renku rerun

Recreate files created by the “run” command.

Commands and options

renku rerun

Recreate files generated by a sequence of run commands.

renku rerun [OPTIONS] PATHS...

Options

-n, --dry-run

Show a preview of plans that will be executed.

--skip-metadata-update

Do not update the metadata store for the execution.

--from <sources>

Start an execution from this file.

-p, --provider <provider>

The workflow engine to use.

Default:

toil

Options:

toil | local | cwltool

-c, --config <config file>

YAML file containing configuration for the provider.

Arguments

PATHS

Required argument(s)

Examples

Assume you have run a step 2 that uses a stochastic algorithm, so each run will be slightly different. The goal is to regenerate output C several times to compare the output. In this situation it is not possible to simply call renku update since the input file A has not been modified after the execution of step 2.

A-[step 1]-B-[step 2*]-C

Recreate a specific output file by running:

$ renku rerun C

If you do not want step 1 to also be rerun, you can specify a starting point using the --from parameter:

$ renku rerun --from B C

Note that all other outputs of the executed workflow will be recreated as well. If the output didn’t change, it will be removed from git and re-added to ensure that the re-execution is properly tracked.

In some cases it may be desirable to avoid updating the renku metadata and to avoid committing this and any other change in the repository when the rerun command is used. If this is the case then you can pass the --skip-metadata-update flag to renku rerun.