DSL2L: Add support for specifying platform in input TSV
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DSL2
enhancement
- Dominant language
- Nextflow
- Stars
- 215
- Forks
- 91
- Avg merge
- 5m
- Merged PRs (30d)
- 1
Description
This is important for read group tags, as it influences genotyping models.
eager1/eager2 hardcoded illumina, which is not yet valid anymore due to rising use of MGI sequencers (as previously reported by @ashildv )
More info: https://github.com/nf-core/eager/pull/964#discussion_r1154379221****
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 input TSV is parsed and how its read group tags reach the genotyping models. Use the linked pull-request discussion for context on the platform values and existing hardcoded Illumina behavior. Done means the input can specify the sequencing platform and that value is used instead of assuming Illumina.
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