Fetch and ingest (on branch) #26
Workflow file for this run
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| name: Fetch and ingest (on branch) | |
| on: | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
| required: false | |
| jobs: | |
| set_config_overrides: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: upload_config | |
| run: | | |
| # Create JSON string for the nested upload config | |
| GITHUB_BRANCH=${GITHUB_REF#refs/heads/} | |
| S3_DST="s3://nextstrain-data/files/workflows/mpox/branch/${GITHUB_BRANCH}" | |
| UPLOAD_CONFIG=$(jq -cn --arg S3_DST "$S3_DST" '{"s3": {"dst": $S3_DST }}') | |
| echo "upload_config=$UPLOAD_CONFIG" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| upload_config: ${{ steps.upload_config.outputs.upload_config }} | |
| fetch-and-ingest: | |
| needs: [set_config_overrides] | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| UPLOAD_CONFIG: ${{ needs.set_config_overrides.outputs.upload_config }} | |
| run: | | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 32 \ | |
| --memory 64gib \ | |
| --env AWS_ACCESS_KEY_ID \ | |
| --env AWS_SECRET_ACCESS_KEY \ | |
| ingest \ | |
| --configfiles config/config.yaml config/optional.yaml \ | |
| --config trigger_rebuild=False send_slack_notifications=False upload="$UPLOAD_CONFIG" |