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Add PlantUML diagram (#146)
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* add plantUML file

* Update SVG images for PlantUML diagrams

* update flow diagram path

* remove old SVG

* update plantuml action version to v1.0.1

* Update CHANGELOG.md

* add query sample names process; update titles

* Update CHANGELOG.md

* Update CHANGELOG.md

* Update CHANGELOG.md

---------

Co-authored-by: Mootor <mmootor@ip-0A125257.rhxrlfvjyzbupc03cc22jkch3c.xx.internal.cloudapp.net>
Co-authored-by: Faizal-Eeman <[email protected]>
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3 people authored Apr 3, 2024
1 parent 9ba216b commit a0c200a
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2 changes: 1 addition & 1 deletion .github/workflows/render-puml.yaml
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Expand Up @@ -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 }}
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5 changes: 5 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -8,6 +8,11 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
---

## [Unreleased]
### Changed
- Update PlantUML action to `v1.0.1`

### Added
- Add PlantUML diagram

---

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -65,7 +65,7 @@ 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:

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1 change: 0 additions & 1 deletion call-sSV-workflow.svg

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35 changes: 35 additions & 0 deletions docs/call-sSV.puml
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@@ -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
41 changes: 41 additions & 0 deletions docs/call-sSV.svg
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