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|
.. include:: global.inc
.. _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**.
================================================
1. Annotate functions with **Ruffus** decorators
================================================
******
Core
******
.. csv-table::
:header: "Decorator", "Syntax"
:widths: 100, 600,1
"@originate (:ref:`Manual <new_manual.originate>`)
", "
:ref:`@originate <decorators.originate>` ( ``output_files``, [``extra_parameters``,...] )
", ""
"@split (:ref:`Manual <new_manual.split>`)
", "
:ref:`@split <decorators.split>` ( ``tasks_or_file_names``, ``output_files``, [``extra_parameters``,...] )
", ""
"@transform (:ref:`Manual <new_manual.transform>`)
", "
| :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 <new_manual.merge>`)
", "
:ref:`@merge <decorators.merge>` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
", ""
"@posttask (:ref:`Manual <new_manual.posttask>`)
", "
| :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 necessary
================================================
- For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::
pipeline_printout_graph ( "flowchart.svg")
.. comment
This requires the `dot programme <http://www.graphviz.org/>`_ to be installed
- For a text printout of all jobs ::
pipeline_printout()
================================================
3. Run the pipeline
================================================
::
pipeline_run(multiprocess = N_PARALLEL_JOBS)
|
