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fix(kofamscan): migrate to topic versions and add stub testing#11436

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HReed1 wants to merge 3 commits intonf-core:masterfrom
HReed1:stub-topics-kofamscan
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fix(kofamscan): migrate to topic versions and add stub testing#11436
HReed1 wants to merge 3 commits intonf-core:masterfrom
HReed1:stub-topics-kofamscan

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@HReed1
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@HReed1 HReed1 commented Apr 30, 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, also make a PR on the nf-core/modules repository to update the 'modules.json' and make sure to update the tool version!
  • Make sure your code lints (nf-core modules lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in module.html is updated unless an exception is made.
  • The test output is attached below and the test dataset is added to the nf-core/test-datasets repository.

Description

This PR standardizes the kofamscan module to the new topic: versions tuple architecture to resolve CI failures and meet project standards.

  • Migrated manual versions.yml generation to tuple emission with dynamic version extraction using eval.
  • Removed legacy versions.yml logic.
  • Implemented robust stub: block.
  • Updated snapshot assertions.
  • Confirmed strict-syntax compliance and 100% nf-core modules lint pass.

Part of #4570

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@SPPearce SPPearce left a comment

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If you move the setup block up to the top (outside of the first test) then it will only run once (and won't require code duplication)

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If you move the setup block up to the top (outside of the first test) then it will only run once (and won't require code duplication)

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