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46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
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// 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 PARACLU {
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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::paraclu=10" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/paraclu%3A10--h9a82719_1"
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} else {
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container "quay.io/biocontainers/paraclu:10--h9a82719_1"
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}
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input:
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tuple val(meta), path(bed)
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val(min_cluster)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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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 VERSION=10
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"""
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awk -F "\t" '{print\$1"\t"\$6"\t"\$2"\t"\$5}' < $bed > ${bed}_4P
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sort -k1,1 -k3n ${bed}_4P > ${bed}_4Ps
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paraclu $min_cluster ${bed}_4Ps > ${prefix}.clustered
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paraclu-cut ${prefix}.clustered > ${prefix}.clustered.simplified
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awk -F '\t' '{print \$1"\t"\$3"\t"\$4"\t"\$1":"\$3".."\$4","\$2"\t"\$6"\t"\$2}' ${prefix}.clustered.simplified > ${prefix}.clustered.simplified.bed
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: $VERSION
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END_VERSIONS
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"""
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}
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