Merge pull request #306 from chuan-wang/master

Handle special case with index 2 only for NovaSeq
NationalGenomicsInfrastructure · Jul 16, 2021 · c336c9f · c336c9f
2 parents c157d72 + 278e33d
commit c336c9f
Show file tree

Hide file tree

Showing 2 changed files with 4 additions and 1 deletion.
diff --git a/VERSIONLOG.md b/VERSIONLOG.md
@@ -1,5 +1,8 @@
 # TACA Version Log
 
+## 20210716.1
+Handle special case with index 2 only for NovaSeq
+
 ## 20210617.1
 Support addtional 10X index types
 

diff --git a/taca/illumina/HiSeqX_Runs.py b/taca/illumina/HiSeqX_Runs.py
@@ -263,7 +263,7 @@ def _generate_per_lane_base_mask(self, sample_type, mask_table):
             index1_size = lane_contents[0]
             index2_size = lane_contents[1]
             is_dual_index = False
-            if index1_size != 0 and index2_size != 0:
+            if (index1_size != 0 and index2_size != 0) or (index1_size == 0 and index2_size != 0):
                 is_dual_index = True
             # Compute the basemask
             base_mask = self._compute_base_mask(runSetup, sample_type, index1_size, is_dual_index, index2_size)