fix: correctly configure retain-artifacts: true/false on the event level, as it is parsed

Author: dlaehnemann

.test/config-sra/config.yaml

@@ -47,44 +47,44 @@ calling:
     moderate: "ANN['IMPACT'] == 'MODERATE'"
     no_filter: "True"
   fdr-control:
-    threshold: 0.05
+    threshold: 0.01
     # Denote FDR control mode.
     # The default (local-smart) is recommended because it provides the most realistic and intuitive results.
     # See see https://varlociraptor.github.io/docs/filtering for details.
     mode: local-smart
     # Retain artifacts upon FDR control (i.e. do not remove them from the callset,
     # see https://varlociraptor.github.io/docs/filtering)
     # Only applies in smart mode (local-smart or global-smart).
-    retain-artifacts: false
     events: 
       moderate:
+        desc: Variants with moderate impact
         varlociraptor: 
           - base_only
           - changed_only
           - both
         filter:
           - moderate
-        desc: Variants with moderate impact
       present:
+        desc: All variants present, unfiltered.
         varlociraptor: 
           - base_only
           - changed_only
           - both
         filter:
           - no_filter
-        desc: Variants with moderate impact
       present_or_artifact:
+        desc: All variants present, unfiltered and with the artifacts probability also considered part of the present probability.
+        retain-artifacts: true
         varlociraptor: 
           - base_only
           - changed_only
           - both
-          - artifact
         filter:
           - no_filter
-        desc: Variants with moderate impact
 
 complement_events:
   filtered_artifacts:
+    desc: All variants that were removed from the present event during fdr control due to a high artifacts probability.
     report: True
     types: ["variants", "fusions"]
     full: present_or_artifact

config/config.yaml

@@ -150,10 +150,6 @@ calling:
     # The default (local-smart) is recommended because it provides the most realistic and intuitive results.
     # See see https://varlociraptor.github.io/docs/filtering for details.
     mode: local-smart
-    # Retain artifacts upon FDR control (i.e. do not remove them from the callset,
-    # see https://varlociraptor.github.io/docs/filtering)
-    # Only applies in smart mode (local-smart or global-smart).
-    retain-artifacts: false
     events:
       # Add any number of events here to filter for.
       # The id of each event can be chosen freely, but needs to contain
@@ -172,6 +168,10 @@ calling:
         # This will occur in the report.
         desc: |
           Some description.
+        # Retain artifacts upon FDR control (i.e. do not remove them from the callset,
+        # see https://varlociraptor.github.io/docs/filtering)
+        # Only applies in smart mode (local-smart or global-smart).
+        retain-artifacts: false
         varlociraptor:
           # Add varlociraptor events to aggregated over.
           # The probability for the union of these events is used for controlling