Snakemake

https://img.shields.io/badge/Gitpod-ready--to--code-blue?logo=gitpod https://img.shields.io/conda/dn/bioconda/snakemake.svg?label=Bioconda https://img.shields.io/pypi/pyversions/snakemake.svg https://img.shields.io/pypi/v/snakemake.svg https://img.shields.io/github/workflow/status/snakemake/snakemake/Publish%20to%20Docker%20Hub?color=blue&label=docker%20container&branch=main https://github.com/snakemake/snakemake/workflows/CI/badge.svg?branch=main&label=tests https://img.shields.io/badge/stack-overflow-orange.svg https://img.shields.io/twitter/follow/johanneskoester.svg?style=social&label=Follow Discord GitHub stars

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 >7 new citations per week. For an introduction, please visit https://snakemake.github.io.

Getting started

Support

Citation

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.

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 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.

Snakemake API documentation

The documentation of the Snakemake API for programmatic access and developement on Snakemake.

Conda-Forge

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

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.