Use new nf-test features #11
Workflow file for this run
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| name: Run Linting | |
| 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: | |
| pre-commit: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # 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@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Install NodeJS | |
| uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # v4 | |
| with: | |
| node-version: "20" | |
| - name: Install Prettier | |
| run: npm install -g [email protected] | |
| - name: Run Prettier --check | |
| run: prettier --check . | |
| editorconfig: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - uses: actions/setup-node@1e60f620b9541d16bece96c5465dc8ee9832be0b # 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-core-lint-modules: | |
| runs-on: ${{ github.event.inputs.runners || 'self-hosted' }} | |
| name: nf-core lint modules | |
| strategy: | |
| fail-fast: false | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | |
| with: | |
| python-version: "3.11" | |
| - uses: actions/cache@0c45773b623bea8c8e75f6c82b208c3cf94ea4f9 # 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@6a0805fcefea3d4657a47ac4c165951e33482018 # 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 modules | |
| run: nf-core --hide-progress modules lint -a | |
| nf-core-lint-subworkflows: | |
| runs-on: ubuntu-latest | |
| name: nf-core lint subworkflows | |
| steps: | |
| - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4 | |
| - name: Set up Python | |
| uses: actions/setup-python@39cd14951b08e74b54015e9e001cdefcf80e669f # v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install pip | |
| run: python -m pip install --upgrade pip | |
| - uses: actions/setup-java@6a0805fcefea3d4657a47ac4c165951e33482018 # v4 | |
| with: | |
| distribution: "temurin" | |
| java-version: "17" | |
| - name: Setup Nextflow | |
| uses: nf-core/setup-nextflow@561fcfc7146dcb12e3871909b635ab092a781f34 # 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 subworkflows | |
| run: nf-core --hide-progress subworkflows lint -a |