add exome flag to exome samples

cg/meta/workflow/balsamic.py

@@ -2,12 +2,13 @@
 
 import logging
 from pathlib import Path
+from typing import Optional
 
 from housekeeper.store.models import File, Version
 from pydantic.v1 import EmailStr, ValidationError
 
 from cg.constants import Workflow
-from cg.constants.constants import FileFormat, SampleType
+from cg.constants.constants import FileFormat, SampleType, AnalysisType
 from cg.constants.housekeeper_tags import BalsamicAnalysisTag
 from cg.constants.observations import ObservationsFileWildcards
 from cg.constants.priority import SlurmQos
@@ -278,6 +279,12 @@ def get_verified_sex(sample_data: dict) -> Sex:
             LOG.error(f"Unable to retrieve a valid sex from samples: {sample_data.keys()}")
             raise BalsamicStartError
 
+    def get_exome_argument_if_exome_sample(self, case_id: str) -> bool:
+        """Returns the exome argument if the application type in sample_data is wes."""
+        application_type: str = self.get_case_application_type(case_id)
+        if application_type == AnalysisType.WHOLE_EXOME_SEQUENCING:
+            return True
+
     def get_verified_samples(self, case_id: str) -> dict[str, str]:
         """Return a verified tumor and normal sample dictionary."""
         tumor_samples: list[Sample] = self.status_db.get_samples_by_type(
@@ -454,6 +461,10 @@ def get_verified_config_case_arguments(
         )
         verified_sex: Sex = sex or self.get_verified_sex(sample_data=sample_data)
 
+        verified_exome_argument: Optional[bool] = self.get_exome_argument_if_exome_sample(
+            case_id=case_id
+        )
+
         config_case: dict[str, str] = {
             "case_id": case_id,
             "analysis_workflow": self.workflow,
@@ -463,7 +474,9 @@ def get_verified_config_case_arguments(
             "pon_cnn": verified_pon,
             "swegen_snv": self.get_swegen_verified_path(Variants.SNV),
             "swegen_sv": self.get_swegen_verified_path(Variants.SV),
+            "exome": verified_exome_argument,
         }
+
         config_case.update(self.get_verified_samples(case_id=case_id))
         config_case.update(self.get_parsed_observation_file_paths(observations))
         (
@@ -580,12 +593,14 @@ def config_case(
                 "--gnomad-min-af5": arguments.get("gnomad_min_af5"),
                 "--normal-sample-name": arguments.get("normal_sample_name"),
                 "--panel-bed": arguments.get("panel_bed"),
+                "--exome": arguments.get("exome"),
                 "--pon-cnn": arguments.get("pon_cnn"),
                 "--swegen-snv": arguments.get("swegen_snv"),
                 "--swegen-sv": arguments.get("swegen_sv"),
                 "--tumor-sample-name": arguments.get("tumor_sample_name"),
                 "--umi-trim-length": arguments.get("umi_trim_length"),
-            }
+            },
+            exclude_true=True,
         )
         parameters = command + options
         self.process.run_command(parameters=parameters, dry_run=dry_run)

tests/meta/workflow/test_balsamic.py

@@ -4,6 +4,7 @@
 
 import pytest
 
+from cg.constants.constants import AnalysisType
 from cg.constants.observations import ObservationsFileWildcards
 from cg.constants.sequencing import Variants
 from cg.constants.subject import Sex