fix: prevent name collisions on input parameters

[rahuldesai1]

In a Snakefile, it is possible for two different input files to have the same parameter name as long as they are defined in different rules. This can lead to name collisions because we use a global mapping (across all rules) of param_name -> input_file.

To avoid this name collision, I add a check and raise an error if it doesn't pass.

I considered adding the job_id to the front of all the variable names, but I suspect that this will make the entrypoint file even less readable. Since this seems like enough of an edge case, I would prefer to just fail and raise an error rather than append the job id to all the variable names.