ngs-fastq-qc
Pass
Audited by Gen Agent Trust Hub on Aug 15, 2026
Risk Level: SAFECOMMAND_EXECUTION
Full Analysis
- [Local Script Execution]: The skill invokes local Python scripts located in
plugins/ngs-analysis/scripts/to handle preflight checks and workflow execution. These scripts are part of the skill's internal logic for managing bioinformatics pipelines. - [Workflow Generation]: The skill utilizes a local runner to generate artifacts including a
Snakefile. Snakemake is a standard workflow management system in scientific computing, and its use here is consistent with the goal of automating quality control processes. - [Indirect Prompt Injection Surface]: The skill processes external data such as FASTQ files and
samplesheet.csv. While the skill includes a validation step before execution, it is a standard security practice to ensure that input filenames and metadata do not contain characters that could be misinterpreted by the underlying shell commands. - [Command Execution]: The skill executes various bioinformatics command-line tools (e.g., FastQC, MultiQC, fastp). These operations are restricted to the local environment and are initiated based on user-approved parameters for sequence analysis.
Audit Metadata