Add error handling and combine test data downloads #19
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| name: Test workflows | |
| on: | |
| push: | |
| workflow_dispatch: | |
| jobs: | |
| run-miniwdl: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: '3.8' | |
| - name: Install Docker | |
| run: | | |
| curl -fsSL https://get.docker.com -o get-docker.sh | |
| sh get-docker.sh | |
| sudo usermod -aG docker $USER | |
| - name: Install MiniWDL | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install miniwdl | |
| - name: Download test data for LCMS metabolomics and Lipidomics | |
| run: | | |
| make get-test-data | |
| - name: Run Lipidomics WDL with lipidomics test data | |
| run: | | |
| miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics.json --verbose --no-cache --copy-input-files | |
| # This will fail until the new Docker image is pushed to Docker Hub | |
| #- name: Run LCMS metabolomics WDL with LCMS metabolomics test data | |
| # run: | | |
| # make wdl-run-lcms-metab | |
| - name: Run GCMS WDL with pushed Docker Image | |
| run: | | |
| miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms.json --verbose --no-cache --copy-input-files | |
| - name: Build Docker Image | |
| run: | | |
| docker build -t local-metams:latest . | |
| - name: Run GCMS WDL with local Docker Image based on Dockerfile | |
| run: | | |
| miniwdl run wdl/metaMS_gcms.wdl -i wdl/metams_input_gcms_local_docker.json --verbose --no-cache --copy-input-files | |
| - name: Run Lipidomics WDL with local Docker Image based on Dockerfile | |
| run: | | |
| miniwdl run wdl/metaMS_lcmslipidomics.wdl -i wdl/metams_input_lipidomics_local_docker.json --verbose --no-cache --copy-input-files | |
| - name: Run LCMS metabolomics WDL with local Docker Image based on Dockerfile | |
| run: make wdl-run-lcms-metab-local | |
| - name: Remove test data | |
| run: | | |
| rm -rf test_data |