Snakemake¶
Snakemake is a popular workflow management system originated in bioinformatics in 2012, for reproducible and scalable data analyses. It describes workflows via a readable, Python-based language, and allows them to be scaled without the need for modifications.
Snakemake workflows can describe the software required to run them, which is automatically deployed in any execution environment.
The integration of Snakemake in the REANA platform allows Snakemake users to profit from the other regular REANA features in their workflows. For example, it is possible to execute hybrid workflows where some parts of calculations are executed on HTCondor high-throughput compute backend, other parts on Slurm high-performance compute backend, and yet other parts on the default Kubernetes compute backend. For more information about this topic please refer to the blog post mentioned below.
For additional information, please see:
- Snakemake documentation: https://snakemake.readthedocs.io
- REANA blog post: https://blog.reana.io/posts/2021/support-for-running-snakemake-workflows
Supported versions¶
| REANA version | Snakemake |
|---|---|
| 0.8 release series | 6.8.0 |