Run the Population Genomics Pipeline — run

Runs deterministic input preparation and quality control, resolves the registered analysis dependency graph, and executes the selected modules in topological order.

Usage

run_pipeline(
  config,
  registry = default_analysis_registry(),
  selected = NULL
)

Arguments

config: A validated configuration list or path to a YAML configuration file.
registry: A PopgenVCFRegistry; defaults to the built-in registry.
selected: Optional module names. Dependencies are included automatically.

Value

Invisibly returns a PopgenVCFAnalysis object. Results are also written to the configured output directory.

Examples

if (FALSE) { # \dontrun{
config <- default_config()
config$input$vcf <- "cohort.vcf.gz"
config$input$metadata <- "populations.tsv"
config$output$directory <- "results"
run_pipeline(config, selected = c("pca", "fst"))
} # }