add d4 to rd scout load config

Clinical-Genomics · Jan 24, 2025 · a54a6e0 · a54a6e0
1 parent 8cec5df
commit a54a6e0
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Showing 4 changed files with 7 additions and 5 deletions.
diff --git a/cg/constants/scout.py b/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"},

diff --git a/cg/meta/upload/scout/hk_tags.py b/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

diff --git a/cg/meta/upload/scout/raredisease_config_builder.py b/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
+        )
diff --git a/cg/models/scout/scout_load_config.py b/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):