Module: LabwareCreators::TaggedPlateBehaviour

Extended by:
ActiveSupport::Concern
Included in:
CustomTaggedPlate, TaggedPlate
Defined in:
app/models/concerns/labware_creators/tagged_plate_behaviour.rb

Overview

Can be included in plate creators which require well aliquots to have concentrations

Instance Method Summary collapse

Instance Method Details

#cross_plate_pool_detection? ⇒ Bool

Note:

This option is safest to enable when:

  • The pipeline has an earlier consolidation step

  • The pipeline will never pool at a higher level than the current late

  • Only one template is available anyway

In other scenarios you may be at risk of introducing tag clashes.

In the LTHR pipeline we begin with 4x96 well plates, which get combined on a single 384 well plate. This means that the cross-plate pool detection enforces unique UDI plates. This causes problems if a tag plate is used in error, and there needs to be a rework loop. As on the second run through, tag clash detection fires.

By setting the disable_cross_plate_pool_detection config option you can turn off this check.

Returns:

  • (Bool) —

    Whether to disable tag uniqueness detection



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# File 'app/models/concerns/labware_creators/tagged_plate_behaviour.rb', line 70

def cross_plate_pool_detection?
  !purpose_config.fetch(:disable_cross_plate_pool_detection, false)
end

#flag_tag_plate_as_exhausted ⇒ Sequencescape::Api::StateChange

Update the state of the tag plate to ‘exhausted’

Returns:

  • (Sequencescape::Api::StateChange) —

    The created state change



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# File 'app/models/concerns/labware_creators/tagged_plate_behaviour.rb', line 19

def flag_tag_plate_as_exhausted
  api.state_change.create!(
    user: user_uuid,
    target: tag_plate.asset_uuid,
    reason: 'Used in Library creation',
    target_state: 'exhausted'
  )
end

#requires_tag2? ⇒ Boolean

Indicated that an i5 tag (tag2) is required for the tagging of this particular plate. i5 tags are required when a submission spans multiple plates, which will be tagged independently, and then pooled.

The combination of i5 and i7 tags help ensure that each sample in the pool has a unique tag. By using a combination of two tags you can maintain strong diversity in tag reads.

Returns:

  • (Boolean) —

    Returns true if any submissions associated with the plate span multiple source plates.



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# File 'app/models/concerns/labware_creators/tagged_plate_behaviour.rb', line 48

def requires_tag2?
  cross_plate_pool_detection? && parent.submission_pools.any? { |pool| pool.plates_in_submission > 1 }
end

#tag_plates ⇒ Object 



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# File 'app/models/concerns/labware_creators/tagged_plate_behaviour.rb', line 32

def tag_plates
  @tag_plates ||= LabwareCreators::Tagging::TagCollection.new(api, labware, purpose_uuid)
end

#transfer_hash ⇒ Object 



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# File 'app/models/concerns/labware_creators/tagged_plate_behaviour.rb', line 28

def transfer_hash
  WellHelpers.stamp_hash(parent.size)
end