kkonganti@101: process KRAKEN2_CLASSIFY {
kkonganti@101:     tag "$meta.id"
kkonganti@101:     label 'process_low'
kkonganti@101: 
kkonganti@101:     module (params.enable_module ? "${params.swmodulepath}${params.fs}kraken2${params.fs}2.1.2" : null)
kkonganti@101:     conda (params.enable_conda ? 'bioconda::kraken2=2.1.2 conda-forge::pigz=2.6' : null)
kkonganti@101:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@101:         'https://depot.galaxyproject.org/singularity/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' :
kkonganti@101:         'quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0' }"
kkonganti@101: 
kkonganti@101:     input:
kkonganti@101:     tuple val(meta), path(reads)
kkonganti@101: 
kkonganti@101:     output:
kkonganti@101:     tuple val(meta), path('*classified*')  , emit: classified
kkonganti@101:     tuple val(meta), path('*unclassified*'), emit: unclassified
kkonganti@101:     tuple val(meta), path('*.report.txt')  , emit: kraken_report
kkonganti@101:     tuple val(meta), path('*.output.txt')  , emit: kraken_output
kkonganti@101:     path "versions.yml"                    , emit: versions
kkonganti@101: 
kkonganti@101:     when:
kkonganti@101:     task.ext.when == null || task.ext.when || reads
kkonganti@101: 
kkonganti@101:     script:
kkonganti@101:     def args = task.ext.args ?: ''
kkonganti@101:     def db = meta.kraken2_db ?: ''
kkonganti@101:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@101:     def readList = reads.collect{ it.toString() }
kkonganti@101:     def is_single_end = (meta.single_end || meta.is_assembly) ? true : false
kkonganti@101:     def paired = is_single_end ? "" : "--paired"
kkonganti@101:     def classified = is_single_end ? "--classified-out ${prefix}.classified.fastq" : "--classified-out ${prefix}.classified#.fastq"
kkonganti@101:     def unclassified = is_single_end ? "--unclassified-out ${prefix}.unclassified.fastq" : "--unclassified-out ${prefix}.unclassified#.fastq"
kkonganti@101:     args += (reads.getName().endsWith(".gz") ? ' --gzip-compressed ' : '')
kkonganti@101:     """
kkonganti@101:     kraken2 \\
kkonganti@101:         --db $db \\
kkonganti@101:         --threads $task.cpus \\
kkonganti@101:         $unclassified \\
kkonganti@101:         $classified \\
kkonganti@101:         --report ${prefix}.kraken2.report.txt \\
kkonganti@101:         --output ${prefix}.kraken2.output.txt \\
kkonganti@101:         $paired \\
kkonganti@101:         $args \\
kkonganti@101:         $reads
kkonganti@101: 
kkonganti@101:     cat <<-END_VERSIONS > versions.yml
kkonganti@101:     "${task.process}":
kkonganti@101:         kraken2: \$(echo \$(kraken2 --version 2>&1) | sed 's/^.*Kraken version //; s/ .*\$//')
kkonganti@101:     END_VERSIONS
kkonganti@101: 
kkonganti@101:     zcmd=""
kkonganti@101:     zver=""
kkonganti@101: 
kkonganti@101:     if type pigz > /dev/null 2>&1; then
kkonganti@101:         pigz -p $task.cpus *.fastq
kkonganti@101:         zcmd="pigz"
kkonganti@101:         zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed -e '1!d' | sed "s/\$zcmd //" )
kkonganti@101:     elif type gzip > /dev/null 2>&1; then
kkonganti@101:         gzip *.fastq
kkonganti@101:         zcmd="gzip"
kkonganti@101:     
kkonganti@101:         if [ "${workflow.containerEngine}" != "null" ]; then
kkonganti@101:             zver=\$( echo \$( \$zcmd --help 2>&1 ) | sed -e '1!d; s/ (.*\$//' )
kkonganti@101:         else
kkonganti@101:             zver=\$( echo \$( \$zcmd --version 2>&1 ) | sed "s/^.*(\$zcmd) //; s/\$zcmd //; s/ Copyright.*\$//" )
kkonganti@101:         fi
kkonganti@101:     fi
kkonganti@101: 
kkonganti@101:     cat <<-END_VERSIONS >> versions.yml
kkonganti@101:         \$zcmd: \$zver
kkonganti@101:     END_VERSIONS
kkonganti@101:     """
kkonganti@101: }