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Core Concepts

This page explains the fundamental concepts that drive BoCoFlow and help you understand how workflows function.

Workflows​

A workflow in BoCoFlow is a directed graph where:

  • Nodes represent computational operations or data sources/sinks
  • Edges represent the flow of data between nodes
  • Execution follows the dependencies defined by the connections

Workflows are stored as JSON files that contain:

  • The visual layout of nodes
  • Node configurations
  • Connection information
  • Environment settings

Nodes​

Nodes are the building blocks of BoCoFlow workflows. Each node represents a specific operation or function and has:

Node Anatomy​

Node Anatomy

  • Header: Contains the node name and action buttons
  • Ports: Input and output connection points
    • Input ports: Accept data from preceding nodes
    • Output ports: Send data to subsequent nodes
    • Flow ports: Special ports for flow control connections
  • Status indicator: Shows the current execution state

Node Configuration​

Nodes are configured through a configuration modal that appears when you click the ⚙️ icon. Configuration options vary by node type but typically include:

  • File paths: Locations for input/output files
  • Parameters: Processing options
  • Flow variables: Dynamic parameters from flow control nodes

Working Directory​

The working directory is a crucial concept in BoCoFlow:

  • It serves as the root location for your workflow project
  • Relative paths in nodes are resolved against this directory
  • Workflow status and execution logs are stored here
  • The directory structure helps maintain portability

Path Handling​

BoCoFlow uses a prefix system to handle file paths:

  • abs: prefix indicates an absolute path on your system
  • rel: prefix indicates a path relative to the working directory

This system ensures workflows can be portable across different environments.

Execution Model​

BoCoFlow's execution follows a dependency-based model:

  1. Dependency Analysis: The system determines the execution order based on node connections
  2. Selective Execution: Only nodes that need to be executed are processed
  3. Force Execution: The "force_to_run" option allows re-execution even when cached results exist
  4. Status Tracking: Execution status is tracked and visualized for each node

Conda Integration​

BoCoFlow can integrate with Conda environments to manage Python dependencies:

  • Conda Path: Path to your Conda installation
  • Default Environment: The Conda environment to use for node execution
  • Environment Management: Different nodes can use different environments

Next Steps​

Now that you understand the core concepts, learn more about: