runCommandline: Execute SYSargs and SYSargs2

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Function to execute system parameters specified in SYSargs and SYSargs2 object.

Usage

runCommandline(args, runid = "01", make_bam = TRUE, del_sam=TRUE, dir = FALSE, dir.name = NULL, force=FALSE, ...)

Arguments

args	object of class SYSargs or SYSargs2.
runid	Run identifier used for log file to track system call commands. Default is "01".
make_bam	Auto detects SAM file outputs and converts them to sorted and indexed BAM files. Default is make_bam=TRUE.
del_sam	This option allows deleting the SAM files created when the make_BAM converts the SAM files to sorted and indexed BAM files. Default is del_sam=TRUE.
dir	This option allows creating an exclusive results folder for each step in the workflow and a sub-folder for each sample defined in the targets file. All the outputs and log files for the particular step will be created in the respective folders. Default is dir=FALSE. Option available only for an object of class SYSargs2.
dir.name	Name of the workflow directory. Default is dir.name=FALSE. Note: This argument is required when the dir=TRUE.
force	Internally, the function checks if the expected output files exist, and it skips the command lines when the respective files exist. If the argument force is set to TRUE, the command line will be executed and the files overwrite. Default is force=FALSE.
...	Additional arguments to pass on to runCommandline().

Value

Output files, their paths can be obtained with outpaths() from SYSargs container or output() from SYSargs2. In addition, a character vector is returned containing the same paths.

Author(s)

Daniela Cassol and Thomas Girke

Examples

#########################################
## Examples with \code{SYSargs} object ##
#########################################
## Construct SYSargs object from param and targets files 
param <- system.file("extdata", "hisat2.param", package="systemPipeR")
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
args <- systemArgs(sysma=param, mytargets=targets)
args
names(args); modules(args); cores(args); outpaths(args); sysargs(args)

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

## Execute SYSargs on multiple machines of a compute cluster. 
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=cores(args), 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)
file.exists(outpaths(args))

## Alignment stats
read_statsDF <- alignStats(args) 
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)

##########################################
## Examples with \code{SYSargs2} object ##
##########################################
## 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)

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

## Execute SYSargs on multiple machines of a compute cluster. 
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(WF, FUN = runCommandline, more.args = list(args = WF, make_bam = TRUE), 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.