nf-core_modules/modules/seqkit/split2/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
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process SEQKIT_SPLIT2 {
tag "$meta.id"
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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::seqkit=0.16.1' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/seqkit:0.16.1--h9ee0642_0"
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} else {
container "quay.io/biocontainers/seqkit:0.16.1--h9ee0642_0"
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}
input:
tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.split/*.gz"), emit: reads
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path("*.version.txt") , emit: version
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script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if(meta.single_end){
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"""
seqkit \
split2 \
$options.args \
--threads $task.cpus \
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-1 ${reads} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
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} else {
"""
seqkit \
split2 \
$options.args \
--threads $task.cpus \
-1 ${reads[0]} \
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-2 ${reads[1]} \
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--out-dir ${prefix}.split
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echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
"""
}
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}