build.yml

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: 100
    strategy:
      fail-fast: false
      matrix:
        java_version: [17, 24]

    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/$COMMIT_SHA | jq -r '.commit.message' | head -n 1)"
                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
            else
                echo "GitHub event=${{ github.event_name }}"
                # Extract only the first line of the commit message
                COMMIT_MESSAGE="$(git log -1 --pretty=format:'%s')"
                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")"
                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" >> $GITHUB_OUTPUT
            fi

      - 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: Compile
        run: make assemble

      - name: Test
        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 }}
          AWS_S3FS_ACCESS_KEY: ${{ secrets.AWS_ACCESS_KEY_ID }}
          AWS_S3FS_SECRET_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
        if: always()
        uses: actions/upload-artifact@v4
        with:
          name: report-unit-tests-jdk-${{ matrix.java_version }}
          path: |
            **/build/reports/tests/test

    outputs:
      commit_message: ${{ steps.get_commit_message.outputs.commit_message }}

  test:
    if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') }}
    needs: build
    runs-on: ubuntu-latest
    timeout-minutes: 90
    strategy:
      fail-fast: false
      matrix:
        java_version: [17, 24]
        test_mode: ["test_integration", "test_parser_v2", "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.gz tests/checks
            tar -cvf validation-tests.tar.gz validation

      - name: Publish tests report
        uses: actions/upload-artifact@v4
        if: always()
        with:
          name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
          path: |
            validation-tests.tar.gz
            integration-tests.tar.gz

  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'

  release:
    if: ${{ always() && contains(needs.build.outputs.commit_message, '[release]') && needs.build.result == 'success' && (needs.test.result == 'success' || needs.test.result == 'skipped') }}
    needs: [build, test]
    runs-on: ubuntu-latest
    timeout-minutes: 10
    permissions:
      actions: write
      contents: write
      packages: write
      pull-requests: write
      issues: write
    steps:
      - name: Checkout
        uses: actions/checkout@v4
        with:
          fetch-depth: 0
          submodules: true

      - name: Setup Java 17
        uses: actions/setup-java@v4
        with:
          java-version: 17
          distribution: 'temurin'
          architecture: x64
          cache: gradle

      - name: Configure Git
        run: |
          git config --global user.name "${{ github.event.pusher.name || github.actor }}"
          git config --global user.email "${{ github.event.pusher.email || format('{0}@users.noreply.github.com', github.actor) }}"

      - name: Docker Login to Docker Hub
        uses: docker/login-action@v3
        with:
          username: ${{ vars.DOCKERHUB_USERNAME }}
          password: ${{ secrets.DOCKERHUB_TOKEN }}

      - name: Docker Login to Seqera public CR
        uses: docker/login-action@v3
        with:
          registry: "public.cr.seqera.io"
          username: ${{ vars.SEQERA_PUBLIC_CR_USERNAME }}
          password: ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}

      - name: Run release
        run: |
          echo "Starting release process..."
          echo "npr.apiUrl=$NPR_API_URL" >> gradle.properties
          echo "npr.apiKey=$NPR_API_KEY" >> gradle.properties
          bash release.sh
        env:
          GRADLE_OPTS: '-Dorg.gradle.daemon=false'
          AWS_JAVA_V1_DISABLE_DEPRECATION_ANNOUNCEMENT: 'true'
          # credentials to pubslish nextflow assets
          NXF_AWS_ACCESS: ${{ vars.NXF_AWS_ACCESS }}
          NXF_AWS_SECRET: ${{ secrets.NXF_AWS_SECRET }}
          # credentials to publish maven libraries
          AWS_ACCESS_KEY_ID: ${{ vars.SEQERA_MAVEN_ACCESS_KEY }}
          AWS_SECRET_ACCESS_KEY: ${{ secrets.SEQERA_MAVEN_SECRET_KEY }}
          # plugin registry
          NPR_API_URL: ${{ vars.NPR_API_URL }}
          NPR_API_KEY: ${{ secrets.NPR_API_KEY }}
          # GitHub secrets
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}