add manifest

Clinical-Genomics · Sep 6, 2024 · ea53580 · ea53580
1 parent ca3fe01
commit ea53580
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Showing 3 changed files with 6 additions and 10 deletions.
diff --git a/cg/cli/upload/scout.py b/cg/cli/upload/scout.py
@@ -86,7 +86,6 @@ def create_scout_load_config(context: CGConfig, case_id: str, print_console: boo
         LOG.warning(repr(error))
         raise click.Abort from error
     LOG.info(f"Found load config: {scout_load_config}")
-    LOG.info(f"Found load config: {scout_load_config.dict()}")
 
     root_dir: str = context.meta_apis["upload_api"].analysis_api.root
     LOG.info(f"Set root dir to {root_dir}")

diff --git a/cg/meta/upload/scout/raredisease_config_builder.py b/cg/meta/upload/scout/raredisease_config_builder.py
@@ -134,22 +134,13 @@ def build_custom_image_sample(self) -> CustomImages:
             eklipse_images.append(eklipse_image)
 
         case_images = CaseImages(eKLIPse=eklipse_images)
-        print(case_images)
         config_custom_images = CustomImages(case_images=case_images)
-        print(config_custom_images)
-        # Create a CaseImages object with the populated eklipse_images list
-        # case_images = CaseImages(eKLIPse=eklipse_images)
-
-        # Finally, create the CustomImages object with the case_images
-        # config_custom_images = CustomImages(case_images=case_images)
-
         return config_custom_images
 
     def include_case_files(self) -> None:
         """Include case level files for mip case"""
         LOG.info("Including RAREDISEASE specific case level files")
         for scout_key in RAREDISEASE_CASE_TAGS.keys():
-            LOG.info(f"Scout key: {scout_key}")
             self._include_case_file(scout_key)
 
     def _include_case_file(self, scout_key) -> None:

diff --git a/cg/resources/raredisease_bundle_filenames.yaml b/cg/resources/raredisease_bundle_filenames.yaml
@@ -1078,3 +1078,9 @@
   path_index: ~
   step: nextflow-config
   tag: nextflow-config
+- format: json
+  id: CASEID
+  path: PATHTOCASE/manifest.json
+  path_index: ~
+  step: manifest
+  tag: manifest