Heudiconv does not support input files with subject IDs, but this should be fairly easy to do in bash.
Consider a file subjects.txt that contains the following
subject1
subject2
subject3
You could pass the contents from that file into your heudiconv subjects by specifying
singularity run ...
....
-s $(cat subjects.txt | tr '\n' ' ')
...
and it should translate to
...
-s subject1 subject2 subject3
...