From 750c1f2c3abf8aa28a1645b8ed9d69bc8f962e94 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Wed, 18 Feb 2026 15:21:16 +0000
Subject: [PATCH 01/29] Add changes for generating screenshots

---
 .../batches/_cherrypick_single_worksheet.html.erb  | 14 +++++++++++++-
 .../workflows/_cherrypick_strategies.html.erb      | 13 +++++++++++++
 .../workflows/_plate_template_batches.html.erb     |  1 -
 3 files changed, 26 insertions(+), 2 deletions(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 6bb66c2c36..ea7c657b99 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -48,6 +48,8 @@
             <td><strong><%= rowchar %></strong></td>
             <% (num_columns).times do |column| -%>
               <% well = plate_wells[row*num_columns+column] -%>
+                <!--Y26-012: flag to check if well is empty and needs to be represented on the chart with 'e' followed by the buffer volume for empty wells, for example e120.0 -->
+                <% empty_well = true %>
                 <% if  well.present? -%>
                   <% request = indexed_requests[well.id]  %>
                   <% source_well = request&.asset %>
@@ -62,6 +64,8 @@
                       <% else %>
                         <td>
                       <% end -%>
+                      <!--Y26-012: flag to set if the well is not empty -->
+                      <% empty_well = false %>
                       <%= source_well.map_description %>
                       <%= source_well.plate.barcode_number %>
                       v<%= "%.#{configatron.tecan_precision}f" % well.get_picked_volume %> b<%= "%.#{configatron.tecan_precision}f" % well.get_buffer_volume %>
@@ -74,6 +78,9 @@
                 <% else %>
                   <td>
                 <% end -%>
+                <% if empty_well -%>
+                  e120.00
+                <% end %>
                 </td>
             <% end -%>
             <td><strong><%= rowchar %></strong></td>
@@ -92,7 +99,12 @@
 </div>
 
 <div id="footer">
-  v = picking volume µl; b = buffer volume µl<br>
+  <!-- Y26-012: Add buffer volume for empty wells to footer if the option was set; remove it otherwise-->
+  <!-- Buffer for empty wells: 120 µl<br> -->
+  
+  <!-- Alternatively, if empty wells are represented on the chart with 'e' followed by the buffer volume, add legend for that here -->
+  v = picking volume µl; b = buffer volume µl; e = buffer for empty wells µl<br>
+  <!-- v = picking volume µl; b = buffer volume µl<br> -->
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>
 </div>
diff --git a/app/views/workflows/_cherrypick_strategies.html.erb b/app/views/workflows/_cherrypick_strategies.html.erb
index c72f3e9d84..a48410fd61 100644
--- a/app/views/workflows/_cherrypick_strategies.html.erb
+++ b/app/views/workflows/_cherrypick_strategies.html.erb
@@ -26,5 +26,18 @@
   </div>
 
 </div>
+<!-- Y26-012: Add form control to collect the buffer volume for empty wells -->
+<p>Additional options:</p>
+
+<div class="row">
+  <div class="col-md-4">
+    <div class ="form-group form-row">
+      <label class="col-12 col-lg-8 col-form-label" for="buffer_volume_for_empty_wells">Buffer volume for empty wells (µl)</label>
+      <div class="col-12 col-lg-4">
+        <input type="text" class="form-control" id="buffer_volume_for_empty_wells" name="buffer_volume_for_empty_wells">
+      </div>
+    </div>
+  </div>
+</div>
 
 <%= vite_javascript_tag 'cherrypick_strategies' %>
diff --git a/app/views/workflows/_plate_template_batches.html.erb b/app/views/workflows/_plate_template_batches.html.erb
index 4aec5ad3ce..62a350b082 100644
--- a/app/views/workflows/_plate_template_batches.html.erb
+++ b/app/views/workflows/_plate_template_batches.html.erb
@@ -55,6 +55,5 @@
     <%= panel(:info, title: "Step 3: Set volumes and concentrations <a href='https://ssg-confluence.internal.sanger.ac.uk/x/NoHdDQ'><small>Information about cherrypicking options</small></a>".html_safe) do %>
       <%= render partial: 'cherrypick_strategies', locals: { form: form } %>
     <% end %>
-
   <%= render partial: "next_stage_submit" %>
 <% end %>

From 918d41289b92fd0da4d2d774157b67732f77af88 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Wed, 18 Feb 2026 17:47:04 +0000
Subject: [PATCH 02/29] Update worksheet screenshot based on feedback

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index ea7c657b99..8c2dc6d897 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -100,9 +100,7 @@
 
 <div id="footer">
   <!-- Y26-012: Add buffer volume for empty wells to footer if the option was set; remove it otherwise-->
-  <!-- Buffer for empty wells: 120 µl<br> -->
-  
-  <!-- Alternatively, if empty wells are represented on the chart with 'e' followed by the buffer volume, add legend for that here -->
+  Buffer for empty wells: 120 µl<br>
   v = picking volume µl; b = buffer volume µl; e = buffer for empty wells µl<br>
   <!-- v = picking volume µl; b = buffer volume µl<br> -->
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>

From 60301fc69d5cd7ff6f34a366cb56c19c20e10688 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 00:11:21 +0000
Subject: [PATCH 03/29] Add poly_metadata association to Batch for storing
 buffer_volume_for_empty_wells option on Cherrypick batches

---
 app/models/batch.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/models/batch.rb b/app/models/batch.rb
index d069a56278..b8e00904ec 100644
--- a/app/models/batch.rb
+++ b/app/models/batch.rb
@@ -50,6 +50,8 @@ class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
   has_many :samples, -> { distinct }, through: :source_assets, source: :samples
   has_many :output_labware, -> { distinct }, through: :assets, source: :labware
   has_many :input_labware, -> { distinct }, through: :source_assets, source: :labware
+  # Y26-012: Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
+  has_many :poly_metadata, as: :metadatable, dependent: :destroy
 
   has_many_events
   has_many_lab_events

From e9a372dae85539bb253039e46c709f567ff55eb1 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 00:26:50 +0000
Subject: [PATCH 04/29] Add buffer volume for empty wells option to params for
 pass through

