cg 83.13.3__py3-none-any.whl → 83.15.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.13.3"
+__version__ = "83.15.0"

cg/exc.py

@@ -354,3 +354,7 @@ class MissingConfigFilesError(CgError):
 
 class SeqeraError(CgError):
     """Exception raised when receiving an unexpected response from Seqera platform"""
+
+
+class ApplicationDoesNotHaveHiFiYieldError(CgError):
+    """Exception raised when application does not have HiFi yield set."""

cg/services/sequencing_qc_service/quality_checks/checks.py

@@ -1,12 +1,14 @@
+from collections.abc import Callable
 from enum import Enum
-from typing import Callable
 
 from cg.constants import Workflow
 from cg.services.sequencing_qc_service.quality_checks.utils import (
     all_samples_in_case_have_reads,
     any_sample_in_case_has_reads,
-    case_pass_sequencing_qc,
-    sample_pass_sequencing_qc,
+    case_pass_sequencing_qc_on_hifi_yield,
+    case_pass_sequencing_qc_on_reads,
+    raw_data_case_pass_qc,
+    sample_pass_sequencing_qc_on_reads,
 )
 from cg.store.models import Case
 
@@ -18,10 +20,12 @@ class QualityCheck(Enum):
 
 
 class SequencingQCCheck(QualityCheck):
-    CASE_PASSES: Callable = case_pass_sequencing_qc
-    SAMPLE_PASSES: Callable = sample_pass_sequencing_qc
+    CASE_PASSES_ON_READS: Callable = case_pass_sequencing_qc_on_reads
+    CASE_PASSES_ON_YIELD: Callable = case_pass_sequencing_qc_on_hifi_yield
+    SAMPLE_PASSES: Callable = sample_pass_sequencing_qc_on_reads
     ALL_SAMPLES_IN_CASE_HAVE_READS: Callable = all_samples_in_case_have_reads
     ANY_SAMPLE_IN_CASE_HAS_READS: Callable = any_sample_in_case_has_reads
+    RAW_DATA_CASE_QC: Callable = raw_data_case_pass_qc
 
 
 def get_sequencing_quality_check_for_case(case: Case) -> Callable:
@@ -29,20 +33,20 @@ def get_sequencing_quality_check_for_case(case: Case) -> Callable:
     workflow: Workflow = case.data_analysis
 
     workflow_qc_mapping = {
-        Workflow.BALSAMIC: SequencingQCCheck.CASE_PASSES,
-        Workflow.BALSAMIC_PON: SequencingQCCheck.CASE_PASSES,
-        Workflow.BALSAMIC_UMI: SequencingQCCheck.CASE_PASSES,
-        Workflow.MIP_DNA: SequencingQCCheck.CASE_PASSES,
-        Workflow.MIP_RNA: SequencingQCCheck.CASE_PASSES,
-        Workflow.RAREDISEASE: SequencingQCCheck.CASE_PASSES,
-        Workflow.RNAFUSION: SequencingQCCheck.CASE_PASSES,
-        Workflow.TOMTE: SequencingQCCheck.CASE_PASSES,
+        Workflow.BALSAMIC: SequencingQCCheck.CASE_PASSES_ON_READS,
+        Workflow.BALSAMIC_PON: SequencingQCCheck.CASE_PASSES_ON_READS,
+        Workflow.BALSAMIC_UMI: SequencingQCCheck.CASE_PASSES_ON_READS,
         Workflow.FLUFFY: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
-        Workflow.RAW_DATA: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
         Workflow.MICROSALT: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
+        Workflow.MIP_DNA: SequencingQCCheck.CASE_PASSES_ON_READS,
+        Workflow.MIP_RNA: SequencingQCCheck.CASE_PASSES_ON_READS,
         Workflow.MUTANT: SequencingQCCheck.ANY_SAMPLE_IN_CASE_HAS_READS,
+        Workflow.NALLO: SequencingQCCheck.CASE_PASSES_ON_YIELD,
+        Workflow.RAREDISEASE: SequencingQCCheck.CASE_PASSES_ON_READS,
+        Workflow.RAW_DATA: SequencingQCCheck.RAW_DATA_CASE_QC,
+        Workflow.RNAFUSION: SequencingQCCheck.CASE_PASSES_ON_READS,
         Workflow.TAXPROFILER: SequencingQCCheck.ALL_SAMPLES_IN_CASE_HAVE_READS,
-        Workflow.NALLO: SequencingQCCheck.ALL_SAMPLES_IN_CASE_HAVE_READS,
+        Workflow.TOMTE: SequencingQCCheck.CASE_PASSES_ON_READS,
     }
 
