nf-core / nf-core/variantbenchmarking
Multiple truth sets within the same run
Open
Nobody has claimed this yet.
enhancement
not urgent
- Dominant language
- Nextflow
- Stars
- 51
- Forks
- 31
- Avg merge
- 1d 22h
- Merged PRs (30d)
- 1
Description
Description of feature
Would it be possible to add the ability to benchmark against multiple truth sets within the same run? E.g. by specifying truth_id, truth_vcf and regions_bed for each row in the samplesheet instead of as parameters.
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 tracing how the samplesheet and the current truth_id, truth_vcf, and regions_bed parameters enter the benchmarking workflow. Determine how each sample row could carry its own truth set and how runs currently select these values. Done means a run can benchmark multiple rows against distinct truth sets, with validation covering the samplesheet inputs.
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
- Mostly clear
- Newbie friendliness
- 35/100