sanger · andrewsparkes · Mar 20, 2026 · Mar 20, 2026 · Mar 23, 2026 · Mar 23, 2026
diff --git a/app/controllers/ultima_sample_sheet/sample_sheet_generator.rb b/app/controllers/ultima_sample_sheet/sample_sheet_generator.rb
@@ -40,7 +40,9 @@ class Generator # rubocop:disable Metrics/ClassLength
     # Index_Barcode_Num column, i.e. Z0001 or Z097.
     ULTIMA_TAG_GROUPS = {
       'Ultima P1' => 1,
-      'Ultima P2' => 2
+      'Ultima P2' => 2,
+      'Ultima P3' => 3,
+      'Ultima P4' => 4
     }.freeze
 
     # Initializes the generator with the given batch.

diff --git a/config/default_records/tag_groups/006_ultima_p3_and_p4.wip.yml b/config/default_records/tag_groups/006_ultima_p3_and_p4.wip.yml
@@ -0,0 +1,201 @@
+Ultima P3:
+  visible: true
+  adapter_type_name: Ultima
+  tags:
+    1: CTGCACATTGTAGAT
+    2: CTCATGGTATATGAT
+    3: CTGCATGCTGGCGTGAT
+    4: CGGCACGATGCTGAT
+    5: CTCTTCATGAGCATGAT
+    6: CTCATGGAGCATATGAT
+    7: CATACTGCCTATGAT
+    8: CAATGCATCTATATGAT
+    9: CGAGCACAATGCATGAT
+    10: CGGCAGCAGACTGAT
+    11: CAACATGCACATCTGAT
+    12: CGTGCATGGCATCTGAT
+    13: CTACAGCAATGTGAT
+    14: CATCAGTCCTGCGAT
+    15: CAAGCGACATGCGAT
+    16: CATGCTCAATATCTGAT
+    17: CGACTCATGCCTGAT
+    18: CATGGCATACTGCTGAT
+    19: CAATCGCATCGTGAT
+    20: CGGCACTGCAGTGAT
+    21: CGGATCGCATGCGAT
+    22: CTATTGCTCTGCATGAT
+    23: CATCTGCGGCACATGAT
+    24: CATCGATGCAGAATGAT
+    25: CACATGACCAGCGAT
+    26: CAATGCTGTAGTGAT
+    27: CGACATGCACCTGAT
+    28: CGCAAGCATGTCGAT
+    29: CATGCTCGGCTGCTGAT
+    30: CAAGTCTGCTCAGAT
+    31: CATCATTGATCATCGAT
+    32: CACTCACAATGCATGAT
+    33: CATGTGGCTATCATGAT
+    34: CATGTATGCGCAATGAT
+    35: CTTGCGCTCTCAGAT
+    36: CGCGCACAATATGAT
+    37: CAGCGCACCAGCATGAT
+    38: CTGCTATCTGGTGAT
+    39: CGATATCATGGTGAT
+    40: CATGCATGTGGATAGAT
+    41: CTCTGCTCCTGCGAT
+    42: CATCGCACCAGAGAT
+    43: CAATCTGATATGATGAT
+    44: CATACTGCAGGAGAT
+    45: CTTCATGACAGAGAT
+    46: CTACATCATGGCATGAT
+    47: CGCTGTTGCATGATGAT
+    48: CTTCACTCATGAGAT
+    49: CATGCGCTTACAGAT
+    50: CAGCATCTCTGCCTGAT
+    51: CACTGCCATATCATGAT
+    52: CTCAGCTGCGGCGAT
+    53: CATGCAGAGCGCCTGAT
+    54: CAATGCTATCGAGAT
+    55: CAGATAAGAGCAGAT
