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migrate lissero module to topic channels#12025

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Anifowak:migrate-lissero-topic
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migrate lissero module to topic channels#12025
Anifowak wants to merge 1 commit into
nf-core:masterfrom
Anifowak:migrate-lissero-topic

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@Anifowak

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PR checklist

Closes #11908

  • 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

@Anifowak Anifowak requested a review from SPPearce June 17, 2026 01:43
@Anifowak

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The remaining failure appears unrelated to the topic-channel migration. The lissero process fails with ModuleNotFoundError: No module named 'pkg_resources', likely due to missing setuptools in the environment.

Please advise whether you’d like me to add setuptools to the module environment or leave this outside the scope of the topic migration.

Thank you

@SPPearce SPPearce left a comment

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Yes, we need to pin setuptools to make it work on conda. There are a bunch of other modules we've had to do this with.

{ assert snapshot(
file(process.out.tsv[0][1]).readLines()[0], // Two line file. Line 2 contains a path.
process.out.versions
process.out.versions_lissero

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Suggested change
process.out.versions_lissero
sanitizeOutput(process.out, unstableKeys: ["tsv"])

@Anifowak Anifowak force-pushed the migrate-lissero-topic branch 4 times, most recently from 85cdcac to a7e3300 Compare June 18, 2026 01:00
@Anifowak Anifowak force-pushed the migrate-lissero-topic branch from a7e3300 to a8a4d4f Compare June 18, 2026 01:06
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Migrate to topic lissero

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