nf-core / nf-core/stableexpression
Check species identifier with g:Profiler API beforehand
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@OlivierCoen is already working on this.
Since Sep 16, 2026.
bug
- Dominant language
- Python
- Stars
- 9
- Forks
- 3
- Avg merge
- 3d 5h
- Merged PRs (30d)
- 3
Description
Description of the bug
In the g:Profiler API, some species identifiers are not formatted as expected. While, for most species, it is the first letter of the genus + the species name (eg. hsapiens, athaliana), for species including subspecies it is different (eg. Canis lupus dingo becomes cldingo).
We need to be able to query the https://biit.cs.ut.ee/gprofiler/api/util/organisms_list endpoint first, and get the exact identifier of the species of interest.
Command used and terminal output
nextflow run main.nf -profile apptainer -resume --species canis_lupus --outdir results/canis_lupus
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