Several updates for making Malaria Joint Calling easier. (#449) #40

	name: Build and deploy site to GitHub Pages

	on:
	push:
	branches:
	- main
	workflow_dispatch:

	jobs:
	github-pages:
	runs-on: macos-latest
	steps:
	- name: Checkout Repository
	uses: actions/checkout@v3

	- name: Cache node_modules
	uses: actions/cache@v3
	with:
	path: "**/node_modules"
	key: ${{ runner.os }}-modules-${{ env.cache-name }}-${{ hashFiles('**/yarn.lock') }}

	- name: Setup Python
	uses: actions/setup-python@v4
	with:
	python-version: '3.10'

	- name: Install Requirements
	run: \|
	brew install graphviz
	python3 -m pip install --upgrade pip
	python3 -m pip install wdldoc~=1.7.0
	python3 -m pip install mkdocs~=1.4.2
	python3 -m pip install graphviz~=0.20.1
	- name: Create Site Homepage
	run: \|
	mkdir -p docs
	cp README.md docs/index.md && sed -i.bak 's/\.\/docs/\.\//g' docs/index.md
	- name: Build Docs
	run: \|
	wdldoc --debug -o docs ./wdl/pipelines ./wdl/tasks

	python3 ./scripts/git_page/md_post_process.py --debug --md_dir ./docs

	python3 ./scripts/git_page/create_wdl_visual.py --debug ./wdl/pipelines ./wdl/tasks --output_path ./docs/dot

	python3 ./scripts/git_page/add_dot_link_to_md.py --md_dir ./docs/workflows --dot_dir ./docs/dot

	mkdocs build
	- name: Deploy
	uses: JamesIves/github-pages-deploy-action@releases/v4
	with:
	BRANCH: gh-pages
	FOLDER: ./site

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