Move nf-test files and container definitions #75
Workflow file for this run
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| name: nf-aggregate CI | |
| # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors | |
| on: | |
| pull_request: | |
| release: | |
| types: | |
| - published | |
| merge_group: | |
| types: | |
| - checks_requested | |
| branches: | |
| - master | |
| env: | |
| NXF_ANSI_LOG: false | |
| concurrency: | |
| group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" | |
| cancel-in-progress: true | |
| jobs: | |
| changes: | |
| name: Check for changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'tags' output variable | |
| tags: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Combine all tags.yml files | |
| id: get_username | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| - uses: dorny/paths-filter@v2 | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| nf-test: | |
| name: nf-test ${{ matrix.tags }} ${{ matrix.profile }} | |
| needs: [changes] | |
| if: needs.changes.outputs.tags != '[]' | |
| runs-on: ubuntu-latest | |
| env: | |
| TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| NXF_VER: | |
| - "23.10.0" | |
| - "latest-everything" | |
| tags: ["${{ fromJson(needs.changes.outputs.tags) }}"] | |
| profile: | |
| - "docker" | |
| - "conda" | |
| steps: | |
| - name: Check out pipeline code | |
| uses: actions/checkout@v3 | |
| - name: Install Nextflow | |
| uses: nf-core/setup-nextflow@v1 | |
| with: | |
| version: "${{ matrix.NXF_VER }}" | |
| - name: Set up miniconda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniconda-version: "latest" | |
| auto-update-conda: true | |
| channels: conda-forge,bioconda,defaults | |
| python-version: ${{ matrix.python-version }} | |
| - name: Conda setup | |
| 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 | |
| - name: Cache nf-test installation | |
| id: cache-software | |
| uses: actions/cache@v3 | |
| with: | |
| path: | | |
| /usr/local/bin/nf-test | |
| /home/runner/.nf-test/nf-test.jar | |
| key: ${{ runner.os }}-${{ env.NFTEST_VER }}-nftest | |
| - name: Install nf-test | |
| if: steps.cache-software.outputs.cache-hit != 'true' | |
| run: | | |
| wget -qO- https://code.askimed.com/install/nf-test | bash | |
| sudo mv nf-test /usr/local/bin/ | |
| - name: Run nf-test | |
| run: | | |
| nf-test test --tag ${{ matrix.tags }} --profile "test,${{ matrix.profile }}" --junitxml=test.xml | |
| - name: Output log on failure | |
| if: failure() | |
| run: | | |
| sudo apt install bat > /dev/null | |
| batcat --decorations=always --color=always ${{ github.workspace }}/.nf-test/tests/*/meta/nextflow.log | |
| - name: Publish Test Report | |
| uses: mikepenz/action-junit-report@v3 | |
| if: always() # always run even if the previous step fails | |
| with: | |
| report_paths: test.xml |