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Migrate to topic channels for versions#431

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jonasscheid merged 29 commits into
devfrom
topics
Feb 6, 2026
Merged

Migrate to topic channels for versions#431
jonasscheid merged 29 commits into
devfrom
topics

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@jonasscheid

@jonasscheid jonasscheid commented Jan 8, 2026 •
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Merge after #429

Nf-core module topic channel merge should be the next step. I did migrate to topic channels in pipeline nf-core modules for consistency reasons.

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 pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/mhcquant branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core pipelines lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions Bot commented Jan 8, 2026 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 52d609f

+| ✅ 300 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   3 tests had warnings |!
Details

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: conf/igenomes_ignored.config
  • pipeline_todos - TODO string in nextflow.config: Specify any additional parameters here

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md

✅ Tests passed:

Run details

  • nf-core/tools version 3.5.1
  • Run at 2026-02-06 14:33:49

@jonasscheid
Add changelog entry for version 3.2.0
57c3e08 
Updated CHANGELOG for version 3.2.0 with changes and dependency updates.
jonasscheid
jonasscheid commented Jan 9, 2026
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Comment thread modules/local/openms/textexporter/main.nf Outdated
Copilot AI mentioned this pull request Jan 9, 2026
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Copilot AI commented Jan 9, 2026

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@jonasscheid I've opened a new pull request, #433, to work on those changes. Once the pull request is ready, I'll request review from you.

Copilot AI and others added 3 commits January 9, 2026 08:38
@jonasscheid
Remove all cache buster comments from local modules
ecd9f94 
Co-authored-by: jonasscheid <43858870+jonasscheid@users.noreply.github.com>
@jonasscheid
Merge pull request #433 from nf-core/copilot/sub-pr-431
9b7245a 
Remove cache buster artifacts from topic channel migration
@jonasscheid
update snapshots with correct versions
f859ec4
@jonasscheid jonasscheid changed the title Migrate to topic channels Migrate to topic channels for versions Jan 9, 2026
Joon-Klaps
Joon-Klaps reviewed Jan 9, 2026
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Not 100% certain if everything went ok with template merge.

Think you might to fix of couple stuff first before the linter will be happy.

Comment thread modules/local/easypqp/convert/main.nf Outdated
Comment thread modules/local/openms/idconflictresolver/main.nf Outdated
Comment thread modules/local/openms/idconflictresolver/main.nf Outdated
Comment thread modules/local/openms/mapaligneridentification/main.nf Outdated
Comment thread modules/nf-core/openms/decoydatabase/main.nf
Comment thread subworkflows/local/prepare_spectra/main.nf Outdated
Comment thread subworkflows/local/quant/main.nf
Comment thread subworkflows/local/rescore/main.nf
Comment thread workflows/mhcquant.nf
jonasscheid
jonasscheid commented Jan 28, 2026
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Comment thread conf/modules.config Outdated
jonasscheid
jonasscheid commented Jan 28, 2026
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jonasscheid
jonasscheid commented Jan 28, 2026
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jonasscheid
jonasscheid commented Jan 28, 2026
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@jonasscheid

jonasscheid commented Jan 28, 2026 •
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@Joon-Klaps Thanks already for having a look! I updated every nf-core module to topics as well. Made the linter happy. Currently tests fail due to sever issue of a tool that we are dependent on. Should resolve itself after 1,2 tries. If you could have a look again, I would be grateful :)

EDIT: Seems to be a mqc issue. On it!

EDIT EDIT: Fixed 👍🏼

jonasscheid
jonasscheid commented Jan 29, 2026
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Comment thread modules/local/openms/idconflictresolver/main.nf Outdated
Joon-Klaps
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Think you still missed some stuff, mostly regarding the topics themselves

Comment thread modules/local/openms/featurefinderidentification/main.nf Outdated
Comment thread modules/local/openms/maprttransformer/main.nf Outdated
Comment thread modules/local/openms/mztabexporter/main.nf Outdated
Comment thread modules/local/openms/psmfeatureextractor/main.nf Outdated
Comment thread modules/local/openms/textexporter/main.nf Outdated
Comment thread subworkflows/local/rescore/main.nf Outdated
Comment thread subworkflows/local/rescore/main.nf Outdated
Comment thread subworkflows/local/rescore/main.nf Outdated
Comment thread modules/local/openms/idmassaccuracy/main.nf
Comment thread CHANGELOG.md
jonasscheid and others added 7 commits January 29, 2026 09:35
@jonasscheid
Fix OpenMS tool formatting to use multi-line style
3b35783
@jonasscheid @Joon-Klaps
Update CHANGELOG.md
91bb0f6 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@jonasscheid @Joon-Klaps
Update subworkflows/local/rescore/main.nf
ae96114 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@jonasscheid @Joon-Klaps
Update subworkflows/local/rescore/main.nf
8ba585a 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@jonasscheid @Joon-Klaps
Update modules/local/openms/featurefinderidentification/main.nf
98fd653 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@jonasscheid @Joon-Klaps
Update subworkflows/local/rescore/main.nf
17e6397 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@jonasscheid @Joon-Klaps
Update subworkflows/local/prepare_spectra/main.nf
c767225 
Co-authored-by: Joon Klaps <joon.klaps@kuleuven.be>
@nf-core nf-core deleted a comment from Joon-Klaps Jan 29, 2026
jonasscheid
jonasscheid commented Jan 29, 2026
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Comment thread subworkflows/local/rescore/main.nf Outdated
@jonasscheid

jonasscheid commented Feb 6, 2026

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Can we merge?

Joon-Klaps
Joon-Klaps approved these changes Feb 6, 2026
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You still have for certain local modules both topic and emit as 'versions' as well as commented out lines that can be deleted but if you really want to merge, don't let me stop you.

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nf-core-bot commented Feb 6, 2026

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Warning

Newer version of the nf-core template is available.

Your pipeline is using an old version of the nf-core template: 3.5.1.
Please update your pipeline to the latest version.

For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation.

@jonasscheid

jonasscheid commented Feb 6, 2026

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Apologies, I thought I should keep version emit even for local modules, but not necessary anymore, your right. Thanks again!

@jonasscheid jonasscheid merged commit 83dba10 into dev Feb 6, 2026
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@jonasscheid jonasscheid deleted the topics branch March 4, 2026 10:26
@jonasscheid jonasscheid mentioned this pull request Apr 22, 2026
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@Joon-Klaps Joon-Klaps Joon-Klaps approved these changes

@marissaDubbelaar marissaDubbelaar Awaiting requested review from marissaDubbelaar marissaDubbelaar is a code owner

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