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# Cheat Sheet

The `ruffus` module is a lightweight way to add support for running computational pipelines.

## Usage

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 python decorators

> Decorator | Examples
> --- | ---
> @follows Indicate task dependency mkdir prerequisite shorthand | @follows ( `task1`, `'task2'` )) @follows ( `task1`, mkdir( `'my/directory/for/results'` ))
> @parallel Parameters for parallel jobs | @parallel ( `parameter_list` ) @parallel ( `parameter_generating_function` )
> @files I/O parameters skips up-to-date jobs | @files( `parameter_list` ) @files( `parameter_generating_function` ) Simplified syntax for tasks with a single job: @files ( `input_file`, `output_file`, `other_params`, `...` )
> @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 ( `glob_str`, `matching_regex`, `output_pattern`, `...` ) @files_re ( `file_names`, `matching_regex`, `input_pattern`, `output_pattern`, `...` ) @files_re ( `glob_str`, `matching_regex`, `output_pattern`, `...` ) @files_re ( `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
> @check_if_uptodate Checks if task needs to be run | @check_if_uptodate ( `is_task_up_to_date_function` )
> @posttask Calls function after task completes touch_file shorthand | @posttask ( `signal_task_completion_function` ) @posttask (@touch_file( `'task1.completed'` ))

### 2. Print dependency graph if you necessary

> - For a graphical flowchart in `jpg`, `svg`, `dot`, `png`, `ps`, `gif` formats:

>       pipeline_printout_graph ( open("flowchart.svg", "w"),
>                                "svg",
>                                list_of_target_tasks)

> This requires dot to be installed

> - For a text printout of all jobs

>       pipeline_printout(sys.stdout, list_of_target_tasks)

### 3. Run the pipeline

> pipeline_run(list_of_target_tasks, [list_of_tasks_forced_to_rerun, multiprocess = N_PARALLEL_JOBS])

See the Full Tutorial for a more complete introduction on how to add support for ruffus.

### Navigation

- index
- modules |
- next |
- previous |
Ruffus v. 1.0.6
- Home |
- Contents |
- Cheat sheet |
- Full tutorial |
- FAQ |
- Future plans |
- Search »