Update NovaSeq X sequencing volumes (#419)(patch)

### Added
- New Enum module
- New constants module for the udf/calculate EPPs
- New constant classes for flow cells and their properties

### Changed
- Updated the recommended volumes of reagents for preparing new NovaSeq X runs

cg_lims/EPPs/files/sample_sheet/models.py

@@ -1,21 +1,11 @@
 from genologics.lims import Process
 from typing import Optional
 import logging
-from enum import Enum
+from cg_lims.enums import StrEnum, IntEnum
 
 LOG = logging.getLogger(__name__)
 
 
-class StrEnum(str, Enum):
-    def __str__(self) -> str:
-        return str.__str__(self)
-
-
-class IntEnum(int, Enum):
-    def __int__(self) -> int:
-        return int.__int__(self)
-
-
 class IndexSetup(IntEnum):
     DUAL_INDEX: int = 2
     SINGLE_INDEX: int = 1

cg_lims/EPPs/udf/calculate/base.py

@@ -28,6 +28,7 @@
 )
 from cg_lims.EPPs.udf.calculate.novaseq_x_volumes import novaseq_x_volumes
 from cg_lims.EPPs.udf.calculate.pool_normalization import pool_normalization
+from cg_lims.EPPs.udf.calculate.novaseq_x_denaturation import novaseq_x_denaturation
 
 # commands
 from cg_lims.EPPs.udf.calculate.twist_pool import twist_pool
@@ -59,3 +60,4 @@ def calculate(ctx):
 calculate.add_command(calculate_average_size_and_set_qc)
 calculate.add_command(novaseq_x_volumes)
 calculate.add_command(pool_normalization)
+calculate.add_command(novaseq_x_denaturation)

cg_lims/EPPs/udf/calculate/constants.py

@@ -0,0 +1,22 @@
+from cg_lims.enums import IntEnum, FloatEnum, StrEnum
+
+
+class FlowCellTypes(StrEnum):
+    """Flow cell types available from Illumina"""
+
+    FLOW_CELL_10B: str = "10B"
+
+
+class FlowCellSize(IntEnum):
+    """The total number of lanes for a flow cell type."""
+
+    FLOW_CELL_10B: int = 8
+
+
+class FlowCellLaneVolumes10B(FloatEnum):
+    """The recommended volume of reagents per flow cell lane. All values are in ul."""
+
+    POOL_VOLUME: float = 34
+    PHIX_VOLUME: float = 1
+    NAOH_VOLUME: float = 8.5
+    BUFFER_VOLUME: float = 127.5

cg_lims/EPPs/udf/set/novaseq_x_denaturation.py → cg_lims/EPPs/udf/calculate/novaseq_x_denaturation.py

@@ -7,19 +7,20 @@
 
 from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.get.artifacts import get_artifacts
+from cg_lims.EPPs.udf.calculate.constants import FlowCellTypes, FlowCellSize, FlowCellLaneVolumes10B
 
 LOG = logging.getLogger(__name__)
 
 DENATURATION_VOLUMES = {
-    "10B": {
-        "Volume of Pool to Denature (ul)": 40,
-        "PhiX Volume (ul)": 1,
-        "NaOH Volume (ul)": 10,
-        "Pre-load Buffer Volume (ul)": 150,
+    FlowCellTypes.FLOW_CELL_10B: {
+        "Volume of Pool to Denature (ul)": FlowCellLaneVolumes10B.POOL_VOLUME,
+        "PhiX Volume (ul)": FlowCellLaneVolumes10B.PHIX_VOLUME,
+        "NaOH Volume (ul)": FlowCellLaneVolumes10B.NAOH_VOLUME,
+        "Pre-load Buffer Volume (ul)": FlowCellLaneVolumes10B.BUFFER_VOLUME,
     }
 }
 
-FLOW_CELL_SIZE = {"10B": 8}
+FLOW_CELL_SIZE = {FlowCellTypes.FLOW_CELL_10B: FlowCellSize.FLOW_CELL_10B}
 
 
 def get_flow_cell_type(process: Process) -> str:
@@ -37,7 +38,8 @@ def get_number_of_lanes(process: Process) -> int:
     flow_cell_type: str = get_flow_cell_type(process=process)
     if not number_of_lanes:
         LOG.info(
-            f"Missing number of lanes to load from previous step, using default value and assuming a fully loaded flow cell ({FLOW_CELL_SIZE[flow_cell_type]} lanes)."
+            f"Missing number of lanes to load from previous step, "
+            f"using default value and assuming a fully loaded flow cell ({FLOW_CELL_SIZE[flow_cell_type]} lanes)."
         )
         return FLOW_CELL_SIZE[flow_cell_type]
     return number_of_lanes

cg_lims/EPPs/udf/calculate/novaseq_x_volumes.py

@@ -7,12 +7,13 @@
 
 from cg_lims.exceptions import LimsError, MissingUDFsError, InvalidValueError
 from cg_lims.get.artifacts import get_artifacts
+from cg_lims.EPPs.udf.calculate.constants import FlowCellTypes, FlowCellSize, FlowCellLaneVolumes10B
 
 LOG = logging.getLogger(__name__)
 
 
-FLOW_CELL_LANE_VOLUMES = {"10B": 40}
-FLOW_CELL_SIZE = {"10B": 8}
+FLOW_CELL_LANE_VOLUMES = {FlowCellTypes.FLOW_CELL_10B: FlowCellLaneVolumes10B.POOL_VOLUME}
+FLOW_CELL_SIZE = {FlowCellTypes.FLOW_CELL_10B: FlowCellSize.FLOW_CELL_10B}
 
 
 def get_flow_cell_type(process: Process) -> str:

cg_lims/EPPs/udf/set/base.py

@@ -4,7 +4,6 @@
 from cg_lims.EPPs.udf.set.set_sample_date import set_sample_date
 from cg_lims.EPPs.udf.set.set_method import method_document
 from cg_lims.EPPs.udf.set.set_barcode import assign_barcode
-from cg_lims.EPPs.udf.set.novaseq_x_denaturation import novaseq_x_denaturation
 
 
 @click.group(invoke_without_command=True)
@@ -18,4 +17,3 @@ def set(context: click.Context):
 set.add_command(set_sample_date)
 set.add_command(method_document)
 set.add_command(assign_barcode)
-set.add_command(novaseq_x_denaturation)

cg_lims/enums.py

@@ -0,0 +1,16 @@
+from enum import Enum
+
+
+class StrEnum(str, Enum):
+    def __str__(self) -> str:
+        return str.__str__(self)
+
+
+class IntEnum(int, Enum):
+    def __int__(self) -> int:
+        return int.__int__(self)
+
+
+class FloatEnum(float, Enum):
+    def __int__(self) -> float:
+        return float.__int__(self)