Merge branch 'master' into write_config_taxprofiler

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 66.0.2
+current_version = 67.0.8
 commit = True
 tag = True
 tag_name = v{new_version}

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "66.0.2"
+__version__ = "67.0.8"

cg/apps/hermes/hermes_api.py

@@ -18,6 +18,7 @@ def __init__(self, config: dict):
         self.process = Process(
             binary=config["hermes"]["binary_path"],
         )
+        self.container_path: str = config["hermes"]["container_path"]
         self.container_mount_volume = config["hermes"]["container_mount_volume"]
 
     def convert_deliverables(
@@ -33,7 +34,7 @@ def convert_deliverables(
             "run",
             "--bind",
             self.container_mount_volume,
-            "/home/proj/stage/singularity_containers/hermes_latest.sif",
+            self.container_path,
             "convert",
             "deliverables",
             "--workflow",

cg/apps/orderform/excel_orderform_parser.py

@@ -12,8 +12,8 @@
 from cg.constants import DataDelivery
 from cg.constants.orderforms import Orderform
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.excel_sample import ExcelSample
-from cg.models.orders.order import OrderType
 
 LOG = logging.getLogger(__name__)
 

cg/apps/orderform/json_orderform_parser.py

@@ -1,8 +1,8 @@
 from cg.apps.orderform.orderform_parser import OrderformParser
 from cg.constants import DataDelivery, Workflow
 from cg.exc import OrderFormError
+from cg.models.orders.constants import OrderType
 from cg.models.orders.json_sample import JsonSample
-from cg.models.orders.order import OrderType
 
 
 class JsonOrderformParser(OrderformParser):

cg/apps/orderform/orderform_parser.py

@@ -7,7 +7,7 @@
 from cg.apps.orderform.utils import ORDER_TYPES_WITH_CASES
 from cg.constants import DataDelivery
 from cg.exc import OrderFormError
-from cg.models.orders.order import OrderType
+from cg.models.orders.constants import OrderType
 from cg.models.orders.orderform_schema import OrderCase, Orderform, OrderPool
 from cg.models.orders.sample_base import OrderSample
 from cg.store.models import Customer

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/orderforms.py

@@ -1,19 +1,11 @@
 from enum import StrEnum
 
 from cg.constants import ANALYSIS_SOURCES, METAGENOME_SOURCES
-from cg.models.orders.order import OrderType
 
 SEX_MAP = {"male": "M", "female": "F", "unknown": "unknown"}
 REV_SEX_MAP = {value: key for key, value in SEX_MAP.items()}
-CONTAINER_TYPES = ["Tube", "96 well plate"]
 SOURCE_TYPES = set().union(METAGENOME_SOURCES, ANALYSIS_SOURCES)
 
-CASE_PROJECT_TYPES = [
-    OrderType.MIP_DNA,
-    OrderType.BALSAMIC,
-    OrderType.MIP_RNA,
-]
-
 
 class Orderform(StrEnum):
     BALSAMIC: str = "1508"
@@ -79,4 +71,5 @@ def get_current_orderform_version(order_form: str) -> str:
     "LaboratorieMedicinskt Centrum Gotland": "621 84 Visby",
     "Unilabs Eskilstuna Laboratorium": "631 88 Eskilstuna",
     "Norrland University Hospital": "901 85 Umeå",
+    "Länssjukhuset Sundsvall": "856 43 Sundsvall",
 }

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/exc.py

@@ -174,6 +174,12 @@ class OrderError(CgError):
     """
 
 
+class OrderSubmissionError(CgError):
+    """
+    Exception related to order submission.
+    """
+
+
 class OrderFormError(CgError):
     """
     Exception related to the order form.

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/cg_config.py

@@ -27,9 +27,7 @@
 from cg.meta.delivery.delivery import DeliveryAPI
 from cg.services.analysis_service.analysis_service import AnalysisService
 from cg.services.decompression_service.decompressor import Decompressor
-from cg.services.deliver_files.factory import (
-    DeliveryServiceFactory,
-)
+from cg.services.deliver_files.factory import DeliveryServiceFactory
 from cg.services.deliver_files.rsync.models import RsyncDeliveryConfig
 from cg.services.deliver_files.rsync.service import DeliveryRsyncService
 from cg.services.fastq_concatenation_service.fastq_concatenation_service import (
@@ -147,6 +145,10 @@ class CommonAppConfig(BaseModel):
     container_mount_volume: str | None = None
 
 
+class HermesConfig(CommonAppConfig):
+    container_path: str
+
+
 class FluffyUploadConfig(BaseModel):
     user: str
     password: str
@@ -427,7 +429,7 @@ class CGConfig(BaseModel):
     genotype_api_: GenotypeAPI = None
     gens: CommonAppConfig = None
     gens_api_: GensAPI = None
-    hermes: CommonAppConfig = None
+    hermes: HermesConfig = None
     hermes_api_: HermesApi = None
     janus: ClientConfig | None = None
     janus_api_: JanusAPIClient | None = None