feat: adapt results output structure to better match current GMS560 p…

…ipeline

config/output_files.yaml

@@ -1,21 +1,21 @@
 files:
   - name: "_copy_detected_variants"
     input: "pgx/detected_variants/{sample}_{type}.annotated.csv"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.detected_variants.csv"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.detected_variants.csv"
     types:
       - T
       - N
 
   - name: "_copy_depth_of_baits"
     input: "pgx/depth_of_coverage/depth_of_baits/{sample}_{type}.output.gdf"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.depth_of_baits.gdf"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.depth_of_baits.gdf"
     types:
       - T
       - N
 
   - name: "_copy_depth_at_missing"
     input: "pgx/append_id_to_gdf/{sample}_{type}.depth_at_missing_annotated.gdf"
-    output: "results/dna/additional_files/pgx/{sample}_{type}.depth_at_missing_annotated.gdf"
+    output: "results/dna/pgx/additional_files/{sample}_{type}.depth_at_missing_annotated.gdf"
     types:
       - T
       - N
@@ -39,4 +39,4 @@ files:
     output: "results/dna/pgx/{sample}_{type}.pgx_report.html"
     types:
       - T
-      - N
+      - N