kkonganti@11: process CAT_FASTQ {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_micro'
kkonganti@11: 
kkonganti@11:     conda (params.enable_conda ? "conda-forge::sed=4.7 conda-forge::gzip" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://containers.biocontainers.pro/s3/SingImgsRepo/biocontainers/v1.2.0_cv1/biocontainers_v1.2.0_cv1.img' :
kkonganti@11:         'biocontainers/biocontainers:v1.2.0_cv1' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(reads, stageAs: "input*/*")
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("*.merged.fastq.gz"), emit: catted_reads
kkonganti@11:         path "versions.yml"                       , emit: versions
kkonganti@11: 
kkonganti@11:     when:
kkonganti@11:         task.ext.when == null || task.ext.when
kkonganti@11: 
kkonganti@11:     script:
kkonganti@11:         def args = task.ext.args ?: ''
kkonganti@11:         def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@11:         def readList = reads.collect{ it.toString() }
kkonganti@11:         def is_in_gz = readList[0].endsWith('.gz')
kkonganti@11:         def gz_or_ungz = (is_in_gz ? '' : ' | gzip')
kkonganti@11:         def pigz_or_ungz = (is_in_gz ? '' : " | pigz -p ${task.cpus}")
kkonganti@11:         if (meta.single_end) {
kkonganti@11:             if (readList.size > 1) {
kkonganti@11:                 """
kkonganti@11:                 zcmd="gzip"
kkonganti@11:                 zver=""
kkonganti@11: 
kkonganti@11:                 if type pigz > /dev/null 2>&1; then
kkonganti@11:                     cat ${readList.join(' ')} ${pigz_or_ungz} > ${prefix}.merged.fastq.gz
kkonganti@11:                     zcmd="pigz"
kkonganti@11:                     zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@11:                 else
kkonganti@11:                     cat ${readList.join(' ')} ${gz_or_ungz} > ${prefix}.merged.fastq.gz
kkonganti@11:                     zcmd="gzip"
kkonganti@11: 
kkonganti@11:                     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@11:                         zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@11:                     else
kkonganti@11:                         zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@11:                     fi
kkonganti@11:                 fi
kkonganti@11: 
kkonganti@11:                 cat <<-END_VERSIONS > versions.yml
kkonganti@11:                 "${task.process}":
kkonganti@11:                     cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
kkonganti@11:                     \$zcmd: \$zver
kkonganti@11:                 END_VERSIONS
kkonganti@11:                 """
kkonganti@11:             }
kkonganti@11:         } else {
kkonganti@11:             if (readList.size > 2) {
kkonganti@11:                 def read1 = []
kkonganti@11:                 def read2 = []
kkonganti@11:                 readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v }
kkonganti@11:                 """
kkonganti@11:                 zcmd="gzip"
kkonganti@11:                 zver=""
kkonganti@11: 
kkonganti@11:                 if type pigz > /dev/null 2>&1; then
kkonganti@11:                     cat ${read1.join(' ')} ${pigz_or_ungz} > ${prefix}_1.merged.fastq.gz
kkonganti@11:                     cat ${read2.join(' ')} ${pigz_or_ungz} > ${prefix}_2.merged.fastq.gz
kkonganti@11:                     zcmd="pigz"
kkonganti@11:                     zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@11:                 else
kkonganti@11:                     cat ${read1.join(' ')} ${gz_or_ungz} > ${prefix}_1.merged.fastq.gz
kkonganti@11:                     cat ${read2.join(' ')} ${gz_or_ungz} > ${prefix}_2.merged.fastq.gz
kkonganti@11:                     zcmd="gzip"
kkonganti@11: 
kkonganti@11:                     if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@11:                         zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@11:                     else
kkonganti@11:                         zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@11:                     fi
kkonganti@11:                 fi
kkonganti@11: 
kkonganti@11:                 cat <<-END_VERSIONS > versions.yml
kkonganti@11:                 "${task.process}":
kkonganti@11:                     cat: \$( echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//' )
kkonganti@11:                     \$zcmd: \$zver
kkonganti@11:                 END_VERSIONS
kkonganti@11:                 """
kkonganti@11:             }
kkonganti@11:         }
kkonganti@11: }