Changes between Initial Version and Version 1 of net.sf.basedb.reggie/notes423


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Timestamp:
Aug 6, 2019, 10:03:37 AM (2 years ago)
Author:
Nicklas Nordborg
Comment:

Started to write the update notes for Reggie 4.23

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  • net.sf.basedb.reggie/notes423

    v1 v1  
     1= Updating to Reggie 4.23 =
     2
     3TODO - when to do the different steps!
     4
     5TODO - state requirements: no current sequencing or secondary analysis jobs
     6
     7== 1. Set value for Pipeline annotation on existing items ==
     8
     9Almost all existing items from Library and downstream must be given a value for the **Pipeline** annotation. The table below specifies the value
     10to 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.
     11
     12|| **Item type** || **Subtypes** || **Additional filter** || **Pipeline value** ||
     13|| Extract || Library, !PooledLibrary, !PooledLibraryAliquot ||  -  || RNAseq ||
     14|| Physical bioassay || !FlowCell ||  -  || RNAseq ||
     15|| Derived bioassay || !SequencingRun, !DemuxedSequences, !MergedSequences ||  -  || RNAseq ||
     16|| Derived bioassay || !MaskedSequences, !AlignedSequences || Job type = !HisatAlign || TODO ||
     17|| Derived bioassay || !MaskedSequences, !AlignedSequences || Job type <> !HisatAlign || Legacy ||
     18|| Raw bioassay || Cufflinks ||  -  || Legacy ||
     19|| Raw bioassay || !StringTie ||  -  || TODO ||
     20|| Protocol || Demuxing ||  -  || RNAseq ||
     21|| Software || Demuxing ||  -  || RNAseq ||
     22
     23== 2. Other updates to existing items ==
     24
     25Existing Hardware items of type=Sequencer should be updated with a value for the **!FlowCellType** annotation. It should be either !NextSeq or !HiSeq.
     26
     27== 3. New items that should be created ==
     28
     29|| **Item type** || **Subtypes** || **Additional settings** || **Comment** ||
     30|| Protocol || DNANormalization || !TargetAmount, !TargetMinimalAmount, !TargetVolume, MIPS_Pool || The protocol to use for normalizing DNA that should go into the MIPs pipeline. ||
     31|| Protocol || Library preparation || !LibPrepTarget=MIPs || One or more protocols that will appear in the "MIPs library registration" wizard ||
     32|| Protocol || Pooling || !LibPrepTarget=MIPs || One or more protocols that will appear in the MIPs pooling wizard ||
     33|| Protocol || Demuxing || Pipeline=MIPs || One or more protocols that will appear in the MIPs demux wizard ||
     34|| Software || Demuxing || Pipeline=MIPs || One or more software entries that will appear in the MIPs demux wizard ||
     35
     36