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.

Engine	Type	Version	Local	Slurm	IBM LSF	Amazon AWS	Microsoft Azure	Google Cloud
AWS HealthOmics	Hosted	v1.1	—	—	—	✓	—	—
Cromwell	Binary	v1.0	✓	✓	✓	✓	—	✓
dxCompiler	Binary	v1.1	—	—	—	✓ (DNAnexus)	✓ (DNAnexus)	—
miniwdl	Binary	v1.2	✓	✓ (plugin)	✓ (plugin)	✓ (plugin)	—	—
Sprocket	Binary	v1.3	✓	✓	✓	✓ (TES)	✓ (TES)	✓ (TES)
Terra	Hosted	v1.0	—	—	—	—	—	✓
Toil	Binary	v1.1	✓	✓	✓	✓	—	✓

IDE Support

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

Name	Active*	Editor	Supports
Sprocket (LSP)	★	Editors with LSP	Formatting, linting, snippets, syntax highlighting, and validation.
wdl-mode	☆	Emacs	Syntax highlighting.
poly-wdl	☆	Emacs	Integration with polymode.
Sprocket for IntelliJ	★	JetBrains IDEs	Formatting, completions, diagnostics, navigation, and syntax highlighting.
Winstanly WDL	☆	JetBrains IDEs	Linting and syntax highlighting.
wdl-sublime	☆	Sublime Text	Syntax highlighting.
sprocket.nvim	★	Neovim	Formatting, linting, snippets, syntax highlighting, and validation.
wdl-vim	☆	Vim	Syntax highlighting.
Sprocket (extension)	★	Visual Studio Code	Formatting, linting, snippets, syntax highlighting, and validation.
Syntax Highlighter	☆	Visual Studio Code	Syntax highlighting.
Sprocket for Zed	★	Zed	Completions, diagnostics, navigation, and syntax highlighting.

* Active: A filled star (★) marks a project with a commit or release within the past 12 months; an unfilled star (☆) marks one without qualifying activity. Archived and deprecated projects receive an unfilled star.

Development Tools

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

Name	Active*	Category	Description
wdl-tests	☆	Conformance testing	Conformance tests for WDL execution engines. (Deprecated)
wdl-aid	☆	Documentation generation	"Automatic input generation for WDL worflows."
pytest-workflow	☆	Testing	Testing framework for workflow languages (including WDL).
wdl-atlas	★	Documentation generation	Generate interactive HTML and workflow diagrams.
wdldoc	☆	Documentation generation	"Create WDL documentation using Markdown."
wdl-packager	☆	Package management	"Package a WDL and imports into a zip file."
pytest-wdl	☆	Testing	"WDL plugin for pytest."
spectool	★	Conformance testing	"A conformance testing tool for WDL."

Community Workflows

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

Name	Description
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 WDL Library — Fred Hutch Cancer Center	A centralized collection of reusable WDL modules and pipelines for bioinformatics research, featuring tested components for tools like STAR, BWA, GATK, and more. See documentation for guides and usage examples.