replace str with Path objects and rename method

Author: peterpru

cg/meta/workflow/nallo.py

@@ -46,14 +46,14 @@ def sample_sheet_headers(self) -> list[str]:
 
     def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[list[str]]:
         """Collect and format information required to build a sample sheet for a single sample."""
-        bam_unmapped_read_paths = self.get_unmapped_bam_read_paths(sample=case_sample.sample)
+        read_file_paths = self.get_bam_read_file_paths(sample=case_sample.sample)
         sample_sheet_entries = []
 
-        for bam_path in bam_unmapped_read_paths:
+        for bam_path in read_file_paths:
             sample_sheet_entry = NalloSampleSheetEntry(
                 project=case_sample.case.internal_id,
                 sample=case_sample.sample.internal_id,
-                bam_unmapped_read_path=Path(bam_path),
+                read_file=Path(bam_path),
                 family_id=case_sample.case.internal_id,
                 paternal_id=case_sample.get_paternal_sample_id or "0",
                 maternal_id=case_sample.get_maternal_sample_id or "0",

cg/meta/workflow/nf_analysis.py

@@ -253,10 +253,10 @@ def get_paired_read_paths(self, sample=Sample) -> tuple[list[str], list[str]]:
         )
         return fastq_forward_read_paths, fastq_reverse_read_paths
 
-    def get_unmapped_bam_read_paths(self, sample=Sample) -> list[str]:
+    def get_bam_read_file_paths(self, sample=Sample) -> list[Path]:
         """Gather BAM file path for a sample based on the BAM tag."""
         return [
-            hk_file.full_path
+            Path(hk_file.full_path)
             for hk_file in self.housekeeper_api.files(
                 bundle=sample.internal_id, tags={AlignmentFileTag.BAM}
             )

cg/models/nallo/nallo.py

@@ -12,7 +12,7 @@ class NalloSampleSheetEntry(BaseModel):
 
     project: str
     sample: str
-    bam_unmapped_read_path: Path
+    read_file: Path
     family_id: str
     paternal_id: str
     maternal_id: str
@@ -26,7 +26,7 @@ def reformat_sample_content(self) -> list[list[str]]:
             [
                 self.project,
                 self.sample,
-                self.bam_unmapped_read_path,
+                self.read_file,
                 self.family_id,
                 self.paternal_id,
                 self.maternal_id,
@@ -35,9 +35,9 @@ def reformat_sample_content(self) -> list[list[str]]:
             ]
         ]
 
-    @field_validator("bam_unmapped_read_path")
+    @field_validator("read_file")
     @classmethod
-    def unmapped_bam_file_exists(cls, bam_path: Path) -> Path:
+    def read_file_exists(cls, bam_path: Path) -> Path:
         """Verify that bam files exist."""
         if not bam_path.is_file():
             raise NfSampleSheetError(f"Bam file does not exist: {str(bam_path)}")