     if workflow in workflow_qc_mapping:
@@ -55,5 +59,5 @@ def get_sample_sequencing_quality_check() -> Callable:
     return SequencingQCCheck.SAMPLE_PASSES
 
 
-def run_quality_checks(quality_checks: list[QualityCheck], **kwargs) -> bool:
+def run_quality_checks(quality_checks: list[Callable], **kwargs) -> bool:
     return all(quality_check(**kwargs) for quality_check in quality_checks)

cg/services/sequencing_qc_service/quality_checks/utils.py

@@ -1,13 +1,15 @@
 import logging
 
+from cg.constants.devices import DeviceType
 from cg.constants.priority import Priority
 from cg.constants.sequencing import SeqLibraryPrepCategory
+from cg.exc import ApplicationDoesNotHaveHiFiYieldError
 from cg.store.models import Case, Sample
 
 LOG = logging.getLogger(__name__)
 
 
-def case_pass_sequencing_qc(case: Case) -> bool:
+def case_pass_sequencing_qc_on_reads(case: Case) -> bool:
     """
     Get the sequencing QC of a case. The checks are performed in the following order:
     1. If the case is a ready-made library, the ready made library QC is used.
@@ -21,22 +23,66 @@ def case_pass_sequencing_qc(case: Case) -> bool:
     if is_case_ready_made_library(case):
         return ready_made_library_case_pass_sequencing_qc(case)
     if is_case_express_priority(case):
-        return express_case_pass_sequencing_qc(case)
+        return express_case_pass_sequencing_qc_on_reads(case)
     return all(sample_has_enough_reads(sample) for sample in case.samples)
 
 
-def express_case_pass_sequencing_qc(case: Case) -> bool:
+def case_pass_sequencing_qc_on_hifi_yield(case: Case) -> bool:
+    """
+    Get the sequencing QC of a case using yield. The checks are performed in the following order:
+    1. If the case is express priority, the express QC is used.
+    2. If the above condition is not met then it checks if all samples have enough yield.
+
+    The express QC should be checked before the standard QC.
+    """
+    if is_case_express_priority(case):
+        return express_case_pass_sequencing_qc_on_hifi_yield(case)
+    return all(sample_has_enough_hifi_yield(sample) for sample in case.samples)
+
+
+def express_case_pass_sequencing_qc_on_reads(case: Case) -> bool:
     """
     Checks if all samples in an express case have enough reads.
     """
     return all(express_sample_has_enough_reads(sample) for sample in case.samples)
 
 
-def express_sample_pass_sequencing_qc(sample: Sample) -> bool:
+def express_case_pass_sequencing_qc_on_hifi_yield(case: Case) -> bool:
+    """
+    Checks if all samples in an express case have enough hifi yield.
+    """
+    return all(express_sample_has_enough_yield(sample) for sample in case.samples)
+
+
+def express_sample_pass_sequencing_qc_on_reads(sample: Sample) -> bool:
     return express_sample_has_enough_reads(sample)
 
