Ruffus Decorators¶
See also
Core¶
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Combinatorics¶
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@permutations (Summary / Manual)
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@combinations (Summary / Manual)
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@combinations_with_replacement (Summary / Manual)
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Advanced¶
Decorator Examples @subdivide (Summary / Manual) - 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.
- @subdivide ( tasks_or_file_names, regex(regex_pattern), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
- @subdivide ( tasks_or_file_names, formatter([regex_pattern] ), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
- Infers input as well as output from regular expression substitutions
- Useful for adding additional file dependencies
- @transform ( tasks_or_file_names, regex(regex_pattern), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
- @transform ( tasks_or_file_names, formatter(regex_pattern), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
- Groups multiple input files using regular expression matching
- Input resulting in the same output after substitution will be collated together.
- @collate (tasks_or_file_names, regex(regex_pattern), inputs | add_inputs(input_pattern), output_pattern, [extra_parameters,...] )
- @collate (tasks_or_file_names, formatter(formatter_pattern), inputs | add_inputs(input_pattern), output_pattern, [extra_parameters,...] )
- Indicates task dependency
- optional mkdir prerequisite (see Manual)
- Calls function after task completes
- Optional touch_file indicator (Manual)
- @posttask ( signal_task_completion_function )
- @posttask (touch_file( 'task1.completed' ))
- Switches tasks on and off at run time depending on its parameters
- Evaluated each time pipeline_run(...), pipeline_printout(...) or pipeline_printout_graph(...) is called.
- Dormant tasks behave as if they are up to date and have no output.
- @active_if ( on_or_off1, [on_or_off2, ...] )
@jobs_limit (Summary / Manual)
- 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 pipeline_run(...)
- @jobs_limit ( NUMBER_OF_JOBS_RUNNING_CONCURRENTLY )
- Generates paths for os.makedirs
- Customise the graphic for each task in printed flowcharts
- @graphviz ( graphviz_parameter = XXX, [graphviz_parameter2 = YYY ...])
Esoteric!¶
Decorator Examples
- I/O parameters
- skips up-to-date jobs
- Should use @transform etc instead
- By default, does not check if jobs are up to date
- Best used in conjuction with @check_if_uptodate
- @parallel ( parameter_list ) (see Manual)
- @parallel ( parameter_generating_function ) (see Manual)
@check_if_uptodate (Summary / Manual)
- Custom function to determine if jobs need to be run
- @check_if_uptodate ( is_task_up_to_date_function )
- @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