The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language. They can be seamlessly scaled to server, cluster, grid and cloud environments, without the need to modify the workflow definition. Finally, Snakemake workflows can entail a description of required software, which will be automatically deployed to any execution environment.
- To get a first impression, please visit https://snakemake.github.io.
- To properly understand what Snakemake can do for you please read our “rolling” paper.
- News about Snakemake are published via Twitter.
- To learn Snakemake, please do the Snakemake Tutorial, and see the FAQ.
- Best practices for writing Snakemake workflows can be found here.
- For more advanced usage on various platforms, see the Snakemake Executor Tutorials.
- For releases, see Changelog.
- Check frequently asked questions (FAQ).
- In case of questions, please post on stack overflow.
- To discuss with other Snakemake users, use the discord server. Please do not post questions there. Use stack overflow for questions.
- For bugs and feature requests, please use the issue tracker.
- For contributions, visit Snakemake on Github and read the guidelines.
When using Snakemake, please cite our “rolling” paper
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., Köster, J., 2021. Sustainable data analysis with Snakemake. F1000Res 10, 33.
This paper will also be regularly updated when Snakemake receives new features. See Citations for more information.
- Snakemake Wrappers Repository
- The Snakemake Wrapper Repository is a collection of reusable wrappers that allow to quickly use popular tools from Snakemake rules and workflows.
- Snakemake Workflow Catalog
- An automatically scraped catalog of publicly available Snakemake workflows for any kind of data analysis.
- Snakemake Workflows Project
- This project provides a collection of high quality modularized and re-usable workflows. The provided code should also serve as a best-practices of how to build production ready workflows with Snakemake. Everybody is invited to contribute.
- Snakemake Profiles Project
- This project provides Snakemake configuration profiles for various execution environments. Please consider contributing your own if it is still missing.
- Conda-Forge is a community driven distribution of Conda packages that can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries.
- Bioconda, a partner project of conda-forge, is a community driven distribution of bioinformatics-related Conda packages that can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries.