kkonganti@11: process CAT_CAT {
kkonganti@11:     tag "$meta.id"
kkonganti@11:     label 'process_micro'
kkonganti@11: 
kkonganti@11:     module (params.enable_module ? "${params.swmodulepath}${params.fs}pigz${params.fs}2.7" : null)
kkonganti@11:     conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
kkonganti@11:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@11:         'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
kkonganti@11:         'quay.io/biocontainers/pigz:2.3.4' }"
kkonganti@11: 
kkonganti@11:     input:
kkonganti@11:         tuple val(meta), path(files_in)
kkonganti@11: 
kkonganti@11:     output:
kkonganti@11:         tuple val(meta), path("*${prefix}"), emit: concatenated_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 args2 = task.ext.args2 ?: ''
kkonganti@11:         def file_list = files_in.collect { it.toString() }
kkonganti@11: 
kkonganti@11:         // | input     | output     | command1 | command2 |
kkonganti@11:         // |-----------|------------|----------|----------|
kkonganti@11:         // | gzipped   | gzipped    | cat      |          |
kkonganti@11:         // | ungzipped | ungzipped  | cat      |          |
kkonganti@11:         // | gzipped   | ungzipped  | zcat     |          |
kkonganti@11:         // | ungzipped | gzipped    | cat      | pigz     |
kkonganti@11: 
kkonganti@11:         // Use input file ending as default
kkonganti@11:         prefix   = task.ext.prefix ? "${meta.id}.${task.ext.prefix}" : "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
kkonganti@11:         out_zip  = prefix.endsWith('.gz')
kkonganti@11:         in_zip   = file_list[0].endsWith('.gz')
kkonganti@11:         command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
kkonganti@11:         command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
kkonganti@11:         """
kkonganti@11:         $command1 \\
kkonganti@11:             $args \\
kkonganti@11:             ${file_list.join(' ')} \\
kkonganti@11:             $command2 \\
kkonganti@11:             > ${prefix}
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
kkonganti@11:         END_VERSIONS
kkonganti@11:         """
kkonganti@11: 
kkonganti@11:         stub:
kkonganti@11:         def file_list = files_in.collect { it.toString() }
kkonganti@11:         prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
kkonganti@11:         """
kkonganti@11:         touch $prefix
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS > versions.yml
kkonganti@11:         "${task.process}":
kkonganti@11:             pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
kkonganti@11:         END_VERSIONS
kkonganti@11: 
kkonganti@11:         catver=""
kkonganti@11:         zver=""
kkonganti@11: 
kkonganti@11:         if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@11:             catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
kkonganti@11:             zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@11: 
kkonganti@11:         else
kkonganti@11:             catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@11:             zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
kkonganti@11:         fi
kkonganti@11: 
kkonganti@11:         cat <<-END_VERSIONS >> versions.yml
kkonganti@11:             cat: \$catver
kkonganti@11:             zcat: \$zver
kkonganti@11:         END_VERSIONS
kkonganti@11:     """
kkonganti@11: }