bulk-rnaseq
Pass
Audited by Gen Agent Trust Hub on Oct 2, 2026
Risk Level: SAFE
Full Analysis
- [SAFE]: The skill uses established and well-documented bioinformatics tools (FastQC, fastp, STAR, Salmon, MultiQC) and well-known pipeline frameworks (nf-core/rnaseq via Nextflow) which are standard for the field.
- [SAFE]: The included Python scripts (
build_counts_matrix.pyandvalidate_samplesheet.py) perform standard data validation, transformation, and aggregation using established libraries likepandasandpytximport. No dangerous shell execution, arbitrary code execution, or unauthorized network operations were identified in the source code. - [SAFE]: External dependencies are limited to standard Python packages and specialized bioinformatics tools typically managed via conda or Nextflow. The use of pinned versions for pipelines (e.g., nf-core/rnaseq -r 3.26.0) is a security and reproducibility best practice.
- [SAFE]: The skill provides thorough documentation on experimental design and quality control (QC), encouraging defensible and reproducible scientific practices while accurately describing the tools and data flow.
Audit Metadata