Merge pull request #204 from hydra-genetics/action_v3 #157
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| name: small integration test | |
| # Controls when the action will run. | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the master and develop branch | |
| push: | |
| branches: | |
| - develop | |
| - master | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| jobs: | |
| integration-small-singularity: | |
| name: integration small data set singularity | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: 3.8 | |
| - name: Build | |
| run: | | |
| echo "Free space:" | |
| df -h | |
| - name: Remove stuff | |
| run: | | |
| sudo rm -rf /usr/share/dotnet | |
| sudo rm -rf /usr/local/lib/android | |
| sudo rm -rf /opt/hostedtoolcache/CodeQL | |
| sudo docker image prune --all --force | |
| - name: Build | |
| run: | | |
| echo "Free space:" | |
| df -h | |
| - name: Install apptainer/singularity | |
| run: | | |
| sudo add-apt-repository -y ppa:apptainer/ppa && sudo apt install -y software-properties-common && sudo apt install -y apptainer-suid | |
| - name: Install requirements.txt | |
| run: | | |
| pip install -r requirements.txt | |
| - name: Install requirements.test.txt | |
| run: | | |
| pip install -r requirements.test.txt | |
| - name: Integration test - small dataset | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs --configfile config.yaml --use-singularity --singularity-args " --cleanenv --bind /home/runner " | |
| - name: Integration test - small dataset PACBIO | |
| working-directory: .tests/integration | |
| run: | | |
| snakemake -s ../../workflow/Snakefile -j 1 --show-failed-logs --configfile config_pacbio.yaml --use-singularity --singularity-args " --cleanenv --bind /home/runner " | |