8000 Refactor repeat annotation by fellen31 · Pull Request #702 · nf-core/raredisease · GitHub
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Refactor repeat annotation #702

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Merged
merged 2 commits into from
May 23, 2025
Merged

Refactor repeat annotation #702

merged 2 commits into from
May 23, 2025

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fellen31
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@fellen31 fellen31 commented May 20, 2025 •
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This PR simplifies the repeat annotation by updating the stranger module with bgzip and tabix.

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/raredisease 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>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,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).

@fellen31 fellen31 force-pushed the refactor-annotate-repeat-expansions branch from dc40644 to 7b2d5ab Compare May 20, 2025 08:41
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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: 3.2.0.
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.

@fellen31 fellen31 force-pushed the refactor-annotate-repeat-expansions branch from 7b2d5ab to a71c20a Compare May 20, 2025 08:43
@fellen31 fellen31 marked this pull request as ready for review May 20, 2025 09:53
ramprasadn
ramprasadn approved these changes May 23, 2025
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LGTM! Thanks for the PR, Felix!

@ramprasadn ramprasadn merged commit 7c3e79d into nf-core:dev May 23, 2025
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@ramprasadn ramprasadn ramprasadn approved these changes

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