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.. include:: ../global.inc
#######################
Ruffus Decorators
#######################
.. seealso::
:ref:`Indicator objects <decorators.indicator_objects>`
.. _decorators:
=============================================
*Core*
=============================================
.. csv-table::
:header: "Decorator", "Examples"
:widths: 400, 600,1
"**@originate** (:ref:`Summary <decorators.originate>` / :ref:`Manual <new_manual.originate>`)
- Creates (originates) a set of starting file without dependencies from scratch (*ex nihilo*!)
- Only called to create files which do not exist.
- Invoked onces (a job created) per item in the ``output_files`` list.
", "
* :ref:`@originate <decorators.originate>` ( ``output_files``, [``extra_parameters``,...] )
\
", ""
"**@split** (:ref:`Summary <decorators.split>` / :ref:`Manual <new_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:`Summary <decorators.transform>` / :ref:`Manual <new_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``,...] )
\
* :ref:`@transform <decorators.transform>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.transform.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@merge** (:ref:`Summary <decorators.merge>` / :ref:`Manual <new_manual.merge>`)
- Merges multiple input files into a single output.
", "
* :ref:`@merge <decorators.merge>` (``tasks_or_file_names``, ``output``, [``extra_parameters``,...] )
\
", ""
.. _decorators.combinatorics:
=============================================
*Combinatorics*
=============================================
.. csv-table::
:header: "Decorator", "Examples"
:widths: 400, 600,1
"**@product** (:ref:`Summary <decorators.product>` / :ref:`Manual <new_manual.product>`)
- Generates the **product**, i.e. all vs all comparisons, between sets of input files.
", "
* :ref:`@product <decorators.product>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])* ,*[* ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *]), ]*, ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@permutations** (:ref:`Summary <decorators.permutations>` / :ref:`Manual <new_manual.permutations>`)
- Generates the **permutations**, between all the elements of a set of **Input**
- Analogous to the python `itertools.permutations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
- permutations('ABCD', 2) --> AB AC AD BA BC BD CA CB CD DA DB DC
", "
* :ref:`@permutations <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@combinations** (:ref:`Summary <decorators.combinations>` / :ref:`Manual <new_manual.combinations>`)
- Generates the **permutations**, between all the elements of a set of **Input**
- Analogous to the python `itertools.combinations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
- combinations('ABCD', 3) --> ABC ABD ACD BCD
- Generates the **combinations**, between all the elements of a set of **Input**:
i.e. r-length tuples of *input* elements with no repeated elements (**A A**)
and where order of the tuples is irrelevant (either **A B** or **B A**, not both).
", "
* :ref:`@combinations <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@combinations_with_replacement** (:ref:`Summary <decorators.combinations_with_replacement>` / :ref:`Manual <new_manual.combinations_with_replacement>`)
- Generates the **permutations**, between all the elements of a set of **Input**
- Analogous to the python `itertools.permutations <http://docs.python.org/2/library/itertools.html#itertools.permutations>`__
- combinations('ABCD', 3) --> ABC ABD ACD BCD
- Generates the **combinations_with_replacement**, between all the elements of a set of **Input**:
i.e. r-length tuples of *input* elements with no repeated elements (**A A**)
and where order of the tuples is irrelevant (either **A B** or **B A**, not both).
", "
* :ref:`@combinations_with_replacement <decorators.permutations>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.product.matching_formatter>` *([* ``regex_pattern`` *])*, ``tuple_size``, ``output_pattern``, [``extra_parameters``,...] )
\
", ""
=============================================
*Advanced*
=============================================
.. csv-table::
:header: "Decorator", "Examples"
:widths: 400, 600,1
"**@subdivide** (:ref:`Summary <decorators.subdivide>` / :ref:`Manual <new_manual.subdivide>`)
- Subdivides a set of *Inputs* each further into multiple *Outputs*.
- The number of files in each *Output* can be set at runtime by the use of globs.
- **Many to Even More** operator.
- The use of **split** is a synonym for subdivide is deprecated.
", "
* :ref:`@subdivide <decorators.subdivide>` ( ``tasks_or_file_names``, :ref:`regex <decorators.subdivide.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
\
* :ref:`@subdivide <decorators.subdivide>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.subdivide.matching_formatter>`\ *(*\ [``regex_pattern``] *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@transform** (:ref:`Summary <decorators.transform_ex>` / :ref:`Manual <new_manual.inputs>`)
- Infers input as well as output from regular expression substitutions
- Useful for adding additional file dependencies
", "
* :ref:`@transform <decorators.transform_ex>` ( ``tasks_or_file_names``, :ref:`regex <decorators.transform.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
\
* :ref:`@transform <decorators.transform_ex>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.transform.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , [ :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ] ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@collate** (:ref:`Summary <decorators.collate>` / :ref:`Manual <new_manual.collate>`)
- Groups multiple input files using regular expression matching
- Input resulting in the same output after substitution will be collated together.
