*.{bam}" + - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - results: - type: dir - description: Qualimap results dir - pattern: "*/*" - - 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 ] + - results: + type: dir + description: Qualimap results dir + pattern: "*/*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@phue" + - "@phue" diff --git a/modules/qualimap/bamqccram/main.nf b/modules/qualimap/bamqccram/main.nf new file mode 100644 index 00000000..b9a5538d --- /dev/null +++ b/modules/qualimap/bamqccram/main.nf @@ -0,0 +1,60 @@ +process QUALIMAP_BAMQCCRAM { + tag "$meta.id" + label 'process_medium' + + conda (params.enable_conda ? "bioconda::qualimap=2.2.2d bioconda::samtools=1.12" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' : + 'quay.io/biocontainers/mulled-v2-d3934ca6bb4e61334891ffa2e9a4c87a530e3188:4bf11d12f2c3eccf1eb585097c0b6fd31c18c418-0' }" + + input: + tuple val(meta), path(cram), path(crai) + path gff + path fasta + path fasta_fai + + output: + tuple val(meta), path("${prefix}"), emit: results + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + prefix = task.ext.prefix ?: "${meta.id}" + + def collect_pairs = meta.single_end ? '' : '--collect-overlap-pairs' + def memory = task.memory.toGiga() + "G" + def regions = gff ? "--gff $gff" : '' + + def strandedness = 'non-strand-specific' + if (meta.strandedness == 'forward') { + strandedness = 'strand-specific-forward' + } else if (meta.strandedness == 'reverse') { + strandedness = 'strand-specific-reverse' + } + """ + unset DISPLAY + mkdir tmp + export _JAVA_OPTIONS=-Djava.io.tmpdir=./tmp + + samtools view -hb -T ${fasta} ${cram} | + qualimap \\ + --java-mem-size=$memory \\ + bamqc \\ + $args \\ + -bam /dev/stdin \\ + $regions \\ + -p $strandedness \\ + $collect_pairs \\ + -outdir $prefix \\ + -nt $task.cpus + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + qualimap: \$(echo \$(qualimap 2>&1) | sed 's/^.*QualiMap v.//; s/Built.*\$//') + samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//') + END_VERSIONS + """ +} diff --git a/modules/qualimap/bamqccram/meta.yml b/modules/qualimap/bamqccram/meta.yml new file mode 100644 index 00000000..d72f203d --- /dev/null +++ b/modules/qualimap/bamqccram/meta.yml @@ -0,0 +1,51 @@ +name: qualimap_bamqccram +description: Evaluate alignment data +keywords: + - quality control + - qc + - bam +tools: + - qualimap: + description: | + Qualimap 2 is a platform-independent application written in + Java and R that provides both a Graphical User Interface and + a command-line interface to facilitate the quality control of + alignment sequencing data and its derivatives like feature counts. + homepage: http://qualimap.bioinfo.cipf.es/ + documentation: http://qualimap.conesalab.org/doc_html/index.html + doi: 10.1093/bioinformatics/bts503 + licence: ["GPL-2.0-only"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bacramm: + type: file + description: BAM file + pattern: "*.{bam}" + - gff: + type: file + description: Feature file with regions of interest + pattern: "*.{gff,gtf,bed}" + - fasta: + type: file + description: Reference file of cram file + pattern: "*.{fasta,fa,fna}" +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - results: + type: dir + description: Qualimap results dir + pattern: "*/*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@FriederikeHanssen" diff --git a/modules/quast/meta.yml b/modules/quast/meta.yml index 05faa8b8..f4bc38fc 100644 --- a/modules/quast/meta.yml +++ b/modules/quast/meta.yml @@ -10,7 +10,7 @@ tools: QUAST calculates quality metrics for genome assemblies homepage: http://bioinf.spbau.ru/quast doi: https://doi.org/10.1093/bioinformatics/btt086 - licence: ['GPL-2.0-only'] + licence: ["GPL-2.0-only"] input: - consensus: type: file diff --git a/modules/racon/meta.yml b/modules/racon/meta.yml index 2428f044..0cb3888e 100644 --- a/modules/racon/meta.yml +++ b/modules/racon/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/lbcb-sci/racon tool_dev_url: https://github.com/lbcb-sci/racon doi: https://doi.org/10.1101/gr.214270.116 - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/rapidnj/meta.yml b/modules/rapidnj/meta.yml index ead54e09..968baeb5 100644 --- a/modules/rapidnj/meta.yml +++ b/modules/rapidnj/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://birc.au.dk/software/rapidnj tool_dev_url: https://github.com/somme89/rapidNJ doi: "doi:10.1007/978-3-540-87361-7_10" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - alignment: diff --git a/modules/rasusa/meta.yml b/modules/rasusa/meta.yml index 610afd3f..86bce584 100644 --- a/modules/rasusa/meta.yml +++ b/modules/rasusa/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/mbhall88/rasusa/blob/master/README.md tool_dev_url: https://github.com/mbhall88/rasusa doi: "10.5281/zenodo.3731394" - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -20,14 +20,14 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - reads: - type: file - description: List of input paired-end FastQ files + type: file + description: List of input paired-end FastQ files - genome_size: - type: string - description: Genome size of the species + type: string + description: Genome size of the species - depth_cutoff: - type: integer - description: Depth of coverage cutoff + type: integer + description: Depth of coverage cutoff output: - meta: diff --git a/modules/raven/meta.yml b/modules/raven/meta.yml index 644907a9..53917625 100644 --- a/modules/raven/meta.yml +++ b/modules/raven/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/lbcb-sci/raven#usage tool_dev_url: https://github.com/lbcb-sci/raven doi: doi.org/10.1038/s43588-021-00073-4 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/raxmlng/meta.yml b/modules/raxmlng/meta.yml index 3cc558f4..2a23537a 100644 --- a/modules/raxmlng/meta.yml +++ b/modules/raxmlng/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/amkozlov/raxml-ng/wiki tool_dev_url: https://github.com/amkozlov/raxml-ng doi: doi.org/10.1093/bioinformatics/btz305 - licence: ['GPL v2-or-later'] + licence: ["GPL v2-or-later"] input: - alignment: diff --git a/modules/roary/meta.yml b/modules/roary/meta.yml index 4cf42bdf..a24ae558 100644 --- a/modules/roary/meta.yml +++ b/modules/roary/meta.yml @@ -11,7 +11,7 @@ tools: documentation: http://sanger-pathogens.github.io/Roary/ tool_dev_url: https://github.com/sanger-pathogens/Roary/ doi: "http://dx.doi.org/10.1093/bioinformatics/btv421" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/rsem/calculateexpression/meta.yml b/modules/rsem/calculateexpression/meta.yml index fdfaa0c4..10b54b49 100644 --- a/modules/rsem/calculateexpression/meta.yml +++ b/modules/rsem/calculateexpression/meta.yml @@ -21,7 +21,7 @@ input: - reads: type: file description: Input reads for quantification - pattern: "*.fastq.gz"# + pattern: "*.fastq.gz" - index: type: file description: RSEM index diff --git a/modules/rsem/preparereference/meta.yml b/modules/rsem/preparereference/meta.yml index 062f0256..fbe57b20 100644 --- a/modules/rsem/preparereference/meta.yml +++ b/modules/rsem/preparereference/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/deweylab/RSEM documentation: https://github.com/deweylab/RSEM doi: https://doi.org/10.1186/1471-2105-12-323 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - fasta: type: file diff --git a/modules/rseqc/bamstat/meta.yml b/modules/rseqc/bamstat/meta.yml index 561ba195..2d7fa799 100644 --- a/modules/rseqc/bamstat/meta.yml +++ b/modules/rseqc/bamstat/meta.yml @@ -12,7 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/inferexperiment/meta.yml b/modules/rseqc/inferexperiment/meta.yml index 88eabc8a..b4162059 100644 --- a/modules/rseqc/inferexperiment/meta.yml +++ b/modules/rseqc/inferexperiment/meta.yml @@ -11,7 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/innerdistance/meta.yml b/modules/rseqc/innerdistance/meta.yml index 27bcf242..d10a4c44 100644 --- a/modules/rseqc/innerdistance/meta.yml +++ b/modules/rseqc/innerdistance/meta.yml @@ -11,7 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/junctionannotation/meta.yml b/modules/rseqc/junctionannotation/meta.yml index 56364232..a17b84e9 100644 --- a/modules/rseqc/junctionannotation/meta.yml +++ b/modules/rseqc/junctionannotation/meta.yml @@ -12,7 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/junctionsaturation/meta.yml b/modules/rseqc/junctionsaturation/meta.yml index 05d814ad..340fec0d 100644 --- a/modules/rseqc/junctionsaturation/meta.yml +++ b/modules/rseqc/junctionsaturation/meta.yml @@ -12,7 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/readdistribution/meta.yml b/modules/rseqc/readdistribution/meta.yml index 4c736878..94c64712 100644 --- a/modules/rseqc/readdistribution/meta.yml +++ b/modules/rseqc/readdistribution/meta.yml @@ -12,7 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/readduplication/meta.yml b/modules/rseqc/readduplication/meta.yml index 3623de80..5a866643 100644 --- a/modules/rseqc/readduplication/meta.yml +++ b/modules/rseqc/readduplication/meta.yml @@ -11,7 +11,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/rseqc/tin/meta.yml b/modules/rseqc/tin/meta.yml index 158b4033..6333ae14 100644 --- a/modules/rseqc/tin/meta.yml +++ b/modules/rseqc/tin/meta.yml @@ -12,7 +12,7 @@ tools: homepage: http://rseqc.sourceforge.net/ documentation: http://rseqc.sourceforge.net/ doi: 10.1093/bioinformatics/bts356 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/salmon/index/meta.yml b/modules/salmon/index/meta.yml index 3b0cd853..53c64152 100644 --- a/modules/salmon/index/meta.yml +++ b/modules/salmon/index/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - genome_fasta: type: file diff --git a/modules/salmon/quant/meta.yml b/modules/salmon/quant/meta.yml index 223ca82b..109109d8 100644 --- a/modules/salmon/quant/meta.yml +++ b/modules/salmon/quant/meta.yml @@ -12,7 +12,7 @@ tools: homepage: https://salmon.readthedocs.io/en/latest/salmon.html manual: https://salmon.readthedocs.io/en/latest/salmon.html doi: 10.1038/nmeth.4197 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/samblaster/meta.yml b/modules/samblaster/meta.yml index 4d51f4fe..776bef20 100644 --- a/modules/samblaster/meta.yml +++ b/modules/samblaster/meta.yml @@ -1,13 +1,13 @@ name: samblaster description: | - This module combines samtools and samblaster in order to use - samblaster capability to filter or tag SAM files, with the advantage - of maintaining both input and output in BAM format. - Samblaster input must contain a sequence header: for this reason it has been piped - with the "samtools view -h" command. - Additional desired arguments for samtools can be passed using: - options.args2 for the input bam file - options.args3 for the output bam file + This module combines samtools and samblaster in order to use + samblaster capability to filter or tag SAM files, with the advantage + of maintaining both input and output in BAM format. + Samblaster input must contain a sequence header: for this reason it has been piped + with the "samtools view -h" command. + Additional desired arguments for samtools can be passed using: + options.args2 for the input bam file + options.args3 for the output bam file keywords: - sort tools: @@ -21,7 +21,7 @@ tools: documentation: https://github.com/GregoryFaust/samblaster tool_dev_url: https://github.com/GregoryFaust/samblaster doi: "10.1093/bioinformatics/btu314" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/samtools/ampliconclip/meta.yml b/modules/samtools/ampliconclip/meta.yml index 8959b98d..1107cbcd 100644 --- a/modules/samtools/ampliconclip/meta.yml +++ b/modules/samtools/ampliconclip/meta.yml @@ -7,15 +7,15 @@ keywords: - samtools ampliconclip - samtools tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - meta: diff --git a/modules/samtools/bam2fq/meta.yml b/modules/samtools/bam2fq/meta.yml index f35701c4..319a60cf 100644 --- a/modules/samtools/bam2fq/meta.yml +++ b/modules/samtools/bam2fq/meta.yml @@ -1,7 +1,7 @@ name: samtools_bam2fq description: | - The module uses bam2fq method from samtools to - convert a SAM, BAM or CRAM file to FASTQ format + The module uses bam2fq method from samtools to + convert a SAM, BAM or CRAM file to FASTQ format keywords: - bam2fq - samtools @@ -13,7 +13,7 @@ tools: documentation: http://www.htslib.org/doc/1.1/samtools.html tool_dev_url: None doi: "" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/samtools/depth/meta.yml b/modules/samtools/depth/meta.yml index a46fd332..861b04fa 100644 --- a/modules/samtools/depth/meta.yml +++ b/modules/samtools/depth/meta.yml @@ -12,7 +12,7 @@ tools: documentation: http://www.htslib.org/doc/samtools-depth.html tool_dev_url: https://github.com/samtools/samtools doi: "10.1093/bioinformatics/btp352" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/samtools/faidx/meta.yml b/modules/samtools/faidx/meta.yml index bae97a39..e9767764 100644 --- a/modules/samtools/faidx/meta.yml +++ b/modules/samtools/faidx/meta.yml @@ -1,43 +1,43 @@ name: samtools_faidx description: Index FASTA file keywords: - - index - - fasta + - index + - fasta tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: FASTA file - pattern: "*.{fa,fasta}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fasta: + type: file + description: FASTA file + pattern: "*.{fa,fasta}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fai: - type: file - description: FASTA index file - pattern: "*.{fai}" - - 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 ] + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" - - "@phue" + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/samtools/fastq/meta.yml b/modules/samtools/fastq/meta.yml index 91fd476d..41055cfb 100644 --- a/modules/samtools/fastq/meta.yml +++ b/modules/samtools/fastq/meta.yml @@ -1,43 +1,43 @@ name: samtools_fastq description: Converts a SAM/BAM/CRAM file to FASTQ keywords: - - bam - - sam - - cram - - fastq + - bam + - sam + - cram + - fastq tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: compressed FASTQ file - pattern: "*.fastq.gz" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - fastq: + type: file + description: compressed FASTQ file + pattern: "*.fastq.gz" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - "@suzannejin" diff --git a/modules/samtools/fixmate/meta.yml b/modules/samtools/fixmate/meta.yml index 2cec6e7c..a72c5ca9 100644 --- a/modules/samtools/fixmate/meta.yml +++ b/modules/samtools/fixmate/meta.yml @@ -1,24 +1,24 @@ name: samtools_fixmate description: Samtools fixmate is a tool that can fill in information (insert size, cigar, mapq) about paired end reads onto the corresponding other read. Also has options to remove secondary/unmapped alignments and recalculate whether reads are proper pairs. keywords: - - fixmate - - samtools - - insert size - - repair - - bam - - paired - - read pairs + - fixmate + - samtools + - insert size + - repair + - bam + - paired + - read pairs tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: http://www.htslib.org/doc/samtools.html - tool_dev_url: https://github.com/samtools/samtools - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: http://www.htslib.org/doc/samtools.html + tool_dev_url: https://github.com/samtools/samtools + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - meta: type: map diff --git a/modules/samtools/flagstat/meta.yml b/modules/samtools/flagstat/meta.yml index 9bd9ff89..95269063 100644 --- a/modules/samtools/flagstat/meta.yml +++ b/modules/samtools/flagstat/meta.yml @@ -1,49 +1,49 @@ name: samtools_flagstat description: Counts the number of alignments in a BAM/CRAM/SAM file for each FLAG type keywords: - - stats - - mapping - - counts - - bam - - sam - - cram + - stats + - mapping + - counts + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - flagstat: - type: file - description: File containing samtools flagstat output - pattern: "*.{flagstat}" - - 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 ] + - flagstat: + type: file + description: File containing samtools flagstat output + pattern: "*.{flagstat}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/samtools/idxstats/meta.yml b/modules/samtools/idxstats/meta.yml index ec542f34..3710ab88 100644 --- a/modules/samtools/idxstats/meta.yml +++ b/modules/samtools/idxstats/meta.yml @@ -1,50 +1,50 @@ name: samtools_idxstats description: Reports alignment summary statistics for a BAM/CRAM/SAM file keywords: - - stats - - mapping - - counts - - chromosome - - bam - - sam - - cram + - stats + - mapping + - counts + - chromosome + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - bai: - type: file - description: Index for BAM/CRAM/SAM file - pattern: "*.{bai,crai,sai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - bai: + type: file + description: Index for BAM/CRAM/SAM file + pattern: "*.{bai,crai,sai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - idxstats: - type: file - description: File containing samtools idxstats output - pattern: "*.{idxstats}" - - 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 ] + - idxstats: + type: file + description: File containing samtools idxstats output + pattern: "*.{idxstats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/samtools/index/meta.yml b/modules/samtools/index/meta.yml index 0905b3cd..e5cadbc2 100644 --- a/modules/samtools/index/meta.yml +++ b/modules/samtools/index/meta.yml @@ -1,53 +1,53 @@ name: samtools_index description: Index SAM/BAM/CRAM file keywords: - - index - - bam - - sam - - cram + - index + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - 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}" - - csi: - type: file - description: CSI index file - pattern: "*.{csi}" - - 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 ] + - 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}" + - csi: + type: file + description: CSI index file + pattern: "*.{csi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" - - "@maxulysse" + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/samtools/merge/meta.yml b/modules/samtools/merge/meta.yml index 2576a3a3..fb78e55c 100644 --- a/modules/samtools/merge/meta.yml +++ b/modules/samtools/merge/meta.yml @@ -1,54 +1,54 @@ name: samtools_merge description: Merge BAM or CRAM file keywords: - - merge - - bam - - sam - - cram + - merge + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] 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}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - pattern: "*.{fasta,fa}" + - 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}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" 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}" - - 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 ] + - 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" authors: - - "@drpatelh" - - "@yuukiiwa " - - "@maxulysse" - - "@FriederikeHanssen" + - "@drpatelh" + - "@yuukiiwa " + - "@maxulysse" + - "@FriederikeHanssen" diff --git a/modules/samtools/mpileup/meta.yml b/modules/samtools/mpileup/meta.yml index fac7a5bc..c384f5c6 100644 --- a/modules/samtools/mpileup/meta.yml +++ b/modules/samtools/mpileup/meta.yml @@ -1,48 +1,48 @@ name: samtools_mpileup -description: BAM +description: BAM keywords: - - mpileup - - bam - - sam - - cram + - mpileup + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: file - description: FASTA reference file - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: file + description: FASTA reference file + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - mpileup: - type: file - description: mpileup file - pattern: "*.{mpileup}" - - 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 ] + - mpileup: + type: file + description: mpileup file + pattern: "*.{mpileup}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@joseespinosa" + - "@drpatelh" + - "@joseespinosa" diff --git a/modules/samtools/sort/meta.yml b/modules/samtools/sort/meta.yml index 3402a068..a820c55a 100644 --- a/modules/samtools/sort/meta.yml +++ b/modules/samtools/sort/meta.yml @@ -1,44 +1,44 @@ name: samtools_sort description: Sort SAM/BAM/CRAM file keywords: - - sort - - bam - - sam - - cram + - sort + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - 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 ] + - bam: + type: file + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" + - "@drpatelh" + - "@ewels" diff --git a/modules/samtools/stats/meta.yml b/modules/samtools/stats/meta.yml index 869e62e3..cac50b1c 100644 --- a/modules/samtools/stats/meta.yml +++ b/modules/samtools/stats/meta.yml @@ -1,53 +1,53 @@ name: samtools_stats description: Produces comprehensive statistics from SAM/BAM/CRAM file keywords: - - statistics - - counts - - bam - - sam - - cram + - statistics + - counts + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: - type: file - description: BAI/CRAI file from alignment - pattern: "*.{bai,crai}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - pattern: "*.{fasta,fa}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - input: + type: file + description: BAM/CRAM file from alignment + pattern: "*.{bam,cram}" + - input_index: + type: file + description: BAI/CRAI file from alignment + pattern: "*.{bai,crai}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - stats: - type: file - description: File containing samtools stats output - pattern: "*.{stats}" - - 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 ] + - stats: + type: file + description: File containing samtools stats output + pattern: "*.{stats}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@FriederikeHanssen" + - "@drpatelh" + - "@FriederikeHanssen" diff --git a/modules/samtools/view/meta.yml b/modules/samtools/view/meta.yml index 8abf34af..5604bfa7 100644 --- a/modules/samtools/view/meta.yml +++ b/modules/samtools/view/meta.yml @@ -1,53 +1,53 @@ name: samtools_view description: filter/convert SAM/BAM/CRAM file keywords: - - view - - bam - - sam - - cram + - view + - bam + - sam + - cram tools: - - samtools: - description: | - SAMtools is a set of utilities for interacting with and post-processing - short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. - These files are generated as output by short read aligners like BWA. - homepage: http://www.htslib.org/ - documentation: hhttp://www.htslib.org/doc/samtools.