SYSargs-class: Class '"SYSargs"'

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

S4 class container for storing parameters of command-line- or R-based software. SYSargs instances are constructed by the systemArgs function from two simple tablular files: a targets file and a param file. The latter is optional for workflow steps lacking command-line software. Typically, a SYSargs instance stores all sample-level inputs as well as the paths to the corresponding outputs generated by command-line- or R-based software generating sample-level output files. Each sample level input/outfile operation uses its own SYSargs instance. The outpaths of SYSargs usually define the sample inputs for the next SYSargs instance. This connectivity is achieved by writing the outpaths with the writeTargetsout function to a new targets file that serves as input to the next systemArgs call. By chaining several SYSargs steps together one can construct complex workflows involving many sample-level input/output file operations with any combinaton of command-line or R-based software.

Objects from the Class

Objects can be created by calls of the form new("SYSargs", ...).

Slots

targetsin:

Object of class "data.frame" storing tabular data from targets input file

targetsout:

Object of class "data.frame" storing tabular data from targets output file

targetsheader:

Object of class "character" storing header/comment lines of targets file

modules:

Object of class "character" storing software versions from module system

software:

Object of class "character" name of executable of command-line software

cores:

Object of class "numeric" number of CPU cores to use

other:

Object of class "character" additional arguments

reference:

Object of class "character" path to reference genome file

results:

Object of class "character" path to results directory

infile1:

Object of class "character" paths to first FASTQ file

infile2:

Object of class "character" paths to second FASTQ file if data is PE

outfile1:

Object of class "character" paths to output files generated by command-line software

sysargs:

Object of class "character" full commands used to execute external software

outpaths:

Object of class "character" paths to final outputs including postprocessing by Rsamtools

Methods

SampleName

signature(x = "SYSargs"): extracts sample names

[

signature(x = "SYSargs"): subsetting of class with bracket operator

coerce

signature(from = "list", to = "SYSargs"): as(list, "SYSargs")

cores

signature(x = "SYSargs"): extracts data from cores slot

infile1

signature(x = "SYSargs"): extracts data from infile1 slot

infile2

signature(x = "SYSargs"): extracts data from infile2 slot

modules

signature(x = "SYSargs"): extracts data from modules slot

names

signature(x = "SYSargs"): extracts slot names

length

signature(x = "SYSargs"): extracts number of samples

other

signature(x = "SYSargs"): extracts data from other slot

outfile1

signature(x = "SYSargs"): extracts data from outfile1 slot

outpaths

signature(x = "SYSargs"): extracts data from outpath slot

reference

signature(x = "SYSargs"): extracts data from reference slot

results

signature(x = "SYSargs"): extracts data from results slot

show

signature(object = "SYSargs"): summary view of SYSargs objects

software

signature(x = "SYSargs"): extracts data from software slot

targetsheader

signature(x = "SYSargs"): extracts data from targetsheader slot

targetsin

signature(x = "SYSargs"): extracts data from targetsin slot

targetsout

signature(x = "SYSargs"): extracts data from targetsout slot

Author(s)

Thomas Girke

See Also

systemArgs and runCommandline

Examples

showClass("SYSargs")
## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "tophat.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
args
names(args); targetsin(args); targetsout(args); targetsheader(args); 
software(args); modules(args); cores(args); outpaths(args) 
sysargs(args); other(args); reference(args); results(args); infile1(args)
infile2(args); outfile1(args); SampleName(args)

## Return sample comparisons
readComp(args, format = "vector", delim = "-")

## The subsetting operator '[' allows to select specific samples
args[1:4]

## Not run: 
## Execute SYSargs on single machine
runCommandline(args=args)

## Execute SYSargs on multiple machines  
qsubargs <- getQsubargs(queue="batch", Nnodes="nodes=1", cores=cores(args), memory="mem=10gb", time="walltime=20:00:00")
qsubRun(appfct="runCommandline(args=args)", appargs=args, qsubargs=qsubargs, Nqsubs=1, submitdir="results", package="systemPipeR")

## Write outpaths to new targets file for next SYSargs step
writeTargetsout(x=args, file="default")

## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.