dot-apply_config_patches: Apply YAML config patches to package-bundled configs.

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

Apply YAML config patches to package-bundled configs.

Description

This is used in tests/testthat/test-run_pipeline.R tests where some modifications of default config files are needed. The patches are located in tests/testthat/run_pipeline_config_patches.

Before the patches are applied, their local versions are updated from the default ones, similar to standard behaviour (update_config()).

Usage

.apply_config_patches(
  patches_dir,
  analysis_config_dir,
  pipeline_config_dir = getOption("scdrake_pipeline_config_dir")
)

Arguments

patches_dir	A character scalar: path to directory with config patches. The files there must be named the same as the bundled ones, e.g. ⁠02_norm_clustering.yaml⁠.
analysis_config_dir	A character scalar: path to directory with analysis config files.
pipeline_config_dir	A character scalar: path to directory with pipeline config file (pipeline.yaml).

Details

pipeline_config_dir directory will be used if pipeline.default.yaml file is present in patches_dir.

Value

Invisibly NULL.

bioinfocz/scdrake documentation built on Jan. 29, 2024, 10:24 a.m.