We cannot pass an array of integers as a command line argument.

[yamaken37]

We cannot pass an array of integers as a command line argument.
Please let me know if there is a workaround for it.

Workflow Code

#!/usr/bin/env cwl-runner

class: CommandLineTool
cwlVersion: v1.1

requirements:
  InlineJavascriptRequirement: {}

baseCommand: echo

inputs:
  input_A:
    type: int[]

arguments:
  - valueFrom: ${ return inputs.input_A.join(" "); }
    position: 1

outputs: []

Expected Behavior

• I expect it to work the same way it did when yaml was given to me.

$ cwltool test.cwl --input_A 0 --input_A 1
0 1

• Here is the output given yaml

$ cwltool test.cwl test.yaml
INFO /bin/cwltool 3.1.20220224085855
INFO Resolved 'test.cwl' to 'file:///cwl-test/test.cwl'
INFO [job test.cwl] /tmp/ixzpdr_f$ echo \
    '0 1'
0 1
INFO [job test.cwl] completed success
{}
INFO Final process status is success

• yaml

input_A:
  - 0
  - 1

Actual Behavior

$ cwltool test.cwl --input_A 1 --input_A 2
INFO /bin/cwltool 3.1.20220224085855
INFO Resolved 'test.cwl' to 'file:///cwl-test/test.cwl'
ERROR Workflow error, try again with --debug for more information:
Invalid job input record:
the `input_A` field is not valid because
  item is invalid because
    `'1'` is not int

Full Traceback

$ cwltool --debug test.cwl --input_A 1 --input_A 2

INFO /bin/cwltool 3.1.20220224085855
INFO Resolved 'test.cwl' to 'file:///cwl-test/test.cwl'
DEBUG Parsed job order from command line: {
    "id": "test.cwl",
    "input_A": [
        "1",
        "2"
    ]
}
ERROR Workflow error:
Invalid job input record:
the `input_A` field is not valid because
  item is invalid because
    `'1'` is not int
Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/cwltool/process.py", line 799, in _init_job
    validate_ex(
  File "/usr/lib/python3/dist-packages/schema_salad/validate.py", line 460, in validate_ex
    raise ValidationException("", None, errors, "*")
schema_salad.exceptions.ValidationException: the `input_A` field is not valid because
  item is invalid because
    `'1'` is not int

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/cwltool/main.py", line 1343, in main
    (out, status) = real_executor(
  File "/usr/lib/python3/dist-packages/cwltool/executors.py", line 60, in __call__
    return self.execute(process, job_order_object, runtime_context, logger)
  File "/usr/lib/python3/dist-packages/cwltool/executors.py", line 143, in execute
    self.run_jobs(process, job_order_object, logger, runtime_context)
  File "/usr/lib/python3/dist-packages/cwltool/executors.py", line 228, in run_jobs
    for job in jobiter:
  File "/usr/lib/python3/dist-packages/cwltool/command_line_tool.py", line 990, in job
    builder = self._init_job(job_order, runtimeContext)
  File "/usr/lib/python3/dist-packages/cwltool/process.py", line 850, in _init_job
    raise WorkflowException("Invalid job input record:\n" + str(err)) from err
cwltool.errors.WorkflowException: Invalid job input record:
the `input_A` field is not valid because
  item is invalid because
    `'1'` is not int

Your Environment

• cwltool version: 3.1.20220224085855

[mr-c]

Thank you for your report @yamaken37 , the only work around right now is to use an input object file

You can generate a template inputs object file using --make-template:

cwltool --make-template test.cwl  > inputs.yaml

(You don't have to use the name inputs.yaml)

And then edit inputs.yaml as you wish, for example

input_A:  # array of type 'int'
  - 1
  - 2

Now run using the inputs object:

$ cwltool test.cwl inputs.yaml
INFO [job 2034.cwl] /tmp/mhpvoy7j$ echo \
    '1 2'
1 2
INFO [job 2034.cwl] completed success
{}INFO Final process status is success

[yamaken37]

Thanks！

[mr-c]

This is still worth fixing 🙂