[FEATURE] adapt mygene to also extract pathway annotations
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Description
Is your feature request related to a problem? Please describe
For some functionalities (eg. enrichment analysis), genes need to be annotated.
However, the currently implemented mygene script can only extract go annotations.
Describe the solution you'd like
The original mygene api itself can extract many different annotation types given the gene ids.
We want to make it available through the mygene nf-core module script.
For example, kegg pathways should be able to be extracted, when specified by the user using certain flags.
Describe alternatives you've considered
No response
Additional context
No response
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 locating the existing mygene nf-core module script and review how it currently extracts GO annotations. Then consult the original mygene API for supported annotation types and determine how user-specified flags should expose them, including KEGG pathways. Done means the module can return the requested annotation types through those flags.
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
- Needs clarification
- Newbie friendliness
- 35/100