Enable linter snakemke in snakemkae CI - enforece snakemake qulaity #109

	name: Snakemake CI

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

	jobs:
	build:
	runs-on: ubuntu-latest
	strategy:
	fail-fast: true
	matrix:
	python-version: ["3.11.2"]
	poetry-version: ["1.8.3"]

	steps:
	- name: Checkout Code
	uses: actions/checkout@v4
	with:
	fetch-depth: 0

	# Run Super-Linter only on Snakefile and .smk files
	- name: Lint Snakefiles Only
	uses: github/super-linter/slim@v5
	env:
	VALIDATE_SNAKEMAKE_SNAKEFMT: true
	FILTER_REGEX_INCLUDE: '(^Snakefile$\|.*\.smk$)' # Only include Snakefile and .smk files
	GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
	DISABLE_ERRORS: true

	- name: Set up Python ${{ matrix.python-version }}
	uses: actions/setup-python@v4
	with:
	python-version: ${{ matrix.python-version }}
	cache: "pip"

	- uses: mamba-org/setup-micromamba@v1
	with:
	micromamba-version: '1.5.6-0'
	environment-file: environment.yml
	init-shell: >-
	bash
	cache-environment: true
	post-cleanup: 'all'

	- name: Install dependencies
	run: \|
	pip install -e .
	pip install pytest
	pip install snakefmt==0.10.2
	- name: Snakemake Linting
	run: \|
	snakefmt workflow/

	- name: Snakemake Testing
	run: \|
	pytest workflow/.tests

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