create-lint-wf.yml

name: Create a pipeline and run nf-core linting
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]

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

env:
  NXF_ANSI_LOG: false

jobs:
  MakeTestWorkflow:
    runs-on: ubuntu-latest
    env:
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
    steps:
      # Get the repo code
      - uses: actions/checkout@v3
        name: Check out source-code repository

      # Set up nf-core/tools
      - name: Set up Python 3.11
        uses: actions/setup-python@v4
        with:
          python-version: 3.11

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

      # Set up Nextflow
      - name: Install Nextflow
        uses: nf-core/setup-nextflow@v1
        with:
          version: ${{ matrix.NXF_VER }}

      # Install the Prettier linting tools
      - uses: actions/setup-node@v3

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

      # Install the editorconfig linting tools
      - name: Install editorconfig-checker
        run: npm install -g editorconfig-checker

      # Build a pipeline from the template
      - name: nf-core create
        run: nf-core --log-file log.txt create -n testpipeline -d "This pipeline is for testing" -a "Testing McTestface" --plain

      # Try syncing it before we change anything
      - name: nf-core sync
        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/

      # Build a module from the template
      - name: nf-core modules create
        run: nf-core --log-file log.txt modules create bpipe --dir nf-core-testpipeline --author @nf-core-bot --label process_low --meta

      # Run code style linting
      - name: Run Prettier --check
        run: prettier --check nf-core-testpipeline

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

      # Update modules to the latest version
      - name: nf-core modules update
        run: nf-core --log-file log.txt modules update --dir nf-core-testpipeline --all --no-preview

      # Remove TODO statements
      - name: remove TODO
        run: find nf-core-testpipeline -type f -exec sed -i '/TODO nf-core:/d' {} \;

      # Replace zenodo.XXXXXX to pass readme linting
      - name: replace zenodo.XXXXXX
        run: find nf-core-testpipeline -type f -exec sed -i 's/zenodo.XXXXXX/zenodo.123456/g' {} \;

      # Run nf-core linting
      - name: nf-core lint
        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned

      # Run the other nf-core commands
      - name: nf-core list
        run: nf-core --log-file log.txt list

      # - name: nf-core licences
      #   run: nf-core --log-file log.txt licences nf-core-testpipeline

      - name: nf-core schema
        run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts

      - name: nf-core bump-version
        run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1

      - name: nf-core lint in release mode
        run: nf-core --log-file log.txt --hide-progress lint --dir nf-core-testpipeline --fail-ignored --fail-warned --release

      - name: nf-core modules install
        run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force

      - name: nf-core modules install gitlab
        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git --branch branch-tester install fastp --dir nf-core-testpipeline/

      - name: nf-core modules list local
        run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/

      - name: nf-core modules list remote
        run: nf-core --log-file log.txt modules list remote

      - name: nf-core modules list remote gitlab
        run: nf-core --log-file log.txt modules --git-remote https://gitlab.com/nf-core/modules-test.git list remote

      - name: Upload log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@v3
        with:
          name: nf-core-log-file
          path: log.txt