MIPs pooling

[Nicklas Nordborg]

Pooling of MIPs library plates. Typically, a pool is made up of 1 to 3 MIPs plates. The wizard should verify that barcodes do not overlap.

[Nicklas Nordborg]

In 5389:

References #1133: Re-organize the Reggie front page

Added lots of wizards to the "MIPs library preparation and analysis" section. The wizards will be implemented in other tickets. See #1130, #1135, #1136, #1137, #1138 and more to come.

[Nicklas Nordborg]

In 5426:

References #1138: MIPs pooling

Added a counter for MIPs plates waiting to be pooled. This could not be implemented in the same way as for the RNA-seq pipeline which uses a check that compare original and remaining quantity for the libraries.

In the MIPs pipeline we do not register libraries with quantities, so a new "Plate event type" (=Pooling) was added. The intention is that when a MIPs plate is registered as pooled a "Pooling" plate event is registered and the MIPs plate will go on to the next step.

Also found that we never checked the "Create" plate event type in the installation script. It should be installed by default so it is not a big deal.

[Nicklas Nordborg]

In 5427:

References #1138: MIPs pooling

First version of the pooling wizard for MIPs plates. I turned out to be very hard to get a working query to select plates without a pooling event so this was removed again. Instead the PoolDate annotation is set on the MIPs plate to indicate that it has been part of a pool.

The wziard currently allows any number of MIPs plates to be selected and then creates a single pool from all of them. No check for duplicate barcode usage has been implemented yet.

Pools are currently created using the same name-space as RNA-seq pools (PoolNNNN). If this is not desired we may need a new subtype for MIPs pools.

[Nicklas Nordborg]

In 5428:

References #1138: MIPs pooling

Adding the wizard also (should have been included in [5427]).

[Nicklas Nordborg]

In 5430:

References #1138: MIPs pooling

Implemented a check for duplicate barcodes. A first check is made aldready in the web client and it should be impossible to register if plates with the same barcode are selected. There is also a check on the server side in case the client side check for some reason is not working.

[Nicklas Nordborg]

In 5434:

References #1138: MIPs pooling

Introduced the Pipeline annotation that is intended to be used on several types of items that must be separated in the processing pipeline.

The first use case is PooledLibrary items that appear in the RNAseq and MIPs pipeline. Of course, we do not want pools to appear in the wrong wizard in the next processing step (create flow cell).

So, filters have been added to several places to make queries, etc return only the expected pools. A manual update of existing PooledLibraries is recommended (set Pipeline=RNAseq).

[Nicklas Nordborg]

In 5435:

References #1138: MIPs pooling

Updated the "Create flow cells" wizard in the RNAseq pipeline:

• Added a filter Pipeline=RNAseq to the "Select manually" function
• Added check that selected pools are intended for the RNAseq pipeline

Added a counter for counting MIPs pools that are ready to be used on a flow cell. The filter is not yet complete since it will not detect pools that have actually been used...

[Nicklas Nordborg]

In 5436:

References #1138: MIPs pooling

Updated the "Create manual pool" wizard in the RNAseq pipeline to include a filter when selecting libraries.

This requires that all Library items are also annotated with the Pipeline annotation, so other wizards that create library items have been updated to set that annotation.

A manual update is needed to set Pipeline=RNAseq to all existing library items.

[Nicklas Nordborg]

In 5452:

References #1138: MIPs pooling

Only display pooling protocols of the correct type (LibPrepTarget=MIPs). This also affects the RNAseq pipeline which need a filter (LibPrepTarget=Manual).

Fixed the filter for counting and selected pools that are ready for sequencing. The new filter uses the number of child items (which must be 0) instead of the original and remaining quantities. This also affects the RNAseq pipeline but should give equivalent results.

[Nicklas Nordborg]

In 5473:

References #1138: MIPs pooling

Register any-to-any links from pools to libplate (MIPs-plates) using names "LibPlate", "LibPlate.2", "LibPlate.3", etc.

Sequencing ended and sequencing confirm wizards have been updated to display a list with the plate names.