.. _project_info-citations:

====================
Citing and Citations
====================

This section gives instructions on how to cite Snakemake and lists citing articles.


.. project_info-citing_snakemake:

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Citing Snakemake
----------------

When using Snakemake for a publication, **please cite the following article** in you paper:

Cite This
=========

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


More References
===============

Another publication describing more of Snakemake internals:

`Köster, Johannes and Rahmann, Sven. "Building and Documenting Bioinformatics Workflows with Python-based Snakemake". Proceedings of the GCB 2012. <http://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_

And my PhD thesis which describes all algorithmic details:

`Johannes Köster, "Parallelization, Scalability, and Reproducibility in Next-Generation Sequencing Analysis", TU Dortmund 2014 <http://hdl.handle.net/2003/33940>`_


Project Pages
=============

If you publish a Snakemake workflow, consider to add this badge to your project page:

.. image:: https://img.shields.io/badge/snakemake-≥3.5.2-brightgreen.svg?style=flat-square
   :target: https://snakemake.bitbucket.io

The markdown syntax is

.. sourcecode:: text

    [![Snakemake](https://img.shields.io/badge/snakemake-≥3.5.2-brightgreen.svg?style=flat-square)](https://snakemake.bitbucket.io)

Replace the ``3.5.2`` with the minimum required Snakemake version.
You can also `change the style <http://shields.io/#styles>`_.