---
 app/models/tasks/cherrypick_handler.rb           | 4 ++++
 app/views/workflows/_cherrypick_batches.html.erb | 2 ++
 2 files changed, 6 insertions(+)

diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index 9461e8d4b1..35773b1c34 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -92,6 +92,8 @@ def setup_input_params_for_pass_through # rubocop:todo Metrics/AbcSize
     else
       raise StandardError, "Invalid cherrypicking strategy '#{params[:cherrypick][:strategy]}'"
     end
+    # Y26-012: Add buffer volume for empty wells option to params for pass through
+    @buffer_volume_for_empty_wells = params[:buffer_volume_for_empty_wells]
     @plate_purpose_id = params[:plate_purpose_id]
     @fluidigm_barcode = params[:fluidigm_plate]
   end
@@ -129,6 +131,8 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
           raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_strategy]}"
         end
 
+      binding.pry
+
       # We can preload the well locations so that we can do efficient lookup later.
       well_locations =
         Map
diff --git a/app/views/workflows/_cherrypick_batches.html.erb b/app/views/workflows/_cherrypick_batches.html.erb
index 6d378979b9..d93285264a 100644
--- a/app/views/workflows/_cherrypick_batches.html.erb
+++ b/app/views/workflows/_cherrypick_batches.html.erb
@@ -40,6 +40,8 @@
   <%= hidden_field_tag 'robot_id', @robot_id    %>
   <%= hidden_field_tag 'cherrypick_strategy', @cherrypick_strategy %>
   <%= hidden_field_tag 'plate_type', @plate_type %>
+  <!-- Y26-012: Add hidden field to carry over the buffer volume for empty wells option from the form on the previous page -->
+  <%= hidden_field_tag 'buffer_volume_for_empty_wells', @buffer_volume_for_empty_wells %>
 
   <%= render(partial: 'next_stage_submit', locals: { check_selection: true }) %>
 <% end %>

From 4b7b7e72d8eb917009b8f9c380ab381d10657991 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 00:27:40 +0000
Subject: [PATCH 05/29] Remove pry

---
 app/models/tasks/cherrypick_handler.rb | 2 --
 1 file changed, 2 deletions(-)

diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index 35773b1c34..6201a6a8c5 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -131,8 +131,6 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
           raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_strategy]}"
         end
 
-      binding.pry
-
       # We can preload the well locations so that we can do efficient lookup later.
       well_locations =
         Map

From 6a0d6db93fe2ee04a1639265659d62c7ed648ef9 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 01:08:32 +0000
Subject: [PATCH 06/29] Add HasPolyMetadata concent to set the option on batch

---
 app/models/batch.rb                      |  4 ++--
 app/models/concerns/has_poly_metadata.rb | 29 ++++++++++++++++++++++++
 app/models/tasks/cherrypick_handler.rb   |  5 ++++
 3 files changed, 36 insertions(+), 2 deletions(-)
 create mode 100644 app/models/concerns/has_poly_metadata.rb

diff --git a/app/models/batch.rb b/app/models/batch.rb
index b8e00904ec..96ca15f5bb 100644
--- a/app/models/batch.rb
+++ b/app/models/batch.rb
@@ -16,6 +16,8 @@ class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
   include ::Batch::PipelineBehaviour
   include ::Batch::StateMachineBehaviour
   include UnderRepWellCommentsToBroadcast
+  # Y26-012: Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
+  include HasPolyMetadata
   extend EventfulRecord
 
   # The three states of {Batch} Also @see {SequencingQcBatch}
@@ -50,8 +52,6 @@ class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
   has_many :samples, -> { distinct }, through: :source_assets, source: :samples
   has_many :output_labware, -> { distinct }, through: :assets, source: :labware
   has_many :input_labware, -> { distinct }, through: :source_assets, source: :labware
-  # Y26-012: Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
-  has_many :poly_metadata, as: :metadatable, dependent: :destroy
 
   has_many_events
   has_many_lab_events
diff --git a/app/models/concerns/has_poly_metadata.rb b/app/models/concerns/has_poly_metadata.rb
new file mode 100644
index 0000000000..a984ee94a0
--- /dev/null
+++ b/app/models/concerns/has_poly_metadata.rb
@@ -0,0 +1,29 @@
+# frozen_string_literal: true
+
+module HasPolyMetadata
+  extend ActiveSupport::Concern
+
+  included do
+    has_many :poly_metadata, as: :metadatable, dependent: :destroy, inverse_of: :metadatable
+  end
+
+  # Sets a PolyMetaDatum for the given key and value.
+  # If value is present, it will create or update the PolyMetaDatum with the
+  # given key and value, otherwise it will destroy the PolyMetaDatum with the
+  # given key if that exists.
+  # @param key [String] The key of the PolyMetaDatum to set.
+  # @param value [String] The value of the PolyMetaDatum to set. If nil or empty, the PolyMetaDatum will be destroyed.
+  # @return [void]
+  def set_poly_metadata(key, value)
+    record = poly_metadata.find_by(key:)
+    if value.present?
+      if record
+        record.update!(value:)
+      else
+        poly_metadata.create!(key:, value:)
+      end
+    else
+      record&.destroy!
+    end
+  end
+end
diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index 6201a6a8c5..edee8bed55 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -131,6 +131,11 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
           raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_strategy]}"
         end
 
+      # Y26-012: Store the buffer volume for empty wells option in the batch's
+      # poly_metadata for use in the worksheet rendering and robot driver file
+      key = :buffer_volume_for_empty_wells
+      set_poly_metadata(key, params[key])
+
       # We can preload the well locations so that we can do efficient lookup later.
       well_locations =
         Map

From c5244aab20b888ac1f79c14beb253d248f2889f3 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 01:12:49 +0000
Subject: [PATCH 07/29] Call set_poly_metadata on the batch in cherrypick
 handler

---
 app/models/tasks/cherrypick_handler.rb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index edee8bed55..451c4c3624 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -134,7 +134,7 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
       # Y26-012: Store the buffer volume for empty wells option in the batch's
       # poly_metadata for use in the worksheet rendering and robot driver file
       key = :buffer_volume_for_empty_wells
-      set_poly_metadata(key, params[key])
+      @batch.set_poly_metadata(key, params[key])
 
