Merge pull request #1904 from sanger/1782-y24-198-lcm-wgsem-seq-bed-v…

…erifications Y24-198 LCM Triomics WGS and EMSeq bed verifications
sanger · Oct 10, 2024 · f80c427 · f80c427
2 parents 603dd9b + 7e2eb1b
commit f80c427
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diff --git a/config/purposes/lcm_triomics.wip.yml b/config/purposes/lcm_triomics.wip.yml
@@ -47,6 +47,7 @@ LCMT EM NaOH Denat:
   :stock_plate: false
   :cherrypickable_target: false
   :input_plate: false
+  :presenter_class: Presenters::PermissivePresenter
   :size: 96
 LCMT EM APOBEC Deam:
   :asset_type: plate

diff --git a/config/robots.rb b/config/robots.rb
@@ -3727,4 +3727,320 @@
         }
       }
     )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Verify initial setup
+    custom_robot(
+      'bravo-verify-initial-setup',
+      name: 'Bravo Verify Initial Setup',
+      require_robot: true, # Robot barcode must be scanned in.
+      verify_robot: false, # First robot step; no previous robot.
+      beds: {
+        bed(4).barcode => {
+          purpose: 'LCMT Lysate',
+          states: ['passed'],
+          label: 'Bed 4'
+        },
+        car('1,4').barcode => {
+          purpose: 'LCMT DNA Frag',
+          states: ['pending'],
+          label: 'Carousel 1,4',
+          parent: bed(4).barcode,
+          target_state: 'started'
+        },
+        car('2,4').barcode => {
+          purpose: 'LCMT DNA End Prep',
+          states: ['pending'],
+          label: 'Carousel 2,4',
+          parent: car('1,4').barcode,
+          target_state: 'started'
+        },
+        car('3,5').barcode => {
+          purpose: 'LCMT DNA Adp Lig',
+          states: ['pending'],
+          label: 'Carousel 3,5',
+          parent: car('2,4').barcode,
+          target_state: 'started'
+        },
+        car('4,4').barcode => {
+          purpose: 'LCMT EM TET2 Ox',
+          states: ['pending'],
+          label: 'Carousel 4,4',
+          parent: car('3,5').barcode,
+          target_state: 'started'
+        },
+        car('4,3').barcode => {
+          purpose: 'LCMT EM TET2 Stop',
+          states: ['pending'],
+          label: 'Carousel 4,3',
+          parent: car('4,4').barcode,
+          target_state: 'started'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT DNA Frag Verification
+    custom_robot(
+      'bravo-lcmt-dna-frag-verification',
+      name: 'Bravo LCMT DNA Frag Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT DNA Frag',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT DNA End Prep Verification
+    custom_robot(
+      'bravo-lcmt-dna-end-prep-verification',
+      name: 'Bravo LCMT DNA End Prep Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT DNA End Prep',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT DNA Adp Lig to LCMT DNA Lib PCR
+    custom_robot(
+      'bravo-lcmt-dna-adp-lig-to-lcmt-dna-lib-pcr',
+      name: 'Bravo LCMT DNA Adp Lig => LCMT DNA Lib PCR',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(6).barcode => {
+          purpose: 'LCMT DNA Adp Lig',
+          states: ['passed'],
+          label: 'Bed 6'
+        },
+        bed(7).barcode => {
+          purpose: 'LCMT DNA Lib PCR',
+          states: ['pending'],
+          label: 'Bed 7',
+          parent: bed(6).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT DNA Adp Lig Verification
+    custom_robot(
+      'bravo-lcmt-dna-adp-lig-verification',
+      name: 'Bravo LCMT DNA Adp Lig Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT DNA Adp Lig',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM TET2 Ox Verification
+    custom_robot(
+      'bravo-lcmt-em-tet2-ox-verification',
+      name: 'Bravo LCMT EM TET2 Ox Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT EM TET2 Ox',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM TET2 Stop Verification
+    custom_robot(
+      'bravo-lcmt-em-tet2-stop-verification',
+      name: 'Bravo LCMT EM TET2 Stop Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT EM TET2 Stop',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM TET2 Stop to Denat and Deam Setup
