Project Roadmap (v0.2 to v0.4)

[sdhutchins]

After much consideration, I think labrat needs to be merged into a tool closer to what I tend to frequently use. The below features should help refine the tool and give it more value to me.

Labrat Roadmap

This document outlines the prioritized feature roadmap for Labrat, organized into Critical, High, Medium, and Low priority tiers.

Critical Priority

These features define the core identity of Labrat and should be implemented first.

• Changelog generation from git log (create and append)
• Template engine (R Markdown, Python, README, Snakemake, Nextflow, HPC scripts, workflow docs)
• Template registry (add, list, store in ~/.labrat/templates)
• SLURM queue viewer (labrat slurm queue)
• SLURM summary (labrat slurm summary)
• Organize scientific files within a project (labrat organize)
• Internal state management using ~/.labrat/ (no project.yml or intrusive metadata)
• Gene and variant lookup (labrat query --gene, labrat query --variant)
• Variant or gene report generation
• Modulefile templates (Lmod and Tcl)
• Generate variant links or text for input into notebooklm

High Priority

Important features that extend utility and improve everyday usage.

• SLURM watch mode (auto-refresh)
• SLURM job cancellation (labrat slurm kill)
• Auto-fill modulefile fields
• Add GitHub-based template import
• Analysis SOP templates
• Snakemake rule templates
• Nextflow module and process templates
• Shiny app skeleton templates
• HPC submission script templates
• Workflow documentation templates
• Timestamped project backups (labrat backup)

Medium Priority

Enhancements that improve usability and support teaching and reproducibility.

• Directory skeleton templates
• GitHub Actions CI templates
• Dockerfile templates
• environment.yml and requirements.txt templates
• Internal annotation notes storage
• Internal annotation history (annotations.json)
• HPC environment auto-detection
• Structured note-taking for gene/variant annotations
• Organization of non-scientific files (images, archives)
• Optional GUI in the future
• Specialized README templates
• Snakemake cluster-config templates
• Nextflow config templates

Low Priority

Nice-to-have additions or future expansion areas.

• Project scaffolding (not currently desired)
• Support for non-SLURM schedulers (SGE, PBS, LSF)
• Extended variant report templates
• Extended gene report templates
• Rarely used template categories
• Workflow diagram generation
• Auto-tagging changelog for GitHub releases
• Advanced modulefile generators
• Configuration file templates (.ini, .cfg)
• Project type auto-detection
• Interactive template filling mode
• Web UI for browsing templates
• Multi-user template sharing
• Template ranking or rating
• Remote template syncing
• Telemetry or usage analytics