github actions tests in docker container

        with:

          image: docker:latest

          run: echo "hello world"

      - name: Pull Docker image

        run: docker pull tomkellygenetics/cellranger_clean:3.0.2

      - name: Run image

        run: docker run -it -d --name builder -v $GITHUB_WORKSPACE:/workspace -w tomkellygenetics/cellranger_clean:3.0.2 echo "hello from cellranger_clean"

      - name: Call Cell Ranger

        uses: addnab/docker-run-action@v1

        with:

  test-cellranger:

    runs-on: ubuntu-latest

    container:

      image: tomkellygenetics/cellranger_clean:3.0.2

          run: echo "cellranger:" $(which cellranger)

      - name: Pull Docker image

        run: docker pull tomkellygenetics/universc:1.0.2

      - name: Run image

        run: docker run -it -d --name builder -v $GITHUB_WORKSPACE:/workspace -w tomkellygenetics/universc:1.0.2 echo "hello from universc"

      - name: Call UniverSC

        uses: addnab/docker-run-action@v1

        with:

          image: tomkellygenetics/universc:latest

    steps:  

      - uses: actions/checkout@v2

      - name: What OS is running

        run: uname -a

      - name: Where am i

        run: pwd; ls

      - name: call Cell Ranger

        run: which cellranger; cellranger -v

  test-universc:

    runs-on: ubuntu-latest

    container:

      image: tomkellygenetics/universc:1.0.2

    steps:

      - uses: actions/checkout@v2

      - name: What OS is running

        run: uname -a

      - name: Where am i                

        run: pwd; ls

      - name: pull updates:

        run: cd universc; git pull origin master

      - name: call UniverSC

        run: bash /universc/launch_universc.sh -v

      - name: test callas

        run: bash /universc/test/test_call.sh