Tests

black formatting #162

	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: .test_se
	snakefile: workflow/Snakefile
	args: "--lint"

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

	- name: Test workflow SE
	uses: snakemake/[email protected]
	with:
	directory: .test_se
	snakefile: workflow/Snakefile
	args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"

	- name: Test report SE
	uses: snakemake/[email protected]
	with:
	directory: .test_se
	snakefile: workflow/Snakefile
	args: "--report report.zip"

	# - name: Test workflow PE
	# uses: snakemake/[email protected]
	# with:
	# directory: .test_pe
	# snakefile: workflow/Snakefile
	# args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache"
	#
	# - name: Test report PE
	# uses: snakemake/[email protected]
	# with:
	# directory: .test_pe
	# snakefile: workflow/Snakefile
	# args: "--report report.zip"

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