Run models #1295
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| 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 }} |