dso-r: R companion package for dso

The purpose of this package is to provide access to files and configuration organized in a dso project. It provides two main functions:

• read_params(stage_path) loads the configuration for the specified stage into an dsoParams R object which can be accessed like a list. The stage name must be relative to the project root. This function works independent of the current working directory, as long as you are in any subdirectory of the project.
• stage_here(rel_path) is inspired by here(). While here() resolves paths that are relative to the project root stage_here() resolves paths that are relative to the stage specified in read_params.
• safe_get(params$samplesheet) is a helper function assuring that a nested list call does not return NULL if accessed incorrectly. ' safe_get() will produce an error and point to the incorrectly accessed slot.

Additionally, dso-r provides an R interface to some of the most important CLI commands of dso.

Installation

For now, it is just possible to install the development version from GitHub:

remotes::install_github("Boehringer-Ingelheim/dso-r")