fetch-and-ingest-branch.yaml

name: Fetch and ingest (on branch)

on:
  # Manually triggered using GitHub's UI
  workflow_dispatch:
    inputs:
      image:
        description: 'Specific container image to use for build (will override the default of "nextstrain build")'
        required: false


jobs:
  set_config_overrides:
    runs-on: ubuntu-latest
    steps:
      - id: upload_config
        run: |
          # Create JSON string for the nested upload config
          GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
          S3_DST="s3://nextstrain-data/files/workflows/mpox/branch/${GITHUB_BRANCH}"
          UPLOAD_CONFIG=$(jq -cn --arg S3_DST "$S3_DST" '{"s3": {"dst": $S3_DST }}')

          echo "upload_config=$UPLOAD_CONFIG" >> "$GITHUB_OUTPUT"
    outputs:
      upload_config: ${{ steps.upload_config.outputs.upload_config }}

  fetch-and-ingest:
    needs: [set_config_overrides]
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      runtime: aws-batch
      env: |
        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }}
        GITHUB_RUN_ID: ${{ github.run_id }}
        SLACK_CHANNELS: ${{ vars.TEST_SLACK_CHANNEL }}
        UPLOAD_CONFIG: ${{ needs.set_config_overrides.outputs.upload_config }}
      run: |
        nextstrain build \
          --aws-batch \
          --detach \
          --no-download \
          --cpus 32 \
          --memory 64gib \
          --env GITHUB_RUN_ID \
          --env SLACK_TOKEN \
          --env SLACK_CHANNELS \
          ingest \
            nextstrain_automation \
              --configfiles build-configs/nextstrain-automation/config.yaml \
              --config trigger_rebuild=False send_slack_notifications=True upload="$UPLOAD_CONFIG"