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - samtools: + description: | + SAMtools is a set of utilities for interacting with and post-processing + short DNA sequence read alignments in the SAM, BAM and CRAM formats, written by Heng Li. + These files are generated as output by short read aligners like BWA. + homepage: http://www.htslib.org/ + documentation: hhttp://www.htslib.org/doc/samtools.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - input: - type: file - description: BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" - - fasta: - type: optional file - description: Reference file the CRAM was created with - 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/SAM file + pattern: "*.{bam,cram,sam}" + - fasta: + type: optional file + description: Reference file the CRAM was created with + pattern: "*.{fasta,fa}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: filtered/converted BAM/SAM file - pattern: "*.{bam,sam}" - - cram: - type: file - description: filtered/converted 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 ] + - bam: + type: file + description: filtered/converted BAM/SAM file + pattern: "*.{bam,sam}" + - cram: + type: file + description: filtered/converted CRAM file + pattern: "*.cram" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@joseespinosa" - - "@FriederikeHanssen" + - "@drpatelh" + - "@joseespinosa" + - "@FriederikeHanssen" diff --git a/modules/scoary/meta.yml b/modules/scoary/meta.yml index e8e8515e..941064c3 100644 --- a/modules/scoary/meta.yml +++ b/modules/scoary/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/AdmiralenOla/Scoary tool_dev_url: https://github.com/AdmiralenOla/Scoary doi: "10.1186/s13059-016-1108-8" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/seacr/callpeak/meta.yml b/modules/seacr/callpeak/meta.yml index 53b3415f..3e215bfb 100644 --- a/modules/seacr/callpeak/meta.yml +++ b/modules/seacr/callpeak/meta.yml @@ -1,54 +1,53 @@ - name: seacr_callpeak description: Call peaks using SEACR on sequenced reads in bedgraph format keywords: - - peak-caller - - peaks - - bedgraph - - cut&tag - - cut&run - - chromatin - - seacr + - peak-caller + - peaks + - bedgraph + - cut&tag + - cut&run + - chromatin + - seacr tools: - - seacr: - description: | - SEACR is intended to call peaks and enriched regions from sparse CUT&RUN - or chromatin profiling data in which background is dominated by "zeroes" - (i.e. regions with no read coverage). - homepage: https://github.com/FredHutch/SEACR - documentation: https://github.com/FredHutch/SEACR - licence: ['GPL-2.0-only'] + - seacr: + description: | + SEACR is intended to call peaks and enriched regions from sparse CUT&RUN + or chromatin profiling data in which background is dominated by "zeroes" + (i.e. regions with no read coverage). + homepage: https://github.com/FredHutch/SEACR + documentation: https://github.com/FredHutch/SEACR + licence: ["GPL-2.0-only"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bedgraph: - type: file - description: | - The target bedgraph file from which the peaks will be calculated. - - ctrlbedgraph: - type: file - description: | - Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. - - threshold: - type: value - description: | - Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bedgraph: + type: file + description: | + The target bedgraph file from which the peaks will be calculated. + - ctrlbedgraph: + type: file + description: | + Control (IgG) data bedgraph file to generate an empirical threshold for peak calling. + - threshold: + type: value + description: | + Threshold value used to call peaks if the ctrlbedgraph input is set to []. Set to 1 if using a control bedgraph output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Bed file containing the calculated peaks. - pattern: "*.bed" - - 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 ] + - bed: + type: file + description: Bed file containing the calculated peaks. + pattern: "*.bed" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@chris-cheshire" + - "@chris-cheshire" diff --git a/modules/seqkit/split2/meta.yml b/modules/seqkit/split2/meta.yml index 90eec7f9..91c74b0c 100644 --- a/modules/seqkit/split2/meta.yml +++ b/modules/seqkit/split2/meta.yml @@ -1,39 +1,39 @@ name: seqkit_split2 description: Split single or paired-end fastq.gz files keywords: - - split - - fastq + - split + - fastq tools: - - seqkit: - description: | - Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. - homepage: https://github.com/shenwei356/seqkit - documentation: https://bioinf.shenwei.me/seqkit/ - doi: 10.1371/journal.pone.0163962 - licence: ['MIT'] + - seqkit: + description: | + Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen. + homepage: https://github.com/shenwei356/seqkit + documentation: https://bioinf.shenwei.me/seqkit/ + doi: 10.1371/journal.pone.0163962 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: FastQ files - pattern: "*.{fq.gz/fastq.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: FastQ files + pattern: "*.{fq.gz/fastq.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Split fastq files - pattern: "*.{fq.gz/fastq.gz}" - - 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 ] + - reads: + type: file + description: Split fastq files + pattern: "*.{fq.gz/fastq.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@FriederikeHanssen" + - "@FriederikeHanssen" diff --git a/modules/seqsero2/meta.yml b/modules/seqsero2/meta.yml index ceea80e3..f20c194e 100644 --- a/modules/seqsero2/meta.yml +++ b/modules/seqsero2/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/denglab/SeqSero2 tool_dev_url: https://github.com/denglab/SeqSero2 doi: "10.1128/AEM.01746-19" - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: diff --git a/modules/seqtk/mergepe/meta.yml b/modules/seqtk/mergepe/meta.yml index a342f60b..8248ee09 100644 --- a/modules/seqtk/mergepe/meta.yml +++ b/modules/seqtk/mergepe/meta.yml @@ -6,9 +6,9 @@ tools: - seqtk: description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. Seqtk mergepe command merges pair-end reads into one interleaved file. homepage: https://github.com/lh3/seqtk - documentation: https://docs.csc.fi/apps/seqtk/ + documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/seqtk/rename/main.nf b/modules/seqtk/rename/main.nf new file mode 100644 index 00000000..f50aad69 --- /dev/null +++ b/modules/seqtk/rename/main.nf @@ -0,0 +1,40 @@ +process SEQTK_RENAME { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::seqtk=1.3" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : + 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" + + input: + tuple val(meta), path(sequences) + + output: + tuple val(meta), path("*.gz") , emit: sequences + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def extension = "fasta" + if ("$sequences" ==~ /.+\.fq|.+\.fq.gz|.+\.fastq|.+\.fastq.gz/) { + extension = "fastq" + } + """ + seqtk \\ + rename \\ + $args \\ + $sequences \\ + $prefix | \\ + gzip -c --no-name > ${prefix}.renamed.${extension}.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') + END_VERSIONS + """ +} diff --git a/modules/seqtk/rename/meta.yml b/modules/seqtk/rename/meta.yml new file mode 100644 index 00000000..b68dec8e --- /dev/null +++ b/modules/seqtk/rename/meta.yml @@ -0,0 +1,42 @@ +name: seqtk_rename +description: Rename sequence names in FASTQ or FASTA files. +keywords: + - rename +tools: + - seqtk: + description: Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. The seqtk rename command renames sequence names. + homepage: https://github.com/lh3/seqtk + documentation: https://docs.csc.fi/apps/seqtk/ + tool_dev_url: https://github.com/lh3/seqtk + licence: ['MIT'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - sequences: + type: file + description: A FASTQ or FASTA file + pattern: "*.{fastq.gz, fastq, fq, fq.gz, fasta, fastq.gz, fa, fa.gz, fas, fas.gz, fna, fna.gz}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test' ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - sequences: + type: file + description: FASTQ/FASTA file containing renamed sequences + pattern: "*.{fastq.gz, fasta.gz}" + +authors: + - "@hseabolt" + - "@mjcipriano" + - "@sateeshperi" diff --git a/modules/seqtk/sample/meta.yml b/modules/seqtk/sample/meta.yml index 6cc4d657..d92e54e5 100644 --- a/modules/seqtk/sample/meta.yml +++ b/modules/seqtk/sample/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/seqtk/subseq/meta.yml b/modules/seqtk/subseq/meta.yml index 0d9a802b..d06efb55 100644 --- a/modules/seqtk/subseq/meta.yml +++ b/modules/seqtk/subseq/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://github.com/lh3/seqtk documentation: https://docs.csc.fi/apps/seqtk/ tool_dev_url: https://github.com/lh3/seqtk - licence: ['MIT'] + licence: ["MIT"] input: - sequences: diff --git a/modules/sequenzautils/bam2seqz/meta.yml b/modules/sequenzautils/bam2seqz/meta.yml index e05d2fa9..0168bd68 100755 --- a/modules/sequenzautils/bam2seqz/meta.yml +++ b/modules/sequenzautils/bam2seqz/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/sequenzautils/gcwiggle/meta.yml b/modules/sequenzautils/gcwiggle/meta.yml index 616e073b..6e9a1483 100644 --- a/modules/sequenzautils/gcwiggle/meta.yml +++ b/modules/sequenzautils/gcwiggle/meta.yml @@ -8,7 +8,7 @@ tools: homepage: https://sequenza-utils.readthedocs.io/en/latest/index.html documentation: https://sequenza-utils.readthedocs.io/en/latest/index.html doi: 10.1093/annonc/mdu479 - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - meta: type: map diff --git a/modules/seqwish/induce/meta.yml b/modules/seqwish/induce/meta.yml index 281e3994..b40360c6 100644 --- a/modules/seqwish/induce/meta.yml +++ b/modules/seqwish/induce/meta.yml @@ -1,47 +1,47 @@ name: seqwish_induce description: Induce a variation graph in GFA format from alignments in PAF format keywords: - - induce - - paf - - gfa - - graph - - variation graph + - induce + - paf + - gfa + - graph + - variation graph tools: - - seqwish: - description: | - seqwish implements a lossless conversion from pairwise alignments between - sequences to a variation graph encoding the sequences and their alignments. - homepage: https://github.com/ekg/seqwish - documentation: https://github.com/ekg/seqwish - licence: ['MIT'] + - seqwish: + description: | + seqwish implements a lossless conversion from pairwise alignments between + sequences to a variation graph encoding the sequences and their alignments. + homepage: https://github.com/ekg/seqwish + documentation: https://github.com/ekg/seqwish + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - paf: - type: file - description: PAF file of alignments - pattern: "*.{paf,paf.gz}" - - fasta: - type: file - description: FASTA file used to generate alignments - pattern: "*.{fa,fa.gz,fasta,fasta.gz}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - paf: + type: file + description: PAF file of alignments + pattern: "*.{paf,paf.gz}" + - fasta: + type: file + description: FASTA file used to generate alignments + pattern: "*.{fa,fa.gz,fasta,fasta.gz}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - gfa: - type: file - description: Variation graph in GFA 1.0 format - pattern: "*.{gfa}" - - 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 ] + - gfa: + type: file + description: Variation graph in GFA 1.0 format + pattern: "*.{gfa}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@heuermh" + - "@heuermh" diff --git a/modules/snpdists/meta.yml b/modules/snpdists/meta.yml index bf4366ff..4eee3902 100644 --- a/modules/snpdists/meta.yml +++ b/modules/snpdists/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/tseemann/snp-dists tool_dev_url: https://github.com/tseemann/snp-dists doi: "" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/snpeff/meta.yml b/modules/snpeff/meta.yml index 8ba18683..c191b9ac 100644 --- a/modules/snpeff/meta.yml +++ b/modules/snpeff/meta.yml @@ -1,58 +1,58 @@ name: snpEff description: Genetic variant annotation and functional effect prediction toolbox keywords: - - annotation + - annotation tools: - - snpeff: - description: | - SnpEff is a variant annotation and effect prediction tool. - It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). - homepage: https://pcingola.github.io/SnpEff/ - documentation: https://pcingola.github.io/SnpEff/se_introduction/ - licence: ['MIT'] + - snpeff: + description: | + SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants on genes and proteins (such as amino acid changes). + homepage: https://pcingola.github.io/SnpEff/ + documentation: https://pcingola.github.io/SnpEff/se_introduction/ + licence: ["MIT"] params: - - use_cache: - type: boolean - description: | - boolean to enable the usage of containers with cache - Enable the usage of containers with cache - Does not work with conda - - snpeff_tag: - type: value - description: | - Specify the tag for the container - https://hub.docker.com/r/nfcore/snpeff/tags + - use_cache: + type: boolean + description: | + boolean to enable the usage of containers with cache + Enable the usage of containers with cache + Does not work with conda + - snpeff_tag: + type: value + description: | + Specify the tag for the container + https://hub.docker.com/r/nfcore/snpeff/tags 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: value - 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: value + description: | + which db to annotate with + - cache: + type: file + description: | + path to snpEff cache (optional) output: - - vcf: - type: file - description: | - annotated vcf - pattern: "*.ann.vcf" - - report: - type: file - description: snpEff report file - pattern: "*.html" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - vcf: + type: file + description: | + annotated vcf + pattern: "*.ann.vcf" + - report: + type: file + description: snpEff report file + pattern: "*.html" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/snpsift/split/meta.yml b/modules/snpsift/split/meta.yml index 5a125b62..48673c47 100644 --- a/modules/snpsift/split/meta.yml +++ b/modules/snpsift/split/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://pcingola.github.io/SnpEff/ss_introduction/ tool_dev_url: https://github.com/pcingola/SnpEff doi: "10.3389/fgene.2012.00035" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/snpsites/meta.yml b/modules/snpsites/meta.yml index 381d25cc..4149aeef 100644 --- a/modules/snpsites/meta.yml +++ b/modules/snpsites/meta.yml @@ -9,7 +9,7 @@ tools: description: Rapidly extracts SNPs from a multi-FASTA alignment. homepage: https://www.sanger.ac.uk/tool/snp-sites/ documentation: https://github.com/sanger-pathogens/snp-sites - licence: ['GPL-3.0-or-later'] + licence: ["GPL-3.0-or-later"] input: - alignment: type: file diff --git a/modules/sourmash/sketch/main.nf b/modules/sourmash/sketch/main.nf new file mode 100644 index 00000000..e16b605f --- /dev/null +++ b/modules/sourmash/sketch/main.nf @@ -0,0 +1,35 @@ +process SOURMASH_SKETCH { + tag "$meta.id" + label 'process_low' + + conda (params.enable_conda ? "bioconda::sourmash=4.2.4" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/sourmash:4.2.4--hdfd78af_0': + 'quay.io/biocontainers/sourmash:4.2.4--hdfd78af_0' }" + + input: + tuple val(meta), path(sequence) + + output: + tuple val(meta), path("*.sig"), emit: signatures + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: "dna --param-string 'scaled=1000,k=31'" + def prefix = task.ext.prefix ?: "${meta.id}" + """ + sourmash sketch \\ + $args \\ + --merge '${prefix}' \\ + --output '${prefix}.sig' \\ + $sequence + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' ) + END_VERSIONS + """ +} diff --git a/modules/sourmash/sketch/meta.yml b/modules/sourmash/sketch/meta.yml new file mode 100644 index 00000000..9fb552bc --- /dev/null +++ b/modules/sourmash/sketch/meta.yml @@ -0,0 +1,42 @@ +name: sourmash_sketch +description: Create a signature (a hash sketch) of a sequence using sourmash +keywords: + - hash sketch + - signature +tools: + - sourmash: + description: Compute and compare MinHash signatures for DNA data sets. + homepage: https://sourmash.readthedocs.io/ + documentation: https://sourmash.readthedocs.io/ + tool_dev_url: https://github.com/dib-lab/sourmash + doi: "10.1186/s13059-016-0997-x" + licence: ['BSD-3-clause'] + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - sequence: + type: file + description: FastA file containing (genomic) sequence data + pattern: "*.{fna,fa,fasta}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + - signatures: + type: file + description: MinHash signature of the given sequence + pattern: "*.{sig}" + +authors: + - "@Midnighter" diff --git a/modules/spades/meta.yml b/modules/spades/meta.yml index b6878d3d..e49cd139 100644 --- a/modules/spades/meta.yml +++ b/modules/spades/meta.yml @@ -13,7 +13,7 @@ tools: documentation: http://cab.spbu.ru/files/release3.15.0/manual.html tool_dev_url: https://github.com/ablab/spades doi: 10.1089/cmb.2012.0021 - licence: ['GPL v2'] + licence: ["GPL v2"] input: - meta: type: map @@ -36,8 +36,7 @@ input: List of input FastQ files of size 1, originating from Oxford Nanopore technology. - hmm: type: file - description: - File or directory with amino acid HMMs for Spades HMM-guided mode. + description: File or directory with amino acid HMMs for Spades HMM-guided mode. output: - meta: type: map diff --git a/modules/spatyper/meta.yml b/modules/spatyper/meta.yml index 94f17a69..5fb7cc18 100644 --- a/modules/spatyper/meta.yml +++ b/modules/spatyper/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/HCGB-IGTP/spaTyper tool_dev_url: https://github.com/HCGB-IGTP/spaTyper doi: https://doi.org/10.5281/zenodo.4063625 - licence: ['LGPL v3'] + licence: ["LGPL v3"] input: - meta: diff --git a/modules/sratools/fasterqdump/meta.yml b/modules/sratools/fasterqdump/meta.yml index 1478bed8..ec5f69a5 100644 --- a/modules/sratools/fasterqdump/meta.yml +++ b/modules/sratools/fasterqdump/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/ncbi/sra-tools documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools - licence: ['US-Government-Work'] + licence: ["US-Government-Work"] input: - meta: diff --git a/modules/sratools/prefetch/meta.yml b/modules/sratools/prefetch/meta.yml index 22213b29..e08b708c 100644 --- a/modules/sratools/prefetch/meta.yml +++ b/modules/sratools/prefetch/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/ncbi/sra-tools documentation: https://github.com/ncbi/sra-tools/wiki tool_dev_url: https://github.com/ncbi/sra-tools - licence: ['US-Government-Work'] + licence: ["US-Government-Work"] input: - meta: diff --git a/modules/staphopiasccmec/meta.yml b/modules/staphopiasccmec/meta.yml index 006e5389..38c920ed 100644 --- a/modules/staphopiasccmec/meta.yml +++ b/modules/staphopiasccmec/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/staphopia/staphopia-sccmec tool_dev_url: https://github.com/staphopia/staphopia-sccmec doi: https://doi.org/10.7717/peerj.5261 - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/star/align/meta.yml b/modules/star/align/meta.yml index 2d78b81a..7ee10f1c 100644 --- a/modules/star/align/meta.yml +++ b/modules/star/align/meta.yml @@ -13,7 +13,7 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/star/genomegenerate/meta.yml b/modules/star/genomegenerate/meta.yml index 04ade195..8181157a 100644 --- a/modules/star/genomegenerate/meta.yml +++ b/modules/star/genomegenerate/meta.yml @@ -13,7 +13,7 @@ tools: homepage: https://github.com/alexdobin/STAR manual: https://github.com/alexdobin/STAR/blob/master/doc/STARmanual.pdf doi: 10.1093/bioinformatics/bts635 - licence: ['MIT'] + licence: ["MIT"] input: - fasta: type: file diff --git a/modules/strelka/germline/main.nf b/modules/strelka/germline/main.nf index 1ce0da31..3f47d86f 100644 --- a/modules/strelka/germline/main.nf +++ b/modules/strelka/germline/main.nf @@ -8,11 +8,9 @@ process STRELKA_GERMLINE { 'quay.io/biocontainers/strelka:2.9.10--0' }" input: - tuple val(meta), path(input), path(input_index) + tuple val(meta), path(input), path(input_index), path (target_bed), path (target_bed_tbi) path fasta path fai - path target_bed - path target_bed_tbi output: tuple val(meta), path("*variants.vcf.gz") , emit: vcf @@ -27,7 +25,7 @@ process STRELKA_GERMLINE { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def regions = target_bed ? "--exome --callRegions ${target_bed}" : "" + def regions = target_bed ? "--callRegions ${target_bed}" : "" """ configureStrelkaGermlineWorkflow.py \\ --bam $input \\ diff --git a/modules/strelka/germline/meta.yml b/modules/strelka/germline/meta.yml index 2eeb0f8f..c119532d 100644 --- a/modules/strelka/germline/meta.yml +++ b/modules/strelka/germline/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/strelka/somatic/main.nf b/modules/strelka/somatic/main.nf index 22cce8cb..b61c09bd 100644 --- a/modules/strelka/somatic/main.nf +++ b/modules/strelka/somatic/main.nf @@ -8,11 +8,9 @@ process STRELKA_SOMATIC { 'quay.io/biocontainers/strelka:2.9.10--h9ee0642_1' }" input: - tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi) + tuple val(meta), path(input_normal), path(input_index_normal), path(input_tumor), path(input_index_tumor), path(manta_candidate_small_indels), path(manta_candidate_small_indels_tbi), path(target_bed), path(target_bed_index) path fasta path fai - path target_bed - path target_bed_tbi output: tuple val(meta), path("*.somatic_indels.vcf.gz") , emit: vcf_indels @@ -27,15 +25,16 @@ process STRELKA_SOMATIC { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - def