add Sentieon arg

BALSAMIC/commands/config/case.py

@@ -33,6 +33,7 @@
     OPTION_PANEL_BED,
     OPTION_PON_CNN,
     OPTION_QUALITY_TRIM,
+    OPTION_SENTIEON_INSTALL_DIR,
     OPTION_SWEGEN_SNV,
     OPTION_SWEGEN_SV,
     OPTION_TUMOR_SAMPLE_NAME,
@@ -84,6 +85,7 @@
 @OPTION_PANEL_BED
 @OPTION_PON_CNN
 @OPTION_QUALITY_TRIM
+@OPTION_SENTIEON_INSTALL_DIR
 @OPTION_SWEGEN_SNV
 @OPTION_SWEGEN_SV
 @OPTION_TUMOR_SAMPLE_NAME
@@ -117,6 +119,7 @@ def case_config(
     panel_bed: Path,
     pon_cnn: Path,
     quality_trim: bool,
+    sentieon_install_dir: Path,
     swegen_snv: Path,
     swegen_sv: Path,
     tumor_sample_name: str,
@@ -188,6 +191,7 @@ def case_config(
         directory.mkdir(exist_ok=True)
 
     config_collection_dict = ConfigModel(
+        sentieon_install_dir=sentieon_install_dir.as_posix(),
         QC={
             "quality_trim": quality_trim,
             "adapter_trim": adapter_trim,

BALSAMIC/commands/options.py

@@ -370,6 +370,13 @@
     help="Sample configuration file",
 )
 
+OPTION_SENTIEON_INSTALL_DIR = click.option(
+    "--sentieon-install-dir",
+    type=click.Path(exists=True, resolve_path=True),
+    required=False,
+    help="Path to Sentieon install directory",
+)
+
 OPTION_SHOW_ONLY_MISSING_FILES = click.option(
     "-m",
     "--show-only-missing",

BALSAMIC/models/config.py

@@ -220,6 +220,7 @@ class ConfigModel(BaseModel):
     background_variants: Optional[str] = None
     analysis: AnalysisModel
     custom_filters: CustomFilters | None = None
+    sentieon_install_dir: Annotated[Optional[str], AfterValidator(is_dir)]
 
     @field_validator("reference")
     def abspath_as_str(cls, reference: Dict[str, Path]):

BALSAMIC/workflows/balsamic.smk

@@ -148,6 +148,50 @@ params = BalsamicWorkflowConfig.model_validate(WORKFLOW_PARAMS)
 if config_model.custom_filters and config_model.custom_filters.umi_min_reads:
     params.umiconsensuscall.filter_minreads = config_model.custom_filters.umi_min_reads
 
+# Set Sentieon license
+try:
+    config["SENTIEON_LICENSE"] = os.environ["SENTIEON_LICENSE"]
+except KeyError as error:
+    LOG.error(
+        "Set environment variable SENTIEON_LICENSE to a valid Sentieon license"
+    )
+    raise BalsamicError
+
+# Set Sentieon binary from Sentieon path argument
+sentieon_install_dir: str = config_model.sentieon_install_dir
+if sentieon_install_dir:
+    config["SENTIEON_INSTALL_DIR"] = Path(sentieon_install_dir).as_posix()
+    config["SENTIEON_EXEC"] = Path(sentieon_install_dir, "bin", "sentieon").as_posix()
+else:
+    # Find and set Sentieon binary and license server from env variables
+    try:
+        config["SENTIEON_INSTALL_DIR"] = os.environ["SENTIEON_INSTALL_DIR"]
+
+        if os.getenv("SENTIEON_EXEC") is not None:
+            config["SENTIEON_EXEC"] = os.environ["SENTIEON_EXEC"]
+        else:
+            config["SENTIEON_EXEC"] = Path(
+                os.environ["SENTIEON_INSTALL_DIR"], "bin", "sentieon"
+            ).as_posix()
+
+    except KeyError as error:
+        LOG.error(
+            "Set environment variables SENTIEON_INSTALL_DIR and optionally SENTIEON_EXEC"
+        )
+        raise BalsamicError
+
+config["SENTIEON_TNSCOPE"] = SENTIEON_TNSCOPE_DIR.as_posix()
+config["SENTIEON_DNASCOPE"] = SENTIEON_DNASCOPE_DIR.as_posix()
+
+
+if not Path(config["SENTIEON_EXEC"]).exists():
+    LOG.error(
+        "Sentieon executable not found {}".format(
+            Path(config["SENTIEON_EXEC"]).as_posix()
+        )
+    )
+    raise BalsamicError
+
 # vcfanno annotations
 research_annotations.append(
     {
@@ -293,35 +337,6 @@ if config["analysis"]["sequencing_type"] != "wgs":
 if len(cluster_config.keys()) == 0:
     cluster_config = config
 
-# Find and set Sentieon binary and license server from env variables
-try:
-    config["SENTIEON_LICENSE"] = os.environ["SENTIEON_LICENSE"]
-    config["SENTIEON_INSTALL_DIR"] = os.environ["SENTIEON_INSTALL_DIR"]
-
-    if os.getenv("SENTIEON_EXEC") is not None:
-        config["SENTIEON_EXEC"] = os.environ["SENTIEON_EXEC"]
-    else:
-        config["SENTIEON_EXEC"] = Path(
-            os.environ["SENTIEON_INSTALL_DIR"], "bin", "sentieon"
-        ).as_posix()
-
-    config["SENTIEON_TNSCOPE"] = SENTIEON_TNSCOPE_DIR.as_posix()
-    config["SENTIEON_DNASCOPE"] = SENTIEON_DNASCOPE_DIR.as_posix()
-
-except KeyError as error:
-    LOG.error(
-        "Set environment variables SENTIEON_LICENSE, SENTIEON_INSTALL_DIR, SENTIEON_EXEC "
-        "to run SENTIEON variant callers"
-    )
-    raise BalsamicError
-
-if not Path(config["SENTIEON_EXEC"]).exists():
-    LOG.error(
-        "Sentieon executable not found {}".format(
-            Path(config["SENTIEON_EXEC"]).as_posix()
-        )
-    )
-    raise BalsamicError
 
 if "hg38" in config["reference"]["reference_genome"]:
     config["reference"]["genome_version"] = "hg38"