genbank/clade-counts #861
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: Open SARS-CoV-2 clade counts | |
| on: | |
| repository_dispatch: | |
| types: | |
| - clade-counts | |
| - open/clade-counts | |
| - genbank/clade-counts | |
| 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. WARNING: without this we will overwrite files in s3://nextstrain-data/files/workflows/forecasts-ncov/open' | |
| required: false | |
| jobs: | |
| set_s3_dst: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: s3_dst | |
| run: | | |
| S3_DST=s3://nextstrain-data/files/workflows/forecasts-ncov | |
| if [[ "$TRIAL_NAME" ]]; then | |
| S3_DST+=/trial/"$TRIAL_NAME" | |
| fi | |
| echo "s3_dst=$S3_DST" >> "$GITHUB_OUTPUT" | |
| env: | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| outputs: | |
| s3_dst: ${{ steps.s3_dst.outputs.s3_dst }} | |
| open_clade_counts: | |
| needs: [set_s3_dst] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| run: | | |
| nextstrain build \ | |
| --cpus 8 \ | |
| --memory 16gib \ | |
| --env SLACK_TOKEN \ | |
| --env SLACK_CHANNELS \ | |
| --env S3_DST \ | |
| ingest \ | |
| upload_all_sequence_counts \ | |
| --config data_provenances=["open"] s3_dst="$S3_DST" | |
| env: | | |
| SLACK_CHANNELS: ${{ inputs.slack_channel || vars.SLACK_CHANNELS }} | |
| S3_DST: ${{ needs.set_s3_dst.outputs.s3_dst }} | |
| trigger_model_runs: | |
| needs: [open_clade_counts] | |
| if: ${{ !github.event.inputs.trial_name }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - run: gh workflow run run-models.yaml --repo nextstrain/forecasts-ncov -f data_provenance=open | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }} |