dunnlab_code

YCRC HPC cluster reference for the Dunn Lab. Use when writing SLURM batch scripts, configuring job resources, managing storage, or running analyses on Bouchet, McCleary, or Misha clusters. Covers partitions, storage, job scheduling, and cluster-specific details.

Add a .devcontainer configuration to a project for secure, reproducible Claude Code development environments. Use when setting up devcontainers, Docker-based dev environments, or configuring container-based workflows.

Applies Dunn Lab coding conventions and defaults. Use when starting and modifying new analysis scripts, writing documentation, or setting up project structure. Includes preferred languages, formatting, and file organization patterns.

Step-by-step workflow for scaffolding a new Dunn Lab project from scratch. Use whenever starting a new analysis, pipeline, tool, or package — including when the user says "new project", "set up a repo", "start a new analysis", "initialize a project", or asks to create project structure, directory layout, or boilerplate for a new codebase. Also trigger when the user describes a new analysis goal (e.g., "I need to analyze some RNA-seq data", "let's build a phylogenetics pipeline") and the working directory is empty or lacks project structure (no README.md, no CLAUDE.md, no src/ or scripts/ directory).

Code review checklist and process for Dunn Lab projects. Use when reviewing pull requests, auditing code quality, or giving feedback on scripts and analyses.

Standards and workflow for managing bibliographic references in manuscripts. Covers BibTeX formatting conventions, author lists, title capitalization, and conservative editing rules.

Bioinformatics workflow conventions for the Dunn Lab. Use when building or modifying sequence analysis pipelines, phylogenetics, gene annotation, or multi-species comparative analyses. Covers data hygiene, tool defaults, and naming conventions.