- The code that adds things in the `jobs/scripts` directory as executables is also picking up the `.pyc` byte-compiled files. Doesn't really break anything, but should be cleaned up.
- The Picard version used (1.139) is quite old. Would be nice to be able to use the current 2.9.0 version.
- The two SPP scripts (`run_spp.R` and `run_spp_nodups.R`) need to be packaged up in Conda in a sane way.