Merge branch 'master' into include-hidden-analysis-trailblazer

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 64.5.24
+current_version = 64.5.25
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "64.5.24"
+__version__ = "64.5.25"

cg/apps/hermes/hermes_api.py

@@ -15,7 +15,10 @@ class HermesApi:
     """Class to communicate with hermes"""
 
     def __init__(self, config: dict):
-        self.process = Process(binary=config["hermes"]["binary_path"])
+        self.process = Process(
+            binary=config["hermes"]["binary_path"],
+        )
+        self.container_mount_volume = config["hermes"]["container_mount_volume"]
 
     def convert_deliverables(
         self,
@@ -27,6 +30,10 @@ def convert_deliverables(
         """Convert deliverables file in raw workflow format to CG format with Hermes."""
         LOG.info("Converting workflow deliverables to CG deliverables")
         convert_command = [
+            "run",
+            "--bind",
+            self.container_mount_volume,
+            "/home/proj/stage/singularity_containers/hermes_latest.sif",
             "convert",
             "deliverables",
             "--workflow",

cg/models/cg_config.py

@@ -144,6 +144,7 @@ class StatinaConfig(BaseModel):
 class CommonAppConfig(BaseModel):
     binary_path: str | None = None
     config_path: str | None = None
+    container_mount_volume: str | None = None
 
 
 class FluffyUploadConfig(BaseModel):

cg/utils/commands.py

@@ -16,7 +16,7 @@ class Process:
     """Class to handle communication with other programs via the shell.
 
     The other parts of the code should not need to have any knowledge about how the processes are
-    called, that will be handled in this module.Output form stdout and stdin will be handled here.
+    called; that will be handled in this module.Output form stdout and stdin will be handled here.
     """
 
     def __init__(

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "poetry.core.masonry.api"
 
 [tool.poetry]
 name = "cg"
-version = "64.5.24"
+version = "64.5.25"
 description = "Clinical Genomics command center"
 authors = ["Clinical Genomics <[email protected]>"]
 readme = "README.md"

tests/conftest.py

@@ -1220,7 +1220,12 @@ def hermes_process() -> ProcessMock:
 @pytest.fixture(name="hermes_api")
 def hermes_api(hermes_process: ProcessMock) -> HermesApi:
     """Return a Hermes API with a mocked process."""
-    hermes_config = {"hermes": {"binary_path": "/bin/true"}}
+    hermes_config = {
+        "hermes": {
+            "binary_path": "/bin/true",
+            "container_mount_volume": "a_str",
+        }
+    }
     hermes_api = HermesApi(config=hermes_config)
     hermes_api.process = hermes_process
     return hermes_api