SYSargs2Pipe_ls {systemPipeR}R Documentation

SYSargs2Pipe accessor methods

Description

Methods to access information from SYSargs2Pipe object.

Usage

	SYSargs2Pipe_ls(x)

Arguments

x

object of class SYSargs2Pipe.

Value

various outputs

Author(s)

Daniela Cassol and Thomas Girke

Examples

## Construct SYSargs2 object number 1
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

## Construct SYSargs2 object number 2
targetsPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl", package="systemPipeR")
WF1 <- loadWorkflow(targets=targetsPE, wf_file="hisat2-pe/hisat2-mapping-pe.cwl",
                   input_file="hisat2-pe/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]

[Package systemPipeR version 1.18.2 Index]