lint.yml

name: Run Linting
on:
  push:
    branches:
      # https://docs.renovatebot.com/key-concepts/automerge/#branch-vs-pr-automerging
      - "renovate/**" # branches Renovate creates
  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 }}
  # renovate: datasource=github-releases depName=nextflow/nextflow versioning=semver
  NXF_VER: "24.10.1"

jobs:
  pre-commit:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
      - uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
      - uses: pre-commit/action@2c7b3805fd2a0fd8c1884dcaebf91fc102a13ecd # v3.0.1
        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:
      # https://github.com/dorny/paths-filter?tab=readme-ov-file#custom-processing-of-changed-files
      modules: ${{ steps.filter.outputs.modules }}
      modules_files: ${{ steps.module_names.outputs.result }}
      subworkflows: ${{ steps.filter.outputs.subworkflows }}
      subworkflows_files: ${{ steps.subworkflow_names.outputs.result }}
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4
        with:
          fetch-depth: 2 # To retrieve the preceding commit.

      - uses: dorny/paths-filter@de90cc6fb38fc0963ad72b210f1f284cd68cea36 # v3
        id: filter
        with:
          filters: |
            modules:
              - 'modules/nf-core/**'
              - 'tests/modules/nf-core/**'
            subworkflows:
              - 'subworkflows/nf-core/**'
              - 'tests/subworkflows/nf-core/**'
          token: ""
          list-files: "json"

      - name: Get module name
        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
        id: module_names
        with:
          script: |
            return [...new Set(${{ steps.filter.outputs.modules_files }}
              .map(path => path.replace('modules/nf-core/', '')
              .split('/')
              .slice(0, 2)
              .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml')
              .join('/')))];

      - name: Get subworkflow name
        uses: actions/github-script@60a0d83039c74a4aee543508d2ffcb1c3799cdea # v7
        id: subworkflow_names
        with:
          script: |
            return [...new Set(${{ steps.filter.outputs.subworkflows_files }}
              .map(path => path.replace('subworkflows/nf-core/', '')
              .split('/')
              .slice(0,2)
              .filter(x => x !== 'main.nf' && x !== 'tests' && x !== 'meta.yml' && x !== 'environment.yml')
              .join('/')))];

      - name: debug
        run: |
          echo ${{ steps.filter.outputs.modules_files }}
          echo ${{ steps.filter.outputs.subworkflows_files }}
          echo ${{ steps.module_names.outputs.result }}
          echo ${{ steps.subworkflow_names.outputs.result }}

  nf-core-lint-modules:
    runs-on: ${{ github.event.inputs.runners  || 'self-hosted' }}
    name: nf-core lint modules
    needs: nf-core-changes
    if: ${{ (needs.nf-core-changes.outputs.modules == 'true') }}
    strategy:
      fail-fast: false
      matrix:
        module: "${{ fromJson(needs.nf-core-changes.outputs.modules_files) }}"
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Set up Python
        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
        with:
          python-version: "3.11"

      - uses: actions/cache@6849a6489940f00c2f30c0fb92c6274307ccb58a # 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@8df1039502a15bceb9433410b1a100fbe190c53b # 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.module }}
        run: nf-core modules lint ${{ matrix.module }}

  nf-core-lint-subworkflows:
    runs-on: ubuntu-latest
    name: nf-core lint subworkflows
    needs: nf-core-changes
    if: ${{ (needs.nf-core-changes.outputs.subworkflows == 'true') }}
    strategy:
      fail-fast: false
      matrix:
        subworkflow: "${{ fromJson(needs.nf-core-changes.outputs.subworkflows_files) }}"
    steps:
      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4

      - name: Set up Python
        uses: actions/setup-python@0b93645e9fea7318ecaed2b359559ac225c90a2b # v5
        with:
          python-version: "3.11"

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

      - uses: actions/setup-java@8df1039502a15bceb9433410b1a100fbe190c53b # 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 subworkflow ${{ matrix.subworkflow }}
        run: nf-core subworkflows lint ${{ matrix.subworkflow }}

  confirm-pass:
    runs-on: ubuntu-latest
    needs: [nf-core-lint-modules, nf-core-lint-subworkflows]
    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) }}"