SYSargs2Pipe-methods: Deprecated '"SYSargs2Pipe"' accessor methods

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

These methods are deprecated and should be replaced by SYSargsList-methods. Methods to access information from SYSargs2Pipe object.

Usage

	SYSargs2Pipe_ls(x)

Arguments

x	object of class SYSargs2Pipe.

Details

The following methods are deprecated and will be made defunct; use the replacement indicated below:

• SYSargsList: help("SYSargsList-class")

Value

various outputs

Author(s)

Daniela Cassol and Thomas Girke

Examples

## Not run: 
## Construct SYSargs2 object number 1
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

## Construct SYSargs2 object number 2
targetsPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl/hisat2/hisat2-pe", package="systemPipeR")
WF1 <- loadWorkflow(targets=targetsPE, wf_file="hisat2-mapping-pe.cwl", 
                  input_file="hisat2-mapping-pe.yml", dir_path=dir_path)
WF1 <- renderWF(WF1, inputvars=c(FileName1="_FASTQ_PATH1_", FileName2="_FASTQ_PATH2_", SampleName="_SampleName_"))
WF1

## Keep track 
WF_set <- run_track(WF_ls = c(WF1, WF))
WF_steps(WF_set)
track(WF_set)
summaryWF(WF_set)[1]

## End(Not run)

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