Snakemake workflow: single-cell-preprocess

A Snakemake workflow for for processing 10X single-cell data

• Snakemake workflow: single-cell-preprocess
  • Usage
  • Deployment options
  • Authors
  • References
  • TODO

Usage

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.

Deployment options

To run the workflow from command line, change the working directory.

cd path/to/snakemake-workflow-name

Adjust options in the default config file config/config.yml. Before running the complete workflow, you can perform a dry run using:

snakemake --dry-run

To run the workflow with test files using conda:

snakemake --cores 2 --sdm conda --directory .test

To run the workflow with apptainer / singularity, add a link to a container registry in the Snakefile, for example container: "oras://ghcr.io/<user>/<repository>:<version>" for Github's container registry. Run the workflow with:

snakemake --cores 2 --sdm conda apptainer --directory .test

Authors

• Liezel Tamon
  • University of Oxford
  • ORCID profile
  • https://www.imm.ox.ac.uk/people/liezel-tamon

References

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.

TODO

• Replace <owner> and <repo> everywhere in the template with the correct user name/organization, and the repository name. The workflow will be automatically added to the snakemake workflow catalog once it is publicly available on Github.
• Replace <name> with the workflow name (can be the same as <repo>).
• Replace <description> with a description of what the workflow does.
• Update the deployment, authors and references sections.
• Update the README.md badges. Add or remove badges for conda/singularity/apptainer usage depending on the workflow's deployment options.
• Do not forget to also adjust the configuration-specific config/README.md file.