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81 lines
2.5 KiB
Plaintext
81 lines
2.5 KiB
Plaintext
process CAT_FASTQ {
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tag "$meta.id"
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label 'process_single'
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conda "conda-forge::sed=4.7"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/ubuntu:20.04' :
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'ubuntu:20.04' }"
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input:
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tuple val(meta), path(reads, stageAs: "input*/*")
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output:
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tuple val(meta), path("*.merged.fastq.gz"), emit: reads
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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 prefix = task.ext.prefix ?: "${meta.id}"
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def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
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if (meta.single_end) {
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if (readList.size >= 1) {
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"""
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cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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} else {
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if (readList.size >= 2) {
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def read1 = []
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def read2 = []
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readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
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"""
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cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz
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cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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}
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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()]
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if (meta.single_end) {
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if (readList.size > 1) {
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"""
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touch ${prefix}.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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} else {
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if (readList.size > 2) {
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"""
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touch ${prefix}_1.merged.fastq.gz
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touch ${prefix}_2.merged.fastq.gz
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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}
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}
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