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Update scdrake project files.

Source: R/project.R
update_project.Rd

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.