/data/results/
         TestFolder1/
         subfolder1/Variants/MD-14-11856_RNA_v2.vcf
         subfoder2/Variants/SU-16-16117_RNA_v2.vcf
         matrix.txt
         matrixkey.txt

         TestFolder2/
         subfolder1/Variants/SU-15-2542_v2.vcf
         subfolder2/Variants/SU-16-16117_v2.vcf
         matrix.txt
         matrixkey.txt

Barcode        SampleName
barcode_003    SU-15-2542
barcode-005    MD-14-11856
barcode-002    SU-16-16117

#!/usr/bin/perl
use warnings;
use strict;

use File::Copy qw(move);
use List::Util 'first';
use File::Find;
use File::Spec;
use Data::Dumper;

use File::Basename;
use File::Spec::Functions 'splitdir';

my $current_directory = "/data/results";

if (grep -d, glob("$current_directory/*")) {
    print "$current_directory has subfolder(s)n";
    }
    else
    {
    print "there are no foldersn";

    die;
}

my %files;
my @dirs = grep { -d } glob '/data/results/*';

for my $dir ( @dirs ) {

        print "the directory is $dirn";
        my $run_folder = (split '/', $dir)[3];
        print "the folder is $run_foldern";


        my $key2 = $run_folder;

       # checks if barcode matrix and barcode summary files exist

            #shortens the folder names and unzips them.

            #check if each sample is present in the matrix file for each folder.
            my $location = "/data/results/".$run_folder;

            my $matrix_key = "/data/results/".$run_folder."/matrixkey.txt";

            open my $key, '<', $matrix_key or die $!; # key file

            <$key>; # throw away header line in key file (first line)
            my @matrix_key = ();

            @matrix_key = sort {length($b->[1]) <=> length($a->[1])} map [ split ],  <$key>;
            close $key or die $!;

            print Dumper(@matrix_key) . "===nn";

        sub find_vcf {
            my $F = $File::Find::name;

            if ($F =~ /vcf$/ ) {
                print "$Fn";

                $F =~ m|([^/]+).vcf$| or die "Can't extract Sample ID";
                my $sample_id = $1; print "the short vcf name is: $sample_idn";

                if ( my $aref = first { index($sample_id, $_->[1]) != -1 } @matrix_key ) {
                    #the code fails to match sample_id to matrix_key eventhough it's printed out correctly

                    print "$sample_id t MATCHES $aref->[1]n";
                    print "t$aref->[1]_$aref->[0]nn";

                    } else {
                # handle all other possible exceptions

                #print "folder name is $run_foldern";

                die("The VCF file doesn't match the Summary Barcode file: $sample_idn");
                           }

                }

            }

        find({ wanted => &find_vcf, no_chdir=>1}, $location);


  }

exit();