Ruffus Decorators

Note

See also:

• Indicator Objects

Basic

Decorator	Examples
@follows Indicates task dependency (see Manual) optional mkdir prerequisite (see Manual)	@follows ( task1, 'task2' )) @follows ( task1, mkdir( 'my/directory/' ))
@files (see Manual) I/O parameters skips up-to-date jobs	@files( parameter_list ) @files( parameter_generating_function ) @files ( input_file, output_file, other_params, ... )

Core

Decorator	Examples
@split (see Manual) Splits a single input into multiple output Globs in output can specify an indeterminate number of files.	@split ( tasks_or_file_names, output_files, [extra_parameters,...] )
@transform (see Manual) Applies the task function to transform input data to output.	@transform ( tasks_or_file_names, suffix(suffix_string), output_pattern, [extra_parameters,...] ) @transform ( tasks_or_file_names, regex(regex_pattern), output_pattern, [extra_parameters,...] )
@merge (see Manual) Merges multiple input files into a single output.	@merge (tasks_or_file_names, output, [extra_parameters,...] )
@posttask Calls function after task completes (see Manual) Optional touch_file indicator (see Manual)	@posttask ( signal_task_completion_function ) @posttask (touch_file( 'task1.completed' ))

Advanced

Decorator	Examples
@collate (See Manual here and here) 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), output_pattern, [extra_parameters,...] ) @collate (tasks_or_file_names, regex(regex_pattern), inputs | add_inputs(input_pattern), output_pattern, [extra_parameters,...] )
@transform (Manual) Infers input as well as output from regular expression substitutions Useful for adding additional file dependencies	@transform ( tasks_or_file_names, suffix(suffix_string), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] ) @transform ( tasks_or_file_names, regex(regex_pattern), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
@split (see Manual) Splits multiple input each further into many more output Globs in output can specify an indeterminate number of files.	@split ( tasks_or_file_names, regex(regex_pattern), [ inputs | add_inputs(input_pattern), ] output_pattern, [extra_parameters,...] )
@jobs_limit (see 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 )

Esoteric!

Decorator	Examples
@parallel 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 (see Manual) Custom function to determine if jobs need to be run	@check_if_uptodate ( is_task_up_to_date_function )
Tip The use of this overly complicated function is discouraged. @files_re I/O file names via regular expressions start from lists of file names or glob results skips up-to-date jobs	@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