First Example

Overview

Teaching: 5 min
Exercises: 0 min

Questions

• How do I wrap a simple command line tool?

Objectives

• Learn the basic structure of a CWL description.

The simplest “hello world” program. This accepts one input parameter, writes a message to the terminal or job log, and produces no permanent output. CWL documents are written in JSON or YAML, or a mix of the two.

First, create a file called 1st-tool.cwl, containing the boxed text below. It will help you to use a text editor that can be specified to produce text in YAML or JSON. Whatever text editor you use, the indents you see should not be created using tabs.

1st-tool.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
inputs:
  message:
    type: string
    inputBinding:
      position: 1
outputs: []

Next, create a file called echo-job.yml, containing the following boxed text, which will describe the input of a run:

echo-job.yml

message: Hello world!

Now, invoke cwl-runner with the tool wrapper 1st-tool.cwl and the input object echo-job.yml on the command line. The command is cwl-runner 1st-tool.cwl echo-job.yml. The boxed text below shows this command and the expected output.

$ cwl-runner 1st-tool.cwl echo-job.yml
[job 1st-tool.cwl] /tmp/tmpmM5S_1$ echo \
    'Hello world!'
Hello world!
[job 1st-tool.cwl] completed success
{}
Final process status is success

The command cwl-runner 1st-tool.cwl echo-job.yml is an example of a general form that you will often come across while using CWL. The general form is cwl-runner [tool-or-workflow-description] [input-job-settings]

What’s going on here? Let’s break down the contents of 1st-tool.cwl:

cwlVersion: v1.0
class: CommandLineTool

The cwlVersion field indicates the version of the CWL spec used by the document. The class field indicates this document describes a command line tool.

baseCommand: echo

The baseCommand provides the name of program that will actually run (echo). echo is a built-in program in the bash and C shells.

inputs:
  message:
    type: string
    inputBinding:
      position: 1

The inputs section describes the inputs of the tool. This is a list of input parameters and each parameter includes an identifier, a data type, and optionally an inputBinding which describes how this input parameter should appear on the command line. In this example, the position field indicates where it should appear on the command line.

outputs: []

This tool has no formal output, so the outputs section is an empty list.

Key Points

• CWL documents are written in YAML and/or JSON.

• The command called is specified with baseCommand.

• Each expected input is described in the inputs section.

• Input values are specified in a separate YAML file.

• The tool description and input files are provided as arguments to a CWL runner.