docker-run-tests.yml

name: Run all tests in Docker
on: workflow_dispach
jobs:
  test:
    runs-on: ubuntu-20.04
    steps:
      -
        name: Login to DockerHub
        uses: docker/login-action@v1 
        with:
          username: ${{ secrets.DOCKER_HUB_USERNAME }}
          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}

  build:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false

  run:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: Hello world 
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test echo "hello world"
    - name: Diagnostics
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test pwd;ls

  call:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: Test call
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test bash /universc/test/test_call.sh

  test-10x-v2:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test 10x
      timeout-minutes: 300
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 20m  /universc/test/run_tests_10x_v2_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

  test-10x-v3:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test 10x
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_10x_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

  test-cellranger:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false 
    - name: clear environment
      run: rm -rf *
    - name: Test Cell Ranger
      timeout-minutes: 45      
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_cellranger_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

  test-dropseq:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test DropSeq
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 45m  /universc/test/run_tests_dropseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then echo exit $code; exit $code; fi

  test-icell8:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test ICELL8
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_icell8_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

  test-indrops-v3:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test inDrops v3
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_indropsv3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

  test-sci-seq:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test SCI-Seq3
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_sciseq_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi

  test-smart-seq3:
    runs-on: ubuntu-20.04
    steps:
    - uses: actions/checkout@v2
    - uses: docker/setup-buildx-action@v1
    - uses: docker/login-action@v1
      with:
        username: ${{ secrets.DOCKER_HUB_USERNAME }}
        password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
        registry: ${{ env.REGISTRY }}

    - name: Build and push
      uses: docker/build-push-action@v2
      with:
        context: ./
        file: ./Dockerfile
        tags: ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test
        push: false
    - name: clear environment
      run: rm -rf *
    - name: Test Smart-Seq3
      run: docker run ${{ secrets.DOCKER_HUB_USERNAME }}/universc:test timeout 30m  /universc/test/run_tests_smartseq3_gh_actions.sh || code=$?; if [[ $code -ne 124 && $code -ne 0 ]]; then exit $code; fi