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Bioinformatics Pipeline Run Mode

When you rerun a pipeline after making some changes to it, the pipeline detects these changes and reruns only those blocks that are affected by these changes. This automatic change detection enables quick and efficient iterative workflows where you can tweak some parameters of a block or change the input values or data for your analysis.

By default, the pipeline uses the Minimal run mode. In this mode, the pipeline runs only the blocks for which one of the following statements is true:

  • The block has not been run before or its results have been deleted.

  • You have modified the block since the last time it ran.

  • Input data, including new runtime inputs, to the block has changed since the last run.

  • The block has one or more upstream blocks which have run since the last time the block was run.

If you are running only a subset of blocks within a pipeline, these rules are applied only to those selected blocks.

The other run mode is the Full mode. The pipeline runs all blocks even if they have previously computed results and there have been no changes affecting the block results.


Use the default Minimal run mode whenever possible because skipping up-to-date blocks can save significant time running the pipeline, especially when the pipeline has long-running blocks that do not need to rerun.

See Also