Argument with prefix = empty string and separate = false is omitted from cmd line

[bogdang989]

Expected Behavior

Argument with prefix: "" and separate: false should be in the command line.
Command line should be echo non_existing_app.

Actual Behavior

Argument is not in the command line.
Command line is non_existing_app.

Workflow Code

class: CommandLineTool
cwlVersion: v1.0
baseCommand: []
inputs:
  echo: boolean
outputs: []
arguments:
- position: 1
  shellQuote: false
  prefix: ''
  valueFrom: "non_existing_app"
- position: 0
  prefix: ''
  separate: false
  shellQuote: false
  valueFrom: "echo"
requirements:
- class: ShellCommandRequirement

Your Environment

• cwltool version: 1.0.20190621234233
  works fine with cwltool version: 1.0.20190228155703

[sivkovic]

I believe this caused the error 239499d#diff-bfbf952b5c2585de423b12dcf6f43938R424. Is this the proper behavior if we don't include the prefix that value should not be added? Either that or there should probably be additional clarification in the spec (https://www.commonwl.org/v1.1/CommandLineTool.html#CommandLineBinding)

[bogdang989]

Hi @sivkovic 👋 It's definitely a bug, value shouldn't be excluded if prefix is empty string, nothing in the spec indicates that.
Here's a PR for the cwltool fix (basically just to revert the check from if not prefix to if prefix is None) - #1166 and a PR for a conformance test that covers this case for v1.1 spec - common-workflow-language/cwl-v1.1#64

EDIT: Actually, when separate is false, prefix must be defined or validation would fail. Therefore, there is no need to even check for prefix at all, just append should work.

[mr-c]

Since this is a change in behaviour, I guess it would have to wait for CWL v1.3 or 2.0...