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