Run models #1283
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| 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 }} |