Implement support for library preparation that uses Illumina Unique Dual indexes

[Nicklas Nordborg]

The current library preparation pipeline only support the TruSeqSingle barcodes (with names starting with AD) and pool layouts are hard-coded into the various wizards.

Since we already have support for other barcode types in other places it should be possible to do something like this:

• Assign a BarcodeSet annotation to a library preparation protocol. If not specified we use the TruSeqSingle as default.
• Pool layouts still need to be coded into the wizards, but they should now also be able to use barcodes from the actual BarcodeSet.
• The "Create flow cell" wizard must support a second index read and default values depend on the barcode length.
• Maybe something more...

[Nicklas Nordborg]

In 7989:

References #1630: Implement support for library preparation that uses Illumina Unique Dual indexes

Added BarcodeSet.ILLUMINA_UNIQUE_DUAL_A and enabled the BarcodeSet annotation for mRNA, cDNA and Library plates.

The "Create new library plate" has been modified to include a setting for which barcode set to use. There are currently two options: "TruSeqSingle" (default) and "IlluminaUniqueDual (Set A)". Changing the barcode set also changes the available pool layouts. Currently, only the "1x16 (offest)" layout is available for "IlluminaUniqueDual (Set A)".

The "Assign barcodes to cDNA plates" wizard have been updated so that it supports the "IlluminaUniqueDual (Set A)" barcode set and there are variants that use barcodes from two consecutive columns at a time (eg. C1-2, C3-4, C5-6, C7-8, C9-10 and C11-12).

[Nicklas Nordborg]

In 7990:

References #1630: Implement support for library preparation that uses Illumina Unique Dual indexes

Some minor changes in the printable libprep protocol that now include the barcode set and variant that should be used.

[Nicklas Nordborg]

In 7991:

References #1630: Implement support for library preparation that uses Illumina Unique Dual indexes

Added BarcodePosition annotation that can be set on the barcodes that are distributed on plates. IF set, the value will be displayed in the library preparation protocol.

[Nicklas Nordborg]

In 7992:

References #1630: Implement support for library preparation that uses Illumina Unique Dual indexes

Updated the "Create flow cell" wizard so that it support setting planned sequencing cycles for a second index.

[Nicklas Nordborg]

In 7993:

References #1630: Implement support for library preparation that uses Illumina Unique Dual indexes

Minor change in the "Start sequencing" protocol so that it display "Read1 - Index1 - Index2 - Read2" when dual indexing is used.