load_custom_plan: Source a file returning a custom drake plan.

In bioinfocz/scdrake: A pipeline for droplet-based single-cell RNA-seq data secondary analysis implemented in the drake Make-like toolkit for R language

Source a file returning a custom drake plan.

Description

This function is used in drakes init scripts ⁠_drake_single_sample.R⁠ and ⁠_drake_integration.R⁠. It sources an R script (plan_custom.R by default) which must return a drake::drake_plan() object. In the R script, all variables defined in the init script are available, mainly cfg and cfg_pipeline lists holding pipeline parameters. At the same time, all those variables are locked and cannot be modified in file script.

Usage

load_custom_plan(
  file = getOption("scdrake_plan_custom_file"),
  envir = parent.frame()
)

Arguments

file	A character scalar: path to R script returning a drake::drake_plan().
envir	An environment in which the R script will be sourced (defaults to caller env).

Value

A drake::drake_plan() object (tibble).

bioinfocz/scdrake documentation built on Sept. 19, 2024, 4:43 p.m.