deeptools
Pass
Audited by Gen Agent Trust Hub on Sep 15, 2026
Risk Level: SAFEDYNAMIC_EXECUTIONINDIRECT_PROMPT_INJECTION
Full Analysis
- [DYNAMIC_EXECUTION]: The
scripts/workflow_generator.pyscript generates bash templates by interpolating user-provided parameters into predefined shell command structures. This is a legitimate utility for creating complex command-line sequences for bioinformatics workflows and does not represent a threat as the generated scripts are intended for user review. - [INDIRECT_PROMPT_INJECTION]: The skill has an attack surface where untrusted data (file paths or parameter values) could be processed.
- Ingestion points:
scripts/workflow_generator.pyaccepts parameters via command-line arguments;scripts/validate_files.pyreads and parses BED file content. - Boundary markers: None present in the interpolation logic.
- Capability inventory: The skill can write files to the filesystem (
workflow_generator.py) and generate scripts that execute a variety of bioinformatics tools (e.g.,bamCoverage,samtools,plotHeatmap). - Sanitization:
scripts/validate_files.pyperforms format validation on BED files, but input parameters in the workflow generator are interpolated directly into shell templates. - [SAFE]: The skill provides standard documentation and utilities for the established 'deepTools' bioinformatics suite. All external references and package installations target official and well-known repositories.
Audit Metadata