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/meta.yml b/modules/bakta/meta.yml index 29e6edbe..b2bbbf7a 100644 --- a/modules/bakta/meta.yml +++ b/modules/bakta/meta.yml @@ -11,7 +11,7 @@ tools: 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: 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/meta.yml b/modules/biobambam/bammarkduplicates2/meta.yml index c916517b..52e2eb75 100644 --- a/modules/biobambam/bammarkduplicates2/meta.yml +++ b/modules/biobambam/bammarkduplicates2/meta.yml @@ -1,44 +1,44 @@ name: biobambam_bammarkduplicates2 description: Locate and tag duplicate reads in a BAM file keywords: - - markduplicates - - bam - - cram + - 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'] + - 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}" + - 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" + - 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" + - "@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/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/meta.yml b/modules/freebayes/meta.yml index e9fb54c2..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: @@ -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/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/meta.yml b/modules/gatk4/applyvqsr/meta.yml index 746d22ac..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: 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/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/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/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/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/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/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/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/genotypegvcfs/meta.yml b/modules/gatk4/genotypegvcfs/meta.yml index 2c9767b2..e0550687 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: diff --git a/modules/gatk4/getpileupsummaries/meta.yml b/modules/gatk4/getpileupsummaries/meta.yml index ccf6446d..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: 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/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/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/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/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/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/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/meta.yml b/modules/gatk4/mutect2/meta.yml index 94ce72ee..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: 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/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/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/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/meta.yml b/modules/gatk4/variantrecalibrator/meta.yml index aac44b3a..92416a58 100644 --- a/modules/gatk4/variantrecalibrator/meta.yml +++ b/modules/gatk4/variantrecalibrator/meta.yml @@ -45,6 +45,10 @@ input: type: file description: GATK sequence dictionary pattern: "*.dict" + - allelespecific: + type: boolean + description: specify whether to use allele specific annotations + pattern: "{true,false}" - resvcfs: type: list description: resource files to be used as truth, training and known sites resources, this imports the files into the module, file names are specified again in the resource_labels to be called via the command. @@ -53,6 +57,22 @@ input: type: list description: tbis for the corresponding vcfs files to be used as truth, training and known resources. pattern: '*/hapmap_3.3.hg38_chr21.vcf.gz.tbi' + - reslabels: + type: list + description: labels for the resource files to be used as truth, training and known sites resources, label should include an identifier,which kind of resource(s) it is, prior value and name of the file. + pattern: "hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38_chr21.vcf.gz" + - annotation: + type: list + description: specify which annotations should be used for calculations. + pattern: "['QD', 'MQ', 'FS', 'SOR']" + - mode: + type: string + description: specifies which recalibration mode to employ (SNP is default, BOTH is intended for testing only) + pattern: "{SNP,INDEL,BOTH}" + - rscript: + type: boolean + description: specify whether to generate rscript.plot output file + pattern: "{true,false}" output: - recal: type: file 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/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/meta.yml b/modules/manta/germline/meta.yml index b74a9693..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: 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/meta.yml b/modules/mosdepth/meta.yml index 0ca7bce9..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 @@ -73,6 +73,6 @@ output: description: File containing software versions pattern: "versions.yml" authors: - - "@joseespinosa" - - "@drpatelh" - - "@ramprasadn" + - "@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/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/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/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/meta.yml b/modules/qualimap/bamqc/meta.yml index 6888d30e..cf7cfb4f 100644 --- a/modules/qualimap/bamqc/meta.yml +++ b/modules/qualimap/bamqc/meta.yml @@ -1,50 +1,50 @@ 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}" + - use_gff: + type: boolean + description: Specifies if feature file should be used or not 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/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 8ea78f47..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 ] - - fastq: - 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: + - 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: BAM/CRAM file from alignment - pattern: "*.{bam,cram}" - - input_index: + description: File containing samtools stats output + pattern: "*.{stats}" + - versions: 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" + 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/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/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/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/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/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/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/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/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/gatk4/calculatecontamination/test.yml b/tests/modules/gatk4/calculatecontamination/test.yml index 4b73851d..4cd44281 100644 --- a/tests/modules/gatk4/calculatecontamination/test.yml +++ b/tests/modules/gatk4/calculatecontamination/test.yml @@ -4,9 +4,9 @@ - gatk4 - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table + - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: output/gatk4/versions.yml + - path: output/gatk4/versions.yml md5sum: 3da8f1c0de968886330a3f7a3a1c6616 - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_matched_pair @@ -15,9 +15,9 @@ - gatk4 - gatk4/calculatecontamination files: - - path: output/gatk4/test.contamination.table + - path: output/gatk4/test.contamination.table md5sum: 46c708c943b453da89a3da08acfdb2a7 - - path: output/gatk4/versions.yml + - path: output/gatk4/versions.yml md5sum: 14ab12a71b0c2b87d8cd53639a991b3a - name: gatk4 calculatecontamination test_gatk4_calculatecontamination_segmentation @@ -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 + - path: output/gatk4/versions.yml md5sum: d2e61315de31f512e448f0cb4b77db54 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/test.yml b/tests/modules/gatk4/getpileupsummaries/test.yml index e3b25227..e305d412 100644 --- a/tests/modules/gatk4/getpileupsummaries/test.yml +++ b/tests/modules/gatk4/getpileupsummaries/test.yml @@ -6,7 +6,7 @@ files: - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - - path: output/gatk4/versions.yml + - path: output/gatk4/versions.yml md5sum: 059123619f3ed8d4cd178c4390b81e69 - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites @@ -15,9 +15,9 @@ - gatk4/getpileupsummaries - gatk4 files: - - path: output/gatk4/test.pileups.table + - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - - path: output/gatk4/versions.yml + - path: output/gatk4/versions.yml md5sum: 76b5388b0c5b5762d8d33e34b23f181d - name: gatk4 getpileupsummaries test_gatk4_getpileupsummaries_separate_sites_cram @@ -26,7 +26,7 @@ - gatk4/getpileupsummaries - gatk4 files: - - path: output/gatk4/test.pileups.table + - path: output/gatk4/test.pileups.table md5sum: 8e0ca6f66e112bd2f7ec1d31a2d62469 - - path: output/gatk4/versions.yml + - path: output/gatk4/versions.yml md5sum: 2fa51319c2b1d678ee00ab09512cf268 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/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/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/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/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/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/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/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