update_barcodes.yml

name: barcode update

on:
  schedule:
    - cron: '0 0 * * *'

jobs:
  testsuite:
    runs-on: macos-latest
    defaults:
      run:
        shell: bash

    steps:
      - name: Check out repository code
        uses: actions/checkout@main
        with:
          repo-token: ${{ secrets.GITHUB_TOKEN }}

      - name: Setup for conda
        uses: conda-incubator/setup-miniconda@v2
        with:        
          auto-update-conda: true
          channels: bioconda,conda-forge
          channel-priority: true
          python-version: 3.7
          activate-environment: test

      - name: Install
        shell: bash -l {0}
        run: |
          conda install -n base conda-libmamba-solver
          conda config --set solver libmamba
          conda config --add channels bioconda
          conda config --add channels conda-forge          
          conda install --yes --file ci/conda_requirements.txt
          pip install -e . --no-deps 
          
      - name: update
        shell: bash -l {0}
        env:
          TREELINK: ${{ secrets.TREELINK }}
          ZIPNAME: ${{ secrets.ZIPNAME }}
        run: |
          conda activate test
          wget "${TREELINK}"
          freyja barcode-build --pb "${ZIPNAME}" --outdir freyja/data/

      - name: commit if output is different 
        run: |
          echo "running git diff, committing if different"
          if [[($(git status freyja/data/usher_barcodes.csv --porcelain | wc -c) -ne 0)]]; then
            echo "changes were made, updating barcodes"
            git config --local user.name "$GITHUB_ACTOR"
            git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
            echo $(date +"%m_%d_%Y-%H-%M")> freyja/data/last_barcode_update.txt
            git add freyja/data/last_barcode_update.txt
            git add freyja/data/lineages.yml
            git add freyja/data/usher_barcodes.csv
            git add freyja/data/curated_lineages.json
            git commit -m "updating barcodes and metadata"
            git push origin main
          else
              echo "no changes were made, doing nothing."
          fi;