Change workflow subclass/descriptor type from CWL to WDL

Dockstore
1

I accidentally added a .dockstore.yml file to my GitHub repo with the wrong subclass (CWL instead of WDL). I tried changing the subclass to WDL in .dockstore.yml, but it didn’t update in the dockstore interface and I can’t publish the workflow.

If it helps, here are links to my repository and the dockstore workflow page.

How can I change the subclass/descriptor type from CWL to WDL?

2

Hi!
Try changing the name at the same time you change the subclass to WDL.
That should create a new WDL workflow.

We also have a new version of Dockstore coming out in less than a month that will let you delete workflows in this situation (never been published) but the current workaround would be to create a new one with the right info.

Let us know if it works!

3

I tried changing the name in the .dockstore.yml file from “fetch_dbgap_files” to “fetch_dbgap_files_wdl”, but the new workflow hasn’t shown up on Dockstore after ~15 minutes. Here’s the contents of my .dockstore.yml file:

version: 1.2
workflows:
    - name: fetch_dbgap_files_wdl
      subclass: WDL
      primaryDescriptorPath: fetch_dbgap_files.wdl

Also, noting that the ability to delete unpublished workflows will be great, so thanks for implementing that feature!

4

Hmmm, does anything interesting show up in the github app logs?
Here’s a link to how you can find them GitHub App Troubleshooting & FAQs — Dockstore documentation

5

No, nothing in the github app logs. The last thing I see is yesterday’s error saying that I can’d add a WDL version to a CWL workflow.

6

I’ve also created Update .dockstore.yml by denis-yuen · Pull Request #1 · UW-GAC/fetch-dbgap-files · GitHub to address one possible issue

Edit to add: this does seem to work on my (unpublished) fork

7

Thanks for the pull request – I merged it in. I’m still not seeing any new unpublished workflows on my Dockstore page though. I tried refreshing the github organization a couple times. Still nothing new in the app logs.

8

Hmmm, oddly, I don’t see any events at all on the back-end either.

Could you do something trivial for the repo contents such as modifying a readme? I wonder if the PR merge somehow doesn’t count as an event since the origin is my fork.

9

Ah, I figured it out. First, I made a small change to the README and nothing happened. Then I looked at which repositories were being synched with Dockstore. As part of my previous attempts to change CWL to WDL yesterday, I had de-selected the fetch-dbgap-files repo so nothing from it was synching. I re-selected it and now the workflow has synched successfully. Thanks!

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