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fc8cdde2b4
Add all initial suggestions from review (syntax issues) Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
35 lines
1.3 KiB
Text
35 lines
1.3 KiB
Text
// 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_GENOMECOV {
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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=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(bams), path (sizes)
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output:
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tuple val(meta), path("*.bed"), emit: coverage
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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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bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.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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