update_project: Update 'scdrake' project files.

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

Update scdrake project files.

Description

This will overwrite project files by the package-bundled ones:

• RMarkdown documents in ⁠Rmd/⁠

• Initial scripts for drake::r_make(): ⁠_drake_single_sample.R⁠ and ⁠_drake_integration.R⁠

• Default YAML configs. Their location can be set by ⁠*_config_dir⁠ parameters.

Usage

update_project(
  dir = ".",
  pipeline_config_dir = getOption("scdrake_pipeline_config_dir"),
  single_sample_config_dir = getOption("scdrake_single_sample_config_dir"),
  integration_config_dir = getOption("scdrake_integration_config_dir"),
  ask = TRUE,
  verbose = getOption("scdrake_verbose")
)

Arguments

dir	A character scalar: path to scdrake project directory. If NULL, the current working directory will be used (same as the default: ".").
pipeline_config_dir	A character scalar: path to directory with pipeline config file (pipeline.yaml).
single_sample_config_dir	A character scalar: path to directory with ⁠00_main.yaml⁠, ⁠01_input_qc.yaml⁠, ⁠02_norm_clustering.yaml⁠, cluster_markers.yaml, and contrasts.yaml files.
integration_config_dir	A character scalar: path to directory with ⁠00_main.yaml⁠, ⁠01_integration.yaml⁠, ⁠02_int_clustering.yaml⁠, cluster_markers.yaml, and contrasts.yaml files.
ask	A logical scalar: if TRUE, ask before updating the files.
verbose	A logical scalar: if TRUE, be verbose. The default value is obtained from getOption("scdrake_verbose").

Value

Invisibly NULL.

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