+    56: CAGAGCCACTCAGAT
+    57: CATGTAATATCAGAT
+    58: CAGCGCATGATCCTGAT
+    59: CATAGATAGCCAGAT
+    60: CACTAGCATGGCGAT
+    61: CAATAGCATCGAGAT
+    62: CTTCTGTGAGATGAT
+    63: CTCTGCTCATTCATGAT
+    64: CACAATAGCGATGAT
+    65: CTGTAGGCATCTGAT
+    66: CAACAGCTCTCTGAT
+    67: CAGACACAATATGAT
+    68: CTAGCAAGATCAGAT
+    69: CTTGAGACATGAGAT
+    70: CTCAGATGTCCAGAT
+    71: CAGCCGCATGCACAGAT
+    72: CTCGCATGTGGAGAT
+    73: CACATGCATGTCCTGAT
+    74: CGCGGCTGATATGAT
+    75: CTGTGACAAGCTGAT
+    76: CATGCGAGCATGGTGAT
+    77: CAATACATGATCGAT
+    78: CATGGACATATGCAGAT
+    79: CAGCGCGCTGGCATGAT
+    80: CATGCGTCACCTGAT
+    81: CTGCATGTTGCTGAGAT
+    82: CATCCTGCGATAGAT
+    83: CAATATCTGAGTGAT
+    84: CTGTGCAGGAGTGAT
+    85: CGATGTGCCATAGAT
+    86: CTCACATGGAGAGAT
+    87: CAGAACATGTCAGAT
+    88: CGCACAATGCGAGAT
+    89: CATGCACAGAATGTGAT
+    90: CGTATGGCAGCTGAT
+    91: CTGATGGTGCTCATGAT
+    92: CTCAGCCATGCGATGAT
+    93: CATGCACAAGATCAGAT
+    94: CTCTGTTGCTCAGAT
+    95: CACAGCGCTCCAGAT
+    96: CACAGAAGATGCGAT
+
+Ultima P4:
+  visible: true
+  adapter_type_name: Ultima
+  tags:
+    1: CATCATGCTCCGCTGAT
+    2: CTTGCTATGAGCGAT
+    3: CATGTATCAGGTGAT
+    4: CATGCGCAATGTATGAT
+    5: CATGTGAGCGGTGAT
+    6: CGCACAAGTCATGAT
+    7: CATGCAATACATGAGAT
+    8: CATCTATCAGGCGAT
+    9: CGAGCATCAGGTGAT
+    10: CAAGACTGATATGAT
+    11: CATGCGGAGTGAGAT
+    12: CAGATATAGCCTGAT
+    13: CAAGAGAGAGCTGAT
+    14: CTATCAAGCTCAGAT
+    15: CAGAATACATGCGAT
+    16: CTCAAGCGCACAGAT
+    17: CACACACAACATGAT
+    18: CTTACATGTCATGAT
+    19: CAGAAGAGATATGAT
+    20: CAGAGCGCCGCAGAT
+    21: CGCTCAACATGCGAT
+    22: CATGACAGTAATGAT
+    23: CATGCAATCACATCGAT
+    24: CAGTTGATACATGAT
+    25: CTGTGACATAATGAT
+    26: CATAGTGCTGCAATGAT
+    27: CACGAGCGCAATGAT
+    28: CACAATGCAGATGTGAT
+    29: CTGCGCAGCATCCTGAT
+    30: CAAGACATCAGAGAT
+    31: CATGCTTGTGTCATGAT
+    32: CAGTGCGACAATGAT
+    33: CATATGGTGACAGAT
+    34: CAATGATAGTGTGAT
+    35: CATAGCAGCAACATGAT
+    36: CATGACACCAGTGAT
+    37: CAATCTCAGCAGATGAT
+    38: CTCGATGAGCCTGAT
+    39: CAACACTCTGCAGAT
+    40: CTTAGCATCACTGAT
+    41: CTGTTGTGATCAGAT
+    42: CAAGTGTGCGCAGAT
+    43: CATGAGCATGGTCTGAT
