systemArgs: Constructs SYSargs object from param and targets files

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Constructs SYSargs S4 class objects 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 established 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.

Usage

systemArgs(sysma, mytargets, type = "SYSargs")

Arguments

sysma	path to 'param' file; file structure follows a simple name/value syntax that converted into JSON format; for details about the file structure see sample files provided by package. Assign NULL to run the pipeline without 'param' file. This can be useful for running partial workflows, e.g. with pregenerated BAM files.
mytargets	path to targets file
type	type="SYSargs" returns SYSargs, type="json" returns param file content in JSON format (requires rjson library)

Value

SYSargs object or character string in JSON format

Author(s)

Thomas Girke

See Also

showClass("SYSargs")

Examples

## 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); 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
resources <- list(walltime=120, ntasks=1, ncpus=cores(args), memory=1024) 
reg <- clusterRun(args, 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))
sapply(1:length(args), function(x) loadResult(reg, x)) # Works once all jobs have completed successfully.

## Alignment stats
read_statsDF <- alignStats(args) 
write.table(read_statsDF, "results/alignStats.xls", row.names=FALSE, quote=FALSE, sep="\t")

## 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.