SYSargs2-class: Class '"SYSargs2"'

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

SYSargs2 class stores all the information and instructions needed for processing a set of input files with a specific command-line or a series of command-line within a workflow. The SYSargs2 S4 class object is created from the loadWorkflow and renderWF function, which populates all the command-line for each sample in each step of the particular workflow. Each sample level input/outfile operation uses its own SYSargs2 instance. The output of SYSargs2 define all the expected output files for each step in the workflow, which usually it is the sample input for the next step in an SYSargs2 instance. Between different instances, this connectivity is established by writing the subsetting output with the writeTargetsout function to a new targets file that serves as input to the next loadWorkflow and renderWF call. By chaining several SYSargs2 steps together one can construct complex workflows involving many sample-level input/output file operations with any combination of command-line or R-based software.

Objects from the Class

Objects can be created by calls of the form new("SYSargs2", ...).

Slots

targets:

Object of class "list" storing data from each sample from targets file

targetsheader:

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

modules:

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

wf:

Object of class "list" storing data from Workflow CWL param file

clt:

Object of class "list" storing data from each CommandLineTool step in the Workflow or the single CommandLineTool CWL param file

yamlinput:

Object of class "list" storing data from input file

cmdlist:

Object of class "list" storing all command-line used to execute external software

input:

Object of class "list" storing data from each target defined in inputvars

output:

Object of class "list" paths to final outputs files

cwlfiles:

Object of class "list" paths to input and CWL param files

inputvars:

Object of class "list" storing data from each inputvars

Methods

[

signature(x = "SYSargs2"): subsetting of class with bracket operator

[[

signature(x = "SYSargs2", i = "ANY", j = "missing"): subsetting of class with bracket operator

[[<-

signature(x = "SYSargs2"): replacement method for SYSargs2 class

$

signature(x = "SYSargs2"): extracting slots elements by name

clt

signature(x = "SYSargs2"): extracts data from clt slot

cmdlist

signature(x = "SYSargs2"): extracts data from cmdlist slot

coerce

signature(from = "list", to = "SYSargs2"): as(list, "SYSargs2")

cwlfiles

signature(x = "SYSargs2"): extracts data from cwlfiles slot

infile1

signature(x = "SYSargs2"): extracting paths to first FASTQ file

infile2

signature(x = "SYSargs2"): extracting paths to second FASTQ file if data is PE

input

signature(x = "SYSargs2"): extracts data from input slot

inputvars

signature(x = "SYSargs2"): extracts data from inputvars slot

length

signature(x = "SYSargs2"): extracts number of samples

modules

signature(x = "SYSargs2"): extracts data from modules slot

names

signature(x = "SYSargs2"): extracts slot names

output

signature(x = "SYSargs2"): extracts data from cmdlist slot

show

signature(object = "SYSargs2"): summary view of SYSargs2 objects

sysargs2

signature(x = "SYSargs2"): Coerce back to list as(SYSargs2, "list")

targets

signature(x = "SYSargs2"): extract data from targets slot

targetsheader

signature(x = "SYSargs2"): extracts data from targetsheader slot

wf

signature(x = "SYSargs2"): extracts data from wf slot

yamlinput

signature(x = "SYSargs2"): extracts data from yamlinput slot

Author(s)

Daniela Cassol and Thomas Girke

See Also

loadWorkflow and renderWF and runCommandline and clusterRun

Examples

showClass("SYSargs2")

## Construct SYSargs2 object from CWl param, CWL input, and targets files 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", 
                  input_file="hisat2-mapping-se.yml", dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
WF
names(WF); modules(WF); targets(WF)[1]; cmdlist(WF)[1:2]; output(WF)

## The subsetting operator '[' allows to select specific command-line
cmdlist(WF)[1:2]

## Not run: 
## Execute SYSargs2 on single machine
WF <- runCommandline(args=WF)

## Execute SYSargs2 on multiple machines of a compute cluster. The following
## example uses the conf and template files for the Slurm scheduler. Please 
## read the instructions on how to obtain the corresponding files for other schedulers.  
file.copy(system.file("extdata", ".batchtools.conf.R", package="systemPipeR"), ".")
file.copy(system.file("extdata", "batchtools.slurm.tmpl", package="systemPipeR"), ".")
resources <- list(walltime=120, ntasks=1, ncpus=4, memory=1024) 
reg <- clusterRun(args, FUN = runCommandline, conffile=".batchtools.conf.R", template="batchtools.slurm.tmpl", Njobs=18, runid="01", resourceList=resources)

## Monitor progress of submitted jobs
getStatus(reg=reg)

## Updates the path in the object \code{output(WF)}
WF <- output_update(WF, dir=FALSE, replace=TRUE, extension=c(".sam", ".bam"))

## Alignment stats
read_statsDF <- alignStats(WF) 
read_statsDF <- cbind(read_statsDF[targets$FileName,], targets)
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## End(Not run)

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