Deprecate process shell block
#7209
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| name: Nextflow CI | |
| # read more here: https://help.github.com/en/articles/workflow-syntax-for-github-actions#on | |
| # Note: We don't use the `on: path` option for docs, | |
| # because the Build steps are *required* tests. | |
| # Instead, we trigger + skip the tests if the only changes | |
| # are in the docs folder. GitHub treats this as passing. | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| - 'test*' | |
| - 'dev*' | |
| - 'STABLE-*' | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| name: Build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [17, 23] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Get the commit message | |
| id: get_commit_message | |
| run: | | |
| if [ "${{ github.event_name }}" = "pull_request" ]; then | |
| echo "GitHub event=pull_request" | |
| COMMIT_SHA=${{ github.event.pull_request.head.sha }} | |
| COMMIT_MESSAGE=$(curl -s \ | |
| -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \ | |
| https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message') | |
| echo "Commit message=$COMMIT_MESSAGE" | head -n 1 | |
| echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT | |
| else | |
| echo "GitHub event=${{ github.event_name }}" | |
| echo "Commit message=${{ github.event.head_commit.message }}" | head -n 1 | |
| echo "commit_message=${{ github.event.head_commit.message }}" | head -n 1 >> $GITHUB_OUTPUT | |
| fi | |
| - name: Get changed files | |
| id: changed-files | |
| uses: tj-actions/changed-files@v43 | |
| with: | |
| files_ignore: docs/** | |
| - name: List all changed files | |
| env: | |
| ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }} | |
| run: | | |
| for file in ${ALL_CHANGED_FILES}; do | |
| echo "$file was changed" | |
| done | |
| - name: Setup env | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| 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 }} | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: ${{matrix.java_version}} | |
| distribution: 'temurin' | |
| architecture: x64 | |
| cache: gradle | |
| - name: Compile | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: make assemble | |
| - name: Test | |
| if: steps.changed-files.outputs.any_changed == 'true' | |
| run: | | |
| env | sort | |
| # configure test env | |
| if [[ "$GOOGLE_SECRET" ]]; then | |
| echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json | |
| export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json | |
| fi | |
| # run tests | |
| make test | |
| env: | |
| 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 }} | |
| 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: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| - name: Publish tests report | |
| uses: actions/upload-artifact@v4 | |
| if: steps.changed-files.outputs.any_changed == 'true' && always() | |
| with: | |
| name: report-unit-tests-jdk-${{ matrix.java_version }} | |
| path: | | |
| **/build/reports/tests/test | |
| outputs: | |
| any_changed: ${{ steps.changed-files.outputs.any_changed }} | |
| commit_message: ${{ steps.get_commit_message.outputs.commit_message }} | |
| test: | |
| if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }} | |
| needs: build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 90 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [17, 23] | |
| test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| 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@v4 | |
| with: | |
| java-version: ${{matrix.java_version}} | |
| distribution: 'temurin' | |
| architecture: x64 | |
| cache: gradle | |
| - name: Run tests | |
| run: | | |
| env | sort | |
| # configure test env | |
| if [[ "$GOOGLE_SECRET" ]]; then | |
| echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json | |
| export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json | |
| fi | |
| cat $HOME/.nextflow/scm | |
| make clean assemble install | |
| bash test-ci.sh | |
| env: | |
| TEST_JDK: ${{ matrix.java_version }} | |
| TEST_MODE: ${{ matrix.test_mode }} | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| 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 }} | |
| 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: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }} | |
| - name: Tar integration tests | |
| if: always() | |
| run: tar -cvf integration-tests.tar tests/checks | |
| - name: Publish tests report | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }} | |
| path: | | |
| validation/**/* | |
| validation/**/.* | |
| integration-tests.tar | |
| test-e2e: | |
| if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }} | |
| needs: build | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| permissions: | |
| actions: write # Allow writing to actions | |
| contents: write # Allow writing to repository contents | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup Java 17 | |
| uses: actions/setup-java@v4 | |
| with: | |
| java-version: 17 | |
| distribution: 'temurin' | |
| architecture: x64 | |
| cache: gradle | |
| - name: Setup env | |
| run: | | |
| wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64 | |
| chmod +x wave | |
| mv wave /usr/local/bin/ | |
| echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV | |
| - name : Docker Login to Seqera public CR | |
| uses : docker/login-action@v3 | |
| with : | |
| registry : "public.cr.seqera.io" | |
| username : "public-cr-admin" | |
| password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }} | |
| - name: Launch tests | |
| run: | | |
| cd test-e2e | |
| bash run.sh | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }} | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' |