mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
36 lines
1 KiB
Text
36 lines
1 KiB
Text
process ROARY {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::roary=3.13.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/roary:3.13.0--pl526h516909a_0' :
|
|
'quay.io/biocontainers/roary:3.13.0--pl526h516909a_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(gff)
|
|
|
|
output:
|
|
tuple val(meta), path("results/*") , emit: results
|
|
tuple val(meta), path("results/*.aln"), optional: true, emit: aln
|
|
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}"
|
|
"""
|
|
roary \\
|
|
$args \\
|
|
-p $task.cpus \\
|
|
-f results/ \\
|
|
$gff
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
roary: \$( roary --version )
|
|
END_VERSIONS
|
|
"""
|
|
}
|