Snakemake workflow: IDAT to Graph

A Snakemake workflow for creating graph visualizations of DNA methylation data.

• Snakemake workflow: IDAT to Graph
  • 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.yaml. 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

Authors

• Vojtěch Damian
  • Department of Pathology and Molecular Medicine, Second Faculty of Medicine, Charles University, Motol and Homolka University Hospital
  • ORCID profile

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

• Add an option to choose between using beta values and M-values
• Add report support