 
-def sample_pass_sequencing_qc(sample: Sample) -> bool:
+def express_sample_has_enough_reads(sample: Sample) -> bool:
+    """
+    Checks if given express sample has enough reads. Gets the threshold from the sample's
+    application version.
+    """
+    express_reads_threshold: int = get_express_reads_threshold_for_sample(sample)
+    enough_reads: bool = sample.reads >= express_reads_threshold
+    if not enough_reads:
+        LOG.warning(f"Sample {sample.internal_id} has too few reads.")
+    return enough_reads
+
+
+def express_sample_has_enough_yield(sample: Sample) -> bool:
+    if not sample.hifi_yield:
+        LOG.debug(f"Sample {sample.internal_id} has no hifi yield.")
+        return False
+
+    express_yield_threshold: int = get_express_yield_threshold_for_sample(sample)
+    enough_yield: bool = sample.hifi_yield >= express_yield_threshold
+    if not enough_yield:
+        LOG.warning(f"Sample {sample.internal_id} does not have enough yield.")
+    return enough_yield
+
+
+def sample_pass_sequencing_qc_on_reads(sample: Sample) -> bool:
     """
     Get the standard sequencing QC of a sample. The checks are performed in the following order:
     1. If the sample is express priority, the express QC is used.
@@ -47,7 +93,7 @@ def sample_pass_sequencing_qc(sample: Sample) -> bool:
     checked before the standard QC.
     """
     if is_sample_express_priority(sample):
-        return express_sample_pass_sequencing_qc(sample)
+        return express_sample_pass_sequencing_qc_on_reads(sample)
     if is_sample_ready_made_library(sample):
         return ready_made_library_sample_has_enough_reads(sample)
     return sample_has_enough_reads(sample)
@@ -87,6 +133,31 @@ def any_sample_in_case_has_reads(case: Case) -> bool:
     return passed_quality_check
 
 
+def raw_data_case_pass_qc(case: Case) -> bool:
+    if is_case_ready_made_library(case):
+        return ready_made_library_case_pass_sequencing_qc(case)
+    if is_first_sample_yield_based_and_processed(case):
+        return all(sample_has_enough_hifi_yield(sample) for sample in case.samples)
+    elif is_first_sample_reads_based_and_processed(case):
+        return all(sample_has_enough_reads(sample) for sample in case.samples)
+    LOG.warning(f"Not all samples for case {case.internal_id} have been post-processed.")
+    return False
+
+
+def is_first_sample_yield_based_and_processed(case: Case) -> bool:
+    sample: Sample = case.samples[0]
+    if metrics := sample.sample_run_metrics:
+        return metrics[0].type == DeviceType.PACBIO
+    return False
+
+
+def is_first_sample_reads_based_and_processed(case: Case) -> bool:
+    sample: Sample = case.samples[0]
+    if metrics := sample.sample_run_metrics:
+        return metrics[0].type == DeviceType.ILLUMINA
+    return False
+
+
 def is_case_express_priority(case: Case) -> bool:
     """
     Check if a case is express priority.
@@ -94,18 +165,6 @@ def is_case_express_priority(case: Case) -> bool:
     return case.priority == Priority.express
 
 
-def express_sample_has_enough_reads(sample: Sample) -> bool:
-    """
-    Checks if given express sample has enough reads. Gets the threshold from the sample's
-    application version.
-    """
-    express_reads_threshold: int = get_express_reads_threshold_for_sample(sample)
-    enough_reads: bool = sample.reads >= express_reads_threshold
-    if not enough_reads:
-        LOG.warning(f"Sample {sample.internal_id} has too few reads.")
-    return enough_reads
-
-
 def get_express_reads_threshold_for_sample(sample: Sample) -> int:
     """
     Get the express reads threshold for a sample.
@@ -113,6 +172,15 @@ def get_express_reads_threshold_for_sample(sample: Sample) -> int:
     return round(sample.application_version.application.target_reads / 2)
 
 
+def get_express_yield_threshold_for_sample(sample: Sample) -> int:
+    if threshold := sample.application_version.application.expected_express_hifi_yield:
+        return threshold
+    else:
+        raise ApplicationDoesNotHaveHiFiYieldError(
+            f"Application for sample {sample.internal_id} does not have target HiFi yield."
+        )
+
+
 def is_sample_ready_made_library(sample: Sample) -> bool:
     return sample.prep_category == SeqLibraryPrepCategory.READY_MADE_LIBRARY
 
