File Coverage

lib/Bio/VertRes/Config/Recipes/EukaryotesSnpCallingUsingStampy.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::EukaryotesSnpCallingUsingStampy;
# ABSTRACT: Standard snp calling pipeline for bacteria


use Moose;
extends 'Bio::VertRes::Config::Recipes::Common';
with 'Bio::VertRes::Config::Recipes::Roles::RegisterStudy';
with 'Bio::VertRes::Config::Recipes::Roles::Reference';
with 'Bio::VertRes::Config::Recipes::Roles::CreateGlobal';
with 'Bio::VertRes::Config::Recipes::Roles::EukaryotesSnpCalling';
with 'Bio::VertRes::Config::Recipes::Roles::EukaryotesMapping';

override '_pipeline_configs' => sub {
    my ($self) = @_;
    my @pipeline_configs;

    $self->add_qc_config(\@pipeline_configs);
    $self->add_eukaryotes_stampy_mapping_config(\@pipeline_configs);

    # Insert BAM Improvment here

    $self->add_eukaryotes_snp_calling_config(\@pipeline_configs);

    return \@pipeline_configs;
};

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

__END__

=pod

=head1 NAME

Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy - Standard snp calling pipeline for bacteria

=head1 VERSION

version 1.133090

=head1 SYNOPSIS

Standard snp calling pipeline for eukaryotes.
   use Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy;

   my $obj = Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy->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