Snakemake version
9.14.0

Describe the bug
I was running a command: snakemake -s Snakefile example-output.txt --core 1 --use-apptainer --sdm apptainer and received an error:

WorkflowError:
The apptainer or singularity command has to be available in order to use apptainer/singularity integration.

I'm on a M4 Macbook pro and using LIMA to run apptainer. I spun up a virtual machine using Lima and called it apptainer, so I have an executable called apptainer.lima where I can run apptainer. I made a file in ~/.local/bin/apptainer that basically just ran apptainer.lima:
#!/bin/bash
apptainer.lima "$@"

I tried to run snakemake and this did not work, even after re-sourcing so my apptainer command was in my path. I then did cp ~/.local/bin/apptainer ~/.local/bin/singularity, resourced, and snakemake now recognizes the command and works.

For more context, my snakemake rule had: container: example.sif, which was in my current path.

Minimal example
If apptainer is not in your path and you have some other command to run it (like me - apptainer.lima), a singularity named executable is recognized and works for running apptainer, but apptainer command does not.