@@ -143,6 +211,28 @@ def sample_has_enough_reads(sample: Sample) -> bool:
     return enough_reads
 
 
+def sample_has_enough_hifi_yield(sample: Sample) -> bool:
+    """
+    Return true if the sample's HiFi yield is greater than or equal to the threshold.
+    Returns false if the HiFi yield is lower than the threshold or None.
+    Raises:
+        ApplicationDoesNotHaveHiFiYieldError if the sample doesn't have expected HiFi yield.
+    """
+    if not sample.expected_hifi_yield:
+        raise ApplicationDoesNotHaveHiFiYieldError(
+            f"Application for sample {sample.internal_id} does not have target HiFi yield."
+        )
+
+    if not sample.hifi_yield:
+        LOG.debug(f"Sample {sample.internal_id} has no hifi yield.")
+        return False
+
+    enough_hifi_yield: bool = sample.hifi_yield >= sample.expected_hifi_yield
+    if not enough_hifi_yield:
+        LOG.warning(f"Sample {sample.internal_id} does not have enough HiFi yield.")
+    return enough_hifi_yield
+
+
 def is_sample_express_priority(sample: Sample) -> bool:
     """
     Check if a sample is express priority.

cg/services/sequencing_qc_service/sequencing_qc_service.py

@@ -2,15 +2,13 @@ import logging
 from typing import Callable
 
 from cg.constants.constants import SequencingQCStatus
-from cg.services.sequencing_qc_service.utils import qc_bool_to_status
-from typing import Callable
-
-from cg.store.models import Case, Sample
 from cg.services.sequencing_qc_service.quality_checks.checks import (
-    run_quality_checks,
-    get_sequencing_quality_check_for_case,
     get_sample_sequencing_quality_check,
+    get_sequencing_quality_check_for_case,
+    run_quality_checks,
 )
+from cg.services.sequencing_qc_service.utils import qc_bool_to_status
+from cg.store.models import Case, Sample
 from cg.store.store import Store
 
 LOG = logging.getLogger(__name__)
@@ -24,10 +22,14 @@ class SequencingQCService:
         """Run QC for samples in pending or failed cases and store the aggregated score on each case."""
         cases: list[Case] = self.store.get_cases_for_sequencing_qc()
         for case in cases:
-            passes_qc: bool = self.case_pass_sequencing_qc(case)
-            qc_status: SequencingQCStatus = qc_bool_to_status(passes_qc)
-            self.store.update_sequencing_qc_status(case=case, status=qc_status)
-            LOG.info(f"Sequencing QC status for case {case.internal_id}: {qc_status}")
+            LOG.debug(f"Performing sequencing QC for case: {case.internal_id}")
+            try:
+                passes_qc: bool = self.case_pass_sequencing_qc(case)
+                qc_status: SequencingQCStatus = qc_bool_to_status(passes_qc)
+                self.store.update_sequencing_qc_status(case=case, status=qc_status)
+                LOG.info(f"Sequencing QC status for case {case.internal_id}: {qc_status}")
+            except Exception as e:
+                LOG.error(f"Error found during sequencing QC of case: {case.internal_id}: {e}")
 
     @staticmethod
     def case_pass_sequencing_qc(case: Case) -> bool:

cg/store/models.py

@@ -193,9 +193,20 @@ class Application(Base):
         return self.tag
 
     @property
-    def expected_reads(self):
+    def expected_reads(self) -> float:
         return self.target_reads * self.percent_reads_guaranteed / 100
 
+    @property
+    def expected_hifi_yield(self) -> int | None:
+        if self.target_hifi_yield and self.percent_hifi_yield_guaranteed:
+            return round(self.target_hifi_yield * self.percent_hifi_yield_guaranteed / 100)
+        else:
+            return None
+
+    @property
+    def expected_express_hifi_yield(self) -> int | None:
+        return round(self.target_hifi_yield * 0.5) if self.target_hifi_yield else None
+
     @property
     def analysis_type(self) -> str:
         if self.prep_category == SeqLibraryPrepCategory.WHOLE_TRANSCRIPTOME_SEQUENCING.value:
@@ -774,10 +785,15 @@ class Sample(Base, PriorityMixin):
         return self.customer.data_archive_location
 
