update-pangolin.yaml

name: Check for new pangolin Release

on:
  schedule:
    # At the end of every day
    - cron: "0 0 * * *"

jobs:
  Create-PR-for-new-Pangolin-release:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v2

      - name: Install mamba
        uses: conda-incubator/setup-miniconda@v2
        with:
          mamba-version: "*"
          channels: bioconda,conda-forge,defaults
          channel-priority: true

      - name: Get latest Pangolin release
        shell: bash -l {0}
        run: |
          echo "LATEST_PANGOLIN=$(mamba search -f pangolin -c bioconda | tail -n1 | awk '{print $2}')" >> $GITHUB_ENV
          echo "Latest Pangolin release: $(mamba search -f pangolin -c bioconda | tail -n1 | awk '{print $2}')"

      - name: Get Pangolin release used in UnCoVar
        run: |
          echo "CURRENT_PANGOLIN=$(cat workflow/envs/pangolin.yaml | grep pangolin | awk -F "=" '{print $2}')" >> $GITHUB_ENV
          echo "Current Pangolin release: $(cat workflow/envs/pangolin.yaml | grep pangolin | awk -F "=" '{print $2}')"

      - name: Update Pangolin release used in UnCoVar
        if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }}
        run: |
          sed -i 's/${{ env.CURRENT_PANGOLIN }}/${{ env.LATEST_PANGOLIN }}/' workflow/envs/pangolin.yaml

      - name: Create Pull Request
        if: ${{ env.LATEST_PANGOLIN != env.CURRENT_PANGOLIN }}
        id: cpr
        uses: peter-evans/create-pull-request@v4
        with:
          token: ${{ secrets.GITHUB_TOKEN }}
          committer: GitHub <noreply@github.com>
          commit-message: Update pangolin to ${{ env.LATEST_PANGOLIN }}
          author: ${{ github.actor }} <${{ github.actor }}@users.noreply.github.com>
          branch: pangolin-update-to-${{ env.LATEST_PANGOLIN }}
          delete-branch: true
          title: "build: update Pangolin to ${{ env.LATEST_PANGOLIN }}"
          body: |
            Hey there, a new release of Pangolin is available: [${{ env.LATEST_PANGOLIN }}](https://github.com/cov-lineages/pangolin/releases/tag/v${{ env.LATEST_PANGOLIN }})

            Auto-generated by [create-pull-request][1]

            [1]: https://github.com/peter-evans/create-pull-request
          labels: |
            automated pr

      - name: Check outputs
        run: |
          echo "Pull Request Number - ${{ steps.cpr.outputs.pull-request-number }}"
          echo "Pull Request URL - ${{ steps.cpr.outputs.pull-request-url }}"