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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process BEDTOOLS_MAKEWINDOWS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--h7d7f7ad_1' :
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'quay.io/biocontainers/bedtools:2.30.0--h7d7f7ad_1' }"
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input:
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tuple val(meta), path(regions)
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val(use_bed)
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output:
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tuple val(meta), path("*.tab"), emit: tab
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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 arg_input = use_bed ? "-b $regions" : "-g $regions"
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"""
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bedtools \\
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makewindows \\
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${arg_input} \\
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$args \\
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> ${prefix}.tab
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
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END_VERSIONS
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"""
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}
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