= 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 ||  -  || RNAseq ||
|| Software || Demuxing ||  -  || 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 ||
|| Software || Demuxing || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard ||