checkout actions update #2


	name: Tests

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

	jobs:
	formatting:
	runs-on: ubuntu-latest
	steps:
	- name: Checkout with submodules
	uses: actions/checkout@v4.1
	with:
	submodules: recursive
	fetch-depth: 0
	- name: Formatting
	uses: github/super-linter@v5
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: main
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4.1
	- name: Linting
	uses: snakemake/snakemake-github-action@v1.25.1
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--lint"

	run-workflow:
	runs-on: ubuntu-latest
	needs:
	- linting
	- formatting
	steps:
	- name: Checkout repository with submodules
	uses: actions/checkout@v4.1
	with:
	submodules: recursive
	- name: Test workflow
	uses: snakemake/snakemake-github-action@v1.25.1
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--use-conda --use-singularity --show-failed-logs --cores 2 --conda-cleanup-pkgs cache"
	# - name: Test report
	# uses: snakemake/snakemake-github-action@v1.25.1
	# with:
	# directory: .test
	# snakefile: workflow/Snakefile
	# args: "--use-conda --use-singularity --cores 2 --report report.zip"

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