.. _cheat_sheet:

#####################
Cheat Sheet
#####################

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

| Each stage or **task** in a computational pipeline is represented by a python function
| Each python function can be called in parallel to run multiple **jobs**.

.. |suffix| replace:: `suffix`
.. _suffix: decorators/indicator_objects.html#decorators.suffix
.. |mkdir| replace:: `mkdir`
.. _mkdir: decorators/indicator_objects.html#decorators.mkdir
.. |touch_file| replace:: `touch_file`
.. _touch_file: decorators/indicator_objects.html#decorators.touch_file
.. |regex| replace:: `regex`
.. _regex: decorators/indicator_objects.html#decorators.regex
.. |inputs| replace:: *inputs*
.. _inputs: decorators/indicator_objects.html#decorators.inputs

================================================
1. Annotate functions with **Ruffus** decorators
================================================


******
Basic 
******
.. csv-table::
   :header: "Decorator", "Examples"
   :widths: 400, 600,1
   
   "**@follows**

   - Indicates task dependency (:ref:`see Manual <manual.follows>`)
   - optional :ref:`mkdir <decorators.follows.directory_name>` prerequisite (:ref:`see Manual <manual.follows.mkdir>`)
   
   ", "
   | :ref:`@follows <decorators.follows>` ( ``task1``, ``'task2'`` ))
   | :ref:`@follows <decorators.follows>` ( ``task1``,  :ref:`mkdir <decorators.follows.directory_name>`\ ( ``'my/directory/for/results'`` ))
   
   ", ""
   "**@files** (:ref:`Manual <manual.files>`)
   
   - I/O parameters
   - skips up-to-date jobs
   
   ", "
   | :ref:`@files <decorators.files>`\ ( ``parameter_list`` )
   | :ref:`@files <decorators.files>`\ ( ``parameter_generating_function`` )
   | :ref:`@files <decorators.files>` ( ``input_file``, ``output_file``, ``other_params``, ... )
   
   ", ""

******
Core
******
.. csv-table::
   :header: "Decorator", "Examples"
   :widths: 400, 600,1

   "**@split** (:ref:`Manual <manual.split>`)   
   
   - Splits a single input into multiple output
   - Globs in ``output`` can specify an indeterminate number of files.
   
   ", "
   :ref:`@split <decorators.split>` ( ``tasks_or_file_names``, ``output_files``, [``extra_parameters``,...] )
   ", ""
   "**@transform** (:ref:`Manual <manual.transform>`)   
    
   - Applies the task function to transform input data to output.
    
   ", "
   | :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`suffix <decorators.transform.suffix_string>`\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
   | :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`regex <decorators.transform.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
   
   ", ""
   "**@merge** (:ref:`Manual <manual.merge>`)   

   - Merges multiple input files into a single output.
   
   ", "
   :ref:`@merge <decorators.merge>` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
   ", ""
   "**@posttask**

   - Calls function after task completes (:ref:`see Manual <posttask>`)
   - Optional :ref:`touch_file <decorators.posttask.file_name>` indicator (:ref:`see Manual <manual.posttask.touch_file>`)

   ", "
   | :ref:`@posttask <decorators.posttask>` ( ``signal_task_completion_function`` )
   | :ref:`@posttask <decorators.posttask>` (:ref:`touch_file <decorators.touch_file>`\ ( ``'task1.completed'`` ))
   
   ", ""

************************************************************************************************
See :ref:`Decorators <decorators>` for a complete list of decorators
************************************************************************************************


================================================
2. Print dependency graph if you necessary
================================================

- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::

        pipeline_printout_graph ( open("flowchart.svg", "w"),
                                 "svg",
                                 list_of_target_tasks)

.. comment
    
        This requires `dot <http://www.graphviz.org/>`_ to be installed

- For a text printout of all jobs ::

        pipeline_printout(sys.stdout, list_of_target_tasks)


================================================
3. Run the pipeline
================================================

::

    pipeline_run(list_of_target_tasks, [list_of_tasks_forced_to_rerun, multiprocess = N_PARALLEL_JOBS])


See the :ref:`Simple Tutorial <Simple_Tutorial>` for a quick introduction on how to add support
for ruffus.


