workflow-template-wdl

This repository is a template WDL respository.

Creating a repository from a template is similar to forking a repository, but there are important differences:

• A new fork includes the entire commit history of the parent repository, while a repository created from a template starts with a single commit.
• Commits to a fork don't appear in your contributions graph, while commits to a repository created from a template do appear in your contribution graph.
• A fork can be a temporary way to contribute code to an existing project, while creating a repository from a template starts a new project quickly.

Devcontainer

This repo includes a devcontainer configuration which will create a GitHub Codespace for WDL development!

Devcontainer specs:

• DevContainer config
• Dockerfile

Tools included in container for development:

• MiniWDL
• Cromwell
• WOMTool
• sprocket
• shellcheck

Dockstore template

This repo includes a Dockestore template for automatic registering of you workflow using the Dockstore Github App

Unit and Integration Tests

This repo uses pytest-workflow for testing WDL for unit and integration tests. Examples can be found in;

• unit test
• integration test

Additionally, the wdl syntax is checked using the following tools:

• MiniWDL
• WOMTool
• sprocket

Getting started

• Create a new repo in GitHub using this template.
• Open the repo in Codespaces

Setup Verification

Verify tools

• verify miniwdl via miniwdl --help
• verify cromwell via cromwell --help

Test miniwdl installation

• open a command prompt and run...
• miniwdl run_self_test
• …30 second test of the installation with a built-in workflow
• should print numerous log messages, and conclude with...
• miniwdl run_self_test OK

Test cromwell/womtools installation

• open a command prompt and run...
• cromwell run test/test.wdl
• …test of the example workflow
• should print numerous log messages, and conclude with...
• Workflow HelloWorld complete. Final Outputs:
• womtool --help
• should print help documentation

Test sprocket installation

• open a command prompt and run...
• sprocket lint test/test.wdl
• should print the following error

workflow HelloWorld {
^ The following tokens are required: document.