File Coverage

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

# ABSTRACT: A base class for generating an Assembly pipeline config file using velvet



use Moose;
extends 'Bio::VertRes::Config::Pipelines::Assembly';

has '_assembler'           => ( is => 'ro', isa => 'Str', default => 'velvet' );
has '_assembler_exec'      => ( is => 'ro', isa => 'Str', default => '/software/pathogen/external/apps/usr/bin/velvet' );
has '_optimiser_exec'      => ( is => 'ro', isa => 'Str', default => '/software/pathogen/external/apps/usr/bin/VelvetOptimiser.pl' );
has '_max_threads'         => ( is => 'ro', isa => 'Int', default => 2 );

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

__END__

=pod

=head1 NAME

Bio::VertRes::Config::Pipelines::VelvetAssembly - A base class for generating an Assembly pipeline config file using velvet

=head1 VERSION

version 1.133090

=head1 SYNOPSIS

A class for generating the Assembly pipeline config file using the velvet assembler
   use Bio::VertRes::Config::Pipelines::VelvetAssembly;

   my $pipeline = Bio::VertRes::Config::Pipelines::VelvetAssembly->new(database    => 'abc'
                                                                       config_base => '/path/to/config/base',
                                                                       limits      => { project => ['project name']);
   $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