graph LR
Core_Workflow_Engine["Core Workflow Engine"]
Execution_Layer["Execution Layer"]
Data_Management["Data Management"]
User_Interaction_Configuration["User Interaction & Configuration"]
Reporting_Utilities["Reporting & Utilities"]
Core_Workflow_Engine -- "Receives workflow commands, definitions, and parameters." --> User_Interaction_Configuration
Core_Workflow_Engine -- "Dispatches jobs for execution and receives their completion status." --> Execution_Layer
Core_Workflow_Engine -- "Interacts for file path resolution, metadata, and managing workflow data dependencies." --> Data_Management
Core_Workflow_Engine -- "Provides workflow status and job metrics for reporting, and utilizes general-purpose utilities." --> Reporting_Utilities
Execution_Layer -- "Receives jobs and environment requirements, and reports job completion status." --> Core_Workflow_Engine
Execution_Layer -- "Accesses input files and stores output files for job execution." --> Data_Management
Execution_Layer -- "Receives environment and resource settings for job execution." --> User_Interaction_Configuration
Execution_Layer -- "Provides execution logs and benchmark data, and utilizes shell command execution and other utilities." --> Reporting_Utilities
Data_Management -- "Provides resolved file paths and cached data, and receives file paths and metadata for management." --> Core_Workflow_Engine
Data_Management -- "Provides access to input/output files for job execution." --> Execution_Layer
Data_Management -- "Receives configurations for storage backends." --> User_Interaction_Configuration
Data_Management -- "Utilizes general-purpose utilities for data handling." --> Reporting_Utilities
User_Interaction_Configuration -- "Initiates workflow execution and provides workflow definitions and parameters." --> Core_Workflow_Engine
User_Interaction_Configuration -- "Provides environment and resource settings for job execution." --> Execution_Layer
User_Interaction_Configuration -- "Provides configurations for storage backends." --> Data_Management
User_Interaction_Configuration -- "Utilizes general-purpose utilities for parsing configurations and other tasks." --> Reporting_Utilities
Reporting_Utilities -- "Receives workflow status and job metrics for reporting." --> Core_Workflow_Engine
Reporting_Utilities -- "Receives execution logs and benchmark data for reporting." --> Execution_Layer
Reporting_Utilities -- "Provides common utilities for data processing and formatting." --> Data_Management
Reporting_Utilities -- "Provides common utilities for configuration parsing and other interface-related tasks." --> User_Interaction_Configuration
click Core_Workflow_Engine href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/snakemake/Core_Workflow_Engine.md" "Details"
click Execution_Layer href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/snakemake/Execution_Layer.md" "Details"
click Data_Management href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/snakemake/Data_Management.md" "Details"
click User_Interaction_Configuration href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/snakemake/User_Interaction_Configuration.md" "Details"
click Reporting_Utilities href "https://github.com/CodeBoarding/GeneratedOnBoardings/blob/main/snakemake/Reporting_Utilities.md" "Details"
Snakemake High-Level Architecture Overview: Scientific Workflow Management System (WMS) with Pipeline/Workflow Pattern, Plugin Architecture, Interpreter Pattern, Command-Query Responsibility Segregation (CQRS), State Machine, Facade Pattern, Strategy Pattern, Dependency Graph.
Core Workflow Engine [Expand]
The central orchestrator of Snakemake, responsible for interpreting workflow definitions, constructing and managing the Directed Acyclic Graph (DAG) of jobs, and scheduling jobs for execution based on dependencies and resource availability. This component embodies the core logic of workflow execution and state management.
Related Classes/Methods:
snakemake.workflow(1:1)snakemake.dag(1:1)snakemake.jobs(1:1)snakemake.scheduler(1:1)snakemake.parser(1:1)
Execution Layer [Expand]
Manages the actual execution of individual jobs and the provisioning of their required software environments. It handles various execution modes (e.g., local, dry run) and ensures reproducibility by managing containerized (Singularity/Docker) or Conda environments.
Related Classes/Methods:
snakemake.executors(1:1)snakemake.deployment.conda(1:1)snakemake.deployment.singularity(1:1)snakemake.script(1:1)
Data Management [Expand]
Provides comprehensive management for all data-related operations, including file I/O, path resolution, metadata persistence, and efficient caching of source code and output files. It abstracts various storage backends (e.g., local, cloud storage).
Related Classes/Methods:
snakemake.io(1:1)snakemake.persistence(1:1)snakemake.sourcecache(1:1)snakemake.caching(1:1)snakemake.storage(1:1)
User Interaction & Configuration [Expand]
Serves as the primary interface for users and external tools to interact with Snakemake. It handles command-line argument parsing, initiates workflow runs, and provides a programmatic API. This component also centralizes the management of all configurable parameters, including resource allocations, deployment options, and execution profiles.
Related Classes/Methods:
Reporting & Utilities [Expand]
Responsible for generating comprehensive reports of workflow execution, including provenance information, job summaries, and performance benchmarks. It also provides a collection of general-purpose helper functions, common data structures, and low-level utilities (e.g., shell command execution) used across various components of the system.
Related Classes/Methods:
snakemake.report(1:1)snakemake.benchmark(1:1)snakemake.utils(1:1)snakemake.common(1:1)