ngs-bcl-to-fastq
Pass
Audited by Gen Agent Trust Hub on Aug 15, 2026
Risk Level: SAFECOMMAND_EXECUTION
Full Analysis
- Command Execution: The skill is designed to execute local Python scripts (
ngs_preflight.py,run_bcl_to_fastq.py) and standard bioinformatics utilities (bcl-convert,bcl2fastq). These commands are used to automate the demultiplexing process and validate run folders, which is the primary function of the skill. - Data Processing Surface: The skill ingests and processes external metadata files such as
RunInfo.xmlandSampleSheet.csv. While this is a standard requirement for NGS analysis, processing data from external files presents a theoretical surface for indirect prompt injection if the inputs are not strictly validated before being passed to sub-processes. - External Software Management: The instructions explicitly caution against the automatic download of proprietary RPM-distributed software (
bcl-convert), requiring explicit user approval instead. This demonstrates a security-conscious approach to managing external dependencies and software licenses.
Audit Metadata