options_target_bed = target_bed ? "--exome --callRegions ${target_bed}" : "" + def options_target_bed = target_bed ? "--callRegions ${target_bed}" : "" def options_manta = manta_candidate_small_indels ? "--indelCandidates ${manta_candidate_small_indels}" : "" """ + configureStrelkaSomaticWorkflow.py \\ --tumor $input_tumor \\ --normal $input_normal \\ --referenceFasta $fasta \\ - $options_target_bed \\ - $options_manta \\ + ${options_target_bed} \\ + ${options_manta} \\ $args \\ --runDir strelka diff --git a/modules/strelka/somatic/meta.yml b/modules/strelka/somatic/meta.yml index 076c1036..b2a25504 100644 --- a/modules/strelka/somatic/meta.yml +++ b/modules/strelka/somatic/meta.yml @@ -13,7 +13,7 @@ tools: documentation: https://github.com/Illumina/strelka/blob/v2.9.x/docs/userGuide/README.md tool_dev_url: https://github.com/Illumina/strelka doi: 10.1038/s41592-018-0051-x - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/stringtie/merge/meta.yml b/modules/stringtie/merge/meta.yml index 02899766..df66696f 100644 --- a/modules/stringtie/merge/meta.yml +++ b/modules/stringtie/merge/meta.yml @@ -1,37 +1,37 @@ name: stringtie_merge description: Merges the annotation gtf file and the stringtie output gtf files keywords: - - merge - - gtf - - reference + - merge + - gtf + - reference tools: - - stringtie2: - description: | - Transcript assembly and quantification for RNA-Seq - homepage: https://ccb.jhu.edu/software/stringtie/index.shtml - documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual - licence: ['MIT'] + - stringtie2: + description: | + Transcript assembly and quantification for RNA-Seq + homepage: https://ccb.jhu.edu/software/stringtie/index.shtml + documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual + licence: ["MIT"] input: - - stringtie_gtf: - type: file - description: | - Stringtie transcript gtf output(s). - pattern: "*.gtf" - - annotation_gtf: - type: file - description: | - Annotation gtf file. - pattern: "*.gtf" + - stringtie_gtf: + type: file + description: | + Stringtie transcript gtf output(s). + pattern: "*.gtf" + - annotation_gtf: + type: file + description: | + Annotation gtf file. + pattern: "*.gtf" output: - - merged_gtf: - type: map - description: | - Merged gtf from annotation and stringtie output gtfs. - pattern: "*.gtf" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - merged_gtf: + type: map + description: | + Merged gtf from annotation and stringtie output gtfs. + pattern: "*.gtf" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@yuukiiwa" + - "@yuukiiwa" diff --git a/modules/stringtie/stringtie/meta.yml b/modules/stringtie/stringtie/meta.yml index 7e854caa..a462c574 100644 --- a/modules/stringtie/stringtie/meta.yml +++ b/modules/stringtie/stringtie/meta.yml @@ -1,57 +1,57 @@ name: stringtie description: Transcript assembly and quantification for RNA-Se keywords: - - transcript - - assembly - - quantification - - gtf + - transcript + - assembly + - quantification + - gtf tools: - - stringtie2: - description: | - Transcript assembly and quantification for RNA-Seq - homepage: https://ccb.jhu.edu/software/stringtie/index.shtml - documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual - licence: ['MIT'] + - stringtie2: + description: | + Transcript assembly and quantification for RNA-Seq + homepage: https://ccb.jhu.edu/software/stringtie/index.shtml + documentation: https://ccb.jhu.edu/software/stringtie/index.shtml?t=manual + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - Stringtie transcript gtf output(s). - - gtf: - type: file - description: | - Annotation gtf file. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + Stringtie transcript gtf output(s). + - gtf: + type: file + description: | + Annotation gtf file. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - transcript_gtf: - type: file - description: transcript gtf - pattern: "*.{transcripts.gtf}" - - coverage_gtf: - type: file - description: coverage gtf - pattern: "*.{coverage.gtf}" - - abudance: - type: file - description: abudance - pattern: "*.{abudance.txt}" - - ballgown: - type: file - description: for running ballgown - pattern: "*.{ballgown}" - - 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 ] + - transcript_gtf: + type: file + description: transcript gtf + pattern: "*.{transcripts.gtf}" + - coverage_gtf: + type: file + description: coverage gtf + pattern: "*.{coverage.gtf}" + - abudance: + type: file + description: abudance + pattern: "*.{abudance.txt}" + - ballgown: + type: file + description: for running ballgown + pattern: "*.{ballgown}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" + - "@drpatelh" diff --git a/modules/subread/featurecounts/meta.yml b/modules/subread/featurecounts/meta.yml index 1100a091..cf02f1ea 100644 --- a/modules/subread/featurecounts/meta.yml +++ b/modules/subread/featurecounts/meta.yml @@ -1,10 +1,10 @@ name: subread_featurecounts description: Count reads that map to genomic features keywords: - - counts - - fasta - - genome - - reference + - counts + - fasta + - genome + - reference tools: - featurecounts: @@ -12,14 +12,14 @@ tools: homepage: http://bioinf.wehi.edu.au/featureCounts/ documentation: http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf doi: "10.1093/bioinformatics/btt656" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - bam: type: file description: BAM/SAM file containing read alignments @@ -33,8 +33,8 @@ output: - meta: type: map description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] - counts: type: file description: Counts of reads mapping to features diff --git a/modules/svdb/merge/meta.yml b/modules/svdb/merge/meta.yml index 2092ddd9..e166bad0 100644 --- a/modules/svdb/merge/meta.yml +++ b/modules/svdb/merge/meta.yml @@ -7,7 +7,7 @@ tools: description: structural variant database software homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md - licence: ['MIT'] + licence: ["MIT"] input: - meta: type: map diff --git a/modules/svdb/query/meta.yml b/modules/svdb/query/meta.yml index 264b1904..e2a9e456 100644 --- a/modules/svdb/query/meta.yml +++ b/modules/svdb/query/meta.yml @@ -7,7 +7,7 @@ tools: description: structural variant database software homepage: https://github.com/J35P312/SVDB documentation: https://github.com/J35P312/SVDB/blob/master/README.md - licence: ['MIT'] + licence: ["MIT"] input: - meta: @@ -36,7 +36,7 @@ output: pattern: "versions.yml" - vcf: type: file - description: Annotated output VCF file + description: Annotated output VCF file pattern: "*_ann_svdbq.vcf" authors: diff --git a/modules/tabix/bgzip/meta.yml b/modules/tabix/bgzip/meta.yml index f8318c7c..207427e4 100644 --- a/modules/tabix/bgzip/meta.yml +++ b/modules/tabix/bgzip/meta.yml @@ -1,41 +1,41 @@ name: tabix_bgzip description: Compresses files keywords: - - compress - - bgzip - - tabix + - compress + - bgzip + - tabix tools: - - bgzip: - description: | - Bgzip compresses files in a similar manner to, and compatible with, gzip. - homepage: https://www.htslib.org/doc/tabix.html - documentation: http://www.htslib.org/doc/bgzip.html - doi: 10.1093/bioinformatics/btp352 - licence: ['MIT'] + - bgzip: + description: | + Bgzip compresses files in a similar manner to, and compatible with, gzip. + homepage: https://www.htslib.org/doc/tabix.html + documentation: http://www.htslib.org/doc/bgzip.html + doi: 10.1093/bioinformatics/btp352 + licence: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: text file + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: text file output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - file: - type: file - description: Output compressed file - pattern: "*.{gz}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - file: + type: file + description: Output compressed file + pattern: "*.{gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@maxulysse" + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/tabix/bgziptabix/main.nf b/modules/tabix/bgziptabix/main.nf index 3f42ad21..12657599 100644 --- a/modules/tabix/bgziptabix/main.nf +++ b/modules/tabix/bgziptabix/main.nf @@ -22,7 +22,7 @@ process TABIX_BGZIPTABIX { def args2 = task.ext.args2 ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - bgzip -c $args $input > ${prefix}.gz + bgzip --threads ${task.cpus} -c $args $input > ${prefix}.gz tabix $args2 ${prefix}.gz cat <<-END_VERSIONS > versions.yml diff --git a/modules/tabix/bgziptabix/meta.yml b/modules/tabix/bgziptabix/meta.yml index f2aed84d..49c03289 100644 --- a/modules/tabix/bgziptabix/meta.yml +++ b/modules/tabix/bgziptabix/meta.yml @@ -1,45 +1,45 @@ name: tabix_bgziptabix description: bgzip a sorted tab-delimited genome file and then create tabix index keywords: - - bgzip - - compress - - index - - tabix - - vcf + - bgzip + - compress + - index + - tabix + - vcf tools: - - tabix: - description: Generic indexer for TAB-delimited genome position files. - homepage: https://www.htslib.org/doc/tabix.html - documentation: https://www.htslib.org/doc/tabix.1.html - doi: 10.1093/bioinformatics/btq671 - licence: ['MIT'] + - tabix: + description: Generic indexer for TAB-delimited genome position files. + homepage: https://www.htslib.org/doc/tabix.html + documentation: https://www.htslib.org/doc/tabix.1.html + doi: 10.1093/bioinformatics/btq671 + licence: ["MIT"] 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 ] + - tab: + type: file + description: TAB-delimited genome position file + pattern: "*.{bed,gff,sam,vcf}" 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}" - - 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 ] + - gz: + type: file + description: Output compressed file + pattern: "*.{gz}" + - tbi: + type: file + description: tabix index file + pattern: "*.{gz.tbi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/tabix/tabix/meta.yml b/modules/tabix/tabix/meta.yml index 2e37c4ff..89478abe 100644 --- a/modules/tabix/tabix/meta.yml +++ b/modules/tabix/tabix/meta.yml @@ -1,41 +1,41 @@ name: tabix_tabix description: create tabix index from a sorted bgzip tab-delimited genome file keywords: - - index - - tabix - - vcf + - index + - tabix + - vcf tools: - - tabix: - description: Generic indexer for TAB-delimited genome position files. - homepage: https://www.htslib.org/doc/tabix.html - documentation: https://www.htslib.org/doc/tabix.1.html - doi: 10.1093/bioinformatics/btq671 - licence: ['MIT'] + - tabix: + description: Generic indexer for TAB-delimited genome position files. + homepage: https://www.htslib.org/doc/tabix.html + documentation: https://www.htslib.org/doc/tabix.1.html + doi: 10.1093/bioinformatics/btq671 + licence: ["MIT"] 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}" - - 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 ] + - tbi: + type: file + description: tabix index file + pattern: "*.{tbi}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@maxulysse" + - "@joseespinosa" + - "@drpatelh" + - "@maxulysse" diff --git a/modules/tbprofiler/profile/meta.yml b/modules/tbprofiler/profile/meta.yml index 0cac6d6b..5923cb32 100644 --- a/modules/tbprofiler/profile/meta.yml +++ b/modules/tbprofiler/profile/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://jodyphelan.gitbook.io/tb-profiler/ tool_dev_url: https://github.com/jodyphelan/TBProfiler doi: "10.1186/s13073-019-0650-x" - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: diff --git a/modules/tiddit/sv/meta.yml b/modules/tiddit/sv/meta.yml index f788ffa6..fc307081 100644 --- a/modules/tiddit/sv/meta.yml +++ b/modules/tiddit/sv/meta.yml @@ -1,51 +1,51 @@ name: tiddit_sv description: Identify chromosomal rearrangements. keywords: - - structural - - variants - - vcf + - structural + - variants + - vcf tools: - - sv: - description: Search for structural variants. - homepage: https://github.com/SciLifeLab/TIDDIT - documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md - doi: 10.12688/f1000research.11168.1 - licence: ['GPL-3.0-or-later'] + - sv: + description: Search for structural variants. + homepage: https://github.com/SciLifeLab/TIDDIT + documentation: https://github.com/SciLifeLab/TIDDIT/blob/master/README.md + doi: 10.12688/f1000research.11168.1 + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - fasta: - type: file - description: Input FASTA file - pattern: "*.{fasta,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 ] + - fasta: + type: file + description: Input FASTA file + pattern: "*.{fasta,fa}" + - fai: + type: file + description: FASTA index file + pattern: "*.{fai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - vcf: - type: file - description: vcf - pattern: "*.{vcf}" - - ploidy: - type: file - description: tab - pattern: "*.{ploidy.tab}" - - signals: - type: file - description: tab - pattern: "*.{signals.tab}" - - 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 ] + - vcf: + type: file + description: vcf + pattern: "*.{vcf}" + - ploidy: + type: file + description: tab + pattern: "*.{ploidy.tab}" + - signals: + type: file + description: tab + pattern: "*.{signals.tab}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@maxulysse" + - "@maxulysse" diff --git a/modules/transdecoder/longorf/meta.yml b/modules/transdecoder/longorf/meta.yml index d4749f4b..b039a261 100644 --- a/modules/transdecoder/longorf/meta.yml +++ b/modules/transdecoder/longorf/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder doi: "" - licence: ['Broad Institute'] + licence: ["Broad Institute"] input: - meta: diff --git a/modules/transdecoder/predict/meta.yml b/modules/transdecoder/predict/meta.yml index e25ce3a2..cb972112 100644 --- a/modules/transdecoder/predict/meta.yml +++ b/modules/transdecoder/predict/meta.yml @@ -11,7 +11,7 @@ tools: documentation: https://github.com/TransDecoder/TransDecoder/wiki tool_dev_url: https://github.com/TransDecoder/TransDecoder doi: "" - licence: ['Broad Institute'] + licence: ["Broad Institute"] input: - meta: diff --git a/modules/trimgalore/meta.yml b/modules/trimgalore/meta.yml index c7e1df1d..e99a8833 100644 --- a/modules/trimgalore/meta.yml +++ b/modules/trimgalore/meta.yml @@ -1,59 +1,59 @@ name: trimgalore description: Trim FastQ files using Trim Galore! keywords: - - trimming - - adapters - - sequencing adapters - - fastq + - trimming + - adapters + - sequencing adapters + - fastq tools: - - trimgalore: - description: | - A wrapper tool around Cutadapt and FastQC to consistently apply quality - and adapter trimming to FastQ files, with some extra functionality for - MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ - documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md - licence: ['GPL-3.0-or-later'] + - trimgalore: + description: | + A wrapper tool around Cutadapt and FastQC to consistently apply quality + and adapter trimming to FastQ files, with some extra functionality for + MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries. + homepage: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ + documentation: https://github.com/FelixKrueger/TrimGalore/blob/master/Docs/Trim_Galore_User_Guide.md + licence: ["GPL-3.0-or-later"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input adapter trimmed FastQ files of size 1 and 2 for - single-end and paired-end data, respectively. - pattern: "*.{fq.gz}" - - html: - type: file - description: FastQC report (optional) - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive (optional) - pattern: "*_{fastqc.zip}" - - log: - type: file - description: Trim Galore! trimming report - pattern: "*_{report.txt}" - - 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 ] + - reads: + type: file + description: | + List of input adapter trimmed FastQ files of size 1 and 2 for + single-end and paired-end data, respectively. + pattern: "*.{fq.gz}" + - html: + type: file + description: FastQC report (optional) + pattern: "*_{fastqc.html}" + - zip: + type: file + description: FastQC report archive (optional) + pattern: "*_{fastqc.zip}" + - log: + type: file + description: Trim Galore! trimming report + pattern: "*_{report.txt}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@ewels" - - "@FelixKrueger" + - "@drpatelh" + - "@ewels" + - "@FelixKrueger" diff --git a/modules/ucsc/bedclip/meta.yml b/modules/ucsc/bedclip/meta.yml index c7372925..e6dd8ceb 100755 --- a/modules/ucsc/bedclip/meta.yml +++ b/modules/ucsc/bedclip/meta.yml @@ -9,7 +9,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['varies; see http://genome.ucsc.edu/license'] + licence: ["varies; see http://genome.ucsc.edu/license"] input: - meta: diff --git a/modules/ucsc/bigwigaverageoverbed/meta.yml b/modules/ucsc/bigwigaverageoverbed/meta.yml index c2b31f88..96a3cabd 100644 --- a/modules/ucsc/bigwigaverageoverbed/meta.yml +++ b/modules/ucsc/bigwigaverageoverbed/meta.yml @@ -10,7 +10,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['varies; see http://genome.ucsc.edu/license'] + licence: ["varies; see http://genome.ucsc.edu/license"] input: - meta: diff --git a/modules/ucsc/liftover/meta.yml b/modules/ucsc/liftover/meta.yml index 5c2febdc..9047558c 100644 --- a/modules/ucsc/liftover/meta.yml +++ b/modules/ucsc/liftover/meta.yml @@ -9,7 +9,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['varies; see http://genome.ucsc.edu/license'] + licence: ["varies; see http://genome.ucsc.edu/license"] input: - meta: diff --git a/modules/ucsc/wigtobigwig/meta.yml b/modules/ucsc/wigtobigwig/meta.yml index 5ca94bb4..8eed29bb 100644 --- a/modules/ucsc/wigtobigwig/meta.yml +++ b/modules/ucsc/wigtobigwig/meta.yml @@ -12,7 +12,7 @@ tools: documentation: None tool_dev_url: None doi: "" - licence: ['varies; see http://genome.ucsc.edu/license'] + licence: ["varies; see http://genome.ucsc.edu/license"] input: - meta: diff --git a/modules/ultra/pipeline/meta.yml b/modules/ultra/pipeline/meta.yml index fa8366e8..1f1f7f11 100644 --- a/modules/ultra/pipeline/meta.yml +++ b/modules/ultra/pipeline/meta.yml @@ -10,7 +10,7 @@ tools: documentation: https://github.com/ksahlin/uLTRA tool_dev_url: https://github.com/ksahlin/uLTRA doi: "10.1093/bioinformatics/btab540" - licence: ['GNU GPLV3'] + licence: ["GNU GPLV3"] input: - meta: diff --git a/modules/umitools/dedup/meta.yml b/modules/umitools/dedup/meta.yml index f89cc1ea..2038b40d 100644 --- a/modules/umitools/dedup/meta.yml +++ b/modules/umitools/dedup/meta.yml @@ -1,47 +1,47 @@ name: umitools_dedup description: Deduplicate reads based on the mapping co-ordinate and the UMI attached to the read. keywords: - - umitools - - deduplication + - umitools + - deduplication tools: - - umi_tools: - description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) - and single cell RNA-Seq cell barcodes - documentation: https://umi-tools.readthedocs.io/en/latest/ - license: ['MIT'] + - umi_tools: + description: > + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) + and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ + license: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: | - BAM file containing reads to be deduplicated via UMIs. - pattern: "*.{bam}" - - bai: - type: file - description: | - BAM index files corresponding to the input BAM file. - pattern: "*.{bai}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bam: + type: file + description: | + BAM file containing reads to be deduplicated via UMIs. + pattern: "*.{bam}" + - bai: + type: file + description: | + BAM index files corresponding to the input BAM file. + pattern: "*.{bai}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bam: - type: file - description: BAM file with deduplicated UMIs. - pattern: "*.{bam}" - - 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 ] + - bam: + type: file + description: BAM file with deduplicated UMIs. + pattern: "*.{bam}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" - - "@klkeys" + - "@drpatelh" + - "@grst" + - "@klkeys" diff --git a/modules/umitools/extract/meta.yml b/modules/umitools/extract/meta.yml index ae6f9fee..7fc23f72 100644 --- a/modules/umitools/extract/meta.yml +++ b/modules/umitools/extract/meta.yml @@ -1,46 +1,47 @@ name: umitools_extract description: Extracts UMI barcode from a read and add it to the read name, leaving any sample barcode in place keywords: - - umitools - - extract + - umitools + - extract tools: - - umi_tools: - description: > - UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) - and single cell RNA-Seq cell barcodes - documentation: https://umi-tools.readthedocs.io/en/latest/ - license: ['MIT'] + - umi_tools: + description: > + UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random Molecular Tags (RMTs) + and single cell RNA-Seq cell barcodes + documentation: https://umi-tools.readthedocs.io/en/latest/ + license: ["MIT"] input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: list - description: | - List of input FASTQ files whose UMIs will be extracted. + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: list + description: | + List of input FASTQ files whose UMIs will be extracted. output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: Extracted FASTQ files. | - For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | - For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. - pattern: "*.{fastq.gz}" - - log: - type: file - description: Logfile for umi_tools - pattern: "*.{log}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: > + Extracted FASTQ files. | + For single-end reads, pattern is \${prefix}.umi_extract.fastq.gz. | + For paired-end reads, pattern is \${prefix}.umi_extract_{1,2}.fastq.gz. + pattern: "*.{fastq.gz}" + - log: + type: file + description: Logfile for umi_tools + pattern: "*.