File Coverage

lib/Bio/VertRes/Config/Recipes/VirusAssemblyAndAnnotation.pm

Criterion	Covered	Total	%
statement	1	3	33.3
branch			n/a
condition			n/a
subroutine	1	1	100.0
pod			n/a
total	2	4	50.0

package Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation;
# ABSTRACT: Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first


use Moose;
extends 'Bio::VertRes::Config::Recipes::Common';
with 'Bio::VertRes::Config::Recipes::Roles::VirusRegisterStudy';

has 'assembler'            => ( is => 'ro', isa => 'Str',  default => 'spades' );
has '_error_correct'       => ( is => 'ro', isa => 'Bool', default => 1 );
has '_remove_primers'      => ( is => 'ro', isa => 'Bool', default => 1 );
has '_pipeline_version'    => ( is => 'ro', isa => 'Num',  default => 3.1 );
has '_normalise'           => ( is => 'ro', isa => 'Bool', default => 1 );
has '_kingdom'             => ( is => 'ro', isa => 'Str',  default => "Viruses" );

override '_pipeline_configs' => sub {
    my ($self) = @_;
    my @pipeline_configs;
    if($self->assembler eq 'velvet')
    {
        $self->add_virus_velvet_assembly_config(\@pipeline_configs);
    }
    else
    {
        $self->add_virus_spades_assembly_config(\@pipeline_configs);
    }
    $self->add_virus_annotate_config(\@pipeline_configs);

    return \@pipeline_configs;
};

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

__END__

=pod

=head1 NAME

Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation - Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first

=head1 VERSION

version 1.133090

=head1 SYNOPSIS

Create the assembly and anntation files only, so no reference required, but for it to run you need to have done QC first
   use Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation;

   my $obj = Bio::VertRes::Config::Recipes::VirusAssemblyAndAnnotation->new(
     database => 'abc',
     limits => {project => ['Study ABC']});
   $obj->create;

=head1 AUTHOR

Andrew J. Page <[e-mail]>

=head1 COPYRIGHT AND LICENSE

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

This is free software, licensed under:

  The GNU General Public License, Version 3, June 2007

=cut