bulk-rnaseq
Pass
Audited by Gen Agent Trust Hub on Aug 17, 2026
Risk Level: SAFEEXTERNAL_DOWNLOADSCOMMAND_EXECUTION
Full Analysis
- [REMOTE_CODE_EXECUTION]: The skill facilitates the use of the nf-core/rnaseq pipeline via Nextflow. This involves executing curated workflow code from the nf-core GitHub organization, which is a recognized and trusted community resource in the bioinformatics field.
- [REMOTE_CODE_EXECUTION]: The skill instructs the installation of dependencies through official package managers (uv and conda) using established repositories like PyPI and Bioconda.
- [INDIRECT_PROMPT_INJECTION]: The skill processes user-supplied configuration and data files, which presents a surface for indirect prompt injection.
- Ingestion points: Samplesheet CSV files are parsed by scripts/validate_samplesheet.py, and transcript-to-gene maps (TSV) are read by scripts/build_counts_matrix.py.
- Boundary markers: There are no specific boundary markers or instructions to ignore embedded commands within the input data files.
- Capability inventory: The skill is designed to manage file system resources and execute shell-based biological analysis tools.
- Sanitization: The provided scripts include validation logic to check for file existence, column structure, and consistency of the experimental design.
Audit Metadata