Mercurial > repos > simon-gladman > trimmomatic_032

comparison trimmomatic_wrapper.pl @ 10:f6cf40363396 draft

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Uploaded
author simon-gladman
date Thu, 10 Jul 2014 13:38:23 -0400
parents 18bd222a110e
children e99104027742
comparison
equal deleted inserted replaced
9:2c4e0eab2cae 10:f6cf40363396
58 58
59 if($stuff{"log"} eq "True"){ 59 if($stuff{"log"} eq "True"){
60 $cmd .= " -trimlog " . $stuff{"logfile"}; 60 $cmd .= " -trimlog " . $stuff{"logfile"};
61 } 61 }
62 62
63 if($stuff{"paired"} eq "True"){ 63 if($stuff{"paired"} ne "single"){
64 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp)); 64 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"revfile"},$stuff{"fwdpairs"},$fwdtemp,$stuff{"revpairs"},$revtemp));
65 } 65 }
66 else { 66 else {
67 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"})); 67 $cmd .= " " . join(" ",($stuff{"fwdfile"},$stuff{"singles"}));
68 } 68 }
82 $cmd .= " " .join(":",("MINLEN",$stuff{"minlen"})); 82 $cmd .= " " .join(":",("MINLEN",$stuff{"minlen"}));
83 83
84 print "Command:\t$cmd\n"; 84 print "Command:\t$cmd\n";
85 85
86 if(system($cmd) == 0){ 86 if(system($cmd) == 0){
87 if ($stuff{"paired"} eq "True"){ 87 if ($stuff{"paired"} ne "single"){
88 my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"}; 88 my $catcmd = "cat $fwdtemp $revtemp > " . $stuff{"singles"};
89 system($catcmd) == 0 or die "Something went wrong with the cat command $!"; 89 system($catcmd) == 0 or die "Something went wrong with the cat command $!";
90 } 90 }
91 } 91 }
92 else{ 92 else{