miniwdl

miniwdl is a local runner and developer toolkit for the bioinformatics-focused Workflow Description Language (WDL). It includes:

• miniwdl run, which runs WDL tasks and workflows on the local host using Docker (or another container runtime), scheduling tasks in parallel up to the available CPUs and memory

• miniwdl check, a static code quality checker for the WDL development cycle

• the Python WDL package, which provides programmatic access to miniwdl’s WDL parser, type-checker, and runtime

It supports WDL versions 1.2, 1.1, 1.0, and draft-2. To get started:

pip3 install miniwdl   # or: conda install -c conda-forge miniwdl
miniwdl run_self_test

Then follow the Getting Started tutorial. The documentation is organized into:

• Getting started: the tutorial and FAQ

• miniwdl run: reference (run directory structure, task requirements, URI downloads, configuration, caching), optimization guidelines, alternate container runtimes, and command-line options

• Other tools: miniwdl check, miniwdl input_template, and miniwdl zip

• Python development: the WDL package API reference, and codelabs on syntax tree traversal, visualizing workflows, adding WDL functions, and adding a language feature

Links

• miniwdl GitHub repo for source code, issues, and contributions

• OpenWDL GitHub repo for the WDL specification and proposals

• OpenWDL Slack #miniwdl for discussion

• CZI Science sponsors this project

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