SYSargs2list {systemPipeR} | R Documentation

## SYSargs2 accessor methods

### Description

Methods to access information from `SYSargs2` object.

### Usage

    	SYSargs2list(x)

### Arguments

`x` | object of class `SYSargs2`

### Value

various outputs

### Author(s)

Daniela Cassol and Thomas Girke

### Examples

    ## 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", 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
    names(WF); modules(WF); targets(WF)[1]; cmdlist(WF)[1:2]; output(WF)

[Package systemPipeR version 1.18.2 Index]