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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:

Tools included in container for development:

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;

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

  • MiniWDL
  • WOMTool
  • sprocket

Getting started

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.