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72 lines
2.8 KiB
Text
72 lines
2.8 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process GENRICH {
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tag "$meta.id"
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label 'process_high'
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publishDir "${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::genrich=0.6.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/genrich:0.6.1--h5bf99c6_1"
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} else {
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container "quay.io/biocontainers/genrich:0.6.1--h5bf99c6_1"
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}
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input:
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tuple val(meta), path(treatment_bam)
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path control_bam
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path blacklist_bed
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val save_pvalues
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val save_pileup
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val save_bed
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val save_duplicates
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output:
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tuple val(meta), path("*narrowPeak") , emit: peaks
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tuple val(meta), path("*pvalues.bedGraph"), optional:true, emit: bedgraph_pvalues
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tuple val(meta), path("*pileup.bedGraph") , optional:true, emit: bedgraph_pileup
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tuple val(meta), path("*intervals.bed") , optional:true, emit: bed_intervals
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tuple val(meta), path("*duplicates.txt") , optional:true, emit: duplicates
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def control = control_bam ? "-c $control_bam" : ''
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def blacklist = blacklist_bed ? "-E $blacklist_bed" : ""
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def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
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def pileup = save_pileup ? "-k ${prefix}.pileup.bedGraph" : ""
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def bed = save_bed ? "-b ${prefix}.intervals.bed" : ""
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def duplicates = ""
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if (save_duplicates) {
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if (options.args.contains('-r')) {
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duplicates = "-R ${prefix}.duplicates.txt"
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} else {
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log.info '[Genrich] Duplicates can only be saved if they are filtered, defaulting to -r option (Remove PCR duplicates).'
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duplicates = "-r -R ${prefix}.duplicates.txt"
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}
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}
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"""
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Genrich \\
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-t $treatment_bam \\
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$options.args \\
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$control \\
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$blacklist \\
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-o ${prefix}.narrowPeak \\
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$pvalues \\
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$pileup \\
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$bed \\
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$duplicates \\
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$control
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(Genrich --version 2>&1) | sed 's/^Genrich, version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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