Use lane 1s matrix when pipeline was set to build matrix from all.

(HiSeq's pipeline doesn't make the lane-less matrix file)

diff --git a/htsworkflow/pipelines/bustard.py b/htsworkflow/pipelines/bustard.py
index 2c68f674ad77a7d1cfdc637e2553fc57ffcbd87f..dd831a197afa7bbf9d8628f29e9992cc4eea0112 100644 (file)
--- a/htsworkflow/pipelines/bustard.py
+++ b/htsworkflow/pipelines/bustard.py
@@ -170,7 +170,8 @@ 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:
-            auto_lane_fragment = ""
+            # its defaulting to all of the lanes, so just pick one
+            auto_lane_fragment = "_1"
         else:
             auto_lane_fragment = "_%d" % ( matrix_auto_lane,)