Re-instate the CLI for non-wdl work #4

	name: Test GC/MS workflow

	on:
	push:
	workflow_dispatch:

	jobs:
	run-miniwdl:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout repository
	uses: actions/checkout@v2

	- name: Set up Python
	uses: actions/setup-python@v2
	with:
	python-version: '3.8'

	- name: Install Docker
	run: \|
	curl -fsSL https://get.docker.com -o get-docker.sh
	sh get-docker.sh
	sudo usermod -aG docker $USER

	- name: Build Docker Image
	run: \|
	docker build -t local-metams:latest .

	- name: Install MiniWDL
	run: \|
	python -m pip install --upgrade pip
	pip install miniwdl

	- name: Run GCMS WDL with pushed Docker Image
	run: \|
	miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files

	- name: Run GCMS WDL with local Docker Image based on Dockerfile
	run: \|
	miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms_local_docker.json --verbose --no-cache --copy-input-files

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