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45 lines
1.5 KiB
Text
45 lines
1.5 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 PAIRTOOLS_PARSE {
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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::pairtools=0.3.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5"
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} else {
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container "quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5"
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}
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input:
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tuple val(meta), path(bam)
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path chromsizes
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output:
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tuple val(meta), path("*.pairsam.gz") , emit: pairsam
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tuple val(meta), path("*.pairsam.stat"), emit: stat
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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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"""
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pairtools \\
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parse \\
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-c $chromsizes \\
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$options.args \\
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--output-stats ${prefix}.pairsam.stat \\
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-o ${prefix}.pairsam.gz \\
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$bam
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echo \$(pairtools --version 2>&1) | sed 's/pairtools.*version //' > ${software}.version.txt
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"""
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}
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