Mercurial > repos > simon-gladman > trimmomatic_032
changeset 14:cb56fdcbe0a5 draft default tip
Uploaded
author | simon-gladman |
---|---|
date | Thu, 10 Jul 2014 14:38:53 -0400 |
parents | 476184b9b2f7 |
children | |
files | trimmomatic_wrapper.pl |
diffstat | 1 files changed, 5 insertions(+), 5 deletions(-) [+] |
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--- a/trimmomatic_wrapper.pl Thu Jul 10 14:38:25 2014 -0400 +++ b/trimmomatic_wrapper.pl Thu Jul 10 14:38:53 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"; @@ -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 $!"; }