featurecounts-rna-counting
Warn
Audited by Gen Agent Trust Hub on Oct 14, 2026
Risk Level: MEDIUMCOMMAND_EXECUTIONPRIVILEGE_ESCALATIONEXTERNAL_DOWNLOADSINDIRECT_PROMPT_INJECTION
Full Analysis
- [COMMAND_EXECUTION]: The skill executes shell commands directly and via Python's subprocess module to run featureCounts, samtools, and wget for data processing and retrieval.
- [PRIVILEGE_ESCALATION]: The instructions suggest using the sudo command for package installation (sudo apt-get install subread), which requires administrative access to the system.
- [EXTERNAL_DOWNLOADS]: The skill fetches genomic annotation data from the European Bioinformatics Institute (EBI) GENCODE repository at ftp.ebi.ac.uk, which is an established and trusted source for scientific data.
- [INDIRECT_PROMPT_INJECTION]: The skill processes external BAM and GTF files, representing a potential surface for indirect injection if malicious data is interpreted by the agent. 1. Ingestion points: Reads local BAM files from the results/ directory and GTF annotations from ebi.ac.uk. 2. Boundary markers: Absent; the skill does not use specific delimiters to isolate external data from command logic. 3. Capability inventory: Includes directory creation (mkdir), file system writes (to_csv), and shell execution (subprocess.run). 4. Sanitization: Uses basic regular expressions for filename cleaning but lacks comprehensive sanitization of data file content.
Audit Metadata