Y24-266 LCM Triomics pipeline configuration and integration test for EMSeq branch

config/pipelines/high_throughput_lcm_triomics.wip.yml

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+---
+# Pipeline configuration for EMSeq
+LCM Triomics EMSeq:
+  pipeline_group: LCM Triomics WGS and EMSeq
+  filters:
+    request_type_key: limber_lcm_triomics_emseq
+    library_type: LCM Triomics EMSeq
+  library_pass: LCMT EM PCR XP
+  relationships:
+    LCMT Lysate: LCMT DNA Frag
+    LCMT DNA Frag: LCMT DNA End Prep
+    LCMT DNA End Prep: LCMT DNA Adp Lig
+    LCMT DNA Adp Lig: LCMT EM TET2 Ox
+    LCMT EM TET2 Ox: LCMT EM TET2 Stop
+    LCMT EM TET2 Stop: LCMT EM NaOH Denat
+    LCMT EM NaOH Denat: LCMT EM APOBEC Deam
+    LCMT EM APOBEC Deam: LCMT EM Lib PCR
+    LCMT EM Lib PCR: LCMT EM PCR XP
+
+LCM Triomics EMSeq Custom Pooling:
+  pipeline_group: LCM Triomics WGS and EMSeq
+  filters:
+    request_type_key: limber_lcm_triomics_emseq
+    state: passed
+  relationships:
+    LCMT EM PCR XP: LCMT EM Pool XP
+    LCMT EM Pool XP: LCMT EM Pool XP Norm

config/purposes/lcm_triomics.wip.yml

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+# EMSeq plate purposes
+---
+LCMT Lysate:
+  :asset_type: plate
+  :stock_plate: true
+  :cherrypickable_target: false
+  :input_plate: true
+  :presenter_class: Presenters::StockPlatePresenter
+  :creator_class: LabwareCreators::Uncreatable
+  :size: 96
+LCMT DNA Frag:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :presenter_class: Presenters::PermissivePresenter
+  :size: 96
+LCMT DNA End Prep:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :presenter_class: Presenters::PermissivePresenter
+  :size: 96
+LCMT DNA Adp Lig:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :presenter_class: Presenters::PermissivePresenter
+  :size: 96
+LCMT EM TET2 Ox:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :presenter_class: Presenters::PermissivePresenter
+  :size: 96
+LCMT EM TET2 Stop:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :size: 96
+LCMT EM NaOH Denat:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :size: 96
+LCMT EM APOBEC Deam:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :size: 96
+LCMT EM Lib PCR:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :presenter_class: Presenters::PcrPresenter
+  :creator_class: LabwareCreators::TaggedPlate
+  :tag_layout_templates:
+    - TS_pWGSA_UDI96v2
+    - TS_pWGSB_UDI96
+    - TS_pWGSC_UDI96
+    - TS_pWGSC_UDI_tag60_61_swap
+    - TS_pWGSD_UDI96
+  :size: 96
+LCMT EM PCR XP:
+  :asset_type: plate
+  :stock_plate: false
+  :cherrypickable_target: false
+  :input_plate: false
+  :file_links:
+    - name: Download Concentration (nM) CSV
+      id: concentrations_nm
+    - name: Download Concentration (ng/ul) CSV
+      id: concentrations_ngul
+  :size: 96
+# Change all 'pool' refs to 'pool XP' (libraries are clean-up prior to
+# pooling so the flow is directly from PCR XP to Pool XP).
+LCMT EM Pool XP:
+  :asset_type: tube
+  :target: StockMultiplexedLibraryTube
+  :type: IlluminaHtp::InitialStockTubePurpose
+  :creator_class: LabwareCreators::CustomPooledTubes
+  :presenter_class: Presenters::SimpleTubePresenter
+  :default_printer_type: :tube
+LCMT EM Pool XP Norm:
+  :asset_type: tube
+  :target: MultiplexedLibraryTube
+  :type: IlluminaHtp::InitialStockTubePurpose
+  :creator_class: LabwareCreators::TubeFromTube
+  :presenter_class: Presenters::FinalTubePresenter
+  :default_printer_type: :tube