Test pipeline on GHA #5

	name: Test snakemake 🐍 pipeline
	on:
	pull_request:
	branches:
	- main

	jobs:
	test-pipeline:
	runs-on: ubuntu-latest
	services:
	mysql:
	image: mysql:8.0
	env:
	MYSQL_ROOT_PASSWORD: root
	ports:
	- "8888:3306"
	options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
	steps:
	- name: Setup pipeline 🚰
	uses: actions/checkout@v4

	- name: Setup slurm 🐌
	uses: koesterlab/setup-slurm-action@v1

	- name: Cache conda 🏦
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if environment.yml has not changed
	CACHE_NUMBER_CONDA: 0
	with:
	path: ~/conda_pkgs_dir
	key:
	${{ runner.os }}-conda-${{ env.CACHE_NUMBER_CONDA }}-${{hashFiles('environment.yml') }}

	- name: Setup conda 🐍
	uses: conda-incubator/setup-miniconda@v3
	with:
	activate-environment: aatrnaseqpipe
	environment-file: environment.yml
	use-only-tar-bz2: true

	- name: Cache test data 🏦
	uses: actions/cache@v4
	env:
	# Increase this value to reset cache if environment.yml has not changed
	CACHE_NUMBER_TEST_DATA: 0
	with:
	path: ~/.test
	key:
	${{ runner.os }}-test-data-${{ env.CACHE_NUMBER_TEST_DATA }}

	- name: Download test data
	run: \|
	cd .test
	bash dl_test_data.sh

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