verbose: Verbose levels, defining verboseness of messages
In flowr: Streamlining Design and Deployment of Complex Workflows

There are several levels of verboseness one can choose from.

levels:

level 0 is almost silent, producing only necessary messages
level 1 is good for most purposes, where as,
level 2 is good when developing a new pipeline.
level 3 is good for debugging, especially when getting un-expected results.

One can set the level of verboseness using opts_flow$set(verbose=2), which will be used across flowr and ngsflows packages. Additionally one may set this value in the configurations files: ~/flowr/conf/flowr.conf OR ~/flowr/conf/ngsflows.conf.

verbose

An object of class NULL of length 0.

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

Loading required package: params
Loading required package: whisker
Flowr: streamlining workflows

Attaching package: 'flowr'

The following objects are masked from 'package:params':

    check_args, get_opts, load_opts, set_opts

def seems to be a file, reading it...
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 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