MONSDA
======

.. toctree::
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   :maxdepth: 2
   :caption: GETTING STARTED

   source/installation
   source/first

.. toctree::
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   :caption: PREPARING YOUR PROJECT

   source/preparation
   source/configurator

.. toctree::
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   :caption: EXECUTING MONSDA

   source/runsmk
   source/cluster


.. toctree::
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   :caption: TUTORIAL

   source/tutorial


.. toctree::
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   :caption: WORKFLOW AND TOOL OVERVIEW

   source/workflows


.. toctree::
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   :caption: DETAILS

   source/wrapper
   source/conditiontree
   source/config

.. toctree::
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   :caption: CONTRIBUTE

   source/integrate
   source/contribute


Welcome to **MONSDA**, Modular Organizer of Nextflow and Snakemake driven hts Data Analysis

Automizing HTS analysis from data download, preprocessing and mapping to postprocessing/analysis and track generation centered on a single config file. **MONSDA** can create **Snakemake** and **Nextflow** workflows centered on a user friendly, sharable **Json** config file and reproducible subworkflows. These workflows can either be saved to disk for manual inspection and execution or automatically executed.

For details on **Snakemake** and **Nextflow** and their features please refer to the corresponding Snakemake_  or Nextflow_ documentation.

.. _Snakemake: https://Snakemake.readthedocs.io/en/stable/tutorial/tutorial.html
.. _Nextflow: https://www.Nextflow.io/docs/latest/index.html

In general it is necessary to write a configuration file containing workflows to execute, information on paths, files to process and settings beyond default for mapping tools and others.
The template on which **MONSDA** is based on can be found in the **config** directory.

For **MONSDA** to be as FAIR as possible, one needs to use **conda** or the alternative **mamba**. For details on either please refer to the corresponding conda_ or mamba_ manual.

.. _conda: https://docs.conda.io/en/latest/
.. _mamba: https://mamba.readthedocs.io/en/latest/

This workflow organizer makes heavy use of **conda** and especially the bioconda_ channel.

.. _bioconda: https://bioconda.github.io