Make regex patterns raw strings to avoid deprecation warnings

Author: ssjunnebo

dataflow_transfer/run_classes/element_runs.py

@@ -22,6 +22,6 @@ class AVITIRun(ElementRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{8}_AV\d{6}_(A|BP)\d{10}$"  # 20251007_AV242106_A2507535225
+            r"^\d{8}_AV\d{6}_(A|BP)\d{10}$"  # 20251007_AV242106_A2507535225
         )
         super().__init__(run_dir, configuration)

dataflow_transfer/run_classes/illumina_runs.py

@@ -20,7 +20,7 @@ class NovaSeqXPlusRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{8}_[A-Z0-9]+_\d{4}_[A-Z0-9]+$"  # 20251010_LH00202_0284_B22CVHTLT1
+            r"^\d{8}_[A-Z0-9]+_\d{4}_[A-Z0-9]+$"  # 20251010_LH00202_0284_B22CVHTLT1
         )
         super().__init__(run_dir, configuration)
 
@@ -33,7 +33,7 @@ class NextSeqRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{6}_[A-Z0-9]+_\d{3}_[A-Z0-9]+$"  # 251015_VH00203_572_AAHFHCCM5
+            r"^\d{6}_[A-Z0-9]+_\d{3}_[A-Z0-9]+$"  # 251015_VH00203_572_AAHFHCCM5
         )
         super().__init__(run_dir, configuration)
 
@@ -46,7 +46,7 @@ class MiSeqRun(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # 251015_M01548_0646_000000000-M6D7K
+            r"^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # 251015_M01548_0646_000000000-M6D7K
         )
         super().__init__(run_dir, configuration)
 
@@ -59,6 +59,6 @@ class MiSeqi100Run(IlluminaRun):
 
     def __init__(self, run_dir, configuration):
         self.run_id_format = (
-            "^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # TODO: Need to update this
+            r"^\d{6}_[A-Z0-9]+_\d{4}_[A-Z0-9\-]+$"  # TODO: Need to update this
         )
         super().__init__(run_dir, configuration)

dataflow_transfer/run_classes/ont_runs.py

@@ -19,7 +19,7 @@ class PromethIONRun(ONTRun):
     run_type = "PromethION"
 
     def __init__(self, run_dir, configuration):
-        self.run_id_format = "^\d{8}_\d{4}_[A-Z0-9]{2}_P[A-Z0-9]+_[a-f0-9]{8}$"  # 20251015_1051_3B_PBG60686_0af3a2e0
+        self.run_id_format = r"^\d{8}_\d{4}_[A-Z0-9]{2}_P[A-Z0-9]+_[a-f0-9]{8}$"  # 20251015_1051_3B_PBG60686_0af3a2e0
         super().__init__(run_dir, configuration)
 
 
@@ -30,5 +30,5 @@ class MinIONRun(ONTRun):
     run_type = "MinION"
 
     def __init__(self, run_dir, configuration):
-        self.run_id_format = "^\d{8}_\d{4}_MN[A-Z0-9]+_[A-Z0-9]+_[a-f0-9]{8}$"  # 20240229_1404_MN19414_ASH657_7a74bf8f
+        self.run_id_format = r"^\d{8}_\d{4}_MN[A-Z0-9]+_[A-Z0-9]+_[a-f0-9]{8}$"  # 20240229_1404_MN19414_ASH657_7a74bf8f
         super().__init__(run_dir, configuration)