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Add module BCFTOOLS_PLUGINFIXPLOIDY (#10276)
* Add BCFTOOLS_PLUGINFIXPLOIDY * run linter * nf-core module lint * Add tests * reviewer comments
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‎modules/nf-core/bcftools/pluginfixploidy/environment.yml‎

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---
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# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
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channels:
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- conda-forge
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- bioconda
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dependencies:
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# renovate: datasource=conda depName=bioconda/htslib
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- bioconda::bcftools=1.22
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- bioconda::htslib=1.22.1

‎modules/nf-core/bcftools/pluginfixploidy/main.nf‎

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process BCFTOOLS_PLUGINFIXPLOIDY {
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tag "${meta.id}"
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label 'process_single'
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conda "${moduleDir}/environment.yml"
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container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container
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? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/47/474a5ea8dc03366b04df884d89aeacc4f8e6d1ad92266888e7a8e7958d07cde8/data'
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: 'community.wave.seqera.io/library/bcftools_htslib:0a3fa2654b52006f'}"
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input:
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tuple val(meta), path(vcf), path(index)
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path ploidy
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path sex
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path regions
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path targets
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output:
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tuple val(meta), path("*.{vcf,vcf.gz,bcf,bcf.gz}"), emit: vcf
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tuple val(meta), path("*.tbi"), emit: tbi, optional: true
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tuple val(meta), path("*.csi"), emit: csi, optional: true
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tuple val("${task.process}"), val('bcftools'), eval("bcftools --version | sed '1!d; s/^.*bcftools //'"), topic: versions, emit: versions_bcftools
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: '' // bcftools/common args before `--`
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def args2 = task.ext.args2 ?: '' // plugin args after `--` (e.g. -f 2 -t GT)
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def prefix = task.ext.prefix ?: "${meta.id}"
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def regions_arg = regions ? "--regions-file ${regions}" : ""
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def targets_arg = targets ? "--targets-file ${targets}" : ""
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def ploidy_arg = ploidy ? "-p ${ploidy}" : ""
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def sex_arg = sex ? "-s ${sex}" : ""
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def extension = args.contains("--output-type b") || args.contains("-Ob")
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? "bcf.gz"
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: args.contains("--output-type u") || args.contains("-Ou")
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? "bcf"
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: args.contains("--output-type z") || args.contains("-Oz")
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? "vcf.gz"
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: args.contains("--output-type v") || args.contains("-Ov")
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? "vcf"
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: "vcf"
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"""
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bcftools +fixploidy \\
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--output ${prefix}.${extension} \\
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${regions_arg} \\
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${targets_arg} \\
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${args} \\
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--threads ${task.cpus} \\
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${vcf} \\
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-- \\
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${ploidy_arg} \\
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${sex_arg} \\
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${args2}
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"""
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stub:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def extension = args.contains("--output-type b") || args.contains("-Ob")
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? "bcf.gz"
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: args.contains("--output-type u") || args.contains("-Ou")
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? "bcf"
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: args.contains("--output-type z") || args.contains("-Oz")
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? "vcf.gz"
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: args.contains("--output-type v") || args.contains("-Ov")
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? "vcf"
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: "vcf"
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def stub_index = args.contains("--write-index=tbi") || args.contains("-W=tbi")
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? "tbi"
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: args.contains("--write-index=csi") || args.contains("-W=csi")
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? "csi"
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: args.contains("--write-index") || args.contains("-W")
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? "csi"
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: ""
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def create_cmd = extension.endsWith(".gz") ? "echo '' | gzip >" : "touch"
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def create_index = extension.endsWith(".gz") && stub_index.matches("csi|tbi") ? "touch ${prefix}.${extension}.${stub_index}" : ""
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"""
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${create_cmd} ${prefix}.${extension}
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${create_index}
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"""
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}

