Update the singularity command line parameter for apptainer

Placeholder issue for future work after Singularity has moved to under the Linux Foundation as “Apptainer”.

From @mr-c on Element about renaming --singularity to --apptainer in cwltool:

Sure, but we’ll likely keep the other name as a fallback. Or better yet, auto detect which engine is installed. I believe there is an issue for that already

[salexan2001]

Sure, I will have a look at the contribution guidelines and prepare a pull request. I have no experience with podman so far.

[salexan2001]

However, there seems to be an error regarding the “version check”, as apptainer and singularity seem to have different versioning conventions. I am currently receiving the following error with apptainer:

ERROR Workflow error, try again with --debug for more information:
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.: invalid literal for int() with base 10: 'a'

… while it works perfectly with the syslabs-singularity (and also with standard docker in this case).

(I started the job using $ cwltool --singularity 1st-tool.yml echo-job.yml)

So probably either the two command lines (–singularity / --apptainer) need a specific version check or the versioning scheme needs to be auto-detected depending on whether the one or the other singularity distribution is used.

I have attached the (slightly shortened) full output with --debug option:

bug_report_cwltool.txt