File Coverage

lib/Bio/VertRes/Config/Pipelines/Tradis.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::Pipelines::Tradis;

# ABSTRACT: Create TraDIS config files


use Moose;
use Bio::VertRes::Config::Pipelines::Common;
use Bio::VertRes::Config::References;
use Bio::VertRes::Config::Pipelines::Roles::MetaDataFilter;
use Bio::VertRes::Config::Pipelines::Roles::MultiplePrefix;
extends 'Bio::VertRes::Config::Pipelines::RnaSeqExpression';
with 'Bio::VertRes::Config::Pipelines::Roles::MetaDataFilter';
with 'Bio::VertRes::Config::Pipelines::Roles::MultiplePrefix';
with 'Bio::VertRes::Config::Pipelines::Roles::FilenameWithReference';

has 'protocol'           => ( is => 'ro', isa => 'Str',  default => 'TradisProtocol' );
has '_mapping_quality'    => ( is => 'ro', isa => 'Int',  default => 10 );

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

__END__

=pod

=head1 NAME

Bio::VertRes::Config::Pipelines::Tradis - Create TraDIS config files

=head1 VERSION

version 1.133090

=head1 SYNOPSIS

Create TraDIS config files
   use Bio::VertRes::Config::Pipelines::Tradis;

   my $pipeline = Bio::VertRes::Config::Pipelines::Tradis->new(
     database => 'abc',
     reference => 'Staphylococcus_aureus_subsp_aureus_ABC_v1',
     limits => {
       project => ['ABC study'],
       species => ['EFG']
     }

     );
   $pipeline->to_hash();

=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