sysargs2-methods: SYSargs2 accessor methods

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

Methods to access information from SYSargs2 object.

Usage

	sysargs2(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/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)
sysargs2(WF)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.