Skill Claude CodeCodex
Generate Galaxy-branded workflow visualization SVGs for IWC workflows. Creates static diagrams matching Galaxy's workflow editor style with bezier connections, node cards, and proper terminal positioning. Use when creating visual diagrams for workflows in this repository.
Skill Claude CodeCodex
Maintain per-workflow developer logs in Obsidian when working on Galaxy workflows. Use whenever creating, version-bumping, fixing, or updating an IWC/Galaxy .ga workflow or its -tests.yml. Logs detailed changes, test YAML edits, and planemo invocation history so the correct planemo command (full planemo test vs fast…
Skill Claude CodeCodex
Expert in building and testing conda/bioconda recipes, including recipe creation, linting, dependency management, and debugging common build errors.
Skill Claude CodeCodex
Smart automated backup system with skill integration. Detects project type (notebooks, data files, HackMD docs) and applies appropriate cleanup before backup. Rolling daily backups, compressed milestones, and CHANGELOG tracking.
Skill Claude CodeCodex
Best practices for organizing project folders, file naming conventions, and directory structure standards for research and development projects.
Skill Claude CodeCodex
Best practices for managing development environments including Python venv and conda. Always check environment status before installations and confirm with user before proceeding.
Skill Claude CodeCodex
Integration with Obsidian vault for managing notes, tasks, and knowledge when working with Claude. Supports adding notes, creating tasks, and organizing project documentation. Updated with 2025-2026 best practices including MOCs, properties, practical organization patterns, and Obsidian CLI (1.12+).
Skill Claude CodeCodex
Access and navigate GenomeArk AWS S3 bucket - VGP assemblies, QC data, and species directory structure.
Skill Claude CodeCodex
VGP assembly pipeline - Galaxy workflow selection, execution patterns, QC checkpoints, and batch orchestration.