nf-core_modules/modules/cellranger/count/main.nf
2022-06-23 12:43:06 +02:00

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process CELLRANGER_COUNT {
tag "$meta.gem"
label 'process_high'
if (params.enable_conda) {
exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers."
}
container "nfcore/cellranger:7.0.0"
input:
tuple val(meta), path(reads)
path reference
output:
tuple val(meta), path("sample-${meta.gem}/outs/*"), emit: outs
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def sample_arg = meta.samples.unique().join(",")
def reference_name = reference.name
"""
cellranger \\
count \\
--id='sample-${meta.gem}' \\
--fastqs=. \\
--transcriptome=$reference_name \\
--sample=$sample_arg \\
--localcores=$task.cpus \\
--localmem=${task.memory.toGiga()} \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cellranger: \$(echo \$( cellranger --version 2>&1) | sed 's/^.*[^0-9]\\([0-9]*\\.[0-9]*\\.[0-9]*\\).*\$/\\1/' )
END_VERSIONS
"""
stub:
"""
mkdir -p "sample-${meta.gem}/outs/"
touch sample-${meta.gem}/outs/fake_file.txt
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
"""
}