name: bioinformatics-workflows
description: Patterns for building, maintaining, and scaling bioinformatics workflows. Covers Nextflow, Snakemake, WDL/Cromwell, container orchestration, and best practices for reproducible computational biology. Use when ", " mentioned.

Bioinformatics Workflows

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.