Mercurial > repos > simon-gladman > trimmomatic_032

changeset 10:f6cf40363396 draft

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Uploaded
author simon-gladman
date Thu, 10 Jul 2014 13:38:23 -0400
parents 2c4e0eab2cae
children 70953ccd575a
files trimmomatic_wrapper.pl
diffstat 1 files changed, 2 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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 $!";
     }