cg 83.17.0__py3-none-any.whl → 83.18.0__py3-none-any.whl

cg/__init__.py

@@ -1,2 +1,2 @@
 __title__ = "cg"
-__version__ = "83.17.0"
+__version__ = "83.18.0"

cg/clients/chanjo2/models.py

@@ -27,6 +27,12 @@ class CoverageMetrics(BaseModel):
     mean_coverage: float
 
 
+class CoverageMetricsChanjo1(CoverageMetrics):
+    """Chanjo1 sample coverage metrics model."""
+
+    pass
+
+
 class CoveragePostResponse(RootModel):
     """Coverage sample data model returned from the POST request."""
 

cg/constants/nf_analysis.py

@@ -60,5 +60,3 @@ NALLO_COVERAGE_INTERVAL_TYPE: str = "genes"
 NALLO_COVERAGE_THRESHOLD: int = 10
 
 RAREDISEASE_COVERAGE_FILE_TAGS: list[str] = ["coverage", "d4"]
-RAREDISEASE_COVERAGE_INTERVAL_TYPE: str = "genes"
-RAREDISEASE_COVERAGE_THRESHOLD: int = 10

cg/meta/workflow/analysis.py

@@ -781,7 +781,7 @@ class AnalysisAPI(MetaAPI):
     def get_sample_coverage(
         self, case_id: str, sample_id: str, gene_ids: list[int]
     ) -> CoverageMetrics | None:
-        """Return sample coverage data from Chanjo2."""
+        """Return sample coverage data from Chanjo or Chanjo2."""
         raise NotImplementedError
 
     def get_scout_upload_case_tags(self):

cg/meta/workflow/raredisease.py

@@ -7,18 +7,11 @@ from typing import Any
 
 from housekeeper.store.models import File
 
-from cg.clients.chanjo2.models import (
-    CoverageMetrics,
-    CoveragePostRequest,
-    CoveragePostResponse,
-    CoverageSample,
-)
+from cg.clients.chanjo2.models import CoverageMetricsChanjo1
 from cg.constants import Workflow
 from cg.constants.constants import GenomeVersion
 from cg.constants.nf_analysis import (
     RAREDISEASE_COVERAGE_FILE_TAGS,
-    RAREDISEASE_COVERAGE_INTERVAL_TYPE,
-    RAREDISEASE_COVERAGE_THRESHOLD,
     RAREDISEASE_METRIC_CONDITIONS_WES,
     RAREDISEASE_METRIC_CONDITIONS_WGS,
     RAREDISEASE_PARENT_PEDDY_METRIC_CONDITION,
@@ -154,25 +147,17 @@ class RarediseaseAnalysisAPI(NfAnalysisAPI):
 
     def get_sample_coverage(
         self, case_id: str, sample_id: str, gene_ids: list[int]
-    ) -> CoverageMetrics | None:
-        """Return sample coverage metrics from Chanjo2."""
-        genome_version: GenomeVersion = self.get_genome_build(case_id)
-        coverage_file_path: str | None = self.get_sample_coverage_file_path(
-            bundle_name=case_id, sample_id=sample_id
+    ) -> CoverageMetricsChanjo1 | None:
+        sample_coverage: dict = self.chanjo_api.sample_coverage(
+            sample_id=sample_id, panel_genes=gene_ids
         )
-        try:
-            post_request = CoveragePostRequest(
-                build=self.translate_genome_reference(genome_version),
-                coverage_threshold=RAREDISEASE_COVERAGE_THRESHOLD,
-                hgnc_gene_ids=gene_ids,
-                interval_type=RAREDISEASE_COVERAGE_INTERVAL_TYPE,
-                samples=[CoverageSample(coverage_file_path=coverage_file_path, name=sample_id)],
+        if sample_coverage:
+            return CoverageMetricsChanjo1(
+                coverage_completeness_percent=sample_coverage.get("mean_completeness"),
+                mean_coverage=sample_coverage.get("mean_coverage"),
             )
-            post_response: CoveragePostResponse = self.chanjo2_api.get_coverage(post_request)
-            return post_response.get_sample_coverage_metrics(sample_id)
-        except Exception as error:
-            LOG.error(f"Error getting coverage for sample '{sample_id}', error: {error}")
-            return None
+        LOG.warning(f"Could not calculate sample coverage for: {sample_id}")
+        return None
 
     def get_scout_upload_case_tags(self) -> dict:
         """Return Raredisease Scout upload case tags."""