     @property
-    def expected_reads_for_sample(self) -> int:
+    def expected_reads_for_sample(self) -> float | None:
         """Return the expected reads of the sample."""
         return self.application_version.application.expected_reads
 
+    @property
+    def expected_hifi_yield(self) -> int | None:
+        """Return the expected HiFi yield of the sample."""
+        return self.application_version.application.expected_hifi_yield
+
     @property
     def has_reads(self) -> bool:
         return bool(self.reads)

{cg-83.13.3.dist-info → cg-83.15.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.13.3
+Version: 83.15.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.13.3.dist-info → cg-83.15.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=7BuDkW3ecOxdQ17R23C4DkKxsn1kIqKjJSk0PKbZr7U,41
+cg/__init__.py,sha256=LzHKmL8dVmAmq-6AHs2IvH5WkbB5nsiiArjFCiCZoEA,41
 cg/apps/__init__.py,sha256=pYf0vxo4iYQqURzFRYzqpOCdV8Cm9MWx0GHvJOz0EMg,315
 cg/apps/coverage/__init__.py,sha256=dJtsmNf8tODE2-VEomMIoYA7ugLYZAk_upsfOQCZeF8,27
 cg/apps/coverage/api.py,sha256=e_ozC3QeNKoEfpjjMaL-XjeBLtz-JySWccrtw0E9mLM,2940
@@ -225,7 +225,7 @@ cg/constants/slurm.py,sha256=_Y_InISKpGKT-oVMnES7k7Csz2G1l52MNtJwBZm0prI,313
 cg/constants/subject.py,sha256=EE26Emu6T3_HWvsWeuI5GRGGIvB0BwCjN53KHrsr18U,577
 cg/constants/symbols.py,sha256=c06D1mYFWstZbVEgiby2lUNriswUPVRU5TnSSy889tY,71
 cg/constants/tb.py,sha256=UJHdsu109oR_zxvQrko9SqFANiSUn_UJTw5BFebWcds,621
-cg/exc.py,sha256=QUeoBKw6V4w4G3w2uts9smCd7LejfsLTuza5O0FI6r4,8289
+cg/exc.py,sha256=IYYRa6saq17OT8pA_PBdiorf2XyXTaxNV20JBkdx8QE,8418
 cg/io/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/io/api.py,sha256=WaiompYmK4bkl94fZkGzP2CTsQPmHaTSvy0oD0SKw4s,1037
 cg/io/controller.py,sha256=4TTHm9fNY7Ti3S0r-uhxB3oycJ-Ni5Y44lFj5Yvl3_I,2978
@@ -853,9 +853,9 @@ cg/services/sample_run_metrics_service/dtos.py,sha256=bJ0BL-QkqXIAAIg3F9edIdzAa_
 cg/services/sample_run_metrics_service/sample_run_metrics_service.py,sha256=aQvOuorTG97lUbw7OREO8nsPhO3ouQ38RwksstGwguQ,1795
 cg/services/sample_run_metrics_service/utils.py,sha256=BwICxptnhGg8oBghCLhzHaMNu0LuEV40cSYz1e8mB0A,829
 cg/services/sequencing_qc_service/__init__.py,sha256=OaL9dyyI6B8uRjopTIoD1zcX_H-SbGj46ZM-V-aoq6w,88
-cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=3V_N0jecDkqF9KBEPIZa3RVuzFEDLJnlmQ9c6FIwpfM,2293
-cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=54dvy30YMbbwfo99hnSQAfnIoV7m0G-BQ00BnsumULQ,5325
-cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=uE5bu7xfTHB8CYRZ4uVzryfaSE42Ou6YbkvyormCobE,1754
+cg/services/sequencing_qc_service/quality_checks/checks.py,sha256=qdcHRwZD7uxrOmacyiAG4-EN6nG5z-r4rLxcReU5kSI,2593
+cg/services/sequencing_qc_service/quality_checks/utils.py,sha256=2WN7S4kYsN_9iYPx7d4coAYcWHeueQWrPP2pJ8ztMMc,8969
+cg/services/sequencing_qc_service/sequencing_qc_service.py,sha256=2QIJ9IDZeMtO74ZHJ9bfzyK3-RhDK-m9xaoKsi9RHt8,1969
 cg/services/sequencing_qc_service/utils.py,sha256=5WHJltBICfRODEzFVPFTdCbGNaMKCaVeOswHgIOGgFc,199
 cg/services/slurm_service/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/services/slurm_service/slurm_cli_service.py,sha256=t-XZoAOPgL-eufwK0A6H8WJvGtfWnlIYxnvKZJIX5-Y,702
@@ -904,7 +904,7 @@ cg/store/filters/status_panel_filters.py,sha256=qMYhIsrF9G3mjCvL9b9O2l_cmD3SfPWh
 cg/store/filters/status_pool_filters.py,sha256=XcYqe2z5k_q09xpp4cleDMQ4Q3o2y7UPCkB0QUkl1ck,4308
 cg/store/filters/status_sample_filters.py,sha256=mRpt_ik7niMjBo9K7pP8cmdfDMdr0B3I6Tt2MWXkLoc,9656
 cg/store/filters/status_user_filters.py,sha256=sMwKeWqgEtqv8gyhbN_Uf5huPUxbOt5qEqMWVu67Zys,1328
-cg/store/models.py,sha256=MsKSG9UBiXySCEsODMRDmntjpjkVCd_rlRpqTEw2TZ8,43274
+cg/store/models.py,sha256=dSJRWdvqFmgIbYTlQbsZD8utH10BIjbtUKERybnlssI,43915
 cg/store/store.py,sha256=mz1TfKPlanH2uQyhZdwe_8VKg0IdFolmromKLu668IY,630
 cg/utils/__init__.py,sha256=gGjdV2l_hfWFCTybU6dwDk_FcItM88EIHNPaX6g1qUk,30
 cg/utils/calculations.py,sha256=zLVJO6nNw6n7AW7fHZI56UnQ23lqJrShB4Hh2ow6-TQ,349
@@ -923,7 +923,7 @@ cg/utils/flask/enum.py,sha256=xwNVtFPkSzoloJctLHu7obRyxcng1GJrhkeYkqwf9tw,1052
 cg/utils/mapping.py,sha256=oZpZW2kgsbtAP2FZ7RtRPELiEE1zZk_nAGisHGtCOUo,491
 cg/utils/time.py,sha256=_VOglhrFEZ5cwHK1U1g36SdwzB7UvV-Nvlt4ymuZUho,1501
 cg/utils/utils.py,sha256=RciI_UhWcnG_pMZrmQZ1ZYb-O1N0DweTYMmhE0SIRgQ,1410
-cg-83.13.3.dist-info/METADATA,sha256=DhvQrRopWX7HGbwF1GgTJthjXpxPR4BgcpxTs9hMhg4,4940
-cg-83.13.3.dist-info/WHEEL,sha256=zp0Cn7JsFoX2ATtOhtaFYIiE2rmFAD4OcMhtUki8W3U,88
-cg-83.13.3.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.13.3.dist-info/RECORD,,
+cg-83.15.0.dist-info/METADATA,sha256=wj51NyMN6wmwfhFYzc6eCNr6yc2UzVNWHh5V_r30Vgs,4940
+cg-83.15.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.15.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.15.0.dist-info/RECORD,,

{cg-83.13.3.dist-info → cg-83.15.0.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: poetry-core 2.2.1
+Generator: poetry-core 2.3.0
 Root-Is-Purelib: true
 Tag: py3-none-any