TES tags support + Configurable polling interval + Log request URL on error #81
Workflow file for this run
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| name: nf-ga4gh CI | |
| on: | |
| push: | |
| branches: | |
| - 'master' | |
| pull_request: | |
| types: [opened, reopened, synchronize] | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| name: Build nf-ga4gh | |
| if: "!contains(github.event.head_commit.message, '[ci skip]')" | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 10 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| java_version: [ | |
| 17, | |
| 21, | |
| ] | |
| steps: | |
| - name: Environment | |
| run: env | sort | |
| - name: Checkout | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup Java ${{ matrix.java_version }} | |
| uses: actions/setup-java@v5 | |
| with: | |
| java-version: ${{matrix.java_version}} | |
| distribution: 'temurin' | |
| cache: 'gradle' | |
| - name: Unit tests | |
| run: make test | |
| env: | |
| GRADLE_OPTS: '-Dorg.gradle.daemon=false' | |
| e2e-test: | |
| needs: build | |
| name: Test nf-ga4gh | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 5 | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| nextflow_version: [ | |
| '25.10', | |
| ] | |
| java_version: [ | |
| 21, | |
| ] | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v6 | |
| with: | |
| fetch-depth: 1 | |
| submodules: true | |
| - name: Setup Java ${{ matrix.java_version }} | |
| uses: actions/setup-java@v5 | |
| with: | |
| java-version: ${{ matrix.java_version }} | |
| distribution: 'temurin' | |
| cache: 'gradle' | |
| - name: Install Nextflow ${{ matrix.nextflow_version }} | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ matrix.nextflow_version }} | |
| - name: Install Plugin | |
| run: | | |
| make install | |
| - name: Install TES Server | |
| run: | | |
| # https://github.com/ohsu-comp-bio/funnel/releases/tag/v0.11.8 | |
| curl -fsSL https://ohsu-comp-bio.github.io/funnel/install.sh | bash -s -- v0.11.8 | |
| - name: Start TES Server | |
| run: | | |
| funnel server run > funnel.log 2>&1 & | |
| - name: Get plugin version | |
| shell: bash | |
| run: | | |
| PLUGIN_VERSION="$(cat VERSION)" | |
| echo "PLUGIN_VERSION=${PLUGIN_VERSION}" >> "$GITHUB_ENV" | |
| echo "Using plugin version: ${PLUGIN_VERSION}" | |
| - name: Install nf-canary | |
| run: | | |
| cat <<EOF > nextflow.config | |
| // Nextflow config file for running on TES Backend | |
| plugins { | |
| id 'nf-ga4gh@${PLUGIN_VERSION}' | |
| } | |
| process { | |
| executor = 'tes' | |
| container = 'ubuntu:latest' | |
| } | |
| params { | |
| // TES | |
| endpoint = 'http://localhost:8000' | |
| basicUsername = null | |
| basicPassword = null | |
| } | |
| report.enabled = true | |
| timeline.enabled = true | |
| EOF | |
| - name: Run nf-canary | |
| run: | | |
| export NXF_ANSI_LOG=false | |
| nextflow run seqeralabs/nf-canary | |
| - name: Stage Reports | |
| if: always() | |
| run: | | |
| mkdir -p $GITHUB_WORKSPACE/results | |
| # Nextflow Logs | |
| cp -f report.html timeline.html .nextflow.log $GITHUB_WORKSPACE/results/ || true | |
| # Funnel Logs | |
| cp -f $GITHUB_WORKSPACE/funnel.log $GITHUB_WORKSPACE/results/ || true | |
| - name: Upload Reports | |
| uses: actions/upload-artifact@v4 | |
| if: always() | |
| with: | |
| name: test-results-nxf-${{ matrix.nextflow_version }}-java-${{ matrix.java_version }} | |
| path: results/ | |
| retention-days: 7 |