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46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
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// 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 EXPANSIONHUNTER {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::expansionhunter=4.0.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/expansionhunter:4.0.2--he785bd8_0"
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} else {
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container "quay.io/biocontainers/expansionhunter:4.0.2--he785bd8_0"
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}
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input:
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tuple val(meta), path(bam), path(bai)
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path fasta
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path variant_catalog
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output:
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tuple val(meta), path("*.vcf"), 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}" : "${meta.id}"
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def gender = (meta.gender == 'male' || meta.gender == 1 || meta.gender == 'XY') ? "male" : "female"
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"""
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ExpansionHunter \\
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$options.args \\
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--reads $bam \\
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--output-prefix $prefix \\
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--reference $fasta \\
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--variant-catalog $variant_catalog \\
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--sex $gender
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echo \$(ExpansionHunter --version 2>&1) | sed 's/^.*ExpansionHunter //' > ${software}.version.txt
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"""
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}
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