Update Barcodes #2
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| name: Update Barcodes | |
| on: | |
| schedule: | |
| - cron: '0 0 */7 * *' | |
| 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 "$GITHUB_ACTOR" | |
| git config --local user.email "[email protected]" | |
| git remote set-url origin https://github.com/andersen-lab/Freyja-nf | |
| if [[($(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 |