Added liftoff, integrated with pfr/nxf-modules, and some minor improvements #2
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| # Adopted from https://github.com/nf-core/modules/blob/master/.github/workflows/test.yml | |
| name: Run tests | |
| on: | |
| pull_request: | |
| branches: [main] | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| jobs: | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: actions/setup-node@v4 | |
| with: | |
| node-version: "20" | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test | grep -v LICENSE) | |
| stub-test: | |
| runs-on: ubuntu-latest | |
| name: Run stub test with docker | |
| env: | |
| NXF_ANSI_LOG: false | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Get test data from pangene-test | |
| run: | | |
| if [ ! -d pangene-test ]; then | |
| echo "pangene-test not cloned yet. Cloning now..." | |
| mkdir -p pangene-test | |
| ssh-keyscan github.com >> ~/.ssh/known_hosts | |
| echo "${{ secrets.PANGENE_TEST_DEPLOY_KEY }}" > ~/.ssh/id_rsa | |
| chmod 600 ~/.ssh/id_rsa | |
| git clone [email protected]:PlantandFoodResearch/pangene-test.git | |
| else | |
| echo "pangene-test already cloned. Running a sync..." | |
| cd pangene-test | |
| git pull | |
| cd - | |
| fi | |
| cd pangene | |
| ln -s ../pangene-test | |
| cd - | |
| - uses: actions/setup-java@v3 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| - name: Run stub-test | |
| run: | | |
| nextflow \ | |
| main.nf \ | |
| -profile local,docker \ | |
| -resume \ | |
| -stub \ | |
| -params-file conf/test_params.json | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [prettier, editorconfig, stub-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |