So the problem why the CI did not pass for most PRs was that nf-core #scdownstream

So the problem why the CI did not pass for most PR...

Nico Trummer

03/12/2026, 7:26 PM

So the problem why the CI did not pass for most PRs was that

hugounifier

(explanation in the thread) relies on data that comes from the HUGO database. Apparently they changed the database multiple times in the last weeks. In nf-core, tests are mostly based on hash snapshots of the output files of processes. So if the data from the API changes, the snapshots mismatch. If this would occur once every few months it would not really be a problem, but recently it has happened every few days. So I changed the tests that have this dependency to use less strict testing. You can see the changes here. With this merged, the CI for the SingleR PR from @Kim Fehl started working. Then I took the freedom to merge this changes into the other PRs (@Kurayi @Ze Yu @Miguel Rosell Hidalgo) so hopefully these will pass too now and can soon be merged

pr 2

cattyping 1

Nico Trummer

03/12/2026, 7:29 PM

hugounifier

is a little package I developed that is useful when you want to integrate multiple public datasets where you only have the expression matrices, and not the raw data. Often they use different sets of gene symbols/IDs and making them match is not always easy (e.g. some non-approved symbols are aliases for multiple approved symbols). It tries to intelligently resolve these situations

✨ 3

Kurayi

03/12/2026, 8:21 PM

I feel like this will be super useful sometime soon. Definitely starring 🤩🤩

Mariia Selifanova

03/12/2026, 9:30 PM

@Nico Trummer just added a question to our GitHub issue, please check when you have a moment. Thanks! https://github.com/nf-core/scdownstream/issues/171

✅ 1

Nico Trummer

03/12/2026, 9:51 PM

@Mariia Selifanova did my response answer your question?

❤️ 1

Mariia Selifanova

03/12/2026, 10:04 PM

@Nico Trummer That clears things up a lot! Thanks a bunch 🙂

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