|
0
|
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 } |
