nf-core / nf-core/genomeannotator
Parallelize repeatmasking
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enhancement
- Dominant language
- Nextflow
- Stars
- 44
- Forks
- 17
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
Currently, RepeatMasker runs on chunks of the assembly, containing full scaffolds/chromosomes. For highly contiguous assemblies, this can mean excessively long run times. Investigate whether repeat masking can be performed on sub-regions of the scaffolds in parallel without losing repeat regions.
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 by investigating how RepeatMasker currently processes assembly chunks containing full scaffolds or chromosomes. Determine whether sub-region processing can run in parallel without losing repeat regions; the work is done when a technically sound approach and its scope are established.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100