pre-commit #459

	name: MosaiCatcher basic checks

	on:
	schedule:
	# Run every Sunday at 00:00 UTC on the master branch
	- cron: "0 0 * * 0"
	# branches:
	# - master
	push:
	branches:
	- "*"
	- "!master"

	jobs:
	# WORK
	Formatting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/[email protected]

	- name: Formatting
	uses: github/super-linter@v4
	env:
	VALIDATE_ALL_CODEBASE: false
	DEFAULT_BRANCH: master
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	VALIDATE_SNAKEMAKE_SNAKEFMT: true

	Linting:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/[email protected]
	- name: Linting
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	args: "--lint"
	Testing:
	runs-on: ubuntu-latest
	# needs:
	# - Linting
	# - Formatting
	steps:
	- uses: actions/[email protected]
	- name: Testing data
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	stagein: "conda config --set channel_priority flexible"
	args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba -p --verbose --debug"
	- name: Testing report
	uses: snakemake/[email protected]
	with:
	directory: .
	snakefile: ./workflow/Snakefile
	args: "--cores 1 --use-conda --latency-wait 60 --configfile .tests/config/simple_config.yaml --conda-frontend mamba --report report.zip"

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