From 8146d09b8b6a97ba09042232ccfb9aa03e03689c Mon Sep 17 00:00:00 2001
From: Ida Lindegaard <82438141+idalindegaard@users.noreply.github.com>
Date: Mon, 25 Nov 2024 16:41:36 +0100
Subject: [PATCH] New Novaseq X volume constants (#561)

A patch after the change in issue #522

### Added

- new denaturation volume constants in constants.py
- updated which constants to use in novaseq_x_denaturation.py
---
 cg_lims/EPPs/udf/calculate/constants.py            |  3 +++
 .../EPPs/udf/calculate/novaseq_x_denaturation.py   | 14 +++++++++++---
 2 files changed, 14 insertions(+), 3 deletions(-)

diff --git a/cg_lims/EPPs/udf/calculate/constants.py b/cg_lims/EPPs/udf/calculate/constants.py
index 0d249e5c..00d056a5 100644
--- a/cg_lims/EPPs/udf/calculate/constants.py
+++ b/cg_lims/EPPs/udf/calculate/constants.py
@@ -21,6 +21,7 @@ class FlowCellLaneVolumes10B(FloatEnum):
     """The recommended volume of reagents per 10B flow cell lane. All values are in ul."""
 
     POOL_VOLUME: float = 35
+    DENATURATION_VOLUME: float = 34
     PHIX_VOLUME: float = 1
     NAOH_VOLUME: float = 8.5
     BUFFER_VOLUME: float = 127.5
@@ -30,6 +31,7 @@ class FlowCellLaneVolumes15B(FloatEnum):
     """The recommended volume of reagents per 1.5B flow cell lane. All values are in ul."""
 
     POOL_VOLUME: float = 35
+    DENATURATION_VOLUME: float = 34
     PHIX_VOLUME: float = 1
     NAOH_VOLUME: float = 8.5
     BUFFER_VOLUME: float = 127.5
@@ -39,6 +41,7 @@ class FlowCellLaneVolumes25B(FloatEnum):
     """The recommended volume of reagents per 25B flow cell lane. All values are in ul."""
 
     POOL_VOLUME: float = 57
+    DENATURATION_VOLUME: float = 56
     PHIX_VOLUME: float = 1.6
     NAOH_VOLUME: float = 14
     BUFFER_VOLUME: float = 210
diff --git a/cg_lims/EPPs/udf/calculate/novaseq_x_denaturation.py b/cg_lims/EPPs/udf/calculate/novaseq_x_denaturation.py
index 9fd30c1c..90691094 100644
--- a/cg_lims/EPPs/udf/calculate/novaseq_x_denaturation.py
+++ b/cg_lims/EPPs/udf/calculate/novaseq_x_denaturation.py
@@ -25,12 +25,17 @@ def __init__(self, per_lane_udf: str, total_udf: str, volume: float):
 
 
 class NovaSeqXDenaturation:
-    def __init__(self, pool: float, phix: float, naoh: float, buffer: float):
+    def __init__(self, pool: float, denaturation: float, phix: float, naoh: float, buffer: float):
         self.pool: DenaturationReagent = DenaturationReagent(
-            per_lane_udf="Volume of Pool to Denature (ul) per Lane",
+            per_lane_udf="Per Lane Volume Total (ul)",
             total_udf="Total Volume of Pool to Denature (ul)",
             volume=pool,
         )
+        self.denaturation: DenaturationReagent = DenaturationReagent(
+            per_lane_udf="Volume of Pool to Denature (ul) per Lane",
+            total_udf="Total Volume Denaturation (ul)",
+            volume=denaturation,
+        )
         self.phix: DenaturationReagent = DenaturationReagent(
             per_lane_udf="PhiX Volume (ul) per Lane",
             total_udf="Total PhiX Volume (ul)",
@@ -48,24 +53,27 @@ def __init__(self, pool: float, phix: float, naoh: float, buffer: float):
         )
 
     def get_reagent_list(self):
-        return [self.pool, self.phix, self.naoh, self.buffer]
+        return [self.pool, self.denaturation, self.phix, self.naoh, self.buffer]
 
 
 DENATURATION_VOLUMES = {
     FlowCellTypes.FLOW_CELL_10B: NovaSeqXDenaturation(
         pool=FlowCellLaneVolumes10B.POOL_VOLUME,
+        denaturation=FlowCellLaneVolumes10B.DENATURATION_VOLUME,
         phix=FlowCellLaneVolumes10B.PHIX_VOLUME,
         naoh=FlowCellLaneVolumes10B.NAOH_VOLUME,
         buffer=FlowCellLaneVolumes10B.BUFFER_VOLUME,
     ),
     FlowCellTypes.FLOW_CELL_15B: NovaSeqXDenaturation(
         pool=FlowCellLaneVolumes15B.POOL_VOLUME,
+        denaturation=FlowCellLaneVolumes15B.DENATURATION_VOLUME,
         phix=FlowCellLaneVolumes15B.PHIX_VOLUME,
         naoh=FlowCellLaneVolumes15B.NAOH_VOLUME,
         buffer=FlowCellLaneVolumes15B.BUFFER_VOLUME,
     ),
     FlowCellTypes.FLOW_CELL_25B: NovaSeqXDenaturation(
         pool=FlowCellLaneVolumes25B.POOL_VOLUME,
+        denaturation=FlowCellLaneVolumes25B.DENATURATION_VOLUME,
         phix=FlowCellLaneVolumes25B.PHIX_VOLUME,
         naoh=FlowCellLaneVolumes25B.NAOH_VOLUME,
         buffer=FlowCellLaneVolumes25B.BUFFER_VOLUME,