nf-core_modules/modules/seqkit/stats/main.nf
2022-03-30 23:01:17 +02:00

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process SEQKIT_STATS {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::seqkit=2.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/seqkit:2.2.0--h9ee0642_0':
'quay.io/biocontainers/seqkit:2.2.0--h9ee0642_0' }"
input:
tuple val(meta), path(reads)
output:
tuple val(meta), path("*.tsv"), emit: stats
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: '--all'
def prefix = task.ext.prefix ?: "${meta.id}"
"""
seqkit stats \\
--tabular \\
$args \\
$reads > '${prefix}.tsv'
cat <<-END_VERSIONS > versions.yml
"${task.process}":
seqkit: \$( seqkit version | sed 's/seqkit v//' )
END_VERSIONS
"""
}