Added tesorter #5
Workflow file for this run
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| name: Run tests | |
| on: | |
| push: | |
| branches: [main] | |
| pull_request: | |
| branches: [main] | |
| # 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: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
| - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1 | |
| # FIXME Flip this off once we get to less than a couple hundred. Adding | |
| # this so it will only run against changed files. It'll make it much | |
| # easier to fix these as they come up rather than everything at once. | |
| with: | |
| extra_args: "" | |
| prettier: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g prettier@3.1.0 | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - uses: actions/setup-node@60edb5dd545a775178f52524783378180af0d1f8 # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install editorconfig-checker | |
| run: npm install -g editorconfig-checker | |
| - name: Run ECLint check | |
| run: editorconfig-checker -exclude README.md $(git ls-files | grep -v test) | |
| nf-test-changes: | |
| name: nf-test-changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| # Expose matched filters as job 'modules' output variable | |
| modules: ${{ steps.filter.outputs.changes }} | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| with: | |
| fetch-depth: 2 # To retrieve the preceding commit. | |
| - name: Combine all tags.yml files | |
| id: get_tags | |
| run: find . -name "tags.yml" -not -path "./.github/*" -exec cat {} + > .github/tags.yml | |
| - name: debug | |
| run: cat .github/tags.yml | |
| # TODO: change back to using dorny/paths-filter when https://github.com/dorny/paths-filter/pull/133 is implemented | |
| - uses: mirpedrol/paths-filter@main | |
| id: filter | |
| with: | |
| filters: ".github/tags.yml" | |
| token: "" | |
| nf-core-lint: | |
| runs-on: ubuntu-latest | |
| name: nf-core-lint | |
| needs: [nf-test-changes] | |
| if: ${{ (needs.nf-test-changes.outputs.modules != '[]') }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # v4 | |
| id: cache-pip | |
| with: | |
| path: ~/.cache/pip | |
| key: ${{ runner.os }}-pip | |
| restore-keys: | | |
| ${{ runner.os }}-pip | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-core tools development version | |
| run: python -m pip install --upgrade --force-reinstall git+https://github.com/nf-core/tools.git@dev | |
| - name: Lint module ${{ matrix.tags }} | |
| run: nf-core modules lint ${{ matrix.tags }} | |
| if: ${{ !startsWith(matrix.tags, 'subworkflows/') }} | |
| - name: Remove substring from matrix.tags | |
| id: remove_substring | |
| run: echo subworkflow_names=$(echo "${{ matrix.tags }}" | sed 's/subworkflows\///g') >> $GITHUB_OUTPUT | |
| - name: Lint subworkflow ${{ matrix.tags }} | |
| run: nf-core subworkflows lint ${{steps.remove_substring.outputs.subworkflow_names}} | |
| if: ${{ startsWith(matrix.tags, 'subworkflows/') }} | |
| nf-test: | |
| runs-on: ubuntu-latest | |
| name: nf-test | |
| needs: [nf-test-changes] | |
| if: needs.nf-test-changes.outputs.modules != '[]' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| tags: ["${{ fromJson(needs.nf-test-changes.outputs.modules) }}"] | |
| profile: [conda, docker, singularity] | |
| env: | |
| NXF_ANSI_LOG: false | |
| NFTEST_VER: "0.8.4" | |
| steps: | |
| - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4 | |
| - uses: actions/setup-java@99b8673ff64fbf99d8d325f52d9a5bdedb8483e9 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@v2 | |
| - name: Install nf-test | |
| uses: nf-core/setup-nf-test@v1 | |
| - 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@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@ab5e6d0c87105b4c9c2047343972218f562e4319 # 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 | |
| uses: conda-incubator/setup-miniconda@030178870c779d9e5e1b4e563269f3aa69b04081 # v3 | |
| 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) >> $GITHUB_PATH | |
| # Test the module | |
| - name: Run nf-test | |
| env: | |
| NFT_DIFF: "pdiff" | |
| NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2" | |
| run: | | |
| PROFILE=${{ matrix.profile }} | |
| NFT_WORKDIR=~ \ | |
| nf-test test \ | |
| --profile=$PROFILE \ | |
| --tag ${{ matrix.tags }} \ | |
| --tap=test.tap \ | |
| --verbose | |
| - uses: pcolby/tap-summary@0959cbe1d4422e62afc65778cdaea6716c41d936 # v1 | |
| with: | |
| path: >- | |
| test.tap | |
| - name: Clean up | |
| if: always() | |
| run: | | |
| sudo rm -rf /home/ubuntu/tests/ | |
| confirm-pass: | |
| runs-on: ubuntu-latest | |
| needs: [pre-commit, prettier, editorconfig, nf-core-lint, nf-test-changes, nf-test] | |
| if: always() | |
| steps: | |
| - name: All tests ok | |
| if: ${{ success() || !contains(needs.*.result, 'failure') }} | |
| run: exit 0 | |
| - name: One or more tests failed | |
| if: ${{ contains(needs.*.result, 'failure') }} | |
| run: exit 1 | |
| - name: debug-print | |
| if: always() | |
| run: | | |
| echo "toJSON(needs) = ${{ toJSON(needs) }}" | |
| echo "toJSON(needs.*.result) = ${{ toJSON(needs.*.result) }}" |