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906577873b
* New functions.nf * Convert code to create versions.yml * Update meta.yml * update output channel * Fix more meta.yml * Manually update remaining modules * remove superflous echo * Fix misformatted meta.yml files * Fix yaml, was list instead of dict * fix version for bcftools Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
52 lines
1.8 KiB
Text
52 lines
1.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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 "versions.yml" , 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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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(bcftools --version 2>&1 | head -n1 | sed 's/^.*bcftools //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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