diff --git a/README.md b/README.md index 66a82d8..3220cf5 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,48 @@ # workflow-template-wdl -This repo includes a devcontainer configuration which will create a GitHub Codespace for WDL development! +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](.devcontainer/devcontainer.json) - [Dockerfile](.devcontainer/Dockerfile) -# Getting started +Tools included in container for development: +- [MiniWDL](https://github.com/chanzuckerberg/miniwdl) +- [Cromwell](https://github.com/broadinstitute/cromwell) +- [WOMTool](https://cromwell.readthedocs.io/en/stable/WOMtool/) +- [sprocket](https://github.com/stjude-rust-labs/sprocket) +- [shellcheck](https://github.com/koalaman/shellcheck) + +## Dockstore template + +This repo includes a [Dockestore](https://dockstore.org/) [template](.github/.dockstore.yml) for automatic registering of you workflow using the [Dockstore Github App](https://docs.dockstore.org/en/stable/getting-started/github-apps/github-apps-landing-page.html) + +## Unit and Integration Tests + +This repo uses [pytest-workflow](https://pytest-workflow.readthedocs.io/) for testing WDL for unit and integration tests. Examples can be found in; +- [unit test](.github/workflows/unit.yml) +- [integration test](.github/workflows/integration.yml) + +Additionally, the [wdl syntax](.github/workflows/lint.yml) is checked using the following tools: +- MiniWDL +- WOMTool +- sprocket + +## Getting started - Create a new repo in GitHub using this [template](https://github.com/openwdl/workflow-template-wdl/generate). - Open the repo in [Codespaces](../../codespaces) -## Setup Verification +### Setup Verification #### Verify tools @@ -40,7 +72,7 @@ Devcontainer specs: - open a command prompt and run... - `sprocket lint test/test.wdl` - should print the following error -- ``` +``` workflow HelloWorld { ^ The following tokens are required: document. ```