Tweak to make sure Simple_prep.sh works outside of main repo

[eroesch]

The original design of simple_prep.sh was assuming that the user would not have cloned the repo, and simply used the script. The modifications make it such that:

• if the user calls simple_prep.sh outside of the repo, it creates a folder "workflow" to host "miniconda" and "scripts",
• if the user calls simple_prep.sh from inside the repo (because they would have cloned from github), it does not git clone again, uses local files and store miniconda inside the same folder.