init_project: Initialize a new 'scdrake' project.

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

Initialize a new scdrake project.

Description

Initialize a new scdrake project.

Usage

init_project(
  dir = ".",
  use_rstudio = TRUE,
  set_active_project = TRUE,
  set_wd = TRUE,
  download_example_data = FALSE,
  ask = TRUE,
  verbose = getOption("scdrake_verbose"),
  ...
)

Arguments

dir	A character scalar: path to directory in which the project will be created. If NULL, the current working directory will be used (same as the default: "."). Subdirectories will be created recursively.
use_rstudio	A logical scalar: if TRUE, initiate an RStudio project inside dir.
set_active_project	A logical scalar: if TRUE, set active project to dir.
set_wd	A logical scalar: if TRUE, change the current working directory to dir.
download_example_data	A logical scalar: if TRUE, download example PBMC 1k and 3k data to {dir}/example_data. See download_pbmc1k() and download_pbmc3k() for more details on these datasets.
ask	A logical scalar: if TRUE, do not prompt and overwrite an existing project.
verbose	A logical scalar: if TRUE, be verbose. The default value is obtained from getOption("scdrake_verbose").
...	Passed to download_yq().

Details

This function will:

• Create the project's root directory.

• (Optional) Switch the current working directory to the project's root and call here::i_am().

• Copy config, RMarkdown, and ⁠_drake_*.R⁠ files.

• Create an empty .here file. This ensures that the here package will be able to find the project's root directory in case an RStudio project is not initialized.

• Check whether the yq tool is available in PATH environment variable.

• (Optional) Download the example data using download_pbmc1k() and download_pbmc3k().

• (Optional) Initialize an RStudio project and set it as the active project.

Examples

## Not run: 
init_project("my_project")

## End(Not run)

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