output panel as tsv file

cg/cli/workflow/nallo/base.py

@@ -45,4 +45,4 @@ def panel(context: CGConfig, case_id: str, dry_run: bool) -> None:
     if dry_run:
         echo_lines(lines=bed_lines)
         return
-    analysis_api.write_panel(case_id=case_id, content=bed_lines)
+    analysis_api.write_panel_as_tsv(case_id=case_id, content=bed_lines)

cg/constants/scout.py

@@ -14,6 +14,7 @@ class GenomeBuild(StrEnum):
 class ScoutExportFileName(StrEnum):
     MANAGED_VARIANTS: str = f"managed_variants{FileExtensions.VCF}"
     PANELS: str = f"gene_panels{FileExtensions.BED}"
+    PANELS_TSV: str = f"gene_panels{FileExtensions.TSV}"
 
 
 class UploadTrack(StrEnum):

cg/meta/workflow/analysis.py

@@ -705,6 +705,17 @@ def _write_panel(out_dir: Path, content: list[str]) -> None:
             file_path=Path(out_dir, ScoutExportFileName.PANELS),
         )
 
+    @staticmethod
+    def _write_panel_as_tsv(out_dir: Path, content: list[str]) -> None:
+        """Write the gene panel to case dir while omitted the commented BED lines."""
+        filtered_content = [line for line in content if not line.startswith("##")]
+        out_dir.mkdir(parents=True, exist_ok=True)
+        WriteFile.write_file_from_content(
+            content="\n".join(filtered_content),
+            file_format=FileFormat.TXT,
+            file_path=Path(out_dir, ScoutExportFileName.PANELS_TSV),
+        )
+
     def _get_gene_panel(self, case_id: str, genome_build: str, dry_run: bool = False) -> list[str]:
         """Create and return the aggregated gene panel file."""
         case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
@@ -725,6 +736,10 @@ def write_panel(self, case_id: str, content: list[str]) -> None:
         """Write the gene panel to case dir."""
         self._write_panel(out_dir=Path(self.root, case_id), content=content)
 
+    def write_panel_as_tsv(self, case_id: str, content: list[str]) -> None:
+        """Write the gene panel to case dir."""
+        self._write_panel_as_tsv(out_dir=Path(self.root, case_id), content=content)
+
     @staticmethod
     def get_aggregated_panels(customer_id: str, default_panels: set[str]) -> list[str]:
         """Check if customer is collaborator for gene panel master list