Merge branch 'master' into ticket-tag-existing-data

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 67.0.3
+current_version = 67.0.9
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "67.0.3"
+__version__ = "67.0.9"

cg/cli/workflow/fluffy/base.py

@@ -13,6 +13,7 @@
 
 ARGUMENT_CASE_ID = click.argument("case_id", required=True)
 OPTION_EXTERNAL_REF = click.option("-e", "--external-ref", is_flag=True)
+OPTION_USE_BWA_MEM = click.option("-b", "--use-bwa-mem", is_flag=True)
 
 LOG = logging.getLogger(__name__)
 
@@ -51,15 +52,27 @@ def create_samplesheet(context: CGConfig, case_id: str, dry_run: bool):
 @DRY_RUN
 @click.option("-c", "--config", help="Path to fluffy config in .json format")
 @OPTION_EXTERNAL_REF
+@OPTION_USE_BWA_MEM
 @click.pass_obj
-def run(context: CGConfig, case_id: str, dry_run: bool, config: str, external_ref: bool = False):
+def run(
+    context: CGConfig,
+    case_id: str,
+    dry_run: bool,
+    config: str,
+    external_ref: bool,
+    use_bwa_mem: bool,
+):
     """
     Run Fluffy analysis
     """
     analysis_api: FluffyAnalysisAPI = context.meta_apis["analysis_api"]
     analysis_api.status_db.verify_case_exists(case_internal_id=case_id)
     analysis_api.run_fluffy(
-        case_id=case_id, workflow_config=config, dry_run=dry_run, external_ref=external_ref
+        case_id=case_id,
+        workflow_config=config,
+        dry_run=dry_run,
+        external_ref=external_ref,
+        use_bwa_mem=use_bwa_mem,
     )
     if dry_run:
         return
@@ -78,12 +91,14 @@ def run(context: CGConfig, case_id: str, dry_run: bool, config: str, external_re
 @DRY_RUN
 @click.option("-c", "--config", help="Path to fluffy config in .json format")
 @OPTION_EXTERNAL_REF
+@OPTION_USE_BWA_MEM
 @click.pass_context
 def start(
     context: click.Context,
     case_id: str,
     dry_run: bool,
-    external_ref: bool = False,
+    external_ref: bool,
+    use_bwa_mem: bool,
     config: str = None,
 ):
     """
@@ -96,7 +111,14 @@ def start(
     analysis_api.prepare_fastq_files(case_id=case_id, dry_run=dry_run)
     context.invoke(link, case_id=case_id, dry_run=dry_run)
     context.invoke(create_samplesheet, case_id=case_id, dry_run=dry_run)
-    context.invoke(run, case_id=case_id, config=config, dry_run=dry_run, external_ref=external_ref)
+    context.invoke(
+        run,
+        case_id=case_id,
+        config=config,
+        dry_run=dry_run,
+        external_ref=external_ref,
+        use_bwa_mem=use_bwa_mem,
+    )
 
 
 @fluffy.command("start-available")

cg/constants/scout.py

@@ -106,6 +106,7 @@ class ScoutUploadKey(StrEnum):
 
 RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict(
     alignment_file={AlignmentFileTag.CRAM},
+    d4_file={"d4"},
     vcf2cytosure={"vcf2cytosure"},
     mt_bam={"bam-mt"},
     eklipse_path={"eklipse-png"},

cg/meta/upload/scout/hk_tags.py

@@ -71,6 +71,7 @@ class SampleTags(BaseModel):
     bam_file: set[str] | None = None
     alignment_file: set[str] | None = None
     alignment_path: set[str] | None = None
+    d4_file: set[str] | None = None
     vcf2cytosure: set[str] | None = None
     eklipse_path: set[str] | None = None
     mt_bam: set[str] | None = None

