From 1f7131450d1e160f1fdf29268517c60988ce0c80 Mon Sep 17 00:00:00 2001
From: Mootor
 <mmootor@ip-0A125257.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
Date: Wed, 13 Mar 2024 18:27:22 -0700
Subject: [PATCH] add Regenotyping to DAG

---
 docs/call-gSV.puml | 32 ++++++++++++++++++++++++--------
 1 file changed, 24 insertions(+), 8 deletions(-)

diff --git a/docs/call-gSV.puml b/docs/call-gSV.puml
index c3177b07..4ed6a528 100644
--- 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