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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process COOLER_CLOAD {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0' :
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'quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0' }"
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input:
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tuple val(meta), path(pairs), path(index)
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val cool_bin
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path chromsizes
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output:
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tuple val(meta), val(cool_bin), path("*.cool"), emit: cool
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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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def nproc = args.contains('pairix') || args.contains('tabix')? "--nproc $task.cpus" : ''
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"""
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cooler cload \\
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$args \\
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$nproc \\
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${chromsizes}:${cool_bin} \\
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$pairs \\
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${prefix}.${cool_bin}.cool
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cooler: \$(cooler --version 2>&1 | sed 's/cooler, version //')
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END_VERSIONS
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"""
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}
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