Integration Tests #99

	name: Integration Tests

	on:
	workflow_call:

	workflow_dispatch:

	schedule:
	- cron: '0 0 * * *'

	jobs:
	test-slurm:
	name: Slurm Test
	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:
	- uses: actions/checkout@v4
	- uses: s-weigand/setup-conda@v1.2.1
	- uses: koesterlab/setup-slurm-action@v1

	- name: Install Sunbeam
	shell: bash
	run: \|
	cd $GITHUB_WORKSPACE
	bash install.sh -e sunbeam -v

	- name: Run Sunbeam
	shell: bash
	run: \|
	cd $GITHUB_WORKSPACE
	source activate sunbeam
	mkdir projects/

	pip install snakemake-executor-plugin-slurm

	sunbeam init --data_fp tests/data/reads/ --profile slurm projects/test/

	sunbeam run --default-resources slurm_account=runner --profile projects/test/ test

	- name: Check output
	shell: bash
	run: \|
	cd $GITHUB_WORKSPACE
	ls -l .snakemake/slurm_logs/ \| grep "rule_test"

	test-apptainer:
	name: Apptainer Test
	runs-on: ubuntu-latest

	steps:
	- uses: actions/checkout@v4
	- uses: s-weigand/setup-conda@v1.2.1
	- uses: eWaterCycle/setup-apptainer@v2
	with:
	apptainer-version: 1.1.2

	- name: Install Sunbeam
	shell: bash
	run: \|
	cd $GITHUB_WORKSPACE
	bash install.sh -e sunbeam -v

	- name: Run Sunbeam
	shell: bash
	run: \|
	cd $GITHUB_WORKSPACE
	source activate sunbeam
	mkdir projects/

	sunbeam init --data_fp tests/data/reads/ --profile apptainer projects/test/

	sunbeam run --profile projects/test/ --docker_tag latest

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