This hackathon project focuses on updating the Sarek pipeline with more Parabricks GPU modules as optional replacements for CPU-based steps. This will reduce the total runtime of Sarek for select workflows. There is a GitHub Issue open on this topic which details previous work.
Goal
Add more GPU modules to the Sarek pipeline.
Presently, Sarek utilizes the Parabricks fq2bam module as a GPU accelerated version of BWA-Mem. However, there are other Parabricks modules that can be added to Sarek:
What participants will do
Each contributor will:
- Choose a module to work on with the team
- Add it to the Sarek pipeline
- Run tests and lint checks locally.
- Open a Pull Request for review.
Each module will have its own branch and PR.
Recommended preparation
Participants should ideally have:
- Basic familiarity with Git and GitHub (forking repositories, creating branches, and opening pull requests)
- Basic knowledge of Nextflow
- Familiarity with nf-core modules and pipelines
The following training material is recommended:
