Ensure that only directories get picked up for sample names #46

	name: Tests

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

	jobs:
	formatting:

	runs-on: ubuntu-latest

	steps:

	- uses: actions/checkout@v1
	- name: Formatting
	uses: github/super-linter@v4
	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@v1
	- name: Set up test data
	working-directory: .test
	run: \|
	python make_test_data.py

	run-workflow:

	runs-on: ubuntu-latest

	steps:

	- name: Checkout repository
	uses: actions/checkout@v2
	with:
	submodules: recursive

	- name: Download test data
	working-directory: .test
	run: \|
	python make_test_data.py

	- name: Test workflow
	uses: snakemake/snakemake-github-action@v1.23.0
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--use-conda --show-failed-logs --cores 2 --conda-cleanup-pkgs cache --all-temp"

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