nf-core_modules/modules/cellranger/mkgtf/main.nf
Alexander Peltzer e499abe572
Update main.nf
2022-06-10 10:53:48 +02:00

34 lines
816 B
Text

process CELLRANGER_MKGTF {
tag "$gtf"
label 'process_low'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:7.0.0"
input:
path gtf
output:
path "*.filtered.gtf", emit: gtf
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
"""
cellranger \\
mkgtf \\
$gtf \\
${gtf.baseName}.filtered.gtf \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
}