Dependency-aware analysis registry — analysis

Register analysis modules, resolve their dependency graph, and execute them against a validated popgenVCF analysis state through the unified execution engine.

Usage

new_analysis_registry()

register_analysis(
  registry,
  name,
  run,
  requires = character(),
  enabled = TRUE,
  description = "",
  validate = validate_module_result,
  outputs = name,
  references = character(),
  resource_class = "standard",
  parallel_safe = FALSE,
  contract_version = "1.0"
)

list_analyses(registry)

resolve_analysis_order(registry, config, selected = NULL)

execute_analysis_registry(
  analysis,
  context,
  registry,
  selected = NULL,
  engine = new_execution_engine(),
  checkpoint_path = NULL
)

default_analysis_registry()

Arguments

registry: A PopgenVCFRegistry object.
name: Unique module name.
run: Module runner accepting analysis and context.
requires: Character vector of prerequisite module names.
enabled: Logical value or function accepting the validated config.
description: Short module description.
validate: Result validator accepting result, analysis, and context.
outputs: Declared analysis-result names.
references: Scientific references supporting the module.
resource_class: Expected resource class.
parallel_safe: Whether the module may run concurrently with independent modules. Parallel-safe modules must not modify the shared runtime context.
contract_version: Module-contract version.
config: Validated popgenVCF configuration.
selected: Optional module names.
analysis: A PopgenVCFAnalysis object.
context: Runtime context shared by module runners.
engine: A PopgenVCFExecutionEngine object.
checkpoint_path: Optional .rds path forwarded to execute_analysis_plan() for unconditional per-batch checkpointing.

Value

A registry, module table, execution order, or updated analysis/context bundle depending on the function.