nf-core-linting.yml

name: nf-core-lint
run-name: nf-core-lint
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` tests to ensure that the module code meets the nf-core guidelines
on:
  push:
    branches: [master]
  pull_request:
    branches: [master]

# Cancel if a newer run is started
concurrency:
  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
  cancel-in-progress: true

jobs:
  changes:
    name: check-changes
    runs-on: ubuntu-latest
    outputs:
      # Expose matched filters as job 'modules' output variable
      modules: ${{ steps.filter.outputs.changes }}
    steps:
      - uses: actions/checkout@v3

      - uses: dorny/paths-filter@v2
        id: filter
        with:
          filters: "tests/config/pytest_modules.yml"

  lint:
    runs-on: ubuntu-20.04
    name: lint
    needs: changes
    if: needs.changes.outputs.modules != '[]'
    strategy:
      fail-fast: false
      matrix:
        tags: ["${{ fromJson(needs.changes.outputs.modules) }}"]
    steps:
      - uses: actions/checkout@v3

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

      - uses: actions/cache@v3
        with:
          path: ~/.cache/pip
          key: ${{ runner.os }}-pip-${{ hashFiles('**/requirements.txt') }}
          restore-keys: |
            ${{ runner.os }}-pip-

      - name: Set up Python
        uses: actions/setup-python@v4
        with:
          python-version: "3.x"

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

      - name: Install nf-core tools
        run: python -m pip install nf-core

      - name: Install Nextflow
        env:
          CAPSULE_LOG: none
        run: |
          wget -qO- get.nextflow.io | bash
          sudo mv nextflow /usr/local/bin/

      - name: Lint ${{ matrix.tags }}
        run: nf-core modules lint ${{ matrix.tags }}
        # HACK
        if: startsWith( matrix.tags, 'subworkflow' ) != true

      - uses: actions/cache@v3
        with:
          path: /usr/local/bin/nextflow
          key: ${{ runner.os }}
          restore-keys: |
            ${{ runner.os }}