format #30

	name: Tests

	on:
	push:
	branches:
	- main
	pull_request:
	branches-ignore: []

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout with submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Formatting
	uses: github/super-linter@v5
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: main
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Linting
	uses: snakemake/snakemake-github-action@v1.22.0
	with:
	directory: tests
	snakefile: workflow/Snakefile
	args: "--configfile tests/config.yaml --lint"

	run-workflow:
	runs-on: ubuntu-latest
	needs:
	- linting
	- formatting
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v3
	with:
	submodules: recursive
	lfs: true
	- name: Setup Python 3.11
	uses: actions/setup-python@v2
	with:
	python-version: 3.11
	- name: Add Conda to system path
	run: \|
	echo $CONDA/bin >> $GITHUB_PATH
	- name: Install dependencies
	run: \|
	conda install -c conda-forge mamba
	- name: Setup snakemake
	run: \|
	mamba install -c conda-forge -c bioconda snakemake singularity
	- name: Run workflow
	run: \|
	snakemake --directory tests --configfile tests/config.yaml --profile tests/profile --snakefile workflow/Snakefile

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