Simplify strun commands by using config files

[bhilbert4]

Rather than creating very long (in some cases close to 1000 character) strun commands, it might be better to switch to using configuration files for the strun commands. We would need lots of copies of the configuration files, but assuming we can write some functions to create these rather than the extra long commands, it may be better in the long run.

Using configuration files could potentially make everything easier to trace and track after the pipeline has been run, as opposed to parsing the long strun commands.

@arminrest