Updating to Reggie 4.23

TODO - when to do the different steps!

TODO - state requirements: no current sequencing or secondary analysis jobs

1. Set value for Pipeline annotation on existing items

Almost all existing items from Library and downstream must be given a value for the Pipeline annotation. The table below specifies the value to set for the Pipeline annotation for different types of items. It should be possible to do a manual batch export/import for each row or groups of rows.

Item type	Subtypes	Additional filter	Pipeline value
Extract	Library, PooledLibrary, PooledLibraryAliquot	-	RNAseq
Physical bioassay	FlowCell	-	RNAseq
Derived bioassay	SequencingRun, DemuxedSequences, MergedSequences	-	RNAseq
Derived bioassay	MaskedSequences, AlignedSequences	Job type = HisatAlign	TODO
Derived bioassay	MaskedSequences, AlignedSequences	Job type <> HisatAlign	Legacy
Raw bioassay	Cufflinks	-	Legacy
Raw bioassay	StringTie	-	TODO
Protocol	Demuxing, Merging	-	RNAseq
Software	Demuxing, Merging	-	RNAseq

2. Other updates to existing items

Existing Hardware items of type=Sequencer should be updated with a value for the FlowCellType annotation. It should be either NextSeq or HiSeq.

3. New items that should be created

Item type	Subtypes	Additional settings	Comment
Protocol	DNANormalization	TargetAmount, TargetMinimalAmount, TargetVolume, MIPS_Pool	The protocol to use for normalizing DNA that should go into the MIPs pipeline.
Protocol	Library preparation	LibPrepTarget=MIPs	One or more protocols that will appear in the "MIPs library registration" wizard
Protocol	Pooling	LibPrepTarget=MIPs	One or more protocols that will appear in the MIPs pooling wizard
Protocol	Demuxing	Pipeline=MIPs	One or more protocols that will appear in the MIPs demux wizard (demux section)
Software	Demuxing	Pipeline=MIPs	One or more software entries that will appear in the MIPs demux wizard (demux section)
Protocol	Merging	Pipeline=MIPs	One or more protocols that will appear in the MIPs demux wizard (merge section)
Software	Merging	Pipeline=MIPs	One or more software entries that will appear in the MIPs demux wizard (merge section)

4. Barcode templates

Most of the barcode information (such as the sequences, positions, etc.) should be available as a file that can be used with batch importers. Some steps need to be done manually.

1. A barcode templates is represented as a Bioplate item where each coordinate is linked to a Tag item. Start by manually creating the required number of bioplates. They should have the following values:

Bioplate type	BarcodeTemplate
Plate geometry	96-well (8x12)
Pipeline (annotation)	MIPs

2. Import/create Tag items from file using the batch Tag importer and then add annotations with the Annotation importer. The following values are required:

Name	Name of the barcode/tag which must be unique
Pipeline	All items should be set to MIPs
BarcodeSequence	The barcode sequence for the first index read
BarcodeSequence2	The barcode sequence for the second index read

3. Link the barcodes to templates. This is done by creating (virtual) extracts and link them with tags and positions on one of the bioplates created in the first step. It should be possible to do this with the batch Extract importer:

Name	Name of the extract (recommended to be the same as the name of the Tag)
Tag	Name of the tag
Bioplate	Name of the template bioplate
Biowell row	Row coordinate on the template bioplate (A-H)
Biowell column	Column coordinate on the template bioplate (1-12)