RNAFUSION: use config files instead of nf-core hasta profile (#3868)

### Changed

- Unified the config and param file generation for rnafusion with the other nf workflows, using Clinical-Genomics/servers#1467

cg/meta/workflow/rnafusion.py

@@ -5,7 +5,7 @@
 
 from cg.constants import Workflow
 from cg.constants.constants import GenomeVersion, Strandedness
-from cg.constants.nf_analysis import MULTIQC_NEXFLOW_CONFIG, RNAFUSION_METRIC_CONDITIONS
+from cg.constants.nf_analysis import RNAFUSION_METRIC_CONDITIONS
 from cg.constants.scout import RNAFUSION_CASE_TAGS
 from cg.exc import MissingMetrics
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
@@ -34,6 +34,9 @@ def __init__(
         self.profile: str = config.rnafusion.profile
         self.conda_env: str = config.rnafusion.conda_env
         self.conda_binary: str = config.rnafusion.conda_binary
+        self.config_platform: str = config.rnafusion.config_platform
+        self.config_params: str = config.rnafusion.config_params
+        self.config_resources: str = config.rnafusion.config_resources
         self.tower_binary_path: str = config.tower_binary_path
         self.tower_workflow: str = config.rnafusion.tower_workflow
         self.account: str = config.rnafusion.slurm.account
@@ -61,10 +64,6 @@ def get_genome_build(self, case_id: str) -> GenomeVersion:
         """Return reference genome for a case. Currently fixed for hg38."""
         return GenomeVersion.HG38
 
-    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 Rnafusion bundle filenames path."""
@@ -88,11 +87,9 @@ def get_workflow_parameters(
     ) -> RnafusionParameters:
         """Get Rnafusion parameters."""
         return RnafusionParameters(
-            cluster_options=f"--qos={self.get_slurm_qos_for_case(case_id=case_id)}",
             genomes_base=genomes_base or self.get_references_path(),
             input=self.get_sample_sheet_path(case_id=case_id),
             outdir=self.get_case_path(case_id=case_id),
-            priority=self.account,
         )
 
     def get_references_path(self, genomes_base: Path | None = None) -> Path:

cg/models/cg_config.py

@@ -258,6 +258,9 @@ class RnafusionConfig(CommonAppConfig):
     compute_env: str
     conda_binary: str | None = None
     conda_env: str
+    config_platform: str
+    config_params: str
+    config_resources: str
     launch_directory: str
     profile: str
     references: str

cg/models/rnafusion/rnafusion.py

@@ -1,7 +1,5 @@
 from pathlib import Path
 
-from pydantic import Field
-
 from cg.constants.constants import Strandedness
 from cg.models.nf_analysis import NextflowSampleSheetEntry, WorkflowParameters
 from cg.models.qc_metrics import QCMetrics
@@ -29,15 +27,6 @@ class RnafusionParameters(WorkflowParameters):
     """Rnafusion parameters."""
 
     genomes_base: Path
-    all: bool = False
-    arriba: bool = True
-    cram: str = "arriba,starfusion"
-    fastp_trim: bool = True
-    fusioncatcher: bool = True
-    starfusion: bool = True
-    trim_tail: int = 50
-    clusterOptions: str = Field(str, alias="cluster_options")
-    priority: str
 
 
 class RnafusionSampleSheetEntry(NextflowSampleSheetEntry):

tests/conftest.py

@@ -12,8 +12,8 @@
 from typing import Any, Generator
 
 import pytest
-from pytest_mock import MockFixture
 from housekeeper.store.models import File, Version
+from pytest_mock import MockFixture
 from requests import Response
 
 from cg.apps.crunchy import CrunchyAPI
@@ -68,9 +68,7 @@
     TaxprofilerSampleSheetEntry,
 )
 from cg.models.tomte.tomte import TomteParameters, TomteSampleSheetHeaders
-from cg.services.deliver_files.rsync.service import (
-    DeliveryRsyncService,
-)
+from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.illumina.backup.encrypt_service import IlluminaRunEncryptionService
 from cg.services.illumina.data_transfer.data_transfer_service import (
     IlluminaDataTransferService,
@@ -2139,6 +2137,9 @@ def context_config(
             "compute_env": "nf_tower_compute_env",
             "conda_binary": conda_binary.as_posix(),
             "conda_env": "S_RNAFUSION",
+            "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(),
             "profile": "myprofile",
@@ -2696,7 +2697,6 @@ def raredisease_context(
     mocker.patch.object(RarediseaseAnalysisAPI, "get_target_bed_from_lims")
     RarediseaseAnalysisAPI.get_target_bed_from_lims.return_value = "some_target_bed_file"
 
-    samples = [sample_enough_reads, another_sample_enough_reads]
     return cg_context