A scatter workflow that should make several empty directories makes only one directory

[tom-tan]

It does not happen when a scattered step makes non-empty directories.

Version

$ toil-cwl-runner --version
5.7.1

How to reproduce

scatter.cwl:

cwlVersion: v1.0
class: Workflow

requirements:
  ScatterFeatureRequirement: {}
inputs:
  - id: strs
    type: string[]
outputs:
  - id: dirs
    type: Directory[]
    outputSource: mkdir/dir

steps:
  - id: mkdir
    run:
      class: CommandLineTool
      baseCommand: mkdir
      inputs:
        - id: str
          type: string
          inputBinding: {}
      outputs:
        - id: dir
          type: Directory
          outputBinding:
            glob: "$(inputs.str)"
    scatter: str
    in:
        str: strs
    out: [dir]

job.yml:

strs: [a, b, c]

and run the following:

$ toil-cwl-runner scatter.cwl job.yml

Expected behavior

It makes directories named a, b and c.

$ toil-cwl-runner scatter-workflow.cwl job.yml
...
{
    "dirs": [
        {
            "location": "file:///workspaces/a",
            "basename": "a",
            "nameroot": "a",
            "nameext": "",
            "class": "Directory",
            "listing": []
        },
        {
            "location": "file:///workspaces/b",
            "basename": "b",
            "nameroot": "b",
            "nameext": "",
            "class": "Directory",
            "listing": []
        },
        {
            "location": "file:///workspaces/c",
            "basename": "c",
            "nameroot": "c",
            "nameext": "",
            "class": "Directory",
            "listing": []
        }
    ]
}
$ ls
a  b  c  job.yml  scatter.cwl

Actual behavior

It only makes a.
It also returns output object that consists of directories with basename a, b and c but they have the same location value.

$ toil-cwl-runner scatter-workflow.cwl job.yml
...
{
    "dirs": [
        {
            "location": "file:///workspaces/a",
            "basename": "a",
            "nameroot": "a",
            "nameext": "",
            "class": "Directory",
            "listing": []
        },
        {
            "location": "file:///workspaces/a",
            "basename": "b",
            "nameroot": "b",
            "nameext": "",
            "class": "Directory",
            "listing": []
        },
        {
            "location": "file:///workspaces/a",
            "basename": "c",
            "nameroot": "c",
            "nameext": "",
            "class": "Directory",
            "listing": []
        }
    ]
}
$ ls
a   job.yml  scatter.cwl

┆Issue is synchronized with this Jira Story
┆epic: AGC
┆friendlyId: TOIL-1216

[DailyDreaming]

@tom-tan Thanks for the detailed report and how to reproduce the problem. Will look into a fix.

[adamnovak]

We need to update cwltest to at least the version in common-workflow-language/cwltest#146 (comment) so that we can see this bug, and then fix it.

[DailyDreaming]

This should be done and included in current CWL tests.