# HG changeset patch
# User simon-gladman
# Date 1405013110 14400
# Node ID 18bd222a110eeaa31906c1ed62cc4cf90fdf045e
# Parent  76d1aebc44bfaacd4dea1c1f6f0865fd9c95cc67
Uploaded

diff -r 76d1aebc44bf -r 18bd222a110e trimmomatic_wrapper.pl
--- a/trimmomatic_wrapper.pl	Thu Jul 10 13:24:53 2014 -0400
+++ b/trimmomatic_wrapper.pl	Thu Jul 10 13:25:10 2014 -0400
@@ -45,11 +45,11 @@
 
 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
 
-if($stuff{"paired"} eq "True"){
-    $cmd .= "PE";
+if($stuff{"paired"} eq "single"){
+    $cmd .= "SE";
 }
 else {
-    $cmd .= "SE";
+    $cmd .= "PE";
 }
 
 $cmd .= " -threads $numthreads";