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https://github.com/MillironX/nf-core_modules.git
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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
44 lines
1.4 KiB
Text
44 lines
1.4 KiB
Text
// 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 COOLER_DIGEST {
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tag "$fasta"
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label 'process_medium'
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publishDir "${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:[:], publish_by_meta:[]) }
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conda (params.enable_conda ? "bioconda::cooler=0.8.11" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/cooler:0.8.11--pyh3252c3a_0"
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} else {
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container "quay.io/biocontainers/cooler:0.8.11--pyh3252c3a_0"
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}
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input:
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path fasta
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path chromsizes
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val enzyme
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output:
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path "*.bed" , emit: bed
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path "versions.yml" , emit: versions
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script:
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"""
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cooler digest \\
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$options.args \\
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-o "${fasta.baseName}_${enzyme.replaceAll(/[^0-9a-zA-Z]+/, '_')}.bed" \\
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$chromsizes \\
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$fasta \\
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$enzyme
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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