using ammonite and cwltool to preprocess CWL

salad.scala

package wdl4s.cwl.other

import ammonite.ops._
import ammonite.ops.ImplicitWd._
import lenthall.validation.ErrorOr.ErrorOr
import wdl4s.cwl.{CwlCodecs, CwlFile}


object Salad extends App{

  //case class SaladOutput(outputAsJson: String, relativePath: Path)

  /**
    *
    * @param in Needs to take a file to get relative file paths.
    * @return
    */

  def salad(in: Path): String = {
    //val relPath: RelPath = in relativeTo pwd

    val toolresult = cwlTool(in.toString())

    toolresult.out.string
  }

  def cwlTool(filePath: String): CommandResult = %%('cwltool, "--print-pre", filePath.toString())

  def saladAndParse(in: Path): ErrorOr[(CwlFile, Map[String, CwlFile])] = {

    val json = salad(in)
    ???

     val cwl = CwlCodecs.decodeSingleFileCwlAsJson(json)

    ???
  }

  val x = 'cwl/'src/'test/'resources/"arguments.cwl"

  val y = pwd/x

  println(salad(y))
}