Changeset 5857


Ignore:
Timestamp:
Mar 10, 2020, 8:12:25 AM (21 months ago)
Author:
Nicklas Nordborg
Message:

References #1231: Add support for sequencing with NovaSeq?

The "Register sequencing ended" has been updated to work with a NovaSeq run.

Location:
extensions/net.sf.basedb.reggie/trunk
Files:
2 edited

Legend:

Unmodified
Added
Removed
  • extensions/net.sf.basedb.reggie/trunk/resources/sequencing/sequencing_ended.js

    r5488 r5857  
    354354        }
    355355        info.SequencingStart = '20'+sequencing.getTextValue(doc, 'RunStartDate');
     356      }
     357      else if (fc.FlowCellType == 'NovaSeq')
     358      {
     359        info.ExperimentName = sequencing.getTextValue(doc, 'ExperimentName');
     360        info.RunID = sequencing.getTextValue(doc, 'RunId'); // Note! "RunId" instead of "RunID"
     361        info.HiSeqPosition = sequencing.getTextValue(doc, 'Side');
     362        info.ScannerID = sequencing.getTextValue(doc, 'InstrumentName');
     363        info.ScanNumber = parseInt(sequencing.getTextValue(doc, 'RunNumber'));
     364        info.FlowCellID = sequencing.getTextValue(doc, 'RfidsInfo>FlowCellSerialBarcode');
     365        if (numReads == 4)
     366        {
     367          info.SequencingCycles = sequencing.getTextValue(doc, 'Read1NumberOfCycles') + '-' + sequencing.getTextValue(doc, 'IndexRead1NumberOfCycles') + '-' + sequencing.getTextValue(doc, 'IndexRead2NumberOfCycles') + '-' + sequencing.getTextValue(doc, 'Read2NumberOfCycles');
     368        }
     369        else
     370        {
     371          info.SequencingCycles = sequencing.getTextValue(doc, 'Read1NumberOfCycles') + '-' + sequencing.getTextValue(doc, 'IndexRead1NumberOfCycles') + '-' + sequencing.getTextValue(doc, 'Read2NumberOfCycles');
     372        }
     373        info.SequencingStart = '20'+sequencing.getTextValue(doc, 'RunStartDate');
     374       
    356375      }
    357376    }
  • extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/SequencingRunServlet.java

    r5855 r5857  
    742742    script.cmd("if [ -f \"$RUN_ARCHIVE/RunParameters.xml\" ]; then");
    743743    script.cmd("  RUN_PARAMETERS=RunParameters.xml");
    744     script.cmd("  RUN_COMPLETE=RunCompletionStatus.xml");
    745744    script.cmd("elif [ -f \"$RUN_ARCHIVE/runParameters.xml\" ]; then");
    746745    script.cmd("  RUN_PARAMETERS=runParameters.xml");
    747     script.cmd("  RUN_COMPLETE=RTAComplete.txt");
    748746    script.cmd("else");
    749747    script.cmd("echo \"Can't find RunParameters.xml or runParameters.xml in folder ${RUN_ARCHIVE}\" 1>&2");
    750748    script.cmd("exit 1");
     749    script.cmd("fi");
     750    script.cmd("if [ -f \"$RUN_ARCHIVE/RunCompletionStatus.xml\" ]; then");
     751    script.cmd("  RUN_COMPLETE=RunCompletionStatus.xml");
     752    script.cmd("elif [ -f \"$RUN_ARCHIVE/RTAComplete.txt\" ]; then");
     753    script.cmd("  RUN_COMPLETE=RTAComplete.txt");
    751754    script.cmd("fi");
    752755    script.cmd("echo $RUN_ARCHIVE");
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