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        cpus            => $self->cpus
	);
    $kraken_runner_obj->run();
    for my $filename(@{$kraken_files})
    {
        unlink($filename);
    }
    return \@kraken_report_output_files;
}

sub _build__kraken_data {
	my $self = shift;
    my $nuc_files = $self->_extract_nuc_files_from_all_gffs();
    my $kraken_files = $self->_run_kraken_on_nuc_files($nuc_files);
    my $kraken_report_files = $self->_run_kraken_report_on_kraken_files( $kraken_files );
    
	return $self->_parse_kraken_reports($kraken_report_files);
}

sub _parse_kraken_reports
{
    my ( $self, $kraken_report_files ) = @_;
    
    my @report_rows;
    for my $kraken_report(@{$kraken_report_files})
    {
        push(@report_rows, $self->_parse_kraken_report($kraken_report));
    }
    
    for my $kraken_report(@{$kraken_report_files})
    {
        unlink($kraken_report);
    }   
    
    return \@report_rows;
}

sub _parse_kraken_report {
	my ( $self, $kraken_report ) = @_;

	# parse report
	open( my $report_fh, '<', $kraken_report );
    
    my $sample_name = $kraken_report;
    $sample_name =~ s/.report$//;
    $sample_name =~ s/.kraken$//;
    my($sample_base_name, $dirs, $suffix) = fileparse($sample_name);
    
	my ( $top_genus, $top_species );
	while ( <$report_fh> ){
		my @parts = split( "\t" );
		chomp @parts;

		$top_genus = $parts[5] if ( (! defined $top_genus) && $parts[3] eq 'G' );
		$top_species = $parts[5] if ( (! defined $top_species) && $parts[3] eq 'S' );

		last if (defined $top_genus && defined $top_species);
	}
    close($report_fh);

	$top_genus   ||= "not_found";
	$top_genus   =~ s/^\s+//g;
	$top_species ||= "not_found";
	$top_species =~ s/^\s+//g;

	return [ $sample_base_name, $top_genus, $top_species ];
}


sub _build__header {
	return join( ',', ( 'Sample', 'Genus', 'Species' ) );
}

sub _build__tmp_directory_obj {
	return File::Temp->newdir(DIR => getcwd, CLEANUP => 1 ); 
}

sub _build__tmp_directory {
	my $self = shift;
	return $self->_tmp_directory_obj->dirname();
}

sub report {
	my $self = shift;

	open( OUTFILE, '>', $self->outfile );
	print OUTFILE $self->_header . "\n";
	for my $line ( @{ $self->_kraken_data } ){
		print OUTFILE join( ',', @{ $line } ) . "\n";
	}
	close OUTFILE;
}


__PACKAGE__->meta->make_immutable;
no Moose;
1;

__END__

=pod

=encoding UTF-8

=head1 NAME

Bio::Roary::QC::Report - generate a report based on kraken output

=head1 VERSION

version 3.13.0

=head1 SYNOPSIS

=head1 AUTHOR

Andrew J. Page <ap13@sanger.ac.uk>

=head1 COPYRIGHT AND LICENSE

This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute.

This is free software, licensed under: