deeptools
Pass
Audited by Gen Agent Trust Hub on Sep 25, 2026
Risk Level: SAFECOMMAND_EXECUTIONDYNAMIC_EXECUTIONINDIRECT_PROMPT_INJECTION
Full Analysis
- [DYNAMIC_EXECUTION]: The skill uses
scripts/workflow_generator.pyto produce customized bash scripts for specific analysis pipelines. This dynamic generation is a core feature for reproducible research in bioinformatics. - [INDIRECT_PROMPT_INJECTION]: The
scripts/workflow_generator.pyscript ingests user-provided filenames and parameters to populate bash templates. - Ingestion points: Command-line arguments to
scripts/workflow_generator.py(e.g.,--input-bam,--chip-bams). - Boundary markers: None explicitly present in the generated shell output, but shell escaping is consistently applied.
- Capability inventory: The generated scripts invoke various deepTools binaries (e.g.,
bamCoverage,plotHeatmap) via shell execution. - Sanitization: The skill employs
shlex.quoteand a restrictive regular expression ([A-Za-z0-9._/-]+) to ensure file paths and numeric parameters cannot contain malicious shell metacharacters. - [COMMAND_EXECUTION]: The skill facilitates the execution of deepTools command-line utilities and provides guidance on setting file permissions (
chmod +x) for locally generated workflow scripts.
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