Y26-088 - [PR] Library Prep from Ultima UG200 (support new tags and add UG200 automated submission)

config/pipelines/ultima_ug200_high_throughtput_pcr_free.wip.yml

@@ -0,0 +1,28 @@
+---
+# Ultima UG200 PCR Free Pipeline
+Ultima UG200 High Throughput PCR Free:
+  pipeline_group: Ultima UG200 High Throughput PCR Free
+  filters:
+    request_type_key: limber_ultima_ug200_htp_pcr_free
+    library_type:
+      - Ultima High Throughput PCR Free 96 # same as UG100
+  library_pass: UPF2 Lib XP2
+  relationships:
+    UPF2 Cherrypicked: UPF2 Shear
+    UPF2 Shear: UPF2 Post Shear
+    UPF2 Post Shear: UPF2 End Prep
+    UPF2 End Prep: UPF2 Lib
+    UPF2 Lib: UPF2 Lib XP2
+Ultima UG200 Multiplexing:
+  pipeline_group: Ultima UG200 High Throughput PCR Free
+  filters:
+    request_type_key:
+      - limber_multiplexing_ultima_ug200
+  relationships:
+    UPF2 Lib XP2: UPF2 EqVol Pool
+    UPF2 EqVol Pool: UPF2 EqVol Norm
+Ultima UG200 Balancing:
+  pipeline_group: Ultima UG200 High Throughput PCR Free
+  relationships:
+    UPF2 Lib XP2: UPF2 Balanced Pool
+    UPF2 Balanced Pool: UPF2 Balanced Norm

config/purposes/ultima_ug200_pcr_free.wip.yml

@@ -0,0 +1,76 @@
+---
+# Ultima UG200 PCR Free Pipeline purposes
+UPF2 Cherrypicked:
+  :asset_type: plate
+  :stock_plate: true
+  :cherrypickable_target: true
+  :input_plate: true
+  :default_printer_type: :plate_a
+  :presenter_class: Presenters::StockPlatePresenter
+UPF2 Shear:
+  :asset_type: plate
+UPF2 Post Shear:
+  :asset_type: plate
+UPF2 End Prep:
+  :asset_type: plate
+  :default_printer_type: :ultima_lib_plate
+UPF2 Lib:
+  :asset_type: plate
+  :presenter_class: Presenters::StandardPresenter
+  :creator_class: LabwareCreators::TaggedPlate
+  :tag_layout_templates:
+    - 'Ultima P3'
+    - 'UG-RD-1916 (Solaris 2.0 V1 PCR-Free Adapters for Ultima Genomics P4)'
+  :default_printer_type: :ultima_lib_plate
+UPF2 Lib XP2:
+  :asset_type: plate
+  :manual_transfer:
+    states:
+      - 'pending'
+  :default_printer_type: :plate_xp2
+UPF2 EqVol Pool:
+  :asset_type: tube
+  :target: StockMultiplexedLibraryTube
+  :type: IlluminaHtp::InitialStockTubePurpose
+  :creator_class: LabwareCreators::PooledTubesBySubmission
+  :presenter_class:
+    name: Presenters::SimpleTubePresenter
+    args:
+      downstream_mx_tube:
+        child_tube_purposes_to_limit:
+          - 'UPF2 EqVol Norm'
+  :default_printer_type: :ultima_balanced_tube
+UPF2 EqVol Norm:
+  :asset_type: tube
+  :target: MultiplexedLibraryTube
+  :type: IlluminaHtp::MxTubePurpose
+  :creator_class: LabwareCreators::TubeFromTube
+  :presenter_class: Presenters::FinalTubePresenter
+  :default_printer_type: :ultima_balanced_norm_tube
+UPF2 Balanced Pool:
+  :asset_type: tube
+  :type: IlluminaHtp::InitialStockTubePurpose
+  :creator_class: LabwareCreators::BalancedPooledTube
+  :target: LibraryTube
+  :number_of_parent_labwares: 1
+  :transfer_template: 'Whole plate to tube'
+  :presenter_class: Presenters::SimpleTubePresenter
+  :default_printer_type: :ultima_balanced_tube
+  :file_links:
+    - name: 'Download balanced Library Pooling file'
+      id: 'ultima_balancing'
+UPF2 Balanced Norm:
+  :asset_type: tube
+  :type: IlluminaHtp::StockTubePurpose
+  :default_printer_type: :ultima_balanced_norm_tube
+  :creator_class: LabwareCreators::TubeFromTube
+  :presenter_class: Presenters::SubmissionTubePresenter
+  :submission_options:
+    Ultima Sequencing - Automated Submission:
+      template_name: 'Limber-Htp - Ultima PCR Free - Ultima UG200 sequencing Automated'
+      allowed_extra_barcodes: false
+      request_options:
+        ot_recipe: Free
+        fragment_size_required_from: 300
+        fragment_size_required_to: 400
+        wafer_size: 10TB

