check.output: Checking if the outfiles files exist

Description Usage Arguments Value Author(s) See Also Examples

View source: R/sysargs2_utilities.R

Description

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

Usage

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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

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## 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 July 20, 2021, 10:45 p.m.