Creating Files at Runtime

Overview

Teaching: 10 min
Exercises: 0 min

Questions

• How do I create required input files from input parameters at runtime?

Objectives

• Learn how to create files on the fly during runtime.

Sometimes you need to create a file on the fly from input parameters, such as tools which expect to read their input configuration from a file rather than the command line parameters. To do this, use InitialWorkDirRequirement.

createfile.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool
cwlVersion: v1.0
baseCommand: ["cat", "example.conf"]

requirements:
  InitialWorkDirRequirement:
    listing:
      - entryname: example.conf
        entry: |
          CONFIGVAR=$(inputs.message)

inputs:
  message: string
outputs: []

echo-job.yml

message: Hello world!

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

$ cwltool createfile.cwl echo-job.yml
[job 140528604979344] /home/example$ cat example.conf
CONFIGVAR=Hello world!
Final process status is success
{}

Key Points

• Use InitialWorkDirRequirement to specify input files that need to be created during tool runtime.