bwa-mem aligner not using GPU
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enhancement
- Dominant language
- Nextflow
- Stars
- 198
- Forks
- 181
- Avg merge
- 6d 17h
- Merged PRs (30d)
- 1
Description
Description of feature
seems like the bwamem aligner doesn't take the use_gpu flag or use the gpu implementation of bwamem. Is it possible to use it (for processing TAPs etc, as bwamem is recommended over bwameth)
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with subworkflows/nf-core/fastq_align_dedup_bwamem/main.nf and trace how the bwa-mem aligner is invoked and whether the use_gpu flag is handled. Determine whether a GPU implementation is available for the TAPs and related processing, then confirm that the workflow uses it when requested.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100