Mercurial > repos > simon-gladman > trimmomatic_032

changeset 12:e99104027742 draft

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Uploaded
author simon-gladman
date Thu, 10 Jul 2014 14:06:31 -0400
parents 70953ccd575a
children 476184b9b2f7
files trimmomatic_wrapper.pl
diffstat 1 files changed, 5 insertions(+), 5 deletions(-) [+]
line wrap: on
line diff
--- a/trimmomatic_wrapper.pl	Thu Jul 10 14:06:14 2014 -0400
+++ b/trimmomatic_wrapper.pl	Thu Jul 10 14:06:31 2014 -0400
@@ -45,11 +45,11 @@
 
 my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";
 
-if($stuff{"paired"} eq "single"){
-    $cmd .= "SE";
+if($stuff{"paired"} eq "True"){
+    $cmd .= "PE";
 }
 else {
-    $cmd .= "PE";
+    $cmd .= "SE";
 }
 
 $cmd .= " -threads $numthreads";
@@ -60,7 +60,7 @@
     $cmd .= " -trimlog " . $stuff{"logfile"};
 }
 
-if($stuff{"paired"} ne "single"){
+if($stuff{"paired"} eq "True"){
     $cmd .= " " . join(" ",($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"} ne "single"){
+    if ($stuff{"paired"} eq "True"){
         my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
         system($catcmd) == 0 or die "Something went wrong with the cat command $!";
     }