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Propr topics - #12387

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SPPearce wants to merge 22 commits into
masterfrom
propr_topics
Open

Propr topics#12387
SPPearce wants to merge 22 commits into
masterfrom
propr_topics

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@SPPearce

@SPPearce SPPearce commented Jul 20, 2026

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Swap propr to topics

SPPearce added 11 commits July 15, 2026 09:22
@SPPearce
Remove unused ch_versions from subworkflows
7cc2850
@SPPearce
Convert propr/grea to topic channels and add stub
f0ec521 
- Changed versions.yml output to emit to topic channel
- Added stub section that creates empty output files
- Added stub test
- All tests pass on docker profile

Generated by GitHub Copilot
@SPPearce
Swap propr/grea to topic
05dcee8
@SPPearce
Update subworkflow test
ae3f869
@SPPearce
Remove null versions from snap
559ea4f
@SPPearce
Merge branch 'master' into propr_grea_topics
41e61a2
@SPPearce
Merge remote-tracking branch 'origin/subworkflow_unused_versions' int…
4eacb6f 
…o propr_grea_topics
@SPPearce
Actually add topic
eeb90ea
@SPPearce
Merge remote-tracking branch 'origin/master' into propr_topics
bc637c1
@SPPearce
Convert all propr modules to topic channels and add stubs
712a57c 
- propr/grea: Added topic to versions.yml emit
- propr/logratio: Added topic to versions.yml emit, added stub test
- propr/propd: Added stub section, added stub test
- propr/propr: Added topic to versions.yml emit, added stub section, added stub test
- All tests pass on docker profile
- Conda tests fail due to general conda plugin error (not module-specific)

Generated by GitHub Copilot
@SPPearce
Swap propr to topics
32bbf17
@github-actions github-actions Bot added size/xl and removed size/l labels Jul 27, 2026
@SPPearce
SPPearce marked this pull request as ready for review July 30, 2026 08:07
Joon-Klaps
Joon-Klaps reviewed Jul 30, 2026
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@Joon-Klaps Joon-Klaps left a comment

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Notice you didn't rename the versions to module_versions, you'll probably now the guidelines better but was that mandatory? I mean, it won't break users pipelines now if when they patch.

Comment thread modules/nf-core/propr/propd/tests/main.nf.test
@SPPearce

SPPearce commented Jul 30, 2026

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Notice you didn't rename the versions to module_versions, you'll probably now the guidelines better but was that mandatory? I mean, it won't break users pipelines now if when they patch.

The versions channel? I thought we were just using emit: versions, topic: versions, but will check.

@SPPearce

SPPearce commented Jul 30, 2026

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Notice you didn't rename the versions to module_versions, you'll probably now the guidelines better but was that mandatory? I mean, it won't break users pipelines now if when they patch.

https://nf-co.re/docs/specifications/components/modules/general#topic-qualifiers-should-be-used-for-emitting-versions says to keep with path "versions.yml", emit: versions, topic: versions (as is used by ~50 modules currently).

@SPPearce
SPPearce requested a review from pinin4fjords as a code owner August 3, 2026 09:16
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@Joon-Klaps Joon-Klaps Joon-Klaps approved these changes
@pinin4fjords pinin4fjords Awaiting requested review from pinin4fjords pinin4fjords is a code owner

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