nf-core_modules/modules/cellranger/mkgtf/main.nf
2022-02-04 09:53:32 +01:00

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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:6.1.2"
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
"""
}