added MakeNewReference.pl to sub

#!/usr/bin/perl

#########################################

#                                       #

#     Written by Kai Battenberg         #

#     Plant Symbiosis Research Team     #

#                                       #

#########################################

use strict;

use warnings;

use Getopt::Long;

#####SCRIPT DESCRIPTION#####

#Script "MakeNewReference.pl" given a genome file (FASTA), annotation file (GTF), and a genome name, generates a reference for cellranger.

###########

#####Options#####

print "\n\#\#\#\#\#Running MakeNewReference\#\#\#\#\#\n";

print "checking options.\n";

#setting the default values.

my $genome = "";

my $annotation = "";

my $name = "";

#making the options into external arguments.

GetOptions (

	'genome=s' => \$genome,

	'annotation=s' => \$annotation,

	'name=s' => \$name

	);

#checking for sequence type

if (!$genome) {

	die "USAGE: option --genome <FASTA file> is required.\n";

}

elsif (!$annotation){

	die "USAGE: option --annotation <GTF file> is required.\n";

}

elsif (!$name) {

	die "USAGE: option --name <reference name> is required.\n";

}

print "check complete.\n\n";

##########

#####MAIN#####

print "making cellranger reference.\n";

system "cellranger mkref --genome=$name --fasta=$genome --genes=$annotation";

print "reference made.\n";

print "\#\#\#\#\#MakeNewReference COMPLETE\#\#\#\#\#\n\n";

##########

#####SUB#####

##########

__END__