nf-core_modules/modules/megan/rma2info/main.nf
James A. Fellows Yates 2d38566eca
Add MEGAN/RMA2INFO (#1513)
* fix: remove left-over unnecessary code

* Add megan/rma2info

* Attempt at fixing test

* Right yml formatting

* Get the versios reporting correct
2022-04-12 08:35:36 +02:00

38 lines
1.2 KiB
Text

process MEGAN_RMA2INFO {
tag "$meta.id"
label 'process_low'
conda (params.enable_conda ? "bioconda::megan=6.21.7" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/megan:6.21.7--h9ee0642_0':
'quay.io/biocontainers/megan:6.21.7--h9ee0642_0' }"
input:
tuple val(meta), path(rma6)
val(megan_summary)
output:
tuple val(meta), path("*.txt.gz") , emit: txt
tuple val(meta), path("*.megan"), optional: true, emit: megan_summary
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 summary = megan_summary ? "-es ${prefix}.megan" : ""
"""
rma2info \\
-i ${rma6} \\
-o ${prefix}.txt.gz \\
${summary} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
megan: \$(echo \$(rma2info 2>&1) | grep version | sed 's/.*version //g;s/, built.*//g')
END_VERSIONS
"""
}