gisaid/clade-counts #878
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| name: GISAID SARS-CoV-2 clade counts | |
| on: | |
| repository_dispatch: | |
| types: | |
| - clade-counts | |
| - gisaid/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/gisaid' | |
| 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: ${{ steps.s3_dst.outputs.s3_dst }} | |
| gisaid_clade_counts: | |
| needs: [set_s3_dst] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| run: | | |
| nextstrain build \ | |
| --cpus 8 \ | |
| --memory 32gib \ | |
| --env SLACK_TOKEN \ | |
| --env SLACK_CHANNELS \ | |
| --env S3_DST \ | |
| ingest \ | |
| upload_all_sequence_counts \ | |
| --config data_provenances=["gisaid"] s3_dst="$S3_DST" | |
| env: | | |
| SLACK_CHANNELS: ${{ inputs.slack_channel || vars.SLACK_CHANNELS }} | |
| S3_DST: ${{ needs.set_s3_dst.outputs.s3_dst }} | |
| trigger_model_runs: | |
| needs: [gisaid_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=gisaid | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH }} |