Tests

option to run hipstr #34

	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: create conda env
	uses: conda-incubator/setup-miniconda@v2
	with:
	mamba-version: "*"
	channels: conda-forge,bioconda,defaults
	auto-activate-base: false
	activate-environment: TriosCompassV2
	environment-file: environment.yaml

	- name: check env
	shell: bash -el {0}
	run: \|
	conda info
	pip list \| grep peds
	which snakemake

	- name: Lint workflow alternatively
	shell: bash -el {0}
	run: \|
	snakemake --lint --configfile config/config.yaml

	- 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"

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

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