+    44: CACTGATGCATGGAGAT
+    45: CTTATATCTCATGAT
+    46: CATCAGCTGAAGATGAT
+    47: CACACATCCAGCGAT
+    48: CAACATGTGATCGAT
+    49: CGGCTATGCATCGAT
+    50: CAAGTGAGCTGCGAT
+    51: CAATAGACAGCTGAT
+    52: CAGTCTGATCCTGAT
+    53: CTTGCATAGCGTGAT
+    54: CTCGTGGCATGCATGAT
+    55: CGCTGCCTGCTGCTGAT
+    56: CATAGTTCATCTGAT
+    57: CAATCAGCAGACGAT
+    58: CATGAGCATGAGGCGAT
+    59: CACATCAGTGGCGAT
+    60: CTGCATGCACACCTGAT
+    61: CTACTGGCAGCTGAT
+    62: CTATTGATATGAGAT
+    63: CTCATAGCCTGCATGAT
+    64: CACATGCTCAATGCGAT
+    65: CAACTCATATGCGAT
+    66: CATGGCTGTCTCGAT
+    67: CATCTAGCCATAGAT
+    68: CAGTCAACAGCAGAT
+    69: CTAGCGCAATGAGAT
+    70: CATCATTAGCGCGAT
+    71: CGCTTCATGCTGCAGAT
+    72: CTGATGGCGCGCATGAT
+    73: CTGATCTATGCAATGAT
+    74: CACTGAATGTGCGAT
+    75: CGCAATCTATCTGAT
+    76: CGGCATGCTGTAGAT
+    77: CTCATGTGTGGTGAT
+    78: CTGCATATTGTGATGAT
+    79: CGCATGTATGGCGAT
+    80: CATATAACATGCATGAT
+    81: CATATCTCCTGTGAT
+    82: CTGATACAGAATGAT
+    83: CTGTGCGCCATAGAT
+    84: CAGAGCATGCTAATGAT
+    85: CATAAGATGCGTGAT
+    86: CATACAAGAGCTGAT
+    87: CATGCTGAATGTGTGAT
+    88: CTCATGATTACTGAT
+    89: CATGACGCATTAGAT
+    90: CGTGTGCAACATGAT
+    91: CGGTGCATATCAGAT
+    92: CTTCGATGCTGTGAT
+    93: CAATAGATGTGAGAT
+    94: CGATGCCATCTCATGAT
+    95: CGATCACAAGCTGAT
+    96: CTGTGATGTAATGAT
diff --git a/config/default_records/tag_layout_templates/ultima_p3_and_p4.wip.yml b/config/default_records/tag_layout_templates/ultima_p3_and_p4.wip.yml
@@ -0,0 +1,8 @@
+Ultima P3:
+  :tag_group_name: Ultima P3
+  :direction_algorithm: TagLayout::InColumns
+  :walking_algorithm: TagLayout::WalkWellsOfPlate
+Ultima P4:
+  :tag_group_name: Ultima P4
+  :direction_algorithm: TagLayout::InColumns
+  :walking_algorithm: TagLayout::WalkWellsOfPlate
diff --git a/spec/controllers/ultima_sample_sheet/sample_sheet_generator_spec.rb b/spec/controllers/ultima_sample_sheet/sample_sheet_generator_spec.rb
@@ -53,6 +53,8 @@
   # First oligo sequences for the two tag groups.
   let(:plate1_first_oligo) { 'CAGCTCGAATGCGAT' }
   let(:plate2_first_oligo) { 'CAGTCAGTTGCAGAT' }
+  let(:plate3_first_oligo) { 'CTGCACATTGTAGAT' }
+  let(:plate4_first_oligo) { 'CATCATGCTCCGCTGAT' }
 
