Workflow not showing when using GitHub App

Tools and Workflows
1

Hello,

I was trying to use Dockstore’s GitHub App to publish our workflows. I followed your instructions to successfully install it (see the screen shot below). However, none of the workflows showed up in “My Workflows” panel.

Screen Shot 2022-03-13 at 14.37.52
Screen Shot 2022-03-13 at 14.37.52986×716 54.3 KB

2

I checked the GitHub App Logs, but only see that this failure was due to “must not be null”, which I totally have no idea about how to fix it. (please see the screen shot below)

Screen Shot 2022-03-13 at 14.38.44
Screen Shot 2022-03-13 at 14.38.44751×203 7.95 KB

3

Could you please give me a hand? You can see my .dockstore.yml for reference.

Thanks!

Sincerely,
Yiming

4

Sorry you’re running into an issue getting cumulus onto Dockstore! Please give us some time to look over the logs and the information you provided to figure out the best next steps. We will post to this thread with updates as soon as they are available.

5

Hi Yiming,

After looking over the linked .dockstore.yml file, we noticed a typo in one of the YAML keys for Cellranger_create_reference: cumulus/.dockstore.yml at a5d26f791a8edcd9d0a66b9f703663e647ef4586 · lilab-bcb/cumulus · GitHub.
Note that the current text is sublicass and should be subclass. Renaming this key will allow the GitHub App to sync successfully.

We’ve also opened an issue on our GitHub page to improve the error reporting for invalid keys in the .dockstore.yml to be more verbose. Here is a link to the GitHub issue: Vague GitHub Apps error on invalid YAML key · Issue #4791 · dockstore/dockstore · GitHub.

Let us know if this solves the issue, or if you have any further questions!

Thanks,
Richard

7

Hi Richard-Hansen,

Thank you so much for your suggestion! It fixed my sync issue.

However, I still have one issue left. In my .dockstore.yml file, I specified that only tags and “master” branch are exposed to the public. However, after sync via GitHub App, I still see that all my branches are exposed (please see the screen shot below):

Screen Shot 2022-03-14 at 16.52.40
Screen Shot 2022-03-14 at 16.52.40892×720 62 KB

Did I still do something wrong in my .dockstore.yml file?

Sincerely,
Yiming

8

Hi Yiming,

The filters set in the .dockstore.yml file indicate which branches/tags are refreshed on Dockstore when the GitHub App is triggered. Branches and tags that have already been synced over to Dockstore will remain public by default.

Looking through the commit history of the .dockstore.yml file, it appears the initial commit (Add Dockstore config file for automated workflow synchronization · lilab-bcb/cumulus@631304b · GitHub) synced changes on all branches and tags from your repository. The current version of the .dockstore.yml file (cumulus/.dockstore.yml at 0d2bf4e1a180ee3b54c007770cb19a395527992a · lilab-bcb/cumulus · GitHub) will sync changes on tags and the master branch only.

You can hide versions via the UI. There is not currently support for hiding a version using the .dockstore.yml config file. To hide a version:

  1. Navigate to a workflow’s Versions tab, as shown in your screenshot above.
  2. Select the Actions dropdown.
  3. Click Edit
  4. Check the box with text Hidden
  5. Click Save Changes

Let me know if you have any questions!

Thanks,
Richard

9

I see. Thank you for this clarification. It really helps.

Sincerely,
Yiming