Running a workflow with a different version?

[amstilp]

Is there a (supported or recommended) way to run a different version of a workflow than the current version that's set on AnVIL? As an example, I have a workflow with versions "combined_checks" and "main". The version that's currently saved in AnVIL is "combined_checks", but I would like to run the "main" version.

I found one of two ways to potentially set the version:

1. Modify the config object returned by avworkspace_configuration_get() to replace the methodUri and methodVersion elements, eg:

config$methodRepoMethod$methodUri <- str_replace(config$methodRepoMethod$methodUri, "combined_checks", "main")
config$methodRepoMethod$methodVersion <- str_replace(config$methodRepoMethod$methodVersion, "combined_checks", "main")

2. From the AnVIL page for the workflow in my web browser, manually select the "main" branch and save the workflow, then run avworkspace_configuration_get().

While option 2 is a workaround, it would be nice to do everything from the command line/within R.

• Is there a better way to specify the version of the workflow that I would like to run, eg something like avworkflow_configuration_get("primed_cc/validate_phenotype_model", version="main")?
• If not, is this something the Bioconductor::AnVIL R package could support in the future?

---

For some more detailed background, this is part of what was causing the underlying error in my #80 issue.

The workflow I am trying to run is hosted on Dockstore (primed-cc/validate_phenotype_model), with underlying code hosted on GitHub (UW-GAC/primed-file-checks). When the workflow was imported into the workspace, it was set to use the "combined_checks" branch. This branch has since
been merged into main and deleted, so avworkspace_configuration_inputs() was trying to get the inputs from a branch of the code that no longer exists.

Doing either of the two fixes above let me get the inputs with avworkspace_configuration_inputs().

[amstilp]

Also if it's helpful, here's the error I got after the #80 fix (when trying to pull config inputs for a branch that longer existed):

> inputs <- avworkflow_configuration_inputs(config)
Error: 'avworkflow_response' failed:
  Not Found (HTTP 404).
  Cannot get dockstore://github.com%2FUW-GAC%2Fprimed-file-checks%2Fvalidate_phenotype_model/combined_checks from method repo.

so that led me down this path.

[mtmorgan]

I don't think there is currently a better way to do this.

It seems like there are two things to do to implement a new feature...

• discover available versions
• easily update version to be used

I will look into this

[amstilp]

Thanks! Given that there are some workarounds, this would be a nice feature but isn't a blocker for anything.