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.
- 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 :ref:`tutorial`, and see the :ref:`FAQ <project_info-faq>`.
- Best practices for writing Snakemake workflows can be found :ref:`here <snakefiles-best_practices>`.
- For more advanced usage on various platforms, see the :ref:`executor_tutorial`.
- For releases, see :ref:`Changelog <changelog>`.
- Check :ref:`frequently asked questions (FAQ) <project_info-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 :ref:`guidelines <project_info-contributing>`.
When using Snakemake, please cite our "rolling" paper
This paper will also be regularly updated when Snakemake receives new features. See :doc:`Citations <project_info/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.
- 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.
.. toctree:: :caption: Getting started :name: getting_started :hidden: :maxdepth: 1 getting_started/installation tutorial/tutorial tutorial/short executor_tutorial/tutorial snakefiles/best_practices
.. toctree:: :caption: Executing workflows :name: execution :hidden: :maxdepth: 1 executing/cli executing/cluster executing/cloud executing/grouping executing/caching executing/interoperability executing/monitoring
.. toctree::
:caption: Defining workflows
:name: snakefiles
:hidden:
:maxdepth: 1
snakefiles/writing_snakefiles
snakefiles/rules
snakefiles/configuration
snakefiles/modularization
snakefiles/remote_files
snakefiles/utils
snakefiles/deployment
snakefiles/reporting
snakefiles/testing
snakefiles/foreign_wms
.. toctree::
:caption: Project Info
:name: project-info
:hidden:
:maxdepth: 1
project_info/citations
project_info/more_resources
project_info/faq
project_info/contributing
project_info/authors
project_info/history
project_info/license