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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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@@ -13,7 +13,7 @@ jobs: | |
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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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@startuml | ||
skinparam SwimlaneTitleFontStyle bold | ||
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start | ||
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:==Input | ||
--- | ||
Input Matched Tumor/Normal BAMs; | ||
:==Input Validation | ||
--- | ||
Validate the input BAMs and corresponding index files; | ||
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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; | ||
} | ||
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split again | ||
partition "Manta" { | ||
:==Manta sSV | ||
--- | ||
Call SVs using Manta; | ||
} | ||
end split | ||
stop | ||
@enduml |
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