       # We can preload the well locations so that we can do efficient lookup later.
       well_locations =

From f2d190d049640e75c50afbab743115b241ea6b6e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 01:29:24 +0000
Subject: [PATCH 08/29] Update worksheet with buffer_volume_for_empty_wells
 option from batch metadata

---
 app/models/concerns/has_poly_metadata.rb             |  7 +++++++
 .../batches/_cherrypick_single_worksheet.html.erb    | 12 ++++++++----
 2 files changed, 15 insertions(+), 4 deletions(-)

diff --git a/app/models/concerns/has_poly_metadata.rb b/app/models/concerns/has_poly_metadata.rb
index a984ee94a0..df51d6456a 100644
--- a/app/models/concerns/has_poly_metadata.rb
+++ b/app/models/concerns/has_poly_metadata.rb
@@ -26,4 +26,11 @@ def set_poly_metadata(key, value)
       record&.destroy!
     end
   end
+
+  # Returns the value of the PolyMetaDatum with the given key.
+  # @param key [String] The key of the PolyMetaDatum to retrieve.
+  # @return [String, nil] The value of the PolyMetaDatum, or nil if it does not exist.
+  def get_poly_metadata(key)
+    poly_metadata.find_by(key:)&.value
+  end
 end
diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 8c2dc6d897..637c300c55 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -14,6 +14,8 @@
 <%# see Robot::Verification::Base#pick_number_to_expected_layout for structure of robot_plate_layout %>
 <% destination_layout, source_layout, control_layout = robot_plate_layout %>
 <% source_plate_colour = source_layout.transform_values { |sort_order| "colour#{sort_order%12}" } %>
+<!-- Y26-012 Get buffer_volume_for_empty_wells from batch poly_metadata -->
+<% buffer_volume_for_empty_wells = batch.get_poly_metadata(:buffer_volume_for_empty_wells) %>
 
 <div id="plate_details">
   <%= render partial: 'cherrypick_worksheet_plate_list', locals: { section_name: 'Source plates', plates: source_layout, bed_prefix: 'SCRC' } %>
@@ -78,8 +80,8 @@
                 <% else %>
                   <td>
                 <% end -%>
-                <% if empty_well -%>
-                  e120.00
+                <% if empty_well && buffer_volume_for_empty_wells.present? -%>
+                  e<%= "%.#{configatron.tecan_precision}f" % buffer_volume_for_empty_wells %>
                 <% end %>
                 </td>
             <% end -%>
@@ -100,8 +102,10 @@
 
 <div id="footer">
   <!-- Y26-012: Add buffer volume for empty wells to footer if the option was set; remove it otherwise-->
-  Buffer for empty wells: 120 µl<br>
-  v = picking volume µl; b = buffer volume µl; e = buffer for empty wells µl<br>
+  <% if buffer_volume_for_empty_wells.present? -%>
+    Buffer for empty wells: <%= buffer_volume_for_empty_wells %> µl<br>
+  <% end -%>
+  v = picking volume µl; b = buffer volume µl<% if buffer_volume_for_empty_wells.present? -%>; e = buffer for empty wells µl<br><% end -%>
   <!-- v = picking volume µl; b = buffer volume µl<br> -->
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>

From 0247d437e100ac257cb4f4c96e0c9dd52d452f11 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 22:20:34 +0000
Subject: [PATCH 09/29] Add buffer steps for empty wells in tecan behaviour

---
 .../generator/behaviours/tecan_default.rb     | 39 +++++++++++++++++--
 1 file changed, 36 insertions(+), 3 deletions(-)

diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index f7c46f64e6..6f072ce407 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -1,7 +1,7 @@
 # frozen_string_literal: true
 
 # Module with the file generation functionality for Tecan robots
-module Robot::Generator::Behaviours::TecanDefault
+module Robot::Generator::Behaviours::TecanDefault # rubocop:disable Metrics/ModuleLength
   def mapping(data_object: picking_data)
     raise ArgumentError, 'Data object not present for Tecan mapping' if data_object.nil?
 
@@ -70,10 +70,11 @@ def buffer_separator
     'C;'
   end
 
-  def buffers(data_object)
+  def buffers(data_object) # rubocop:disable Metrics/AbcSize
+    data_object = data_object_for_buffers(data_object)
     buffer = []
     each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
-      next unless total_volume > mapping['volume']
+      next if mapping.key?('src_well') && total_volume <= mapping['volume']
 
       dest_name = data_object['destination'][dest_plate_barcode]['name']
       volume = mapping['buffer_volume']
@@ -113,4 +114,36 @@ def sorted_destination_plates
   def description_to_column_index(well_name, plate_size)
     Map::Coordinate.description_to_vertical_plate_position(well_name, plate_size)
   end
+
+  def column_index_to_description(index, plate_size)
+    Map::Coordinate.vertical_plate_position_to_description(index, plate_size)
+  end
+
+  def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
+    buffer_volume_for_empty_wells = @batch.get_poly_metadata(:buffer_volume_for_empty_wells)
+    return data_object unless buffer_volume_for_empty_wells
+
+    obj = { 'destination' => {} }
+    data_object['destination'].each do |dest_plate_barcode, plate_details|
+      plate_size = plate_details['plate_size']
+      # Initialise the destination section
+      obj['destination'][dest_plate_barcode] = {
+        'name' => plate_details['name'],
+        'plate_size' => plate_size
+      }
+      # Create a hash of column index to the existing mapping entries
+      index_to_mapping = plate_details['mapping'].index_by do |entry|
+        description_to_column_index(entry['dst_well'], plate_size)
+      end
+      # Loop through the column order and generate new mapping entries
+      mapping = (1..plate_size).map do |index|
+        index_to_mapping[index] || {
+          'dst_well' => column_index_to_description(index, plate_size),
+          'buffer_volume' => buffer_volume_for_empty_wells
+        }
+      end
+      obj['destination'][dest_plate_barcode]['mapping'] = mapping
+    end
+    obj
+  end
 end

