Add support to run raredisease with WES

cg/constants/constants.py

@@ -57,7 +57,7 @@ class ControlOptions(StrEnum):
     EMPTY: str = ""
 
 
-DEFAULT_CAPTURE_KIT = "twistexomerefseq_9.1_hg19_design.bed"
+DEFAULT_CAPTURE_KIT = "twistexomerefseq_10.2_hg19_design.bed"
 
 
 class CustomerId(StrEnum):

cg/meta/workflow/nf_analysis.py

@@ -263,15 +263,19 @@ def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[l
         """Collect and format information required to build a sample sheet for a single sample."""
         raise NotImplementedError
 
-    def get_sample_sheet_content(self, case_id: str) -> list[list[Any]]:
-        """Collect and format information required to build a sample sheet for a case.
-        This contains information for all samples linked to the case."""
+    def get_validated_case(self, case_id: str) -> Case:
         case: Case = self.status_db.get_case_by_internal_id(internal_id=case_id)
         if len(case.links) == 0:
             raise CgError(f"No samples linked to {case_id}")
         if nlinks := len(case.links) > 1 and not self.is_multiple_samples_allowed:
             raise CgError(f"Only one sample per case is allowed. {nlinks} found")
+        return case
+
+    def get_sample_sheet_content(self, case_id: str) -> list[list[Any]]:
+        """Return formatted information required to build a sample sheet for a case.
+        This contains information for all samples linked to the case."""
         sample_sheet_content = []
+        case = self.get_case_from_string(case_id)
         LOG.info(f"Samples linked to case {case_id}: {len(case.links)}")
         LOG.debug("Getting sample sheet information")
         for link in case.links:

cg/meta/workflow/raredisease.py

@@ -4,15 +4,15 @@
 from pathlib import Path
 from typing import Any
 
-from cg.constants import Workflow
-from cg.constants.constants import GenomeVersion
+from cg.constants import DEFAULT_CAPTURE_KIT, Workflow
+from cg.constants.constants import AnalysisType, GenomeVersion
 from cg.constants.gene_panel import GenePanelGenomeBuild
 from cg.constants.nf_analysis import RAREDISEASE_METRIC_CONDITIONS
 from cg.constants.subject import PlinkPhenotypeStatus, PlinkSex
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
-from cg.models.nf_analysis import WorkflowParameters
 from cg.models.raredisease.raredisease import (
+    RarediseaseParameters,
     RarediseaseSampleSheetEntry,
     RarediseaseSampleSheetHeaders,
 )
@@ -74,11 +74,39 @@ def get_sample_sheet_content_per_sample(self, case_sample: CaseSample) -> list[l
         )
         return sample_sheet_entry.reformat_sample_content
 
-    def get_workflow_parameters(self, case_id: str) -> WorkflowParameters:
+    def get_analysis_type(self, case_id: str):
+        case = self.get_case_from_string(case_id)
+        sample_analysis_type = ""
+        for link in case.links:
+            case_sample = link
+            sample_analysis_type_tmp = (
+                case_sample.sample.application_version.application.analysis_type
+            )
+            if sample_analysis_type_tmp != sample_analysis_type and sample_analysis_type != "":
+                raise ValueError(
+                    f"{sample_analysis_type_tmp} has not the same analysis type as other samples in the case"
+                )
+            sample_analysis_type = sample_analysis_type_tmp
+        return sample_analysis_type
+
+    def set_target_bed(self, case_id: str, analysis_type: str) -> str:
+        if analysis_type == AnalysisType.WHOLE_GENOME_SEQUENCING:
+            target_bed = self.get_target_bed_from_lims(case_id=case_id) or DEFAULT_CAPTURE_KIT
+        else:
+            target_bed = self.get_target_bed_from_lims(case_id=case_id)
+            if not target_bed:
+                raise ValueError("No capture kit was found in LIMS")
+        return target_bed
+
+    def get_workflow_parameters(self, case_id: str) -> RarediseaseParameters:
         """Return parameters."""
-        return WorkflowParameters(
+        analysis_type: AnalysisType = self.get_analysis_type(case_id=case_id)
+        target_bed: str = self.set_target_bed(case_id=case_id, analysis_type=analysis_type)
+        return RarediseaseParameters(
             input=self.get_sample_sheet_path(case_id=case_id),
             outdir=self.get_case_path(case_id=case_id),
+            analysis_type=analysis_type,
+            target_bed=target_bed,
         )
 
