Multipe auto-confirmation steps for a single item

[Nicklas Nordborg]

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.

[Nicklas Nordborg]

In 6021:

References #1272: Multipe auto-confirmation steps for a single item

Started to implement a new strategy for auto-confirmation for some kind of jobs. Tested with the mBAF calculation.

The new strategy uses a specific parameter (AutoConfirmHandler) on the Job item instead of an any-to-any link that is temporarily pointing to the job instead of the expected result file.

Auto-confirmation is performed for jobs with this parameter when they have ended. The value of the parameter is used to specify which handler to use. Once the job has been handled the parameter is removed from the job. The strategy is more similar to the original strategy that uses the AutoProcessing annotation and the important thing is that we now can detect when a job is successful and use that to start other analysis.

[Nicklas Nordborg]

In 6022:

References #1272: Multipe auto-confirmation steps for a single item

Auto-confirmation for raw-only variant calling has been updated to use the new strategy.

[Nicklas Nordborg]

In 6023:

References #1272: Multipe auto-confirmation steps for a single item

The gene and pilot reports now uses the new strategy for auto-confirmation. New item lists for the reports has been created since the strategy doesn't work well if only checking for missing reports.

[Nicklas Nordborg]

In 6025:

References #1272: Multipe auto-confirmation steps for a single item

Implemented auto-confirm support for the SSP plug-in. This will automatically create a job for SCAN-B report generation.

[Nicklas Nordborg]

In 6040:

References #1272: Multipe auto-confirmation steps for a single item

Removing unused code.