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2ade120249
* Add --paired flag to umitools dedup and bump to 1.1.2 * paired not paired_end * Fix ECLint
57 lines
2 KiB
Text
57 lines
2 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process UMITOOLS_EXTRACT {
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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::umi_tools=1.1.2" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0"
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} else {
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container "quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0"
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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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tuple val(meta), path("*.log") , emit: log
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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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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umi_tools \\
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extract \\
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-I $reads \\
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-S ${prefix}.umi_extract.fastq.gz \\
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$options.args \\
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> ${prefix}.umi_extract.log
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echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
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"""
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} else {
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"""
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umi_tools \\
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extract \\
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-I ${reads[0]} \\
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--read2-in=${reads[1]} \\
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-S ${prefix}.umi_extract_1.fastq.gz \\
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--read2-out=${prefix}.umi_extract_2.fastq.gz \\
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$options.args \\
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> ${prefix}.umi_extract.log
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echo \$(umi_tools --version 2>&1) | sed 's/^.*UMI-tools version://; s/ *\$//' > ${software}.version.txt
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"""
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}
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}
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