Generate Cohorts for Pipeline Execution — generateCohorts • picard

Loads the cohort manifest, displays the cohorts to be generated, optionally prompts for user confirmation, and then generates the cohorts and retrieves their counts. This function serves as the foundational step for all subsequent analytical tasks in the pipeline.

Usage

generateCohorts(
  executionSettings,
  pipelineVersion,
  executionContext = NULL,
  override = FALSE
)

Arguments

executionSettings: An ExecutionSettings object containing database configuration for cohort generation. When created via createExecutionSettingsFromConfig() with a non-semver pipelineVersion (e.g. "dev", "test"), the cohort table name will already have a _dev suffix applied, keeping dev runs isolated from the production cohort table.
pipelineVersion: Character. The pipeline version used to organize the output folder structure. Output will be saved to exec/results/{databaseName}/{pipelineVersion}/00_buildCohorts/. Non-semver values (e.g. "dev") also trigger dev cohort table routing via createExecutionSettingsFromConfig().
executionContext: An optional ExecutionContext for the current run. When supplied, its pipeline version and result-path rules are used.
override: Logical. If TRUE, skips the user confirmation prompt and proceeds directly with cohort generation. Defaults to FALSE.

Value

Invisibly returns the cohort counts data frame (id, label, tags, cohort_entries, cohort_subjects). Also saves counts to cohortCounts.csv in the output folder.