A Snakemake workflow for counting single cell RNAseq (scRNA-seq) data with Cell Ranger (Cell Ranger licensing requires a manual download of the software).
The usage of this workflow is described in the Snakemake Workflow Catalog.
Detailed information about input data and workflow configuration can also be found in the config/README.md.
If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.
To run the workflow from command line, change the working directory.
cd path/to/snakemake-workflow-nameAdjust options in the default config file config/config.yml.
Before running the complete workflow, you can perform a dry run using:
snakemake --dry-runTo run the workflow with test files using conda (this will download several GB of example data):
snakemake --cores 2 --sdm conda --directory .test/ --snakefile .test/Snakefile- David Lähnemann
- German Cancer Consortium (DKTK), partner site Essen-Düsseldorf, A partnership between DKFZ and University Hospital Essen
- https://orcid.org/0000-0002-9138-4112
- Smiths Sengkwawoh Lueong
- German Cancer Consortium (DKTK), partner site Essen-Düsseldorf, A partnership between DKFZ and University Hospital Essen
- https://orcid.org/0000-0002-2776-6706
Köster, J., Mölder, F., Jablonski, K. P., Letcher, B., Hall, M. B., Tomkins-Tinch, C. H., Sochat, V., Forster, J., Lee, S., Twardziok, S. O., Kanitz, A., Wilm, A., Holtgrewe, M., Rahmann, S., & Nahnsen, S. Sustainable data analysis with Snakemake. F1000Research, 10:33, 10, 33, 2021. https://doi.org/10.12688/f1000research.29032.2.