kkonganti@0: process CENTRIFUGE_CLASSIFY {
kkonganti@0:     tag "$meta.id"
kkonganti@0:     label 'process_medium'
kkonganti@0: 
kkonganti@0:     module (params.enable_module ? 'centrifuge' : null)
kkonganti@0:     conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
kkonganti@0:     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0:         'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
kkonganti@0:         'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
kkonganti@0: 
kkonganti@0:     input:
kkonganti@0:     tuple val(meta), path(reads)
kkonganti@0: 
kkonganti@0:     output:
kkonganti@0:     tuple val(meta), path('*.report.txt')                 , emit: report
kkonganti@0:     tuple val(meta), path('*.output.txt')                 , emit: output
kkonganti@0:     tuple val(meta), path('*.kreport.txt')                , emit: kreport
kkonganti@0:     tuple val(meta), path('*.sam')                        , optional: true, emit: sam
kkonganti@0:     tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')    , optional: true, emit: fastq_mapped
kkonganti@0:     tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz')  , optional: true, emit: fastq_unmapped
kkonganti@0:     path "versions.yml"                                   , emit: versions
kkonganti@0: 
kkonganti@0:     when:
kkonganti@0:     task.ext.when == null || task.ext.when
kkonganti@0: 
kkonganti@0:     script:
kkonganti@0:     def args = task.ext.args ?: ''
kkonganti@0:     def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0:     def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
kkonganti@0:     def db = meta.centrifuge_x ?: ''
kkonganti@0:     def db_name = db.toString().replace(".tar.gz","")
kkonganti@0:     def unaligned = ''
kkonganti@0:     def aligned = ''
kkonganti@0:     if (meta.single_end) {
kkonganti@0:         unaligned = params.centrifuge_save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
kkonganti@0:         aligned = params.centrifuge_save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
kkonganti@0:     } else {
kkonganti@0:         unaligned = params.centrifuge_save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
kkonganti@0:         aligned = params.centrifuge_save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
kkonganti@0:     }
kkonganti@0:     def sam_output = params.centrifuge_out_fmt_sam ? "--out-fmt 'sam'" : ''
kkonganti@0:     """
kkonganti@0:     centrifuge \\
kkonganti@0:         -x $db \\
kkonganti@0:         -p $task.cpus \\
kkonganti@0:         $paired \\
kkonganti@0:         --report-file ${prefix}.centrifuge.report.txt \\
kkonganti@0:         -S ${prefix}.centrifuge.output.txt \\
kkonganti@0:         $unaligned \\
kkonganti@0:         $aligned \\
kkonganti@0:         $sam_output \\
kkonganti@0:         $args
kkonganti@0: 
kkonganti@0:     centrifuge-kreport -x $db_name ${prefix}.centrifuge.output.txt > ${prefix}.centrifuge.kreport.txt
kkonganti@0: 
kkonganti@0:     cat <<-END_VERSIONS > versions.yml
kkonganti@0:     "${task.process}":
kkonganti@0:         centrifuge: \$( centrifuge --version  | sed -n 1p | sed 's/^.*centrifuge-class version //')
kkonganti@0:     END_VERSIONS
kkonganti@0:     """
kkonganti@0: }