Get pathogen barcodes #22
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| 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 | |