Added OverrideCycles in bclconvert samplesheet

Author: nkongenelly

checkQC/qc_data_utils.py

@@ -15,6 +15,7 @@ def bclconvert_test_runfolder(qc_data):
                     "index": "GAACTGAGCG",
                     "index2": "TCGTGGAGCG",
                     "sample_project": "AB-1234",
+                    "overridecycles": "Y36;I10;I10",
                     "custom_description": "LIBRARY_NAME:test",
                 },
                 {
@@ -23,6 +24,7 @@ def bclconvert_test_runfolder(qc_data):
                     "index": "AGGTCAGATA",
                     "index2": "CTACAAGATA",
                     "sample_project": "CD-5678",
+                    "overridecycles": "Y36;I10;I10",
                      "custom_description": "LIBRARY_NAME:test",
                 },
                 {
@@ -31,6 +33,7 @@ def bclconvert_test_runfolder(qc_data):
                     "index": "GAACTGAGCG",
                     "index2": "TCGTGGAGCG",
                     "sample_project": "AB-1234",
+                    "overridecycles": "Y36;I10;I10",
                      "custom_description": "LIBRARY_NAME:test",
                 },
                 {
@@ -39,6 +42,7 @@ def bclconvert_test_runfolder(qc_data):
                     "index": "AGGTCAGATA",
                     "index2": "CTACAAGATA",
                     "sample_project": "CD-5678",
+                    "overridecycles": "Y36;I10;I10",
                      "custom_description": "LIBRARY_NAME:test",
                 },
             ],

tests/parsers/test_illumina_parser.py

@@ -107,5 +107,6 @@ def test_read_samplesheet(runfolder_path):
         'lane': 1,
         'sample_id': 'Sample_14574-Qiagen-IndexSet1-SP-Lane1',
         'sample_project': 'AB-1234',
+        "overridecycles": "Y36;I10;I10",
         'custom_description': 'LIBRARY_NAME:test',
     }

tests/resources/bclconvert/200624_A00834_0183_BHMTFYTINY/SampleSheet.csv

@@ -18,8 +18,8 @@ FastqCompressionFormat,gzip,,
 SoftwareVersion,4.1.5,,
 ,,,
 [BCLConvert_Data],,,
-Lane,Sample_ID,Index,Index2,Sample_Project,custom_Description
-1,Sample_14574-Qiagen-IndexSet1-SP-Lane1,GAACTGAGCG,TCGTGGAGCG,AB-1234,LIBRARY_NAME:test
-1,Sample_14575-Qiagen-IndexSet1-SP-Lane1,AGGTCAGATA,CTACAAGATA,CD-5678,LIBRARY_NAME:test
-2,Sample_14574-Qiagen-IndexSet1-SP-Lane2,GAACTGAGCG,TCGTGGAGCG,AB-1234,LIBRARY_NAME:test
-2,Sample_14575-Qiagen-IndexSet1-SP-Lane2,AGGTC  AGATA,C TACAA GATA,CD-5678,LIBRARY_NAME:test
+Lane,Sample_ID,Index,Index2,Sample_Project,OverrideCycles,custom_Description
+1,Sample_14574-Qiagen-IndexSet1-SP-Lane1,GAACTGAGCG,TCGTGGAGCG,AB-1234,Y36;I10;I10,LIBRARY_NAME:test
+1,Sample_14575-Qiagen-IndexSet1-SP-Lane1,AGGTCAGATA,CTACAAGATA,CD-5678,Y36;I10;I10,LIBRARY_NAME:test
+2,Sample_14574-Qiagen-IndexSet1-SP-Lane2,GAACTGAGCG,TCGTGGAGCG,AB-1234,Y36;I10;I10,LIBRARY_NAME:test
+2,Sample_14575-Qiagen-IndexSet1-SP-Lane2,AGGTC  AGATA,C TACAA GATA,CD-5678,Y36;I10;I10,LIBRARY_NAME:test