add alignment_path

Clinical-Genomics · Sep 3, 2024 · 7512278 · 7512278
1 parent 5e95c19
commit 7512278
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Showing 3 changed files with 3 additions and 1 deletion.
diff --git a/cg/constants/scout.py b/cg/constants/scout.py
@@ -104,7 +104,7 @@ class ScoutUploadKey(StrEnum):
 )
 
 RAREDISEASE_SAMPLE_TAGS: dict[str, set[str]] = dict(
-    alignment_file={"cram"},
+    alignment_path={"cram"},
     vcf2cytosure={"vcf2cytosure"},
     mt_bam={"bam-mt"},
     chromograph_autozyg={"chromograph", "autozyg"},

diff --git a/cg/meta/upload/scout/hk_tags.py b/cg/meta/upload/scout/hk_tags.py
@@ -70,6 +70,7 @@ class SampleTags(BaseModel):
     # If cram does not exist
     bam_file: set[str] | None = None
     alignment_file: set[str] | None = None
+    alignment_path: set[str] | None = None
     vcf2cytosure: set[str] | None = None
     mt_bam: set[str] | None = None
     chromograph_autozyg: set[str] | None = None

diff --git a/cg/models/scout/scout_load_config.py b/cg/models/scout/scout_load_config.py
@@ -68,6 +68,7 @@ class ScoutMipIndividual(ScoutIndividual):
 
 
 class ScoutRarediseaseIndividual(ScoutIndividual):
+    alignment_path: str | None = None
     mt_bam: str | None = None
     bam_file: str | None = None
     chromograph_autozyg: str | None = None