Workflows¶

FlowAgent supports various bioinformatics workflows, each with a standardized structure and the ability to integrate custom scripts.

Supported Workflows¶

RNA-seq¶

Quality control and preprocessing
Alignment and quantification
Differential expression analysis
Custom normalization options
Single-cell analysis support

ChIP-seq¶

Quality assessment
Read alignment
Peak calling
Motif analysis
Signal visualization

Hi-C¶

Quality control
Contact matrix generation
TAD calling
Interaction analysis
3D structure prediction

ATAC-seq¶

Quality metrics
Peak calling
Accessibility analysis
Footprinting
Integration with ChIP-seq

Bisulfite-seq¶

Quality control
Methylation calling
Differential methylation
Pattern analysis
Integration with gene expression

Single-cell Multi-omics¶

RNA velocity
CITE-seq analysis
Multimodal integration
Trajectory analysis
Cell type annotation

Workflow Structure¶

Each workflow follows a standardized structure:

Data Quality & Preprocessing
Raw data quality metrics (FastQC, MultiQC)
Data cleaning and filtering
Format validation
Alignment & Quantification
Mapping statistics
Tool-specific metrics
Quality filtering
Analysis-Specific Steps
Workflow-specific analyses
Custom script integration
Result generation
Resource Management
CPU/Memory monitoring
Runtime tracking
Performance optimization
Results & Visualization
Quality reports
Analysis summaries
Visualization outputs

Custom Script Integration¶

Workflows can be extended with custom scripts:

workflow = WorkflowExecutor(llm_interface)
results = await workflow.execute_workflow(
    input_data={"fastq": "input.fastq"},
    workflow_type="rna_seq",
    custom_script_requests=["deseq2_normalize"]
)

See the Custom Scripts section for more details.