Merge pull request #11 from openwdl/docs

update documentation. Closes #5

.github/workflows/integration.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       matrix:
         test:
-          - integration
+          - test-example
     steps:
     - uses: actions/checkout@v4
     - name: Set up Python
@@ -26,15 +26,16 @@ jobs:
         pip3 install miniwdl
         pip3 install pytest-workflow
         mkdir ~/temp
-    - name: Run unit tests
+    - name: Run integration tests
       # Use --symlink to limit disk usage.
       run: >- 
         pytest --keep-workflow-wd-on-fail --git-aware --tag ${{ matrix.test }} 
         --symlink tests/ --basetemp ~/temp
     - name: Check miniwdl log in case of failure.
       if: ${{ failure() }}
-      # Get the last 1000 lines of the miniwdl log to catch the error.
-      run: bash -c 'tail -n 1000 /home/runner/temp/*/task.out'
+      run: >-
+         # Get the last 1000 lines of the miniwdl log to catch the error.
+         bash -c 'tail -n 1000 /home/runner/temp/*/workflow.log'
     - name: Check job stderr messages in case of failure
       if: ${{ failure() }}
       run: >- 
@@ -46,4 +47,4 @@ jobs:
       run: >- 
         bash -c '
         for file in $(find /home/runner/temp/ -name stdout.txt); 
-        do echo $file; cat $file; done'
+        do echo $file; cat $file; done'

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.
 ```

tests/inputs/example.inputs.json

@@ -0,0 +1,5 @@
+{
+    "example.hello.name": "Test"
+  }
+
+

tests/test.example.yaml

@@ -0,0 +1,6 @@
+- name: test-example
+  command: miniwdl run -i tests/inputs/example.inputs.json -d test-output/ hello.wdl
+  files:
+    - path: test-output/_LAST/out/hello.response/stdout.txt
+      contains:                        
+        - 'hello Test!'