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fix lint - #337

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fix-jaffal-pr336-dev
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fix lint#337
yinshiyi wants to merge 7 commits into
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fix-jaffal-pr336-dev

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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/nanoseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile 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).

@yinshiyi
yinshiyi force-pushed the fix-jaffal-pr336-dev branch from 7166e96 to 48deb2b Compare August 19, 2026 01:29
@yinshiyi
yinshiyi force-pushed the fix-jaffal-pr336-dev branch from 48deb2b to c385723 Compare August 19, 2026 01:33
@yinshiyi

yinshiyi commented Aug 19, 2026

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Likely need to update test data from newer library prep kits for the basecaller module.

  • dna_r10.4.1_e8.2_400bps_hac@v4.1.0' is not a valid model name
  • tried 2 fixes
    Fix 1: If using R9.4.1 data (FLO-MIN106)
    Match the basecalling model to the R9 flow cell:
    dorado_model = 'dna_r9.4.1_e8.1_hac@v3.0.1'
    This model is not found in latest version of dorado.
    Fix 2: If using R10.4.1 data (FLO-MIN114)
    Update the model string to a current version supported by modern Dorado releases:
    dorado_model = 'dna_r10.4.1_e8.2_400bps_hac@v4.2.0'
    This model is there but the sampling frequency is not the same as the test dataset.
[2026-08-19 21:41:40.270] [error] Exception thrown: Failed to resolve basecaller models: Sample rate for model (5000) and data (4000) are not compatible.

terminate called after throwing an instance of 'std::runtime_error'

  what():  Failed to resolve basecaller models: Sample rate for model (5000) and data (4000) are not compatible.

  • instead of hacking the nextflow older version, update the mainfest and validation call to reflect the newer standard

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