cg/resources/nallo_bundle_filenames.yaml

@@ -282,32 +282,67 @@
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz
   step: methylation_pileup
-  tag: hap1
+  tag: modkit_hap1
 - format: bed
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_1.bed.gz.tbi
   step: methylation_pileup
-  tag: hap1_index
+  tag: modkit_hap1_index
 - format: bed
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz
   step: methylation_pileup
-  tag: hap2
+  tag: modkit_hap2
 - format: bed
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_2.bed.gz.tbi
   step: methylation_pileup
-  tag: hap2_index
+  tag: modkit_hap2_index
 - format: bed
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz
   step: methylation_pileup
-  tag: ungrouped
+  tag: modkit_ungrouped
 - format: bed
   id: SAMPLEID
   path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_modkit_pileup_ungrouped.bed.gz.tbi
   step: methylation_pileup
-  tag: ungrouped_index
+  tag: modkit_ungrouped_index
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.hap1.bed.gz
+  step: methylation_pileup
+  tag: methbat_hap1
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.hap1.bed.gz.tbi
+  step: methylation_pileup
+  tag: methbat_hap1_index
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.hap2.bed.gz
+  step: methylation_pileup
+  tag: methbat_hap2
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.hap2.bed.gz.tbi
+  step: methylation_pileup
+  tag: methbat_hap2_index
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.combined.bed.gz
+  step: methylation_pileup
+  tag: methbat_combined
+- format: bed
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/pileup/SAMPLEID/SAMPLEID_pbcpgtools.combined.bed.gz.tbi
+  step: methylation_pileup
+  tag: methbat_combined_index
+- format: tsv
+  id: SAMPLEID
+  path: PATHTOCASE/methylation/profile/SAMPLEID/SAMPLEID_methbat_profile.tsv
+  step: methylation_calling
+  tag: methbat_profile
 - format: meta
   id: SAMPLEID
   path: PATHTOCASE/qc/mosdepth/SAMPLEID/SAMPLEID.per-base.d4

{cg-83.17.0.dist-info → cg-83.18.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: cg
-Version: 83.17.0
+Version: 83.18.0
 Summary: Clinical Genomics command center
 Requires-Python: >=3.11,<3.13
 Classifier: Programming Language :: Python

