Content
50%Reviews the quality of instructions and guidance provided to agents. Good implementation is clear, handles edge cases, and produces reliable results.
The body is well-structured with concrete quantified thresholds and a clear phased pipeline, but it suffers from redundancy between the workflow diagram and phase summaries, missing inline executable code, absent error-recovery feedback loops, and dangling references to bundle files that are not present.
Suggestions
Merge the ASCII Workflow Overview with the Phase Summaries into a single representation to remove the duplicated per-phase descriptions and improve conciseness.
Add explicit feedback loops for QC/batch failures (e.g., 'if CV >30% in QC samples, re-run calibration or exclude the batch') to raise workflow clarity.
Either inline a minimal executable Python snippet for key phases or create the referenced code_examples.md and report_template.md files so the progressive-disclosure references resolve to real bundle files.
| Dimension | Reasoning | Score |
|---|---|---|
Conciseness | The ASCII Workflow Overview diagram and the subsequent Phase Summaries restate the same per-phase content, and the Domain Reasoning section explains normalization/batch-effect concepts Claude largely already knows; mostly efficient but could be tightened by merging the two. | 2 / 3 |
Actionability | Concrete thresholds are given (CV <30%, blank >3x, ±5 ppm, adj p<0.05, |log2FC|>1.0), but no executable code is inline and the referenced code_examples.md does not exist, leaving guidance specific but incomplete. | 2 / 3 |
Workflow Clarity | The 8-phase pipeline is clearly sequenced with embedded QC validation criteria (Phase 2), but there are no explicit feedback/error-recovery loops describing what to do when a QC gate fails, and batch correction lacks a verification checkpoint. | 2 / 3 |
Progressive Disclosure | Sections are organized and a one-level-deep 'Reference Files' section signals report_template.md and code_examples.md, but those files (and any references/scripts/assets bundles) do not exist, so the references are dangling rather than backed by an actual bundle structure. | 2 / 3 |
Total | 8 / 12 Passed |