   # Eagerly create tag groups and tags to get consistent IDs.
   let!(:tag_group1) do
@@ -67,14 +69,28 @@
       tg.tags.first.update!(oligo: plate2_first_oligo)
     end
   end
-  let(:tag_groups) { [tag_group1, tag_group2] }
+  let!(:tag_group3) do
+    create(:tag_group_with_tags, tag_count: 96, name: 'Ultima P3').tap do |tg|
+      # To test Z0193 matching with the oligo sequence.
+      tg.tags.first.update!(oligo: plate3_first_oligo)
+    end
+  end
+  let!(:tag_group4) do
+    create(:tag_group_with_tags, tag_count: 96, name: 'Ultima P4').tap do |tg|
+      # To test Z0289 matching with the oligo sequence.
+      tg.tags.first.update!(oligo: plate4_first_oligo)
+    end
+  end
+  let(:tag_groups) { [tag_group1, tag_group2, tag_group3, tag_group4] }
 
   let(:request_type) { create(:ultima_sequencing) }
   let(:pipeline) { create(:ultima_sequencing_pipeline, request_types: [request_type]) }
   let(:batch) { create(:ultima_sequencing_batch, pipeline:, requests:) }
-  let(:requests) { [request1, request2] }
+  let(:requests) { [request1, request2, request3, request4] }
   let(:request1) { create(:ultima_sequencing_request, asset: tube1.receptacle, request_type: request_type) }
   let(:request2) { create(:ultima_sequencing_request, asset: tube2.receptacle, request_type: request_type) }
+  let(:request3) { create(:ultima_sequencing_request, asset: tube3.receptacle, request_type: request_type) }
+  let(:request4) { create(:ultima_sequencing_request, asset: tube4.receptacle, request_type: request_type) }
 
   # Eagerly create tubes with aliquots to get consistent IDs.
   let!(:tube1) do
@@ -91,9 +107,23 @@
     create(:event, content: Time.zone.today.to_s, message: 'scanned in', family: 'scanned_into_lab', eventful: tube)
     tube
   end
+  let!(:tube3) do
+    receptacle = create(:receptacle)
+    tag_group3.tags.first(3).map { |tag| create(:aliquot, tag:, receptacle:) }
+    tube = create(:multiplexed_library_tube, receptacle:)
+    create(:event, content: Time.zone.today.to_s, message: 'scanned in', family: 'scanned_into_lab', eventful: tube)
+    tube
+  end
+  let!(:tube4) do
+    receptacle = create(:receptacle)
+    tag_group4.tags.first(3).map { |tag| create(:aliquot, tag:, receptacle:) }
+    tube = create(:multiplexed_library_tube, receptacle:)
+    create(:event, content: Time.zone.today.to_s, message: 'scanned in', family: 'scanned_into_lab', eventful: tube)
+    tube
+  end
 
   # Expected mapping of tag groups to their respective 1-based plate numbers.
-  let(:tag_group_index_map) { { tag_group1 => 1, tag_group2 => 2 } }
+  let(:tag_group_index_map) { { tag_group1 => 1, tag_group2 => 2, tag_group3 => 3, tag_group4 => 4 } }
 
   # Expected mapping of tags to their respective 1-based index numbers.
   let(:tag_index_map) do
@@ -169,27 +199,47 @@ def map_description(map_id)
       csv = "#{request2.id_wafer_lims}.csv"
       "#{folder}/#{csv}"
     end
+    let(:zip_entry3_name) do
+      folder = "batch_#{batch.id}_sample_sheets"
+      csv = "#{request3.id_wafer_lims}.csv"
+      "#{folder}/#{csv}"
+    end
+    let(:zip_entry4_name) do
+      folder = "batch_#{batch.id}_sample_sheets"
+      csv = "#{request4.id_wafer_lims}.csv"
+      "#{folder}/#{csv}"
+    end
     # Expected CSV section headers from Zip; to peek at the content.
     let(:zip_content1_header) do
       "[Header],,,,,,,\r\nBatch #{batch.id} #{tube1.human_barcode},,,,,,,\r\n"
     end
     let(:zip_content2_header) do
       "[Header],,,,,,,\r\nBatch #{batch.id} #{tube2.human_barcode},,,,,,,\r\n"
     end
+    let(:zip_content3_header) do
+      "[Header],,,,,,,\r\nBatch #{batch.id} #{tube3.human_barcode},,,,,,,\r\n"
+    end
+    let(:zip_content4_header) do
+      "[Header],,,,,,,\r\nBatch #{batch.id} #{tube4.human_barcode},,,,,,,\r\n"
+    end
 
     it 'generates valid zip entries' do
       # Test: The sample manifest (csv file) is generated on user request per pool.
       # Test: The name should be uniquely identifiable (file name : batchId_NT_number)
       zip_hash = extract_zip(described_class.generate(batch))
-      expect(zip_hash.keys).to contain_exactly(zip_entry1_name, zip_entry2_name)
+      expect(zip_hash.keys).to contain_exactly(
+        zip_entry1_name, zip_entry2_name, zip_entry3_name, zip_entry4_name
+      )
     end
 
