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taxprofiler/modules/nf-core/krona/ktimporttaxonomy/main.nf

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process KRONA_KTIMPORTTAXONOMY {
tag "${meta.id}"
2022-10-05 10:24:18 +00:00
label 'process_single'
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda (params.enable_conda ? "bioconda::krona=2.8" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krona:2.8--pl5262hdfd78af_2' :
'quay.io/biocontainers/krona:2.8--pl5262hdfd78af_2' }"
input:
tuple val(meta), path(report)
path taxonomy, stageAs: 'taxonomy.tab'
output:
tuple val(meta), path ('*.html'), emit: html
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
def VERSION = '2.8' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
TAXONOMY=\$(find -L . -name '*.tab' -exec dirname {} \\;)
echo \$TAXONOMY
ktImportTaxonomy \\
$args \\
-o ${prefix}.html \\
-tax \$TAXONOMY/ \\
$report
cat <<-END_VERSIONS > versions.yml
"${task.process}":
krona: $VERSION
END_VERSIONS
"""
}