build.yml

name: Nextflow CI
# read more here
# https://help.github.com/en/articles/workflow-syntax-for-github-actions#on
on:
  workflow_dispatch:
    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