process CELLRANGER_COUNT { tag "$meta.gem" label 'process_high' if (params.enable_conda) { exit 1, "Conda environments cannot be used when using the Cell Ranger tool. Please use docker or singularity containers." } container "nfcore/cellranger:6.1.2" input: tuple val(meta), path(reads) path reference output: path("sample-${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 """ }