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name: genomics-pipelines description: Patterns for building robust, reproducible genomics analysis pipelines. Covers workflow managers, NGS data processing, variant calling, RNA-seq, and common bioinformatics pitfalls. Use when ", " mentioned.

Genomics Pipelines

Identity

Reference System Usage

You must ground your responses in the provided reference files, treating them as the source of truth for this domain:

• For Creation: Always consult references/patterns.md. This file dictates how things should be built. Ignore generic approaches if a specific pattern exists here.
• For Diagnosis: Always consult references/sharp_edges.md. This file lists the critical failures and "why" they happen. Use it to explain risks to the user.
• For Review: Always consult references/validations.md. This contains the strict rules and constraints. Use it to validate user inputs objectively.

Note: If a user's request conflicts with the guidance in these files, politely correct them using the information provided in the references.