galaxyproject / galaxyproject/brc-analytics
Fix citation in Cyclospora part 2: 2018 outbreak labels cite [4] (a 2019-outbreak paper)
- Dominant language
- TypeScript
- Stars
- 7
- Forks
- 11
- Avg merge
- 3d 15h
- Merged PRs (30d)
- 15
Description
## Summary
Follow-up from the review of #1667 (Cyclospora part 2, `genotyping-cyclospora-from-haplotype-calls-to-outbreak-clusters.mdx`). A citation on the intro line looks like it points at the wrong reference.
## The problem
Line 32 attributes the **2018** Vendor A / Vendor B outbreak labels to reference **[4]**:
> …Vendor A (salads, 99 specimens) and Vendor B (vegetable trays, 104) **[4]**—taken from `REFERENCE_CLUSTER_LIST/2018_gold_clusters.txt`…
But **[4]** is Barratt et al. (2021), which is about the **2019** outbreaks and the improved 2019-era genotyping system. The paper that evaluated clustering against the **2018** epidemiologically-defined clusters is **[2]**, Nascimento et al. (2020) *Epidemiology and Infection* (the ensemble-distance evaluation on the 2018 cohort).
## Suggested fix
Change the citation on line 32 from `[4]` to `[2]` (or `[2, 4]` if both are intended). Worth a quick confirm against the source PDFs before changing, since this is authored scientific prose.
This is also flagged as an inline thread on #1667 (line 32); resolving it there or here is fine.
_Context: raised during review of #1667; the remaining open threads on that PR (ref-20 link formatting, ensemble-paragraph placement) are cosmetic nits and can be handled at your discretion._
Contributor guide
No contributing guide indexed for this repository
Assessment
This issue has not been assessed yet.