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
@@ -31,6 +30,10 @@ def __init__(
         self.nfcore_workflow_path: str = config.taxprofiler.workflow_path
         self.conda_env: str = config.taxprofiler.conda_env
         self.conda_binary: str = config.taxprofiler.conda_binary
+        self.conda_binary: str = config.taxprofiler.conda_binary
+        self.config_platform: str = config.taxprofiler.config_platform
+        self.config_params: str = config.taxprofiler.config_params
+        self.config_resources: str = config.taxprofiler.config_resources
         self.profile: str = config.taxprofiler.profile
         self.revision: str = config.taxprofiler.revision
         self.hostremoval_reference: Path = Path(config.taxprofiler.hostremoval_reference)
@@ -47,25 +50,21 @@ def sample_sheet_headers(self) -> list[str]:
         """Headers for sample sheet."""
         return TaxprofilerSampleSheetEntry.headers()
 
-    @property
-    def is_params_appended_to_nextflow_config(self) -> bool:
-        """Return True if parameters should be added into the nextflow config file instead of the params file."""
-        return False
-
     @property
     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."""
         return TAXPROFILER_BUNDLE_FILENAMES_PATH
 
+    @property
+    def is_params_appended_to_nextflow_config(self) -> bool:
+        """Return True if parameters should be added into the nextflow config file instead of the params file."""
+        return False
+
     def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[list[str]]:
         """Collect and format information required to build a sample sheet for a single sample."""
         sample_name: str = case_sample.sample.name
@@ -85,12 +84,10 @@ def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[l
     def get_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

@@ -276,6 +276,9 @@ class TaxprofilerConfig(CommonAppConfig):
     conda_binary: str | None = None
     conda_env: str
     compute_env: str
+    config_platform: str
+    config_params: str
+    config_resources: str
     databases: str
     hostremoval_reference: str
     workflow_path: str

cg/models/taxprofiler/taxprofiler.py

@@ -23,26 +23,7 @@ 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
 
 
 class TaxprofilerSampleSheetEntry(NextflowSampleSheetEntry):

tests/conftest.py

@@ -2160,6 +2160,9 @@ def context_config(
             "root": str(taxprofiler_dir),
             "conda_binary": conda_binary.as_posix(),
             "conda_env": "S_taxprofiler",
+            "config_platform": str(nf_analysis_platform_config_path),
+            "config_params": str(nf_analysis_pipeline_params_path),
+            "config_resources": str(nf_analysis_pipeline_resource_optimisation_path),
             "launch_directory": Path("path", "to", "launchdir").as_posix(),
             "workflow_path": Path("workflow", "path").as_posix(),
             "databases": Path("path", "to", "databases").as_posix(),