Update CHANGELOG.md

.github/workflows/render-puml.yaml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
       - name: Generate PUML diagrams
-        uses: uclahs-cds/[email protected].0
+        uses: uclahs-cds/[email protected].1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           ghcr-username: ${{ github.actor }}

CHANGELOG.md

@@ -11,6 +11,12 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ### Added
 - Add supported Nextflow version to `README.md`
 
+### Changed
+- Update PlantUML action to `v1.0.1`
+
+### Added
+- Add PlantUML diagram
+
 ---
 
 ## [6.1.0] - 2024-03-12

README.md

@@ -68,7 +68,7 @@ In the above command, the partition type can be changed based on the size of the
 
 ## Flow Diagram:
 
-![call-sSV flow diagram](call-sSV-workflow.svg?raw=true)
+![call-sSV flow diagram](docs/call-sSV.svg)
 
 ## Pipeline Steps:
 

docs/call-sSV.puml

@@ -0,0 +1,35 @@
+@startuml
+skinparam SwimlaneTitleFontStyle bold
+
+start
+
+:==Input
+---
+Input Matched Tumor/Normal BAMs;
+:==Input Validation
+---
+Validate the input BAMs and corresponding index files;
+
+split
+partition "DELLY" {
+    :==DELLY sSV
+    ---
+    Call sSVs using DELLY;
+    :==Query Sample Name
+    ---
+    Query Tumor/Normal sample names
+    using BCFtools;
+    :==Filter sSV
+    ---
+    Filter out germline SVs using DELLY;
+    }
+
+split again
+partition "Manta" {
+    :==Manta sSV
+    ---
+    Call SVs using Manta;
+    }
+end split
+stop
+@enduml