name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core pipelines lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

jobs:
  pre-commit:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - name: Set up Python 3.12
        uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
        with:
          python-version: "3.12"

      - name: Install pre-commit
        run: pip install pre-commit

      - name: Run pre-commit
        run: pre-commit run --all-files

  nf-core:
    runs-on: ubuntu-latest
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@0ad4b8fadaa221de15dcec353f45205ec38ea70b # v4

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v2

      - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
        with:
          python-version: "3.12"
          architecture: "x64"

      - name: read .nf-core.yml
        uses: pietrobolcato/action-read-yaml@1.1.0
        id: read_yml
        with:
          config: ${{ github.workspace }}/.nf-core.yml

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}

      - name: Run nf-core pipelines lint
        if: ${{ github.base_ref != 'master' }}
        env:
          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
        run: nf-core -l lint_log.txt pipelines lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

      - name: Run nf-core pipelines lint --release
        if: ${{ github.base_ref == 'master' }}
        env:
          GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }}
          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
          GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }}
        run: nf-core -l lint_log.txt pipelines lint --release --dir ${GITHUB_WORKSPACE} --markdown lint_results.md

      - name: Save PR number
        if: ${{ always() }}
        run: echo ${{ github.event.pull_request.number }} > PR_number.txt

      - name: Upload linting log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
        with:
          name: linting-logs
          path: |
            lint_log.txt
            lint_results.md
            PR_number.txt
