template-version-comment.yml

name: nf-core template version comment
# This workflow is triggered on PRs to check if the pipeline template version matches the latest nf-core version.
# It posts a comment to the PR, even if it comes from a fork.

on:
  pull_request:

permissions: {}

jobs:
  check_template_version:
    runs-on: ubuntu-latest
    steps:
      - name: Check out pipeline code
        uses: actions/checkout@de0fac2e4500dabe0009e67214ff5f5447ce83dd # v6
        with:
          ref: ${{ github.event.pull_request.head.sha }}

      - name: Read template version from .nf-core.yml
        uses: nichmor/minimal-read-yaml@1f7205277e25e156e1f63815781db80a6d490b8f # v0.0.2
        id: read_yml
        with:
          config: ${{ github.workspace }}/.nf-core.yml

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

      - name: Build PR comment if template is outdated
        # The fork-controlled version is passed via the environment and only ever
        # used as quoted shell data (never interpolated into a command), so it
        # cannot be used for script injection.
        env:
          PR_VERSION: ${{ steps.read_yml.outputs['nf_core_version'] }}
          PR_NUMBER: ${{ github.event.pull_request.number }}
        run: |
          mkdir -p pr-comment
          echo "$PR_NUMBER" > pr-comment/pr_number.txt
          echo "template-version" > pr-comment/header.txt

          latest_version=$(nf-core --version | grep -oE '[0-9]+\.[0-9]+\.[0-9]+' | head -n1)

          if [ -n "$PR_VERSION" ] && [ -n "$latest_version" ] && [ "$PR_VERSION" != "$latest_version" ]; then
            cat > pr-comment/comment.md <<EOF
          > [!WARNING]
          > Newer version of the nf-core template is available.
          >
          > Your pipeline is using an old version of the nf-core template: ${PR_VERSION}.
          > Please update your pipeline to the latest version.
          >
          > For more documentation on how to update your pipeline, please see the [Synchronisation documentation](https://nf-co.re/docs/developing/template-syncs/overview).
          EOF
          fi

      - name: Upload PR comment artifact
        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7
        with:
          name: pr-comment
          path: pr-comment/