Only run update_biocontainers on containers in the registry

[georgiastuart]

Describe the bug

Update biocontainers runs on a set of containers not necessarily in the registry.

To Reproduce Steps to reproduce the behavior:

• Create your own registry
• Delete all the biocontainers
• update_biocontainers still runs on all biocontainers

Expected behavior A clear and concise description of what you expected to happen.

I'd expect it to skip containers that aren't in the registry.

Version of Singularity and Singularity Registry HPC Client

https://github.com/georgiastuart/resistry-test

[georgiastuart]

I think I can fix this, I just can't do it right away so I wanted to bookmark with an issue!

[vsoch]

The listing comes from the galaxy project, here https://github.com/georgiastuart/resistry-test/blob/0a803915bcc1ae525e41248721c123eb8a869462/.github/scripts/get_biocontainers.py#L34 and the purpose is to add biocontainers that aren't in the registry. Can you help me understand why this needs fixing?

[georgiastuart]

My registry doesn't have any biocontainers in it and the script running tries to add them. This may be a "delete this workflow file if you don't want it" docs issue rather than a code issue!

[vsoch]

Yes - we should definitely add a “delete this workflow file” to the developer tutorial! Do you want to add it or would you like me to?

[georgiastuart]

I can! I should have time later today.

[vsoch]

yay! Thank you! <3