nf-core_modules/modules/kleborate/main.nf
2022-02-04 09:53:32 +01:00

34 lines
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Text

process KLEBORATE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' :
'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1' }"
input:
tuple val(meta), path(fastas)
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}"
"""
kleborate \\
$args \\
--outfile ${prefix}.results.txt \\
--assemblies $fastas
cat <<-END_VERSIONS > versions.yml
"${task.process}":
kleborate: \$( echo \$(kleborate --version | sed 's/Kleborate v//;'))
END_VERSIONS
"""
}