Possible to combine inputs using valueFrom for scatter

Question

[ionox0]

Is it possible to combine multiple inputs from another step using valueFrom so that they can be scattered over?

For example something like:

inputs:

  input_one: Directory
  input_two: Directory

steps: 

  a_step:
    run: ../../cwl_tools/noise/calculate_noise.cwl
    in:
      input_thing:
        valueFrom: |
          ${
            return [
              inputs.input_one,
              inputs.input_two
            ]
          }

    out: [output_thing]
    scatter: input_thing

I get this error:

[workflow workflow.cwl] starting step a_step
Unhandled exception
Traceback (most recent call last):
  File "/home/johnsoni/virtualenvs/pipeline_test/lib/python2.7/site-packages/cwltool-1.0.20180306140409-py2.7.egg/cwltool/workflow.py", line 401, in try_make_job
    emptyscatter = [shortname(s) for s in scatter if len(inputobj[s]) == 0]
TypeError: object of type 'NoneType' has no len()

Answer 1

[Michael R. Crusoe]

Hello ionox0,

Yes, this is possible. Just wire up the other inputs to non-existent names and reference them from your expression

inputs:

  input_one: Directory
  input_two: Directory

steps: 

  a_step:
    run: ../../cwl_tools/noise/calculate_noise.cwl
    in:
      fake_input_two: input_two
      input_thing:
        source: input_one
        valueFrom: |
          ${
            return [
              self,
              inputs.fake_input_two
            ]
          }

    out: [output_thing]
    scatter: input_thing

Though, in your case this can be accomplished using linkMerge: merge_flattened

requirements:
  MultipleInputFeatureRequirement: {}

inputs:

  input_one: Directory
  input_two: Directory

steps: 

  a_step:
    run: ../../cwl_tools/noise/calculate_noise.cwl
    in:
      input_thing:
        source: input_one, input_two
        linkMerge: merge_flattened

    out: [output_thing]
    scatter: input_thing