check.output: Checking if the outfiles files exist

View source: R/sysargs2_utilities.R

check.outputR 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)

tgirke/systemPipeR documentation built on Aug. 30, 2022, 10 p.m.