run-models.yaml

name: Run models

on:
  repository_dispatch:
    types:
      - run-models
  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 that does not send Slack notifications. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/forecasts-ncov'
        required: false
      data_provenance:
        description: 'Data provenance of data inputs for model: gisaid or open. Will run both if left empty.'
        required: false

jobs:
  set_config_overrides:
    runs-on: ubuntu-latest
    steps:
      - id: s3_dst
        run: |
          S3_DST=s3://nextstrain-data/files/workflows/forecasts-ncov

          if [[ -n "$TRIAL_NAME" ]]; then
            S3_DST+=/trial/"$TRIAL_NAME"
          fi

          echo "s3_dst=$S3_DST" >> "$GITHUB_OUTPUT"
        env:
          TRIAL_NAME: ${{ inputs.trial_name }}

      - id: data_provenances
        run: |
          DATA_PROVENANCES='["gisaid", "open"]'

          if [[ -n "$INPUT_DATA_PROVENANCE" ]]; then
            DATA_PROVENANCES="$INPUT_DATA_PROVENANCE"
          fi

          echo "data_provenances=$DATA_PROVENANCES" >> "$GITHUB_OUTPUT"
        env:
          INPUT_DATA_PROVENANCE: ${{ inputs.data_provenance }}
    outputs:
      s3_dst: ${{ steps.s3_dst.outputs.s3_dst }}
      data_provenances: ${{ steps.data_provenances.outputs.data_provenances }}

  run_models:
    needs: [set_config_overrides]
    permissions:
      id-token: write
    uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
    secrets: inherit
    with:
      runtime: aws-batch
      run: |
        nextstrain build \
          --aws-batch \
          --detach \
          --no-download \
          --image nextstrain/base \
          --cpus 8 \
          --memory 16GiB \
          --env AWS_DEFAULT_REGION \
          --env GITHUB_RUN_ID \
          --env SLACK_TOKEN \
          --env SLACK_CHANNELS \
          . \
            --configfile config/config.yaml config/optional.yaml \
            --config s3_dst="$S3_DST" data_provenances="$DATA_PROVENANCES" \
            --keep-going
      env: |
        DATA_PROVENANCES: ${{ needs.set_config_overrides.outputs.data_provenances }}
        GITHUB_RUN_ID: ${{ github.run_id }}
        SLACK_CHANNELS: ${{ github.event.inputs.slack_channel || vars.SLACK_CHANNELS }}
        S3_DST: ${{ needs.set_config_overrides.outputs.s3_dst }}