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migrate leviosam2/lift module to topic channels#12000

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Anifowak:migrate-leviosam2-lift-topic
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migrate leviosam2/lift module to topic channels#12000
Anifowak wants to merge 1 commit into
nf-core:masterfrom
Anifowak:migrate-leviosam2-lift-topic

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@Anifowak

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PR checklist

Closes #11907

  • 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 force-pushed the migrate-leviosam2-lift-topic branch 4 times, most recently from dff7ba2 to c8bd796 Compare June 13, 2026 14:38
@Anifowak Anifowak requested a review from GallVp June 13, 2026 14:42
@Anifowak Anifowak force-pushed the migrate-leviosam2-lift-topic branch from c8bd796 to 6f6fced Compare June 13, 2026 14:47
@Anifowak Anifowak requested review from mashehu and mirpedrol June 13, 2026 14:48
@Anifowak Anifowak force-pushed the migrate-leviosam2-lift-topic branch from 6f6fced to 7385428 Compare June 13, 2026 14:55
@Anifowak Anifowak force-pushed the migrate-leviosam2-lift-topic branch from 7385428 to 046dc20 Compare June 13, 2026 15:07

@SPPearce SPPearce left a comment

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Thanks for your contribution.
A few suggestions to get this to pass. You'll need to regenerate the snapshots too.

Comment on lines +146 to +149
{ assert snapshot(
process.out.bam,
process.out.versions_leviosam2
).match()

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The stub test can always be this:

Suggested change
{ assert snapshot(
process.out.bam,
process.out.versions_leviosam2
).match()
{ assert snapshot(sanitizeOutput(process.out)).match()

assert snapshot(
process.out.bam.collect { file(it[1]).getName() },
process.out.versions
process.out.versions_leviosam2

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This passes the linting:

Suggested change
process.out.versions_leviosam2
process.out.findAll { key, val -> key.startsWith('versions') },

Alternatively, the whole snapshot could be `snapshot(sanitizeOutput(process.out, unstableKeys: ["bam"])).match()

@Anifowak

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Alright.

Thank you

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Migrate to topic leviosam2/lift

2 participants