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Migrate slamdunk to topics - #12711

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SPPearce merged 6 commits into
nf-core:masterfrom
kurt-0130:seqera-co-scientist/slamdunk-all--b89d
Aug 18, 2026
Merged

Migrate slamdunk to topics#12711
SPPearce merged 6 commits into
nf-core:masterfrom
kurt-0130:seqera-co-scientist/slamdunk-all--b89d

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@kurt-0130

@kurt-0130 kurt-0130 commented Aug 16, 2026

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PR checklist

Closes #12702

  • 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
    • For subworkflows:
      • nf-core subworkflows test <SUBWORKFLOW> --profile docker
      • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
      • nf-core subworkflows test <SUBWORKFLOW> --profile conda

@kurt-0130
kurt-0130 requested a review from HaidYi August 16, 2026 18:26
Migrate slamdunk/all and slamdunk/map modules from YAML-based
versions output to the new topic-based versions pattern using
eval() for version extraction.

Changes:
- Replace VERSIONS_BLOCK with eval-based version output
- Add topic: versions channel for version reporting
- Update stub tests to use snapshot-based assertions
- Update meta.yml to reflect new output structure
- Remove versions.yml from expected outputs
@kurt-0130
kurt-0130 force-pushed the seqera-co-scientist/slamdunk-all--b89d branch from f71b13b to f33a4c7 Compare August 16, 2026 19:07
@mribeirodantas mribeirodantas changed the title Seqera co scientist/slamdunk all b89d Migrate slamdunk to topics Aug 16, 2026
@SPPearce SPPearce linked an issue Aug 17, 2026 that may be closed by this pull request

@LouisLeNezet LouisLeNezet left a comment

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Just a small change needed.
Great job.

Comment thread modules/nf-core/slamdunk/all/tests/main.nf.test Outdated
Comment thread modules/nf-core/slamdunk/map/tests/main.nf.test Outdated
Comment thread modules/nf-core/slamdunk/map/tests/main.nf.test Outdated
@SPPearce
SPPearce added this pull request to the merge queue Aug 18, 2026
Merged via the queue into nf-core:master with commit 7942c43 Aug 18, 2026
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Migrate to topic slamdunk/all

4 participants