nf-core / nf-core/proteinannotator
Aggregate annotations across tools
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- Dominant language
- Nextflow
- Stars
- 15
- Forks
- 12
- Avg merge
- 1d 20h
- Merged PRs (30d)
- 2
Description
Description of feature
For each protein fasta, aggregate the results across tools. Will probably require reading all annotations into Python or equivalent using pandas or polars, then doing a groupby/group_by per sequence ID.
Then, we can output:
- Union of all annotations
- Consensus annotations (annotations agreed upon by all tools) -- this will probably be the rare case
- Mild consensus annotations (e.g. annotations with evidence from 2 or more tools)
See also reportho's output documentation for how they report the outputs
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 how the pipeline currently emits annotations for each protein FASTA and read the reportho output documentation linked in the issue. Define the grouped sequence-ID output for the union, unanimous consensus, and annotations supported by at least two tools; done means these results are produced consistently across tool outputs.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- pandas, python
- Domain
- bioinformatics, data-engineering
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100