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********
pipemake
********
pipemake is a lightweight, flexible, and easy-to-use tool for creating and managing `Snakemake <https://snakemake.readthedocs.io/>`_ pipelines. It was designed with three primary goals: 

1. Offer a collection of curated, customizable genomic analysis pipelines for researchers seeking to rapidly integrate Snakemake-based workflows into their research.
2. Optimize computational efficiency and reproducibility by fully operating in the Snakemake ecosystem.
3. Streamline development by creating a flexible platform with swappable pipelines that easily reuse previously written Snakemake code.

.. toctree::
    :hidden:
    :caption: pipemake Documentation

    about
    installation
    pipelines
    usage
    create
    filetypes
    
    contact

================
Getting pipemake
================

-----
mamba
-----

.. code-block:: bash

    mamba create -c conda-forge -c bioconda -c kocherlab -n pipemake pipemake

For more information, see the :ref:`installation`.

======
Issues
======

1. Check the `docs <https://pipemake.rtfd.io/>`_.
2. Search the `issues on GitHub <https://github.com/kocherlab/pipemake/issues>`_ or open a new one.

============
Contributors
============

* **Andrew Webb**, Department of Ecology and Evolutionary Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Howard Hughes Medical Institute, Chevy Chase, MD, USA
* **Scott Wolf**, Research Computing, Princeton University, Princeton, NJ, USA
* **Ian M Traniello**, Department of Ecology and Evolutionary Biology and Lewis-Sigler Institute for Integrative Genomics, Princeton University
* **Sarah Kocher**, Department of Ecology and Evolutionary Biology, Lewis-Sigler Institute for Integrative Genomics, Princeton University, Howard Hughes Medical Institute, Chevy Chase, MD, USA

=======
License
=======

Pipemake is licensed under the MIT license. See the `LICENSE <https://github.com/kocherlab/pipemake/blob/main/LICENSE>`_ file for details.