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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

Getting started

To get a first impression, please visit 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.



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