Issue with "Insert Indel Qualities" Step in Galaxy Training Material after recent upgrade

usegalaxy.org support
1

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:

  1. For SRR12733957, the step Insert Indel Qualities remains stuck in a green “queued” state and does not proceed to execution.
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    → As a result, the downstream step Call Variants fails due to missing input.
  2. 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.
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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:

2

The previous issue seems to be resolved — thank you! However, there is now still a new problem: when running the SnpEff step on the same datasets (SRR12733957 and SRR11954102), the job finishes successfully (green), but the output is empty — 0 lines and 0 columns. This did not happen before the platform upgrade.