Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/modules/centrifuge/classify/main.nf @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 process CENTRIFUGE_CLASSIFY {
2 tag "$meta.id"
3 label 'process_medium'
4
5 module (params.enable_module ? 'centrifuge' : null)
6 conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6' :
9 'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
10
11 input:
12 tuple val(meta), path(reads)
13
14 output:
15 tuple val(meta), path('*.report.txt') , emit: report
16 tuple val(meta), path('*.output.txt') , emit: output
17 tuple val(meta), path('*.kreport.txt') , emit: kreport
18 tuple val(meta), path('*.sam') , optional: true, emit: sam
19 tuple val(meta), path('*.mapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_mapped
20 tuple val(meta), path('*.unmapped.fastq{,.1,.2}.gz') , optional: true, emit: fastq_unmapped
21 path "versions.yml" , emit: versions
22
23 when:
24 task.ext.when == null || task.ext.when
25
26 script:
27 def args = task.ext.args ?: ''
28 def prefix = task.ext.prefix ?: "${meta.id}"
29 def paired = meta.single_end ? "-U ${reads}" : "-1 ${reads[0]} -2 ${reads[1]}"
30 def db = meta.centrifuge_x ?: ''
31 def db_name = db.toString().replace(".tar.gz","")
32 def unaligned = ''
33 def aligned = ''
34 if (meta.single_end) {
35 unaligned = params.centrifuge_save_unaligned ? "--un-gz ${prefix}.unmapped.fastq.gz" : ''
36 aligned = params.centrifuge_save_aligned ? "--al-gz ${prefix}.mapped.fastq.gz" : ''
37 } else {
38 unaligned = params.centrifuge_save_unaligned ? "--un-conc-gz ${prefix}.unmapped.fastq.gz" : ''
39 aligned = params.centrifuge_save_aligned ? "--al-conc-gz ${prefix}.mapped.fastq.gz" : ''
40 }
41 def sam_output = params.centrifuge_out_fmt_sam ? "--out-fmt 'sam'" : ''
42 """
43 centrifuge \\
44 -x $db \\
45 -p $task.cpus \\
46 $paired \\
47 --report-file ${prefix}.centrifuge.report.txt \\
48 -S ${prefix}.centrifuge.output.txt \\
49 $unaligned \\
50 $aligned \\
51 $sam_output \\
52 $args
53
54 centrifuge-kreport -x $db_name ${prefix}.centrifuge.output.txt > ${prefix}.centrifuge.kreport.txt
55
56 cat <<-END_VERSIONS > versions.yml
57 "${task.process}":
58 centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
59 END_VERSIONS
60 """
61 }