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
.