add Regenotyping to DAG

uclahs-cds · Mar 14, 2024 · 1f71314 · 1f71314
1 parent d0281ad
commit 1f71314
Showing 1 changed file with 24 additions and 8 deletions.
diff --git a/docs/call-gSV.puml b/docs/call-gSV.puml
@@ -1,21 +1,25 @@
 @startuml
 skinparam SwimlaneTitleFontStyle bold
 
+start
+
 :==Normal BAM
 ---
 Input Normal BAM;
 :==Input Validation
 ---
 Validate the input BAM and corresponding index file;
-split
+fork
 if (run_discovery) is (true) then
     split
         :==DELLY gSV
         ---
-        Call germline SVs using DELLY;
+        Call germline SVs using DELLY
+        (BCF);
         :==DELLY gCNV
         ---
-        Call germline CNVs using DELLY;
+        Call germline CNVs using DELLY
+        (BCF);
         :==QC
         ---
         Quality Check variant calls;
@@ -25,22 +29,34 @@ if (run_discovery) is (true) then
     split again
         :==Manta gSV
         ---
-        Call germline SVs using Manta;
+        Call germline SVs using Manta
+        (VCF);
     end split
 else (false)
 endif
+stop
 
-split again
+fork again
 if (run_regenotyping) is (true) then
+    split
     :==Regenotype gSV
     ---
-    Regenotype SVs using DELLY germline SV calls;
+    Regenotype SVs
+    using DELLY gSV calls
+    (BCF);
+    note right: input\nmerged\ngSV sites
+    split again
     :==Regenotype gCNV
     ---
-    Regenotype CNVs using DELLY germline CNV calls;
+    Regenotype CNVs
+    using DELLY gCNV calls
+    (BCF);
+    note left: input\nmerged\ngCNV sites
+    end split
+
 else (false)
 endif
-end split
+stop
 
 @enduml