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lib/Bio/VertRes/Config/Pipelines/Assembly.pm  view on Meta::CPAN

    my ($self) = @_;
    my $output_hash = super();
    $output_hash->{limit}                   = $self->_limit;
    $output_hash->{max_lanes_to_search}     = $self->_max_lanes_to_search;
    $output_hash->{max_failures}            = $self->_max_failures;
    $output_hash->{vrtrack_processed_flags} = { stored => 1, assembled => 0, rna_seq_expression => 0 };
    $output_hash->{limits}                  = $self->_escaped_limits;

    $output_hash->{data}{tmp_directory} = $self->_tmp_directory;

    # rough guess at the maximum you expect to get
    $output_hash->{data}{genome_size}       = $self->_genome_size;
    $output_hash->{data}{seq_pipeline_root} = $self->root;
    $output_hash->{data}{assembler}         = $self->_assembler;
    $output_hash->{data}{assembler_exec}    = $self->_assembler_exec;
    $output_hash->{data}{optimiser_exec}    = $self->_optimiser_exec;
    $output_hash->{data}{max_threads}       = $self->_max_threads;
    $output_hash->{data}{pipeline_version}  = $self->_pipeline_version;
    $output_hash->{data}{error_correct}     = $self->_error_correct;
    $output_hash->{data}{sga_exec}          = $self->_sga_exec;
    $output_hash->{data}{normalise}         = $self->_normalise;