add sample id to hk tage

Clinical-Genomics · Sep 3, 2024 · aef457e · aef457e
1 parent 7512278
commit aef457e
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/cg/meta/upload/scout/raredisease_config_builder.py b/cg/meta/upload/scout/raredisease_config_builder.py
@@ -94,7 +94,7 @@ def build_config_sample(self, case_sample: CaseSample) -> ScoutRarediseaseIndivi
         config_sample = ScoutRarediseaseIndividual()
         self.add_common_sample_info(config_sample=config_sample, case_sample=case_sample)
         # self.add_common_sample_files(config_sample=config_sample, case_sample=case_sample)
-        self.include_sample_files(config_sample)
+        self.include_sample_files(config_sample=config_sample, case_sample=case_sample)
         config_sample.father = (
             case_sample.father.internal_id
             if case_sample.father
@@ -114,13 +114,13 @@ def include_case_files(self) -> None:
             LOG.info(f"Scout key: {scout_key}")
             self._include_case_file(scout_key)
 
-    def include_sample_files(self, config_sample: ScoutIndividual = None) -> None:
+    def include_sample_files(self, case_sample: CaseSample, config_sample: ScoutIndividual = None, ) -> None:
         for scout_key in RAREDISEASE_SAMPLE_TAGS.keys():
             LOG.info(f"Scout key: {scout_key}")
             scout_key = scout_key.replace("chromograph_", "chromograph_images.")
             scout_key = scout_key.replace("reviewer_", "reviewer.")
 
-            self._include_sample_file(scout_key)
+            self._include_sample_file(scout_key, case_sample)
 
     def _include_case_file(self, scout_key) -> None:
         """Include the file path associated to a scout configuration parameter if the corresponding housekeeper tags
@@ -131,13 +131,14 @@ def _include_case_file(self, scout_key) -> None:
             self.get_file_from_hk(getattr(self.case_tags, scout_key)),
         )
 
-    def _include_sample_file(self, scout_key) -> None:
+    def _include_sample_file(self, scout_key, case_sample) -> None:
         """Include the file path associated to a scout configuration parameter if the corresponding housekeeper tags
         are found. Otherwise return None."""
+        tags = getattr(self.sample_tags, scout_key)
         setattr(
             self.load_config,
             scout_key,
-            self.get_file_from_hk(getattr(self.sample_tags, scout_key)),
+            self.get_sample_file(hk_tags=tags, sample_id=case_sample),
         )
 
     @staticmethod

diff --git a/cg/models/scout/scout_load_config.py b/cg/models/scout/scout_load_config.py
@@ -68,7 +68,6 @@ 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