", "
* :ref:`@collate <decorators.collate>` (``tasks_or_file_names``, :ref:`regex <decorators.collate.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
\
* :ref:`@collate <decorators.collate_ex>` (``tasks_or_file_names``, :ref:`regex <decorators.collate_ex.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
\
* :ref:`@collate <decorators.collate>` (``tasks_or_file_names``, :ref:`formatter <decorators.collate.matching_formatter>`\ *(*\ ``formatter_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
\
* :ref:`@collate <decorators.collate_ex>` (``tasks_or_file_names``, :ref:`formatter <decorators.collate_ex.matching_formatter>`\ *(*\ ``formatter_pattern``\ *)*\ , :ref:`inputs <decorators.inputs>` | :ref:`add_inputs <decorators.add_inputs>`\ *(*\ ``input_pattern``\ *)*\ , ``output_pattern``, [``extra_parameters``,...] )
\
", ""
"**@follows** (:ref:`Summary <decorators.follows>` / :ref:`Manual <new_manual.follows>`)
- Indicates task dependency
- optional :ref:`mkdir <decorators.follows.directory_name>` prerequisite (:ref:`see Manual <new_manual.follows.mkdir>`)
", "
* :ref:`@follows <decorators.follows>` ( ``task1``, ``'task2'`` ))
\
* :ref:`@follows <decorators.follows>` ( ``task1``, :ref:`mkdir <decorators.follows.directory_name>`\ ( ``'my/directory/'`` ))
\
", ""
"**@posttask** (:ref:`Summary <decorators.posttask>` / :ref:`Manual <new_manual.posttask>`)
- Calls function after task completes
- Optional :ref:`touch_file <decorators.posttask.file_name>` indicator (:ref:`Manual <new_manual.posttask.touch_file>`)
", "
* :ref:`@posttask <decorators.posttask>` ( ``signal_task_completion_function`` )
\
* :ref:`@posttask <decorators.posttask>` (:ref:`touch_file <decorators.touch_file>`\ ( ``'task1.completed'`` ))
\
", ""
"**@active_if** (:ref:`Summary <decorators.active_if>` / :ref:`Manual <new_manual.active_if>`)
- Switches tasks on and off at run time depending on its parameters
- Evaluated each time :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`, :ref:`pipeline_printout(...) <pipeline_functions.pipeline_printout>` or :ref:`pipeline_printout_graph(...) <pipeline_functions.pipeline_printout_graph>` is called.
- Dormant tasks behave as if they are up to date and have no output.
", "
* :ref:`@active_if <decorators.active_if>` ( ``on_or_off1, [on_or_off2, ...]`` )
\
", ""
"**@jobs_limit** (:ref:`Summary <decorators.jobs_limit>` / :ref:`Manual <new_manual.jobs_limit>`)
- Limits the amount of multiprocessing for the specified task
- Ensures that fewer than N jobs for this task are run in parallel
- Overrides ``multiprocess`` parameter in :ref:`pipeline_run(...) <pipeline_functions.pipeline_run>`
", "
* :ref:`@jobs_limit <decorators.jobs_limit>` ( ``NUMBER_OF_JOBS_RUNNING_CONCURRENTLY`` )
\
", ""
"**@mkdir** (:ref:`Summary <decorators.mkdir>` / :ref:`Manual <new_manual.mkdir>`)
- Generates paths for `os.makedirs <http://docs.python.org/2/library/os.html#os.makedirs>`__
", "
* :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`suffix <decorators.mkdir.suffix_string>`\ *(*\ ``suffix_string``\ *)*\ , ``output_pattern`` )
\
* :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`regex <decorators.mkdir.matching_regex>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern`` )
\
* :ref:`@mkdir <decorators.mkdir>` ( ``tasks_or_file_names``, :ref:`formatter <decorators.mkdir.matching_formatter>`\ *(*\ ``regex_pattern``\ *)*\ , ``output_pattern``)
\
", ""
"**@graphviz** (:ref:`Summary <decorators.graphviz>` / :ref:`Manual <new_manual.pipeline_printout_graph>`)
- Customise the graphic for each task in printed flowcharts
", "
* :ref:`@graphviz <decorators.graphviz>` ( ``graphviz_parameter = XXX``, ``[graphviz_parameter2 = YYY ...]``)
\
", ""
=============================================
*Esoteric!*
=============================================
.. csv-table::
:header: "Decorator", "Examples"
:widths: 400, 600,1
"**@files** (:ref:`Summary <decorators.files>` / :ref:`Manual <new_manual.deprecated_files>`)
- I/O parameters
- skips up-to-date jobs
- Should use :ref:`@transform <decorators.transform>` etc instead
", "
* :ref:`@files <decorators.files>`\ ( ``parameter_list`` )
\
* :ref:`@files <decorators.files>`\ ( ``parameter_generating_function`` )
\
* :ref:`@files <decorators.files>` ( ``input_file``, ``output_file``, ``other_params``, ... )
\
", ""
"**@parallel** (:ref:`Summary <decorators.parallel>` / :ref:`Manual <new_manual.deprecated_parallel>`)
- By default, does not check if jobs are up to date
- Best used in conjuction with :ref:`@check_if_uptodate <decorators.check_if_uptodate>`
", "
* :ref:`@parallel <decorators.parallel>` ( ``parameter_list`` ) (:ref:`see Manual <new_manual.deprecated_parallel>`)
\
* :ref:`@parallel <decorators.parallel>` ( ``parameter_generating_function`` ) (:ref:`see Manual <new_manual.on_the_fly>`)
\
", ""
"**@check_if_uptodate** (:ref:`Summary <decorators.check_if_uptodate>` / :ref:`Manual <new_manual.check_if_uptodate>`)
- Custom function to determine if jobs need to be run
", "
* :ref:`@check_if_uptodate <decorators.check_if_uptodate>` ( ``is_task_up_to_date_function`` )
\
", ""
".. tip::
The use of this overly complicated function is discouraged.
**@files_re** (:ref:`Summary <decorators.files_re>`)
- I/O file names via regular
expressions
- start from lists of file names
or |glob|_ results
- skips up-to-date jobs
", "
* :ref:`@files_re <decorators.files_re>` ( ``tasks_or_file_names``, ``matching_regex``, [``input_pattern``,] ``output_pattern``, ``...`` )
``input_pattern``/``output_pattern`` are regex patterns
used to create input/output file names from the starting
list of either glob_str or file names
", ""
|
