Use "run" with singularity/apptainer instead of "exec", when possible

[sameeul]

Context for the PR:
Currently if the user uses a docker image in a workflow and depending on the choice of the container engine (docker vs singularity), the execution can be different, if the docker image has an entrypoint.

I understand that CWL community encourages docker images w/o entrypoints, however there are a good number of images produced by various scientific communities that comes with entrypoints. When this images are used in HPC environment, in most cases, due to security policies (not having access to root), singularity is chosen as the container engine. In these cases, docker images with entrypoint fails to execute.

I also know that creating CommandLineTools with a baseCommand can bypass the entrypoint issue when running with singularity but that also makes those CommandLineTools container engine dependent, in turn making the CWL workflows themselves container engine dependent.

With those observations, if there is no other strong reason for choosing singularity exec in the initial implementation, I would propose to change it to singularity run.

Here is also a link of relevant discussion: https://cwl.discourse.group/t/singularity-exec-vs-docker-run/956/4

[codecov]

Codecov Report

Attention: Patch coverage is 70.00000% with 3 lines in your changes missing coverage. Please review.

Project coverage is 83.98%. Comparing base (048eb55) to head (d2f9f24).
Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
cwltool/singularity.py	70.00%	1 Missing and 2 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #2065      +/-   ##
==========================================
- Coverage   84.05%   83.98%   -0.07%     
==========================================
  Files          46       46              
  Lines        8302     8312      +10     
  Branches     1957     1959       +2     
==========================================
+ Hits         6978     6981       +3     
- Misses        848      854       +6     
- Partials      476      477       +1     

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[mr-c]

6 conformance tests fail when running with Singularity: https://github.com/common-workflow-language/cwltool/actions/runs/11769747600/job/32791926095?pr=2065#step:7:905

[sameeul]

Thanks for the feedback. I ran the CI on my fork and looks like the singularity tests are passing now.

[mr-c]

A new cwltool release has been made with your fix; thank you @sameeul !

https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20241112140730 / https://github.com/common-workflow-language/cwltool/releases/tag/3.1.20241112140730