What problem does it solve? Developing SUSHI pipeline applications at FGCZ requires coordinating an R backend method (ezRun), a Ruby on Rails frontend, and an Rmd report template while following strict institutional coding standards. This Skill provides the complete workflow, templates, and reference documentation so developers avoid parameter-passing bugs, style violations, and deployment errors. ## Core Features & Use Cases - End-to-End App Templates: Ready-to-use R method template (template_app.R), Ruby app template (template_app.rb), and Rmd report template covering the full SUSHI app structure. - Coding Standards Enforcement: Mandatory FGCZ style rules (camelCase variables, underscore_separated functions, seq_along iteration, ezLoadPackage usage) with a detailed style guide and checklist. - ezRun Function Reference: Documentation of 100+ helper functions (ezRead.table, ezNorm, ezMclapply, makeRmdReport) plus a concise quick-reference for logging, I/O, and system calls. - Working Example: A complete XeniumQC spatial transcriptomics QC app demonstrating multi-sample processing, JSON parsing, and tabset report generation. - Use Case: A bioinformatician asks to create a new ATAC-seq QC app; the Skill supplies the R method skeleton, Ruby frontend with resource parameters, report template, and a testing checklist for deployment to SUSHI. ## Quick Start Ask the agent to create a new SUSHI app for your analysis type, for example by saying: create a SUSHI app that processes bulk RNA-seq QC metrics with an interactive report.
