From a25e6c2ec2d869f54e5694c38eef836534d74fb7 Mon Sep 17 00:00:00 2001
From: kohleman <kohleman>
Date: Thu, 16 Apr 2015 07:42:50 +0000
Subject: [PATCH] fixed problem with separate lanes
SVN: 33846
---
.../source/Jython/createSampleSheet_nextseq.py | 13 +++++++------
1 file changed, 7 insertions(+), 6 deletions(-)
diff --git a/deep_sequencing_unit/source/Jython/createSampleSheet_nextseq.py b/deep_sequencing_unit/source/Jython/createSampleSheet_nextseq.py
index dbe898920c4..0186e2a21a9 100644
--- a/deep_sequencing_unit/source/Jython/createSampleSheet_nextseq.py
+++ b/deep_sequencing_unit/source/Jython/createSampleSheet_nextseq.py
@@ -199,6 +199,9 @@ def readConfig(logger):
configMap['miSeqWorkflow'] = configParameters.get(ILLUMINA, 'miSeqWorkflow')
configMap['miSeqApplication'] = configParameters.get(ILLUMINA, 'miSeqApplication')
configMap['miSeqChemistry'] = configParameters.get(ILLUMINA, 'miSeqChemistry')
+
+ configMap['nextSeqDataSectionSingleRead'] = configParameters.get(ILLUMINA, 'nextSeqDataSectionSingleRead')
+ configMap['nextSeqDataSectionDualRead'] = configParameters.get(ILLUMINA, 'nextSeqDataSectionDualRead')
configMap['truSeqAdapter1'] = configParameters.get(ILLUMINA, 'truSeqAdapter1')
configMap['truSeqAdapter2'] = configParameters.get(ILLUMINA, 'truSeqAdapter2')
@@ -480,9 +483,9 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary
headerList.append('')
if int(flowCellDict['INDEXREAD2']) > 0:
- miSeqDataSection = configMap['miSeqDataSectionDualRead'].split(',')
+ miSeqDataSection = configMap['nextSeqDataSectionDualRead'].split(',')
else:
- miSeqDataSection = configMap['miSeqDataSectionSingleRead'].split(',')
+ miSeqDataSection = configMap['nextSeqDataSectionSingleRead'].split(',')
miSeqDataSection.reverse()
headerList.append(miSeqDataSection.pop())
@@ -511,8 +514,7 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary
if int(flowCellDict['INDEXREAD2']) > 0:
sampleSheetDict[lane + '_' + key] = [
- lane + separator
- + key + separator
+ key + separator
+ key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + '_' + index2[0:len_index2] + separator
+ separator
+ separator
@@ -524,8 +526,7 @@ def createMiSeqSampleSheet(parentDict, flowCellDict, configMap, index1Vocabulary
]
else:
sampleSheetDict[lane + '_' + key] = [
- lane + separator
- + key + separator
+ key + separator
+ key + '_' + sanitizeString(parentDict[key][configMap['externalSampleName']]) + '_' + index1[0:len_index1] + separator
+ separator
+ separator
--
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