Create a Pre-Pipeline Builder Script — makeInputBuilderScript • picard

Creates a new R script in the pre-pipeline builder directories (inputs/cohorts/R/ or inputs/conceptSets/R/) for loading, building, and maintaining manifests before executing the study pipeline. Unlike task files, builder scripts execute in sequence as part of manifest setup.

Usage

makeInputBuilderScript(
  type,
  category = c("cohorts", "conceptSets"),
  projectPath = here::here(),
  open = TRUE
)

Arguments

type: Character. Type of builder script. For cohorts: "importAtlas", "importCapr", "importSql", or "buildDependentCohorts" For concept sets: "importAtlas" or "importCapr"
category: Character. Category of manifest to build. Options: "cohorts" or "conceptSets"
projectPath: Character. Path to the project root (defaults to current project)
open: Logical. Whether to open the file after creating it (default TRUE)

Value

Invisibly returns the template content as a character string

Details

Builder scripts are organized in two main pre-pipeline directories:

inputs/cohorts/R/: Scripts for loading and building cohorts
inputs/conceptSets/R/: Scripts for loading and building concept sets

Available script types:

importAtlas: Import definitions from ATLAS using manifest API
importCapr: Build definitions programmatically using Capr
importSql: Load custom SQL-based definitions
buildDependentCohorts: Build derived cohorts (cohorts only)

All scripts are sourced in sequence by main.R before the production pipeline executes. Users can delete unused scripts (e.g., if they only need ATLAS imports).

Examples

if (FALSE) {
# Create a script for importing ATLAS cohorts
makeInputBuilderScript(type = "importAtlas", category = "cohorts")

# Create a script for building Capr-based cohorts
makeInputBuilderScript(type = "importCapr", category = "cohorts")

# Create a script for importing ATLAS concept sets
makeInputBuilderScript(type = "importAtlas", category = "conceptSets")
}