.. _project_info-citations:

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

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


.. project_info-citing_snakemake:

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

When using Snakemake for a publication, **please cite the following article** in you 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. <https://doi.org/10.12688/f1000research.29032.1>`_

This "rolling" paper will be regularly updated when Snakemake receives new features.

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

The initial Snakemake publication was:

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

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. <https://drops.dagstuhl.de/opus/volltexte/oasics-complete/oasics-vol26-gcb2012-complete.pdf>`_

And my PhD thesis which describes all algorithmic details as of 2015:

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

The most comprehensive publication is our "rolling" paper (see above):

`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. <https://doi.org/10.12688/f1000research.29032.1>`_


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

If you publish a Snakemake workflow, consider adding a link to `the documentation <https://snakemake.readthedocs.io>`_ with `this badge <https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat>`_ to your project page.

The markdown syntax is

.. sourcecode:: text

    [![Snakemake](https://img.shields.io/badge/snakemake-≥5.6.0-brightgreen.svg?style=flat)](https://snakemake.readthedocs.io)

Replace the ``5.6.0`` with the minimum required Snakemake version.
You can also `change the style <https://shields.io/#styles>`_.
