check.output: Checking if the outfiles files exist

In tgirke/systemPipeR: systemPipeR: NGS workflow and report generation environment

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