update nf-core module: MYGENE
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update module
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Description
This module is used to create a .gmt file given a list of genes.
Currently, it only parses info from GO terms.
Ideally, one can chose to parse info from GO, KEGG, Reactome, TF, etc.
- update it so that it can parse info from different databases.
- Or if there is any other alternative to mygene is also welcomed
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 nf-core module for MYGENE and reviewing how it currently creates a .gmt file from GO terms. Define which databases should be supported, or evaluate an alternative to mygene; done means the module can parse the agreed sources from a gene list.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100