comparison trimmomatic_wrapper.pl @ 14:cb56fdcbe0a5 draft default tip

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13:476184b9b2f7

my $numthreads = $stuff{"threads"};


my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";

if($stuff{"paired"} eq "True"){
    $cmd .= "PE";
}
else {
    $cmd .= "SE";
}

$cmd .= " -threads $numthreads";

$cmd .= " -phred33" if($stuff{"phred"} eq "phred33");

if($stuff{"log"} eq "True"){
    $cmd .= " -trimlog " . $stuff{"logfile"};
}

if($stuff{"paired"} eq "True"){
    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
}
else {
    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"}));
}

$cmd .= " " .join(":",("MINLEN",$stuff{"minlen"}));

print "Command:\t$cmd\n";

if(system($cmd) == 0){
    if ($stuff{"paired"} eq "True"){
        my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
        system($catcmd) == 0 or die "Something went wrong with the cat command $!";
    }
}
else{

14:cb56fdcbe0a5

my $numthreads = $stuff{"threads"};


my $cmd = "java -cp $jar org.usadellab.trimmomatic.Trimmomatic";

if($stuff{"paired"} eq "single"){
    $cmd .= "SE";
}
else {
    $cmd .= "PE";
}

$cmd .= " -threads $numthreads";

$cmd .= " -phred33" if($stuff{"phred"} eq "phred33");

if($stuff{"log"} eq "True"){
    $cmd .= " -trimlog " . $stuff{"logfile"};
}

if($stuff{"paired"} ne "single"){
    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
}
else {
    $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"}));
}

$cmd .= " " .join(":",("MINLEN",$stuff{"minlen"}));

print "Command:\t$cmd\n";

if(system($cmd) == 0){
    if ($stuff{"paired"} ne "single"){
        my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 
        system($catcmd) == 0 or die "Something went wrong with the cat command $!";
    }
}
else{