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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/variantbenchmarking 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).

@kubranarci
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@georgiakes Hello! would you mind reviving this?

@georgiakes
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From the tests, it looks like only Truvari has an unstable snapshot.
For the report, MultiQC already lets the user create custom plots by selecting fields (see the image).
I think keeping only the tables and letting the user generate plots makes the report cleaner. What are your thoughts on this? :)
Screenshot from 2025-11-18 11-27-37

@kubranarci
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I think keeping only the tables and letting the user generate plots makes the report cleaner. What are your thoughts on this? :)

Yea, I just fixed truvari snapshots (It is always a bit painfull). The problem is only truvari has this function for now (unfortunately), for svbenchmark or wittyer or rtgtools multiqc doesnt support anything. I think it is better to have everything as united there now is better. But later, if mutliqc supports all I would remove those extra plots as you suggested :)

@georgiakes
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Hmmm yeah for sure I get your point.
If you want I can open an issue in multiqc to support all the other tools!
So having that in mind, it LGTM :)
FYI: The image is from the the happy report and I think it also works with sompy, so we have less work to do :)

@kubranarci
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@georgiakes that sounds great! Thank you (both for opening the issue and the review)

@kubranarci kubranarci merged commit 7c2cf41 into nf-core:dev Nov 18, 2025
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@kubranarci kubranarci linked an issue Nov 18, 2025 that may be closed by this pull request
This was linked to issues Nov 18, 2025
@kubranarci kubranarci deleted the 239-add-happy-sompy-and-truvari-in-multiqc-report branch November 18, 2025 14:03
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Add truvari to multiqc Add sompy to multiqc Add happy to multiqc

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