fetch-and-ingest.yaml

name: Fetch and ingest

on:
  schedule:
    # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings.
    #
    # Note the actual runs might be late.
    # Numerous people were confused, about that, including me:
    #  - https://g.nite07.orgmunity/t/scheduled-action-running-consistently-late/138025/11
    #  - https://github.com/github/docs/issues/3059
    #
    # Note, '*' is a special character in YAML, so you have to quote this string.
    #
    # Docs:
    #  - https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows#schedule
    #
    # Tool that deciphers this particular format of crontab string:
    #  - https://crontab.guru/
    #
    # Runs at 4pm UTC (12pm EDT) since curation by NCBI happens on the East Coast.
    - cron:  '0 16 * * *'

  repository_dispatch:
    types:
      - fetch-and-ingest

  # 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
    env:
      GITHUB_RUN_ID: ${{ github.run_id }}
      SLACK_CHANNELS: monkeypox-updates
      SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }}
    steps:
    - uses: actions/checkout@v2
    - uses: nextstrain/.github/actions/setup-nextstrain-cli@master
      with:
        cli-version: ">=7.1.0"
        python-version: "3.10"

    - name: run_pipeline
      run: |
        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 \
          --env SLACK_TOKEN \
          --env SLACK_CHANNELS \
          --env PAT_GITHUB_DISPATCH \
          ingest \
            --configfiles config/config.yaml config/optional.yaml
      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 }}
        PAT_GITHUB_DISPATCH: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }}

    - name: notify_pipeline_failed
      if: ${{ failure() }}
      run: ./ingest/bin/notify-on-job-fail