From: Diane Trout <diane@caltech.edu>
Date: Thu, 12 Jul 2012 17:59:19 +0000 (-0700)
Subject: Use lane 1s matrix when pipeline was set to build matrix from all.
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=dca410f958fd60ab2a3cddf217501b7820ef19c7

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 2c68f67..dd831a1 100644
--- 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,)