Mercurial > repos > galaxytrakr > hfp_bettercallsal_konda

comparison 1.0.0/modules/gather_hits/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 GATHER_HITS {
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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/pigz:2.3.4' :
9 'quay.io/biocontainers/pigz:2.3.4' }"
10
11 input:
12 tuple val(meta), path(genomes_fasta)
13
14 output:
15 tuple val(meta), path("*_template_hits.txt"), emit: sm_template_hits
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def args2 = task.ext.args2 ?: ''
24
25 // Use input file ending as default
26 prefix = task.ext.prefix ?: "${meta.id}"
27 command = genomes_fasta.toString().endsWith('.gz') ? 'zcat' : 'cat'
28 """
29 $command \\
30 $args \\
31 $genomes_fasta | \\
32 grep -F '>' | grep -E -o 'GC[AF]\\_[0-9]+\\.*[0-9]*' > ${prefix}.sm_template_hits.txt
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
37 END_VERSIONS
38
39 mkdirver=""
40 catver=""
41 zver=""
42 grepver=""
43
44 if [ "${workflow.containerEngine}" != "null" ]; then
45 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
46 catver=\$( cat --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
47 zver=\$( zcat --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
48 grepver="\$mkdirver"
49 else
50 catver=\$( cat --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
51 zver=\$( zcat --version 2>&1 | sed '1!d; s/^.*(gzip) //' )
52 grepver=\$( echo \$(grep --version 2>&1) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
53 fi
54
55 cat <<-END_VERSIONS >> versions.yml
56 cat: \$catver
57 zcat: \$zver
58 grep: \$grepver
59 END_VERSIONS
60 """
61 }