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6ff995e93d
* initial commit [ci skip] * add basic structure [ci skip] * finalized the bcftools/query module * add optional files [ci skip] * Add the vcf index file as param [ci skip] * update the md5sum for output file [ci skip] * all tests passing
49 lines
1.6 KiB
Text
49 lines
1.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process BCFTOOLS_QUERY {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bcftools=1.13" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bcftools:1.13--h3a49de5_0"
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} else {
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container "quay.io/biocontainers/bcftools:1.13--h3a49de5_0"
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}
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input:
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tuple val(meta), path(vcf), path(index)
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path(regions)
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path(targets)
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path(samples)
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output:
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tuple val(meta), path("*.gz") , emit: vcf
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def regions_file = regions ? "--regions-file ${regions}" : ""
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def targets_file = targets ? "--targets-file ${targets}" : ""
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def samples_file = samples ? "--samples-file ${samples}" : ""
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"""
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bcftools query \\
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--output ${prefix}.vcf.gz \\
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${regions_file} \\
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${targets_file} \\
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${samples_file} \\
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$options.args \\
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${vcf}
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echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
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"""
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}
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