subsetWF {systemPipeR}R Documentation

Subsetting SYSargs2 class slots

Description

Return subsets of character for the input, output or the list of command-line for each workflow step.

Usage

subsetWF(args, slot, subset = NULL, delete = FALSE)

Arguments

args

object of class SYSargs2.

slot

three options available: type="input" returns input slot from SYSargs2 object; type="output" returns output slot from SYSargs2 object; and type="step" returns all the command-line for each workflow step from SYSargs2 object.

subset

name or numeric position of the values to be subsetting in the slot.

delete

allows to delete a subset of files in the case of slot="output". Default is delete=NULL.

Author(s)

Daniela Cassol and Thomas Girke

See Also

loadWorkflow renderWF

Examples

## Construct SYSargs2 object 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
WF <- loadWorkflow(targets=targets, wf_file="hisat2-se/hisat2-mapping-se.cwl",
                   input_file="hisat2-se/hisat2-mapping-se.yml",
                   dir_path=dir_path)
WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH_", SampleName="_SampleName_"))
WF

## Testing subset_wf function
input <- subsetWF(WF, slot="input", subset='FileName')
output <- subsetWF(WF, slot="output", subset=1)
step.cmd <- subsetWF(WF, slot="step", subset=1) ## subset all the HISAT2 commandline 

[Package systemPipeR version 1.18.2 Index]