wiki:net.sf.basedb.reggie/notes423

Version 1 (modified by Nicklas Nordborg, 16 months ago) (diff)

Started to write the update notes for Reggie 4.23

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