Preserve error messages for user-friendliness #5097
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| name: Nextflow CI | |
| # read more here | |
| # https://help.github.com/en/articles/workflow-syntax-for-github-actions#on | |
| on: | |
| push: | |
| branches: | |
| - '*' | |
| - '!refs/tags/.*' | |
| tags-ignore: | |
| - '*' | |
| paths-ignore: | |
| - 'docs/**' | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| jobs: | |
| build: | |
| if: "github.event == 'push' || github.repository != github.event.pull_request.head.repo.full_name" | |
| name: Build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [11, 19] | |
| steps: | |
| - name: Environment | |
| run: env | sort | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup env | |
| run: | | |
| rm -f $HOME/.gitconfig; | |
| mkdir -p "$HOME/.nextflow"; | |
| echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm" | |
| env: | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| - name: Setup Java ${{ matrix.java_version }} | |
| uses: actions/setup-java@v3 | |
| with: | |
| java-version: ${{matrix.java_version}} | |
| distribution: 'adopt' | |
| architecture: x64 | |
| cache: gradle | |
| - name: Compile | |
| run: make assemble | |
| - name: Test | |
| run: make test | |
| - name: Publish tests report | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: report-unit-tests-jdk-${{ matrix.java_version }} | |
| path: | | |
| **/build/reports/tests/test | |
| test: | |
| if: "!contains(github.event.head_commit.message, '[ci fast]')" | |
| needs: build | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [11, 19] | |
| test_mode: ["test_integration", "test_aws", "test_azure", "test_google", "test_wave"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup env | |
| run: | | |
| rm -f $HOME/.gitconfig; | |
| mkdir -p "$HOME/.nextflow"; | |
| echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm" | |
| env: | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| - name: Run tests | |
| run: | | |
| cat $HOME/.nextflow/scm | |
| make assemble install | |
| bash test-ci.sh | |
| env: | |
| TEST_JDK: ${{ matrix.java_version }} | |
| TEST_MODE: ${{ matrix.test_mode }} | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| AWS_DEFAULT_REGION: eu-west-1 | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }} | |
| NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }} | |
| NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }} | |
| NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }} | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }} | |
| AZURE_STORAGE_ACCOUNT_NAME: nfazurestore | |
| AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }} | |
| AZURE_BATCH_ACCOUNT_NAME: nfbatchtest | |
| AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| - name: Tar integration tests | |
| if: always() | |
| run: tar -cvf integration-tests.tar tests/checks | |
| - name: Publish tests report | |
| uses: actions/upload-artifact@v3 | |
| if: always() | |
| with: | |
| name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }} | |
| path: | | |
| validation/** | |
| integration-tests.tar |