diff --git a/.github/workflows/continuous_integration.yml b/.github/workflows/continuous_integration.yml index d01a2b98..25c10f20 100644 --- a/.github/workflows/continuous_integration.yml +++ b/.github/workflows/continuous_integration.yml @@ -13,12 +13,13 @@ jobs: runs-on: ubuntu-latest env: - NXF_VER: ${{ matrix.nxf_ver }} NXF_ANSI_LOG: false strategy: matrix: - nxf_ver: ['21.10.6', ''] + NXF_VER: + - "22.10.1" + - "latest" profile: - docker workflow: @@ -29,22 +30,15 @@ jobs: # Steps represent a sequence of tasks that will be executed as part of the job steps: - # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 + # https://github.com/marketplace/actions/checkout + - name: Check out repository code + uses: actions/checkout@v4 + # https://github.com/marketplace/actions/setup-nextflow - name: Install Nextflow - run: | - wget -qO- get.nextflow.io | bash - sudo mv nextflow /usr/local/bin/ - - # Use https://github.com/marketplace/actions/setup-conda to setup conda - # - name: Setup Conda - # uses: s-weigand/setup-conda@v1 - # with: - # update-conda: true - - # - name: Alias local interproscan to docker container. - # run: alias interproscan.sh='docker run biocontainers/interproscan:v5.30-69.0_cv3 /opt/interproscan/interproscan.sh' + uses: nf-core/setup-nextflow@v1 + with: + version: "${{ matrix.NXF_VER }}" - name: Test ${{ matrix.workflow }} with profile ${{ matrix.profile }} run: nextflow run -profile test,${{ matrix.profile }} main.nf --subworkflow ${{ matrix.workflow }}