singularity/apptainer sandbox images are not handled

[natthan-pigoux]

I want to use Singularity/Apptainer sandbox images that are already present locally.

While using --singularity and --disable-pull options it doesn't find the image because it looks for .sif extension which doesn't exists in my case because the image is a sandbox (e.g. unpacked).

Here is an example:

cwlVersion: v1.2
class: CommandLineTool
inputs:
  local_script:
    type: File
    inputBinding:
      position: 1
outputs:
  local_output:
    type: File
    outputBinding:
      glob: "output.txt"
baseCommand: ["python"]
hints:
  DockerRequirement:
    dockerPull: /path/to/containers/python/3.12-slim

cwltool --debug --disable-pull --singularity hello_world_docker.cwl inputs.yaml
[...]
DEBUG Singularity error
Traceback (most recent call last):
  File "cwltool/job.py", line 759, in run
  File "cwltool/singularity.py", line 361, in get_from_requirements
cwl_utils.errors.WorkflowException: Container image _path_to_containers_python_3.12-slim_latest.sif not found
ERROR Workflow error:
Singularity is not available for this tool, try --no-container to disable Singularity, or install a user space Docker replacement like uDocker with --user-space-docker-cmd.: Container image _cvmfs_sw.cta-observatory.org_software_containers_python_3.12-slim_latest.sif not found
[...]