nf-core / nf-core/funcprofiler
Benchmark ideal parameters for eggnog-mapper
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 3
- Forks
- 5
- Avg merge
- 2d 23m
- Merged PRs (30d)
- 1
Description
Description of feature
For v1 I added some approximate defaults of 95% identity and 60% read coverage for a hit to be called. This may or may not be ideal, but I think is a better starting point than no filtering at all for a tool expecting assemblies or contigs. For v1.1, it would be nice to have some benchmarking to show what parameters would yield the best F1 score (or best by some other metric). Additionally, it would be nice to have some scripts for summarizing the outputs into a convenient feature table.
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, datasets, or entry points. Start by defining the benchmark inputs, evaluation metric, and parameter search, then locate how outputs could be summarized into a feature table. Done means benchmark results identify suitable parameters and the requested summary scripts are available.
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