ngs-bulk-rnaseq-counts-qc
Pass
Audited by Gen Agent Trust Hub on Aug 15, 2026
Risk Level: SAFECOMMAND_EXECUTION
Full Analysis
- [Command Execution]: The skill provides instructions for executing local Python scripts (
run_bulk_rnaseq_counts_qc.pyandngs_preflight.py) located within the skill's own directory structure. These scripts are used to manage complex bioinformatics pipelines, including input validation and workflow orchestration via Snakemake or Nextflow. - [Integration with Established Tools]: The workflow leverages widely recognized bioinformatics tools such as Salmon, STAR, and MultiQC. References to external frameworks like
nf-core/rnaseqare standard practice in genomics and are provided as architectural guidance for standard processing. - [Data Ingestion Surface]: The skill is designed to process sample sheets (CSV) and sequence data (FASTQ). While these represent external data ingestion points, the skill incorporates validation steps (e.g., preflight checks and strandedness inference) to ensure data integrity before processing.
Audit Metadata