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Fix sequence validation to handle NaN values in DRAMP database download#538

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jfy133 merged 4 commits into
nf-core:devfrom
hindrek:fix/dramp-missing-sequences
Jul 3, 2026
Merged

Fix sequence validation to handle NaN values in DRAMP database download#538
jfy133 merged 4 commits into
nf-core:devfrom
hindrek:fix/dramp-missing-sequences

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@hindrek

@hindrek hindrek commented Jul 1, 2026

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Fixes #537.

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/funcscan 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).

@github-actions

github-actions Bot commented Jul 1, 2026

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This PR is against the main branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @hindrek,

It looks like this pull-request is has been made against the hindrek/funcscan main branch.
The main branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to main are only allowed if they come from the hindrek/funcscan dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@hindrek hindrek changed the base branch from main to dev July 1, 2026 09:19

@jfy133 jfy133 left a comment

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Thank you very much @hindrek ! DRAMP is being the bane of my life at the moment 🙃

Simple enough fix, so it's ready to go - please however add an entry in the CHANGELOG and add yourself to the contributors list in README and the nextflow.config manifest section :), then I will merge

@jfy133

jfy133 commented Jul 3, 2026

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Thanks @hindrek

@jfy133 jfy133 merged commit e571215 into nf-core:dev Jul 3, 2026
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TypeError: expected string or bytes-like object, got 'float' during DRAMP database download

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