Pipeline annotation in secondary analysis

[Nicklas Nordborg]

The "Pipeline" annotation was added to be able to separate items in the RNAseq from item in the MIPs pipeline since they share common subtypes (Library, PooledLibrary, etc.).

We should extend this annotation to cover items in the downstream secondary analysis. For example, we could set Pipeline=Legacy to alignments and raw bioassays in the old Tophat/Cufflinks? pipeline.

[Nicklas Nordborg]

In 5543:

References #1164: Pipeline annotation in secondary analysis

Added "Legacy" as a valid value to the Pipeline annotation. Items in the old Tophat/Cufflinks? path are created with this annotation and it is also used for filtering.

[Nicklas Nordborg]

In 5544:

References #1164: Pipeline annotation in secondary analysis

Added pipeline check also to auto-confirmation of jobs. Not really required since we only have Cufflinks data in the legacy pipeline.

[Nicklas Nordborg]

In 5546:

References #1164: Pipeline annotation in secondary analysis

Renamed the "Legacy" pipeline to "RNAseq/Legacy" and added "RNAseq/Hisat/StringTie". Counters and servlets for loading items have been updated to filter out the expected items.

[Nicklas Nordborg]

In 5547:

References #1164: Pipeline annotation in secondary analysis

The wizards for starting genotype and stringtie have been updated to add a filter for pipeline when using the "Select manually" function and to check that the pipeline is the expected (RNAseq/Hisat/StringTie).

[Nicklas Nordborg]

In 5548:

References #1164 and #1157. Added pipeline to "Mask+align" and "Raw bioassays" sections in the case summary.