JavaScript & CWL

Part 1: InlineJavascriptRequirement

If you need to do a computation while running a cwltool, you can do so using a snippet of javascript.

#!/usr/bin/env cwl-runner

$namespaces:
  s: https://schema.org/

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-0326-7494
    s:email: andrew.lamb@sagebase.org

s:name: Andrew Lamb

cwlVersion: v1.0

class: CommandLineTool

requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
  listing:
  - entry: $(inputs.file)
    writable: true

baseCommand:
- gzip

inputs:

- id: file
  type: File
  inputBinding:
    position: 1

outputs:

- id: gziped_file
  type: File
  outputBinding:
    glob: $(inputs.file.path + ".gz")

The above tool gzips the given input file. The gzip util will tack on the the .gz suffix, so we don’t know what the exact file name will be. But we can figure it out using a little bit of javascript:

- id: gziped_file
  type: File
  outputBinding:
    glob: $(inputs.file.path + ".gz")

1. Inputs.file.path returns the path of the input file
2. ‘+ “.gz”’ concatenates the gz suffix
3. $() returns the result of the javscript expression contained between the parens

Part 2: Expression tools

Expression tools are cwltools that only perform javascript, and don’t call any other script or command.

#!/usr/bin/env cwl-runner

$namespaces:
  s: https://schema.org/

s:author:
  - class: s:Person
    s:identifier: https://orcid.org/0000-0002-0326-7494
    s:email: andrew.lamb@sagebase.org

s:name: Andrew Lamb

cwlVersion: v1.0
class: ExpressionTool

requirements:
- class: InlineJavascriptRequirement

inputs:

- id: input_file
  type: File
- id: new_file_name
  type: string

outputs:

- id: output_file
  type: File

expression: |
  ${
    inputs.input_file.basename = inputs.new_file_name;
    return {output_file: inputs.input_file};
  }

Expression tools are like command line tools in terms of input and outputs. The difference is that instead of execution a commnad, expression tools execute a javascript expression:

expression: |
  ${
    inputs.input_file.basename = inputs.new_file_name;
    return {output_file: inputs.input_file};
  }

This expression simply renames the file, and returns it.