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--- | ||
name: PlantUML Generation | ||
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on: | ||
push: | ||
paths: | ||
- '**.puml' | ||
workflow_dispatch: | ||
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jobs: | ||
plantuml: | ||
runs-on: ubuntu-latest | ||
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steps: | ||
- name: Generate PUML diagrams | ||
uses: uclahs-cds/[email protected] | ||
with: | ||
github-token: ${{ secrets.GITHUB_TOKEN }} | ||
ghcr-username: ${{ github.actor }} | ||
ghcr-password: ${{ secrets.GITHUB_TOKEN }} |
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@startuml | ||
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skinparam SwimlaneTitleFontStyle bold | ||
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|s| Parallelized by sample | ||
|i| Parallelized by interval | ||
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|s| | ||
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start | ||
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partition "**Unparallelized Setup**\nThis block is run once\nregardless of sample count" { | ||
if (Parallelize by\nchromosome?) is (Yes) then | ||
:==run_SplitIntervals_GATK | ||
---- | ||
Split reference genome into | ||
interval lists by chomosome | ||
(1-22, X, Y, M, nonassembled); | ||
else (No) | ||
:==run_SplitIntervals_GATK | ||
---- | ||
Split reference genome into | ||
**scatter_count** interval lists; | ||
endif | ||
} | ||
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:==run_validate_PipeVal | ||
---- | ||
Validate the input BAM and index file; | ||
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|i| | ||
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:==run_RealignerTargetCreator_GATK | ||
---- | ||
Split input BAMs by interval and identify | ||
potentially misaligned sub-intervals to | ||
target across all input samples; | ||
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:==run_IndelRealigner_GATK | ||
---- | ||
Realign indels across all input | ||
samples simultaneously; | ||
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|s| | ||
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:==run_BaseRecalibrator_GATK | ||
---- | ||
Generate base quality score recalibration | ||
(BQSR) table based on read group, reported | ||
quality score, machine cycle, and nucleotide | ||
context; | ||
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|i| | ||
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:==run_ApplyBQSR_GATK | ||
---- | ||
Apply the recalibration to each input | ||
sample sequentially; | ||
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|s| | ||
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:==run_MergeSamFiles_Picard | ||
---- | ||
Merge interval BAMS into recalibrated BAM; | ||
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if (Parallelize by\nchromosome?) is (No) then | ||
:==deduplicate_records_SAMtools | ||
---- | ||
Remove duplicate reads due to | ||
overlap on interval splitting sites; | ||
else (Yes) | ||
endif | ||
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:==run_index_SAMtools | ||
---- | ||
Create index file for recalibrated BAM; | ||
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:==calculate_sha512 | ||
---- | ||
Generate sha512 checksum for | ||
recalibrated BAM and index file; | ||
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split | ||
:==run_GetPileupSummaries_GATK | ||
---- | ||
Summarize counts of reads that support | ||
reference, alternate, and other alleles | ||
for given sites; | ||
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:==run_CalculateContamination_GATK | ||
---- | ||
Calculate the fraction of reads coming | ||
from cross-sample contamination. | ||
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If the input is a paired sample, run | ||
again in matched normal mode; | ||
split again | ||
if (Compute depth\nof coverage?) is (Yes) then | ||
:==run_DepthOfCoverage_GATK | ||
---- | ||
Assess sequence coverage by a wide array | ||
of metrics, partioned by sample, read | ||
group, and library; | ||
endif | ||
end split | ||
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stop | ||
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@enduml | ||
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