The Workflow Designer allows you to create custom analysis pipelines by connecting multiple tools together. This enables:
- **Complex analyses**: Chain multiple tools in sequence - **Reproducible workflows**: Save and reuse analysis pipelines - **Custom pipelines**: Design analyses specific to your needs - **Automated processing**: Execute multi-step analyses automatically
Workflow capabilities
- Drag-and-drop interface - Tool chaining and connections - Data flow between tools - Workflow saving and loading
Building Workflows
1. Add input nodes (FASTA/FASTQ files) 2. Drag tools from the toolbox to the canvas 3. Connect tools in sequence (drag from output to input) 4. Configure tool parameters 5. Run the workflow
Tool Categories
- **Data Sources**: FASTA/FASTQ input nodes - **Sequence Tools**: Basic sequence manipulation - **Analysis Tools**: Advanced analysis tools
Connections
- Connect tools by dragging from output to input - Tools execute in the order of connections - Data flows automatically between connected tools
Running Workflows
- Click "Run Workflow" to execute - Tools execute sequentially based on connections - Results from each step are displayed - View results for individual tools
Workflow Results
- Step-by-step execution results - Output from each tool in the workflow - Error messages if any step fails - Download results from individual steps
Best Practices
- Test workflows with sample data first - Verify tool order before execution - Check results at each step - Save successful workflows for reuse
**1. Multi-Step Analyses** - Combine quality control, alignment, and analysis - Chain preprocessing with main analysis - Create complete analysis pipelines
**2. Reproducible Research** - Save workflows for reproducibility - Share workflows with collaborators - Document analysis procedures
**3. Automated Processing** - Process multiple samples - Standardize analysis procedures - Reduce manual steps
1. **Plan your workflow**: Think about tool order before building 2. **Start simple**: Begin with 2-3 tools, then expand 3. **Test incrementally**: Test each connection before adding more 4. **Save workflows**: Save successful workflows for reuse 5. **Document workflows**: Add notes about workflow purpose and parameters 6. **Validate results**: Check results at each step to catch errors early