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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
45 lines
1.4 KiB
Text
45 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 BEDTOOLS_SLOP {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
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}
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input:
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tuple val(meta), path(bed)
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path sizes
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output:
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tuple val(meta), path("*.bed"), emit: bed
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path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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bedtools \\
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slop \\
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-i $bed \\
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-g $sizes \\
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$options.args \\
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> ${prefix}.bed
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(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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