shallow_listing data loss issue

[mr-c]

Found via DataBiosphere/toil#5099 (comment)

Setup

mkdir 5099-test
mkdir 5099-test/subdir
touch 5099-test/a 5099-test/b 5099-test/c 5099-test/subdir/d
find 5099-test/
# 5099-test/
# 5099-test/a
# 5099-test/c
# 5099-test/subdir
# 5099-test/subdir/d
# 5099-test/b

5099-minimal-example.cwl

class: Workflow
cwlVersion: v1.2
id: minimal_example
label: minimal_example
inputs:
  - id: msin
    type: Directory[]
outputs:
  - id: msout
    outputSource:
      - second_pass/msout
    type: Directory[]
steps:
  - id: pass
    in:
      - id: msin
        source: msin
    out:
      - id: msout
    run: 5099-pass.cwl
  - id: second_pass
    in:
      - id: msin
        source: pass/msout
    out:
      - id: msout
    run: 5099-pass.cwl

5099-pass.cwl

class: CommandLineTool
cwlVersion: v1.2
id: pass
baseCommand: echo
# arguments:
#  - $(inputs.msin[0].listing)
inputs:
  - id: msin
    type: 
      - Directory[]
outputs:
  - id: msout
    type:
      - Directory[]
    outputBinding:
      outputEval: $(inputs.msin)
requirements:
  - class: LoadListingRequirement
    #loadListing: no_listing
    loadListing: shallow_listing

5099-debug.json

{
         "msin":    [  {"class": "Directory", "path": "5099-test"}]
}

Expected Behavior

cwltool 5099-minimal-example.cwl 5099-debug.json without --outdir does not delete any files from the input directory 5099-test

Actual Behavior

The directory 5099-test/subdir and its contents are deleted

$ find 5099-test/
5099-test/
5099-test/a
5099-test/c
5099-test/b

Your Environment

• cwltool version: 3.1.20241112140731.dev10+gf1d192dd.d202412
  Check using cwltool --version