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_case_from_string(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]]:
+        """Collect and format 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 = self.get_analysis_type(case_id=case_id)
+        target_bed = 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_config_case.py

@@ -13,6 +13,7 @@
 from cg.constants import EXIT_SUCCESS, Workflow
 from cg.constants.constants import FileFormat, MetaApis
 from cg.io.controller import ReadFile
+from cg.meta.workflow.raredisease import RarediseaseAnalysisAPI
 from cg.meta.workflow.nf_analysis import NfAnalysisAPI
 from cg.models.cg_config import CGConfig
 from cg.utils import Process
@@ -46,6 +47,7 @@ def test_config_case_without_options(
 )
 def test_config_with_missing_case(
     cli_runner: CliRunner,
+    mocker,
     caplog: LogCaptureFixture,
     case_id_does_not_exist: str,
     workflow: Workflow,
@@ -55,6 +57,11 @@ def test_config_with_missing_case(
     caplog.set_level(logging.ERROR)
     context: CGConfig = request.getfixturevalue(f"{workflow}_context")
 
+    # 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"
+
     # GIVEN a case not in the StatusDB database
     assert not context.status_db.get_case_by_internal_id(internal_id=case_id_does_not_exist)
 
@@ -120,6 +127,11 @@ def test_config_case_default_parameters(
     nexflow_config_file_path: Path = request.getfixturevalue(f"{workflow}_nexflow_config_file_path")
     sample_sheet_content_expected: str = request.getfixturevalue(f"{workflow}_sample_sheet_content")
 
+    # 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"
+
     # Mocking external Scout call
     mocker.patch.object(Process, "run_command", return_value=None)
 
@@ -211,6 +223,11 @@ def test_config_case_dry_run(
     # 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, "config-case", case_id, "-d"], obj=context)
 

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/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)