process

This library contains code for processing and executing CWL documents, such as CommandLineTools.

This code is experimental, young, and buggy, however it is able to bind inputs, generate command line arguments, and bind outputs. Currently the focus is on supporting CommandLineTool processing. Last checked (3/14/2018), about 15/68 conformance tests were passing.

Example

package main

import (
  "fmt"
  "github.com/buchanae/cwl"
  "github.com/buchanae/cwl/process"
  localfs "github.com/buchanae/cwl/process/fs/local"
)

func main() {
  // must be run from /examples dir
  path := "tar-param.cwl"
  inputsPath := "tar-param.inputs.yml"

  vals, err := cwl.LoadValuesFile(inputsPath)
  if err != nil {
    fmt.Println("error loading inputs:", err)
    return
  }

  doc, err := cwl.Load(path)
  if err != nil {
    panic(err)
  }

  tool, ok := doc.(*cwl.Tool)
  if !ok {
    panic("can only run command line tools")
  }

  rt := process.Runtime{}
  fs := localfs.NewLocal(".")

  proc, err := process.NewProcess(tool, vals, rt, fs)
  if err != nil {
    panic(err)
  }

  cmd, err := proc.Command()
  if err != nil {
    panic(err)
  }
  fmt.Println(cmd)
}

TODO / Questions

• This may be a relative reference, in which case it must be resolved using the base IRI of the document. Does this mean relative to the inputs document?