Merge pull request #157 from uclahs-cds/nwiltsie-add-plantuml

Add PlantUML flow diagram

.github/workflows/render-puml.yaml

@@ -13,7 +13,7 @@ jobs:
 
     steps:
       - name: Generate PUML diagrams
-        uses: uclahs-cds/tool-PlantUML-action@v1.0.0
+        uses: uclahs-cds/tool-PlantUML-action@v1.0.1
         with:
           github-token: ${{ secrets.GITHUB_TOKEN }}
           ghcr-username: ${{ github.actor }}

CHANGELOG.md

@@ -8,6 +8,9 @@ This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.htm
 ---
 
 ## [Unreleased]
+### Changed
+- Replace workflow diagram with PlantUML version
+- Update PlantUML action to v1.0.1
 
 ---
 

README.md

@@ -42,7 +42,7 @@ python submit_nextflow_pipeline.py \
 
 ## Flow Diagram
 
-![call-gSNP flow diagram](call-gSNP-DSL2.png)
+![call-gSNP flow diagram](docs/call-gsnp-flow.svg)
 
 ---
 

docs/call-gsnp-flow.puml

@@ -0,0 +1,87 @@
+@startuml
+
+skinparam ConditionEndStyle hline
+
+start
+
+if (Explicit intervals?) is (Yes) then
+    :==run_SplitIntervals_GATK
+    ----
+    Split reference genome into up
+    to **scatter_count** interval lists,
+    without subdividing any of the
+    input intervals;
+else (No)
+    :==run_SplitIntervals_GATK
+    ----
+    Split reference genome into
+    **scatter_count** interval lists;
+endif
+
+split
+
+:==run_HaplotypeCallerVCF_GATK
+----
+Generate VCFs for each split interval
+using HaplotypeCaller;
+
+:==run_MergeVcfs_Picard_VCF
+----
+Merge raw variants into whole VCF file;
+
+#palegreen:Per-sample raw VCF + index files>
+
+partition "Recalibrate Variants" {
+
+:==run_VariantRecalibratorSNP_GATK
+----
+Generate Variant Quality Score Recalibration
+(VQSR) table for SNPs;
+
+:==run_ApplyVQSR_GATK_SNP
+----
+Filter SNPs based on VQSR table;
+
+:==run_VariantRecalibratorINDEL_GATK
+----
+Generate VQSR table for INDELs;
+
+:==run_ApplyVQSR_GATK_INDEL
+----
+Filter INDELs based on VQSR table;
+
+}
+
+#palegreen:SNP and INDEL recalibrated
+variants + index files>
+
+:==filter_gSNP_GATK
+----
+Filter ambiguous variants with
+customized Perl script;
+
+#palegreen:Filtered germline
+variants + index files>
+
+detach
+
+split again
+
+:==run_HaplotypeCallerGVCF_GATK
+----
+Generate GVCFs for each split interval
+using HaplotypeCaller;
+
+:==run_MergeVcfs_Picard_GVCF
+----
+Merge raw variants into whole GVCF file;
+
+#palegreen:Per-sample GVCF + index files>
+
+detach
+
+endsplit
+
+
+@enduml
+