.. include:: ../../global.inc
.. include:: manual_chapter_numbers.inc

.. index::
    pair: Ruffus names list; Tutorial

.. _new_manual.ruffus_names:

##########################################################################################################################################################################################################################################
|new_manual.ruffus_names.chapter_num|: Names exported from Ruffus
##########################################################################################################################################################################################################################################

.. seealso::

    * :ref:`Manual Table of Contents <new_manual.table_of_contents>`

******************
Ruffus Names
******************

    This is a list of all the names *Ruffus* makes available:


    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    | Category                                                      | Manual                                                                                                                                                        |
    +===============================================================+===============================================================================================================================================================+
    |  **Pipeline functions**                                       | | :ref:`pipeline_printout() <pipeline_functions.pipeline_printout>` (:ref:`Manual <new_manual.pipeline_printout>`)                                            |
    |                                                               | | :ref:`pipeline_printout() <pipeline_functions.pipeline_printout_graph>` (:ref:`Manual <new_manual.pipeline_printout_graph>`)                                |
    |                                                               | | :ref:`pipeline_printout() <pipeline_functions.pipeline_run>` (:ref:`Manual <new_manual.pipeline_run>`)                                                      |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |  **Decorators**                                               |                                                                                                                                                               |
    |                                                               | | :ref:`@active_if <decorators.active_if>` (:ref:`Manual <new_manual.active_if>`)                                                                             |
    |                                                               | | :ref:`@check_if_uptodate <decorators.check_if_uptodate>` (:ref:`Manual <new_manual.check_if_uptodate>`)                                                     |
    |                                                               | | :ref:`@collate <decorators.collate>` (:ref:`Manual <new_manual.collate>`)                                                                                   |
    |                                                               | | :ref:`@files <decorators.files>` (:ref:`Manual <new_manual.deprecated_files>`)                                                                              |
    |                                                               | | :ref:`@follows <decorators.follows>` (:ref:`Manual <new_manual.follows>`)                                                                                   |
    |                                                               | | :ref:`@jobs_limit <decorators.jobs_limit>` (:ref:`Manual <new_manual.jobs_limit>`)                                                                          |
    |                                                               | | :ref:`@merge <decorators.merge>` (:ref:`Manual <new_manual.merge>`)                                                                                         |
    |                                                               | | :ref:`@mkdir <decorators.mkdir>` (:ref:`Manual <new_manual.mkdir>`)                                                                                         |
    |                                                               | | :ref:`@originate <decorators.originate>` (:ref:`Manual <new_manual.originate>`)                                                                             |
    |                                                               | | :ref:`@parallel <decorators.parallel>` (:ref:`Manual <new_manual.deprecated_parallel>`)                                                                     |
    |                                                               | | :ref:`@posttask <decorators.posttask>` (:ref:`Manual <new_manual.posttask>`)                                                                                |
    |                                                               | | :ref:`@split <decorators.split>` (:ref:`Manual <new_manual.split>`)                                                                                         |
    |                                                               | | :ref:`@subdivide <decorators.subdivide>` (:ref:`Manual <new_manual.subdivide>`)                                                                             |
    |                                                               | | :ref:`@transform <decorators.transform>` (:ref:`Manual <new_manual.transform>`)                                                                             |
    |                                                               | | :ref:`@files_re <decorators.files_re>` (:ref:`Manual <new_manual.deprecated_files_re>`)                                                                     |
    |                                                               |                                                                                                                                                               |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |  **Loggers**                                                  |                                                                                                                                                               |
    |                                                               | | stderr_logger                                                                                                                                               |
    |                                                               | | black_hole_logger                                                                                                                                           |
    |                                                               |                                                                                                                                                               |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |  **Parameter disambiguating Indicators**                      | | :ref:`suffix <decorators.suffix>` (:ref:`Manual <new_manual.suffix>`)                                                                                       |
    |                                                               | | :ref:`regex <decorators.regex>` (:ref:`Manual <new_manual.regex>`)                                                                                          |
    |                                                               | | :ref:`formatter <decorators.formatter>` (:ref:`Manual <new_manual.formatter>`)                                                                              |
    |                                                               | | :ref:`inputs <decorators.inputs>` (:ref:`Manual <new_manual.inputs>`)                                                                                       |
    |                                                               | | :ref:`inputs <decorators.add_inputs>` (:ref:`Manual <new_manual.inputs>`)                                                                                   |
    |                                                               | | :ref:`touch_file <decorators.touch_file>` (:ref:`Manual <new_manual.posttask.touch_file>`)                                                                  |
    |                                                               | | :ref:`combine <decorators.combine>`                                                                                                                         |
    |                                                               | | :ref:`mkdir <decorators.follows.mkdir>` (:ref:`Manual <new_manual.follows.mkdir>`)                                                                          |
    |                                                               | | :ref:`output_from <decorators.output_from>` (:ref:`Manual <new_manual.output_from>`)                                                                        |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |  **Decorators in ruffus.combinatorics**                       |                                                                                                                                                               |
    |                                                               | | :ref:`@combinations <decorators.combinations>` (:ref:`Manual <new_manual.combinations>`)                                                                    |
    |                                                               | | :ref:`@combinations_with_replacement <decorators.combinations_with_replacement>` (:ref:`Manual <new_manual.combinations_with_replacement>`)                 |
    |                                                               | | :ref:`@permutations <decorators.permutations>` (:ref:`Manual <new_manual.permutations>`)                                                                    |
    |                                                               | | :ref:`@product <decorators.product>` (:ref:`Manual <new_manual.product>`)                                                                                   |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+
    |  **Decorators in ruffus.cmdline**                             |                                                                                                                                                               |
    |                                                               | | :ref:`get_argparse <new_manual.cmdline.get_argparse>`                                                                                                       |
    |                                                               | | :ref:`setup_logging <new_manual.cmdline.setup_logging>`                                                                                                     |
    |                                                               | | :ref:`run <new_manual.cmdline.run>`                                                                                                                         |
    |                                                               | | :ref:`MESSAGE <new_manual.cmdline.MESSAGE>`                                                                                                                 |
    +---------------------------------------------------------------+---------------------------------------------------------------------------------------------------------------------------------------------------------------+