kkonganti@17: process CAT_CAT {
kkonganti@17:     tag "$meta.id"
kkonganti@17:     label 'process_micro'
kkonganti@17: 
kkonganti@17:     module (params.enable_module ? "${params.swmodulepath}${params.fs}pigz${params.fs}2.7" : null)
kkonganti@17:     conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
kkonganti@17:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@17:         'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
kkonganti@17:         'quay.io/biocontainers/pigz:2.3.4' }"
kkonganti@17: 
kkonganti@17:     input:
kkonganti@17:         tuple val(meta), path(files_in)
kkonganti@17: 
kkonganti@17:     output:
kkonganti@17:         tuple val(meta), path("*${prefix}"), emit: concatenated_reads
kkonganti@17:         path "versions.yml"                , emit: versions
kkonganti@17: 
kkonganti@17:     when:
kkonganti@17:         task.ext.when == null || task.ext.when
kkonganti@17: 
kkonganti@17:     script:
kkonganti@17:         def args = task.ext.args ?: ''
kkonganti@17:         def args2 = task.ext.args2 ?: ''
kkonganti@17:         def file_list = files_in.collect { it.toString() }
kkonganti@17: 
kkonganti@17:         // | input     | output     | command1 | command2 |
kkonganti@17:         // |-----------|------------|----------|----------|
kkonganti@17:         // | gzipped   | gzipped    | cat      |          |
kkonganti@17:         // | ungzipped | ungzipped  | cat      |          |
kkonganti@17:         // | gzipped   | ungzipped  | zcat     |          |
kkonganti@17:         // | ungzipped | gzipped    | cat      | pigz     |
kkonganti@17: 
kkonganti@17:         // Use input file ending as default
kkonganti@17:         prefix   = task.ext.prefix ? "${meta.id}.${task.ext.prefix}" : "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
kkonganti@17:         out_zip  = prefix.endsWith('.gz')
kkonganti@17:         in_zip   = file_list[0].endsWith('.gz')
kkonganti@17:         command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
kkonganti@17:         command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
kkonganti@17:         """
kkonganti@17:         $command1 \\
kkonganti@17:             $args \\
kkonganti@17:             ${file_list.join(' ')} \\
kkonganti@17:             $command2 \\
kkonganti@17:             > ${prefix}
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
kkonganti@17:         END_VERSIONS
kkonganti@17:         """
kkonganti@17: 
kkonganti@17:         stub:
kkonganti@17:         def file_list = files_in.collect { it.toString() }
kkonganti@17:         prefix   = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
kkonganti@17:         """
kkonganti@17:         touch $prefix
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS > versions.yml
kkonganti@17:         "${task.process}":
kkonganti@17:             pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
kkonganti@17:         END_VERSIONS
kkonganti@17: 
kkonganti@17:         catver=""
kkonganti@17:         zver=""
kkonganti@17: 
kkonganti@17:         if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@17:             catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' |  cut -f1-2 -d' ' )
kkonganti@17:             zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
kkonganti@17: 
kkonganti@17:         else
kkonganti@17:             catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
kkonganti@17:             zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
kkonganti@17:         fi
kkonganti@17: 
kkonganti@17:         cat <<-END_VERSIONS >> versions.yml
kkonganti@17:             cat: \$catver
kkonganti@17:             zcat: \$zver
kkonganti@17:         END_VERSIONS
kkonganti@17:     """
kkonganti@17: }