Multipe auto-confirmation steps for a single item
The secondary analysis pipelines are becoming more and more complex and the current auto-confirmation implementation is becoming too limited since it more or less assumes that once a given item has been confirmed the processing will continue by creating new child items. There are exceptions for the gene and pilot reports but this only works because they are endpoints.
With the new SCAN-B report coming for StringTie raw bioassays the auto-confirmation is already "taken" by the SSP analysis. Since the SSP analysis only create new annotations there is no new child item to hook into to be able to start the SCAN-B report plug-in after. Another complication is that for the report we also need the variant calling to be completed. Since this is in a parallel path there is no guarantee which one will be completed first.
So, we need a way to put back the StringTie raw bioassay into the auto-confirmation pipeline after each step (eg. after SSP and after variant calling) and it should automatically know which step to start next.