R/verbose.R

In sahilseth/flowr: Streamlining Design and Deployment of Complex Workflows

#' @rdname verbose
#' @title Verbose levels, defining verboseness of messages
#' 
#' @description 
#' There are several levels of verboseness one can choose from.
#' 
#' \strong{levels:}
#' 
#' \itemize{
#' 	\item level 0 is almost silent, producing only necessary messages 
#' 	\item level 1 is good for most purposes, where as, 
#' 	\item level 2 is good when developing a new pipeline.
#' 	\item level 3 is good for debugging, especially when getting un-expected results.
#' }
#' 	
#' 	One can set the level of verboseness using \code{opts_flow$set(verbose=2)}, which 
#' 	will be used across flowr and ngsflows packages. Additionally one may set this value in 
#' 	the configurations files: \code{~/flowr/conf/flowr.conf} OR \code{~/flowr/conf/ngsflows.conf}.
#' 	
#' @examples
#' fl = system.file("pipelines/abcd.def", package = "flowr")
#' def = as.flowdef(fl, verbose = 0)
#'	# def seems to be a file, reading it...
#' def = as.flowdef(fl, verbose = 1)
#'	# def seems to be a file, reading it...
#'	# checking if required columns are present...
#'	# checking if resources columns are present...
#'	# checking if dependency column has valid names...
#'	# checking if submission column has valid names...
#'	# checking for missing rows in def...
#'	# checking for extra rows in def...
#'	# checking submission and dependency types...
#' def = as.flowdef(fl, verbose = 2)
#'	# def seems to be a file, reading it...
#'	# checking if required columns are present...
#'	# checking if resources columns are present...
#'	# checking if dependency column has valid names...
#'	# checking if submission column has valid names...
#'	# checking for missing rows in def...
#'	# checking for extra rows in def...
#'	# checking submission and dependency types...
#'	# jobname	prev.sub_type --> dep_type --> sub_type: relationship
#'	# 	1: A	none --> none --> scatter 
#'	# 	2: B	scatter --> serial --> scatter rel: complex one:one
#'	# 	3: C	scatter --> gather --> serial rel: many:one
#'	# 	4: D	serial --> burst --> scatter rel: one:many
verbose = opts_flow$get("verbose")