diagnostic_rt_qpcr/libraries/prepareqpcrplatehelper/source.rb
# Make sure that proper samples exist in plate (currently
# Validation steps rubber stamp everything)
Make sure that proper samples exist in plate (currently
Validation steps rubber stamp everything)
Make sure that proper samples exist in plate ( currently Validation steps rubber stamp everything )
def run_job(default_job_params:, default_operation_params:, op:)
    @job_params = update_plan_params(plan_params: default_job_params,
                                     opts: default_operation_params)
    @job_params = update_plan_params(plan_params: job_params,
                                     opts: get_op_opts(op))
    input_collection = op.input(INPUT_PLATE).collection
    input_collection = Collection.find(DEBUG_CONTAINER) if debug
    output_collection = relabel_plate(input_collection)
    op.output(OUTPUT_PLATE).set(collection: output_collection)
    input_collection.mark_as_deleted unless debug
    layout_generator = PlateLayoutGeneratorFactory.build(
      group_size: job_params[:group_size],
      method: job_params[:method]
    )
    if debug
      operation_inputs = generate_samples
    else
      operation_inputs = op.input_array(TEMPLATE).map { |fv| fv.item }
    end
    sample_inputs, negative_controls, positive_controls =
      sort_inputs(neg_control: job_params[:negative_controls],
                  pos_control: job_params[:positive_controls],
                  operation_inputs: operation_inputs)
    setup_control_samples(operation_inputs: negative_controls,
                        collection: output_collection,
                        layout_generator: layout_generator,
                        controls: job_params[:negative_controls])
    setup_control_samples(operation_inputs: positive_controls,
                        collection: output_collection,
                        layout_generator: layout_generator,
                        controls: job_params[:positive_controls])
    setup_samples(operation_inputs: sample_inputs,
                           collection: output_collection,
                           layout_generator: layout_generator)
    associate_plate_to_plate(to_collection: output_collection,
                             from_collection: input_collection)
    add_additional_components(rc_list: make_sample_rc_list(output_collection,
                                                    operation_inputs),
                              collection: output_collection,
                              recipe_list: job_params[:additional_inputs],
                              operation: op)
    add_negative_controls(collection: output_collection, samples: negative_controls,
                          recipe: job_params[:negative_controls], operation: op)
    add_inputs(collection: output_collection, samples: sample_inputs,
               recipe: job_params[:standard_samples], operation: op)
    add_inputs(collection: output_collection, samples: positive_controls,
               recipe: job_params[:positive_controls], operation: op)
    {}
  end
def run_job ( default_job_params : , default_operation_params : , op : ) @job_params = update_plan_params ( plan_params : default_job_params , opts : default_operation_params ) @job_params = update_plan_params ( plan_params : job_params , opts : get_op_opts ( op ) ) input_collection = op . input ( INPUT_PLATE ) . collection input_collection = Collection . find ( DEBUG_CONTAINER ) if debug output_collection = relabel_plate ( input_collection ) op . output ( OUTPUT_PLATE ) . set ( collection : output_collection ) input_collection . mark_as_deleted unless debug layout_generator = PlateLayoutGeneratorFactory . build ( group_size : job_params [ :group_size ] , method : job_params [ :method ] ) if debug operation_inputs = generate_samples else operation_inputs = op . input_array ( TEMPLATE ) . map { | fv | fv . item } end sample_inputs , negative_controls , positive_controls = sort_inputs ( neg_control : job_params [ :negative_controls ] , pos_control : job_params [ :positive_controls ] , operation_inputs : operation_inputs ) setup_control_samples ( operation_inputs : negative_controls , collection : output_collection , layout_generator : layout_generator , controls : job_params [ :negative_controls ] ) setup_control_samples ( operation_inputs : positive_controls , collection : output_collection , layout_generator : layout_generator , controls : job_params [ :positive_controls ] ) setup_samples ( operation_inputs : sample_inputs , collection : output_collection , layout_generator : layout_generator ) associate_plate_to_plate ( to_collection : output_collection , from_collection : input_collection ) add_additional_components ( rc_list : make_sample_rc_list ( output_collection , operation_inputs ) , collection : output_collection , recipe_list : job_params [ :additional_inputs ] , operation : op ) add_negative_controls ( collection : output_collection , samples : negative_controls , recipe : job_params [ :negative_controls ] , operation : op ) add_inputs ( collection : output_collection , samples : sample_inputs , recipe : job_params [ :standard_samples ] , operation : op ) add_inputs ( collection : output_collection , samples : positive_controls , recipe : job_params [ :positive_controls ] , operation : op ) { } end
Make sure that proper samples exist in plate (currently
Validation steps rubber stamp everything)
Make sure that proper samples exist in plate ( currently Validation steps rubber stamp everything )
default_job_params
<not_specific>
default_operation_params
<not_specific>
op
<not_specific>