How To Write Cwl In R
How to write CWL in R?
Here is an example to wrap echo in Common Workflow Language (CWL) using the Rcwl package.
library(Rcwl)
input1 <- InputParam(id = "sth")
echo <- cwlParam(baseCommand = "echo", inputs = InputParamList(input1))
echo$sth <- "Hello World!"
echo
## class: cwlParam
## cwlClass: CommandLineTool
## cwlVersion: v1.0
## baseCommand: echo
## inputs:
## sth (string): Hello World!
## outputs:
## output:
## type: stdout
To write echo to CWL and YML.
out <- tempfile()
writeCWL(echo, out)
cat(readLines(paste0(out, ".cwl")), sep = "\n")
## cwlVersion: v1.0
## class: CommandLineTool
## baseCommand: echo
## inputs:
## sth:
## type: string
## inputBinding:
## separate: true
## outputs:
## output:
## type: stdout
cat(readLines(paste0(out, ".yml")), sep = "\n")
## sth: Hello World!
Run CWL directly in R.
runCWL(echo)
More tutorial: https://hubentu.github.io/Rcwl
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