Tests

5' trimming option for fastp optional (to be used only with Arima Hi-… #89

	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/snakemake-github-action@v1.24.0
	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/snakemake-github-action@v1.24.0
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--use-conda --show-failed-logs --cores 3 --conda-cleanup-pkgs cache --all-temp"

	- name: Test report
	uses: snakemake/snakemake-github-action@v1.24.0
	with:
	directory: .test
	snakefile: workflow/Snakefile
	args: "--report report.zip"

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