Fixing bug where files are saved to launch directory by moving the output to working directory #38

	name: End-to-end MGS workflow test

	on: [pull_request]

	jobs:
	test:
	runs-on: ubuntu-latest

	steps:
	- name: Checkout
	uses: actions/checkout@v4

	- name: Set up JDK 11
	uses: actions/setup-java@v4
	with:
	java-version: '11'
	distribution: 'adopt'

	- name: Setup Nextflow latest-edge
	uses: nf-core/setup-nextflow@v1
	with:
	version: "latest-edge"

	- name: Install nf-test
	run: \|
	wget -qO- https://get.nf-test.com \| bash
	sudo mv nf-test /usr/local/bin/

	- name: Run index workflow
	run: nf-test test --tag index --verbose

	- name: Clean docker for more space
	run: \|
	docker kill $(docker ps -q) 2>/dev/null \|\| true
	docker rm $(docker ps -a -q) 2>/dev/null \|\| true
	docker rmi $(docker images -q) -f 2>/dev/null \|\| true
	docker system prune -af --volumes

	- name: Clean up nf-test dir
	run: sudo rm -rf .nf-test

	- name: Run run workflow
	run: nf-test test --tag run --verbose

	- name: Run run_validation workflow
	run: nf-test test --tag validation --verbose

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