From 03927d530965b6f8f7dbd6f11365abb7df02c54f Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 22:22:00 +0000
Subject: [PATCH 10/29] Add buffer steps for empty wells in TecanV3 driver file
 generator

---
 app/models/robot/generator/tecan_v3.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/models/robot/generator/tecan_v3.rb b/app/models/robot/generator/tecan_v3.rb
index e6a1bdadde..95f59649a8 100644
--- a/app/models/robot/generator/tecan_v3.rb
+++ b/app/models/robot/generator/tecan_v3.rb
@@ -14,9 +14,10 @@ class Robot::Generator::TecanV3 < Robot::Generator::TecanV2
   # @see Robot::Generator::Behaviours::TecanDefault#buffers
   # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
   def buffers(data_object)
+    data_object = data_object_for_buffers(data_object)
     groups = Hash.new { |h, k| h[k] = [] } # channel => [steps]
     each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
-      next unless total_volume > mapping['volume']
+      next if mapping.key?('src_well') && total_volume <= mapping['volume']
 
       dest_name = data_object['destination'][dest_plate_barcode]['name']
       volume = mapping['buffer_volume']

From 13e85a36f202e3bb3258f4f396759a965e0c3012 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 22:50:53 +0000
Subject: [PATCH 11/29] Check if the destination well is empty, in case of
 partial plate

---
 .../generator/behaviours/tecan_default.rb     | 22 ++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index 6f072ce407..4fbf0e5857 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -125,6 +125,7 @@ def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metri
 
     obj = { 'destination' => {} }
     data_object['destination'].each do |dest_plate_barcode, plate_details|
+      plate = Plate.find_by_barcode(dest_plate_barcode)
       plate_size = plate_details['plate_size']
       # Initialise the destination section
       obj['destination'][dest_plate_barcode] = {
@@ -135,10 +136,25 @@ def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metri
       index_to_mapping = plate_details['mapping'].index_by do |entry|
         description_to_column_index(entry['dst_well'], plate_size)
       end
+
       # Loop through the column order and generate new mapping entries
-      mapping = (1..plate_size).map do |index|
-        index_to_mapping[index] || {
-          'dst_well' => column_index_to_description(index, plate_size),
+      # Add existing mappings if present and skip non-empty wells in case it is partial plate.
+      mapping = []
+      (1..plate_size).each do |index|
+        # Add existing mapping if present for this column index.
+        if index_to_mapping.key?(index)
+          mapping << index_to_mapping[index]
+          next
+        end
+
+        # Check if the destination well empty, in case of partial plate.
+        dst_well = column_index_to_description(index, plate_size) # A1, B1, etc.
+        well = plate.find_well_by_name(dst_well) # Well object or nil
+        next if well.present? && !well.empty? # Skip non-empty wells
+
+        # Add buffer for empty well
+        mapping << {
+          'dst_well' => dst_well,
           'buffer_volume' => buffer_volume_for_empty_wells
         }
       end

From e755668a19e59eaba4bdc105f5ee6640550d8e3e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Thu, 19 Feb 2026 23:55:09 +0000
Subject: [PATCH 12/29] Add guard for generator test without batch

---
 app/models/robot/generator/behaviours/tecan_default.rb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index 4fbf0e5857..607380c95c 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -119,8 +119,8 @@ def column_index_to_description(index, plate_size)
     Map::Coordinate.vertical_plate_position_to_description(index, plate_size)
   end
 
-  def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength
-    buffer_volume_for_empty_wells = @batch.get_poly_metadata(:buffer_volume_for_empty_wells)
+  def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
+    buffer_volume_for_empty_wells = @batch&.get_poly_metadata(:buffer_volume_for_empty_wells)
     return data_object unless buffer_volume_for_empty_wells
 
     obj = { 'destination' => {} }

From 521a3ddc9f05260d2b401cf131b8e804c0bc8146 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 01:03:46 +0000
Subject: [PATCH 13/29] Add the word volume to the note and legend in worksheet

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 637c300c55..ae73b9f9cf 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -103,9 +103,9 @@
 <div id="footer">
   <!-- Y26-012: Add buffer volume for empty wells to footer if the option was set; remove it otherwise-->
   <% if buffer_volume_for_empty_wells.present? -%>
-    Buffer for empty wells: <%= buffer_volume_for_empty_wells %> µl<br>
+    Buffer volume for empty wells: <%= buffer_volume_for_empty_wells %> µl<br>
   <% end -%>
-  v = picking volume µl; b = buffer volume µl<% if buffer_volume_for_empty_wells.present? -%>; e = buffer for empty wells µl<br><% end -%>
+  v = picking volume µl; b = buffer volume µl<% if buffer_volume_for_empty_wells.present? -%>; e = buffer volume for empty wells µl<br><% end -%>
   <!-- v = picking volume µl; b = buffer volume µl<br> -->
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>

From 0d0787c02bc9a2a0169d16656f19264dc35e8db7 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 01:04:50 +0000
Subject: [PATCH 14/29] Add Automatic buffer addition for empty wells required?
 checkbox

---
 .../workflows/_cherrypick_strategies.html.erb      | 14 ++++++++++----
 1 file changed, 10 insertions(+), 4 deletions(-)

diff --git a/app/views/workflows/_cherrypick_strategies.html.erb b/app/views/workflows/_cherrypick_strategies.html.erb
index a48410fd61..07cad95a5c 100644
--- a/app/views/workflows/_cherrypick_strategies.html.erb
+++ b/app/views/workflows/_cherrypick_strategies.html.erb
@@ -1,4 +1,4 @@
-<%# locals: { form: } -%>
+<%# locals: { form: } %>
 
 <p>Choose a strategy below:</p>
 
@@ -26,15 +26,21 @@
   </div>
 
 </div>
-<!-- Y26-012: Add form control to collect the buffer volume for empty wells -->
+<%# Add form controls to collect the options for the buffer volume for empty wells -%>
 <p>Additional options:</p>
 
