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Ecosystem

WDL has a rich, distributed ecosystem of interconnected developer tools and execution engines to ensure (a) users can quickly write high-quality, idiomatic workflows, and (b) scaling the execution of those workflows within any computation environment is a breeze.

TIP

The WDL ecosystem is rapidly evolving, and, while we're always looking to expand the list of known ecosystem tools, sometimes tools get missed. If you know of a tool that needs to be listed here but isn't, we encourage you to create a pull request and let us know!

Execution Engines

The following list contains the known execution engines listed alphabetically.

EngineLocalHPCCloud
AWS HealthOmics
Hosted Platform
Support WDL v1.1
Slurm
IBM LSF
Amazon AWS
Microsoft Azure
Google Cloud
Cromwell
Binary/Executable
Support WDL v1.0
Slurm
IBM LSF
Amazon AWS
Microsoft Azure
Google Cloud
dxCompiler
Binary/Executable
Support WDL v1.1 and v2.0
Slurm
IBM LSF
Amazon AWS*
Microsoft Azure*
Google Cloud

* via DNAnexus
miniwdl
Binary/Executable
Support WDL v1.1
Slurm (plugin)
IBM LSF (plugin)
Amazon AWS (plugin)
Microsoft Azure
Google Cloud
Terra
Hosted Platform
Support WDL v1.0
Slurm
IBM LSF
Amazon AWS
Microsoft Azure
Google Cloud
Toil
Binary/Executable
Support WDL v1.1
Slurm
IBM LSF
Amazon AWS
Microsoft Azure
Google Cloud

IDE Support

Extensions and other IDE support tools listed sorted by the editor.

NameEditorSupports
Sprocket (LSP)Editors with LSPFormatting, linting, snippets, syntax highlighting, and validation.
wdl-modeEmacsSyntax highlighting.
poly-wdlEmacsIntegration with polymode.
Winstanly WDLJetBrainsLinting and syntax highlighting.
wdl-sublimeSublime TextSyntax highlighting.
wdl-vimVimSyntax highlighting.
Sprocket (extension)Visual Studio CodeFormatting, linting, snippets, syntax highlighting, and validation.
Syntax HighlighterVisual Studio CodeSyntax highlighting.

Development Tools

The following are tools to enhance the experience of working with WDL sorted by the category.

NameCategoryDescription
wdl-testsConformance testingConformance tests for WDL execution engines.
wdl-aidDocumentation generation"Automatic input generation for WDL worflows."
pytest-workflowTestingTesting framework for workflow languages (including WDL).
wdldocDocumentation generation"Create WDL documentation using Markdown."
wdl-packagerPackage management"Package a WDL and imports into a zip file."
pytest-wdlTesting"WDL plugin for pytest."

Community Workflows

The following is an incomplete list of large WDL workflow repositories sorted by name.

NameDescription
BioWDL
LUMC
"Bioinformatics workflows and tasks, written in WDL." BioWDL is a large GitHub organization that contains the WDL workflows developed at LUMC (link).
Chan Zuckerberg
Chan Zuckerberg Initiative
Official repository for the WDL workflows developed at the Chan Zuckerberg Initiative for the CZID platform (link).
Dockstore
Multiple
Dockstore describes itself as "an app store for bioinformatics"—it's an open source platform for sharing analytical tools and workflows. WDL is one of the supported languages.
ENCODE
ENCODE Consortium
Official repository of the ENCODE Data Coordinating Center's Uniform Processing Pipelines. These pipelines are designed to "create high-quality, consistent, and reproducible data" for the ENCODE project.
GATK
Broad Institute
Official GATK best practices workflows developed at and published by the Broad Institute's Data Sciences Platform.
PacBio
Pacific Biosciences
Official repository for the best practices workflows for PacBio data.
St. Jude Cloud
St. Jude Children's Research Hospital
Official repository for data processing pipelines used on St. Jude Cloud (link).
Thiagen
Theiagen Genomics
Official repository of Thiagen's WDL workflows.
WARP
Broad Institute
WARP stands for "WDL Research Analysis Pipelines" and contains cloud-optimized pipelines for processing biological data from the Broad Institute Data Sciences Platform.
WILDS
Fred Hutch
Official repositories of the Workflows for Integration of Large Data and Software (WILDS) developed at the Fred Hutch Data Science Lab.