Class: RunCsv::PacbioSampleSheetV25

Inherits:
PacbioSampleSheet show all
Defined in:
app/exchanges/run_csv/pacbio_sample_sheet_v25.rb

Overview

RunCsv::PacbioSampleSheet

Instance Method Summary collapse

Methods inherited from PacbioSampleSheet

#generate_smrt_cells, #generate_wells, #payload, #plate_well_names, #run_settings, #sample_data, #samples_csv, #smrt_cell_settings, #transpose_smrt_cells

Methods included from DataStructureBuilder

#data_structure, #instance_value

Instance Method Details

#bio_sample_name(sample) ⇒ Object

Returns the formatted bio sample name for the given sample. This method overrides the bio_sample_name method in the parent class. It returns the sample names with colons replaced by hyphens.



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# File 'app/exchanges/run_csv/pacbio_sample_sheet_v25.rb', line 13

def bio_sample_name(sample)
  sample.formatted_bio_sample_name
end

#generate_smrt_cell_settings(well) ⇒ Object

Generate a hash of settings for a single cell Overrides the method in the parent class Only difference is removal of ‘Polymerase Kit’ key



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# File 'app/exchanges/run_csv/pacbio_sample_sheet_v25.rb', line 20

def generate_smrt_cell_settings(well) # rubocop:disable Metrics/MethodLength
  {
    'Well Name'	=> well.used_aliquots.first.source.tube.barcode, # TRAC-2-7242
    'Library Type'	=> well.library_type, # Standard
    'Movie Acquisition Time (hours)'	=> well.movie_acquisition_time, # 24
    'Insert Size (bp)'	=> well.insert_size, # 500
    'Assign Data To Project'	=> 1, # (maybe we need to assign a run a project in traction)?
    'Library Concentration (pM)'	=> well.library_concentration, # 250
    'Include Base Kinetics'	=> well.include_base_kinetics,
    'Indexes'	=> well.barcode_set, # 244d96c6-f3b2-4997-5ae3-23ed33ab925f
    'Sample is indexed'	=> well.tagged?, # Set to True to Multiplex
    'Bio Sample Name' => well.tagged? ? nil :  well.formatted_bio_sample_name,
    'Use Adaptive Loading'	=> well.use_adaptive_loading,
    'Consensus Mode'	=> 'molecule', # (default to molecule do we need a custom field)
    'Same Barcodes on Both Ends of Sequence'	=> well.same_barcodes_on_both_ends_of_sequence,
    'Full Resolution Base Qual' => well.full_resolution_base_qual
  }
end