Add snpEff support
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DSL2
enhancement
feature
- Dominant language
- Nextflow
- Stars
- 215
- Forks
- 91
- Avg merge
- 5m
- Merged PRs (30d)
- 1
Description
Is your feature request related to a problem? Please describe.
In some cases, a user may want to know if there is any differences in terms of gene functionality/expression. One possible method could be: http://snpeff.sourceforge.net/, as also implemented in nf-core-sarek
This could be particularly relevent to bacteiral work looking into changes in pathogenicity.
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 reviewing snpEff and the referenced nf-core/sarek implementation to determine what support would mean for nf-core/eager. Define the integration scope, expected inputs and outputs, and how the result should address bacterial pathogenicity analysis before implementation.
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