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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process PAIRTOOLS_FLIP {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::pairtools=0.3.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pairtools:0.3.0--py37hb9c2fc3_5' :
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'quay.io/biocontainers/pairtools:0.3.0--py37hb9c2fc3_5' }"
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input:
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tuple val(meta), path(sam)
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path chromsizes
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output:
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tuple val(meta), path("*.flip.gz"), emit: flip
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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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pairtools \\
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flip \\
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-c $chromsizes \\
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$args \\
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-o ${prefix}.flip.gz \\
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$sam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pairtools: \$(pairtools --version 2>&1 | sed 's/pairtools.*version //')
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END_VERSIONS
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"""
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}
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