feat: warn when CUR cost data is incomplete

[FloWuenne]

PR checklist

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool, parameter, or workflow path, update the relevant docs.
• If plugin declarations changed, update CITATIONS.md, README.md, and agent/context guidance in the same PR.
• Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
• Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).

Description

Add explicit CUR coverage reporting so the benchmark report warns when a supplied CUR does not cover all included tasks. Instead of silently presenting unmatched tasks as zero-cost totals, the report now summarizes missing-cost runs and processes in a short warning card.

What changed

• track CUR match coverage per included task during report aggregation
• add cost_coverage metadata to report_data.json
• render a concise warning card in the report when a supplied CUR is incomplete
• add tests for both the aggregation contract and rendered warning logic

Walkthrough

benchmark_report_warning_walkthrough.mp4
Incomplete CUR warning in compiled benchmark report

Testing

• python3 -m pytest -v modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py modules/local/render_benchmark_report/tests/test_render.py
• python3 -m pytest -v modules/local/aggregate_benchmark_report_data/tests/test_aggregate.py modules/local/normalize_benchmark_jsonl/tests/test_normalize.py modules/local/render_benchmark_report/tests/test_render.py bin/test_benchmark_report_fetch.py
• python3 bin/benchmark_report.py normalize-jsonl --data-dir /tmp/cur-warning-demo/data --costs /tmp/cur-warning-demo/partial_cur.parquet --output-dir /tmp/cur-warning-demo/jsonl_bundle
• python3 bin/benchmark_report.py aggregate-report-data --jsonl-dir /tmp/cur-warning-demo/jsonl_bundle --output /tmp/cur-warning-demo/report_data.json
• python3 bin/benchmark_report.py render-html --data /tmp/cur-warning-demo/report_data.json --brand assets/brand.yml --output /tmp/cur-warning-demo/report.html
• /root/.local/bin/pre-commit run --all-files

Notes

Container-backed nf-test / full Nextflow docker verification remains blocked in this VM because Docker launches hit the known cgroup/socket environment issue, but the Python stage tests and local normalize/aggregate/render compile flow all passed.

_{To show artifacts inline, enable in settings.}