Start Demux and Merge

[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 flow cells

The wizard also creates one MergedSequences for each Library that has been sequenced:

• Name of item: <lib-name>.g, <lib-name>.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:

• Start date (=SequencingStart annotation on SequencingRun)
• Serial number of !HiSEQ (=Hardcoded; in BASE 3.3 -> annotation on Hardware item)
• Run number (=not known but CASA2 can find out; or should we keep annotation on SequencingRun item??)
• Lane (=HiSeqPosition annotation on FlowCell)
• Flow cell ID (=FlowCellID annotation on FlowCell)
• 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.