update_barcodes.yml

name: Update Barcodes

on:
  schedule:
      - cron:  '0 0 */3 * *'
  workflow_dispatch:

jobs:
  update_barcodes:
    runs-on: ubuntu-latest

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

      - name: 'Get updated barcodes and lineages from Freyja repo'
        run: |
              git clone http://github.com/andersen-lab/Freyja
              cp Freyja/freyja/data/usher_barcodes.feather data/barcodes
              cp Freyja/freyja/data/last_barcode_update.txt data/barcodes
              cp Freyja/freyja/data/lineages.yml data/

      - name: 'Commit and push changes'
        run: |
              git config --local user.name "$GITHUB_ACTOR"
              git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
              git remote set-url origin https://github.com/andersen-lab/Freyja-nf
              if [[($(git status data/barcodes/usher_barcodes.feather --porcelain | wc -c) -ne 0)]]; then
                git add data/barcodes/usher_barcodes.feather
                git add data/barcodes/last_barcode_update.txt
                git add data/lineages.yml
              fi
              git commit -m "Update barcodes"
              git push