+    custom_robot(
+      'bravo-lcmt-em-tet2-stop-to-denat-and-deam-setup',
+      name: 'Bravo LCMT EM TET2 Stop to Denat and Deam Setup',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(4).barcode => {
+          purpose: 'LCMT EM TET2 Stop',
+          states: ['passed'],
+          label: 'Bed 4'
+        },
+        car('3,3').barcode => {
+          purpose: 'LCMT EM NaOH Denat',
+          states: ['pending'],
+          label: 'Carousel 3,3',
+          parent: bed(4).barcode,
+          target_state: 'started'
+        },
+        car('3,4').barcode => {
+          purpose: 'LCMT EM APOBEC Deam',
+          states: ['pending'],
+          label: 'Carousel 3,4',
+          parent: car('3,3').barcode,
+          target_state: 'started'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM NaOH Denat Verification
+    custom_robot(
+      'bravo-lcmt-em-naoh-denat-verification',
+      name: 'Bravo LCMT EM NaOH Denat Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT EM NaOH Denat',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM APOBEC Deam Verification
+    custom_robot(
+      'bravo-lcmt-em-apobec-deam-verification',
+      name: 'Bravo LCMT EM APOBEC Deam Verification',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT EM APOBEC Deam',
+          states: ['started'],
+          label: 'Bed 5',
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Bravo LCMT EM APOBEC Deam => LCMT EM Lib PCR
+    custom_robot(
+      'bravo-lcmt-em-apobec-deam-to-lcmt-em-lib-pcr',
+      name: 'Bravo LCMT EM APOBEC Deam => LCMT EM Lib PCR',
+      require_robot: true,
+      verify_robot: true,
+      beds: {
+        bed(5).barcode => {
+          purpose: 'LCMT EM APOBEC Deam',
+          states: ['passed'],
+          label: 'Bed 5'
+        },
+        bed(6).barcode => {
+          purpose: 'LCMT EM Lib PCR',
+          states: ['pending'],
+          label: 'Bed 6',
+          parent: bed(5).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Hamilton LCMT DNA Lib PCR => LCMT DNA PCR XP
+    custom_robot(
+      'hamilton-lcmt-dna-lib-pcr-to-lcmt-dna-pcr-xp',
+      name: 'Hamilton LCMT DNA Lib PCR => LCMT DNA PCR XP',
+      require_robot: true,
+      verify_robot: false, # Previous robot is Bravo.
+      beds: {
+        bed(7).barcode => {
+          purpose: 'LCMT DNA Lib PCR',
+          states: ['passed'],
+          label: 'Bed 7'
+        },
+        bed(9).barcode => {
+          purpose: 'LCMT DNA PCR XP',
+          states: ['pending'],
+          label: 'Bed 9',
+          parent: bed(7).barcode,
+          target_state: 'passed'
+        },
+        bed(12).barcode => {
+          purpose: 'LCMT DNA Lib PCR',
+          states: ['passed'],
+          label: 'Bed 12'
+        },
+        bed(14).barcode => {
+          purpose: 'LCMT DNA PCR XP',
+          states: ['pending'],
+          label: 'Bed 14',
+          parent: bed(12).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
+
+    # LCM Triomics WGS and EMSeq bed verification
+    # Hamilton LCMT EM Lib PCR => LCMT EM PCR XP
+    custom_robot(
+      'hamilton-lcmt-em-lib-pcr-to-lcmt-em-pcr-xp',
+      name: 'Hamilton LCMT EM Lib PCR => LCMT EM PCR XP',
+      require_robot: true,
+      verify_robot: false, # Previous robot is Bravo.
+      beds: {
+        bed(7).barcode => {
+          purpose: 'LCMT EM Lib PCR',
+          states: ['passed'],
+          label: 'Bed 7'
+        },
+        bed(9).barcode => {
+          purpose: 'LCMT EM PCR XP',
+          states: ['pending'],
+          label: 'Bed 9',
+          parent: bed(7).barcode,
+          target_state: 'passed'
+        },
+        bed(12).barcode => {
+          purpose: 'LCMT EM Lib PCR',
+          states: ['passed'],
+          label: 'Bed 12'
+        },
+        bed(14).barcode => {
+          purpose: 'LCMT EM PCR XP',
+          states: ['pending'],
+          label: 'Bed 14',
+          parent: bed(12).barcode,
+          target_state: 'passed'
+        }
+      }
+    )
   end