## Define CL call
library(systemPipeR)
command2 <- "
    hisat2 \
    -S <F, out: ./results/_SampleName_.sam> \
    -x <F: ./data/tair10.fasta> \
    -k <int: 1> \
    -min-intronlen <int: 30> \
    -max-intronlen <int: 3000> \
    -threads <int: 4> \
    -U <F: _FASTQ_PATH1_>
"

WF <- createParam(command2, overwrite = TRUE, writeParamFiles = TRUE, confirm = TRUE)
yml <- yaml::read_yaml("param/cwl/hisat2/hisat2.yml"); yml <- c(SampleName = "_SampleName_", yml); yaml::write_yaml(yml, "param/cwl/hisat2/hisat2.yml")
targetspath <- system.file("extdata", "targets.txt", package = "systemPipeR")
WF_test <- loadWorkflow(targets = targetspath, wf_file = "hisat2.cwl", input_file = "hisat2.yml",
    dir_path = "param/cwl/hisat2/")
WF_test <- renderWF(WF_test, inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"))
cmdlist(WF_test)[1:2]

## Use CL call in a WF step
dir.create("data") # create data directory if it doesn't exist
sal <- SPRproject(overwrite=TRUE) # Use overwrite only for testing
appendStep(sal) <- LineWise(code = {
    library(systemPipeR)
}, step_name = "load_SPR")

appendStep(sal) <- SYSargsList(step_name = "hisat2_mapping",
    targets = targetspath, wf_file = "hisat2.cwl",
    input_file = "hisat2.yml", dir_path = "param/cwl/hisat2",
    inputvars = c(FileName = "_FASTQ_PATH1_", SampleName = "_SampleName_"),
    dependency=c("load_SPR")
)
cmdlist(sal)