--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/centrifuge/classify/main.nf	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,61 @@
+process CENTRIFUGE_CLASSIFY {
+    tag "$meta.id"
+    label 'process_medium'
+
+    module (params.enable_module ? 'centrifuge' : null)
+    conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
+        'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path('*.report.txt')                 , emit: report
+    tuple val(meta), path('*.output.txt')                 , emit: output
+    tuple val(meta), path('*.kreport.txt')                , emit: kreport
+    tuple val(meta), path('*.sam')                        , optional: true, emit: sam
+    tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz')    , optional: true, emit: fastq_mapped
+    tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz')  , optional: true, emit: fastq_unmapped
+    path "versions.yml"                                   , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def paired = meta.single_end ? "-U ${reads}" :  "-1 ${reads[0]} -2 ${reads[1]}"
+    def db = meta.centrifuge_x ?: ''
+    def db_name = db.toString().replace(".tar.gz","")
+    def unaligned = ''
+    def aligned = ''
+    if (meta.single_end) {
+        unaligned = params.centrifuge_save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
+        aligned = params.centrifuge_save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
+    } else {
+        unaligned = params.centrifuge_save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
+        aligned = params.centrifuge_save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
+    }
+    def sam_output = params.centrifuge_out_fmt_sam ? "--out-fmt 'sam'" : ''
+    """
+    centrifuge \\
+        -x $db \\
+        -p $task.cpus \\
+        $paired \\
+        --report-file ${prefix}.centrifuge.report.txt \\
+        -S ${prefix}.centrifuge.output.txt \\
+        $unaligned \\
+        $aligned \\
+        $sam_output \\
+        $args
+
+    centrifuge-kreport -x $db_name ${prefix}.centrifuge.output.txt > ${prefix}.centrifuge.kreport.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        centrifuge: \$( centrifuge --version  | sed -n 1p | sed 's/^.*centrifuge-class version //')
+    END_VERSIONS
+    """
+}
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