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]