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https://github.com/MillironX/nf-core_modules.git
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90aef30f43
* Set process label to `process_single` for modules with no `task.cpus` usage * Fix tests of 'borked' modules * prettier * More modules are single-threaded and can use process_single * Adding process_single to hmmer/esl* modules * Fix failing tests * Prettier Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk> Co-authored-by: Daniel Lundin <erik.rikard.daniel@gmail.com>
59 lines
1.7 KiB
Text
59 lines
1.7 KiB
Text
process BEDTOOLS_GENOMECOV {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0' :
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'quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0' }"
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input:
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tuple val(meta), path(intervals), val(scale)
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path sizes
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val extension
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output:
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tuple val(meta), path("*.${extension}"), emit: genomecov
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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 args_list = args.tokenize()
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args += (scale > 0 && scale != 1) ? " -scale $scale" : ""
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if (!args_list.contains('-bg') && (scale > 0 && scale != 1)) {
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args += " -bg"
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}
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (intervals.name =~ /\.bam/) {
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"""
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bedtools \\
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genomecov \\
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-ibam $intervals \\
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$args \\
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> ${prefix}.${extension}
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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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} else {
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"""
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bedtools \\
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genomecov \\
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-i $intervals \\
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-g $sizes \\
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$args \\
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> ${prefix}.${extension}
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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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}
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