Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/cat_cat/main.nf @ 0:0a8dda29956e draft default tip

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planemo upload
author galaxytrakr
date Thu, 28 May 2026 20:41:10 +0000
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-1:000000000000 0:0a8dda29956e
1 process CAT_CAT {
2 tag "$meta.id"
3 label 'process_micro'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}pigz${params.fs}2.7" : null)
6 conda (params.enable_conda ? "conda-forge::pigz=2.6" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
9 'quay.io/biocontainers/pigz:2.3.4' }"
10
11 input:
12 tuple val(meta), path(files_in)
13
14 output:
15 tuple val(meta), path("*${prefix}"), emit: concatenated_reads
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def args2 = task.ext.args2 ?: ''
24 def file_list = files_in.collect { it.toString() }
25
26 // | input | output | command1 | command2 |
27 // |-----------|------------|----------|----------|
28 // | gzipped | gzipped | cat | |
29 // | ungzipped | ungzipped | cat | |
30 // | gzipped | ungzipped | zcat | |
31 // | ungzipped | gzipped | cat | pigz |
32
33 // Use input file ending as default
34 prefix = task.ext.prefix ? "${meta.id}.${task.ext.prefix}" : "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
35 out_zip = prefix.endsWith('.gz')
36 in_zip = file_list[0].endsWith('.gz')
37 command1 = (in_zip && !out_zip) ? 'zcat' : 'cat'
38 command2 = (!in_zip && out_zip) ? "| pigz -c -p $task.cpus $args2" : ''
39 """
40 $command1 \\
41 $args \\
42 ${file_list.join(' ')} \\
43 $command2 \\
44 > ${prefix}
45
46 cat <<-END_VERSIONS > versions.yml
47 "${task.process}":
48 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
49 END_VERSIONS
50 """
51
52 stub:
53 def file_list = files_in.collect { it.toString() }
54 prefix = task.ext.prefix ?: "${meta.id}${file_list[0].substring(file_list[0].lastIndexOf('.'))}"
55 """
56 touch $prefix
57
58 cat <<-END_VERSIONS > versions.yml
59 "${task.process}":
60 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
61 END_VERSIONS
62
63 catver=""
64 zver=""
65
66 if [ "${workflow.containerEngine}" != "null" ]; then
67 catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
68 zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
69
70 else
71 catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
72 zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
73 fi
74
75 cat <<-END_VERSIONS >> versions.yml
76 cat: \$catver
77 zcat: \$zver
78 END_VERSIONS
79 """
80 }