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

env:
  NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }}

jobs:
  fetch-and-ingest:
    runs-on: ubuntu-latest
    steps:
      - uses: actions/checkout@v3
      - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
        with:
          cli-version: ">=7.1.0"
          python-version: "3.10"

      - name: install-pyyaml
        run: python3 -m pip install pyyaml

      - name: run_pipeline
        run: |
          GITHUB_BRANCH=${GITHUB_REF#refs/heads/}
          ./phylogenetic/bin/set-branch-ingest-config \
            --config-yaml ingest/config/optional.yaml \
            --s3-dst s3://nextstrain-data/files/workflows/monkeypox/branch/"${GITHUB_BRANCH}" \
            > ingest/config/optional-branch.yaml

          nextstrain build \
            --aws-batch \
            --detach \
            --no-download \
            --cpus 32 \
            --memory 64gib \
            --env AWS_DEFAULT_REGION \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            ingest \
              --configfiles config/config.yaml config/optional-branch.yaml \
              --config trigger_rebuild=False
        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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}