nf-core / nf-core/funcprofiler
Should we support aligning reads to annotated contigs?
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Description
My vote would be yes! But it does have the potential for introducing a potentially strange interdependence between funcscan and funcprofiler. But still, if the goal of this pipeline is to functionally annotate reads, it does seem like one reasonable way to do that is to assemble contigs, annotate them and then (at this stage) align the raw reads back to those annotated contigs.
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
The issue names no files, tests, or entry points. Start by reviewing how funcscan and funcprofiler interact and clarify whether aligning raw reads to annotated contigs is in scope; completion criteria and affected workflow components still need to be defined.
Written by the indexing model from the issue text.
Assessment
- Domain
- data-engineering
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100