Use new nf-test features #2680
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Run nf-test | |
| on: | |
| pull_request: | |
| branches: [master] | |
| merge_group: | |
| types: [checks_requested] | |
| branches: [master] | |
| workflow_dispatch: | |
| inputs: | |
| runners: | |
| description: "Runners to test on" | |
| type: choice | |
| options: | |
| - "ubuntu-latest" | |
| - "self-hosted" | |
| default: "self-hosted" | |
| # Cancel if a newer run is started | |
| concurrency: | |
| group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: true | |
| env: | |
| NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity | |
| NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| jobs: | |
| nf-test: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| # NOTE I think this is the cleanest way to get them organized | |
| # process | conda | 1 | |
| # process | conda | 2 | |
| # process | conda | 3 | |
| # process | docker_self_hosted | 1 | |
| # ... | |
| # workflow | singularity | 3 | |
| name: ${{ matrix.filter }} | ${{ matrix.profile }} | ${{ matrix.shard }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| filter: [process, workflow] | |
| profile: [conda, docker_self_hosted, singularity] | |
| shard: [1, 2, 3] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NXF_VER: "24.04.4" | |
| NFTEST_VER: "0.9.0" | |
| TOTAL_SHARDS: 3 | |
| SENTIEON_LICENSE_MESSAGE: ${{ secrets.SENTIEON_LICENSE_MESSAGE }} | |
| SENTIEON_ENCRYPTION_KEY: ${{ secrets.SENTIEON_ENCRYPTION_KEY }} | |
| steps: | |
| # TODO If conda-fail.yml exists and matrix = conda skip | |
| # https://github.com/askimed/nf-test/issues/260 | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| with: | |
| fetch-depth: 0 | |
| - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| with: | |
| version: ${{ env.NXF_VER }} | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| with: | |
| version: ${{ env.NFTEST_VER }} | |
| - name: Setup apptainer | |
| if: matrix.profile == 'singularity' | |
| uses: eWaterCycle/setup-apptainer@main | |
| - name: Set up Singularity | |
| if: matrix.profile == 'singularity' | |
| run: | | |
| mkdir -p $NXF_SINGULARITY_CACHEDIR | |
| mkdir -p $NXF_SINGULARITY_LIBRARYDIR | |
| - name: Set up Python | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # v4 | |
| id: cache-pip-pdiff | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip-pdiff | |
| restore-keys: | | |
| ${{ runner.os }}-pip-pdiff | |
| - name: Install Python dependencies | |
| run: python -m pip install --upgrade pip pdiff cryptography | |
| - name: Set up miniconda | |
| if: matrix.profile == 'conda' | |
| uses: conda-incubator/setup-miniconda@a4260408e20b96e80095f42ff7f1a15b27dd94ca # v3 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| - name: Conda setup | |
| if: matrix.profile == 'conda' | |
| run: | | |
| conda clean -a | |
| conda install -n base conda-libmamba-solver | |
| conda config --set solver libmamba | |
| echo $(realpath $CONDA)/condabin >> $GITHUB_PATH | |
| echo $(realpath python) >> $GITHUB_PATH | |
| # Set up secrets | |
| - name: Set up nextflow secrets | |
| # TODO Only run if the tag includes `sentieon` | |
| if: env.SENTIEON_ENCRYPTION_KEY != null && env.SENTIEON_LICENSE_MESSAGE != null | |
| run: | | |
| nextflow secrets set SENTIEON_AUTH_DATA $(python3 tests/modules/nf-core/sentieon/license_message.py encrypt --key "${{ secrets.SENTIEON_ENCRYPTION_KEY }}" --message "${{ secrets.SENTIEON_LICENSE_MESSAGE }}") | |
| # Test the module | |
| - name: Run Tests (Shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }}) | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| SENTIEON_LICSRVR_IP: ${{ secrets.SENTIEON_LICSRVR_IP }} | |
| SENTIEON_AUTH_MECH: "GitHub Actions - token" | |
| run: | | |
| # use "docker_self_hosted" if it runs on self-hosted runner and matrix.profile=docker | |
| if [ "${{ matrix.profile }}" == "docker" ]; then | |
| PROFILE="docker_self_hosted" | |
| else | |
| PROFILE=${{ matrix.profile }} | |
| fi | |
| NFT_WORKDIR=~ \ | |
| nf-test test \ | |
| --profile=${{ matrix.profile }} \ | |
| --tap=test.tap \ | |
| --ci \ | |
| --verbose \ | |
| --changed-since HEAD^ \ | |
| --shard ${{ matrix.shard }}/${{ env.TOTAL_SHARDS }} \ | |
| --filter ${{ matrix.filter }} \ | |
| --follow-dependencies | |
| # TODO If matrix == conda create a conda-fail.yml and commit it | |
| # TODO If no test.tap, then make one to spoof? | |
| # - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | |
| # with: | |
| # path: >- | |
| # test.tap | |
| - name: Clean up | |
| if: always() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ |