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:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

jobs:
  EditorConfig:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - uses: actions/setup-node@v3

      - 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@v3

      - uses: actions/setup-node@v3

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

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

  PythonBlack:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3

      - name: Check code lints with Black
        uses: psf/black@stable

      # If the above check failed, post a comment on the PR explaining the failure
      - name: Post PR comment
        if: failure()
        uses: mshick/add-pr-comment@v1
        with:
          message: |
            ## Python linting (`black`) is failing

            To keep the code consistent with lots of contributors, we run automated code consistency checks.
            To fix this CI test, please run:

            * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black`
            * Fix formatting errors in your pipeline: `black .`

            Once you push these changes the test should pass, and you can hide this comment :+1:

            We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help!

            Thanks again for your contribution!
          repo-token: ${{ secrets.GITHUB_TOKEN }}
          allow-repeats: false

  nf-core:
    runs-on: ubuntu-latest
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@v3

      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1

      - uses: actions/setup-python@v4
        with:
          python-version: "3.7"
          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@v3
        with:
          name: linting-logs
          path: |
            lint_log.txt
            lint_results.md
            PR_number.txt