mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
30 lines
815 B
Text
30 lines
815 B
Text
process GFFREAD {
|
|
tag "$gff"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::gffread=0.12.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/gffread:0.12.1--h8b12597_0' :
|
|
'quay.io/biocontainers/gffread:0.12.1--h8b12597_0' }"
|
|
|
|
input:
|
|
path gff
|
|
|
|
output:
|
|
path "*.gtf" , emit: gtf
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${gff.baseName}"
|
|
"""
|
|
gffread \\
|
|
$gff \\
|
|
$args \\
|
|
-o ${prefix}.gtf
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
gffread: \$(gffread --version 2>&1)
|
|
END_VERSIONS
|
|
"""
|
|
}
|