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31 lines
1.2 KiB
Text
31 lines
1.2 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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def options = initOptions(params.options)
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process BEDTOOLS_INTERSECT {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null)
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container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0"
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input:
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tuple val(meta), path(beds)
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output:
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tuple val(meta), path("*.intersect.bed"), emit: intersect
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path "*.version.txt", emit: version
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script: // TODO change script to account for multiple possible intersections
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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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bedtools intersect -a ${beds[0]} -b ${beds[1]} ${options.args} > ${prefix}.intersect.bed
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bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt
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"""
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}
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