# HG changeset patch
# User greg
# Date 1700766172 0
# Node ID f959d99d1758423e64ce58c8c4f1195299ba5bb7
# Parent  610251aac6ef2400e3f3e7eaf40055c21e6f4ac2
Uploaded

diff -r 610251aac6ef -r f959d99d1758 cfsan_snp_pipeline_snp_matrix.xml
--- a/cfsan_snp_pipeline_snp_matrix.xml	Wed Nov 22 22:40:03 2023 +0000
+++ b/cfsan_snp_pipeline_snp_matrix.xml	Thu Nov 23 19:02:52 2023 +0000
@@ -6,9 +6,9 @@
     <expand macro="requirements"/>
     <command detect_errors="exit_code"><![CDATA[
 #if str($reference_cond.reference_source) == 'cached'
-    set reference = '$reference_cond.reference.fields.path'
+    #set reference = $reference_cond.reference.fields.path
 #else:
-    set reference = '$reference_cond.reference'
+    #set reference = $reference_cond.reference
 #end if
 
 python '$__tool_directory__/snp_wind.py' ./ -p 'consensus.fasta'