Capturing Standard Output

Overview

Teaching: 10 min
Exercises: 0 min
Questions
  • How do I capture a tool’s standard output stream?

Objectives
  • Learn how to capture streamed output from a tool.

To capture a tool’s standard output stream, add the stdout field with the name of the file where the output stream should go. Then add type: stdout on the corresponding output parameter.

stdout.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: echo
stdout: output.txt
inputs:
  message:
    type: string
    inputBinding:
      position: 1
outputs:
  example_out:
    type: stdout

echo-job.yml

message: Hello world!

Now invoke cwl-runner providing the tool wrapper and the input object on the command line:

$ cwl-runner stdout.cwl echo-job.yml
[job stdout.cwl] /tmp/tmpE0gTz7$ echo \
    'Hello world!' > /tmp/tmpE0gTz7/output.txt
[job stdout.cwl] completed success
{
    "example_out": {
        "checksum": "sha1$47a013e660d408619d894b20806b1d5086aab03b",
        "basename": "output.txt",
        "nameroot": "output",
        "nameext": ".txt",
        "location": "file:///home/me/cwl/user_guide/output.txt",
        "path": "/home/me/cwl/user_guide/output.txt",
        "class": "File",
        "size": 13
    }
}
Final process status is success

Key Points

  • Use the stdout field to specify a filename to capture streamed output.

  • The corresponding output parameter must have type: stdout.