Add GENS upload for TGA

cg/meta/upload/balsamic/balsamic.py

@@ -40,10 +40,8 @@ def upload(self, ctx: click.Context, case: Case, restart: bool) -> None:
 
         self.upload_files_to_customer_inbox(case)
 
-        if GensAPI.is_suitable_for_upload(case):
-            ctx.invoke(upload_to_gens, case_id=case.internal_id)
-        else:
-            LOG.info(f"Balsamic case {case.internal_id} is not compatible for Gens upload")
+        # Upload CNV and BAF profile to GENS
+        ctx.invoke(upload_to_gens, case_id=case.internal_id)
 
         # Scout specific upload
         if DataDelivery.SCOUT in case.data_delivery:

cg/meta/workflow/balsamic.py

@@ -399,8 +399,12 @@ def get_parsed_observation_file_paths(self, observations: list[str]) -> dict:
 
         return verified_observations
 
-    def get_verified_gens_file_paths(self, sex: Sex) -> dict[str, str] | None:
+    def get_verified_gens_file_paths(self, sex: Sex, panel_bed: str) -> dict[str, str] | None:
         """Return a list of file path arguments for Gens."""
+        if panel_bed:
+            return {
+                "gnomad_min_af5": self.gnomad_af5_path,
+            }
         return {
             "genome_interval": self.genome_interval_path,
             "gnomad_min_af5": self.gnomad_af5_path,
@@ -461,8 +465,10 @@ def get_verified_config_case_arguments(
         config_case.update(self.get_verified_samples(case_id=case_id))
         config_case.update(self.get_parsed_observation_file_paths(observations))
         (
-            config_case.update(self.get_verified_gens_file_paths(sex=verified_sex))
-            if not verified_panel_bed and genome_version == GenomeVersion.HG19
+            config_case.update(
+                self.get_verified_gens_file_paths(sex=verified_sex, panel_bed=verified_panel_bed)
+            )
+            if genome_version == GenomeVersion.HG19
             else None
         )