{cg-83.17.0.dist-info → cg-83.18.0.dist-info}/RECORD

@@ -1,4 +1,4 @@
-cg/__init__.py,sha256=TDL5feL1tS5hjQE-OqSwP0vhH9a3_iODEb0iTevqItQ,41
+cg/__init__.py,sha256=NOsHCvBNWH45eSTwdtkm_GlvJYAU4UfbXhDZgKKdGSQ,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
@@ -176,7 +176,7 @@ cg/clients/arnold/dto/create_case_request.py,sha256=tXD7EZSgHL6bOHhph65dgYoGKIut
 cg/clients/arnold/exceptions.py,sha256=w9J9TLie5tcgqzaO0L3lrF3OlowtjzkeGR4R7quXzko,384
 cg/clients/chanjo2/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/clients/chanjo2/client.py,sha256=je48Wx3nvyerYKwezZFBjuLHD3C7XaXDQSBeaTOtBlU,1197
-cg/clients/chanjo2/models.py,sha256=9Rw7fZKcqjSIXL48DaxHiugTwAJnbxKwJPWEKQZjWTk,1328
+cg/clients/chanjo2/models.py,sha256=W5Zgb94pplbM2x5QkoHDJXovWLRmh4vbOlsc08ZjzbE,1436
 cg/clients/chanjo2/utils.py,sha256=q6pJEjV90JVTK2ad3OKtLM_vBMpY8PzC-iFG9xg4Y5o,948
 cg/clients/freshdesk/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 cg/clients/freshdesk/constants.py,sha256=SwGJsLggJe5QrrnPVSURe1JSaIwMwKIT09e_1Lhmta4,244
@@ -207,7 +207,7 @@ cg/constants/invoice.py,sha256=Tdd3PY_Z7wz4eSfKaTapSFlkmk_FWM1bwWMOj5D5F5Y,95
 cg/constants/lims.py,sha256=vhATu1UtIXdfPZWEu8pne3uq4ZhCAdPNJcjSotD8AE8,6559
 cg/constants/metrics.py,sha256=jBLp8buIG_3fKFraerFvpfSJ6s-0H42jI1qysjjAXFc,847
 cg/constants/nextflow.py,sha256=o5VxtsyZNJaA1bh_AyKQQ0Iov6grZIeik_hhE8zO268,197
-cg/constants/nf_analysis.py,sha256=r3bfzzIAL3fU3dxMSwIUmN_jYLhcF70L0NXymGLTj5M,2541
+cg/constants/nf_analysis.py,sha256=D1pzSyBz3IcX8lg-m0GJIW2qCp60tIdMkFSyBx5Yc_I,2450
 cg/constants/nipt.py,sha256=KGy7Y08jIUmT9FKKdjGzfRwvklAkOHRLKXqDOQx4aPc,19
 cg/constants/observations.py,sha256=Sjxo3R7DCkcMkSWNSeg2Sznkjr3werFRRsSREjd6CCU,3887
 cg/constants/orderforms.py,sha256=pLD_ufw11aE-Fn4x87el3F_KRITi2lbrgpBYU7eJgpM,2362
@@ -348,7 +348,7 @@ cg/meta/upload/scout/uploadscoutapi.py,sha256=FJfr-rvTG7chU3y8Z-jmdQISUx_QQ3OsxF
 cg/meta/upload/tomte/tomte.py,sha256=QYuW-YlOxXQLs1i15iotswe5CNHi4--aSbMQyxealcw,1662
 cg/meta/upload/upload_api.py,sha256=hi25r35L7bEJMicH8qc4poAd2TNvP5SJwpS_3lf9eo4,3926
 cg/meta/workflow/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-cg/meta/workflow/analysis.py,sha256=oj-hOhp8mlH-KVvB6B6Krsm961K4_avAl6TZ6mWPYlQ,34727
+cg/meta/workflow/analysis.py,sha256=Pwy62B8Ot6aIG7zEQHsqqUZbmOHqF1AO4WHNV6pL0W0,34737
 cg/meta/workflow/balsamic.py,sha256=TB2nLyq8r-CtCBgOD4Kz3WDJi6lgDs78nagItLyVHjo,31149
 cg/meta/workflow/balsamic_pon.py,sha256=gMo9eKxxEtUR61cQtIWcxFRqSgo0IeBSPe9k8XnF_pc,2700
 cg/meta/workflow/balsamic_umi.py,sha256=W1onPhiqfvVhs8d4M0-EbiVvLys2TBp2fihQ7HrV-Uw,757
@@ -386,7 +386,7 @@ cg/meta/workflow/mutant/quality_controller/utils.py,sha256=8zbn210O5RIKRIsaZUkVv
 cg/meta/workflow/nallo.py,sha256=V0yBQLIlRvWS-gtOfJ6OgxGXTTEjx5Yp-KObyBMCNjs,10035
 cg/meta/workflow/nf_analysis.py,sha256=eXl_1AxwwdzVC_k3ujiONH5q1FCw9wacGoVpVKx2_PI,20466
 cg/meta/workflow/prepare_fastq.py,sha256=HbkrsuqlZgb_7kQPf_j_Mqowh6nEms9jl7043ybxK4U,6149
-cg/meta/workflow/raredisease.py,sha256=-bENb0f1f9bptMsP_PBy4niMmkxDnIxCOF32OBgDxts,8898
+cg/meta/workflow/raredisease.py,sha256=yKrPKMfrowUPRYhWaHBJF4EFPbNB6mL3JkkRejZlhAI,8222
 cg/meta/workflow/rnafusion.py,sha256=Mcmn_HTAHpH-M6Pl_bOG2oSfIgZe11GqtTKrk6lFpPU,3646
 cg/meta/workflow/taxprofiler.py,sha256=pphhUfe-CguO1PIwR3orRoaNnVWi_8V23MkYORHcAh0,3045
 cg/meta/workflow/tomte.py,sha256=-WtxossQMfQjYR9CBdxS1V_gTix3gAVqjDR5tIBTHcE,2345
@@ -460,7 +460,7 @@ cg/models/workflow/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuF
 cg/models/workflow/mutant.py,sha256=Y5cwG7UninrAWCn6R9rTNhSDAkDprCebCilyCBlPIcY,685
 cg/models/workflow/validators.py,sha256=BzbmB9QVDjM1C_7F874PR0QD6xhCZvDG01ItITmFy_s,70
 cg/resources/__init__.py,sha256=mRMKpOEL-NO4JEzQsjTrtDFf8toOtBXK0BhDbPnZGVE,1247
-cg/resources/nallo_bundle_filenames.yaml,sha256=pjJaBgtZtsYAqd-sQ1bCq365u9fcsoN0Gn34JjDduJE,16724
+cg/resources/nallo_bundle_filenames.yaml,sha256=04mNM5DFovMTct0OixgspKtaP91_hENoo1lMf-YUSjY,17899
 cg/resources/raredisease_bundle_filenames.yaml,sha256=IN8QDcYQNxFVWghvSNLJ2-Udsd5ts3uBqD9rnJGj4kg,25278
 cg/resources/rnafusion_bundle_filenames.yaml,sha256=hoXuTobKbjH7W7dld87rSF7X0r4KxLXuUllX0ISDDXU,3281
 cg/resources/taxprofiler_bundle_filenames.yaml,sha256=AULMEAYkMzADYUtVtuSmBj7UaAIlLGRDyBMEOO0xWz8,2871
@@ -922,7 +922,7 @@ 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-83.17.0.dist-info/METADATA,sha256=3vkrM4YOxhmXatZvtpUfE_YaFE8zwb2hphnZScPj_Qo,4940
-cg-83.17.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
-cg-83.17.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
-cg-83.17.0.dist-info/RECORD,,
+cg-83.18.0.dist-info/METADATA,sha256=6hSRs_fWC9gpUCmi5yXMHqRa7qkH6ggaYDh7C_sIT_Q,4940
+cg-83.18.0.dist-info/WHEEL,sha256=3ny-bZhpXrU6vSQ1UPG34FoxZBp3lVcvK0LkgUz6VLk,88
+cg-83.18.0.dist-info/entry_points.txt,sha256=q5f47YQQGltzK_xnIq1mDopRXXEItr85Xe1BCtG-Wts,39
+cg-83.18.0.dist-info/RECORD,,