 <div class="row">
-  <div class="col-md-4">
+  <div class="col-md-8">
+    <div class="form-group form-row">
+      <label class="col-12 col-lg-8 col-form-label" for="automatic_buffer_addition">Automatic buffer addition for empty wells required?</label>
+      <div class="col-12 col-lg-4">
+        <input type="checkbox" class="form-control text-right" name="automatic_buffer_addition" id="automatic_buffer_addition" />
+      </div>
+    </div>
     <div class ="form-group form-row">
       <label class="col-12 col-lg-8 col-form-label" for="buffer_volume_for_empty_wells">Buffer volume for empty wells (µl)</label>
       <div class="col-12 col-lg-4">
-        <input type="text" class="form-control" id="buffer_volume_for_empty_wells" name="buffer_volume_for_empty_wells">
+        <input type="text" class="form-control" id="buffer_volume_for_empty_wells" name="buffer_volume_for_empty_wells" value="120">
       </div>
     </div>
   </div>

From 7349453b0688c3d239922d6ebb4ddaf60fe05b46 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 01:05:48 +0000
Subject: [PATCH 15/29] Add script to toggle buffer_volume_for_empty_wells
 textbox based on automatic_buffer_addition checkbox

---
 app/frontend/entrypoints/cherrypick_strategies.js | 12 ++++++++++++
 1 file changed, 12 insertions(+)

diff --git a/app/frontend/entrypoints/cherrypick_strategies.js b/app/frontend/entrypoints/cherrypick_strategies.js
index c0b227d38a..45ed8cddcf 100644
--- a/app/frontend/entrypoints/cherrypick_strategies.js
+++ b/app/frontend/entrypoints/cherrypick_strategies.js
@@ -1,3 +1,15 @@
+// Toggle buffer_volume_for_empty_wells input based on automatic_buffer_addition checkbox
+document.addEventListener("DOMContentLoaded", function () {
+  const bufferInput = document.getElementById("buffer_volume_for_empty_wells");
+  const autoBufferCheckbox = document.getElementById("automatic_buffer_addition");
+  if (bufferInput && autoBufferCheckbox) {
+    function toggleBufferInput() {
+      bufferInput.disabled = !autoBufferCheckbox.checked;
+    }
+    autoBufferCheckbox.addEventListener("change", toggleBufferInput);
+    toggleBufferInput(); // Set initial state
+  }
+});
 // apply a border highlight to the card, based on the cherrypick strategy selected
 // this is admittedly a gratuitous addition to the user experience, but it's a nice touch
 

From df316273b49f74f129523f310f61137eda955824 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 01:20:21 +0000
Subject: [PATCH 16/29] Add code documentation about new data_object generation

---
 .../generator/behaviours/tecan_default.rb     | 38 +++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index 607380c95c..c335db3f39 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -74,6 +74,8 @@ def buffers(data_object) # rubocop:disable Metrics/AbcSize
     data_object = data_object_for_buffers(data_object)
     buffer = []
     each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
+      # src_well is checked to distinguish between buffer for sample wells
+      # and buffer for empty wells.
       next if mapping.key?('src_well') && total_volume <= mapping['volume']
 
       dest_name = data_object['destination'][dest_plate_barcode]['name']
@@ -119,6 +121,42 @@ def column_index_to_description(index, plate_size)
     Map::Coordinate.vertical_plate_position_to_description(index, plate_size)
   end
 
+  # Returns a new data object with buffer entries added for empty destination
+  # wells, if the option is enabled; otherwise returns the original data object.
+  # Only the fields used by the buffer steps are added to the new data object.
+  # @param data_object [Hash] the original data object
+  # @return [Hash] the new data object with buffer entries for empty wells,
+  #   or the original data object if the option is not enabled
+  # @example input data_object
+  #  {"destination" =>
+  #   {"SQPD-9101" =>
+  #     {"name" => "ABgene 0765",
+  #      "plate_size" => 96,
+  #      "control" => false,
+  #      "mapping" =>
+  #       [{"src_well" => ["SQPD-9089", "A1"], "dst_well" => "A1", "volume" => 100.0, "buffer_volume" => 0.0},
+  #        {"src_well" => ["SQPD-9089", "A2"], "dst_well" => "B1", "volume" => 100.0, "buffer_volume" => 0.0}]},
+  #  "source" =>
+  #   {"SQPD-9089" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false},
+  #    "SQPD-9090" => {"name" => "ABgene 0800", "plate_size" => 96, "control" => false}},
+  #  "time" => Thu, 19 Feb 2026 15:20:20.785717000 GMT +00:00,
+  #  "user" => "admin"}
+  #
+  # @example output data_object
+  #  {"destination" =>
+  #   {"SQPD-9101" =>
+  #     {"name" => "ABgene 0765",
+  #      "plate_size" => 96,
+  #      "control" => false,
+  #      "mapping" =>
+  #       [{"src_well" => ["SQPD-9089", "A1"], "dst_well" => "A1", "volume" => 100.0, "buffer_volume" => 0.0},
+  #        {"src_well" => ["SQPD-9089", "A2"], "dst_well" => "B1", "volume" => 100.0, "buffer_volume" => 0.0},
+  #        {"dst_well" => "C1", "buffer_volume" => 120.0}]},
+  #        {"dst_well" => "D1", "buffer_volume" => 120.0}]},
+  #        ...
+  #        ]},
+  #     }
+  #   }
   def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
     buffer_volume_for_empty_wells = @batch&.get_poly_metadata(:buffer_volume_for_empty_wells)
     return data_object unless buffer_volume_for_empty_wells

From 416ab295b821e7e62226941c2b6a2cdd4b574c79 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 01:21:05 +0000
Subject: [PATCH 17/29] Add comment to explain why src_well is checked

---
 app/models/robot/generator/tecan_v3.rb | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/app/models/robot/generator/tecan_v3.rb b/app/models/robot/generator/tecan_v3.rb
index 95f59649a8..625ff034b0 100644
--- a/app/models/robot/generator/tecan_v3.rb
+++ b/app/models/robot/generator/tecan_v3.rb
@@ -17,6 +17,8 @@ def buffers(data_object)
     data_object = data_object_for_buffers(data_object)
     groups = Hash.new { |h, k| h[k] = [] } # channel => [steps]
     each_mapping(data_object) do |mapping, dest_plate_barcode, plate_details|
+      # src_well is checked to distinguish between buffer for sample wells
+      # and buffer for empty wells.
       next if mapping.key?('src_well') && total_volume <= mapping['volume']
 
       dest_name = data_object['destination'][dest_plate_barcode]['name']