     @staticmethod

cg/models/raredisease/raredisease.py

@@ -2,7 +2,7 @@
 
 from pydantic import BaseModel
 
-from cg.models.nf_analysis import NextflowSampleSheetEntry
+from cg.models.nf_analysis import NextflowSampleSheetEntry, WorkflowParameters
 
 
 class RarediseaseQCMetrics(BaseModel):
@@ -62,3 +62,10 @@ class RarediseaseSampleSheetHeaders(StrEnum):
     @classmethod
     def list(cls) -> list[str]:
         return list(map(lambda header: header.value, cls))
+
+
+class RarediseaseParameters(WorkflowParameters):
+    """Model for Raredisease parameters."""
+
+    target_bed: str
+    analysis_type: str

tests/cli/workflow/nf_analysis/test_cli_start.py

@@ -8,6 +8,7 @@
 from cg.apps.lims import LimsAPI
 from cg.cli.workflow.base import workflow as workflow_cli
 from cg.constants import EXIT_SUCCESS, Workflow
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 from tests.cli.workflow.conftest import mock_analysis_flow_cell
@@ -40,6 +41,11 @@ def test_start(
     # GIVEN that the sample source in LIMS is set
     mocker.patch.object(LimsAPI, "get_source", return_value="blood")
 
+    # In the RAREDISEASE case, we need to mock lims fetching of the target bed file
+    if workflow == Workflow.RAREDISEASE:
+        mocker.patch.object(RarediseaseAnalysisAPI, "get_target_bed_from_lims")
+        RarediseaseAnalysisAPI.get_target_bed_from_lims.return_value = "some_target_bed_file"
+
     # WHEN invoking the command with dry-run specified
     result = cli_runner.invoke(workflow_cli, [workflow, "start", case_id, "--dry-run"], obj=context)
 
@@ -82,6 +88,11 @@ def test_start_available(
     # GIVEN that the sample source in LIMS is set
     mocker.patch.object(LimsAPI, "get_source", return_value="blood")
 
+    # In the RAREDISEASE case, we need to mock lims fetching of the target bed file
+    if workflow == Workflow.RAREDISEASE:
+        mocker.patch.object(RarediseaseAnalysisAPI, "get_target_bed_from_lims")
+        RarediseaseAnalysisAPI.get_target_bed_from_lims.return_value = "some_target_bed_file"
+
     # WHEN invoking the command with dry-run specified
     result = cli_runner.invoke(
         workflow_cli, [workflow, "start-available", "--dry-run"], obj=context

tests/conftest.py

@@ -2445,6 +2445,77 @@ def raredisease_deliverables_file_path(raredisease_dir, raredisease_case_id) ->
     ).with_suffix(FileExtensions.YAML)
 
 
+@pytest.fixture(scope="function")
+def raredisease_context(
+    cg_context: CGConfig,
+    helpers: StoreHelpers,
+    nf_analysis_housekeeper: HousekeeperAPI,
+    trailblazer_api: MockTB,
+    raredisease_case_id: str,
+    sample_id: str,
+    no_sample_case_id: str,
+    total_sequenced_reads_pass: int,
+    apptag_rna: str,
+    case_id_not_enough_reads: str,
+    sample_id_not_enough_reads: str,
+    total_sequenced_reads_not_pass: int,
+    mocker,
+) -> CGConfig:
+    """context to use in cli"""
+    cg_context.housekeeper_api_ = nf_analysis_housekeeper
+    cg_context.trailblazer_api_ = trailblazer_api
+    cg_context.meta_apis["analysis_api"] = RarediseaseAnalysisAPI(config=cg_context)
+    status_db: Store = cg_context.status_db
+
+    # Create ERROR case with NO SAMPLES
+    helpers.add_case(status_db, internal_id=no_sample_case_id, name=no_sample_case_id)
+
+    # Create textbook case with enough reads
+    case_enough_reads: Case = helpers.add_case(
+        store=status_db,
+        internal_id=raredisease_case_id,
+        name=raredisease_case_id,
+        data_analysis=Workflow.RAREDISEASE,
+    )
+
+    sample_raredisease_case_enough_reads: Sample = helpers.add_sample(
+        status_db,
+        internal_id=sample_id,
+        last_sequenced_at=datetime.now(),
+        reads=total_sequenced_reads_pass,
+        application_tag=apptag_rna,
+    )
+
+    helpers.add_relationship(
+        status_db,
+        case=case_enough_reads,
+        sample=sample_raredisease_case_enough_reads,
+    )
+
+    # Create case without enough reads
+    case_not_enough_reads: Case = helpers.add_case(
+        store=status_db,
+        internal_id=case_id_not_enough_reads,
+        name=case_id_not_enough_reads,
+        data_analysis=Workflow.RAREDISEASE,
+    )
+
+    sample_not_enough_reads: Sample = helpers.add_sample(
+        status_db,
+        internal_id=sample_id_not_enough_reads,
+        last_sequenced_at=datetime.now(),
+        reads=total_sequenced_reads_not_pass,
+        application_tag=apptag_rna,
+    )
+
+    helpers.add_relationship(status_db, case=case_not_enough_reads, sample=sample_not_enough_reads)
+
+    mocker.patch.object(RarediseaseAnalysisAPI, "get_target_bed_from_lims")
+    RarediseaseAnalysisAPI.get_target_bed_from_lims.return_value = "some_target_bed_file"
+
+    return cg_context
+
+
 @pytest.fixture(scope="function")
 def deliverable_data(raredisease_dir: Path, raredisease_case_id: str, sample_id: str) -> dict:
     return {
@@ -3882,73 +3953,6 @@ def downsample_api(
     )
 
