Skip to content

Long-read GENS PON#66

Merged
fellen31 merged 18 commits intodevfrom
lrs-gens-pon
Feb 11, 2026
Merged

Long-read GENS PON#66
fellen31 merged 18 commits intodevfrom
lrs-gens-pon

Conversation

@fellen31
Copy link
Contributor

@fellen31 fellen31 commented Feb 4, 2026

This PR adds gens panel of normals generation for long-read data. Since long-reads usually contains a lot less reads compared to short-reads (e.g. 8M vs 400M) resulting in a more uneven coverage, we use coverage instead of read counts in the bins.

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/createpanelrefs 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).

@nf-core-bot
Copy link
Member

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.

@fellen31 fellen31 linked an issue Feb 4, 2026 that may be closed by this pull request
@fellen31 fellen31 marked this pull request as ready for review February 6, 2026 14:47
@fellen31 fellen31 requested a review from ramprasadn February 6, 2026 14:47
Copy link
Member

@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Can you add an entry in the CHANGELOG?

@fellen31 fellen31 merged commit 1168e3f into dev Feb 11, 2026
18 checks passed
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Labels

None yet

Projects

None yet

Development

Successfully merging this pull request may close these issues.

Long-read gens PoN

3 participants