SYSargs2Pipe_ls {systemPipeR} | R Documentation |
"SYSargs2Pipe"
accessor methodsThese methods are deprecated and should be replaced by SYSargsList-methods
.
Methods to access information from SYSargs2Pipe
object.
SYSargs2Pipe_ls(x)
x |
object of class |
The following methods are deprecated and will be made defunct; use the replacement indicated below:
SYSargsList
: help("SYSargsList-class"
)
various outputs
Daniela Cassol and Thomas Girke
## Not run: ## Construct SYSargs2 object number 1 targets <- system.file("extdata", "targets.txt", package="systemPipeR") dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR") WF <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", input_file="hisat2-mapping-se.yml", dir_path=dir_path) WF <- renderWF(WF, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_")) WF ## Construct SYSargs2 object number 2 targetsPE <- system.file("extdata", "targetsPE.txt", package="systemPipeR") dir_path <- system.file("extdata/cwl/hisat2/hisat2-pe", package="systemPipeR") WF1 <- loadWorkflow(targets=targetsPE, wf_file="hisat2-mapping-pe.cwl", input_file="hisat2-mapping-pe.yml", dir_path=dir_path) WF1 <- renderWF(WF1, inputvars=c(FileName1="_FASTQ_PATH1_", FileName2="_FASTQ_PATH2_", SampleName="_SampleName_")) WF1 ## Keep track WF_set <- run_track(WF_ls = c(WF1, WF)) WF_steps(WF_set) track(WF_set) summaryWF(WF_set)[1] ## End(Not run)