.. ruffus documentation master file, created by
   sphinx-quickstart on Tue Apr 21 16:55:56 2009.

***************************
*Ruffus* documentation
***************************


The :mod:`ruffus` module is a lightweight way to add support 
for running computational pipelines.

=====================
Start Here:
=====================

.. toctree::
   :maxdepth: 1

   introduction.rst
   tutorials/simple_tutorial/simple_tutorial.rst

=====================
Overview:
=====================
.. toctree::
   :maxdepth: 2

   cheatsheet.rst
   introduction.rst   
   design.rst
   Bugs and Updates <history>
   Future plans <todo>
   faq.rst
   glossary.rst



=====================
Simple Tutorial
=====================

.. toctree::
    :maxdepth: 1

    tutorials/simple_tutorial/simple_tutorial.rst
    tutorials/simple_tutorial/step1_follows.rst
    tutorials/simple_tutorial/step2_files.rst
    tutorials/simple_tutorial/step3_run_pipeline.rst
    tutorials/simple_tutorial/step4_split.rst
    tutorials/simple_tutorial/step5_transform.rst
    tutorials/simple_tutorial/step6_merge.rst
    tutorials/simple_tutorial/step7_posttask.rst

*********************
Accompanying code
*********************

.. toctree::
    :maxdepth: 1

    tutorials/simple_tutorial/step2_files_code.rst
    tutorials/simple_tutorial/step3_run_pipeline_code.rst
    tutorials/simple_tutorial/step4_split_code.rst
    tutorials/simple_tutorial/step5_transform_code.rst
    tutorials/simple_tutorial/step6_merge_code.rst
    tutorials/simple_tutorial/step7_posttask_code.rst

=====================
Manual
=====================
.. toctree::
    :maxdepth: 1

    Manual <tutorials/manual/manual_contents.rst>

=====================
Detailed Examples:
=====================
.. toctree::
   :maxdepth: 1

   examples/intermediate_example.rst
   examples/complicated_example.rst
   examples/sharing_data_across_jobs_example.rst

=====================
Decorators:
=====================
.. toctree::
    :maxdepth: 1

    decorators/decorators.rst
    decorators/indicator_objects.rst
    
#######################
Basic:
#######################

.. toctree::
    :maxdepth: 1

    decorators/follows.rst
    decorators/files.rst

#######################
Core:
#######################
.. toctree::
    :maxdepth: 1

    decorators/split.rst
    decorators/transform.rst
    decorators/merge.rst
    decorators/posttask.rst
    
 
#######################
For advanced users:
#######################
.. toctree::
    :maxdepth: 1

    decorators/parallel.rst
    decorators/check_if_uptodate.rst
    decorators/transform_ex.rst
    decorators/collate.rst
    decorators/files_re.rst


   
   
=====================
Example code:
=====================

.. toctree::
   :maxdepth: 1
   
   examples/simpler.rst
   examples/intermediate_example_code.rst
   examples/complicated_example_code.rst
   examples/sharing_data_across_jobs_example_code.rst
    
=====================
Modules:
=====================
   
.. toctree::
   :maxdepth: 2

   task.rst
   proxy_logger.rst
   
.. comment
   graph.rst
   print_dependencies.rst
   adjacent_pairs_iterate.rst


=====================
Indices and tables
=====================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`

