pass arguments for tag and output for TSO and filtering scripts

my $fastq_out = "mock_UMI.fastq";

my $head_length = ""; #number of characters to have before insertion of mock UMI.

my $umi_length = ""; #length of desired UMI

my $out_dir = ".";

##########

GetOptions (

	'fastq=s' => \$fastq_in,

	'head_length=s' => \$head_length,

	'umi_length=s' => \$umi_length

	'umi_length=s' => \$umi_length,

        'out_dir=s' => \$out_dir

	);

#checking for required options.

elsif (!$umi_length) {

	die "USAGE: option --umi_length <INTEGER> is required.\n";

}

elsif (!$out_dir) {

        die "USAGE: option --out_dir <OUTPUT_DIRECTORY> is required.\n";

}

$fastq_out = $out_dir."/".$fastq_out;

$fastq_out =~ s/\/\//\//;

##########

#checking head length

if ( $head_length !~ /^-?\d+\.?\d*$/ ) {

#####Options#####

#SmartSeq3 tag

my $ss3t = "ATTGCGCAATG";

my $tagseq = "ATTGCGCAATG";

#setting the default values.

my $i1 = "";

my $i2 = "";

my $r1 = "";

my $r2 = "";

my $i1_out = "SmartSeq3_parsed_I1.fastq";

my $i2_out = "SmartSeq3_parsed_I2.fastq";

my $r1_out = "SmartSeq3_parsed_R1.fastq";

my $r2_out = "SmartSeq3_parsed_R2.fastq";

my $i1_out = "parsed_I1.fastq";

my $i2_out = "parsed_I2.fastq";

my $r1_out = "parsed_R1.fastq";

my $r2_out = "parsed_R2.fastq";

my $out_dir = "";

#making the options into external arguments.

	'i2=s' => \$i2,

	'r1=s' => \$r1,

	'r2=s' => \$r2,

        'tag=s' => \$tagseq,

	'out_dir=s' => \$out_dir

	);

#####MAIN#####

#get list of reads to keep

my @keepreads = map { ($_ + 2) / 4 } split(/\n/, `grep $ss3t $r1 -n | cut -f1 -d\:`);

my @keepreads = map { ($_ + 2) / 4 } split(/\n/, `grep $tagseq $r1 -n | cut -f1 -d\:`);

my %keepreads = map { $_ => 1 } @keepreads;

#parse reads to keep

	}

	else {

		#trim r1 data

		my @trim = split (/$ss3t/, $r1_seq);

		my @trim = split (/$tagseq/, $r1_seq);

		shift @trim;

		my $new_r1_seq = join ("$ss3t", @trim);

		my $new_r1_seq = join ("$tagseq", @trim);

		my $new_r1_q = $r1_q;

		chomp $new_r1_q;

		$new_r1_q = reverse $new_r1_q;