check.output {systemPipeR}R Documentation

Checking if the output files exist

Description

This function returns a logical vector indicating whether the expected output files for each workflow step exist.

Usage

check.output(args, subset = 1, index = 1)

Arguments

args

object of class SYSargs2.

subset

name or numeric position of the values to be subsetting in the slot. The subset is the path for the expected output files for all the steps in the workflow. Default is subset=1

index

A numeric index positions of the file in SYSargs2 object, slot output. It requires a subset to be defined. Default is index=1.

Author(s)

Daniela Cassol and Thomas Girke

See Also

subsetWF

Examples

## Construct SYSargs2 object 
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

check.output(WF)

[Package systemPipeR version 1.26.3 Index]