Appendix 2: How dependency is checked


How does Ruffus decide how to run your pipeline?

  • In which order should pipelined functions be called?
  • Which parts of the pipeline are up-to-date and do not need to be rerun?

Running all out-of-date tasks and dependents


By default, Ruffus will

  • build a flow chart (dependency tree) of pipelined tasks (functions)
  • start from the most ancestral tasks with the fewest dependencies (task1 and task4 in the flowchart above).
  • walk up the tree to find the first incomplete / out-of-date tasks (i.e. task3 and task5.
  • start running from there
All down-stream (dependent) tasks will be re-run anyway, so we don’t have to test
whether they are up-to-date or not.


This means that Ruffus may ask any task if their jobs are out of date more than once:

  • once when deciding which parts of the pipeline have to be run
  • once just before executing the task.

Ruffus tries to be clever / efficient, and does the minimal amount of querying.

Forced Reruns

Even if a pipeline stage appears to be up to date, you can always force the pipeline to include from one or more task functions.

This is particularly useful, for example, if the pipeline data hasn’t changed but the analysis or computional code has.

pipeline_run(forcedtorun_tasks = [up_to_date_task1])

will run all tasks from up_to_date_task1 to final_task

Both the “target” and the “forced” lists can include as many tasks as you wish. All dependencies are still carried out and out-of-date jobs rerun.

Esoteric option: Minimal Reruns

In the above example, if we were to delete the results of up_to_date_task1, Ruffus would rerun up_to_date_task1, up_to_date_task2 and task3.

However, you might argue that so long as up_to_date_task2 is up-to-date, and it is the only necessary prerequisite for task3, we should not be concerned about up_to_date_task1.

This is enabled with:

pipeline_run([task6], gnu_make_maximal_rebuild_mode = False)

This option walks down the dependency tree and proceeds no further when it encounters an up-to-date task (up_to_date_task2) whatever the state of what lies beyond it.

This rather dangerous option is useful if you don’t want to keep all the intermediate files/results from upstream tasks. The pipeline will only not involve any incomplete tasks which precede an up-to-date result.

This is seldom what you intend, and you should always check that the appropriate stages of the pipeline are executed in the flowchart output.