AutoProcessing flag remains set on raw bioassays
The secondary analysis auto-confirmation wizard managed to process a batch up until the gene report step but the gene report failed due to a problem with the configuration (see #739).
After fixing the configuration the failed jobs were manually restarted and completed successfully, but the raw bioassays still have
AutoProcessing set to
ReProcess. The do not show up in the 'create gene report' wizard.
The annotation should at least be reset but I think we also need to check a few other scenarios to make sure this is handled correctly. For example, what happens if the auto-confirmation is not involved but the gene reports are started manually.