From 85a6b2ae798c544ab22a607a79834fc0dc3c1039 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:47:05 +0000
Subject: [PATCH 18/29] Add batch behaviour to handle poly_metadata for
 cherrypick options

---
 app/models/batch/poly_metadata_behaviour.rb | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 app/models/batch/poly_metadata_behaviour.rb

diff --git a/app/models/batch/poly_metadata_behaviour.rb b/app/models/batch/poly_metadata_behaviour.rb
new file mode 100644
index 0000000000..59458c84a0
--- /dev/null
+++ b/app/models/batch/poly_metadata_behaviour.rb
@@ -0,0 +1,15 @@
+# frozen_string_literal: true
+module Batch::PolyMetadataBehaviour
+  # Returns whether the Cherrypick automatic_buffer_addition option is enabled
+  # @return [Boolean] whether the automatic_buffer_addition option is enabled
+  def automatic_buffer_addition?
+    get_poly_metadata(:automatic_buffer_addition) == '1'
+  end
+
+  # Returns the Cherrypick buffer_volume_for_empty_wells option value if
+  # automatic_buffer_addition is enabled, nil otherwise.
+  # @return [Float, nil] the buffer_volume_for_empty_wells value
+  def buffer_volume_for_empty_wells
+    get_poly_metadata(:buffer_volume_for_empty_wells).to_f if automatic_buffer_addition?
+  end
+end

From 6177332be059d5c4ef897c2ec8fa640b0fa4003c Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:48:38 +0000
Subject: [PATCH 19/29] Add task helper to set form params in batch
 polymetadata

---
 .../buffer_volume_for_empty_wells_option.rb   | 23 +++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb

diff --git a/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
new file mode 100644
index 0000000000..43c4187cc6
--- /dev/null
+++ b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
@@ -0,0 +1,23 @@
+# frozen_string_literal: true
+# frozen_sring_literal: true
+
+module Cherrypick::Task::BufferVolumeForEmptyWellsOption
+  def create_buffer_volume_for_empty_wells_option(params)
+    return unless @batch
+
+    key = :automatic_buffer_addition
+    # The checkbox value is either "1", or nil if not checked.
+    @batch.set_poly_metadata(key, params[key])
+
+    return if params[key] != '1'
+
+    # If automatic buffer addition for empty wells is required.
+    key = :buffer_volume_for_empty_wells
+    unless valid_float_param?(params[key])
+      raise Cherrypick::VolumeError,
+            "Invalid buffer volume for empty wells: #{params[key]}"
+    end
+
+    @batch.set_poly_metadata(key, params[key])
+  end
+end

From e1067094f2ebbfb4936230d412d338e153ebae16 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:48:59 +0000
Subject: [PATCH 20/29] Add PolyMetadataBehaviour to batch

---
 app/models/batch.rb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/models/batch.rb b/app/models/batch.rb
index 96ca15f5bb..aa156c7abd 100644
--- a/app/models/batch.rb
+++ b/app/models/batch.rb
@@ -16,8 +16,9 @@ class Batch < ApplicationRecord # rubocop:todo Metrics/ClassLength
   include ::Batch::PipelineBehaviour
   include ::Batch::StateMachineBehaviour
   include UnderRepWellCommentsToBroadcast
-  # Y26-012: Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
+  # Added for storing buffer_volume_for_empty_wells option on Cherrypick batches.
   include HasPolyMetadata
+  include ::Batch::PolyMetadataBehaviour
   extend EventfulRecord
 
   # The three states of {Batch} Also @see {SequencingQcBatch}

From 0dad66a4b6ada278f65e9c944d42e0fa56ba395e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:49:31 +0000
Subject: [PATCH 21/29] Add option handling in pick helpers

---
 app/models/cherrypick/task/pick_helpers.rb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/models/cherrypick/task/pick_helpers.rb b/app/models/cherrypick/task/pick_helpers.rb
index a1ff1891f4..45e349ab19 100644
--- a/app/models/cherrypick/task/pick_helpers.rb
+++ b/app/models/cherrypick/task/pick_helpers.rb
@@ -5,6 +5,7 @@ def self.included(base)
       include Cherrypick::Task::PickByNanoGramsPerMicroLitre
       include Cherrypick::Task::PickByNanoGrams
       include Cherrypick::Task::PickByMicroLitre
+      include Cherrypick::Task::BufferVolumeForEmptyWellsOption
     end
   end
 

From 0655cfed969d2fd0d6d0d06c04fd9d7f2c7ecc54 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:50:37 +0000
Subject: [PATCH 22/29] Add pass through for automatic_buffer_addition

---
 app/models/tasks/cherrypick_handler.rb | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/app/models/tasks/cherrypick_handler.rb b/app/models/tasks/cherrypick_handler.rb
index 451c4c3624..926e3952cc 100644
--- a/app/models/tasks/cherrypick_handler.rb
+++ b/app/models/tasks/cherrypick_handler.rb
@@ -92,7 +92,8 @@ def setup_input_params_for_pass_through # rubocop:todo Metrics/AbcSize
     else
       raise StandardError, "Invalid cherrypicking strategy '#{params[:cherrypick][:strategy]}'"
     end
-    # Y26-012: Add buffer volume for empty wells option to params for pass through
+    # Add buffer volume for empty wells option to params for pass through
+    @automatic_buffer_addition = params[:automatic_buffer_addition]
     @buffer_volume_for_empty_wells = params[:buffer_volume_for_empty_wells]
     @plate_purpose_id = params[:plate_purpose_id]
     @fluidigm_barcode = params[:fluidigm_plate]
@@ -131,10 +132,8 @@ def do_cherrypick_task(_task, params) # rubocop:todo Metrics/CyclomaticComplexit
           raise StandardError, "Invalid cherrypicking type #{params[:cherrypick_strategy]}"
         end
 
