nf-core / nf-core/stableexpression
Check species name at the very beginning of the pipeline using the NCBI Datasets API
Open
@OlivierCoen is already working on this.
Since Sep 16, 2026.
enhancement
- Dominant language
- Python
- Stars
- 9
- Forks
- 3
- Avg merge
- 3d 5h
- Merged PRs (30d)
- 3
Description
Description of feature
Currently, species are just reformatted but no check is performed to ensure that they correspond to a real species.
If there is a typo in the species name provided as input (eg. aspergilus fumigatus instead of aspergillus fumigatus), the pipeline will fail with a message saying that Expression Atlas could not find data for it. Instead, I want to check beforehand if this is a real species name, and log an error message saying that the provided species does not exist.
It should be implemented with the NCBI Dataset API.
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