Add parameters to the nextflow config

cg/meta/workflow/taxprofiler.py

@@ -5,7 +5,6 @@
 
 from cg.constants import Workflow
 from cg.constants.constants import GenomeVersion
-from cg.constants.nf_analysis import MULTIQC_NEXFLOW_CONFIG
 from cg.constants.sequencing import SequencingPlatform
 from cg.constants.symbols import EMPTY_STRING
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
@@ -29,12 +28,14 @@ def __init__(
         super().__init__(config=config, workflow=workflow)
         self.root_dir: str = config.taxprofiler.root
         self.workflow_bin_path: str = config.taxprofiler.workflow_bin_path
+        self.profile: str = config.taxprofiler.profile
         self.conda_env: str = config.taxprofiler.conda_env
         self.conda_binary: str = config.taxprofiler.conda_binary
-        self.profile: str = config.taxprofiler.profile
+        self.platform: str = config.taxprofiler.platform
+        self.params: str = config.taxprofiler.params
+        self.workflow_config_path: str = config.taxprofiler.config
+        self.resources: str = config.taxprofiler.resources
         self.revision: str = config.taxprofiler.revision
-        self.hostremoval_reference: Path = Path(config.taxprofiler.hostremoval_reference)
-        self.databases: Path = Path(config.taxprofiler.databases)
         self.tower_binary_path: str = config.tower_binary_path
         self.tower_workflow: str = config.taxprofiler.tower_workflow
         self.account: str = config.taxprofiler.slurm.account
@@ -52,10 +53,6 @@ def is_multiqc_pattern_search_exact(self) -> bool:
         """Only exact pattern search is allowed to collect metrics information from multiqc file."""
         return True
 
-    def get_nextflow_config_content(self, case_id: str) -> str:
-        """Return nextflow config content."""
-        return MULTIQC_NEXFLOW_CONFIG
-
     @staticmethod
     def get_bundle_filenames_path() -> Path:
         """Return Taxprofiler bundle filenames path."""
@@ -80,12 +77,8 @@ def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[l
     def get_built_workflow_parameters(self, case_id: str) -> TaxprofilerParameters:
         """Return Taxprofiler parameters."""
         return TaxprofilerParameters(
-            cluster_options=f"--qos={self.get_slurm_qos_for_case(case_id=case_id)}",
             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,
-            priority=self.account,
         )
 
     def get_multiqc_search_patterns(self, case_id: str) -> dict:

cg/models/cg_config.py

@@ -269,8 +269,10 @@ class TaxprofilerConfig(CommonAppConfig):
     conda_binary: str | None = None
     conda_env: str
     compute_env: str
-    databases: str
-    hostremoval_reference: str
+    platform: str
+    params: str
+    config: str
+    resources: str
     workflow_bin_path: str
     profile: str
     revision: str

cg/models/taxprofiler/taxprofiler.py

@@ -20,29 +20,7 @@ class TaxprofilerQCMetrics(BaseModel):
 
 
 class TaxprofilerParameters(WorkflowParameters):
-    """Model for Taxprofiler parameters."""
-
-    databases: Path
-    save_preprocessed_reads: bool = True
-    perform_shortread_qc: bool = True
-    perform_shortread_complexityfilter: bool = True
-    save_complexityfiltered_reads: bool = True
-    perform_shortread_hostremoval: bool = True
-    hostremoval_reference: Path
-    save_hostremoval_index: bool = True
-    save_hostremoval_mapped: bool = True
-    save_hostremoval_unmapped: bool = True
-    perform_runmerging: bool = True
-    run_kraken2: bool = True
-    kraken2_save_reads: bool = True
-    kraken2_save_readclassifications: bool = True
-    run_bracken: bool = True
-    run_centrifuge: bool = True
-    centrifuge_save_reads: bool = True
-    run_krona: bool = True
-    run_profile_standardisation: bool = True
-    clusterOptions: str = Field(alias="cluster_options")
-    priority: str
+    """Taxprofiler parameters."""
 
 
 class TaxprofilerSampleSheetEntry(NextflowSampleSheetEntry):

tests/conftest.py

@@ -2161,11 +2161,13 @@ def context_config(
             "root": str(taxprofiler_dir),
             "conda_binary": conda_binary.as_posix(),
             "conda_env": "S_taxprofiler",
+            "platform": str(nf_analysis_platform_config_path),
+            "params": str(nf_analysis_pipeline_params_path),
+            "config": str(nf_analysis_pipeline_config_path),
+            "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",