-      # Y26-012: Store the buffer volume for empty wells option in the batch's
-      # poly_metadata for use in the worksheet rendering and robot driver file
-      key = :buffer_volume_for_empty_wells
-      @batch.set_poly_metadata(key, params[key])
+      # Store the buffer volume for empty wells option in the batch's poly_metadata
+      create_buffer_volume_for_empty_wells_option(params)
 
       # We can preload the well locations so that we can do efficient lookup later.
       well_locations =

From e70a38e4c1a3bca16f41c0d08073e4074f44b00e Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:51:17 +0000
Subject: [PATCH 23/29] Tidy up the worksheet ERB

---
 .../batches/_cherrypick_single_worksheet.html.erb   | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index ae73b9f9cf..63e0acc68c 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -14,8 +14,8 @@
 <%# see Robot::Verification::Base#pick_number_to_expected_layout for structure of robot_plate_layout %>
 <% destination_layout, source_layout, control_layout = robot_plate_layout %>
 <% source_plate_colour = source_layout.transform_values { |sort_order| "colour#{sort_order%12}" } %>
-<!-- Y26-012 Get buffer_volume_for_empty_wells from batch poly_metadata -->
-<% buffer_volume_for_empty_wells = batch.get_poly_metadata(:buffer_volume_for_empty_wells) %>
+<%# Get buffer_volume_for_empty_wells from batch as float or nil -%>
+<% buffer_volume_for_empty_wells = batch.buffer_volume_for_empty_wells %>
 
 <div id="plate_details">
   <%= render partial: 'cherrypick_worksheet_plate_list', locals: { section_name: 'Source plates', plates: source_layout, bed_prefix: 'SCRC' } %>
@@ -50,7 +50,7 @@
             <td><strong><%= rowchar %></strong></td>
             <% (num_columns).times do |column| -%>
               <% well = plate_wells[row*num_columns+column] -%>
-                <!--Y26-012: flag to check if well is empty and needs to be represented on the chart with 'e' followed by the buffer volume for empty wells, for example e120.0 -->
+                <%# Flag to check if well is empty and needs to be represented on the chart with 'e' followed by the buffer volume for empty wells, for example e120.00 -%>
                 <% empty_well = true %>
                 <% if  well.present? -%>
                   <% request = indexed_requests[well.id]  %>
@@ -66,7 +66,7 @@
                       <% else %>
                         <td>
                       <% end -%>
-                      <!--Y26-012: flag to set if the well is not empty -->
+                      <%# Flag to set if the well is not empty -%>
                       <% empty_well = false %>
                       <%= source_well.map_description %>
                       <%= source_well.plate.barcode_number %>
@@ -101,12 +101,11 @@
 </div>
 
 <div id="footer">
-  <!-- Y26-012: Add buffer volume for empty wells to footer if the option was set; remove it otherwise-->
+  <%# Add buffer volume for empty wells to footer if the option was set -%>
   <% if buffer_volume_for_empty_wells.present? -%>
-    Buffer volume for empty wells: <%= buffer_volume_for_empty_wells %> µl<br>
+    Buffer volume for empty wells: <%= "%.#{configatron.tecan_precision}f" % buffer_volume_for_empty_wells %> %> µl<br>
   <% end -%>
   v = picking volume µl; b = buffer volume µl<% if buffer_volume_for_empty_wells.present? -%>; e = buffer volume for empty wells µl<br><% end -%>
-  <!-- v = picking volume µl; b = buffer volume µl<br> -->
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>
   Printed: <%= Time.now.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= current_user.login %>
 </div>

From 4ca4650f52892a918c987af1cd2872261e235c32 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:51:47 +0000
Subject: [PATCH 24/29] Use ERB comments instead of HTML comments

---
 app/views/workflows/_cherrypick_batches.html.erb | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/app/views/workflows/_cherrypick_batches.html.erb b/app/views/workflows/_cherrypick_batches.html.erb
index d93285264a..a20af1374e 100644
--- a/app/views/workflows/_cherrypick_batches.html.erb
+++ b/app/views/workflows/_cherrypick_batches.html.erb
@@ -40,7 +40,8 @@
   <%= hidden_field_tag 'robot_id', @robot_id    %>
   <%= hidden_field_tag 'cherrypick_strategy', @cherrypick_strategy %>
   <%= hidden_field_tag 'plate_type', @plate_type %>
-  <!-- Y26-012: Add hidden field to carry over the buffer volume for empty wells option from the form on the previous page -->
+  <%# Add hidden fields for the buffer volume for empty wells option to carry over -%>
+  <%= hidden_field_tag 'automatic_buffer_addition', @automatic_buffer_addition %>
   <%= hidden_field_tag 'buffer_volume_for_empty_wells', @buffer_volume_for_empty_wells %>
 
   <%= render(partial: 'next_stage_submit', locals: { check_selection: true }) %>

From 4f00987f6c87d7f03c1406efcedcbcc6eca4990b Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 02:52:12 +0000
Subject: [PATCH 25/29] Revert redundant change

---
 app/views/workflows/_plate_template_batches.html.erb | 1 +
 1 file changed, 1 insertion(+)

diff --git a/app/views/workflows/_plate_template_batches.html.erb b/app/views/workflows/_plate_template_batches.html.erb
index 62a350b082..4aec5ad3ce 100644
--- a/app/views/workflows/_plate_template_batches.html.erb
+++ b/app/views/workflows/_plate_template_batches.html.erb
@@ -55,5 +55,6 @@
     <%= panel(:info, title: "Step 3: Set volumes and concentrations <a href='https://ssg-confluence.internal.sanger.ac.uk/x/NoHdDQ'><small>Information about cherrypicking options</small></a>".html_safe) do %>
       <%= render partial: 'cherrypick_strategies', locals: { form: form } %>
     <% end %>
+
   <%= render partial: "next_stage_submit" %>
 <% end %>

From b7183cd6fa3b17e47e7326da4935aff8facb6459 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 03:14:38 +0000
Subject: [PATCH 26/29] Remove extra closing ERB tag

