Added a test profile based on public data #20

	# Adopted from https://github.com/nf-core/modules/blob/master/.github/workflows/test.yml

	name: Lint and -stub on Linux/Docker
	on:
	push:
	branches:
	- dev
	pull_request:

	# Cancel if a newer run is started
	concurrency:
	group: ${{ github.workflow }}-${{ github.event.pull_request.number \|\| github.ref }}
	cancel-in-progress: true

	jobs:
	pre-commit:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- name: Set up Python 3.11
	uses: actions/setup-python@v5
	with:
	python-version: 3.11
	cache: "pip"

	- name: Install pre-commit
	run: pip install pre-commit

	- name: Run pre-commit
	run: pre-commit run --all-files

	stub-test:
	runs-on: ubuntu-latest
	name: Run stub test with docker
	env:
	NXF_ANSI_LOG: false

	steps:
	- uses: actions/checkout@v4

	- name: Install Nextflow
	uses: nf-core/setup-nextflow@v1
	with:
	version: "23.04.4"

	- name: Run stub-test
	run: \|
	nextflow run \
	main.nf \
	-profile local,docker \
	-stub \
	-params-file tests/stub/params.json

	confirm-pass:
	runs-on: ubuntu-latest
	needs: [pre-commit, stub-test]
	if: always()
	steps:
	- name: All tests ok
	if: ${{ success() \|\| !contains(needs.*.result, 'failure') }}
	run: exit 0
	- name: One or more tests failed
	if: ${{ contains(needs.*.result, 'failure') }}
	run: exit 1

	- name: debug-print
	if: always()
	run: \|
	echo "toJSON(needs) = ${{ toJSON(needs) }}"
	echo "toJSON(needs..result) = ${{ toJSON(needs..result) }}"

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