nextflow-io / nextflow

A DSL for data-driven computational pipelines
http://nextflow.io
Apache License 2.0
2.61k stars 606 forks source link

Implement SIF ORAS protocol to HTTP #5000

Open pditommaso opened 1 month ago

pditommaso commented 1 month ago

This PR draft the mapping of ORAS images names to HTTP ones.

netlify[bot] commented 1 month ago

Deploy Preview for nextflow-docs-staging ready!

Name Link
Latest commit a46d4a166d8e0485e89dcaed76ec4e0522fb16de
Latest deploy log https://app.netlify.com/sites/nextflow-docs-staging/deploys/667051543a4e0900082c777a
Deploy Preview https://deploy-preview-5000--nextflow-docs-staging.netlify.app
Preview on mobile
Toggle QR Code...

QR Code

Use your smartphone camera to open QR code link.

To edit notification comments on pull requests, go to your Netlify site configuration.

marcodelapierre commented 1 month ago

( a lot of extra commits due to fixing commit sign-offs - sorry! )

marcodelapierre commented 1 month ago

@pditommaso ready for review

Maybe we can still improve on messages/behaviour when image is not built, but otherwise the key implementation changes are there.

marcodelapierre commented 3 weeks ago

Still one failing unit test on CI should resolve docker container with wave container in WaveContainerResolverTest, call to resolveImage at line 76.

The responsible bit of code is in WaveContainerResolver, new lines 98-108.

Looking into it.

marcodelapierre commented 2 weeks ago

@pditommaso @ewels following the meeting today, I have implemented the workaround for the URI in the case of Seqera Containers: https://github.com/nextflow-io/nextflow/blob/wave-sif-http/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy#L392-L400

Ready for review (with one last unit test to fix)

marcodelapierre commented 2 weeks ago

OK, last outstanding unit test fixed:

marcodelapierre commented 2 weeks ago

@pditommaso ready for review

marcodelapierre commented 2 weeks ago

Do we need an integration test for running with Wave plugin and using Http over Oras?

pditommaso commented 2 weeks ago

It may be useful. Some wave tests are here

pditommaso commented 1 week ago

Let's put in hold, not sure anymore it makes sense to implement this