Description:
While using the Galaxy NGS Data Logistics training material in a classroom setting, students encountered issues when processing a collection containing the datasets SRR12733957 and SRR11954102. These issues appear to have arisen after a recent upgrade to the Galaxy platform. Prior to the upgrade, the same training workflow and datasets (SRR12733957 and SRR11954102) were processed successfully without encountering the described problems.
Observed Behavior:
- For SRR12733957, the step Insert Indel Qualities remains stuck in a green “queued” state and does not proceed to execution.
→ As a result, the downstream step Call Variants fails due to missing input. - For SRR11954102, although the Call Variants on collection 40 step completes and is marked as green, the resulting dataset contains 0 lines and 0 columns, indicating no output was generated.
Expected Behavior:
- Both datasets in the collection should complete the Insert Indel Qualities and Call Variants steps successfully.
- The final output should include variant call results with actual content, not empty tables.
Impact:
These issues prevent students from completing the training exercise and undermine the learning objectives of the tutorial.
History Link for Reference:
