Add github actions testing pipeline #27
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| on: | |
| pull_request: | |
| branches: | |
| - main | |
| workflow_dispatch: | |
| name: Pull Request | |
| 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 | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| run: mkdir artifacts | |
| - name: Install Miniconda | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| 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 ART Read-Simulation Environment | |
| run: bash .github/scripts/create_art_environment.sh | |
| - name: Download Assemblies | |
| run: bash .github/scripts/download_assemblies.sh | |
| - name: Simulate Reads | |
| run: bash .github/scripts/simulate_reads.sh | |
| - name: Run Pipeline | |
| run: bash .github/scripts/run_pipeline.sh | |
| - name: Create Output Checking Environment | |
| run: bash .github/scripts/create_output_checking_environment.sh | |
| - name: Check Outputs | |
| run: .github/scripts/check_outputs.sh | |
| - name: Prepare Artifacts | |
| if: always() | |
| run: bash .github/scripts/prepare_artifacts.sh | |
| - name: Upload Artifacts | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| env: | |
| NXF_VER: ${{ matrix.nextflow_version }} | |
| with: | |
| name: artifacts-BCCDC-PHL-tbprofiler-nf-nextflow-v${{ matrix.nextflow_version }}-${{ github.run_id }}.${{ env.GITHUB_RUN_ATTEMPT }} | |
| path: artifacts |