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#!/usr/bin/env perl
use strict;
use warnings;
use Getopt::Long qw(:config no_ignore_case bundling pass_through);
use FindBin;
my $usage = <<__EOUSAGE__;
###############################################################
#
# --left <string> left.fq
# --right <string> right.fq
#
# or
#
# --single <string> single.fq
#
# Optional:
#
# --CPU <int> default: 4
#
# --trim_params <string> "SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25"
#
###############################################################
__EOUSAGE__
;
my $left;
my $right;
my $single;
my $threads = 4;
my $trim_params = "SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25";
&GetOptions( 'left=s' => \$left,
'right=s' => \$right,
'single=s' => \$single,
'CPU=i' => \$threads,
'trim_params=s' => \$trim_params,
);
=trimmomatic
java -jar /seq/regev_genome_portal/SOFTWARE/BIN/trimmomatic.jar PE -threads {__THREADS__} -phred33 \
{__LEFT_FQ__} {__RIGHT_FQ__} \
{__LEFT_FQ__}.P.qtrim.fq {__LEFT_FQ__}.U.qtrim.fq \
{__RIGHT_FQ__}.P.qtrim.fq {__RIGHT_FQ__}.U.qtrim.fq \
LEADING:15 TRAILING:15 MINLEN:36 2> {__LOCAL_ANALYSIS_DIR__}/trimmomatic.log.stats
=cut
;
unless ( ($left && $right) || $single) {
die $usage;
}
main: {
my $cmd;
if ($left && $right) {
$cmd = "java -jar $FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar PE -threads $threads -phred33 "
. " $left $right "
. " $left.P.qtrim.fq $left.U.qtrim.fq "
. " $right.P.qtrim.fq $right.U.qtrim.fq "
. " $trim_params ";
}
else {
$cmd = "java -jar $FindBin::RealBin/../../trinity-plugins/Trimmomatic/trimmomatic.jar SE -threads $threads -phred33 "
. " $single "
. " $single.qtrim.fq "
. " $trim_params ";
}
&process_cmd($cmd);
exit(0);
}
####
sub process_cmd {
my ($cmd) = @_;
print STDERR "CMD: $cmd\n";
my $ret = system($cmd);
if ($ret) {
die "Error, cmd: $cmd died with ret $ret";
}
return;
}
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