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Missing input in allow_nested.wdl unit test #664

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stxue1 opened this issue Jun 18, 2024 · 1 comment
Open

Missing input in allow_nested.wdl unit test #664

stxue1 opened this issue Jun 18, 2024 · 1 comment
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@stxue1
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stxue1 commented Jun 18, 2024

For the allow_nested.wdl unit test, these lines call a task and omits a required input:

wdl/SPEC.md

Lines 5655 to 5658 in 9c0b9cf

call lib.repeat as repeat2 {
input:
opt_string = msg2
}

This line clarifies that with allowNestedInputs directive, this input can be supplied elsewhere:

repeat2.i may be set by the caller of the workflow, e.g., by including "allow_nested.repeat2.i": 2, in the input JSON.

However, for the unit test, I don't see this input being passed through:

wdl/SPEC.md

Lines 5677 to 5685 in 9c0b9cf

```json
{
"allow_nested.int_val": 3,
"allow_nested.msg1": "hello",
"allow_nested.msg2": "goodbye",
"allow_nested.my_ints": [1, 2, 3],
"allow_nested.ref_file": "hello.txt"
}
```

Instead, there is an expected output that wants the same variable:

wdl/SPEC.md

Line 5693 in 9c0b9cf

"allow_nested.repeat2.i": 2,

As I don't see where repeat2.i is defined in the workflow/input JSON, it looks like that line in the example output JSON should be moved to the example input JSON; the spec also doesn't say (at least to my knowledge) that the execution engine should output certain task inputs from nested calls when there is a output section.

@stxue1
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stxue1 commented Jun 19, 2024

A similar issue is in the outputs_task.wdl, there's an input in the JSON:

wdl/SPEC.md

Line 3694 in 9c0b9cf

"outputs.write_outstr": false

But it doesn't exist in the inputs:

wdl/SPEC.md

Lines 3671 to 3673 in 9c0b9cf

input {
Int t
}

jdidion added a commit that referenced this issue Jun 26, 2024
jdidion added a commit that referenced this issue Jun 26, 2024
@jdidion jdidion self-assigned this Jun 26, 2024
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