File Coverage

lib/Bio/VertRes/Config/Recipes/BacteriaRegisterAndQCStudy.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::BacteriaRegisterAndQCStudy;
# ABSTRACT: Register and QC a study


use Moose;
use Bio::VertRes::Config::Pipelines::QC;
use Bio::VertRes::Config::RegisterStudy;
extends 'Bio::VertRes::Config::Recipes::Common';
with 'Bio::VertRes::Config::Recipes::Roles::BacteriaRegisterStudy';
with 'Bio::VertRes::Config::Recipes::Roles::Reference';
with 'Bio::VertRes::Config::Recipes::Roles::CreateGlobal';

has 'assembler'            => ( is => 'ro', isa => 'Str',  default => 'velvet' );
has '_error_correct'       => ( is => 'ro', isa => 'Bool', default => 0 );
has '_remove_primers'      => ( is => 'ro', isa => 'Bool', default => 0 );
has '_pipeline_version'    => ( is => 'ro', isa => 'Num',  default => 2.1 );
has '_normalise'           => ( is => 'ro', isa => 'Bool', default => 0 );
has '_kingdom'             => ( is => 'ro', isa => 'Str',  default => "Bacteria" );


override '_pipeline_configs' => sub {
    my ($self) = @_;
    my @pipeline_configs;
    $self->add_bacteria_qc_config(\@pipeline_configs);
    if($self->assembler eq 'spades')
    {
        $self->add_bacteria_spades_assembly_config(\@pipeline_configs);
    }
    else
    {
        $self->add_bacteria_velvet_assembly_config(\@pipeline_configs);
    }
    $self->add_bacteria_annotate_config(\@pipeline_configs);

    return \@pipeline_configs;
};

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

__END__

=pod

=head1 NAME

Bio::VertRes::Config::Recipes::BacteriaRegisterAndQCStudy - Register and QC a study

=head1 VERSION

version 1.133090

=head1 SYNOPSIS

Register and QC a study
   use Bio::VertRes::Config::Recipes::BacteriaRegisterAndQCStudy;

   my $obj = Bio::VertRes::Config::Recipes::BacteriaRegisterAndQCStudy->new(
     database => 'abc',
     limits => {project => ['Study ABC']},
     reference => 'ABC',
     reference_lookup_file => '/path/to/refs.index');
   $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