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: ""

  ###################
  # nf-core linting #
  ###################
  # TODO Move these to pre-commit
  # https://github.com/nf-core/tools/pull/3141
  nf-core-changes:
    name: nf-core-changes
    runs-on: ubuntu-latest
    outputs:
      tags: ${{ steps.filter.outputs.changes }}
      modules: ${{ steps.tags.outputs.modules }}
      subworkflows: ${{ steps.tags.outputs.subworkflows }}
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4
        with:
          fetch-depth: 2 # To retrieve the preceding commit.

      # 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: "tests/config/pytest_modules.yml"
          token: ""

      - name: Fetch module tags
        id: tags
        run: |
          echo modules=$(echo '${{ steps.filter.outputs.changes }}' | jq -c '. | map(select(contains("modules"))) | map(gsub("modules/"; ""))') >> $GITHUB_OUTPUT
          echo subworkflows=$(echo '${{ steps.filter.outputs.changes }}' | jq '. | map(select(contains("subworkflow"))) | map(gsub("subworkflows/"; ""))') >> $GITHUB_OUTPUT

      - name: debug
        run: |
          echo ${{ steps.tags.outputs.modules }}
          echo ${{ steps.tags.outputs.subworkflows }}

  nf-core-lint-modules:
    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
    name: nf-core lint modules
    needs: nf-core-changes
    if: ${{ (needs.nf-core-changes.outputs.modules != '[]') }}
    strategy:
      fail-fast: false
      matrix:
        tags: "${{ fromJson(needs.nf-core-changes.outputs.modules) }}"
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4

      - name: Set up Python
        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # 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@b36c23c0d998641eff861008f374ee103c25ac73 # 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 }}

  nf-core-lint-subworkflows:
    runs-on: ubuntu-latest
    name: nf-core lint subworkflows
    needs: nf-core-changes
    if: ${{ (needs.nf-core-changes.outputs.subworkflows != '[]') }}
    strategy:
      fail-fast: false
      matrix:
        tags: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows) }}"
    steps:
      - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4

      - name: Set up Python
        uses: actions/setup-python@f677139bbe7f9c59b41e40162b753c062f5d49a3 # v5
        with:
          python-version: "3.11"

      - name: Install pip
        run: python -m pip install --upgrade pip

      - uses: actions/setup-java@b36c23c0d998641eff861008f374ee103c25ac73 # 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 module ${{ matrix.tags }}
        run: nf-core subworkflows lint ${{ matrix.tags }}