Check for s_${lane}_02_matrix.txt as well as s_${lane}_1_matrix.txt

[htsworkflow.git] / htsworkflow / pipelines / bustard.py

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 25b273792b6f7a1f0ebad315e36372636f0bac21..49c1f16b703e8a64d1a68fa8d5925dbe52985ac5 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -168,11 +168,20 @@ def crosstalk_matrix_from_bustard_config(bustard_path, bustard_config_tree):
         # we estimated the matrix from something in this run.
         # though we don't really care which lane it was
         if matrix_auto_lane == 0:
-            matrix_path = os.path.join(bustard_path, 
-                                       'Matrix', 's_02_matrix.txt')
+            auto_lane_fragment = ""
         else:
-            matrix_path = os.path.join(bustard_path, 'Matrix',
-                           's_%d_1_matrix.txt' % (matrix_auto_lane,))
+            auto_lane_fragment = "_%d" % ( matrix_auto_lane,)
+            
+        for matrix_name in ['s%s_02_matrix.txt' % (auto_lane_fragment,),
+                            's%s_1_matrix.txt' % (auto_lane_fragment,),
+                            ]:
+            matrix_path = os.path.join(bustard_path, 'Matrix', matrix_name)
+            if os.path.exists(matrix_path):
+                break
+        else:
+            raise RuntimeError("Couldn't find matrix for lane %d" % \
+                               (matrix_auto_lane,))
+
         crosstalk = CrosstalkMatrix(matrix_path)
     else:
         matrix_elements = call_parameters.find('MatrixElements')