How long does it take Dockstore github app to synch/refresh?

Dockstore
1

I connected the Dockstore GitHub app to a repository containing WDL workflows. The integration works as expected when I click the “Refresh” button on Dockstore for the registered workflow. However, I think the GitHub integration should automatically refresh when a new commit is pushed to any branch with .dockstore.yml in it. I pushed new commits and created new branches with .dockstore.yml, but I would still need to manually click on the “Refresh” button on the Dockstore webpage to see the changes.

The GitHub repository is available at: https://github.com/talkowski-lab/pzm/blob/dockstore-test-3/.github/.dockstore.yml

And the Dockstore page is available at: Dockstore

2

Hi,

I think the .dockstore.yml processing is probably not working due to the wildcard in https://github.com/talkowski-lab/pzm/blob/dockstore-test-3/.github/.dockstore.yml#L4 (we don’t support wildcards in that value and the field is really supposed to point at only one workflow anyway)

After fixing it, a new push should update the workflow.

You can also look for an error message via the “app logs” button
https://docs.dockstore.org/en/stable/getting-started/github-apps/github-apps-troubleshooting-tips.html?highlight=App%20logs#how-do-i-view-the-github-app-logs

Edit to add: I also noticed in your link, the workflow is named “Classifier”
You will need to add a name: Classifier if you want to convert the old refresh-based workflow into a .dockstore.yml workflow otherwise you will get a new workflow without a name, which is also ok if that’s what you want

.dockstore.yml for Workflows Templates (version 1.2) — Dockstore documentation has more info

3

Hi, thank you for the suggestions!

I think wildcards are supported when registering a workflow manually, so do you think wildcard support will be added in future versions of the app?

4

Hi,

There probably is a different way to accomplish what you’re expecting. The ‘primaryDescriptorPath’ value is only meant to point at one workflow and we import the other files that it is pointing to in turn automatically.

If you need to import multiple workflows, you would specify multiple workflows as in this example

https://docs.dockstore.org/en/stable/assets/templates/workflows/workflows.html#filled-out-example-of-multiple-workflows-in-the-same-repository

5

That makes sense, thank you!