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Commit 59dd7711 authored by kohleman's avatar kohleman
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added 'lane' into the Sample sheet, so the bcl2fastq 2.17 works with HiSeq data 

SVN: 34366
parent 19a76ca6
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deep_sequencing_unit/source/Jython/createSampleSheet_nextseq.py
+ 6
− 4
View file @ 59dd7711
...@@ -408,7 +408,7 @@ def get_reverse_complement(sequence): ...@@ -408,7 +408,7 @@ def get_reverse_complement(sequence):
return reverse_complement return reverse_complement
def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary, index2Vocabulary, def createSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary, index2Vocabulary,
flowCellName, logger, myoptions): flowCellName, logger, myoptions):
''' '''
''' '''
...@@ -514,7 +514,8 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary ...@@ -514,7 +514,8 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary
if int(flowCellDict['INDEXREAD2']) > 0: if int(flowCellDict['INDEXREAD2']) > 0:
sampleSheetDict[lane + '_' + key] = [ sampleSheetDict[lane + '_' + key] = [
key + separator lane + separator
+ key + separator
+ key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator + key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator
+ separator + separator
+ separator + separator
...@@ -526,7 +527,8 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary ...@@ -526,7 +527,8 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary
] ]
else: else:
sampleSheetDict[lane + '_' + key] = [ sampleSheetDict[lane + '_' + key] = [
key + separator lane + separator
+ key + separator
+ key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + separator + key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + separator
+ separator + separator
+ separator + separator
...@@ -581,7 +583,7 @@ def main (): ...@@ -581,7 +583,7 @@ def main ():
index1Vocabulary = getVocabulary(configMap['index1Name'], service) index1Vocabulary = getVocabulary(configMap['index1Name'], service)
index2Vocabulary = getVocabulary(configMap['index2Name'], service) index2Vocabulary = getVocabulary(configMap['index2Name'], service)
SampleSheetFile = createMiSeqSampleSheet(parentDict, flowCellDict, configMap, SampleSheetFile = createSampleSheet(parentDict, flowCellDict, configMap,
index1Vocabulary, index2Vocabulary, flowCellName, logger, myoptions) index1Vocabulary, index2Vocabulary, flowCellName, logger, myoptions)
if myoptions.maillist: if myoptions.maillist:
......
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