4 weeks ago by
As far as I know, Cuffdiff was not impacted. The tool would (should!) fail if the problems are related to the conda fixes occurring at Galaxy Main right now, not produce incomplete results.
Do you have an example line or two from the Cuffdiff output that presents with missing statistics? Is that record in the iGenomes GTF complete (contains p_id, tss_id, and gene_name)? You can post back both in a comment if you would like feedback.
Or are some output files completely empty? That would mean that more is going on. Let us know and we can look at your history if working at https://usegalaxy.org.