{log}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@drpatelh" - - "@grst" + - "@drpatelh" + - "@grst" diff --git a/modules/unicycler/meta.yml b/modules/unicycler/meta.yml index b04ac882..918faaf8 100644 --- a/modules/unicycler/meta.yml +++ b/modules/unicycler/meta.yml @@ -12,7 +12,7 @@ tools: documentation: https://github.com/rrwick/Unicycler tool_dev_url: https://github.com/rrwick/Unicycler doi: 10.1371/journal.pcbi.1005595 - licence: ['GPL v3'] + licence: ["GPL v3"] input: - meta: type: map @@ -20,14 +20,14 @@ input: Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - shortreads: - type: file - description: | - List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. + type: file + description: | + List of input Illumina FastQ files of size 1 and 2 for single-end and paired-end data, + respectively. - longreads: - type: file - description: | - List of input FastQ files of size 1, PacBio or Nanopore long reads. + type: file + description: | + List of input FastQ files of size 1, PacBio or Nanopore long reads. output: - meta: type: map diff --git a/modules/untar/meta.yml b/modules/untar/meta.yml index 51f94995..e877a97c 100644 --- a/modules/untar/meta.yml +++ b/modules/untar/meta.yml @@ -1,28 +1,28 @@ name: untar description: Extract files. keywords: - - untar - - uncompress + - untar + - uncompress tools: - - untar: - description: | - Extract tar.gz files. - documentation: https://www.gnu.org/software/tar/manual/ - licence: ['GPL-3.0-or-later'] + - untar: + description: | + Extract tar.gz files. + documentation: https://www.gnu.org/software/tar/manual/ + licence: ["GPL-3.0-or-later"] input: - - archive: - type: file - description: File to be untar - pattern: "*.{tar}.{gz}" + - archive: + type: file + description: File to be untar + pattern: "*.{tar}.{gz}" output: - - untar: - type: file - description: - pattern: "*.*" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" + - untar: + type: file + description: + pattern: "*.*" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/unzip/meta.yml b/modules/unzip/meta.yml index 7bca1ec2..79361527 100644 --- a/modules/unzip/meta.yml +++ b/modules/unzip/meta.yml @@ -9,7 +9,7 @@ tools: homepage: https://sourceforge.net/projects/p7zip/ documentation: https://sourceforge.net/projects/p7zip/ tool_dev_url: https://sourceforge.net/projects/p7zip" - licence: ['LGPL-2.1-or-later'] + licence: ["LGPL-2.1-or-later"] input: - archive: @@ -21,7 +21,7 @@ output: - unzipped_archive: type: directory description: Directory contents of the unzipped archive - pattern: '${archive.baseName}/' + pattern: "${archive.baseName}/" - versions: type: file description: File containing software versions diff --git a/modules/variantbam/meta.yml b/modules/variantbam/meta.yml index ddcd0656..aac72448 100644 --- a/modules/variantbam/meta.yml +++ b/modules/variantbam/meta.yml @@ -14,7 +14,7 @@ tools: documentation: https://github.com/walaj/VariantBam#table-of-contents tool_dev_url: https://github.com/walaj/VariantBam doi: 10.1093/bioinformatics/btw111 - licence: ['Apache-2.0'] + licence: ["Apache-2.0"] input: - meta: diff --git a/modules/vcflib/vcfuniq/meta.yml b/modules/vcflib/vcfuniq/meta.yml index 3bfc679b..50a3617a 100644 --- a/modules/vcflib/vcfuniq/meta.yml +++ b/modules/vcflib/vcfuniq/meta.yml @@ -10,7 +10,7 @@ tools: homepage: https://github.com/vcflib/vcflib documentation: https://github.com/vcflib/vcflib#USAGE doi: "https://doi.org/10.1101/2021.05.21.445151" - licence: ['MIT'] + licence: ["MIT"] input: - meta: diff --git a/modules/vcftools/meta.yml b/modules/vcftools/meta.yml index a8f864a9..7a85bdec 100644 --- a/modules/vcftools/meta.yml +++ b/modules/vcftools/meta.yml @@ -9,7 +9,7 @@ tools: documentation: http://vcftools.sourceforge.net/man_latest.html tool_dev_url: None doi: - licence: ['LGPL'] + licence: ["LGPL"] input: - meta: diff --git a/modules/yara/index/meta.yml b/modules/yara/index/meta.yml index 651a67ee..bdd6bf9a 100644 --- a/modules/yara/index/meta.yml +++ b/modules/yara/index/meta.yml @@ -13,7 +13,10 @@ tools: documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan doi: "" - licence: ['https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE'] + licence: + [ + "https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE", + ] input: - fasta: diff --git a/modules/yara/mapper/meta.yml b/modules/yara/mapper/meta.yml index d49823d2..60089474 100644 --- a/modules/yara/mapper/meta.yml +++ b/modules/yara/mapper/meta.yml @@ -11,7 +11,10 @@ tools: documentation: https://github.com/seqan/seqan tool_dev_url: https://github.com/seqan/seqan doi: "" - licence: ['https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE'] + licence: + [ + "https://raw.githubusercontent.com/seqan/seqan/develop/apps/yara/LICENSE", + ] input: - meta: diff --git a/subworkflows/nf-core/align_bowtie2/meta.yml b/subworkflows/nf-core/align_bowtie2/meta.yml index e149a212..40abd5a6 100644 --- a/subworkflows/nf-core/align_bowtie2/meta.yml +++ b/subworkflows/nf-core/align_bowtie2/meta.yml @@ -26,25 +26,25 @@ input: - index: type: file description: Bowtie2 genome index files - pattern: '*.ebwt' + pattern: "*.ebwt" # TODO Update when we decide on a standard for subworkflow docs output: - bam: type: file description: Output BAM file containing read alignments - pattern: '*.{bam}' + pattern: "*.{bam}" - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - fastq: type: file description: Unaligned FastQ files - pattern: '*.fastq.gz' + pattern: "*.fastq.gz" - log: type: file description: Alignment log - pattern: '*.log' - # TODO Add samtools outputs + pattern: "*.log" +# TODO Add samtools outputs authors: - - '@drpatelh' + - "@drpatelh" diff --git a/subworkflows/nf-core/annotation_ensemblvep/meta.yml b/subworkflows/nf-core/annotation_ensemblvep/meta.yml index e7d92ce9..991a8b2f 100644 --- a/subworkflows/nf-core/annotation_ensemblvep/meta.yml +++ b/subworkflows/nf-core/annotation_ensemblvep/meta.yml @@ -20,10 +20,10 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - vcf_tbi: type: file description: Compressed vcf file + tabix index pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]" authors: - - '@maxulysse' + - "@maxulysse" diff --git a/subworkflows/nf-core/annotation_snpeff/meta.yml b/subworkflows/nf-core/annotation_snpeff/meta.yml index 164a0ee2..e0773626 100644 --- a/subworkflows/nf-core/annotation_snpeff/meta.yml +++ b/subworkflows/nf-core/annotation_snpeff/meta.yml @@ -20,10 +20,10 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - vcf_tbi: type: file description: Compressed vcf file + tabix index pattern: "[ *{.vcf.gz,vcf.gz.tbi} ]" authors: - - '@maxulysse' + - "@maxulysse" diff --git a/subworkflows/nf-core/bam_sort_samtools/meta.yml b/subworkflows/nf-core/bam_sort_samtools/meta.yml index a0e3f30b..51124475 100644 --- a/subworkflows/nf-core/bam_sort_samtools/meta.yml +++ b/subworkflows/nf-core/bam_sort_samtools/meta.yml @@ -20,7 +20,7 @@ input: - bam: type: file description: BAM/CRAM/SAM file - pattern: '*.{bam,cram,sam}' + pattern: "*.{bam,cram,sam}" # TODO Update when we decide on a standard for subworkflow docs output: - meta: @@ -31,11 +31,11 @@ output: - bam: type: file description: Sorted BAM/CRAM/SAM file - pattern: '*.{bam,cram,sam}' + pattern: "*.{bam,cram,sam}" - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" authors: - - '@drpatelh' - - '@ewels' + - "@drpatelh" + - "@ewels" diff --git a/subworkflows/nf-core/bam_stats_samtools/meta.yml b/subworkflows/nf-core/bam_stats_samtools/meta.yml index 509c5c97..38fe8647 100644 --- a/subworkflows/nf-core/bam_stats_samtools/meta.yml +++ b/subworkflows/nf-core/bam_stats_samtools/meta.yml @@ -19,11 +19,11 @@ input: - bam: type: file description: BAM/CRAM/SAM file - pattern: '*.{bam,cram,sam}' + pattern: "*.{bam,cram,sam}" - bai: type: file description: Index for BAM/CRAM/SAM file - pattern: '*.{bai,crai,sai}' + pattern: "*.{bai,crai,sai}" # TODO Update when we decide on a standard for subworkflow docs output: - meta: @@ -34,10 +34,10 @@ output: - stats: type: file description: File containing samtools stats output - pattern: '*.{stats}' + pattern: "*.{stats}" - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" authors: - - '@drpatelh' + - "@drpatelh" diff --git a/subworkflows/nf-core/fgbio_create_umi_consensus/meta.yml b/subworkflows/nf-core/fgbio_create_umi_consensus/meta.yml index 2cb61206..af4ad5bc 100644 --- a/subworkflows/nf-core/fgbio_create_umi_consensus/meta.yml +++ b/subworkflows/nf-core/fgbio_create_umi_consensus/meta.yml @@ -48,20 +48,20 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - ubam: type: file description: unmapped bam file - pattern: '*.bam' + pattern: "*.bam" - groupbam: type: file description: mapped bam file, where reads are grouped by UMI tag - pattern: '*.bam' + pattern: "*.bam" - consensusbam: type: file description: | mapped bam file, where reads are created as consensus of those belonging to the same UMI group - pattern: '*.bam' + pattern: "*.bam" authors: - - '@lescai' + - "@lescai" diff --git a/subworkflows/nf-core/gatk_create_som_pon/meta.yml b/subworkflows/nf-core/gatk_create_som_pon/meta.yml index 07404aae..bffb2d50 100644 --- a/subworkflows/nf-core/gatk_create_som_pon/meta.yml +++ b/subworkflows/nf-core/gatk_create_som_pon/meta.yml @@ -46,7 +46,7 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - mutect2_vcf: type: list description: List of compressed vcf files to be used to make the gendb workspace @@ -72,4 +72,4 @@ output: description: Index of pon_vcf file pattern: "*vcf.gz.tbi" authors: - - '@GCJMackenzie' + - "@GCJMackenzie" diff --git a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/meta.yml b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/meta.yml index 4c42addf..d5abdca9 100644 --- a/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/meta.yml +++ b/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/meta.yml @@ -74,7 +74,7 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - mutect2_vcf: type: file description: Compressed vcf file to be used for variant_calling. @@ -124,4 +124,4 @@ output: description: file containing statistics of the filtermutectcalls run. pattern: "*.filteringStats.tsv" authors: - - '@GCJMackenzie' + - "@GCJMackenzie" diff --git a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml index 14329691..4c41f1f2 100644 --- a/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml +++ b/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/meta.yml @@ -67,7 +67,7 @@ output: - versions: type: file description: File containing software versions - pattern: 'versions.yml' + pattern: "versions.yml" - mutect2_vcf: type: file description: Compressed vcf file to be used for variant_calling. @@ -105,4 +105,4 @@ output: description: file containing statistics of the filtermutectcalls run. pattern: "*.filteringStats.tsv" authors: - - '@GCJMackenzie' + - "@GCJMackenzie" diff --git a/subworkflows/nf-core/sra_fastq/meta.yml b/subworkflows/nf-core/sra_fastq/meta.yml index 3db93257..5114bce5 100644 --- a/subworkflows/nf-core/sra_fastq/meta.yml +++ b/subworkflows/nf-core/sra_fastq/meta.yml @@ -34,4 +34,4 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - '@Midnighter' + - "@Midnighter" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 203005da..8ed68dca 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -178,6 +178,10 @@ bedtools/subtract: - modules/bedtools/subtract/** - tests/modules/bedtools/subtract/** +biobambam/bammarkduplicates2: + - modules/biobambam/bammarkduplicates2/** + - tests/modules/biobambam/bammarkduplicates2/** + bismark/align: - modules/bismark/align/** - modules/bismark/genomepreparation/** @@ -396,6 +400,10 @@ deeparg/predict: - modules/deeparg/predict/** - tests/modules/deeparg/predict/** +deeptools/bamcoverage: + - modules/deeptools/bamcoverage/** + - tests/modules/deeptools/bamcoverage/** + deeptools/computematrix: - modules/deeptools/computematrix/** - tests/modules/deeptools/computematrix/** @@ -576,6 +584,10 @@ gatk4/gatherbqsrreports: - modules/gatk4/gatherbqsrreports/** - tests/modules/gatk4/gatherbqsrreports/** +gatk4/gatherpileupsummaries: + - modules/gatk4/gatherpileupsummaries/** + - tests/modules/gatk4/gatherpileupsummaries/** + gatk4/genomicsdbimport: - modules/gatk4/genomicsdbimport/** - tests/modules/gatk4/genomicsdbimport/** @@ -596,6 +608,10 @@ gatk4/indexfeaturefile: - modules/gatk4/indexfeaturefile/** - tests/modules/gatk4/indexfeaturefile/** +gatk4/intervallisttobed: + - modules/gatk4/intervallisttobed/** + - tests/modules/gatk4/intervallisttobed/** + gatk4/intervallisttools: - modules/gatk4/intervallisttools/** - tests/modules/gatk4/intervallisttools/** @@ -612,6 +628,10 @@ gatk4/mergebamalignment: - modules/gatk4/mergebamalignment/** - tests/modules/gatk4/mergebamalignment/** +gatk4/mergemutectstats: + - modules/gatk4/mergemutectstats/** + - tests/modules/gatk4/mergemutectstats/** + gatk4/mergevcfs: - modules/gatk4/mergevcfs/** - tests/modules/gatk4/mergevcfs/** @@ -755,6 +775,14 @@ homer/makeucscfile: - modules/homer/makeucscfile/** - tests/modules/homer/makeucscfile/** +ichorcna/createpon: + - modules/ichorcna/createpon/** + - tests/modules/ichorcna/createpon/** + +ichorcna/run: + - modules/ichorcna/run/** + - tests/modules/ichorcna/run/** + idr: - modules/idr/** - tests/modules/idr/** @@ -1004,6 +1032,14 @@ msisensor/scan: - modules/msisensor/scan/** - tests/modules/msisensor/scan/** +msisensorpro/msi_somatic: + - modules/msisensorpro/msi_somatic/** + - tests/modules/msisensorpro/msi_somatic/** + +msisensorpro/scan: + - modules/msisensorpro/scan/** + - tests/modules/msisensorpro/scan/** + mtnucratio: - modules/mtnucratio/** - tests/modules/mtnucratio/** @@ -1197,6 +1233,10 @@ qualimap/bamqc: - modules/qualimap/bamqc/** - tests/modules/qualimap/bamqc/** +qualimap/bamqccram: + - modules/qualimap/bamqccram/** + - tests/modules/qualimap/bamqccram/** + quast: - modules/quast/** - tests/modules/quast/** @@ -1357,6 +1397,10 @@ seqtk/mergepe: - modules/seqtk/mergepe/** - tests/modules/seqtk/mergepe/** +seqtk/rename: + - modules/seqtk/rename/** + - tests/modules/seqtk/rename/** + seqtk/sample: - modules/seqtk/sample/** - tests/modules/seqtk/sample/** @@ -1397,6 +1441,10 @@ snpsites: - modules/snpsites/** - tests/modules/snpsites/** +sourmash/sketch: + - modules/sourmash/sketch/** + - tests/modules/sourmash/sketch/** + spades: - modules/spades/** - tests/modules/spades/** diff --git a/tests/config/test_data.config b/tests/config/test_data.config index 7d0d3efa..165e8449 100644 --- a/tests/config/test_data.config +++ b/tests/config/test_data.config @@ -122,6 +122,9 @@ params { genome_21_fasta_fai = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai" genome_21_dict = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict" genome_21_interval_list = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.interval_list" + genome_21_multi_interval_bed = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed" + genome_21_multi_interval_bed_gz = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz" + genome_21_multi_interval_bed_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed.gz.tbi" dbsnp_146_hg38_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz" dbsnp_146_hg38_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/genome/vcf/dbsnp_146.hg38.vcf.gz.tbi" @@ -262,6 +265,9 @@ params { test2_genome_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz.tbi" test2_genome_vcf_idx = "${test_data_dir}/genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.idx" + test_genome21_indels_vcf_gz = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz" + test_genome21_indels_vcf_gz_tbi = "${test_data_dir}/genomics/homo_sapiens/illumina/vcf/test.genome_21.somatic_sv.vcf.gz.tbi" + test_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test.broadPeak" test2_broadpeak = "${test_data_dir}/genomics/homo_sapiens/illumina/broadpeak/test2.broadPeak" diff --git a/tests/modules/artic/minion/test.yml b/tests/modules/artic/minion/test.yml index 8b36b224..401a8470 100644 --- a/tests/modules/artic/minion/test.yml +++ b/tests/modules/artic/minion/test.yml @@ -34,7 +34,7 @@ md5sum: e6e184f1fa153868e3acea0eab42e484 - path: output/artic/test.minion.log.txt contains: - - 'artic_vcf_merge' + - "artic_vcf_merge" - path: output/artic/test.muscle.in.fasta md5sum: 40ae4c89de797d1548c642f0da7a86cc - path: output/artic/test.muscle.out.fasta diff --git a/tests/modules/ataqv/ataqv/test.yml b/tests/modules/ataqv/ataqv/test.yml index f9f2a888..5c5a10e0 100644 --- a/tests/modules/ataqv/ataqv/test.yml +++ b/tests/modules/ataqv/ataqv/test.yml @@ -6,7 +6,7 @@ files: - path: output/ataqv/test.ataqv.json contains: - - '"forward_mate_reads": 101' + - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_problem_reads command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_problem_reads -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config @@ -17,8 +17,8 @@ - path: output/ataqv/1.problems md5sum: d41d8cd98f00b204e9800998ecf8427e - path: output/ataqv/test.ataqv.json - contains: - - '"forward_mate_reads": 101' + contains: + - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_peak command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_peak -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config @@ -27,8 +27,8 @@ - ataqv/ataqv files: - path: output/ataqv/test.ataqv.json - contains: - - '"forward_mate_reads": 101' + contains: + - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_tss command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_tss -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config @@ -37,8 +37,8 @@ - ataqv/ataqv files: - path: output/ataqv/test.ataqv.json - contains: - - '"forward_mate_reads": 101' + contains: + - '"forward_mate_reads": 101' - name: ataqv ataqv test_ataqv_ataqv_excluded_regs command: nextflow run ./tests/modules/ataqv/ataqv -entry test_ataqv_ataqv_excluded_regs -c ./tests/config/nextflow.config -c ./tests/modules/ataqv/ataqv/nextflow.config @@ -47,5 +47,5 @@ - ataqv/ataqv files: - path: output/ataqv/test.ataqv.json - contains: - - '"forward_mate_reads": 101' + contains: + - '"forward_mate_reads": 101' diff --git a/tests/modules/bbmap/bbsplit/test.yml b/tests/modules/bbmap/bbsplit/test.yml index add9b519..a1933211 100644 --- a/tests/modules/bbmap/bbsplit/test.yml +++ b/tests/modules/bbmap/bbsplit/test.yml @@ -7,17 +7,17 @@ - path: output/bbmap/bbsplit/ref/genome/1/chr1.chrom.gz - path: output/bbmap/bbsplit/ref/genome/1/info.txt contains: - - 'Chromosome' + - "Chromosome" - path: output/bbmap/bbsplit/ref/genome/1/merged_ref_9222711925172838098.fa.gz - path: output/bbmap/bbsplit/ref/genome/1/namelist.txt md5sum: 45e7a4cdc7a11a39ada56844ca3a1e30 - path: output/bbmap/bbsplit/ref/genome/1/reflist.txt contains: - - 'genome.fasta' + - "genome.fasta" - path: output/bbmap/bbsplit/ref/genome/1/scaffolds.txt.gz - path: output/bbmap/bbsplit/ref/genome/1/summary.txt contains: - - 'scaffolds' + - "scaffolds" - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block md5sum: 385913c1e84b77dc7bf36288ee1c8706 - path: output/bbmap/bbsplit/ref/index/1/chr1_index_k13_c13_b1.block2.gz diff --git a/tests/modules/biobambam/bammarkduplicates2/main.nf b/tests/modules/biobambam/bammarkduplicates2/main.nf new file mode 100644 index 00000000..aeab18b9 --- /dev/null +++ b/tests/modules/biobambam/bammarkduplicates2/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { BIOBAMBAM_BAMMARKDUPLICATES2 } from '../../../../modules/biobambam/bammarkduplicates2/main.nf' + +workflow test_biobambam_bammarkduplicates2 { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + + BIOBAMBAM_BAMMARKDUPLICATES2 ( input ) +} diff --git a/tests/modules/biobambam/bammarkduplicates2/nextflow.config b/tests/modules/biobambam/bammarkduplicates2/nextflow.config new file mode 100644 index 00000000..8730f1c4 --- /dev/null +++ b/tests/modules/biobambam/bammarkduplicates2/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} diff --git a/tests/modules/biobambam/bammarkduplicates2/test.yml b/tests/modules/biobambam/bammarkduplicates2/test.yml new file mode 100644 index 00000000..d046dfe9 --- /dev/null +++ b/tests/modules/biobambam/bammarkduplicates2/test.yml @@ -0,0 +1,12 @@ +- name: biobambam bammarkduplicates2 test_biobambam_bammarkduplicates2 + command: nextflow run tests/modules/biobambam/bammarkduplicates2 -entry test_biobambam_bammarkduplicates2 -c tests/config/nextflow.config + tags: + - biobambam/bammarkduplicates2 + - biobambam + files: + - path: output/biobambam/test.bam + md5sum: 1cf7f957eb20b4ace9f10d0cf0a0649a + - path: output/biobambam/test.metrics.txt + md5sum: 30d6e7d90bb5df46329d4bc0144ce927 + - path: output/biobambam/versions.yml + md5sum: 0d6f3137ed4515333d73c779f2c24445 diff --git a/tests/modules/bwameth/align/test.yml b/tests/modules/bwameth/align/test.yml index f921b5f4..161c627f 100644 --- a/tests/modules/bwameth/align/test.yml +++ b/tests/modules/bwameth/align/test.yml @@ -13,4 +13,3 @@ - bwameth/align files: - path: output/bwameth/test.bam - diff --git a/tests/modules/checkm/lineagewf/test.yml b/tests/modules/checkm/lineagewf/test.yml index 6749f6aa..f81e8c9c 100644 --- a/tests/modules/checkm/lineagewf/test.yml +++ b/tests/modules/checkm/lineagewf/test.yml @@ -32,4 +32,3 @@ - "contigs" - "UID1" - "genome" - diff --git a/tests/modules/chromap/index/test.yml b/tests/modules/chromap/index/test.yml index 430a53b7..dde1aa1b 100644 --- a/tests/modules/chromap/index/test.yml +++ b/tests/modules/chromap/index/test.yml @@ -5,5 +5,3 @@ - chromap files: - path: output/chromap/genome.index - - diff --git a/tests/modules/dastool/dastool/test.yml b/tests/modules/dastool/dastool/test.yml index e2161890..7f7eb19c 100644 --- a/tests/modules/dastool/dastool/test.yml +++ b/tests/modules/dastool/dastool/test.yml @@ -9,8 +9,8 @@ - path: output/dastool/test.tsv md5sum: 6e46c0be14dded7cb13af38f54feea47 - path: output/dastool/test_DASTool.log - contains: - - 'DAS Tool run on' + contains: + - "DAS Tool run on" - path: output/dastool/test_DASTool_scaffolds2bin.txt md5sum: 6e46c0be14dded7cb13af38f54feea47 - path: output/dastool/test_DASTool_summary.txt diff --git a/tests/modules/deeptools/bamcoverage/main.nf b/tests/modules/deeptools/bamcoverage/main.nf new file mode 100644 index 00000000..fb5c1c2d --- /dev/null +++ b/tests/modules/deeptools/bamcoverage/main.nf @@ -0,0 +1,27 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { DEEPTOOLS_BAMCOVERAGE } from '../../../../modules/deeptools/bamcoverage/main.nf' + +workflow test_deeptools_bamcoverage_bam { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) + ] + + DEEPTOOLS_BAMCOVERAGE ( input ) +} + +workflow test_deeptools_bamcoverage_cram { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + + DEEPTOOLS_BAMCOVERAGE ( input ) +} diff --git a/tests/modules/deeptools/bamcoverage/nextflow.config b/tests/modules/deeptools/bamcoverage/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/deeptools/bamcoverage/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/deeptools/bamcoverage/test.yml b/tests/modules/deeptools/bamcoverage/test.yml new file mode 100644 index 00000000..736c2e61 --- /dev/null +++ b/tests/modules/deeptools/bamcoverage/test.yml @@ -0,0 +1,21 @@ +- name: deeptools bamcoverage test_deeptools_bamcoverage_bam + command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_bam -c tests/config/nextflow.config + tags: + - deeptools + - deeptools/bamcoverage + files: + - path: output/deeptools/test.bigWig + md5sum: 95fe9383a9e6c02aea6b785cf074274f + - path: output/deeptools/versions.yml + md5sum: 68c94e73b7a8c0935578bad61fea54c1 + +- name: deeptools bamcoverage test_deeptools_bamcoverage_cram + command: nextflow run tests/modules/deeptools/bamcoverage -entry test_deeptools_bamcoverage_cram -c tests/config/nextflow.config + tags: + - deeptools + - deeptools/bamcoverage + files: + - path: output/deeptools/test.bigWig + md5sum: 95fe9383a9e6c02aea6b785cf074274f + - path: output/deeptools/versions.yml + md5sum: 665bbd2979c49bf3974a24bd44a88e94 diff --git a/tests/modules/deeptools/plotheatmap/test.yml b/tests/modules/deeptools/plotheatmap/test.yml index 9273f840..ddc468e2 100644 --- a/tests/modules/deeptools/plotheatmap/test.yml +++ b/tests/modules/deeptools/plotheatmap/test.yml @@ -6,4 +6,3 @@ files: - path: output/deeptools/test.plotHeatmap.mat.tab - path: output/deeptools/test.plotHeatmap.pdf - diff --git a/tests/modules/diamond/blastp/test.yml b/tests/modules/diamond/blastp/test.yml index 673563cb..32dfacaa 100644 --- a/tests/modules/diamond/blastp/test.yml +++ b/tests/modules/diamond/blastp/test.yml @@ -1,8 +1,8 @@ - name: diamond blastp command: nextflow run ./tests/modules/diamond/blastp -entry test_diamond_blastp -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastp/nextflow.config tags: - - diamond - - diamond/blastp + - diamond + - diamond/blastp files: - - path: ./output/diamond/test.diamond_blastp.txt - md5sum: 3ca7f6290c1d8741c573370e6f8b4db0 + - path: ./output/diamond/test.diamond_blastp.txt + md5sum: 3ca7f6290c1d8741c573370e6f8b4db0 diff --git a/tests/modules/diamond/blastx/test.yml b/tests/modules/diamond/blastx/test.yml index ee94802f..fe7c6938 100644 --- a/tests/modules/diamond/blastx/test.yml +++ b/tests/modules/diamond/blastx/test.yml @@ -1,8 +1,8 @@ - name: diamond blastx command: nextflow run ./tests/modules/diamond/blastx -entry test_diamond_blastx -c ./tests/config/nextflow.config -c ./tests/modules/diamond/blastx/nextflow.config tags: - - diamond - - diamond/blastx + - diamond + - diamond/blastx files: - - path: ./output/diamond/test.diamond_blastx.txt - md5sum: d41d8cd98f00b204e9800998ecf8427e + - path: ./output/diamond/test.diamond_blastx.txt + md5sum: d41d8cd98f00b204e9800998ecf8427e diff --git a/tests/modules/dragmap/hashtable/test.yml b/tests/modules/dragmap/hashtable/test.yml index 59a3ed55..0534bdc2 100644 --- a/tests/modules/dragmap/hashtable/test.yml +++ b/tests/modules/dragmap/hashtable/test.yml @@ -4,16 +4,16 @@ - dragmap - dragmap/hashtable files: - - path: output/dragmap/dragmap/hash_table.cfg - - path: output/dragmap/dragmap/hash_table.cfg.bin - - path: output/dragmap/dragmap/hash_table.cmp - md5sum: bc210e5358fd65656f9aea297b59ec7d - - path: output/dragmap/dragmap/hash_table_stats.txt - - path: output/dragmap/dragmap/reference.bin - md5sum: b6b5c12a42416b990cd2844de8f33c5d - - path: output/dragmap/dragmap/ref_index.bin - md5sum: 8470be9566ecee77eb4aea6a38922a66 - - path: output/dragmap/dragmap/repeat_mask.bin - md5sum: 2439259a2fd32a1d0f4c53d585f3da3a - - path: output/dragmap/dragmap/str_table.bin - md5sum: 302e2b30993973527e69c6bcd1f093d0 + - path: output/dragmap/dragmap/hash_table.cfg + - path: output/dragmap/dragmap/hash_table.cfg.bin + - path: output/dragmap/dragmap/hash_table.cmp + md5sum: bc210e5358fd65656f9aea297b59ec7d + - path: output/dragmap/dragmap/hash_table_stats.txt + - path: output/dragmap/dragmap/reference.bin + md5sum: b6b5c12a42416b990cd2844de8f33c5d + - path: output/dragmap/dragmap/ref_index.bin + md5sum: 8470be9566ecee77eb4aea6a38922a66 + - path: output/dragmap/dragmap/repeat_mask.bin + md5sum: 2439259a2fd32a1d0f4c53d585f3da3a + - path: output/dragmap/dragmap/str_table.bin + md5sum: 302e2b30993973527e69c6bcd1f093d0 diff --git a/tests/modules/ectyper/test.yml b/tests/modules/ectyper/test.yml index 4f909bd9..15e0327d 100644 --- a/tests/modules/ectyper/test.yml +++ b/tests/modules/ectyper/test.yml @@ -6,6 +6,6 @@ - path: output/ectyper/blast_output_alleles.txt md5sum: 27f3f5e84f7da451b2948d61589cdb06 - path: output/ectyper/ectyper.log - contains: ['Serotype', 'RefSeq', 'O-type', 'finished'] + contains: ["Serotype", "RefSeq", "O-type", "finished"] - path: output/ectyper/test.tsv md5sum: ba923d7c7ee7d1047466aafc9a9df208 diff --git a/tests/modules/freebayes/main.nf b/tests/modules/freebayes/main.nf index f8ae0ecb..6ed708c5 100644 --- a/tests/modules/freebayes/main.nf +++ b/tests/modules/freebayes/main.nf @@ -5,91 +5,98 @@ nextflow.enable.dsl = 2 include { FREEBAYES } from '../../../modules/freebayes/main.nf' workflow test_freebayes { - + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_bed { + targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_cram { + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), [], - [] + [], + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_somatic { + targets = [] input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_bam_bai'], checkIfExists: true), + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = [] + samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } workflow test_freebayes_somatic_cram_intervals { + targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) input = [ [ id:'test', single_end:false ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true), + targets ] fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - targets = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) samples = [] populations = [] cnv = [] - FREEBAYES (input, fasta, fai, targets, samples, populations, cnv) + FREEBAYES (input, fasta, fai, samples, populations, cnv) } diff --git a/tests/modules/freebayes/test.yml b/tests/modules/freebayes/test.yml index 6cca692e..c3c8e30b 100644 --- a/tests/modules/freebayes/test.yml +++ b/tests/modules/freebayes/test.yml @@ -4,7 +4,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 81d3e6ce7b6343d088b779567c3803eb + md5sum: f28d0b8e2ccedeac0e590ca2ecaac83d - path: output/freebayes/versions.yml md5sum: 53651eb835af65df829241257584a7d2 @@ -14,7 +14,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 02645d014a63485162a7789007373b2a + md5sum: 1927441d1b7a4c48cbb61821de300ad4 - path: output/freebayes/versions.yml md5sum: becc93c8a0be580c09d55b955d60a5e1 @@ -24,7 +24,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 3d0bfcd2129c62f8863952fa4c1054db + md5sum: 9b8d1d51d779bbea4086c7f7a2ece641 - path: output/freebayes/versions.yml md5sum: 2e5b266edfc6cab81353cfc72c00f67c @@ -34,7 +34,7 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 22fec868210ba3baf685b214bfd8e74b + md5sum: dcaa639912174055c1380913d6102c01 - path: output/freebayes/versions.yml md5sum: 8fbdb4c052fb3e42b5508a966125fa05 @@ -44,6 +44,6 @@ - freebayes files: - path: output/freebayes/test.vcf.gz - md5sum: 527cf2937067bbd4117d95fd472bb928 + md5sum: b0052a2b83c0ba1b9686d0c96e61712f - path: output/freebayes/versions.yml md5sum: af97e3dfdc086188739907c3460e49e0 diff --git a/tests/modules/gatk4/applybqsr/test.yml b/tests/modules/gatk4/applybqsr/test.yml index 7449c210..4520c34b 100644 --- a/tests/modules/gatk4/applybqsr/test.yml +++ b/tests/modules/gatk4/applybqsr/test.yml @@ -5,9 +5,9 @@ - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 908825edf1f229a072f91d8b753d95dd + md5sum: d088422be886dc8507ff97fcc7dd968a - path: output/gatk4/versions.yml - md5sum: b65c46529ae9658db0c596cbc26505c2 + md5sum: d5c6455d8a77aecc63f87c795fc3443e - name: gatk4 applybqsr test_gatk4_applybqsr_intervals command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_intervals -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config @@ -16,9 +16,9 @@ - gatk4/applybqsr files: - path: output/gatk4/test.bam - md5sum: 50f8a79c7d528e02470416f81eb582bc + md5sum: 4bfa18d651abd945e240b05e70107716 - path: output/gatk4/versions.yml - md5sum: 17c8a40b3537e3400edebd1826d28385 + md5sum: cb4cb8a62e117b4adc643ae47883d53c - name: gatk4 applybqsr test_gatk4_applybqsr_cram command: nextflow run tests/modules/gatk4/applybqsr -entry test_gatk4_applybqsr_cram -c tests/config/nextflow.config -c ./tests/modules/gatk4/applybqsr/nextflow.config @@ -27,6 +27,6 @@ - gatk4/applybqsr files: - path: output/gatk4/test.cram - md5sum: cd8d4ba6181f714e74641adeb2f9aa1d + md5sum: 2e0bca197af4f043a4a85152e6edbe04 - path: output/gatk4/versions.yml - md5sum: 35218922e1929c699ea64de9f4c29fb5 + md5sum: 1efaa18be943bab4e4c54191d6eaa260 diff --git a/tests/modules/gatk4/applyvqsr/main.nf b/tests/modules/gatk4/applyvqsr/main.nf index 90a57aaa..c6e99d5c 100644 --- a/tests/modules/gatk4/applyvqsr/main.nf +++ b/tests/modules/gatk4/applyvqsr/main.nf @@ -2,7 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_NO_ALLELSPECIFICITY } from '../../../../modules/gatk4/applyvqsr/main.nf' +include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY} from '../../../../modules/gatk4/applyvqsr/main.nf' workflow test_gatk4_applyvqsr { input = [ [ id:'test'], // meta map @@ -15,11 +16,8 @@ workflow test_gatk4_applyvqsr { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = false - truthsensitivity = '99.0' - mode = 'SNP' - GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) + GATK4_APPLYVQSR_NO_ALLELSPECIFICITY ( input, fasta, fai, dict ) } workflow test_gatk4_applyvqsr_allele_specific { @@ -33,9 +31,6 @@ workflow test_gatk4_applyvqsr_allele_specific { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = true - truthsensitivity = '99.0' - mode = 'SNP' - GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode ) + GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY ( input, fasta, fai, dict) } diff --git a/tests/modules/gatk4/applyvqsr/nextflow.config b/tests/modules/gatk4/applyvqsr/nextflow.config index 19934e76..bf943c23 100644 --- a/tests/modules/gatk4/applyvqsr/nextflow.config +++ b/tests/modules/gatk4/applyvqsr/nextflow.config @@ -1,5 +1,11 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: GATK4_APPLYVQSR_NO_ALLELSPECIFICITY { + ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0' + } -} \ No newline at end of file + withName: GATK4_APPLYVQSR_WITH_ALLELSPECIFICITY { + ext.args = '--mode SNP --truth-sensitivity-filter-level 99.0 -AS' + } +} diff --git a/tests/modules/gatk4/applyvqsr/test.yml b/tests/modules/gatk4/applyvqsr/test.yml index b2acc6d8..7cb91c43 100644 --- a/tests/modules/gatk4/applyvqsr/test.yml +++ b/tests/modules/gatk4/applyvqsr/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/versions.yml - md5sum: 524a78cdfa56c8b09a4ff3f4cb278261 + md5sum: ce9c443375683e7f2958fe958759ad29 - name: gatk4 applyvqsr test_gatk4_applyvqsr_allele_specific command: nextflow run tests/modules/gatk4/applyvqsr -entry test_gatk4_applyvqsr_allele_specific -c tests/config/nextflow.config -c ./tests/modules/gatk4/applyvqsr/nextflow.config @@ -18,4 +18,4 @@ - path: output/gatk4/test.vcf.gz - path: output/gatk4/test.vcf.gz.tbi - path: output/gatk4/versions.yml - md5sum: 7a3c6e97628bd1f5f4e7fd429bf74a8e + md5sum: 521353d12d576de2864f1d18a3e54f14 diff --git a/tests/modules/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml index d598d1c0..4cd44281 100644 --- a/tests/modules/gatk4/calculatecontamination/test.yml +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -4,10 +4,10 @@ - gatk4 - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table + - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: output/gatk4/versions.yml - md5sum: 79575dc2e6a7f0361f2d8b090c496070 + - path: output/gatk4/versions.yml + md5sum: 3da8f1c0de968886330a3f7a3a1c6616 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_matched_pair -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config @@ -15,10 +15,10 @@ - gatk4 - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table + - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: output/gatk4/versions.yml - md5sum: 733f15ef7eb504daec9fd8cd9beef71a + - path: output/gatk4/versions.yml + md5sum: 14ab12a71b0c2b87d8cd53639a991b3a - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation command: nextflow run tests/modules/gatk4/calculatecontamination -entry test_gatk4_calculatecontamination_segmentation -c tests/config/nextflow.config -c ./tests/modules/gatk4/calculatecontamination/nextflow.config @@ -26,9 +26,9 @@ - gatk4 - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table + - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: output/gatk4/test.segmentation.table + - path: output/gatk4/test.segmentation.table md5sum: f4643d9319bde4efbfbe516d6fb13052 - - path: output/gatk4/versions.yml - md5sum: 5396e33146addbe4a59d0f30cb573a3a + - path: output/gatk4/versions.yml + md5sum: d2e61315de31f512e448f0cb4b77db54 diff --git a/tests/modules/gatk4/fastqtosam/test.yml b/tests/modules/gatk4/fastqtosam/test.yml index 7f6357e8..07f9af15 100644 --- a/tests/modules/gatk4/fastqtosam/test.yml +++ b/tests/modules/gatk4/fastqtosam/test.yml @@ -6,7 +6,7 @@ files: - path: output/gatk4/test.bam - path: output/gatk4/versions.yml - md5sum: 03f3accdc3e3c392c1179213286a0b67 + md5sum: 381cdb2496b2fcc7bbc371a6e4156c7e - name: gatk4 fastqtosam test_gatk4_fastqtosam_paired_end command: nextflow run tests/modules/gatk4/fastqtosam -entry test_gatk4_fastqtosam_paired_end -c tests/config/nextflow.config -c ./tests/modules/gatk4/fastqtosam/nextflow.config @@ -16,4 +16,4 @@ files: - path: output/gatk4/test.bam - path: output/gatk4/versions.yml - md5sum: 144e7118d5f277ad5fba863213c810b0 + md5sum: 1d07c90cbd31992c9ba003f02d1b3502 diff --git a/tests/modules/gatk4/gatherbqsrreports/test.yml b/tests/modules/gatk4/gatherbqsrreports/test.yml index 521f2197..576889de 100644 --- a/tests/modules/gatk4/gatherbqsrreports/test.yml +++ b/tests/modules/gatk4/gatherbqsrreports/test.yml @@ -7,7 +7,7 @@ - path: output/gatk4/test.table md5sum: 9603b69fdc3b5090de2e0dd78bfcc4bf - path: output/gatk4/versions.yml - md5sum: b53101f71b0763e80855703ba4e1f101 + md5sum: 8d52c5aaab73294e9ea5491b95f3e1e1 - name: gatk4 gatherbqsrreports test_gatk4_gatherbqsrreports_multiple command: nextflow run tests/modules/gatk4/gatherbqsrreports -entry test_gatk4_gatherbqsrreports_multiple -c tests/config/nextflow.config @@ -18,4 +18,4 @@ - path: output/gatk4/test.table md5sum: 0c1257eececf95db8ca378272d0f21f9 - path: output/gatk4/versions.yml - md5sum: 584a6ebf04f54abcfcf4c8255e13ff2a + md5sum: 91cad396b9f2045c3cd8c0f256672e80 diff --git a/tests/modules/gatk4/gatherpileupsummaries/main.nf b/tests/modules/gatk4/gatherpileupsummaries/main.nf new file mode 100644 index 00000000..2bd7e98c --- /dev/null +++ b/tests/modules/gatk4/gatherpileupsummaries/main.nf @@ -0,0 +1,18 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_GATHERPILEUPSUMMARIES } from '../../../../modules/gatk4/gatherpileupsummaries/main.nf' + +workflow test_gatk4_gatherpileupsummaries { + + input = [ + [ id:'test', single_end:false ], // meta map + [file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)] + //file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true)] + ] + + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + + GATK4_GATHERPILEUPSUMMARIES ( input, dict ) +} diff --git a/tests/modules/gatk4/gatherpileupsummaries/nextflow.config b/tests/modules/gatk4/gatherpileupsummaries/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/gatk4/gatherpileupsummaries/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/gatk4/gatherpileupsummaries/test.yml b/tests/modules/gatk4/gatherpileupsummaries/test.yml new file mode 100644 index 00000000..0c38a602 --- /dev/null +++ b/tests/modules/gatk4/gatherpileupsummaries/test.yml @@ -0,0 +1,8 @@ +- name: gatk4 gatherpileupsummaries + command: nextflow run ./tests/modules/gatk4/gatherpileupsummaries -entry test_gatk4_gatherpileupsummaries -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/gatherpileupsummaries/nextflow.config + tags: + - gatk4 + - gatk4/gatherpileupsummaries + files: + - path: output/gatk4/test.pileupsummaries.table + md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 diff --git a/tests/modules/gatk4/genomicsdbimport/test.yml b/tests/modules/gatk4/genomicsdbimport/test.yml index d1a8f073..5c4ea2bb 100644 --- a/tests/modules/gatk4/genomicsdbimport/test.yml +++ b/tests/modules/gatk4/genomicsdbimport/test.yml @@ -19,7 +19,7 @@ - path: output/gatk4/test/vidmap.json md5sum: 18d3f68bd2cb6f4474990507ff95017a - path: output/gatk4/versions.yml - md5sum: 6fffaf981f099659cf820277d1f3c606 + md5sum: 91f5c3e9529982f9c819860b403576ce - name: gatk4 genomicsdbimport test_gatk4_genomicsdbimport_get_intervalslist command: nextflow run tests/modules/gatk4/genomicsdbimport -entry test_gatk4_genomicsdbimport_get_intervalslist -c tests/config/nextflow.config -c ./tests/modules/gatk4/genomicsdbimport/nextflow.config @@ -30,7 +30,7 @@ - path: output/gatk4/test.interval_list md5sum: 4c85812ac15fc1cd29711a851d23c0bf - path: output/gatk4/versions.yml - md5sum: 4a56022d6e08d54e8ba853637bf3b5f1 + md5sum: a898fe1cbc4acfa5936c0ffdcf121401 - path: output/untar/versions.yml md5sum: 8f080677b109aea2cfca50208b077534 @@ -55,6 +55,6 @@ - path: output/gatk4/test_genomicsdb/vidmap.json md5sum: 18d3f68bd2cb6f4474990507ff95017a - path: output/gatk4/versions.yml - md5sum: da6a815b7340683b1a56bdfd7e66d463 + md5sum: d87baa3f4218c5554cad3c008cb6cbc4 - path: output/untar/versions.yml md5sum: 9b2916aea9790bdf427c0cb38109110c diff --git a/tests/modules/gatk4/genotypegvcfs/test.yml b/tests/modules/gatk4/genotypegvcfs/test.yml index 128a2238..a49673fd 100644 --- a/tests/modules/gatk4/genotypegvcfs/test.yml +++ b/tests/modules/gatk4/genotypegvcfs/test.yml @@ -5,7 +5,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input @@ -15,7 +18,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp @@ -25,7 +31,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_intervals @@ -35,7 +44,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gz_input_dbsnp_intervals @@ -45,7 +57,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693'] + contains: + [ + "AC=2;AF=1.00;AN=2;DB;DP=20;ExcessHet=0.0000;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=24.05;SOR=0.693", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input @@ -55,7 +70,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp @@ -65,7 +83,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DB;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_intervals @@ -75,7 +96,10 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680'] + contains: + [ + "AC=1;AF=0.500;AN=2;BaseQRankSum=0.00;DP=211;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQRankSum=0.00;QD=0.95;ReadPosRankSum=1.09;SOR=0.680", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi - name: gatk4 genotypegvcfs test_gatk4_genotypegvcfs_gendb_input_dbsnp_intervals @@ -85,5 +109,8 @@ - gatk4/genotypegvcfs files: - path: output/gatk4/test.genotyped.vcf.gz - contains: ['AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693'] + contains: + [ + "AC=2;AF=1.00;AN=2;DP=2;ExcessHet=0.0000;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;QD=18.66;SOR=0.693", + ] - path: output/gatk4/test.genotyped.vcf.gz.tbi diff --git a/tests/modules/gatk4/getpileupsummaries/main.nf b/tests/modules/gatk4/getpileupsummaries/main.nf index 54a9b1f5..b0de9d6e 100644 --- a/tests/modules/gatk4/getpileupsummaries/main.nf +++ b/tests/modules/gatk4/getpileupsummaries/main.nf @@ -8,24 +8,45 @@ workflow test_gatk4_getpileupsummaries_just_variants { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + [] + ] variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) - sites = [] - - GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites ) + fasta = [] + fai = [] + dict = [] + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi ) } workflow test_gatk4_getpileupsummaries_separate_sites { input = [ [ id:'test' ], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ] + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) ] variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) - sites = file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) - - GATK4_GETPILEUPSUMMARIES ( input , variants , variants_tbi , sites ) + fasta = [] + fai = [] + dict = [] + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi) +} + +workflow test_gatk4_getpileupsummaries_separate_sites_cram { + + input = [ [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) , + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + ] + + variants = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz'], checkIfExists: true) + variants_tbi = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_21_vcf_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) + dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) + GATK4_GETPILEUPSUMMARIES ( input , fasta, fai, dict, variants , variants_tbi) } diff --git a/tests/modules/gatk4/getpileupsummaries/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml index 65ea30e7..e305d412 100644 --- a/tests/modules/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/gatk4/getpileupsummaries/test.yml @@ -1,17 +1,32 @@ - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_just_variants - command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_just_variants -c tests/config/nextflow.config tags: - - gatk4 - gatk4/getpileupsummaries + - gatk4 files: - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: 059123619f3ed8d4cd178c4390b81e69 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites - command: nextflow run ./tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/getpileupsummaries/nextflow.config + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites -c tests/config/nextflow.config tags: - - gatk4 - gatk4/getpileupsummaries + - gatk4 files: - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: 76b5388b0c5b5762d8d33e34b23f181d + +- name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram + command: nextflow run tests/modules/gatk4/getpileupsummaries -entry test_gatk4_getpileupsummaries_separate_sites_cram -c tests/config/nextflow.config + tags: + - gatk4/getpileupsummaries + - gatk4 + files: + - path: output/gatk4/test.pileups.table + md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 + - path: output/gatk4/versions.yml + md5sum: 2fa51319c2b1d678ee00ab09512cf268 diff --git a/tests/modules/gatk4/indexfeaturefile/test.yml b/tests/modules/gatk4/indexfeaturefile/test.yml index 04c71ea2..938c2b91 100644 --- a/tests/modules/gatk4/indexfeaturefile/test.yml +++ b/tests/modules/gatk4/indexfeaturefile/test.yml @@ -15,7 +15,7 @@ - path: output/gatk4/genome.bed.gz.tbi md5sum: 4bc51e2351a6e83f20e13be75861f941 - path: output/gatk4/versions.yml - md5sum: 9eb24dc17c96971b7991b3e154279aa7 + md5sum: e5003204702f83aabdb4141272c704d2 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf -c tests/config/nextflow.config -c ./tests/modules/gatk4/indexfeaturefile/nextflow.config @@ -25,7 +25,7 @@ files: - path: output/gatk4/test.genome.vcf.idx - path: output/gatk4/versions.yml - md5sum: f76543e715342bf1fcdeb20385e01fe9 + md5sum: 08cd7c49cfb752fc2905f600106a0345 - name: gatk4 indexfeaturefile test_gatk4_indexfeaturefile_vcf_gz command: nextflow run tests/modules/gatk4/indexfeaturefile -entry test_gatk4_indexfeaturefile_vcf_gz -c tests/config/nextflow.config @@ -36,4 +36,4 @@ - path: output/gatk4/test.genome.vcf.gz.tbi md5sum: fedd68eaddf8d31257853d9da8325bd3 - path: output/gatk4/versions.yml - md5sum: a5d988cf62648f700ffac7257e72b2c0 + md5sum: b388d1681831a40264a7a27f67a8b247 diff --git a/tests/modules/gatk4/intervallisttobed/main.nf b/tests/modules/gatk4/intervallisttobed/main.nf new file mode 100644 index 00000000..2963979f --- /dev/null +++ b/tests/modules/gatk4/intervallisttobed/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_INTERVALLISTTOBED } from '../../../../modules/gatk4/intervallisttobed/main.nf' + +workflow test_gatk4_intervallisttobed { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_21_interval_list'], checkIfExists: true) + ] + + GATK4_INTERVALLISTTOBED ( input ) +} diff --git a/tests/modules/gatk4/intervallisttobed/nextflow.config b/tests/modules/gatk4/intervallisttobed/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/gatk4/intervallisttobed/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/gatk4/intervallisttobed/test.yml b/tests/modules/gatk4/intervallisttobed/test.yml new file mode 100644 index 00000000..9e6e38c5 --- /dev/null +++ b/tests/modules/gatk4/intervallisttobed/test.yml @@ -0,0 +1,8 @@ +- name: gatk4 intervallisttobed + command: nextflow run ./tests/modules/gatk4/intervallisttobed -entry test_gatk4_intervallisttobed -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/intervallisttobed/nextflow.config + tags: + - gatk4 + - gatk4/intervallisttobed + files: + - path: output/gatk4/test.bed + md5sum: 9046675d01199fbbee79f2bc1c5dce52 diff --git a/tests/modules/gatk4/markduplicates/test.yml b/tests/modules/gatk4/markduplicates/test.yml index 333de7c9..7bf49b56 100644 --- a/tests/modules/gatk4/markduplicates/test.yml +++ b/tests/modules/gatk4/markduplicates/test.yml @@ -5,12 +5,12 @@ - gatk4/markduplicates files: - path: output/gatk4/test.bai - md5sum: c8f7a9e426c768577f88f59cb1336bf3 + md5sum: e9c125e82553209933883b4fe2b8d7c2 - path: output/gatk4/test.bam - md5sum: fba0c99a0b087c90113a210e4465f91b + md5sum: 2efd50b2e6b7fd9bdf242cd9e266cfa9 - path: output/gatk4/test.metrics - path: output/gatk4/versions.yml - md5sum: dacbab0e112d2403b09df138d4e62895 + md5sum: 0bc949aaa8792cd6c537cdaab0e2c145 - name: gatk4 markduplicates test_gatk4_markduplicates_multiple_bams command: nextflow run tests/modules/gatk4/markduplicates -entry test_gatk4_markduplicates_multiple_bams -c tests/config/nextflow.config -c ./tests/modules/gatk4/markduplicates/nextflow.config @@ -19,9 +19,9 @@ - gatk4/markduplicates files: - path: output/gatk4/test.bai - md5sum: 325932c51f6898b02dfec469c984ba28 + md5sum: bad71df9c876e72a5bc0a3e0fd755f92 - path: output/gatk4/test.bam - md5sum: f7cba8104e3a7024a5e00c02304f7dea + md5sum: 8187febc6108ffef7f907e89b9c091a4 - path: output/gatk4/test.metrics - path: output/gatk4/versions.yml - md5sum: 14d0d085df7d2f9e770578d92c329299 + md5sum: b10d63cf7b2b672915cb30cea081ccd5 diff --git a/tests/modules/gatk4/mergemutectstats/main.nf b/tests/modules/gatk4/mergemutectstats/main.nf new file mode 100644 index 00000000..bf65a6a6 --- /dev/null +++ b/tests/modules/gatk4/mergemutectstats/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { GATK4_MERGEMUTECTSTATS } from '../../../../modules/gatk4/mergemutectstats/main.nf' + +workflow test_gatk4_mergemutectstats { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_test2_paired_mutect2_calls_vcf_gz_stats'], checkIfExists: true) + ] + + GATK4_MERGEMUTECTSTATS ( input ) +} diff --git a/tests/modules/gatk4/mergemutectstats/nextflow.config b/tests/modules/gatk4/mergemutectstats/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/gatk4/mergemutectstats/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/gatk4/mergemutectstats/test.yml b/tests/modules/gatk4/mergemutectstats/test.yml new file mode 100644 index 00000000..44d1c5f2 --- /dev/null +++ b/tests/modules/gatk4/mergemutectstats/test.yml @@ -0,0 +1,8 @@ +- name: gatk4 mergemutectstats + command: nextflow run ./tests/modules/gatk4/mergemutectstats -entry test_gatk4_mergemutectstats -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/mergemutectstats/nextflow.config + tags: + - gatk4 + - gatk4/mergemutectstats + files: + - path: output/gatk4/test.vcf.gz.stats + md5sum: 17d2091015d04cbd4a26b7a67dc659e6 diff --git a/tests/modules/gatk4/mutect2/main.nf b/tests/modules/gatk4/mutect2/main.nf index 94cf0416..19b22914 100644 --- a/tests/modules/gatk4/mutect2/main.nf +++ b/tests/modules/gatk4/mutect2/main.nf @@ -12,12 +12,12 @@ workflow test_gatk4_mutect2_tumor_normal_pair { [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) ], + [], ["normal"] ] run_single = false run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -26,19 +26,19 @@ workflow test_gatk4_mutect2_tumor_normal_pair { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_tumor_single { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [], [] ] run_single = true run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -47,19 +47,19 @@ workflow test_gatk4_mutect2_tumor_single { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_cram_input { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true)], + [], [] ] run_single = true run_pon = false run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -68,19 +68,19 @@ workflow test_gatk4_mutect2_cram_input { panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz'], checkIfExists: true) panel_of_normals_tbi = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_21_vcf_gz_tbi'], checkIfExists: true) - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } workflow test_gatk4_mutect2_generate_pon { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [], [] ] run_single = false run_pon = true run_mito = false - interval_label = [] fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) @@ -89,7 +89,7 @@ workflow test_gatk4_mutect2_generate_pon { panel_of_normals = [] panel_of_normals_tbi = [] - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } // mitochondria mode would ideally have some mitochondria test data, but since the mitochondria settings only increase detection sensitivity, we can use the chr22 data as a stand in as it is already a small dataset, the extra variants detected compared to generate_pon shows the mode is working. @@ -97,12 +97,12 @@ workflow test_gatk4_mutect2_mitochondria { input = [ [ id:'test'], // meta map [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam'], checkIfExists: true)], [ file(params.test_data['homo_sapiens']['illumina']['mitochon_standin_recalibrated_sorted_bam_bai'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)], [] ] run_single = false run_pon = false run_mito = true - interval_label = 'chr22' fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true) @@ -111,5 +111,5 @@ workflow test_gatk4_mutect2_mitochondria { panel_of_normals = [] panel_of_normals_tbi = [] - GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, interval_label, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) + GATK4_MUTECT2 ( input, run_single, run_pon, run_mito, fasta, fai, dict, germline_resource, germline_resource_tbi, panel_of_normals, panel_of_normals_tbi ) } diff --git a/tests/modules/gatk4/mutect2/nextflow.config b/tests/modules/gatk4/mutect2/nextflow.config index 0966fc15..8730f1c4 100644 --- a/tests/modules/gatk4/mutect2/nextflow.config +++ b/tests/modules/gatk4/mutect2/nextflow.config @@ -2,8 +2,4 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - withName: GATK4_TEMPFIX_MUTECT2 { - ext.args = '--mitochondria-mode' - } - } diff --git a/tests/modules/gatk4/splitncigarreads/test.yml b/tests/modules/gatk4/splitncigarreads/test.yml index a18fbb04..059d5e75 100644 --- a/tests/modules/gatk4/splitncigarreads/test.yml +++ b/tests/modules/gatk4/splitncigarreads/test.yml @@ -5,6 +5,6 @@ - gatk4/splitncigarreads files: - path: output/gatk4/test.bam - md5sum: 1d54057d9f403fba2068ac1aaa4b8a28 + md5sum: ceed15c0bd64ff5c38d3816905933b0b - path: output/gatk4/versions.yml - md5sum: f0f29af552075dc6bf8a13028e09f8e4 + md5sum: 27fceace2528a905ddca2b4db47c4bf5 diff --git a/tests/modules/gatk4/variantfiltration/test.yml b/tests/modules/gatk4/variantfiltration/test.yml index b5da0e5c..068e8d63 100644 --- a/tests/modules/gatk4/variantfiltration/test.yml +++ b/tests/modules/gatk4/variantfiltration/test.yml @@ -5,7 +5,10 @@ - gatk4 files: - path: output/gatk4/test.filtered.vcf.gz - contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365'] + contains: + [ + "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365", + ] - path: output/gatk4/test.filtered.vcf.gz.tbi - name: gatk4 variantfiltration test_gatk4_variantfiltration_gz_input @@ -15,5 +18,8 @@ - gatk4 files: - path: output/gatk4/test.filtered.vcf.gz - contains: ['BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365'] + contains: + [ + "BaseQRankSum=-1.318;DP=17;ExcessHet=3.0103;MLEAC=1,0,0;MLEAF=0.500,0.00,0.00;MQRankSum=0.000;RAW_MQandDP=61200,17;ReadPosRankSum=2.365", + ] - path: output/gatk4/test.filtered.vcf.gz.tbi diff --git a/tests/modules/gatk4/variantrecalibrator/main.nf b/tests/modules/gatk4/variantrecalibrator/main.nf index bbc1dff5..be7004e7 100644 --- a/tests/modules/gatk4/variantrecalibrator/main.nf +++ b/tests/modules/gatk4/variantrecalibrator/main.nf @@ -2,7 +2,8 @@ nextflow.enable.dsl = 2 -include { GATK4_VARIANTRECALIBRATOR } from '../../../../modules/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' +include { GATK4_VARIANTRECALIBRATOR as GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY } from '../../../../modules/gatk4/variantrecalibrator/main.nf' workflow test_gatk4_variantrecalibrator { @@ -14,7 +15,6 @@ workflow test_gatk4_variantrecalibrator { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = false resources = [ [ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), @@ -35,11 +35,8 @@ workflow test_gatk4_variantrecalibrator { 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] ] - annotation = ['QD', 'MQ', 'FS', 'SOR'] - mode = 'SNP' - create_rscript = false - GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript) + GATK4_VARIANTRECALIBRATOR_NO_ALLELESPECIFICTY ( input, fasta, fai, dict, resources) } workflow test_gatk4_variantrecalibrator_allele_specific { @@ -52,7 +49,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific { fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true) - allelespecific = true resources = [ [ file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true), @@ -73,9 +69,6 @@ workflow test_gatk4_variantrecalibrator_allele_specific { 'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz' ] ] - annotation = ['QD', 'MQ', 'FS'] - mode = 'SNP' - create_rscript = false - GATK4_VARIANTRECALIBRATOR ( input, fasta, fai, dict, allelespecific, resources, annotation, mode, create_rscript) + GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY ( input, fasta, fai, dict, resources) } diff --git a/tests/modules/gatk4/variantrecalibrator/nextflow.config b/tests/modules/gatk4/variantrecalibrator/nextflow.config index 19934e76..69be3b9c 100644 --- a/tests/modules/gatk4/variantrecalibrator/nextflow.config +++ b/tests/modules/gatk4/variantrecalibrator/nextflow.config @@ -1,5 +1,11 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: GATK4_VARIANTRECALIBRATOR { + ext.args = '--mode SNP -an QD -an MQ -an FS -an SOR' + } -} \ No newline at end of file + withName: GATK4_VARIANTRECALIBRATOR_WITH_ALLELESPECIFICTY { + ext.args = '--mode SNP -an QD -an MQ -an FS -AS' + } +} diff --git a/tests/modules/hmmer/hmmalign/main.nf b/tests/modules/hmmer/hmmalign/main.nf index 3bf6d452..8758b124 100644 --- a/tests/modules/hmmer/hmmalign/main.nf +++ b/tests/modules/hmmer/hmmalign/main.nf @@ -8,10 +8,10 @@ workflow test_hmmer_hmmalign { input = [ [ id:'test' ], // meta map - file('https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/modules/data/delete_me/e_coli_k12_16s.fna') // Change to params.test_data syntax after the data is included in tests/config/test_data.config + file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/e_coli_k12_16s.fna') // Change to params.test_data syntax after the data is included in tests/config/test_data.config ] - hmm = file('https://raw.githubusercontent.com/erikrikarddaniel/test-datasets/modules/data/delete_me/bac.16S_rRNA.hmm') + hmm = file('https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/bac.16S_rRNA.hmm') HMMER_HMMALIGN ( input, hmm ) } diff --git a/tests/modules/ichorcna/createpon/main.nf b/tests/modules/ichorcna/createpon/main.nf new file mode 100644 index 00000000..0e86fb92 --- /dev/null +++ b/tests/modules/ichorcna/createpon/main.nf @@ -0,0 +1,30 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { ICHORCNA_CREATEPON } from '../../../../modules/ichorcna/createpon/main.nf' + +workflow test_ichorcna_createpon { + + input = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) + + gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true) + mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true) + + centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true) + + ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere ) +} + +workflow test_ichorcna_createpon2 { + + input = [file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true), + file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315_T2.ctDNA.reads.wig", checkIfExists: true)] + + gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true) + mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true) + + centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true) + + ICHORCNA_CREATEPON ( input, gcwig, mapwig, centromere ) +} diff --git a/tests/modules/ichorcna/createpon/nextflow.config b/tests/modules/ichorcna/createpon/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/ichorcna/createpon/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/ichorcna/createpon/test.yml b/tests/modules/ichorcna/createpon/test.yml new file mode 100644 index 00000000..53422b78 --- /dev/null +++ b/tests/modules/ichorcna/createpon/test.yml @@ -0,0 +1,21 @@ +- name: ichorcna createpon test_ichorcna_createpon + command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon -c tests/config/nextflow.config + tags: + - ichorcna/createpon + - ichorcna + files: + - path: output/ichorcna/PoN_median.txt + contains: ['seqnames'] + - path: output/ichorcna/versions.yml + md5sum: 59a2121301113cc013bfae65935e07f1 + +- name: ichorcna createpon test_ichorcna_createpon2 + command: nextflow run tests/modules/ichorcna/createpon -entry test_ichorcna_createpon2 -c tests/config/nextflow.config + tags: + - ichorcna/createpon + - ichorcna + files: + - path: output/ichorcna/PoN_median.txt + contains: ['seqnames'] + - path: output/ichorcna/versions.yml + md5sum: 31a5fcc0075dbe747f7736efbdb99644 diff --git a/tests/modules/ichorcna/run/main.nf b/tests/modules/ichorcna/run/main.nf new file mode 100644 index 00000000..8a830f62 --- /dev/null +++ b/tests/modules/ichorcna/run/main.nf @@ -0,0 +1,40 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { ICHORCNA_RUN } from '../../../../modules/ichorcna/run/main.nf' +include { HMMCOPY_READCOUNTER } from '../../../../modules/hmmcopy/readcounter/main.nf' +include { HMMCOPY_GCCOUNTER } from '../../../../modules/hmmcopy/gccounter/main.nf' +include { HMMCOPY_MAPCOUNTER } from '../../../../modules/hmmcopy/mapcounter/main.nf' +include { HMMCOPY_GENERATEMAP } from '../../../../modules/hmmcopy/generatemap/main.nf' + +workflow test_ichorcna_run_no_panel { + + input = [ [ id:'test'], // meta map + file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) + ] + + gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true) + mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true) + + panel_of_normals = [] + centromere = [] + + ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere) +} + +workflow test_ichorcna_run_inc_panel { + + input = [ [ id:'test'], // meta map + file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/MBC_315.ctDNA.reads.wig", checkIfExists: true) + ] + + gcwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/gc_hg19_1000kb.wig", checkIfExists: true) + mapwig = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/map_hg19_1000kb.wig", checkIfExists: true) + + panel_of_normals = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds", checkIfExists: true) + + centromere = file("https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt", checkIfExists: true) + + ICHORCNA_RUN ( input, gcwig, mapwig, panel_of_normals, centromere) +} diff --git a/tests/modules/ichorcna/run/nextflow.config b/tests/modules/ichorcna/run/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/ichorcna/run/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/ichorcna/run/test.yml b/tests/modules/ichorcna/run/test.yml new file mode 100644 index 00000000..af78e4b3 --- /dev/null +++ b/tests/modules/ichorcna/run/test.yml @@ -0,0 +1,25 @@ +- name: ichorcna run test_ichorcna_run_no_panel + command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_no_panel -c tests/config/nextflow.config + tags: + - ichorcna + - ichorcna/run + files: + - path: output/ichorcna/test.cna.seg + contains: ['Corrected_Copy_Number'] + - path: output/ichorcna/test.params.txt + md5sum: e39a579cdcc9576679f06dc5c22605a7 + - path: output/ichorcna/versions.yml + md5sum: effb37e19bec3609417aaccad4b6a294 + +- name: ichorcna run test_ichorcna_run_inc_panel + command: nextflow run tests/modules/ichorcna/run -entry test_ichorcna_run_inc_panel -c tests/config/nextflow.config + tags: + - ichorcna + - ichorcna/run + files: + - path: output/ichorcna/test.cna.seg + contains: ['Corrected_Copy_Number'] + - path: output/ichorcna/test.params.txt + md5sum: 0b97e0269cd0b571f5a85890f6ddb181 + - path: output/ichorcna/versions.yml + md5sum: fc9d96de0a1c15cea59208305b14e535 diff --git a/tests/modules/imputeme/vcftoprs/test.yml b/tests/modules/imputeme/vcftoprs/test.yml index e5152a03..89f2d540 100644 --- a/tests/modules/imputeme/vcftoprs/test.yml +++ b/tests/modules/imputeme/vcftoprs/test.yml @@ -5,4 +5,4 @@ - imputeme/vcftoprs files: - path: output/imputeme/output.json - contains: [ 'type_2_diabetes_32541925":{"GRS":[24.01]' ] + contains: ['type_2_diabetes_32541925":{"GRS":[24.01]'] diff --git a/tests/modules/iqtree/test.yml b/tests/modules/iqtree/test.yml index 06de90d9..291472b0 100644 --- a/tests/modules/iqtree/test.yml +++ b/tests/modules/iqtree/test.yml @@ -5,7 +5,7 @@ files: - path: output/iqtree/informative_sites.fas.treefile contains: - - '(sample1:0.002' - - '(sample2:0.005' - - 'sample3:0.0005' - - 'sample4:0.001' + - "(sample1:0.002" + - "(sample2:0.005" + - "sample3:0.0005" + - "sample4:0.001" diff --git a/tests/modules/isoseq3/cluster/test.yml b/tests/modules/isoseq3/cluster/test.yml index b1f12df7..2df3024c 100644 --- a/tests/modules/isoseq3/cluster/test.yml +++ b/tests/modules/isoseq3/cluster/test.yml @@ -25,4 +25,4 @@ - path: output/isoseq3/test.transcripts.singletons.bam.pbi md5sum: 8e0e0681179c0c36209b49fa60783841 - path: output/isoseq3/test.transcripts.transcriptset.xml - contains: [ 'PacBio.DataSet.TranscriptSet' ] + contains: ["PacBio.DataSet.TranscriptSet"] diff --git a/tests/modules/isoseq3/refine/test.yml b/tests/modules/isoseq3/refine/test.yml index f2c63fda..82180ed9 100644 --- a/tests/modules/isoseq3/refine/test.yml +++ b/tests/modules/isoseq3/refine/test.yml @@ -9,7 +9,7 @@ - path: output/isoseq3/test.refine.bam.pbi md5sum: 8097cad9e472f2f79de6de5fe3dcc822 - path: output/isoseq3/test.refine.consensusreadset.xml - contains: [ 'pbds:ConsensusReadSet' ] + contains: ["pbds:ConsensusReadSet"] - path: output/isoseq3/test.refine.filter_summary.json md5sum: 87f8bdd5c60741f47b8a991e002f7ef3 - path: output/isoseq3/test.refine.report.csv