Snakemake¶

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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.

Snakemake is highly popular with, >5 new citations per week. For an introduction, please visit https://snakemake.github.io.

Getting started¶

To get a first impression, please visit https://snakemake.github.io. News about Snakemake are published via Twitter. To learn Snakemake, please do the Snakemake Tutorial, and see the FAQ. For more advanced usage on various platforms, see the Snakemake Executor Tutorials.

Support¶

For releases, see Changelog.
Check frequently asked questions (FAQ).
In case of questions, please post on stack overflow.
To discuss with other Snakemake users, you can use the mailing list. 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.

Citation¶

Köster, Johannes and Rahmann, Sven. “Snakemake - A scalable bioinformatics workflow engine”. Bioinformatics 2012.

See Citations for more information.

Resources¶

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 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.
Bioconda: Bioconda can be used from Snakemake for creating completely reproducible workflows by defining the used software versions and providing binaries.