Conditional Workflow

[kokleong9406]

Hi Michael,

My current cwltool version is 3.1.20211107152837. Currently I have a conditional workflow. When I tried to run using cwltool in command prompt, I am able to get the output successfully. But when I tried to run it in cwl-airflow, I am not able to. After checking the log file, this is what is shown:

Source 'out2a' of
                                                                                                                                         type ["null",
                                                                                                                                         "File"] may be
                                                                                                                                         incompatible
cwl_tmp_folder/***_11-conditional-workflow-v2_manual__2021-12-02T09_46_06.468109_00_00_ul3lyxy9/step2a/step2a_step_workflow.cwl:29:13:   with sink
                                                                                                                                           'step2a_out2a' of
                                                                                                                                           type "File"
cwl_tmp_folder/***_11-conditional-workflow-v2_manual__2021-12-02T09_46_06.468109_00_00_ul3lyxy9/step2a/step2a_step_workflow.cwl:27:9:    Source is from
                                                                                                                                           conditional step
                                                                                                                                           and may produce
                                                                                                                                           `null`

Below is how my conditional workflow file looks like:

#!/usr/bin/env cwl-runner

class: Workflow
cwlVersion: v1.2

inputs:
  value: int

steps:
  step1:
    in:
      in1: value
    run: 11-foo-v2.cwl
    out: [out1]
  step2a:
    in:
      in2a: step1/out1
    run: 11-step2a-v2.cwl
    when: $(inputs.in2a > 5)
    out: [out2a]
  step2b:
    in:
      in2b: step1/out1
    run: 11-step2b-v2.cwl
    when: $(inputs.in2b < 5)
    out: [out2b]

outputs:
  out2:
    type: 
      - File
      - "null"
    outputSource: 
      - step2a/out2a
      - step2b/out2b
    pickValue: the_only_non_null

requirements:
  InlineJavascriptRequirement: {}
  MultipleInputFeatureRequirement: {}

[Edit: Further supplement with the other CommandLineTool]

Step1: 11-foo-v2.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool

cwlVersion: v1.2

requirements:
  - class: InlineJavascriptRequirement
  - class: InitialWorkDirRequirement
    listing:
      - entryname: echo_job.sh
        entry: |-
          echo $(inputs.in1) > hello1.txt
          echo $(inputs.in1) hahaha > hello2.txt

baseCommand: [sh]

arguments: [echo_job.sh]

inputs:
  in1: 
    type: int

outputs: 
  out1:
    type: int
    outputBinding:
      glob: 
        - "hello1.txt"
      loadContents: true
      outputEval: $(parseInt(self[0].contents))

Step2a: 11-step2a-v2.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool

cwlVersion: v1.2

requirements:
  - class: InlineJavascriptRequirement

baseCommand: [echo]

arguments:
  - $(inputs.in2a)

inputs:
  in2a:
    type: int

outputs:
  out2a:
    type: stdout

stdout: out2a.txt

Step2b: 11-step2b-v2.cwl

#!/usr/bin/env cwl-runner

class: CommandLineTool

cwlVersion: v1.2

requirements:
  - class: InlineJavascriptRequirement

baseCommand: [echo]

arguments:
  - $(inputs.in2b)

inputs:
  in2b:
    type: int

outputs:
  out2b:
    type: stdout

stdout: out2b.txt

I have already specify that out2 may accept "File" and "null" from the outputSource though. Meanwhile I will explore whether there is anything wrong with my cwl syntax despite having ran it successfully with "cwltool". DO you know why I am encountering this when ran in cwl-airflow?

[michael-kotliar]

@kokleong9406 Thank you for submitting an issue. I will investigate it and come back to you shortly.

Michael