- A package for parsing and visualizing WDL files
- Uses MiniWDL to parse a WDL file into edges, nodes, inputs, and outputs
- Creates a
mermaid.jsfile to plot a flowchart of the WDL file
To install, run
pip install git+https://github.com/chanzuckerberg/miniwdl-viz.git
or
git clone https://github.com/chanzuckerberg/miniwdl-viz.git
cd miniwdl-viz
python3 setup.py install
To run just the parser, run
miniwdl_parser /path/to/wdl
To run the wdl to mermaid plot run:
wdl_to_mermaid /path/to/wdl --plot-flowchart
This uses matplotlib and makes a call to the mermaid.ink site to generate the plot
To simply output the mermaid flowchart as a string, run
wdl_to_mermaid /path/to/wdl --print-flowchart
More options can be found using
miniwdl_parser -h
or
wdl_to_mermaid -h
The parser should be able to handle most WDL workflows that miniwdl can handle. An example of a simple vs a more complex WDL file is below:
This was generated with the command wdl_to_mermaid wdl/phylotree-ng/run.wdl --print-flowchart --flowchart-dir TD
flowchart LR
classDef done fill:#f96
call-GetSampleContigFastas{{"GetSampleContigFastas"}}
call-GetReferenceAccessionFastas{{"GetReferenceAccessionFastas"}}
call-RunSKA{{"RunSKA"}}
call-ComputeClusters{{"ComputeClusters"}}
call-GenerateClusterPhylos{{"GenerateClusterPhylos"}}
call-AddSampleNamesToDistances{{"AddSampleNamesToDistances"}}
call-AddSampleNamesToVariants{{"AddSampleNamesToVariants"}}
subgraph if-L88C5["GenerateClusterPhylos.phylotree_newick != None"]
call-AddSampleNamesToNewick{{"AddSampleNamesToNewick"}}
end
call-FetchNCBIMetadata{{"FetchNCBIMetadata"}}
call-GetSampleContigFastas --> call-RunSKA
call-GetReferenceAccessionFastas --> call-RunSKA
call-RunSKA --> call-ComputeClusters
call-ComputeClusters --> call-GenerateClusterPhylos
call-RunSKA --> call-GenerateClusterPhylos
call-RunSKA --> call-AddSampleNamesToDistances
call-GenerateClusterPhylos --> call-AddSampleNamesToVariants
call-GenerateClusterPhylos --> if-L88C5
call-GenerateClusterPhylos --> call-AddSampleNamesToNewick
This was generated with the command: wdl_to_mermaid wdl/complex-miniwdl/joint-discovery-gatk4-local.wdl --print-flowchart
flowchart TD
classDef done fill:#f96
call-DynamicallyCombineIntervals{{"DynamicallyCombineIntervals"}}
decl-unpadded_intervals>"unpadded_intervals"]
subgraph scatter-L120C3-idx["range(length(unpadded_intervals))"]
call-ImportGVCFs{{"ImportGVCFs"}}
call-GenotypeGVCFs{{"GenotypeGVCFs"}}
call-HardFilterAndMakeSitesOnlyVcf{{"HardFilterAndMakeSitesOnlyVcf"}}
end
call-SitesOnlyGatherVcf{{"SitesOnlyGatherVcf"}}
call-IndelsVariantRecalibrator{{"IndelsVariantRecalibrator"}}
subgraph if-L195C3["num_gvcfs > 10000"]
call-SNPsVariantRecalibratorCreateModel{{"SNPsVariantRecalibratorCreateModel"}}
scatter-L219C3-idx
call-SNPGatherTranches{{"SNPGatherTranches"}}
end
subgraph scatter-L219C3-idx["range(length(HardFilterAndMakeSitesOnlyVcf.sites_only_vcf))"]
call-SNPsVariantRecalibratorScattered{{"SNPsVariantRecalibratorScattered"}}
end
subgraph if-L252C3["num_gvcfs <= 10000"]
call-SNPsVariantRecalibratorClassic{{"SNPsVariantRecalibratorClassic"}}
end
decl-is_small_callset>"is_small_callset"]
subgraph scatter-L279C3-idx["range(length(HardFilterAndMakeSitesOnlyVcf.variant_filtered_vcf))"]
call-ApplyRecalibration{{"ApplyRecalibration"}}
if-L299C5
end
subgraph if-L299C5["!is_small_callset"]
call-CollectMetricsSharded{{"CollectMetricsSharded"}}
end
subgraph if-L317C3["is_small_callset"]
call-FinalGatherVcf{{"FinalGatherVcf"}}
call-CollectMetricsOnFullVcf{{"CollectMetricsOnFullVcf"}}
end
subgraph if-L344C3["!is_small_callset"]
call-GatherMetrics{{"GatherMetrics"}}
end
call-DynamicallyCombineIntervals --> decl-unpadded_intervals
decl-unpadded_intervals --> scatter-L120C3-idx
decl-unpadded_intervals --> call-ImportGVCFs
scatter-L120C3-idx --> call-ImportGVCFs
call-ImportGVCFs --> call-GenotypeGVCFs
decl-unpadded_intervals --> call-GenotypeGVCFs
scatter-L120C3-idx --> call-GenotypeGVCFs
call-GenotypeGVCFs --> call-HardFilterAndMakeSitesOnlyVcf
scatter-L120C3-idx --> call-HardFilterAndMakeSitesOnlyVcf
call-HardFilterAndMakeSitesOnlyVcf --> call-SitesOnlyGatherVcf
call-SitesOnlyGatherVcf --> call-IndelsVariantRecalibrator
call-SitesOnlyGatherVcf --> call-SNPsVariantRecalibratorCreateModel
call-HardFilterAndMakeSitesOnlyVcf --> scatter-L219C3-idx
call-HardFilterAndMakeSitesOnlyVcf --> call-SNPsVariantRecalibratorScattered
scatter-L219C3-idx --> call-SNPsVariantRecalibratorScattered
call-SNPsVariantRecalibratorCreateModel --> call-SNPsVariantRecalibratorScattered
call-SNPsVariantRecalibratorScattered --> call-SNPGatherTranches
call-SitesOnlyGatherVcf --> call-SNPsVariantRecalibratorClassic
call-HardFilterAndMakeSitesOnlyVcf --> scatter-L279C3-idx
scatter-L279C3-idx --> call-ApplyRecalibration
call-HardFilterAndMakeSitesOnlyVcf --> call-ApplyRecalibration
call-IndelsVariantRecalibrator --> call-ApplyRecalibration
call-SNPsVariantRecalibratorScattered --> call-ApplyRecalibration
call-SNPsVariantRecalibratorClassic --> call-ApplyRecalibration
call-SNPGatherTranches --> call-ApplyRecalibration
decl-is_small_callset --> if-L299C5
call-ApplyRecalibration --> call-CollectMetricsSharded
scatter-L279C3-idx --> call-CollectMetricsSharded
decl-is_small_callset --> if-L317C3
call-ApplyRecalibration --> call-FinalGatherVcf
call-FinalGatherVcf --> call-CollectMetricsOnFullVcf
decl-is_small_callset --> if-L344C3
call-CollectMetricsSharded --> call-GatherMetrics
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Please disclose security issues responsibly by contacting [email protected].