.. Loosolab snakemake wrappers documentation master file, created by
   sphinx-quickstart on Tue Jun 12 10:48:38 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

Welcome to the snakemake wrapper documentation from Loosolab!
=============================================================

This repository is a collection of reusable wrappers that allow to quickly use popular tools
from `Snakemake <https://snakemake.readthedocs.io/en/stable/>`_ rules and workflows.

Usage
-----

The general strategy is to include a wrapper into your workflow via the `wrapper <http://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html?highlight=wrapper#wrappers>`_ directive, e.g.

.. code-block:: python

    rule samtools_sort:
        input:
            "mapped/{sample}.bam"
        output:
            "mapped/{sample}.sorted.bam"
        params:
            "-m 4G"
        threads: 8
        wrapper:
            "samtools/sort"


To automatically download the corresponding wrapper from the repository, just add ``--wrapper-prefix https://github.molgen.mpg.de/raw/loosolab/snakemake-wrappers/master/`` to your Snakemake call.

Each wrapper defines required software packages and versions. In combination with the ``--use-conda`` flag of Snakemake, these will be deployed automatically.

Contribute
----------

* provide a meta.yaml with name, description and author of the wrapper,
* provide an environment.yaml which lists all required software packages (the packages shall be available via https://anaconda.org),
* follow the python `style guide <http://legacy.python.org/dev/peps/pep-0008>`_,
* use 4 spaces for indentation.

.. toctree::
   :maxdepth: 3
   :glob:
   :caption: Available wrappers

   wrappers/*