linting.yml

name: nf-core linting
# This workflow is triggered on pushes and PRs to the repository.
# It runs the `nf-core lint` and markdown lint tests to ensure
# that the code meets the nf-core guidelines.
on:
  push:
    branches:
      - dev
      - master
  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: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install nf-core

      - name: Run nf-core lint
        run: nf-core lint --dir ${GITHUB_WORKSPACE}