update-loci.yaml

name: Update data

permissions:
  contents: write

on:
  pull_request:
    branches: main
    paths:
      - "data/**"
      - "scripts/**"
      - "workflow/**"
      - ".github/workflows/**"
  workflow_dispatch:

jobs:
  update:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -l {0}
    strategy:
      fail-fast: false

    steps:
      - name: Debug dump
        uses: crazy-max/ghaction-dump-context@v2

      - name: Checkout code
        uses: actions/checkout@v4

      - name: Set up Miniconda environment
        uses: conda-incubator/setup-miniconda@v3
        with:
          auto-update-conda: true
          activate-environment: strchive
          environment-file: scripts/environment.yml
          python-version: 3.12
          auto-activate-base: false
      - run: |
          conda info

      - name: Check loci and update bed files (short)
        #if: ${{ github.event_name == 'pull_request' || github.event_name == 'workflow_dispatch'}}
        run: snakemake --config stages="skip-refs"

      - name: Open pull request with updated files
        if: ${{ !(github.event_name == 'pull_request') }}
        uses: peter-evans/create-pull-request@v7
        with:
          branch: update-data
          title: Update data

      - name: Commit updated files to current pull request
        if: ${{ github.event_name == 'pull_request' }}
        uses: stefanzweifel/git-auto-commit-action@v5
        with:
          commit_message: Update data