     it 'generates valid zip contents' do
       # In the header section (free text), add the batchId and the pool number.
       zip_hash = extract_zip(described_class.generate(batch))
       expect(zip_hash.values).to contain_exactly(
         a_string_including(zip_content1_header),
-        a_string_including(zip_content2_header)
+        a_string_including(zip_content2_header),
+        a_string_including(zip_content3_header),
+        a_string_including(zip_content4_header)
       )
     end
 
@@ -210,19 +260,26 @@ def map_description(map_id)
     # Parse the generated CSV for the tubes into rows and columns.
     let(:csv1) { CSV.parse(generator.csv_string(request1), row_sep: "\r\n", nil_value: '') }
     let(:csv2) { CSV.parse(generator.csv_string(request2), row_sep: "\r\n", nil_value: '') }
+    let(:csv3) { CSV.parse(generator.csv_string(request3), row_sep: "\r\n", nil_value: '') }
+    let(:csv4) { CSV.parse(generator.csv_string(request4), row_sep: "\r\n", nil_value: '') }
 
     # Test: Adding study_id column to the existing column (study_id per sample)
 
     # Expected sample rows
     let(:csv1_samples) { csv_samples_for(request1) }
-
     let(:csv2_samples) { csv_samples_for(request2) }
+    let(:csv3_samples) { csv_samples_for(request3) }
+    let(:csv4_samples) { csv_samples_for(request4) }
 
     it 'generates header sections' do # rubocop:disable RSpec/MultipleExpectations
       expect(csv1[0].compact_blank).to eq(generator.class::HEADER_TITLE)
       expect(csv1[1].compact_blank).to eq(["Batch #{batch.id} #{tube1.human_barcode}"]) # First CSV
       expect(csv1[2].compact_blank).to eq([])
       expect(csv2[1].compact_blank).to eq(["Batch #{batch.id} #{tube2.human_barcode}"]) # Second CSV
+      expect(csv2[2].compact_blank).to eq([])
+      expect(csv3[1].compact_blank).to eq(["Batch #{batch.id} #{tube3.human_barcode}"]) # Third CSV
+      expect(csv3[2].compact_blank).to eq([])
+      expect(csv4[1].compact_blank).to eq(["Batch #{batch.id} #{tube4.human_barcode}"])
     end
 
     it 'generates global sections' do
@@ -239,6 +296,8 @@ def map_description(map_id)
       expect(csv1[8].compact_blank).to eq(generator.class::SAMPLES_HEADERS)
       expect(csv1[9..]).to eq(csv1_samples) # First CSV
       expect(csv2[9..]).to eq(csv2_samples) # Second CSV
+      expect(csv3[9..]).to eq(csv3_samples) # Third CSV
+      expect(csv4[9..]).to eq(csv4_samples) # Fourth CSV
     end
 
     it 'matches the z-indexes, oligo sequences, and plate numbers' do
@@ -251,6 +310,16 @@ def map_description(map_id)
       expect(csv2[9][2]).to eq('Z0097') # Index_Barcode_Num
       expect(csv2[9][3]).to eq(plate2_first_oligo) # Index_Barcode_Sequence
       expect(csv2[9][4]).to eq('2') # Barcode_Plate_Num
+
+      # Third CSV
+      expect(csv3[9][2]).to eq('Z0193') # Index_Barcode_Num
+      expect(csv3[9][3]).to eq(plate3_first_oligo) # Index_Barcode_Sequence
+      expect(csv3[9][4]).to eq('3') # Barcode_Plate_Num
+
+      # Fourth CSV
+      expect(csv4[9][2]).to eq('Z0289') # Index_Barcode_Num
+      expect(csv4[9][3]).to eq(plate4_first_oligo) # Index_Barcode_Sequence
+      expect(csv4[9][4]).to eq('4') # Barcode_Plate_Num
     end
   end
 end