cg/meta/upload/scout/raredisease_config_builder.py

@@ -6,11 +6,7 @@
 from cg.apps.lims import LimsAPI
 from cg.apps.madeline.api import MadelineAPI
 from cg.constants.constants import FileFormat
-from cg.constants.housekeeper_tags import (
-    HK_DELIVERY_REPORT_TAG,
-    AnalysisTag,
-    NFAnalysisTags,
-)
+from cg.constants.housekeeper_tags import HK_DELIVERY_REPORT_TAG, AnalysisTag, NFAnalysisTags
 from cg.constants.scout import (
     RANK_MODEL_THRESHOLD,
     RAREDISEASE_CASE_TAGS,
@@ -206,3 +202,6 @@ def include_sample_files(self, config_sample: ScoutRarediseaseIndividual) -> Non
         config_sample.mitodel_file = self.get_sample_file(
             hk_tags=self.sample_tags.mitodel_file, sample_id=sample_id
         )
+        config_sample.d4_file = self.get_sample_file(
+            hk_tags=self.sample_tags.d4_file, sample_id=sample_id
+        )

cg/meta/workflow/fluffy.py

@@ -227,7 +227,12 @@ def make_sample_sheet(self, case_id: str, dry_run: bool) -> None:
             fluffy_sample_sheet.write_sample_sheet(sample_sheet_out_path)
 
     def run_fluffy(
-        self, case_id: str, dry_run: bool, workflow_config: str, external_ref: bool = False
+        self,
+        case_id: str,
+        dry_run: bool,
+        workflow_config: str,
+        external_ref: bool,
+        use_bwa_mem: bool,
     ) -> None:
         """
         Call fluffy with the configured command-line arguments
@@ -239,10 +244,8 @@ def run_fluffy(
                 shutil.rmtree(output_path, ignore_errors=True)
         if not workflow_config:
             workflow_config = self.fluffy_config.as_posix()
-        if not external_ref:
-            batch_ref_flag = "--batch-ref"
-        else:
-            batch_ref_flag = ""
+        batch_ref_flag = "" if external_ref else "--batch-ref"
+        use_bwa_mem_flag = "--bwa-mem" if use_bwa_mem else ""
         command_args = [
             "--config",
             workflow_config,
@@ -254,6 +257,7 @@ def run_fluffy(
             self.get_output_path(case_id=case_id).as_posix(),
             "--analyse",
             batch_ref_flag,
+            use_bwa_mem_flag,
             "--slurm_params",
             self.get_slurm_param_qos(case_id=case_id),
         ]

cg/models/scout/scout_load_config.py

@@ -93,6 +93,7 @@ class ScoutRarediseaseIndividual(ScoutIndividual):
     vcf2cytosure: str | None = None
     mitodel_file: str | None = None
     reviewer: Reviewer = Reviewer()
+    d4_file: str | None = None
 
 
 class ScoutCancerIndividual(ScoutIndividual):

cg/services/orders/submitter/ticket_handler.py

@@ -122,14 +122,12 @@ def add_sample_case_name_to_message(message: str, case_name: str | None) -> str:
     def add_existing_sample_info_to_message(
         self, message: str, customer_id: str, internal_id: str, case_name: str
     ) -> str:
-
         existing_sample: Sample = self.status_db.get_sample_by_internal_id(internal_id=internal_id)
 
         sample_customer = ""
         if existing_sample.customer_id != customer_id:
             sample_customer = " from " + existing_sample.customer.internal_id
-
-        message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority}"
+        message += f"{existing_sample.name}, application: {existing_sample.application_version.application.tag}, case: {case_name} (already existing sample{sample_customer}), priority: {existing_sample.priority.name.lower()}"
         return message
 
     @staticmethod
@@ -183,6 +181,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str:
             if not case.is_new:
                 db_case = self.status_db.get_case_by_internal_id(case.internal_id)
                 for sample in db_case.samples:
+                    message += self.NEW_LINE
                     message = self.add_existing_sample_info_to_message(
                         message=message,
                         customer_id=sample.customer.internal_id,
@@ -192,6 +191,7 @@ def create_case_xml_sample_list(self, order, message: str) -> str:
             else:
                 for sample in case.samples:
                     if not sample.is_new:
+                        message += self.NEW_LINE
                         message = self.add_existing_sample_info_to_message(
                             message=message,
                             customer_id=order.customer,

cg/services/orders/validation/models/case.py

@@ -6,6 +6,8 @@
 from cg.services.orders.validation.models.discriminators import has_internal_id
 from cg.services.orders.validation.models.existing_sample import ExistingSample
 from cg.services.orders.validation.models.sample_aliases import SampleInCase
+from cg.store.models import Sample as DbSample
+from cg.store.store import Store
 
