This is an Owl Pipeline that runs Cell Ranger to process single-cell data.
An example pipeline definition file is:
# Version of the configuration file version: 1 name: cellranger # Location of the cellranger software # soft: /soft/cellranger # command to run, currently only count command: count # Arguments for the command above id: SITTF9 sample: SITTF9 transcriptome: /storage/shared/cellranger_refs/refdata-gex-mm10-2020-A fastqs: /storage/user/cellranger/SLX-20946 output_dir: /storage/user/cellranger/runs # extra # useful to add localcores and localmem in case cellranger fails to detect them extra: ["--localcores", "20", "--localmem", "64"] requirements: workers: 1 threads: 25 memory: 64