Skip to content

Add Parabricks GPU-accelerated minimap2 to the scnanoseq pipeline#95

Open
gburnett-nvidia wants to merge 15 commits intonf-core:devfrom
gburnett-nvidia:feat-add-gpu-minimap2
Open

Add Parabricks GPU-accelerated minimap2 to the scnanoseq pipeline#95
gburnett-nvidia wants to merge 15 commits intonf-core:devfrom
gburnett-nvidia:feat-add-gpu-minimap2

Conversation

@gburnett-nvidia
Copy link

This PR adds GPU accelerated Parabricks minimap2 module to the align_longread subworkflow in the scnanoseq pipeline.

It also adds basic nf-tests for this subworkflow.

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/scnanoseq 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: 3.2.1.
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.

@gburnett-nvidia
Copy link
Author

@atrull314 I know you were working on adding some pipeline level tests, is that PR somewhere? I added a test for the align_longreads subworkflow that ran locally but this PR doesn't include those so it's easily passing the CI runners.

@gburnett-nvidia gburnett-nvidia linked an issue Mar 13, 2026 that may be closed by this pull request
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.

Evaluate GPU integration where possible

2 participants