Skip to content

Migrate hlala to topic channels and bump version#11282

Open
jonasscheid wants to merge 2 commits intonf-core:masterfrom
jonasscheid:fix-hlala-topic-channels
Open

Migrate hlala to topic channels and bump version#11282
jonasscheid wants to merge 2 commits intonf-core:masterfrom
jonasscheid:fix-hlala-topic-channels

Conversation

@jonasscheid
Copy link
Copy Markdown
Contributor

@jonasscheid jonasscheid commented Apr 23, 2026

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the module conventions in the contribution docs
  • If necessary, include test data in your PR.
  • Remove all TODO statements.
  • Broadcast software version numbers to topic: versions - See version_topics
  • Follow the naming conventions.
  • Follow the parameters requirements.
  • Follow the input/output options guidelines.
  • Add a resource label
  • Use BioConda and BioContainers if possible to fulfil software requirements.
  • Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
    • For modules:
      • nf-core modules test <MODULE> --profile docker
      • nf-core modules test <MODULE> --profile singularity
      • nf-core modules test <MODULE> --profile conda

Description

  • Migrates hlala/preparegraph and hlala/typing from the deprecated versions.yml pattern to the new topic: versions channel system
  • Bump the reported version from 1.0.3 to 1.0.4 to match the pinned container/conda (hla-la=1.0.4).

Additional

hlala/typing

  • Fix the broken output staging: mkdir -p results && mv \${prefix}/ results/ nested results under results/\${prefix}/ instead of matching the declared results/* output paths. Replaced with a plain mv \${prefix} results rename.

@jonasscheid jonasscheid changed the title Migrate hlala/preparegraph and hlala/typing to topic channels Migrate hlala to topic channels and bump version Apr 23, 2026
"${task.process}":
hla-la: ${VERSION}
END_VERSIONS
mv ${prefix} results
Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

ideally we should avoid this. on cloud compute this produces a real copy of the data and not just renames it. but maybe for a different PR as I see it is a pre-existing condition.

Copy link
Copy Markdown
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

2 participants