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: 90
    strategy:
      fail-fast: false
      matrix:
        java_version: [11, 17, 22]

    steps:
      - name: Environment
        run: env | sort

      - name: Checkout
        uses: actions/checkout@v4
        with:
          fetch-depth: 1
          submodules: true

      - 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: |
            # 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 }}

  test:
    if: ${{ !contains(github.event.head_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: [11, 21]
        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: |
          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/**
            integration-tests.tar