# HG changeset patch
# User simon-gladman
# Date 1405013903 14400
# Node ID f6cf403633965a61b98960075290be2809a438d6
# Parent  2c4e0eab2cae5dd1759b1c0b86e4f878df3f8eaf
Uploaded

diff -r 2c4e0eab2cae -r f6cf40363396 trimmomatic_wrapper.pl
--- a/trimmomatic_wrapper.pl	Thu Jul 10 13:30:31 2014 -0400
+++ b/trimmomatic_wrapper.pl	Thu Jul 10 13:38:23 2014 -0400
@@ -60,7 +60,7 @@
     $cmd .= " -trimlog " . $stuff{"logfile"};
 }
 
-if($stuff{"paired"} eq "True"){
+if($stuff{"paired"} ne "single"){
     $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
 }
 else {
@@ -84,7 +84,7 @@
 print "Command:\t$cmd\n";
 
 if(system($cmd) == 0){
-    if ($stuff{"paired"} eq "True"){
+    if ($stuff{"paired"} ne "single"){
         my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
         system($catcmd) == 0 or die "Something went wrong with the cat command $!";
     }