Returning Output Files

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• Where does the output of a command go?

• How can I save the output of a command?

Objectives

• Learn how to describe and handle outputs from a tool.

The outputs of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an id for the name of parameter, and type describing what types of values are valid for that parameter.

When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files.

The following example demonstrates how to return a file that has been extracted from a tar file.

Passing mandatory arguments to the baseCommand

In previous examples, the baseCommand was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an array of strings. The first element is the command to run, and any subsequent elements are mandatory command line arguments

tar.cwl

#!/usr/bin/env cwl-runner

cwlVersion: v1.0
class: CommandLineTool
baseCommand: [tar, --extract]
inputs:
  tarfile:
    type: File
    inputBinding:
      prefix: --file
outputs:
  example_out:
    type: File
    outputBinding:
      glob: hello.txt

tar-job.yml

tarfile:
  class: File
  path: hello.tar

Next, create a tar file for the example and invoke cwl-runner with the tool wrapper and the input object on the command line:

$ touch hello.txt && tar -cvf hello.tar hello.txt
$ cwl-runner tar.cwl tar-job.yml
[job tar.cwl] /tmp/tmpqOeawQ$ tar \
    --extract --file \
    /tmp/tmpGDk8Y1/stg80bbad20-494d-47af-8075-dffc32df03a3/hello.tar
[job tar.cwl] completed success
{
    "example_out": {
        "location": "file:///home/me/cwl/user_guide/hello.txt",
        "basename": "hello.txt",
        "class": "File",
        "checksum": "sha1$da39a3ee5e6b4b0d3255bfef95601890afd80709",
        "size": 0,
        "path": "/home/me/cwl/user_guide/hello.txt"
    }
}
Final process status is success

The field outputBinding describes how to to set the value of each output parameter.

outputs:
  example_out:
    type: File
    outputBinding:
      glob: hello.txt

The glob field consists of the name of a file in the output directory. If you don’t know name of the file in advance, you can use a wildcard pattern like glob: '*.txt'.

Key Points

• Outputs are described in the outputs section of a CWL description.

• The field outputBinding describes how to to set the value of each output parameter.

• Wildcards are allowed in the glob field.