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39 lines
1.3 KiB
Text
39 lines
1.3 KiB
Text
def VERSION = '10' // Version information not provided by tool on CLI
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process PARACLU {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::paraclu=10" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/paraclu:10--h9a82719_1' :
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'quay.io/biocontainers/paraclu:10--h9a82719_1' }"
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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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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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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 > ${prefix}.clustered.simplified.bed
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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paraclu: $VERSION
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END_VERSIONS
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"""
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}
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