ngstk (version 0.2.3)

set_tools: Function to generate tools path object

Description

Function to generate tools path object

Usage

set_tools(config.file = "", config.list = list(), config.vec = c(),
  eval.params = list())

Arguments

config.file

Path of tools configuration file (json, ini, yaml and toml be supported)

config.list

List object of tools that all of tools path (exclude those without names).

config.vec

Vector object of tools that all of tools path (exclude those without names).

eval.params

Params pass to configr::eval.config

Value

List object contain the tools path that can be used by other function in ngstk package

Examples

# NOT RUN {
config.file <- system.file('extdata', 'demo/tools_config.json', package = 'ngstk')
config.list <- list(gatk = '/path/gatk')
config.vec <- c('/path/samtools')
names(config.vec) <- 'samtools'
tools <- set_tools(config.file, config.list, config.vec,
                  eval.params = list(config = 'tools'))
# }