Remove the databases and hostremoval params

Author: sofstam

cg/meta/workflow/taxprofiler.py

@@ -38,8 +38,6 @@ def __init__(
         self.revision: str = config.taxprofiler.revision
         self.tower_binary_path: str = config.tower_binary_path
         self.tower_workflow: str = config.taxprofiler.tower_workflow
-        self.hostremoval_reference: Path = Path(config.taxprofiler.hostremoval_reference)
-        self.databases: Path = Path(config.taxprofiler.databases)
         self.account: str = config.taxprofiler.slurm.account
         self.email: str = config.taxprofiler.slurm.mail_user
         self.nextflow_binary_path: str = config.taxprofiler.binary_path
@@ -86,8 +84,6 @@ def get_built_workflow_parameters(self, case_id: str) -> TaxprofilerParameters:
         return TaxprofilerParameters(
             input=self.get_sample_sheet_path(case_id=case_id),
             outdir=self.get_case_path(case_id=case_id),
-            databases=self.databases,
-            hostremoval_reference=self.hostremoval_reference,
         )
 
     def get_multiqc_search_patterns(self, case_id: str) -> dict:

cg/models/cg_config.py

@@ -273,8 +273,6 @@ class TaxprofilerConfig(CommonAppConfig):
     params: str
     config: str
     resources: str
-    databases: str
-    hostremoval_reference: str
     workflow_bin_path: str
     profile: str
     revision: str

cg/models/taxprofiler/taxprofiler.py

@@ -20,10 +20,7 @@ class TaxprofilerQCMetrics(BaseModel):
 
 
 class TaxprofilerParameters(WorkflowParameters):
-    """Model for Taxprofiler parameters."""
-
-    databases: Path
-    hostremoval_reference: Path
+    """Taxprofiler parameters."""
 
 
 class TaxprofilerSampleSheetEntry(NextflowSampleSheetEntry):

tests/conftest.py

@@ -2167,9 +2167,7 @@ def context_config(
             "resources": str(nf_analysis_pipeline_resource_optimisation_path),
             "launch_directory": Path("path", "to", "launchdir").as_posix(),
             "workflow_bin_path": Path("workflow", "path").as_posix(),
-            "databases": Path("path", "to", "databases").as_posix(),
             "profile": "myprofile",
-            "hostremoval_reference": Path("path", "to", "hostremoval_reference").as_posix(),
             "revision": "2.2.0",
             "slurm": {
                 "account": "development",