---
 app/views/batches/_cherrypick_single_worksheet.html.erb | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/app/views/batches/_cherrypick_single_worksheet.html.erb b/app/views/batches/_cherrypick_single_worksheet.html.erb
index 63e0acc68c..09a5e40a01 100644
--- a/app/views/batches/_cherrypick_single_worksheet.html.erb
+++ b/app/views/batches/_cherrypick_single_worksheet.html.erb
@@ -103,7 +103,7 @@
 <div id="footer">
   <%# Add buffer volume for empty wells to footer if the option was set -%>
   <% if buffer_volume_for_empty_wells.present? -%>
-    Buffer volume for empty wells: <%= "%.#{configatron.tecan_precision}f" % buffer_volume_for_empty_wells %> %> µl<br>
+    Buffer volume for empty wells: <%= "%.#{configatron.tecan_precision}f" % buffer_volume_for_empty_wells %> µl<br>
   <% end -%>
   v = picking volume µl; b = buffer volume µl<% if buffer_volume_for_empty_wells.present? -%>; e = buffer volume for empty wells µl<br><% end -%>
   Created: <%= batch.updated_at.strftime("%I:%M %p on %A %d %B, %Y") %> for <%= batch.user.login %><br>

From 213445af74b647ee96ed04833adfdcb0ec141d1f Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 03:15:41 +0000
Subject: [PATCH 27/29] Handle checkbox value as 1 or on; passing through
 hidden form fields

---
 app/models/batch/poly_metadata_behaviour.rb                     | 2 +-
 .../cherrypick/task/buffer_volume_for_empty_wells_option.rb     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/app/models/batch/poly_metadata_behaviour.rb b/app/models/batch/poly_metadata_behaviour.rb
index 59458c84a0..b23dfe76ce 100644
--- a/app/models/batch/poly_metadata_behaviour.rb
+++ b/app/models/batch/poly_metadata_behaviour.rb
@@ -3,7 +3,7 @@ module Batch::PolyMetadataBehaviour
   # Returns whether the Cherrypick automatic_buffer_addition option is enabled
   # @return [Boolean] whether the automatic_buffer_addition option is enabled
   def automatic_buffer_addition?
-    get_poly_metadata(:automatic_buffer_addition) == '1'
+    %w[1 on].include?(get_poly_metadata(:automatic_buffer_addition))
   end
 
   # Returns the Cherrypick buffer_volume_for_empty_wells option value if
diff --git a/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
index 43c4187cc6..4fdeb4d321 100644
--- a/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
+++ b/app/models/cherrypick/task/buffer_volume_for_empty_wells_option.rb
@@ -9,7 +9,7 @@ def create_buffer_volume_for_empty_wells_option(params)
     # The checkbox value is either "1", or nil if not checked.
     @batch.set_poly_metadata(key, params[key])
 
-    return if params[key] != '1'
+    return unless %w[1 on].include?(params[key])
 
     # If automatic buffer addition for empty wells is required.
     key = :buffer_volume_for_empty_wells

From c66d6ef05c009278b79a7e01e5ae2f682899c102 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 03:23:02 +0000
Subject: [PATCH 28/29] Fix broken TecanV3 tests

---
 app/models/robot/generator/behaviours/tecan_default.rb | 2 +-
 spec/models/robot/generator/tecan_v3_spec.rb           | 5 +++++
 2 files changed, 6 insertions(+), 1 deletion(-)

diff --git a/app/models/robot/generator/behaviours/tecan_default.rb b/app/models/robot/generator/behaviours/tecan_default.rb
index c335db3f39..e716b5b00a 100644
--- a/app/models/robot/generator/behaviours/tecan_default.rb
+++ b/app/models/robot/generator/behaviours/tecan_default.rb
@@ -158,7 +158,7 @@ def column_index_to_description(index, plate_size)
   #     }
   #   }
   def data_object_for_buffers(data_object) # rubocop:disable Metrics/AbcSize,Metrics/MethodLength,Metrics/CyclomaticComplexity
-    buffer_volume_for_empty_wells = @batch&.get_poly_metadata(:buffer_volume_for_empty_wells)
+    buffer_volume_for_empty_wells = @batch&.buffer_volume_for_empty_wells
     return data_object unless buffer_volume_for_empty_wells
 
     obj = { 'destination' => {} }
diff --git a/spec/models/robot/generator/tecan_v3_spec.rb b/spec/models/robot/generator/tecan_v3_spec.rb
index 72b1d5fb18..f505550678 100644
--- a/spec/models/robot/generator/tecan_v3_spec.rb
+++ b/spec/models/robot/generator/tecan_v3_spec.rb
@@ -69,6 +69,11 @@
   # Expected output for the test cases.
   let(:expected_output) { File.read("spec/data/tecan_v3/case_#{case_num}.gwl") }
 
+  before do
+    allow(batch).to receive(:get_poly_metadata).with(:buffer_volume_for_empty_wells).and_return(nil)
+    allow(batch).to receive(:buffer_volume_for_empty_wells).and_return(nil)
+  end
+
   shared_examples 'a TecanV3 generator' do
     it 'generates the expected output' do
       expect(generator.as_text).to eq expected_output

From 733ebc979d0b71614e9dca1cbb06695a2157dbb4 Mon Sep 17 00:00:00 2001
From: yoldas <ay6@sanger.ac.uk>
Date: Fri, 20 Feb 2026 03:37:24 +0000
Subject: [PATCH 29/29] Fix broken Tecan generator tests

---
 spec/models/robot/generator/tecan_spec.rb | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/spec/models/robot/generator/tecan_spec.rb b/spec/models/robot/generator/tecan_spec.rb
index 3fae3deba7..e94a2702bb 100644
--- a/spec/models/robot/generator/tecan_spec.rb
+++ b/spec/models/robot/generator/tecan_spec.rb
@@ -1,7 +1,10 @@
 # frozen_string_literal: true
 
 describe Robot::Generator::Tecan do
-  before { create(:full_plate) }
+  before do
+    create(:full_plate)
+    allow(batch).to receive(:buffer_volume_for_empty_wells).and_return(nil)
+  end
 
   shared_examples 'a generator' do
     describe '.as_text' do