Fix CI Testing (Continued) #6
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| push: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| name: Tests | |
| jobs: | |
| test: | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| nextflow_version: ["21.04.3", "23.10.1"] | |
| name: Run tests | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@master | |
| - name: create artifacts dir to save test logs | |
| run: mkdir artifacts | |
| - name: Cache Miniconda installation | |
| id: cache-miniconda | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-miniconda-installation | |
| with: | |
| path: /opt/miniconda3 | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-miniconda3 | |
| - name: Cache conda environment | |
| id: cache-conda-env | |
| uses: actions/cache@v4 | |
| env: | |
| cache-name: cache-conda-env | |
| with: | |
| path: ~/.conda/envs | |
| key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('environments') }}-x | |
| - name: Install Miniconda | |
| if: steps.cache-miniconda.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/install_conda.sh | |
| - name: Install Nextflow | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| run: bash .github/scripts/install_nextflow.sh | |
| - name: Create Conda Environments | |
| if: steps.cache-conda-env.outputs.cache-hit != 'true' | |
| run: bash .github/scripts/create_conda_env.sh | |
| - name: Generate Inputs | |
| run: bash .github/scripts/generate_inputs.sh | |
| - name: Run Pipeline | |
| run: bash .github/scripts/run_pipeline.sh | |
| - name: if failure, add latest NF log to artifacts | |
| run: mv .nextflow.log artifacts/failure.nextflow.log && mv work artifacts/work_failed | |
| if: failure() | |
| - uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: artifacts-BCCDC-PHL-ncov-tools-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ github.run_attempt }} | |
| path: artifacts |