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comparison 0.1.0/modules/cat/unique/main.nf @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
1 process CAT_UNIQUE {
2 tag "${meta.id}"
3 label "process_pico"
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}perl${params.fs}5.30.0" : null)
6 conda (params.enable_conda ? "conda-forge::perl conda-forge::coreutils bioconda::perl-bioperl=1.7.8" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/perl-bioperl:1.7.8--hdfd78af_1' :
9 'quay.io/biocontainers/perl-bioperl:1.7.8--hdfd78af_1' }"
10
11 input:
12 tuple val(meta), path(file)
13
14 output:
15 path '*_uniq.txt' , emit: txt
16 path 'versions.yml', emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = (task.ext.args ?: '')
23 def skip = (meta.skip_header ?: 1)
24 prefix = (task.ext.prefix ?: meta.id)
25 """
26 newfile=\$(echo "$file" | sed -e 's/_w_dups/_uniq/g')
27
28 head -n$skip "$file" > \$newfile
29 tail -n+\$(($skip + 1)) "$file" | sort -n | uniq >> \$newfile
30
31 uniqver=""
32
33 if [ "${workflow.containerEngine}" != "null" ]; then
34 uniqver=\$( uniq --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
35
36 else
37 uniqver=\$( uniq --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
38 fi
39
40 cat <<-END_VERSIONS > versions.yml
41 "${task.process}":
42 head: \$uniqver
43 tail: \$uniqver
44 sort: \$uniqver
45 uniq: \$uniqver
46 END_VERSIONS
47 """
48 }