config/robots.rb

@@ -5352,4 +5352,121 @@
         }
       }
     )
+
+    # Ultima UG200 bed verification
+    # UPF2 Cherrypicked => UPF2 Shear
+    custom_robot(
+      'bravo-upf2-cherrypicked-to-upf2-shear',
+      name: 'UPF2 Cherrypicked => UPF2 Shear',
+      beds: {
+        bed(7).barcode => {
+          purpose: 'UPF2 Cherrypicked',
+          states: ['passed'],
+          label: 'Bed 7'
+        },
+        bed(9).barcode => {
+          purpose: 'UPF2 Shear',
+          states: ['pending'],
+          label: 'Bed 9',
+          parent: bed(7).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # Ultima UG200 bed verification
+    # UPF2 Shear => UPF2 Post Shear
+    custom_robot(
+      'bravo-upf2-shear-to-upf2-post-shear',
+      name: 'UPF2 Shear => UPF2 Post Shear',
+      beds: {
+        bed(9).barcode => {
+          purpose: 'UPF2 Shear',
+          states: ['passed'],
+          label: 'Bed 9'
+        },
+        bed(7).barcode => {
+          purpose: 'UPF2 Post Shear',
+          states: ['pending'],
+          label: 'Bed 7',
+          parent: bed(9).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # Ultima UG200 bed verification
+    # UPF2 Post Shear => UPF2 End Prep
+    custom_robot(
+      'bravo-upf2-post-shear-to-upf2-end-prep-xp1',
+      name: 'UPF2 Post Shear => UPF2 End Prep',
+      beds: {
+        bed(4).barcode => {
+          purpose: 'UPF2 Post Shear',
+          states: ['passed'],
+          label: 'Bed 4'
+        },
+        bed(14).barcode => {
+          purpose: 'UPF2 End Prep',
+          states: ['pending'],
+          label: 'Bed 14',
+          parent: bed(4).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # Ultima UG200 bed verification
+    # UPF2 End Prep => UPF2 Lib
+    custom_robot(
+      'bravo-upf2-end-prep-xp1-to-upf2-lib',
+      name: 'Bravo UPF2 End Prep => UPF2 Lib',
+      beds: {
+        bed(5).barcode => {
+          purpose: 'UPF2 End Prep',
+          states: ['passed'],
+          label: 'Bed 5'
+        },
+        bed(6).barcode => {
+          purpose: 'UPF2 Lib',
+          states: ['pending'],
+          label: 'Bed 6',
+          target_state: 'passed',
+          parent: bed(5).barcode
+        }
+      }
+    )
+
+    # Ultima UG200 bed verification
+    # UPF2 Lib => UPF2 Lib XP2
+    custom_robot(
+      'hamilton-upf2-lib-to-upf2-lib-xp2',
+      name: 'Hamilton UPF2 Lib => UPF2 Lib XP2',
+      beds: {
+        bed(7).barcode => {
+          purpose: 'UPF2 Lib',
+          states: ['passed'],
+          label: 'Bed 7'
+        },
+        bed(9).barcode => {
+          purpose: 'UPF2 Lib XP2',
+          states: ['pending'],
+          label: 'Bed 9',
+          parent: bed(7).barcode,
+          target_state: 'passed'
+        },
+        bed(12).barcode => {
+          purpose: 'UPF2 Lib',
+          states: ['passed'],
+          label: 'Bed 12'
+        },
+        bed(14).barcode => {
+          purpose: 'UPF2 Lib XP2',
+          states: ['pending'],
+          label: 'Bed 14',
+          parent: bed(12).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
   end