id,summary,reporter,owner,description,type,status,priority,milestone,component,resolution,keywords,cc 547,Start Demux and Merge,Nicklas Nordborg,Nicklas Nordborg,"Part of #533. This wizard is started after confirming a successful sequencing. The wizard should show `SequencingRun` items that has a `SequencingResult=Succes` annotation but no child `DemuxedSequences` item. It should also be possible to manually select a `SequencingRun` if the demux needs to be re-done with different parameters. The wizard creates one `DemuxedSequences` item so that we can keep track of the demux parameters and software: * Name of item: `SequencingRunNNN.dx`, `SequeningRunNNN.dx2` ... * Software and protocol: (Type=Demuxing) * `ReadString`: Annotation automatically calculated from `SequencingCycles` annotation on the parent `SequencingRun` item The wizard also creates one `MergedSequences` for each `Library` that has been sequenced: * Name of item: `.g`, `.g2` * Software and protocol: (Type=Merging) The `MergedSequences` items are child items to the `DemuxedSequences` item. This should give us enough information to be able to start the demux and merge scripts. '''Parameters for the demux program:''' * Data files folder (=`DataFilesFolder` annotation on `SequencingRun`) * Sample sheet (exported from BASE and saved by operator to correct place on cluster). To be able to export the sample sheet the following info is needed * Read string (=`ReadString` annotation on `DemuxedSequences`) * Project (user input; default=generated from current project in BASE) * Sequencing center (user input; default=LuBMC) * Width (user input; default=100) * Concentration (user input; default=12pM) In the first version the wizard could generate scripts for running the demux. One demux command is required for each flow cell. In a future version it would be nice to submit the job to the cluster automatically. '''Parameters for the merge program:''' Currently no information about this. ",task,closed,major,Reggie v2.16,net.sf.basedb.reggie,fixed,,