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Workflow State Management

FlowAgent includes a robust checkpointing system that helps manage long-running RNA-seq analysis workflows. This system allows you to resume interrupted workflows and avoid repeating expensive computations.

Using Checkpoints

Basic Usage:

# Run workflow with checkpointing
flowagent prompt "Analyze RNA-seq data..." --checkpoint-dir workflow_state

Resuming Interrupted Workflows:

# Resume from last successful checkpoint
flowagent prompt "Analyze RNA-seq data..." --checkpoint-dir workflow_state --resume

How It Works

The checkpoint directory (e.g., workflow_state) stores: - Progress tracking for each workflow step - Intermediate computation results - Error logs and debugging information - Workflow configuration and parameters

This allows FlowAgent to: - Resume workflows from the last successful step - Avoid recomputing expensive operations - Maintain workflow state across system restarts - Track errors and provide detailed debugging information

Best Practices

Choose Descriptive Directory Names:

# Use meaningful names for different analyses
flowagent prompt "..." --checkpoint-dir rnaseq_liver_samples_20250225

Backup Checkpoint Directories:

  • Keep checkpoint directories for reproducibility
  • Back up important checkpoints before rerunning analyses
  • Use different checkpoint directories for different analyses

Debugging Using Checkpoints:

  • Examine checkpoint directory contents for troubleshooting
  • Use --resume to retry failed steps without restarting
  • Check error logs in checkpoint directory for detailed information