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https://github.com/MillironX/nf-core_modules.git
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0e9fd9370a
* Remove quotes around input reports variable for ktImportTaxonomy as prevents supplying multiple files * Add using prefix for output files * Tweak meta reflecting more flexible input database specification * Linting * Fix finding the correct directory * Update main.nf * Fix database inport * Prettier
41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
process KRONA_KTIMPORTTAXONOMY {
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tag "${meta.id}"
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label 'process_high'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::krona=2.8" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
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'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
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input:
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tuple val(meta), path(report)
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path taxonomy, stageAs: 'taxonomy.tab'
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output:
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tuple val(meta), path ('*.html'), emit: html
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
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echo \$TAXONOMY
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ktImportTaxonomy \\
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$args \\
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-o ${prefix}.html \\
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-tax \$TAXONOMY/ \\
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$report
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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krona: $VERSION
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END_VERSIONS
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"""
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}
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