diff --git a/.github/workflows/software/trimgalore.yml b/.github/workflows/software/trimgalore.yml index 689a0fa0..16081569 100644 --- a/.github/workflows/software/trimgalore.yml +++ b/.github/workflows/software/trimgalore.yml @@ -17,14 +17,20 @@ jobs: env: NXF_ANSI_LOG: false steps: + - uses: actions/checkout@v2 - - uses: actions/checkout@v2 + - name: Install Nextflow + run: | + export NXF_VER="20.07.1" + wget -qO- get.nextflow.io | bash + sudo mv nextflow /usr/local/bin/ - - name: Install Nextflow - run: | - export NXF_VER="20.07.1" - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ + - name: Set up Python + uses: actions/setup-python@v2 + with: + python-version: "3.x" + - name: Install dependencies + run: python -m pip install --upgrade pip pytest-workflow - # Test the module - - run: nextflow run ./software/trimgalore/test/ -profile docker + # Test the module + - run: pytest --tag trimgalore --symlink --wt 2