Tests

Working to the next release #656

	name: Tests

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

	jobs:
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v2
	- 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@v2
	- name: Lint workflow
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: workflow/Snakefile
	args: "--lint"

	Testing:
	runs-on: ubuntu-latest
	needs:
	- Linting
	- Formatting
	steps:
	- uses: actions/checkout@v2

	- name: Test workflow
	uses: snakemake/[email protected]
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp --configfile config.yml"

	# pixi test
	Test:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4
	- uses: prefix-dev/[email protected]
	with:
	pixi-version: v0.37.0
	cache: true
	#auth-host: prefix.dev
	#auth-token: ${{ secrets.PREFIX_DEV_TOKEN }}
	- run: pixi run test

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