 
-@pytest.fixture(scope="function")
-def raredisease_context(
-    cg_context: CGConfig,
-    helpers: StoreHelpers,
-    nf_analysis_housekeeper: HousekeeperAPI,
-    trailblazer_api: MockTB,
-    sample_id: str,
-    no_sample_case_id: str,
-    total_sequenced_reads_pass: int,
-    apptag_rna: str,
-    raredisease_case_id: str,
-    case_id_not_enough_reads: str,
-    sample_id_not_enough_reads: str,
-    total_sequenced_reads_not_pass: int,
-) -> CGConfig:
-    """Raredisease context to use in CLI."""
-    cg_context.housekeeper_api_ = nf_analysis_housekeeper
-    cg_context.trailblazer_api_ = trailblazer_api
-    cg_context.meta_apis["analysis_api"] = RarediseaseAnalysisAPI(config=cg_context)
-    status_db: Store = cg_context.status_db
-
-    # Create ERROR case with NO SAMPLES
-    helpers.add_case(status_db, internal_id=no_sample_case_id, name=no_sample_case_id)
-
-    # Create a textbook case with enough reads
-    case_enough_reads: Case = helpers.add_case(
-        store=status_db,
-        internal_id=raredisease_case_id,
-        name=raredisease_case_id,
-        data_analysis=Workflow.RAREDISEASE,
-    )
-
-    sample_raredisease_case_enough_reads: Sample = helpers.add_sample(
-        status_db,
-        application_tag=apptag_rna,
-        internal_id=sample_id,
-        reads=total_sequenced_reads_pass,
-        last_sequenced_at=datetime.now(),
-    )
-
-    helpers.add_relationship(
-        status_db,
-        case=case_enough_reads,
-        sample=sample_raredisease_case_enough_reads,
-    )
-
-    # Create a case without enough reads
-    case_not_enough_reads: Case = helpers.add_case(
-        store=status_db,
-        internal_id=case_id_not_enough_reads,
-        name=case_id_not_enough_reads,
-        data_analysis=Workflow.RAREDISEASE,
-    )
-
-    sample_not_enough_reads: Sample = helpers.add_sample(
-        status_db,
-        application_tag=apptag_rna,
-        internal_id=sample_id_not_enough_reads,
-        reads=total_sequenced_reads_not_pass,
-        last_sequenced_at=datetime.now(),
-    )
-
-    helpers.add_relationship(status_db, case=case_not_enough_reads, sample=sample_not_enough_reads)
-
-    return cg_context
-
-
 @pytest.fixture
 def fastq_file_meta_raw(flow_cell_name: str) -> dict:
     return {

tests/meta/workflow/test_raredisease.py

@@ -32,7 +32,7 @@ def test_get_sample_sheet_content(
     assert contains_pattern
 
 
-def test_write_params_file(raredisease_context: CGConfig, raredisease_case_id: str):
+def test_write_params_file(raredisease_context: CGConfig, raredisease_case_id: str, mocker):
     # GIVEN Raredisease analysis API and input (nextflow sample sheet path)/output (case directory) parameters
     analysis_api: RarediseaseAnalysisAPI = raredisease_context.meta_apis["analysis_api"]
 
@@ -42,6 +42,9 @@ def test_write_params_file(raredisease_context: CGConfig, raredisease_case_id: s
     # THEN care directory is created
     assert os.path.exists(analysis_api.get_case_path(case_id=raredisease_case_id))
 
+    mocker.patch.object(RarediseaseAnalysisAPI, "get_target_bed_from_lims")
+    RarediseaseAnalysisAPI.get_target_bed_from_lims.return_value = "some_target_bed_file"
+
     # WHEN writing parameters file
     analysis_api.write_params_file(case_id=raredisease_case_id)