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