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integration-tests.yml
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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/[email protected]
- 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/[email protected]
- 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