create-lint-wf.yml

name: Create a pipeline and run nf-core linting
on:
  push:
    branches:
      - dev
  pull_request:
  release:
    types: [published]
  workflow_dispatch:
    inputs:
      runners:
        description: "Runners to test on"
        type: choice
        options:
          - "ubuntu-latest"
          - "self-hosted"
        default: "self-hosted"

# 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: ${{ github.event.inputs.runners || 'self-hosted' }}
    env:
      NXF_ANSI_LOG: false
    strategy:
      matrix:
        NXF_VER:
          - "23.04.0"
          - "latest-everything"
    steps:
      - name: go to subdirectory and change nextflow workdir
        run: |
          mkdir -p create-lint-wf
          cd create-lint-wf
          export NXF_WORK=$(pwd)

      # Get the repo code
      - uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
        name: Check out source-code repository

      # Set up nf-core/tools
      - name: Set up Python 3.11
        uses: actions/setup-python@0a5c61591373683505ea898e09a3ea4f39ef2b9c # v5
        with:
          python-version: 3.11
          cache: pip

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

      # Set up Nextflow
      - name: Install Nextflow
        uses: nf-core/setup-nextflow@a2aef5d2363ccd4f99661d959a53dd0286010ddf # v1
        with:
          version: ${{ matrix.NXF_VER }}

      # Build a pipeline from the template
      - name: nf-core create
        run: |
          mkdir create-lint-wf && cd create-lint-wf
          export NXF_WORK=$(pwd)
          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/
        working-directory: create-lint-wf

      # 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
        working-directory: create-lint-wf

      # Run code style linting
      - name: run pre-commit
        run: pre-commit run --all-files
        working-directory: create-lint-wf

      # 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
        working-directory: create-lint-wf

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

      # 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' {} \;
        working-directory: create-lint-wf

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

      # Run the other nf-core commands
      - name: nf-core list
        run: nf-core --log-file log.txt list
        working-directory: create-lint-wf

      # - 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
        working-directory: create-lint-wf

      - name: nf-core bump-version
        run: nf-core --log-file log.txt bump-version --dir nf-core-testpipeline/ 1.1
        working-directory: create-lint-wf

      - 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
        working-directory: create-lint-wf

      - name: nf-core modules install
        run: nf-core --log-file log.txt modules install fastqc --dir nf-core-testpipeline/ --force
        working-directory: create-lint-wf

      - 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/
        working-directory: create-lint-wf

      - name: nf-core modules list local
        run: nf-core --log-file log.txt modules list local --dir nf-core-testpipeline/
        working-directory: create-lint-wf

      - name: nf-core modules list remote
        run: nf-core --log-file log.txt modules list remote
        working-directory: create-lint-wf

      - 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
        working-directory: create-lint-wf

      - name: Upload log file artifact
        if: ${{ always() }}
        uses: actions/upload-artifact@26f96dfa697d77e81fd5907df203aa23a56210a8 # v4
        with:
          name: nf-core-log-file-${{ matrix.NXF_VER }}
          path: create-lint-wf/log.txt

      - name: Cleanup work directory
        run: sudo rm -rf create-lint-wf
        if: always()