targetsPE <- system.file("extdata", "targetsPE.txt", package = "systemPipeR")
dir_path <- system.file("extdata/cwl/kallisto/", package="systemPipeR")
kallisto <- loadWorkflow(targets = targetsPE, wf_file = "kallisto.cwl", 
    input_file = "kallisto.yml", dir_path = dir_path)
kallisto <- renderWF(kallisto, inputvars = c(FileName1 = "_FASTQ_PATH1_", FileName2 = "_FASTQ_PATH2_", SampleName = "_SampleName_"))
kallisto
cmdlist(kallisto)[1:2]
output(kallisto)[1:2]
## Single Machine
kallisto <- runCommandline(args= kallisto, make_bam=FALSE) 