Add support for external sequencing

[Nicklas Nordborg]

This is related to the support for NovaSeq sequencing (see #1231).

The workflow starts similar to the "Create new mRNA" plate. It might be possible to re-use the same code with only minor changes. We have already done this with the NeoPrep support. It might be a good time to remove that support as part of this ticket in order to not complicate the code.

The plate geometry might be a 9x9 box instead of 12x8 plate.

Registration should create "LibPlate" compatible plate/box and create child library items (same as for the NeoPrep).

When the plate/box has been created we need a wizard for exporting data to an Excel or tab-separated file that can be sent to the external partner that is going to do the sequencing.

After the sequencing has completed we should get a sample sheet file with information about which barcodes that was used on the libraries and also barcode of the flowcell.

This information is registered in a new wizard which should also create more child items: PooledLibrary, FlowCell and SequencingRun. This should be done in a way to make the structure compatible with the regular RNAseq workflow so that auto-confirm could take over and start demuxing, etc.

[Nicklas Nordborg]

In 5881:

References #1232: Add support for external sequencing

Started to prepare for this by adding the plate type as a parameter to the JSP. For example, MRNA or EXTERNAL_LIBRARY.

It was also decided to remove support for NeoPrep in this wizard so the hidden link on the front page was also removed.

[Nicklas Nordborg]

In 5882:

References #1232: Add support for external sequencing

Removed NeoPrep support from the library plate design wizard.

[Nicklas Nordborg]

In 5883:

References #1232: Add support for external sequencing

Removed NeoPrep support from the rest of library preparation wizards.

[Nicklas Nordborg]

In 5884:

References #1232: Add support for external sequencing

Added two "pool schemas" for external library preparation. One with 32 samples and one with 64. In reality, it doesn't really matter, except that protocols, etc. will look nicer.

[Nicklas Nordborg]

In 5886:

References #1232: Add support for external sequencing

Added "Protocol" to the "Register external sequencing" wizard, otherwise library items will not get any protocol. To make this possible the library creation event must no longer be registered as a "plate event" since the registration wizard is not strictly plate-based.

[Nicklas Nordborg]

In 5887:

References #1232: Add support for external sequencing

Added a wizard for creating lab protocols for sending external samples. It is basically the same as the mRNA dilution protocol but with different header. This means that pre-normalization is not really required in the design phase, since the dilution information is available in this protocol.

Also started on a wizard that will fill in an Excel sample sheet that should be sent with the samples to the external operator. This needs a lot more work.

Also noted that we may need to generate a list with new labels for samples that are not pre-normalized.

[Nicklas Nordborg]

In 5888:

References #1232: Add support for external sequencing

Implemented support for generating a file with tube labels.

Re-organized the links in the wizard.

[Nicklas Nordborg]

In 5889:

References #1231 and #1232.

Added more columns to the exported sample template Excel file. Major difference is that the "Sample ID" now contains the internal ID of the Library item, while the "Name" column now contains the name of the either the pre-normalized RNA or the Library item (trying to match it with what is on the tube labels).

This change also affects the "Register external sequencing" wizard which now assume that the "Sample_ID" column contains the ID of the Library item. The "Sample_Name" column is not needed, but its used to display a warning if the name doesn't match the first part of the Libary name.

[Nicklas Nordborg]

In 5890:

References #1232: Add support for external sequencing

Added missing Excel icon.

[Nicklas Nordborg]

In 5891:

References #1232: Add support for external sequencing

Export delivery volume and concentration in the sample sheet. We choose to always export the theoretical values given in the normalization protocol even if we know that in some cases the concentration can be lower.

To be able to do this we must keep track of the normalization protocol that was selected in the design wizard. We copy the RNATargetAmount and RNATargetVolume annotation to the library plate and also link the protocol via an any-to-any link.

[Nicklas Nordborg]

In 5892:

References #1232: Add support for external sequencing

The labels file and sample sheet file are saved to the BASE file system and linked with the external plate for future reference.

[Nicklas Nordborg]

In 5895:

References #1232: Add support for external sequencing

Display creation date in the case summary for external libraries since they don't have CleanupDate or NeoPrepDate annotations.

[Nicklas Nordborg]

In 5897:

References #1232: Add support for external sequencing

Changed export of delivery concentration and volume to use the calculated results after dilution. In theory, this should be the same as the targets for the selected normalization protocol. They may differ if, for example, the RNA concentration is lower than the target concentration or if a re-processing is made when the remaining quantity is lower than the target quantity.

[Nicklas Nordborg]

In 5899:

References #1232: Add support for external sequencing

Library preparation protocols in the "Register external sequencing" need to be annotated with LibPrepTarget=External. The is a new option to the LibPrepTarget annotation type which also has been modified to allow multiple options to be selected.

[Nicklas Nordborg]

In 5900:

References #1232: Add support for external sequencing

Improve error handling if there is a problem with creating the sample sheet file. The old implementation would not display anything for the user except for logging a stack trace in the log file.