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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.
Expected Behavior
Argument with
prefix: ""
andseparate: 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
Your Environment
works fine with cwltool version: 1.0.20190228155703
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