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taxprofiler/modules/nf-core/krakentools/kreport2krona/main.nf

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process KRAKENTOOLS_KREPORT2KRONA {
tag "$meta.id"
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label 'process_single'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
conda "bioconda::krakentools=1.2"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
input:
tuple val(meta), path(kreport)
output:
tuple val(meta), path("*.txt"), emit: txt
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}"
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def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
"""
kreport2krona.py \\
-r ${kreport} \\
-o ${prefix}.txt \\
${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kreport2krona.py: ${VERSION}
END_VERSIONS
"""
}