run_track {systemPipeR} | R Documentation |
run_track
functions
Keep track of the all SYSargs2
object. This function is deprecated and should be replaced by SYSargsList-class
.
run_track(WF_ls)
WF_ls |
list of |
The following methods are deprecated and will be made defunct; use the replacement indicated below:
SYSargs2Pipe
: SYSargs2-class
SYSargs2Pipe
object
Daniela Cassol and Thomas Girke
showClass("SYSargs2Pipe")
loadWorkflow
renderWF
## 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)