.. SnakeLines documentation master file, created by
   sphinx-quickstart on Thu Sep  6 13:59:16 2018.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. include:: ../README.rst

Contents
========

.. toctree::
   :caption: User documentation
   :maxdepth: 2

   user/example
   user/running
   user/configuration
   user/aliases
   user/tools

.. toctree::
   :caption: Developer notes
   :maxdepth: 2

   development/structure
   development/new_rules
   development/replace_methods
   development/documentation

.. toctree::
   :caption: Pipelines
   :maxdepth: 2

   pipelines/quality_report
   pipelines/preprocess_paired_end
   pipelines/mapping
   pipelines/download_reference_and_mapping
   pipelines/assembly
   pipelines/variant_calling
   pipelines/methylation
   pipelines/transcriptomics
   pipelines/metagenomics
   pipelines/viral_identification
   pipelines/download_reference
   pipelines/infer_phylogeny
   pipelines/illumina_single_end
   pipelines/nanopore_variant
   pipelines/covidseq

.. toctree::
   :caption: Documentation
   :maxdepth: 2

   rules/outline