‎modules/nf-core/bcftools/pluginfixploidy/meta.yml‎

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name: "bcftools_pluginfixploidy"
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description: "The fixploidy plugin fixes ploidy in genotype fields according to specified
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ploidy rules, sample sex assignments, or a forced ploidy value. For example, haploid
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genotypes can be converted to diploid genotypes."
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keywords:
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- fixploidy
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- bcftools
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- ploidy
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- vcf
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tools:
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- "bcftools":
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description: "BCFtools is a set of utilities that manipulate variant calls in
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the Variant Call Format (VCF) and its binary counterpart BCF. All commands work
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transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed.\
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\ Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically
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even when streaming from a pipe. Indexed VCF and BCF will work in all situations.
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Un-indexed VCF and BCF and streams will work in most, but not all situations."
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homepage: "https://samtools.github.io/bcftools/howtos/index.html"
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documentation: "https://samtools.github.io/bcftools/bcftools.html"
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tool_dev_url: "https://github.com/samtools/bcftools"
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doi: "10.1093/bioinformatics/btp352"
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licence:
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- "MIT"
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args_id: "$args"
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identifier: biotools:bcftools
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- "bcftools plugin fixploidy":
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description: "Bcftools plugins are tools that can be used with bcftools to manipulate
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variant calls in Variant Call Format (VCF) and BCF. The fixploidy plugin fixes
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ploidy in genotype fields according to specified ploidy rules, sample sex assignments,
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or a forced ploidy value. For example, haploid genotypes can be converted to
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diploid genotypes."
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homepage: "https://samtools.github.io/bcftools/howtos/plugins.html"
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documentation: "https://samtools.github.io/bcftools/howtos/plugin.setGT.html"
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tool_dev_url: "https://github.com/samtools/bcftools"
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doi: "10.1093/bioinformatics/btp352"
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licence:
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- "MIT"
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args_id: "$args2"
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identifier: biotools:bcftools
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input:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- vcf:
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type: file
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description: |
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Input VCF/BCF file to fix ploidy in.
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e.g. 'sample.vcf.gz'
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ontologies: []
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- index:
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type: file
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description: |
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Index file for the input VCF/BCF (e.g. .tbi or .csi).
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e.g. 'sample.vcf.gz.tbi'
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ontologies: []
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- ploidy:
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type: file
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description: |
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Optional ploidy definition file for the fixploidy plugin (`-p`), with
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space/tab-delimited columns: CHROM, FROM, TO, SEX, PLOIDY.
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e.g. 'ploidy.txt'
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ontologies: []
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- sex:
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type: file
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description: |
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Optional sample sex assignment file for the fixploidy plugin (`-s`),
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containing lines of the form: NAME SEX.
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Samples not listed are treated as female by the plugin.
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e.g. 'samples_sex.txt'
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ontologies: []
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- regions:
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type: file
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description: |
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Optionally restrict the operation to regions listed in this file
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(indexed input required; passed as a bcftools regions file argument).
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e.g. 'regions.bed'
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ontologies: []
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- targets:
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type: file
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description: |
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Optionally restrict the operation to targets listed in this file
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(does not rely on index jumps in the same way as regions; passed as a
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bcftools targets file argument).
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e.g. 'targets.bed'
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ontologies: []
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output:
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vcf:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- "*.{vcf,vcf.gz,bcf,bcf.gz}":
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type: file
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description: VCF output file containing GT fields with modified ploidy
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pattern: "*.{vcf,vcf.gz,bcf,bcf.gz}"
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ontologies: []
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tbi:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- "*.tbi":
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type: file
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description: Alternative VCF file index
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pattern: "*.tbi"
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ontologies: []
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csi:
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- - meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- "*.csi":
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type: file
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description: Default VCF file index
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pattern: "*.csi"
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ontologies: []
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versions_bcftools:
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- - ${task.process}:
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type: string
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description: The process the versions were collected from
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- bcftools:
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type: string
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description: The tool name
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- "bcftools --version | sed '1!d; s/^.*bcftools //'":
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type: eval
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description: The command used to generate the version of the tool
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topics:
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versions:
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- - ${task.process}:
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type: string
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description: The process the versions were collected from
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- bcftools:
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type: string
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description: The tool name
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- "bcftools --version | sed '1!d; s/^.*bcftools //'":
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type: eval
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description: The command used to generate the version of the tool
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authors:
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- "@alkc"
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maintainers:
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- "@alkc"

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