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comparison 0.5.0/modules/krona/ktimporttext/main.nf @ 0:97cd2f532efe

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planemo upload
author kkonganti
date Mon, 31 Mar 2025 14:50:40 -0400
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-1:000000000000 0:97cd2f532efe
1 process KRONA_KTIMPORTTEXT {
2 tag "$meta.id"
3 label 'process_nano'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}krona${params.fs}2.8.1" : null)
6 conda (params.enable_conda ? "conda-forge::curl bioconda::krona=2.8.1" : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/krona:2.8.1--pl5321hdfd78af_1':
9 'quay.io/biocontainers/krona:2.8.1--pl5321hdfd78af_1' }"
10
11 input:
12 tuple val(meta), path(report)
13
14 output:
15 tuple val(meta), path ('*.html'), emit: html
16 path "versions.yml" , emit: versions
17
18 when:
19 task.ext.when == null || task.ext.when
20
21 script:
22 def args = task.ext.args ?: ''
23 def prefix = task.ext.prefix ?: "${meta.id}"
24 def krona_suffix = params.krona_res_suffix ?: '.krona.tsv'
25 def reports = report.collect {
26 it = it.toString() + ',' + it.toString().replaceAll(/(.*)${krona_suffix}$/, /$1/)
27 }.sort().join(' ')
28 """
29 ktImportText \\
30 $args \\
31 -o ${prefix}.html \\
32 $reports
33
34 cat <<-END_VERSIONS > versions.yml
35 "${task.process}":
36 krona: \$( echo \$(ktImportText 2>&1) | sed 's/^.*KronaTools //g; s/- ktImportText.*\$//g')
37 END_VERSIONS
38 """
39 }