False positive: legitimate bioinformatics repo blocked due to keyword-based safety filter

Description

When asking Claude Code to clone a private GitHub repository (mrna-vaccine-pipeline), the request was blocked with a policy violation error. The only action requested was git clone — no code generation, no biological synthesis instructions, nothing dangerous.

What happened

• User asked Claude Code to pull/clone their own private repository
• Claude refused, citing policy violation
• The repository is a computational bioinformatics pipeline for personalized cancer immunotherapy research (neoantigen prediction → mRNA sequence design in silico)
• All tools used are standard open-source bioinformatics software (GATK, MHCflurry, ViennaRNA, ESMFold)

Expected behavior

A git clone command should not be blocked based on repository name or description keywords. If the context is insufficient to determine intent, the default should be permissive (innocent until proven guilty), not blocking.

Root cause (suspected)

Keywords in the repo name/description — mRNA, vaccine, mutation, cancer — appear to trigger the safety filter, even though:

1. The action requested was a simple git operation
2. The project is legitimate computational biology (no wet-lab synthesis, no pathogen engineering)
3. The code only does data analysis: VCF parsing, binding affinity prediction, codon optimization, and protein structure visualization

Suggestion

• Safety filters should consider the action being performed (e.g., git clone), not just keyword matching on metadata
• When context is ambiguous, default to allowing the action rather than blocking
• Bioinformatics/computational biology should be recognized as a legitimate domain

Environment

• Claude Code CLI (VS Code extension)
• Windows 11
• March 2026