Describe the bug
When running the RNA STARsolo tool on usegalaxy.org (tested on versions up to 2.7.11b+galaxy1 and 2.7.10b+galaxy4), the wrapper completely fails to export the Velocyto matrices (spliced.mtx, unspliced.mtx, ambiguous.mtx) to the user’s history, even when the Velocyto feature is explicitly selected.
To Reproduce
Steps to reproduce the behavior:
Run RNA STARsolo with standard 10x scRNA-seq inputs (R1 & R2).
Under Collect UMI counts for these genomic features (–soloFeatures), select Velocyto. (Either alone or alongside Gene).
Run the tool.
Expected behavior
The tool should output the standard Gene matrix PLUS the Velocyto matrices (preferably packaged as a dataset collection containing spliced/unspliced/ambiguous mtx files), exactly as the STAR C++ engine produces them.
Actual behavior (The Flaw)
The job finishes successfully (turns green), but no Velocyto matrices appear in the history.
By inspecting the Log.out (or tool stdout), we can confirm that the underlying STAR C++ engine correctly computed and saved the matrices in the temporary working directory (e.g., Solo.out/Velocyto/raw/).
However, the Galaxy Tool XML wrapper lacks the necessary or tags in its section to discover and export these Velocyto files. The temporary directory is simply purged after the job finishes, destroying the highly valuable RNA velocity data.
Suggested Fix
Please update the rna_starsolo.xml wrapper. Add a dynamic output that triggers when ‘Velocyto’ in $solo.features is true, using <discover_datasets> to harvest the spliced.mtx, unspliced.mtx, and ambiguous.mtx from the Solo.out/Velocyto/raw/ (or filtered) directory.
Thank you for maintaining these amazing tools! Fixing this will hugely benefit the spatial transcriptomics and scRNA-seq community relying on Galaxy for RNA Velocity analysis.
