taxprofiler/.github/workflows/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:
  pull_request:
  release:
    types: [published]

jobs:
  EditorConfig:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - uses: actions/setup-node@v2

      - name: Install editorconfig-checker
        run: npm install -g editorconfig-checker

      - name: Run ECLint check
        run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile')

  Prettier:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - uses: actions/setup-node@v2

      - name: Install Prettier
        run: npm install -g prettier

      - name: Run Prettier --check
        run: prettier --check ${GITHUB_WORKSPACE}

  nf-core:
    runs-on: ubuntu-latest
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v2

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

      - uses: actions/setup-python@v3
        with:
          python-version: "3.6"
          architecture: "x64"

      - name: Install dependencies
        run: |
          python -m pip install --upgrade pip
          pip install nf-core

      - name: Run nf-core lint
        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 lint --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@v2
        with:
          name: linting-logs
          path: |
            lint_log.txt
            lint_results.md
            PR_number.txt