# HG changeset patch # User simon-gladman # Date 1405015591 14400 # Node ID e991040277422e604199e118af7c524497ba79bc # Parent 70953ccd575ad591137222c280b07d671b24b907 Uploaded diff -r 70953ccd575a -r e99104027742 trimmomatic_wrapper.pl --- 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 $!"; }