View source: R/sysargs2_utilities.R
check.output | R Documentation |
This function returns a data.frame
indicating the number of existing files
and how many files are missing.
check.output(sysargs, type="data.frame") check.outfiles(sysargs, type="data.frame")
sysargs |
object of class |
type |
return object option. It can be |
data.frame
or list
containing all the outfiles
file information.
Daniela Cassol and Thomas Girke
- SYSargs2-class
- SYSargsList-class
## 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)
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