SYSargs2Pipe_ls {systemPipeR} | R Documentation

## Deprecated `"SYSargs2Pipe"` accessor methods

### 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)

[Package systemPipeR version 1.22.0 Index]