Mercurial > repos > simon-gladman > trimmomatic_032

diff trimmomatic_wrapper.pl @ 8:18bd222a110e draft

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Uploaded
author simon-gladman
date Thu, 10 Jul 2014 13:25:10 -0400
parents 7d626189cc4c
children f6cf40363396
line wrap: on
line diff
--- 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";