This repository is a community-maintained collection of WDL modules for some of the most widely used tools in bioinformatics. It is not intended to be exhaustive—the goal is to cover the tools the community reaches for most often and to demonstrate best practices for writing WDL tasks and workflows. Each module can be imported directly into your own workflows as a stable, versioned starting point.

Licensing

This repository is dual-licensed under MIT or Apache-2.0 at your option.

Every module in this repository contains only workflow logic—that is, WDL code that describes how to run tools, not the tools themselves. The tools that modules reference are independent software projects with their own licenses, which may include copyleft licenses such as the GPL. Maintaining that separation helps support this repository’s permissive licensing model: we describe how to invoke a tool, but we do not include the tool itself.

Boundaries we maintain

Because including downstream tools in this repository could affect its permissive licensing, we maintain strict separation between our workflow code and the software it orchestrates:

Downstream tools do not live in this repository. We do not check in third-party source code, binaries, libraries, scripts copied from upstream or downstream projects, or container images—regardless of their license. Each external tool is an independent project maintained and distributed by its own authors under its own terms.
No prebuilt artifacts are published from this repository. We do not produce container images, binary bundles, or any other artifact that incorporates third-party software.
No mirroring or caching of external software. This repository does not operate as a registry, mirror, cache, or distribution channel for anything other than the WDL modules themselves.
No linking or embedding. Modules must invoke external tools as separate executables through simple command-line calls. They must not dynamically link to, share memory with, or otherwise incorporate third-party code at the language level.
Care with helper materials. Contributors must not introduce third-party code or other non-workflow material through helper scripts, example assets, test fixtures, CI artifacts, or similar side materials. Any such material must be reviewed carefully to ensure it does not copy, embed, or redistribute third-party software.

Pull requests that introduce third-party source code, binaries, container images, or other non-workflow artifacts into the repository will be closed without merging with this section of the README.md referenced.

Modules do reference external container images—typically those officially distributed by the tool's authors or hosted on BioContainers—but those images are fetched independently by the workflow engine at runtime and remain governed by their own license terms. Contributors and downstream users are responsible for reviewing and complying with any license obligations associated with the software they choose to pull and execute.

Tool licenses

Each tool referenced by a module carries its own license, independent of this repository's dual license. The primary concern when evaluating tool licenses is whether a license imposes obligations that extend beyond simple distribution—in particular, licenses that trigger copyleft requirements through network interaction, SaaS deployment, or similar use-based mechanisms pose risks that architectural separation alone cannot mitigate.

The lists below identify licenses that are pre-approved for use and those that are prohibited outright. If the tool you wish to reference carries a license not found in either list, include a license review in your pull request (follow the template); it will be evaluated before the module is accepted.

Approved Licenses

The following licenses have been approved (listed in alphabetical order):

Prohibited Licenses

The following licenses are incompatible with this repository regardless of how a tool is invoked:

GNU Affero General Public License v3.0 only · AGPL-3.0-only
- The AGPL triggers copyleft obligations when software is accessed over a network—not just when it is distributed. Because workflow engines may execute tools across networked infrastructure, the AGPL's scope extends beyond what architectural separation alone can address.

Expectations for contributors

When you submit a contribution, you are representing that:

You have the right to license your contribution under the terms of this repository.
Your contribution contains only original workflow logic and does not include third-party source code, binaries, container images, or copied third-party scripts or similar materials.
You have identified every external tool your module invokes and included the license for each tool in the pull request description according to the pull request template. Modules that reference tools with an unknown license will not be accepted.
When updating a module to reference a new version of an external tool, you have re-verified that the tool's license has not changed in a way that is incompatible with this repository's policies. The license must be confirmed and stated in the pull request description for every version bump, not just the initial contribution.
None of the tools your module references are released under the licenses in the prohibited list above or any other license that triggers obligations upon the concerns outlined in the tool license section.

We have included a pull request template that outlines these requirements.

Contributing

See CONTRIBUTING.md.