Facs Gating Viz Style

Beautify FACS gating plots for publication

Security Scan

The skill claims to produce publication-ready FACS plots but the provided code is only a stub (it prints messages and does not read or plot data), and the SKILL.md claims features and no dependencies that are inconsistent with real plotting work.

Purpose & Capability

Name/description say 'beautify FACS gating plots' and SKILL.md lists contour/density/dot styling and publication-ready output, but the included script (scripts/main.py) does not read the FCS file, perform plotting, or write output. SKILL.md also states 'No additional Python packages required', which is inconsistent with typical plotting workflows (matplotlib, numpy, etc.). This suggests the package is incomplete or misleading about capabilities.

Instruction Scope

Runtime instructions tell the agent/user to run python scripts/main.py --data fcs_file.fcs and imply reading input and writing output. The actual script accepts a --data argument but only prints messages and does not access the filesystem or network. There are no instructions that read unrelated files, exfiltrate data, or call external endpoints.

Install Mechanism

No install spec (instruction-only plus a small script). Nothing is downloaded or written to disk by an installer. This is the lowest-risk install mechanism.

Credentials

No environment variables, credentials, or config paths are requested. The skill does not ask for unrelated secrets or unusual system access.

Persistence & Privilege

Flags are default (always=false, user-invocable=true, model invocation allowed). The skill does not request persistent presence, nor does it modify other skills or system-wide settings.

What to consider before installing

This package appears to be a stub: the script accepts a data path and style but only prints status messages and does not read the FCS file, generate plots, or write outputs. That mismatch could be an honest incomplete draft or careless packaging rather than malicious code, but you should not assume it performs the advertised work. Before installing or using this in a production workflow: (1) request a full implementation or source that actually performs plotting and specifies required Python packages (e.g., matplotlib, numpy, FlowCal, fcsparser), (2) review any future code that performs file I/O to ensure it validates input paths (prevent ../ traversal) and handles sensitive files safely, (3) run the code in a sandboxed environment and inspect outputs, and (4) prefer a version that declares and pins dependencies. If you need production-grade plotting now, use a known library or a vetted package rather than this draft.

Beautify flow cytometry gating plots for publication.

Parameters

Parameter	Type	Default	Required	Description
--data, -d	string	-	Yes	FCS file path
--style, -s	string	contour	No	Plot style (contour, density, dot)

Usage

python scripts/main.py --data fcs_file.fcs --style contour

Features

• Contour plots
• Density visualization
• Publication-ready styling

Risk Assessment

Risk Indicator	Assessment	Level
Code Execution	Python/R scripts executed locally	Medium
Network Access	No external API calls	Low
File System Access	Read input files, write output files	Medium
Instruction Tampering	Standard prompt guidelines	Low
Data Exposure	Output files saved to workspace	Low

Security Checklist

• No hardcoded credentials or API keys
• No unauthorized file system access (../)
• Output does not expose sensitive information
• Prompt injection protections in place
• Input file paths validated (no ../ traversal)
• Output directory restricted to workspace
• Script execution in sandboxed environment
• Error messages sanitized (no stack traces exposed)
• Dependencies audited

Prerequisites

No additional Python packages required.

Evaluation Criteria

Success Metrics

• Successfully executes main functionality
• Output meets quality standards
• Handles edge cases gracefully
• Performance is acceptable

Test Cases

1. Basic Functionality: Standard input → Expected output
2. Edge Case: Invalid input → Graceful error handling
3. Performance: Large dataset → Acceptable processing time

Lifecycle Status

• Current Stage: Draft
• Next Review Date: 2026-03-06
• Known Issues: None
• Planned Improvements:
  • Performance optimization
  • Additional feature support