diff --git a/tests/modules/khmer/normalizebymedian/test.yml b/tests/modules/khmer/normalizebymedian/test.yml index 0e61588f..f4d687ef 100644 --- a/tests/modules/khmer/normalizebymedian/test.yml +++ b/tests/modules/khmer/normalizebymedian/test.yml @@ -6,9 +6,9 @@ - khmer/normalizebymedian files: - path: output/khmer/only_pe.fastq.gz - # md5sum not stable even locally with docker (gzip done by tool) - #md5sum: 75e05f2e80cf4bd0b534d4b73f7c059c - + # md5sum not stable even locally with docker (gzip done by tool) + # md5sum: 75e05f2e80cf4bd0b534d4b73f7c059c + - name: khmer normalizebymedian only se reads command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_only_se -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config tags: @@ -16,7 +16,7 @@ - khmer/normalizebymedian files: - path: output/khmer/only_se.fastq.gz - + - name: khmer normalizebymedian mixed reads command: nextflow run ./tests/modules/khmer/normalizebymedian -entry test_khmer_normalizebymedian_mixed -c ./tests/config/nextflow.config -c ./tests/modules/khmer/normalizebymedian/nextflow.config tags: diff --git a/tests/modules/kleborate/test.yml b/tests/modules/kleborate/test.yml index 30d854d5..413ac2ae 100644 --- a/tests/modules/kleborate/test.yml +++ b/tests/modules/kleborate/test.yml @@ -4,4 +4,4 @@ - kleborate files: - path: output/kleborate/test.results.txt - contains: ['strain', 'genome', 'scaffolds'] + contains: ["strain", "genome", "scaffolds"] diff --git a/tests/modules/lima/test.yml b/tests/modules/lima/test.yml index 8d927624..2278cc90 100644 --- a/tests/modules/lima/test.yml +++ b/tests/modules/lima/test.yml @@ -8,9 +8,9 @@ - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.bam.pbi md5sum: 6ae7f057304ad17dd9d5f565d72d3f7b - path: output/lima/test.fl.NEB_5p--NEB_Clontech_3p.consensusreadset.xml - contains: [ 'ConsensusReadSet' ] + contains: ["ConsensusReadSet"] - path: output/lima/test.fl.json - contains: [ 'ConsensusReadSet' ] + contains: ["ConsensusReadSet"] - path: output/lima/test.fl.lima.clips md5sum: fa03bc75bd78b2648a139fd67c69208f - path: output/lima/test.fl.lima.counts diff --git a/tests/modules/lissero/test.yml b/tests/modules/lissero/test.yml index 8dd7339e..688cfa82 100644 --- a/tests/modules/lissero/test.yml +++ b/tests/modules/lissero/test.yml @@ -4,4 +4,4 @@ - lissero files: - path: output/lissero/test.tsv - contains: ['ID', 'SEROTYPE', 'FULL'] + contains: ["ID", "SEROTYPE", "FULL"] diff --git a/tests/modules/lofreq/call/test.yml b/tests/modules/lofreq/call/test.yml index b9f42542..c84d08fb 100644 --- a/tests/modules/lofreq/call/test.yml +++ b/tests/modules/lofreq/call/test.yml @@ -5,4 +5,7 @@ - lofreq/call files: - path: output/lofreq/test.vcf.gz - contains: ['##INFO='] + contains: + [ + '##INFO=', + ] diff --git a/tests/modules/lofreq/callparallel/test.yml b/tests/modules/lofreq/callparallel/test.yml index db281012..c21eeaa7 100644 --- a/tests/modules/lofreq/callparallel/test.yml +++ b/tests/modules/lofreq/callparallel/test.yml @@ -5,4 +5,7 @@ - lofreq files: - path: output/lofreq/test.vcf.gz - contains: ['##INFO='] + contains: + [ + '##INFO=', + ] diff --git a/tests/modules/malt/run/test.yml b/tests/modules/malt/run/test.yml index 5b0742e4..335bc977 100644 --- a/tests/modules/malt/run/test.yml +++ b/tests/modules/malt/run/test.yml @@ -6,4 +6,3 @@ files: - path: output/malt/test_1.rma6 - path: output/malt/malt-run.log - diff --git a/tests/modules/manta/germline/main.nf b/tests/modules/manta/germline/main.nf index f8adedb0..bad62629 100644 --- a/tests/modules/manta/germline/main.nf +++ b/tests/modules/manta/germline/main.nf @@ -7,29 +7,46 @@ include { MANTA_GERMLINE } from '../../../../modules/manta/germline/main.nf' workflow test_manta_germline { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = [] - bed_tbi = [] + bed = [[],[]] - MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi ) + MANTA_GERMLINE ( input, fasta, fai, bed ) } workflow test_manta_germline_target_bed { input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true) + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true)], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true)] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + bed = [ + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true), + ] - MANTA_GERMLINE ( input, fasta, fai, bed, bed_tbi ) + MANTA_GERMLINE ( input, fasta, fai, bed ) +} + +workflow test_manta_germline_target_bed_jointcalling { + input = [ + [ id:'test'], // meta map + [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram'], checkIfExists: true)], + [file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_sorted_cram_crai'], checkIfExists: true),] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + bed = [ + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true), + ] + + MANTA_GERMLINE ( input, fasta, fai, bed ) } diff --git a/tests/modules/manta/germline/nextflow.config b/tests/modules/manta/germline/nextflow.config index 8730f1c4..c82e3c5c 100644 --- a/tests/modules/manta/germline/nextflow.config +++ b/tests/modules/manta/germline/nextflow.config @@ -2,4 +2,8 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + withName: MANTA_GERMLINE { + ext.args = '--exome ' + } + } diff --git a/tests/modules/manta/germline/test.yml b/tests/modules/manta/germline/test.yml index c6ead9eb..7ded24ad 100644 --- a/tests/modules/manta/germline/test.yml +++ b/tests/modules/manta/germline/test.yml @@ -22,3 +22,15 @@ - path: output/manta/test.candidate_sv.vcf.gz.tbi - path: output/manta/test.diploid_sv.vcf.gz - path: output/manta/test.diploid_sv.vcf.gz.tbi +- name: manta germline target bed jointcalling + command: nextflow run ./tests/modules/manta/germline -entry test_manta_germline_target_bed_jointcalling -c ./tests/config/nextflow.config -c ./tests/modules/manta/germline/nextflow.config + tags: + - manta + - manta/germline + files: + - path: output/manta/test.candidate_small_indels.vcf.gz + - path: output/manta/test.candidate_small_indels.vcf.gz.tbi + - path: output/manta/test.candidate_sv.vcf.gz + - path: output/manta/test.candidate_sv.vcf.gz.tbi + - path: output/manta/test.diploid_sv.vcf.gz + - path: output/manta/test.diploid_sv.vcf.gz.tbi diff --git a/tests/modules/medaka/test.yml b/tests/modules/medaka/test.yml index 54146bdc..02bd8927 100644 --- a/tests/modules/medaka/test.yml +++ b/tests/modules/medaka/test.yml @@ -4,4 +4,4 @@ - medaka files: - path: output/medaka/test.polished.genome.fa.gz - md5sum: f42303f1d6c2c79175faeb00e10b9a6e \ No newline at end of file + md5sum: f42303f1d6c2c79175faeb00e10b9a6e diff --git a/tests/modules/metaphlan3/test.yml b/tests/modules/metaphlan3/test.yml index 92e731d2..2a3bee01 100644 --- a/tests/modules/metaphlan3/test.yml +++ b/tests/modules/metaphlan3/test.yml @@ -5,7 +5,7 @@ files: - path: output/metaphlan3/test.biom contains: - - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' + - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' - path: output/metaphlan3/test.bowtie2out.txt md5sum: ef46a9c6a8ce9cae26fbfd5527116fd5 - path: output/metaphlan3/test_profile.txt @@ -36,7 +36,7 @@ files: - path: output/metaphlan3/test.biom contains: - - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' + - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' - path: output/metaphlan3/test.bowtie2out.txt md5sum: ce11486fcc0e68fe7152867a3634e09a - path: output/metaphlan3/test_profile.txt @@ -67,7 +67,7 @@ files: - path: output/metaphlan3/test.biom contains: - - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' + - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' - path: output/metaphlan3/test_profile.txt md5sum: e050d49f7df8a23617880ef9ed7745a0 - path: output/samtools/test.sam.bam @@ -98,7 +98,7 @@ files: - path: output/metaphlan3/test.biom contains: - - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' + - '"format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","generated_by"' - path: output/metaphlan3/test.bowtie2out.txt md5sum: fece494a410b8328608a11de10af6396 - path: output/metaphlan3/test_profile.txt diff --git a/tests/modules/minimap2/align/test.yml b/tests/modules/minimap2/align/test.yml index 598a5d25..73dd73e2 100644 --- a/tests/modules/minimap2/align/test.yml +++ b/tests/modules/minimap2/align/test.yml @@ -14,4 +14,4 @@ - minimap2/align files: - path: ./output/minimap2/test.paf - md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28 \ No newline at end of file + md5sum: 5e7b55a26bf0ea3a2843423d3e0b9a28 diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf index 8862204d..ddd68129 100644 --- a/tests/modules/mosdepth/main.nf +++ b/tests/modules/mosdepth/main.nf @@ -7,10 +7,30 @@ include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' workflow test_mosdepth { input = [ [ id:'test', single_end:true ], [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] + + MOSDEPTH ( input, [], [] ) +} + + +workflow test_mosdepth_window { + input = [ [ id:'test', single_end:true ], + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] ] - dummy = file("dummy_file.txt") window = 100 - MOSDEPTH ( input, dummy, window ) + MOSDEPTH ( input, [], window ) +} + + +workflow test_mosdepth_bed { + input = [ [ id:'test', single_end:true ], + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] + bed = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + + MOSDEPTH ( input, bed, [] ) } diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml index e264ef3b..c66e0b89 100644 --- a/tests/modules/mosdepth/test.yml +++ b/tests/modules/mosdepth/test.yml @@ -4,16 +4,50 @@ - mosdepth files: - path: ./output/mosdepth/test.per-base.bed.gz.csi - md5sum: aa68536f55883aa60f4e68ac9b108358 + md5sum: b2aad62c41a7146680d31df505fcc8c5 - path: ./output/mosdepth/test.per-base.bed.gz - md5sum: b5f9c8ca49be6128a486f6b56514a6d0 + md5sum: 11b3f649072c2c7453febb085b1a9c33 + - path: ./output/mosdepth/test.mosdepth.global.dist.txt + md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a + - path: ./output/mosdepth/test.mosdepth.summary.txt + md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d + +- name: mosdepth window + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config + tags: + - mosdepth + files: + - path: ./output/mosdepth/test.per-base.bed.gz.csi + md5sum: b2aad62c41a7146680d31df505fcc8c5 + - path: ./output/mosdepth/test.per-base.bed.gz + md5sum: 11b3f649072c2c7453febb085b1a9c33 - path: ./output/mosdepth/test.mosdepth.global.dist.txt md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a - path: ./output/mosdepth/test.regions.bed.gz - md5sum: 8e020ec602c02d240e0458642cf5ac5a + md5sum: 64e1ced01c4443d7c1796ef553992f0c - path: ./output/mosdepth/test.regions.bed.gz.csi - md5sum: 44aec43fc34785fcbe6d830c907c617a + md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a - path: ./output/mosdepth/test.mosdepth.region.dist.txt md5sum: 65fbc824c4212c6884354d8ac72ad37e - path: ./output/mosdepth/test.mosdepth.summary.txt md5sum: 11804907dab069ddb99ca97bf2698572 + +- name: mosdepth bed + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config + tags: + - mosdepth + files: + - path: ./output/mosdepth/test.per-base.bed.gz.csi + md5sum: b2aad62c41a7146680d31df505fcc8c5 + - path: ./output/mosdepth/test.per-base.bed.gz + md5sum: 11b3f649072c2c7453febb085b1a9c33 + - path: ./output/mosdepth/test.mosdepth.global.dist.txt + md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a + - path: ./output/mosdepth/test.regions.bed.gz + md5sum: 347f877700d1dc42c95157199eff25d5 + - path: ./output/mosdepth/test.regions.bed.gz.csi + md5sum: ed5fbf46e3bdcbf60094df295bc40356 + - path: ./output/mosdepth/test.mosdepth.region.dist.txt + md5sum: 295564628113d2ec0ca34d7f661cfea8 + - path: ./output/mosdepth/test.mosdepth.summary.txt + md5sum: b07817412fd17819c14541e63bc4926c diff --git a/tests/modules/msisensorpro/msi_somatic/main.nf b/tests/modules/msisensorpro/msi_somatic/main.nf new file mode 100644 index 00000000..4516ada5 --- /dev/null +++ b/tests/modules/msisensorpro/msi_somatic/main.nf @@ -0,0 +1,33 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MSISENSORPRO_MSI_SOMATIC } from '../../../../modules/msisensorpro/msi_somatic/main.nf' +include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf' + +workflow test_msisensorpro_msi { + + scan_in = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + + println scan_in + + MSISENSORPRO_SCAN ( scan_in ) + + input = [// meta map + [ id:'test'], + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + [] + ] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + + MSISENSORPRO_SCAN.out.list.map{meta, list -> [list]}.set{list} + MSISENSORPRO_MSI_SOMATIC(input, fasta, list) + + +} diff --git a/tests/modules/msisensorpro/msi_somatic/nextflow.config b/tests/modules/msisensorpro/msi_somatic/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/msisensorpro/msi_somatic/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/msisensorpro/msi_somatic/test.yml b/tests/modules/msisensorpro/msi_somatic/test.yml new file mode 100644 index 00000000..22e7e864 --- /dev/null +++ b/tests/modules/msisensorpro/msi_somatic/test.yml @@ -0,0 +1,18 @@ +- name: msisensorpro msi_somatic test_msisensorpro_msi + command: nextflow run tests/modules/msisensorpro/msi_somatic -entry test_msisensorpro_msi -c tests/config/nextflow.config + tags: + - msisensorpro/msi_somatic + - msisensorpro + files: + - path: output/msisensorpro/test + md5sum: db7f2cc99ea79f79b0ba011c4bcbb43d + - path: output/msisensorpro/test.msisensor_scan.list + md5sum: 309d41b136993db24a9f3dade877753b + - path: output/msisensorpro/test_dis + md5sum: fc3e205b7ca50c9ecf3f70c87781e96f + - path: output/msisensorpro/test_germline + md5sum: ba585b355c08877b8bca4901f49d9311 + - path: output/msisensorpro/test_somatic + md5sum: 836e617ddded07ec1e39089fd595c3d8 + - path: output/msisensorpro/versions.yml + md5sum: b57279502ca6863c5406ed46e6b42994 diff --git a/tests/modules/msisensorpro/scan/main.nf b/tests/modules/msisensorpro/scan/main.nf new file mode 100644 index 00000000..cf57b820 --- /dev/null +++ b/tests/modules/msisensorpro/scan/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { MSISENSORPRO_SCAN } from '../../../../modules/msisensorpro/scan/main.nf' + +workflow test_msisensorpro_scan { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + ] + + MSISENSORPRO_SCAN ( input ) +} diff --git a/tests/modules/msisensorpro/scan/nextflow.config b/tests/modules/msisensorpro/scan/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/msisensorpro/scan/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/msisensorpro/scan/test.yml b/tests/modules/msisensorpro/scan/test.yml new file mode 100644 index 00000000..be5100e2 --- /dev/null +++ b/tests/modules/msisensorpro/scan/test.yml @@ -0,0 +1,10 @@ +- name: msisensorpro scan test_msisensorpro_scan + command: nextflow run tests/modules/msisensorpro/scan -entry test_msisensorpro_scan -c tests/config/nextflow.config + tags: + - msisensorpro + - msisensorpro/scan + files: + - path: output/msisensorpro/test.msisensor_scan.list + md5sum: 309d41b136993db24a9f3dade877753b + - path: output/msisensorpro/versions.yml + md5sum: ed713232c854bce5c74d10097101ed06 diff --git a/tests/modules/nanoplot/test.yml b/tests/modules/nanoplot/test.yml index 6549953e..fc100a12 100644 --- a/tests/modules/nanoplot/test.yml +++ b/tests/modules/nanoplot/test.yml @@ -1,4 +1,3 @@ - - name: nanoplot_summary command: nextflow run ./tests/modules/nanoplot -entry test_nanoplot_summary -c ./tests/config/nextflow.config -c ./tests/modules/nanoplot/nextflow.config tags: diff --git a/tests/modules/nucmer/test.yml b/tests/modules/nucmer/test.yml index 62caced4..cebd0d4e 100644 --- a/tests/modules/nucmer/test.yml +++ b/tests/modules/nucmer/test.yml @@ -4,6 +4,6 @@ - nucmer files: - path: output/nucmer/test.coords - contains: ['MT192765.1'] + contains: ["MT192765.1"] - path: output/nucmer/test.delta - contains: ['MT192765.1'] + contains: ["MT192765.1"] diff --git a/tests/modules/optitype/test.yml b/tests/modules/optitype/test.yml index 7c2ff0d0..bb493077 100644 --- a/tests/modules/optitype/test.yml +++ b/tests/modules/optitype/test.yml @@ -6,4 +6,4 @@ - path: output/optitype/test/test_coverage_plot.pdf - path: output/optitype/test/test_result.tsv contains: - - '1446' + - "1446" diff --git a/tests/modules/pangolin/test.yml b/tests/modules/pangolin/test.yml index 11f715bf..f11c5c1d 100644 --- a/tests/modules/pangolin/test.yml +++ b/tests/modules/pangolin/test.yml @@ -4,4 +4,4 @@ - pangolin files: - path: ./output/pangolin/test.pangolin.csv - md5sum: d92ede51bf3886f696f2089e86189125 + md5sum: 378f211c219bb644dea63adf7c3254fe diff --git a/tests/modules/pbccs/test.yml b/tests/modules/pbccs/test.yml index 5d481923..71549458 100644 --- a/tests/modules/pbccs/test.yml +++ b/tests/modules/pbccs/test.yml @@ -8,8 +8,8 @@ - path: output/pbccs/alz.chunk2.bam.pbi md5sum: 3112cda9744e3facbf38245d41aaf080 - path: output/pbccs/alz.chunk2.metrics.json.gz - contains: [ 'zmws' ] + contains: ["zmws"] - path: output/pbccs/alz.chunk2.report.json - contains: [ 'Created by pbcopper' ] + contains: ["Created by pbcopper"] - path: output/pbccs/alz.chunk2.report.txt md5sum: bbc5bd7a1269345cf7a7f3d4c746024b diff --git a/tests/modules/picard/filtersamreads/test.yml b/tests/modules/picard/filtersamreads/test.yml index a0ab712b..af30d6d2 100644 --- a/tests/modules/picard/filtersamreads/test.yml +++ b/tests/modules/picard/filtersamreads/test.yml @@ -7,7 +7,6 @@ - path: output/picard/test.filtered.bam md5sum: b44a6ca04811a9470c7813c3c9465fd5 - - name: picard filtersamreads readlist command: nextflow run ./tests/modules/picard/filtersamreads -entry test_picard_filtersamreads_readlist -c ./tests/config/nextflow.config -c ./tests/modules/picard/filtersamreads/nextflow.config tags: diff --git a/tests/modules/picard/markduplicates/test.yml b/tests/modules/picard/markduplicates/test.yml index beb54009..cfb5b5de 100644 --- a/tests/modules/picard/markduplicates/test.yml +++ b/tests/modules/picard/markduplicates/test.yml @@ -18,4 +18,3 @@ contains: - "1.0 97 97" - path: ./output/picard/test.bam - diff --git a/tests/modules/pirate/test.yml b/tests/modules/pirate/test.yml index b8d36b95..6ef9e6e0 100644 --- a/tests/modules/pirate/test.yml +++ b/tests/modules/pirate/test.yml @@ -4,23 +4,23 @@ - pirate files: - path: output/pirate/results/PIRATE.gene_families.ordered.tsv - contains: ['allele_name'] + contains: ["allele_name"] - path: output/pirate/results/PIRATE.gene_families.tsv - contains: ['allele_name'] + contains: ["allele_name"] - path: output/pirate/results/PIRATE.genomes_per_allele.tsv - contains: ['g0197'] + contains: ["g0197"] - path: output/pirate/results/PIRATE.log - contains: ['PIRATE input options'] + contains: ["PIRATE input options"] - path: output/pirate/results/PIRATE.pangenome_summary.txt md5sum: 4551c291bc06b21f984f25c09329ed7d - path: output/pirate/results/PIRATE.unique_alleles.tsv - contains: ['allele_name'] + contains: ["allele_name"] - path: output/pirate/results/binary_presence_absence.fasta - contains: ['GCF_000292685'] + contains: ["GCF_000292685"] - path: output/pirate/results/binary_presence_absence.nwk md5sum: 5b5d86bf97d97de37bb9db514abb7762 - path: output/pirate/results/cluster_alleles.tab - contains: ['g0001'] + contains: ["g0001"] - path: output/pirate/results/co-ords/GCF_000292685.co-ords.tab md5sum: d5ca0f06ca7ea1f5486683d5859bc9b8 - path: output/pirate/results/co-ords/GCF_000298385.co-ords.tab @@ -32,9 +32,9 @@ - path: output/pirate/results/genome_list.txt md5sum: 6534b1635c258ad92b829077addc1ff5 - path: output/pirate/results/link_clusters.log - contains: ['parsing paralog file'] + contains: ["parsing paralog file"] - path: output/pirate/results/loci_list.tab - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/loci_paralog_categories.tab md5sum: 6404d2a32526a398f42d7da768a389bd - path: output/pirate/results/modified_gffs/GCF_000292685.gff @@ -46,40 +46,40 @@ - path: output/pirate/results/pan_sequences.fasta md5sum: ed835c77fdb20c36aa9d5208eb7ca0cb - path: output/pirate/results/pangenome.connected_blocks.tsv - contains: ['block_number'] + contains: ["block_number"] - path: output/pirate/results/pangenome.edges - contains: ['g0259'] + contains: ["g0259"] - path: output/pirate/results/pangenome.gfa - contains: ['g0001'] + contains: ["g0001"] - path: output/pirate/results/pangenome.order.tsv - contains: ['g0172'] + contains: ["g0172"] - path: output/pirate/results/pangenome.reversed.tsv md5sum: b2396ce09a6e4178761eca6dc7f4434f - path: output/pirate/results/pangenome.syntenic_blocks.tsv - contains: ['g0091'] + contains: ["g0091"] - path: output/pirate/results/pangenome.temp - path: output/pirate/results/pangenome_iterations/pan_sequences.50.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.60.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.70.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.80.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.90.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.95.