nf-core_modules/modules/cat/fastq/main.nf

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// Import generic module functions
include { initOptions; saveFiles } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process CAT_FASTQ {
tag "$meta.id"
label 'process_low'
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publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:'merged_fastq', meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "conda-forge::sed=4.7" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img"
} else {
container "biocontainers/biocontainers:v1.2.0_cv1"
}
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.merged.fastq.gz"), emit: reads
script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
def readList = reads.collect{ it.toString() }
if (meta.single_end) {
if (readList.size > 1) {
"""
cat ${readList.sort().join(' ')} > ${prefix}.merged.fastq.gz
"""
}
} else {
if (readList.size > 2) {
def read1 = []
def read2 = []
readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
"""
cat ${read1.sort().join(' ')} > ${prefix}_1.merged.fastq.gz
cat ${read2.sort().join(' ')} > ${prefix}_2.merged.fastq.gz
"""
}
}
}