fetch-and-ingest-genbank-master.yml

name: GenBank fetch and ingest

on:
  schedule:
    # Note times are in UTC, which is 1 or 2 hours behind CET depending on daylight savings.
    #
    # Currently, we aim to trigger ingest every day at 18:07 UTC which is 19:07 CET (as of Mar 2022).
    # Note the actual runs might be late. As of right now, the action starts around 20 past the hour.
    # Numerous people were confused, about that, including me:
    #  - https://github.community/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/
    #
    # Looks like you are about to modify this schedule? Make sure you also modify the schedule for the
    # sister GISAID job, so that we don't need to keep two schedules in our heads.
    - cron:  '7 18 * * *'

  # Manually triggered using `./vendored/trigger nextstrain/ncov-ingest genbank/fetch-and-ingest` (or `fetch-and-ingest`, which
  # includes GISAID)
  repository_dispatch:
    types:
      - genbank/fetch-and-ingest
      - fetch-and-ingest

  # Manually triggered using GitHub's UI
  workflow_dispatch:
    inputs:
      trial_name:
        description: >-
          Short name for a trial run.
          If provided, files will be uploaded to s3://nextstrain-data/files/ncov/open/trial/${TRIAL_NAME}/
          and downstream ncov and forecasts-ncov workflows will not be triggered.
          WARNING: without the trial name, workflow will upload files to s3://nextstrain-data/files/ncov/open/
        required: false
      fetch_from_database:
        description: >-
          Whether the workflow should fetch from upstream database.
          If not selected (false), the workflow will start from existing data on S3.
        type: boolean
        required: false
        default: true
      image:
        description: >-
          Specific container image to use for build.
          This will override the default image (nextstrain/ncov-ingest).
        required: false

jobs:
  set_config_overrides:
    runs-on: ubuntu-latest
    steps:
      - id: config
        name: Set config overrides
        env:
          TRIAL_NAME: ${{ inputs.trial_name }}
          FETCH_FROM_DATABASE: ${{ github.event_name != 'workflow_dispatch' && true || inputs.fetch_from_database }}
        run: |
          config="--config"

          if [[ "$FETCH_FROM_DATABASE" == true ]]; then
            config+=" fetch_from_database=True"
          else
            config+=" fetch_from_database=False"
          fi

          if [[ "$TRIAL_NAME" ]]; then
            config+=" trigger_rebuild=False"
            config+=" trigger_counts=False"
            config+=" s3_dst=s3://nextstrain-data/files/ncov/open/trial/${TRIAL_NAME}"
          else
            config+=" trigger_rebuild=True"
            config+=" trigger_counts=True"
          fi

          echo "config=$config" >> "$GITHUB_OUTPUT"
    outputs:
      config_overrides: ${{ steps.config.outputs.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: |
        CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }}
        GITHUB_RUN_ID: ${{ github.run_id }}
        NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image || 'nextstrain/ncov-ingest' }}
        SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || 'ncov-genbank-updates' }}
      run: |
        nextstrain build \
          --aws-batch \
          --detach \
          --no-download \
          --cpus 36 \
          --memory 68GiB \
          --env GITHUB_RUN_ID \
          --env SLACK_TOKEN \
          --env SLACK_CHANNELS \
          --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \
          . \
            --stats snakemake_stats.json \
            --configfile config/genbank.yaml \
            $CONFIG_OVERRIDES