 NewSample = Annotated[SampleInCase, Tag("new")]
 ExistingSampleType = Annotated[ExistingSample, Tag("existing")]
@@ -45,11 +47,17 @@ def enumerated_existing_samples(self) -> list[tuple[int, ExistingSample]]:
                 samples.append((sample_index, sample))
         return samples
 
-    def get_sample(self, sample_name: str) -> SampleInCase | None:
+    def get_new_sample(self, sample_name: str) -> SampleInCase | None:
         for _, sample in self.enumerated_new_samples:
             if sample.name == sample_name:
                 return sample
 
+    def get_existing_sample_from_db(self, sample_name: str, store: Store) -> DbSample | None:
+        for _, sample in self.enumerated_existing_samples:
+            db_sample: DbSample | None = store.get_sample_by_internal_id(sample.internal_id)
+            if db_sample and db_sample.name == sample_name:
+                return db_sample
+
     @model_validator(mode="before")
     def convert_empty_strings_to_none(cls, data):
         if isinstance(data, dict):

cg/services/orders/validation/rules/case/utils.py

@@ -1,3 +1,4 @@
+from cg.services.orders.validation.models.case import Case
 from cg.services.orders.validation.models.existing_case import ExistingCase
 from cg.services.orders.validation.workflows.balsamic.models.case import BalsamicCase
 from cg.services.orders.validation.workflows.balsamic_umi.models.case import BalsamicUmiCase
@@ -34,3 +35,11 @@ def is_case_not_from_collaboration(case: ExistingCase, customer_id: str, store:
     db_case: DbCase | None = store.get_case_by_internal_id(case.internal_id)
     customer: Customer | None = store.get_customer_by_internal_id(customer_id)
     return db_case and customer and db_case.customer not in customer.collaborators
+
+
+def is_sample_in_case(case: Case, sample_name: str, store: Store) -> bool:
+    if case.get_new_sample(sample_name):
+        return True
+    elif case.get_existing_sample_from_db(sample_name=sample_name, store=store):
+        return True
+    return False

cg/services/orders/validation/rules/case_sample/rules.py

@@ -292,48 +292,49 @@ def validate_sample_names_different_from_case_names(
     return errors
 
 
-def validate_fathers_are_male(order: OrderWithCases, **kwargs) -> list[InvalidFatherSexError]:
+def validate_fathers_are_male(
+    order: OrderWithCases, store: Store, **kwargs
+) -> list[InvalidFatherSexError]:
     errors: list[InvalidFatherSexError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[InvalidFatherSexError] = get_father_sex_errors(
-            case=case, case_index=index
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
 def validate_fathers_in_same_case_as_children(
-    order: OrderWithCases, **kwargs
+    order: OrderWithCases, store: Store, **kwargs
 ) -> list[FatherNotInCaseError]:
     errors: list[FatherNotInCaseError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[FatherNotInCaseError] = get_father_case_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
-def validate_mothers_are_female(order: OrderWithCases, **kwargs) -> list[InvalidMotherSexError]:
+def validate_mothers_are_female(
+    order: OrderWithCases, store: Store, **kwargs
+) -> list[InvalidMotherSexError]:
     errors: list[InvalidMotherSexError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[InvalidMotherSexError] = get_mother_sex_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors
 
 
 def validate_mothers_in_same_case_as_children(
-    order: OrderWithCases, **kwargs
+    order: OrderWithCases, store: Store, **kwargs
 ) -> list[MotherNotInCaseError]:
     errors: list[MotherNotInCaseError] = []
     for index, case in order.enumerated_new_cases:
         case_errors: list[MotherNotInCaseError] = get_mother_case_errors(
-            case=case,
-            case_index=index,
+            case=case, case_index=index, store=store
         )
         errors.extend(case_errors)
     return errors