pull.yml

name: Get pathogen barcodes
on:
  repository_dispatch:
    types: [update-barcodes]
  workflow_dispatch:
    inputs:
      pathogen:
        description: 'Pathogen name'
        required: true

jobs:
  get_pathogen_barcodes:
    runs-on: ubuntu-latest
    defaults:
      run:
        shell: bash -el {0}
    steps:
      - uses: actions/checkout@v3.3.0
      - name: Get pathogen barcodes
        env: 
          PATHOGEN: ${{ github.event.client_payload.pathogen || github.event.inputs.pathogen }}
        run: |
          echo "Pathogen: $PATHOGEN"
          # check if folder named pathogen exists
          if [ ! -d "$PATHOGEN" ]; then
            echo "Pathogen $PATHOGEN does not exist"
          else
            cd $PATHOGEN
            # make directory with current date
            date=$(date +%Y-%m-%d)
            mkdir $date
            # download pathogen barcodes
            wget -O $date/barcode.csv https://raw.githubusercontent.com/andersen-lab/Freyja-process-barcodes/main/${{ env.PATHOGEN }}/output/GENERATE_BARCODES/barcode.csv --header 'Authorization: token ${{ secrets.FREYJA_ACTION_KEY }}'
            wget -O $date/barcode.html https://raw.githubusercontent.com/andersen-lab/Freyja-process-barcodes/main/${{ env.PATHOGEN }}/output/GENERATE_BARCODES/barcode.html --header 'Authorization: token ${{ secrets.FREYJA_ACTION_KEY }}'
            wget -O $date/auspice_tree.json https://raw.githubusercontent.com/andersen-lab/Freyja-process-barcodes/main/${{ env.PATHOGEN }}/data/auspice_tree.json --header 'Authorization: token ${{ secrets.FREYJA_ACTION_KEY }}'
            wget -O $date/reference.fasta https://raw.githubusercontent.com/andersen-lab/Freyja-process-barcodes/main/${{ env.PATHOGEN }}/data/reference.fasta --header 'Authorization: token ${{ secrets.FREYJA_ACTION_KEY }}'
            # commit and push
            git pull origin main
            git config --global user.email "github-actions[bot]@users.noreply.github.com"
            git config --global user.name "github-actions[bot]"
            git add $date
            git commit -m "Add pathogen barcodes for $PATHOGEN"
            git push
          fi