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35 lines
1.1 KiB
Text
35 lines
1.1 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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def options = initOptions(params.options)
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process BEDTOOLS_BAMTOBED {
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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::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(sizes), path(bam), path(bai)
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output:
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tuple val(meta), path(sizes), path("*.bed12"), emit: bed12
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path "*.version.txt" , emit: version
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script:
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"""
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bedtools \\
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bamtobed \\
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-bed12 \\
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-cigar \\
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-i ${bam[0]} \\
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| bedtools sort > ${meta.id}.bed12
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bedtools --version | sed -e "s/bedtools v//g" > bedtools.version.txt
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"""
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}
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