Implement Sample Sheets
Implemented comprehensive sample sheet functionality enabling users to define, create, and utilize complex metadata structures through multiple interfaces including workflow editors, spreadsheet programs, and collection tools.
The Pull Request
This PR implements sample sheets for Galaxy, addressing a critical gap in how users manage complex metadata that traditional list structures can’t capture. Sample sheets enable structured, validated metadata alongside scientific datasets.
The Problem
Scientific workflows often require rich metadata about samples that simple lists can’t represent. Researchers need:
- Column-based metadata structures with validation
- Integration with external spreadsheet tools (Excel, Google Sheets)
- Clear, intuitive interfaces for metadata entry
- Seamless workflow integration
Technical Implementation
The solution provides multiple pathways for sample sheet creation and use:
Core Features
- New collection input type for workflow editors supporting sample sheet definitions
- UI wizard for creating sample sheet collections from various sources
- Conversion tool for transforming sample sheets to tabular format within workflows
- “Apply Rules” integration for direct processing using model objects
- Cell validation with column descriptions displayed as tooltips
User Experience
The implementation balances power with accessibility:
- Create sample sheets directly in Galaxy’s workflow editor
- Import from external spreadsheet programs
- Generate from existing collections
- Real-time validation feedback
- Responsive design for various display sizes
Impact & Adoption
Status: Merged (July 30, 2025)
Milestone: 25.1
Labels: area/API, area/dataset-collections, area/UI-UX, area/workflows, highlight, kind/feature
This feature fundamentally expands Galaxy’s capability to handle complex experimental designs, particularly important for:
- Multi-sample experiments with varied conditions
- Clinical/biomedical workflows requiring patient metadata
- Integration with external LIMS systems
- Reproducible research documentation
Personal Notes
Sample sheets represent a significant UI/UX challenge - how do you make complex metadata management intuitive? The multi-pathway approach (wizard, direct editing, spreadsheet import) ensures users can work in their preferred method.
The integration with “Apply Rules” was particularly satisfying - it leverages existing Galaxy functionality while extending it to handle richer data structures. Several refinements during review addressed responsive design and language clarity, resulting in a more polished final implementation.
This work demonstrates the value of thinking beyond traditional bioinformatics interfaces to support real-world research workflows.
Technical Highlights
- Multiple refinements based on community feedback
- Responsive design considerations for smaller displays
- Careful UX language to guide users through complex operations
- Tight integration with existing Galaxy collection and workflow systems