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.98.reclustered.reinflated - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.blast.output md5sum: 9da25d27684bfcc5488987ab2d1fd3a1 - path: output/pirate/results/pangenome_iterations/pan_sequences.cdhit_clusters - contains: ['GCF_000298385_00081'] + contains: ["GCF_000298385_00081"] - path: output/pirate/results/pangenome_iterations/pan_sequences.core_clusters.tab - contains: ['GCF_000298385_00242'] + contains: ["GCF_000298385_00242"] - path: output/pirate/results/pangenome_iterations/pan_sequences.mcl_log.txt - contains: ['chaos'] + contains: ["chaos"] - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta md5sum: 84668b6c65b57026a17a50b0edd02541 - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pdb @@ -87,12 +87,12 @@ - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.ptf - path: output/pirate/results/pangenome_iterations/pan_sequences.representative.fasta.pto - path: output/pirate/results/pangenome_log.txt - contains: ['Creating pangenome on amino acid'] + contains: ["Creating pangenome on amino acid"] - path: output/pirate/results/paralog_clusters.tab - contains: ['g0216'] + contains: ["g0216"] - path: output/pirate/results/representative_sequences.faa - contains: ['representative_genome'] + contains: ["representative_genome"] - path: output/pirate/results/representative_sequences.ffn - contains: ['representative_genome'] + contains: ["representative_genome"] - path: output/pirate/results/split_groups.log - contains: ['g0213'] + contains: ["g0213"] diff --git a/tests/modules/qcat/test.yml b/tests/modules/qcat/test.yml index 47ece983..04ddacff 100644 --- a/tests/modules/qcat/test.yml +++ b/tests/modules/qcat/test.yml @@ -5,4 +5,4 @@ files: - path: ./output/qcat/fastq/barcode06.fastq.gz - path: ./output/qcat/fastq/barcode12.fastq.gz - - path: ./output/qcat/fastq/none.fastq.gz \ No newline at end of file + - path: ./output/qcat/fastq/none.fastq.gz diff --git a/tests/modules/qualimap/bamqc/main.nf b/tests/modules/qualimap/bamqc/main.nf index a17efd59..623634e4 100644 --- a/tests/modules/qualimap/bamqc/main.nf +++ b/tests/modules/qualimap/bamqc/main.nf @@ -8,8 +8,7 @@ workflow test_qualimap_bamqc { input = [ [ id:'test', single_end:false ], // meta map [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ] ] - gff = file("dummy_file.txt") - use_gff = false + gff = [] - QUALIMAP_BAMQC ( input, gff, use_gff ) + QUALIMAP_BAMQC ( input, gff ) } diff --git a/tests/modules/qualimap/bamqccram/main.nf b/tests/modules/qualimap/bamqccram/main.nf new file mode 100644 index 00000000..e4d8433e --- /dev/null +++ b/tests/modules/qualimap/bamqccram/main.nf @@ -0,0 +1,17 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { QUALIMAP_BAMQCCRAM } from '../../../../modules/qualimap/bamqccram/main.nf' + +workflow test_qualimap_bamqc { + input = [ [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) + ] + gff = [] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) + + QUALIMAP_BAMQCCRAM ( input, gff, fasta, fai ) +} diff --git a/tests/modules/qualimap/bamqccram/nextflow.config b/tests/modules/qualimap/bamqccram/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/qualimap/bamqccram/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/qualimap/bamqccram/test.yml b/tests/modules/qualimap/bamqccram/test.yml new file mode 100644 index 00000000..49cf9b24 --- /dev/null +++ b/tests/modules/qualimap/bamqccram/test.yml @@ -0,0 +1,80 @@ +- name: qualimap bamqccram test_qualimap_bamqc + command: nextflow run tests/modules/qualimap/bamqccram -entry test_qualimap_bamqc -c tests/config/nextflow.config + tags: + - qualimap/bamqccram + - qualimap + files: + - path: ./output/qualimap/test/qualimapReport.html + - path: ./output/qualimap/test/genome_results.txt + md5sum: 61d8b36507652fd7d7db9583de708161 + - path: ./output/qualimap/test/css/plus.png + md5sum: 0125e6faa04e2cf0141a2d599d3bb220 + - path: ./output/qualimap/test/css/down-pressed.png + md5sum: ebe8979581eda700fb234a73c661a4b9 + - path: ./output/qualimap/test/css/underscore.js + md5sum: db5ba047a66617d4cd3e8c5099cc51db + - path: ./output/qualimap/test/css/ajax-loader.gif + md5sum: ae6667053ad118020b8e68ccf307b519 + - path: ./output/qualimap/test/css/searchtools.js + md5sum: d550841adeedc8ed47c40ee607620937 + - path: ./output/qualimap/test/css/up.png + - path: ./output/qualimap/test/css/file.png + - path: ./output/qualimap/test/css/up-pressed.png + - path: ./output/qualimap/test/css/down.png + - path: ./output/qualimap/test/css/minus.png + - path: ./output/qualimap/test/css/bgtop.png + - path: ./output/qualimap/test/css/comment.png + - path: ./output/qualimap/test/css/basic.css + md5sum: 25b2823342c0604924a2870eeb4e7e94 + - path: ./output/qualimap/test/css/report.css + md5sum: 7a5f09eaf7c176f966f4e8854168b812 + - path: ./output/qualimap/test/css/pygments.css + md5sum: d625a0adb949f181bd0d3f1432b0fa7f + - path: ./output/qualimap/test/css/comment-close.png + - path: ./output/qualimap/test/css/doctools.js + md5sum: 5ff571aa60e63f69c1890283e240ff8d + - path: ./output/qualimap/test/css/comment-bright.png + - path: ./output/qualimap/test/css/qualimap_logo_small.png + - path: ./output/qualimap/test/css/websupport.js + md5sum: 9e61e1e8a7433c56bd7e5a615affcf85 + - path: ./output/qualimap/test/css/agogo.css + md5sum: bd757b1a7ce6fdc0288ba148680f4583 + - path: ./output/qualimap/test/css/bgfooter.png + - path: ./output/qualimap/test/css/jquery.js + md5sum: 10092eee563dec2dca82b77d2cf5a1ae + - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_histogram.txt + md5sum: b7aeda7558e9b31f027f7dc530df90b8 + - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_nucleotide_content.txt + md5sum: 42774c6edd6e36538acbdb6ffbd019c2 + - path: ./output/qualimap/test/raw_data_qualimapReport/genome_fraction_coverage.txt + md5sum: 972a19d4846bf4e93ba32ae3dff5289c + - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_histogram.txt + md5sum: 4e3918da81202b52395a576f99c1a50f + - path: ./output/qualimap/test/raw_data_qualimapReport/insert_size_across_reference.txt + - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_histogram.txt + md5sum: 353e74d2a6c4281686c9063de570a64d + - path: ./output/qualimap/test/raw_data_qualimapReport/mapping_quality_across_reference.txt + md5sum: 9bf33149528be9a0e154e4ba7cb89420 + - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_gc-content_distribution.txt + md5sum: be36d9346a402ba580718497d5075d06 + - path: ./output/qualimap/test/raw_data_qualimapReport/homopolymer_indels.txt + md5sum: b0e19fcfb60e5f039eb0986ef61ab3ed + - path: ./output/qualimap/test/raw_data_qualimapReport/duplication_rate_histogram.txt + md5sum: 76e80e4ce8d0e01bbd65f1c28f5a92e7 + - path: ./output/qualimap/test/raw_data_qualimapReport/coverage_across_reference.txt + md5sum: b609d33a1f98d24aa84a04e60513cbee + - path: ./output/qualimap/test/raw_data_qualimapReport/mapped_reads_clipping_profile.txt + md5sum: 7c86f7b225b99bc60008d7e4e55d6adb + - path: ./output/qualimap/test/images_qualimapReport/genome_reads_content_per_read_position.png + - path: ./output/qualimap/test/images_qualimapReport/genome_gc_content_per_window.png + - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_0to50_histogram.png + - path: ./output/qualimap/test/images_qualimapReport/genome_uniq_read_starts_histogram.png + - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_across_reference.png + - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_histogram.png + - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_across_reference.png + - path: ./output/qualimap/test/images_qualimapReport/genome_homopolymer_indels.png + - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_histogram.png + - path: ./output/qualimap/test/images_qualimapReport/genome_mapping_quality_histogram.png + - path: ./output/qualimap/test/images_qualimapReport/genome_insert_size_across_reference.png + - path: ./output/qualimap/test/images_qualimapReport/genome_reads_clipping_profile.png + - path: ./output/qualimap/test/images_qualimapReport/genome_coverage_quotes.png diff --git a/tests/modules/raxmlng/test.yml b/tests/modules/raxmlng/test.yml index 735b6a74..8054adac 100644 --- a/tests/modules/raxmlng/test.yml +++ b/tests/modules/raxmlng/test.yml @@ -5,10 +5,10 @@ files: - path: output/raxmlng/output.raxml.bestTree contains: - - 'sample1:0.359' - - 'sample2:1.50' - - 'sample3:0.000001' - - 'sample4:0.111' + - "sample1:0.359" + - "sample2:1.50" + - "sample3:0.000001" + - "sample4:0.111" - name: raxmlng bootstrap command: nextflow run ./tests/modules/raxmlng -entry test_raxmlng_bootstrap -c ./tests/config/nextflow.config -c ./tests/modules/raxmlng/nextflow.config @@ -17,15 +17,15 @@ files: - path: output/raxmlng/output.raxml.bestTree contains: - - 'sample1:0.359' - - 'sample2:1.50' - - 'sample3:0.000001' - - 'sample4:0.111' + - "sample1:0.359" + - "sample2:1.50" + - "sample3:0.000001" + - "sample4:0.111" - path: output/raxmlng/output.raxml.support contains: - - 'sample1:0.359' - - 'sample2:1.50' - - 'sample3:0.000001' - - 'sample4:0.111' + - "sample1:0.359" + - "sample2:1.50" + - "sample3:0.000001" + - "sample4:0.111" contains_regex: - '\)[89]\d:' diff --git a/tests/modules/roary/test.yml b/tests/modules/roary/test.yml index 981ab51c..11bdf2c7 100644 --- a/tests/modules/roary/test.yml +++ b/tests/modules/roary/test.yml @@ -4,36 +4,39 @@ - roary files: - path: output/roary/results/accessory.header.embl - contains: ['ID Genome standard; DNA; PRO; 1234 BP.'] + contains: ["ID Genome standard; DNA; PRO; 1234 BP."] - path: output/roary/results/accessory.tab - contains: ['FT'] + contains: ["FT"] - path: output/roary/results/accessory_binary_genes.fa md5sum: d4191cf748dd8016ad877857a034bef3 - path: output/roary/results/accessory_binary_genes.fa.newick md5sum: d4a2a64e781263ca1b9b3a4bc9d3a6ea - path: output/roary/results/accessory_graph.dot - contains: ['/* list of nodes */'] + contains: ["/* list of nodes */"] - path: output/roary/results/blast_identity_frequency.Rtab md5sum: 829baa25c3fad94b1af207265452a692 - path: output/roary/results/clustered_proteins - contains: ['JKHLNHAL_00087'] + contains: ["JKHLNHAL_00087"] - path: output/roary/results/core_accessory.header.embl - contains: ['ID Genome standard; DNA; PRO; 1234 BP.'] + contains: ["ID Genome standard; DNA; PRO; 1234 BP."] - path: output/roary/results/core_accessory.tab contains: ['FT /taxa="test1 test2 test3"'] - path: output/roary/results/core_accessory_graph.dot - contains: ['/* list of nodes */'] + contains: ["/* list of nodes */"] - path: output/roary/results/gene_presence_absence.Rtab - contains: ['Gene'] + contains: ["Gene"] - path: output/roary/results/gene_presence_absence.csv - contains: ['"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"'] + contains: + [ + '"Gene","Non-unique Gene name","Annotation","No. isolates","No. sequences"', + ] - path: output/roary/results/number_of_conserved_genes.Rtab - contains: ['279'] + contains: ["279"] - path: output/roary/results/number_of_genes_in_pan_genome.Rtab - contains: ['279'] + contains: ["279"] - path: output/roary/results/number_of_new_genes.Rtab - contains: ['279'] + contains: ["279"] - path: output/roary/results/number_of_unique_genes.Rtab - contains: ['279'] + contains: ["279"] - path: output/roary/results/summary_statistics.txt md5sum: 3921b5445df6a7ed59408119b8860a58 diff --git a/tests/modules/seacr/callpeak/test.yml b/tests/modules/seacr/callpeak/test.yml index 63104bd0..83c1c59a 100644 --- a/tests/modules/seacr/callpeak/test.yml +++ b/tests/modules/seacr/callpeak/test.yml @@ -14,4 +14,4 @@ - seacr/callpeak files: - path: output/seacr/test_1.stringent.bed - md5sum: 1d23015c7087f7b48cc3139d53fd3463 \ No newline at end of file + md5sum: 1d23015c7087f7b48cc3139d53fd3463 diff --git a/tests/modules/seqsero2/test.yml b/tests/modules/seqsero2/test.yml index e2dec062..0ebb7324 100644 --- a/tests/modules/seqsero2/test.yml +++ b/tests/modules/seqsero2/test.yml @@ -6,6 +6,6 @@ - path: output/seqsero2/results/SeqSero_log.txt md5sum: d00242dfa734b5abb3622a6048f0b4fb - path: output/seqsero2/results/SeqSero_result.tsv - contains: ['Sample', 'Predicted', 'Note'] + contains: ["Sample", "Predicted", "Note"] - path: output/seqsero2/results/SeqSero_result.txt - contains: ['Sample', 'Predicted', 'Note'] + contains: ["Sample", "Predicted", "Note"] diff --git a/tests/modules/seqtk/rename/main.nf b/tests/modules/seqtk/rename/main.nf new file mode 100644 index 00000000..1f81352d --- /dev/null +++ b/tests/modules/seqtk/rename/main.nf @@ -0,0 +1,19 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SEQTK_RENAME } from '../../../../modules/seqtk/rename/main.nf' + +workflow test_seqtk_rename { + input = [ [ id:'test' ], // meta map + [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ] + ] + SEQTK_RENAME ( input ) +} + +workflow test_seqtk_rename_fq { + input = [ [ id:'test' ], // meta map + [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ] + ] + SEQTK_RENAME ( input ) +} diff --git a/tests/modules/seqtk/rename/nextflow.config b/tests/modules/seqtk/rename/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/seqtk/rename/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/seqtk/rename/test.yml b/tests/modules/seqtk/rename/test.yml new file mode 100644 index 00000000..75e919d9 --- /dev/null +++ b/tests/modules/seqtk/rename/test.yml @@ -0,0 +1,21 @@ +- name: seqtk rename test_seqtk_rename + command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename -c tests/config/nextflow.config + tags: + - seqtk + - seqtk/rename + files: + - path: output/seqtk/test.renamed.fasta.gz + md5sum: 7b407952dcf0d925f1996e04a201d05b + - path: output/seqtk/versions.yml + md5sum: 24127592f1b9e5ee8e5ab04ee748c491 + +- name: seqtk rename test_seqtk_rename_fq + command: nextflow run tests/modules/seqtk/rename -entry test_seqtk_rename_fq -c tests/config/nextflow.config + tags: + - seqtk + - seqtk/rename + files: + - path: output/seqtk/test.renamed.fastq.gz + md5sum: babdfc2a3940a1e32a63479db2c1d600 + - path: output/seqtk/versions.yml + md5sum: 06c19670eb2b4185e8f4fa5dcf8fb0d5 diff --git a/tests/modules/snpsites/test.yml b/tests/modules/snpsites/test.yml index d9c19cd5..9d80dd51 100644 --- a/tests/modules/snpsites/test.yml +++ b/tests/modules/snpsites/test.yml @@ -6,4 +6,4 @@ - path: output/snpsites/filtered_alignment.fas md5sum: f96c7513003e878e16fa9eac9fcda0f4 - path: output/snpsites/constant.sites.txt - md5sum: 8b9b226e3787f7baaefce07405af22c9 \ No newline at end of file + md5sum: 8b9b226e3787f7baaefce07405af22c9 diff --git a/tests/modules/sourmash/sketch/main.nf b/tests/modules/sourmash/sketch/main.nf new file mode 100644 index 00000000..c9288c59 --- /dev/null +++ b/tests/modules/sourmash/sketch/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { SOURMASH_SKETCH } from '../../../../modules/sourmash/sketch/main.nf' + +workflow test_sourmash_sketch { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) + ] + + SOURMASH_SKETCH ( input ) +} diff --git a/tests/modules/sourmash/sketch/nextflow.config b/tests/modules/sourmash/sketch/nextflow.config new file mode 100644 index 00000000..50f50a7a --- /dev/null +++ b/tests/modules/sourmash/sketch/nextflow.config @@ -0,0 +1,5 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + +} \ No newline at end of file diff --git a/tests/modules/sourmash/sketch/test.yml b/tests/modules/sourmash/sketch/test.yml new file mode 100644 index 00000000..5bd18967 --- /dev/null +++ b/tests/modules/sourmash/sketch/test.yml @@ -0,0 +1,10 @@ +- name: sourmash sketch test_sourmash_sketch + command: nextflow run tests/modules/sourmash/sketch -entry test_sourmash_sketch -c tests/config/nextflow.config + tags: + - sourmash + - sourmash/sketch + files: + - path: output/sourmash/test.sig + md5sum: 4b0dee307e35fc670cd0d416321e4961 + - path: output/sourmash/versions.yml + md5sum: ec70dabc3e4b3bf11d39c17a99ca4bc6 diff --git a/tests/modules/strelka/germline/main.nf b/tests/modules/strelka/germline/main.nf index c50d76e1..312a4f72 100644 --- a/tests/modules/strelka/germline/main.nf +++ b/tests/modules/strelka/germline/main.nf @@ -9,28 +9,29 @@ workflow test_strelka_germline { [ id:'test'], // meta map file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + [], + [] ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - target_bed = [] - target_bed_tbi = [] + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi ) + STRELKA_GERMLINE ( input, fasta, fai) } workflow test_strelka_germline_target_bed { + input = [ [ id:'test'], // meta map - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - target_bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - target_bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_GERMLINE ( input, fasta, fai, target_bed, target_bed_tbi ) + STRELKA_GERMLINE ( input, fasta, fai) } diff --git a/tests/modules/strelka/germline/nextflow.config b/tests/modules/strelka/germline/nextflow.config index 8730f1c4..5983e1b8 100644 --- a/tests/modules/strelka/germline/nextflow.config +++ b/tests/modules/strelka/germline/nextflow.config @@ -1,5 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - + withName: STRELKA_GERMLINE { + ext.args = '--exome' + } } diff --git a/tests/modules/strelka/somatic/main.nf b/tests/modules/strelka/somatic/main.nf index b1d4efeb..ab75f0e2 100644 --- a/tests/modules/strelka/somatic/main.nf +++ b/tests/modules/strelka/somatic/main.nf @@ -12,18 +12,19 @@ workflow test_strelka_somatic { file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), - [],[] + [],[], + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_SOMATIC (input, fasta, fai, bed, bed_tbi ) + STRELKA_SOMATIC (input, fasta, fai ) } -workflow test_strelka__best_practices_somatic { +workflow test_strelka_best_practices_somatic { + input = [ [ id:'test', single_end:false ], // meta map @@ -31,14 +32,14 @@ workflow test_strelka__best_practices_somatic { file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram'], checkIfExists: true), file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_cram_crai'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz'], checkIfExists: true), - file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_gz_tbi'], checkIfExists: true) + file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz_tbi'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed_gz_tbi'], checkIfExists: true) ] - fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) - fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true) - bed = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true) - bed_tbi = file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true) + fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true) + fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true) - STRELKA_SOMATIC ( input, fasta, fai, bed, bed_tbi ) + STRELKA_SOMATIC ( input, fasta, fai ) } diff --git a/tests/modules/strelka/somatic/nextflow.config b/tests/modules/strelka/somatic/nextflow.config index 8730f1c4..5676ba15 100644 --- a/tests/modules/strelka/somatic/nextflow.config +++ b/tests/modules/strelka/somatic/nextflow.config @@ -1,5 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - + withName: STRELKA_SOMATIC { + ext.args = '--exome' + } } diff --git a/tests/modules/strelka/somatic/test.yml b/tests/modules/strelka/somatic/test.yml index a56f955a..787f3b19 100644 --- a/tests/modules/strelka/somatic/test.yml +++ b/tests/modules/strelka/somatic/test.yml @@ -6,20 +6,16 @@ files: - path: output/strelka/test.somatic_indels.vcf.gz - path: output/strelka/test.somatic_indels.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - path: output/strelka/test.somatic_snvs.vcf.gz - path: output/strelka/test.somatic_snvs.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 -- name: strelka somatic test_strelka__best_practices_somatic - command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka__best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config +- name: strelka somatic test_strelka_best_practices_somatic + command: nextflow run ./tests/modules/strelka/somatic -entry test_strelka_best_practices_somatic -c ./tests/config/nextflow.config -c ./tests/modules/strelka/somatic/nextflow.config tags: - strelka - strelka/somatic files: - path: output/strelka/test.somatic_indels.vcf.gz - path: output/strelka/test.somatic_indels.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 - path: output/strelka/test.somatic_snvs.vcf.gz - path: output/strelka/test.somatic_snvs.vcf.gz.tbi - md5sum: 4cb176febbc8c26d717a6c6e67b9c905 diff --git a/tests/modules/tbprofiler/profile/test.yml b/tests/modules/tbprofiler/profile/test.yml index 8b40f1fa..6e30b784 100644 --- a/tests/modules/tbprofiler/profile/test.yml +++ b/tests/modules/tbprofiler/profile/test.yml @@ -6,7 +6,7 @@ files: - path: output/tbprofiler/bam/test.bam - path: output/tbprofiler/results/test.results.json - contains: ['genome_positions', 'locus_tag', 'tbprofiler_version'] + contains: ["genome_positions", "locus_tag", "tbprofiler_version"] - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz - name: tbprofiler profile nanopore @@ -17,5 +17,5 @@ files: - path: output/tbprofiler/bam/test.bam - path: output/tbprofiler/results/test.results.json - contains: ['genome_positions', 'locus_tag', 'tbprofiler_version'] + contains: ["genome_positions", "locus_tag", "tbprofiler_version"] - path: output/tbprofiler/vcf/test.targets.csq.vcf.gz diff --git a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml index 63cf64f8..2ce7c595 100644 --- a/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml +++ b/tests/subworkflows/nf-core/gatk_create_som_pon/test.yml @@ -8,7 +8,7 @@ # - gatk4/genomicsdbimport # - gatk4/createsomaticpanelofnormals files: - # gatk4 mutect2 + # gatk4 mutect2 - path: output/gatk4/test1.vcf.gz - path: output/gatk4/test1.vcf.gz.stats md5sum: 4f77301a125913170b8e9e7828b4ca3f diff --git a/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml b/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml index 4b335065..759f4ed3 100644 --- a/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml +++ b/tests/subworkflows/nf-core/gatk_tumor_normal_somatic_variant_calling/test.yml @@ -10,7 +10,7 @@ # - gatk4/calculatecontamination # - gatk4/filtermutectcalls files: - # gatk4 mutect2 + # gatk4 mutect2 - path: ./output/mutect2/test.vcf.gz - path: ./output/mutect2/test.vcf.gz.stats md5sum: 6ecb874e6a95aa48233587b876c2a7a9 diff --git a/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml b/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml index 9d2d5c10..5248f2ea 100644 --- a/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml +++ b/tests/subworkflows/nf-core/gatk_tumor_only_somatic_variant_calling/test.yml @@ -9,7 +9,7 @@ # - gatk4/calculatecontamination # - gatk4/filtermutectcalls files: - # gatk4 mutect2 + # gatk4 mutect2 - path: ./output/mutect2/test.vcf.gz - path: ./output/mutect2/test.vcf.gz.stats md5sum: 106c5828b02b906c97922618b6072169