Fix missing settings for BCL Convert

chuan-wang · Oct 29, 2024 · c89c8b3 · c89c8b3
1 parent 465db72
commit c89c8b3
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diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -1,5 +1,9 @@
 # TACA Version Log
 
+## 20241029.3
+
+Fix missing settings for BCL Convert
+
 ## 20241029.2
 
 Fix issue that index 2 is automatically converted to RC by BCL Convert

diff --git a/taca/illumina/Runs.py b/taca/illumina/Runs.py
@@ -1317,6 +1317,14 @@ def _process_demux_with_complex_lanes(
                     "Recipe",
                     "Operator",
                     "Sample_Project",
+                    "[Settings]",
+                    "OverrideCycles",
+                    "MinimumTrimmedReadLength",
+                    "MaskShortReads",
+                    "CreateFastqForIndexReads",
+                    "BarcodeMismatchesIndex1",
+                    "BarcodeMismatchesIndex2",
+                    "TrimUMI",
                 ]
                 with open(samplesheet) as sub_samplesheet_file:
                     sub_samplesheet_reader = csv.reader(sub_samplesheet_file)