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]