lint.yml

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 prettier@3.1.0

      - 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