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COVID-19 case counts #952

COVID-19 case counts

COVID-19 case counts #952

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:
set_s3_dst:
runs-on: ubuntu-latest
steps:
- id: s3_dst
run: |
S3_DST=s3://nextstrain-data/files/workflows/forecasts-ncov
if [[ "$TRIAL_NAME" ]]; then
S3_DST+=/trial/"$TRIAL_NAME"
fi
echo "s3_dst=$S3_DST" >> "$GITHUB_OUTPUT"
env:
TRIAL_NAME: ${{ inputs.trial_name }}
outputs:
s3_dst: ${{ steps.s3_dst.outputs.s3_dst }}
case_counts:
needs: [set_s3_dst]
permissions:
id-token: write
uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
secrets: inherit
with:
runtime: docker
run: |
nextstrain build \
ingest \
upload_all_case_counts \
--config s3_dst="$S3_DST"
env: |
SLACK_CHANNELS: ${{ inputs.slack_channel || vars.SLACK_CHANNELS }}
S3_DST: ${{ needs.set_s3_dst.outputs.s3_dst }}