New upstream version 5.5.4

[5.5.4] - 2019-07-21

====================

Changed

-------

- Reports now automatically include workflow code and configuration for improved transparency.

[5.5.3] - 2019-07-11

====================

Changed

.. getting_started-installation:

.. _getting_started-installation:

============

Installation

Snakemake is available on PyPi as well as through Bioconda and also from source code.

You can use one of the following ways for installing Snakemake.

.. _conda-install:

Installation via Conda

======================

   getting_started/installation

   getting_started/examples

   tutorial/tutorial

   tutorial/short

.. toctree::

  initialization to the DAG phase. In contrast to input functions, these can

  optionally take additional arguments ``input``, ``output``, ``threads``, and ``resources``.

Similar to input and output files, ``params`` can be accessed from the shell command or the Python based ``run`` block (see :ref:`tutorial-report`).

Similar to input and output files, ``params`` can be accessed from the shell command the Python based ``run`` block, or the script directive (see :ref:`tutorial-script`).

Exercise

........

   :align: center

.. _tutorial-script:

Step 6: Using custom scripts

::::::::::::::::::::

::::::::::::::::::::::::::::

Usually, a workflow not only consists of invoking various tools, but also contains custom code to e.g. calculate summary statistics or create plots.

While Snakemake also allows you to directly :ref:`write Python code inside a rule <.. _snakefiles-rules>`_, it is usually reasonable to move such logic into separate scripts.