.. _manual-main:

=========
Snakemake
=========

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    :target: https://bioconda.github.io/recipes/snakemake/README.html

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    :target: https://www.python.org

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    :target: https://pypi.python.org/pypi/snakemake

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    :target: https://hub.docker.com/r/snakemake/snakemake

.. image:: https://github.com/snakemake/snakemake/workflows/CI/badge.svg?branch=master&label=tests
    :target: https://github.com/snakemake/snakemake/actions?query=branch%3Amaster+workflow%3ACI

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    :target: https://stackoverflow.com/questions/tagged/snakemake

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    :target: https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester

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    :alt: Discord
    :target: https://discord.gg/NUdMtmr

.. image:: https://img.shields.io/github/stars/snakemake/snakemake?style=social
    :alt: GitHub stars
    :target: https://github.com/snakemake/snakemake/stargazers

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          <span class="__dimensions_badge_embed__" data-doi="https://doi.org/10.1093/bioinformatics/bts480" data-legend="always" data-style="large_rectangle"></span><script async src="https://badge.dimensions.ai/badge.js" charset="utf-8"></script>

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 <https://badge.dimensions.ai/details/id/pub.1018944052>`_.
For an introduction, please visit https://snakemake.github.io.


.. _main-getting-started:

---------------
Getting started
---------------

To get a first impression, please visit https://snakemake.github.io.
News about Snakemake are published via `Twitter <https://twitter.com/search?l=&q=%23snakemake%20from%3Ajohanneskoester>`_.
To learn Snakemake, please do the :ref:`tutorial`, and see the :ref:`FAQ <project_info-faq>`.
For more advanced usage on various platforms, see the :ref:`executor_tutorial`.

.. _main-support:

-------
Support
-------

* For releases, see :ref:`Changelog <changelog>`.
* Check :ref:`frequently asked questions (FAQ) <project_info-faq>`.
* In case of **questions**, please post on `stack overflow <https://stackoverflow.com/questions/tagged/snakemake>`_.
* To **discuss** with other Snakemake users, you can use the `mailing list <https://groups.google.com/forum/#!forum/snakemake>`_. **Please do not post questions there. Use stack overflow for questions.**
* For **bugs and feature requests**, please use the `issue tracker <https://github.com/snakemake/snakemake/issues>`_.
* For **contributions**, visit Snakemake on `Github <https://github.com/snakemake/snakemake>`_ and read the :ref:`guidelines <project_info-contributing>`.

--------
Citation
--------

`Köster, Johannes and Rahmann, Sven. "Snakemake - A scalable bioinformatics workflow engine". Bioinformatics 2012. <https://bioinformatics.oxfordjournals.org/content/28/19/2520>`_

See :doc:`Citations <project_info/citations>` for more information.

---------
Resources
---------

`Snakemake Wrappers Repository <https://snakemake-wrappers.readthedocs.org>`_
    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 <https://github.com/snakemake-workflows/docs>`_
    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 <https://github.com/snakemake-profiles/doc>`_
    This project provides Snakemake configuration profiles for various execution environments.
    Please consider contributing your own if it is still missing.

`Bioconda <https://bioconda.github.io/>`_
    Bioconda 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

.. toctree::
  :caption: Executing workflows
  :name: execution
  :hidden:
  :maxdepth: 1

  executing/cli
  executing/cluster
  executing/cloud
  executing/caching
  executing/interoperability

.. 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


.. toctree::
    :caption: API Reference
    :name: api-reference
    :hidden:
    :maxdepth: 1

    api_reference/snakemake
    api_reference/snakemake_utils
    api_reference/internal/modules


.. 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
