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https://github.com/MillironX/nf-core_modules.git
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9402595711
* First step into creating a seqtk/mergepe module to interleave fastQ input * First rewrite of main.nf to make the module perform the desired (interleave/merge of pe reads) task * Modifications to test the new seqtk/mergepe module. * Improving the seqtk/mergepe module to output single end reads as well, and making sure tests work * Modified so that gzip uses -n and that single read entries are symlinked with ln -s instead of copied, therefore updated test.yml as well. * Fix trailing whitespaces Co-authored-by: Daniel Lundin <daniel.lundin@lnu.se>
53 lines
1.7 KiB
Text
53 lines
1.7 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 SEQTK_MERGEPE {
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tag "$meta.id"
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label 'process_low'
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publishDir "${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::seqtk=1.3" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3"
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} else {
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container "quay.io/biocontainers/seqtk:1.3--h5bf99c6_3"
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}
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fastq.gz"), emit: reads
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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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if (meta.single_end) {
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"""
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ln -s ${reads} ${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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seqtk \\
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mergepe \\
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$options.args \\
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${reads} \\
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| gzip -n >> ${prefix}.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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}
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