search

broadinstitute / gatk-sv

A structural variation pipeline for short-read sequencing
BSD 3-Clause "New" or "Revised" License
162 stars 71 forks source link

Setup automatic updates to WDLs on Dockstore #605

Closed VJalili closed 8 months ago

VJalili commented 9 months ago

This PR adds configurations necessary to enable automatic updates of the WDLs on Dockstore. Accordingly, this PR adds .dockstore.yml, which registers the workflows defined on GATK-SV Terra workspace (i.e., [gnomad-v3-sv/gatk-sv-pipeline-1kgp](https://app.terra.bio/#workspaces/gnomad-v3-sv/gatk-sv-pipeline-1kgp-test-noaddress)) for an automatic sync with Dockstore.

Only the root workflows need to be registered for automatic sync, and Dockstore will fetch all the dependencies automatically without a need for explicit registration. Additionally, the dockstore app does not support registering workflows using wildcards; hence, each workflow must be registered separately.

After this PR is merged, dockstore app will automatically sync the registered workflows with dockstore with every commit pushed to any branch on broadinstitute/gatk-sv that has .github/.dockstore.yml file in it.

mwalker174 commented 8 months ago

Thanks for your patience @VJalili. This looks great! I do think we will need to move to a forking development model to avoid spamming Dockstore with pushes, as it already seems we are breaking its limits. Still, IMO the transition is worth it to further automate out deployment process.

VJalili commented 8 months ago

Thanks, @mwalker174! I agree, hopefully this automation will help with dockstore refresh/sync, and one less manual step in the release process.