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package Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy; |
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# ABSTRACT: Standard snp calling pipeline for bacteria |
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use Moose; |
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extends 'Bio::VertRes::Config::Recipes::Common'; |
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with 'Bio::VertRes::Config::Recipes::Roles::RegisterStudy'; |
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with 'Bio::VertRes::Config::Recipes::Roles::Reference'; |
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with 'Bio::VertRes::Config::Recipes::Roles::CreateGlobal'; |
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with 'Bio::VertRes::Config::Recipes::Roles::EukaryotesSnpCalling'; |
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with 'Bio::VertRes::Config::Recipes::Roles::EukaryotesMapping'; |
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override '_pipeline_configs' => sub { |
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my ($self) = @_; |
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my @pipeline_configs; |
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$self->add_qc_config(\@pipeline_configs); |
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$self->add_eukaryotes_stampy_mapping_config(\@pipeline_configs); |
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#Â Insert BAM Improvment here |
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$self->add_eukaryotes_snp_calling_config(\@pipeline_configs); |
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return \@pipeline_configs; |
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}; |
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__PACKAGE__->meta->make_immutable; |
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no Moose; |
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1; |
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__END__ |
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=pod |
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=head1 NAME |
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Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy - Standard snp calling pipeline for bacteria |
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=head1 VERSION |
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version 1.133090 |
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=head1 SYNOPSIS |
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Standard snp calling pipeline for eukaryotes. |
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use Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy; |
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my $obj = Bio::VertRes::Config::Recipes::EukaryotesSnpCallingUsingStampy->new( |
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database => 'abc', |
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limits => {project => ['Study ABC']}, |
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reference => 'ABC', |
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reference_lookup_file => '/path/to/refs.index' |
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); |
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$obj->create; |
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=head1 AUTHOR |
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Andrew J. Page <ap13@sanger.ac.uk> |
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=head1 COPYRIGHT AND LICENSE |
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This software is Copyright (c) 2013 by Wellcome Trust Sanger Institute. |
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This is free software, licensed under: |
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The GNU General Public License, Version 3, June 2007 |
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=cut |