Merge branch 'master' into 2787-confirm-nanopore-transfer

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 54.9.0
+current_version = 54.10.0
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "54.9.0"
+__version__ = "54.10.0"

cg/constants/gene_panel.py

@@ -32,6 +32,7 @@ class GenePanelMasterList(StrEnum):
     NEURODEG: str = "NEURODEG"
     NMD: str = "NMD"
     OMIM_AUTO: str = "OMIM-AUTO"
+    OPTIC: str = "OPTIC"
     PANELAPP_GREEN: str = "PANELAPP-GREEN"
     PEDHEP: str = "PEDHEP"
     PID: str = "PID"

cg/models/downsample/downsample_data.py

@@ -41,8 +41,10 @@ def __init__(
     def downsampled_sample_name(
         self,
     ) -> str:
-        """Return a new sample name with the number of reads to which it is down sampled in millions appended."""
-        return f"{self.sample_id}_{self.number_of_reads}M"
+        """Return a new sample name with the number of reads to which it is down sampled in millions
+        appended. DS stands for downsampled. The number of reads is converted to a string and the
+        decimal point is replaced with a C."""
+        return f"{self.sample_id}DS{self.convert_number_of_reads_to_string}M"
 
     @property
     def downsampled_case_name(
@@ -51,6 +53,11 @@ def downsampled_case_name(
         """Return a case name with _downsampled appended."""
         return f"{self.case_name}_downsampled"
 
+    @property
+    def convert_number_of_reads_to_string(self) -> str:
+        """Convert the number of reads to a string."""
+        return str(self.number_of_reads).replace(".", "C")
+
     def get_sample_to_downsample(self) -> Sample:
         """
         Check if a sample exists in StatusDB.

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "54.9.0"
+version = "54.10.0"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/models/downsample/test_down_sample_meta_data.py

@@ -40,11 +40,10 @@ def test_downsample_meta_data_pass_checks(
         case_name=downsample_case_name,
         out_dir=tmp_path_factory.mktemp("tmp"),
     )
+    # WHEN the number of reads in millionts is converted to a string
+    number_of_reads: str = meta_data.convert_number_of_reads_to_string
 
     # THEN all necessary models to run the down sample command are created
-    assert (
-        meta_data.downsampled_sample.internal_id
-        == f"{sample.internal_id}_{number_of_reads_in_millions}M"
-    )
+    assert meta_data.downsampled_sample.internal_id == f"{sample.internal_id}DS{number_of_reads}M"
     assert meta_data.downsampled_sample.reads == number_of_reads_in_millions * 1_000_000
     assert meta_data.downsampled_case.name == f"{downsample_case_name}_downsampled"