diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet.py b/deep_sequencing_unit/source/Jython/createSampleSheet.py index 119c0f269773c2c6e1ab60fa403f5fdb1f26ddec..e9298777d153ef93ade508501bde7ade31662719 100644 --- a/deep_sequencing_unit/source/Jython/createSampleSheet.py +++ b/deep_sequencing_unit/source/Jython/createSampleSheet.py @@ -1,6 +1,6 @@ ''' @copyright: -Copyright 2012 ETH Zuerich, CISD +Copyright 2014 ETH Zuerich, SIS @license: Licensed under the Apache License, Version 2.0 (the 'License'); @@ -356,7 +356,7 @@ def convertSampleToDict(foundFlowCell): def createDemultiplexCommands(myoptions, configMap, laneIndexDict, endType, cycles, lane, - myFileName): + myFileName, indexRead1Length, indexRead2Length): ''' Builds up a command line for the demultiplexing of a single flow lane ''' @@ -367,13 +367,13 @@ def createDemultiplexCommands(myoptions, configMap, laneIndexDict, endType, cycl basesMask = 'Y' + cycles + COMMA + 'I' + str(indexlength / 2) + 'n' + COMMA + 'I' + \ str(indexlength / 2) + 'n' else: - basesMask = 'Y' + cycles + COMMA + 'I' + str(indexlength) + 'n' + COMMA + (indexlength + 1) * 'n' + basesMask = 'Y' + cycles + COMMA + 'I' + str(indexlength) + (indexRead1Length - indexlength + 1)*'n' if endType == 'PAIRED_END': basesMask = basesMask + COMMA + 'Y' + cycles return ([' '.join([configMap['configureBclToFastqPath'], configMap['failedReads'], configMap['clusterCount'], configMap['clusterCountNumber'], configMap['outputDir'], '../../../Unaligned_' + str(lane), configMap['sampleSheetName'], - myFileName, configMap['baseMask'], basesMask, newline])]) + myFileName, configMap['baseMask'], basesMask, "--no-eamss", newline])]) def createHiseqSampleSheet(parentDict, flowCellDict, samplesPerLaneDict, flowCellName, configMap, logger, myoptions): @@ -422,7 +422,7 @@ def createHiseqSampleSheet(parentDict, flowCellDict, samplesPerLaneDict, flowCel # more than one samples in an non-indexed lane if samplesPerLaneDict[lane] > 1: # if it is not a PhiX and not a Pool Sample - if (parentDict[key]['NCBI_ORGANISM_TAXONOMY'] != '10847') and parentDict[key]['BARCODE_COMPLEXITY_CHECKER'] != 'OK': + if (parentDict[key]['NCBI_ORGANISM_TAXONOMY'] != '10847') and parentDict[key]['BARCODE_COMPLEXITY_CHECKER'] == 'No Pool': # then just use this sample and skip the others if there are more samplesPerLaneDict[lane] = 0 index = ' ' @@ -473,7 +473,7 @@ def createHiseqSampleSheet(parentDict, flowCellDict, samplesPerLaneDict, flowCel flowCellName + '.csv' demultiplexCommandList.append(createDemultiplexCommands(myoptions, configMap, laneIndexDict, - endType, cycles, lane, myFileName)) + endType, cycles, lane, myFileName, indexRead1Length, indexRead2Length)) SamplesheetFile = writeSampleSheet(myoptions, logger, sampleSheetDict, laneSeparatedList, fileName=myFileName) writeDemultiplexCommandList(logger, demultiplexCommandList, @@ -485,7 +485,7 @@ def createHiseqSampleSheet(parentDict, flowCellDict, samplesPerLaneDict, flowCel flowCellName + '.csv' writeSampleSheet(myoptions, logger, sampleSheetDict, sortedSampleSheetList, fileName=myFileName) - return sampleSheetDict, myFileName + return sampleSheetDict, myFileName def writeDemultiplexCommandList(logger, demultiplexCommandList, fileName):