check.output {systemPipeR} | R Documentation

## Checking if the outfiles files exist

### Description

This function returns a `data.frame` indicating the number of existing files and how many files are missing.

### Usage

    check.output(sysargs, type="data.frame")
    check.outfiles(sysargs, type="data.frame")

### Arguments

`sysargs` | object of class `SYSargs2` or `SYSargsList`.
`type` | return object option. It can be `data.frame` or `list`.

### Value

`data.frame` or `list` containing all the `outfiles` file information.

### Author(s)

Daniela Cassol and Thomas Girke

### See Also

- `SYSargs2-class`

- `SYSargsList-class`

### Examples

    ## Construct SYSargs2 object
    targets <- system.file("extdata", "targets.txt", package="systemPipeR")
    dir_path <- system.file("extdata/cwl", package="systemPipeR")
    WF <- loadWorkflow(targets=targets, wf_file="hisat2/hisat2-mapping-se.cwl",
                      input_file="hisat2/hisat2-mapping-se.yml", dir_path=dir_path)
    WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
    WF
    ## Check output
    check.output(WF)
    check.output(WF, "list")

    ## Construct SYSargsList object
    sal <- SPRproject(overwrite=TRUE)
    targetspath <- system.file("extdata/cwl/example/targets_example.txt", package="systemPipeR")
    appendStep(sal) <- SYSargsList(step_name = "echo",
                          targets=targetspath, dir=TRUE,
                          wf_file="example/workflow_example.cwl", input_file="example/example.yml",
                          dir_path = system.file("extdata/cwl", package="systemPipeR"),
                          inputvars = c(Message = "_STRING_", SampleName = "_SAMPLE_"))
    ## Check outfiles
    check.outfiles(sal)

[Package systemPipeR version 2.0.8 Index]