COVID-19 case counts #576
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| name: COVID-19 case counts | |
| on: | |
| schedule: | |
| - cron: '0 16 * * *' | |
| workflow_dispatch: | |
| inputs: | |
| slack_channel: | |
| description: 'Slack channel to push update alerts. Default channel is nextstrain-counts-updates.' | |
| required: false | |
| trial_name: | |
| description: 'Short name for a trial run. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/forecasts-ncov/cases.' | |
| required: false | |
| jobs: | |
| case_counts: | |
| runs-on: ubuntu-latest | |
| env: | |
| SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} | |
| SLACK_CHANNELS: ${{ github.event.inputs.slack_channel || 'nextstrain-counts-updates' }} | |
| defaults: | |
| run: | |
| # Login shell is required to include changes by conda init bash. | |
| shell: bash -l -eo pipefail {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| python-version: "3.9" | |
| miniforge-variant: Mambaforge | |
| channels: conda-forge,bioconda | |
| - name: setup | |
| run: mamba install "csvtk>=0.23.0" | |
| - name: download case counts | |
| run: | | |
| ./ingest/bin/fetch-ncov-global-case-counts > global_case_counts.tsv | |
| - name: upload to S3 | |
| run: | | |
| S3_DST=s3://nextstrain-data/files/workflows/forecasts-ncov/cases | |
| CLOUDFRONT_DOMAIN="data.nextstrain.org" | |
| if [[ "$TRIAL_NAME" ]]; then | |
| S3_DST+=/trial/"$TRIAL_NAME" | |
| fi | |
| ./ingest/vendored/upload-to-s3 global_case_counts.tsv "$S3_DST"/global.tsv.gz $CLOUDFRONT_DOMAIN | |
| env: | |
| AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| TRIAL_NAME: ${{ github.event.inputs.trial_name }} | |
| - name: notify_pipeline_failed | |
| if: ${{ failure() }} | |
| run: ./ingest/vendored/notify-on-job-fail "Case counts ingest" "nextstrain/forecasts-ncov" |