Clean up folders and output chatter

McTavishLab / extensiphy

Pipeline to place taxa in a sequence alignment and phylogeny using NGS reads

GNU General Public License v3.0

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Open snacktavish opened 3 years ago

snacktavish commented 3 years ago

[x] Many of the folders on the main page of the repo can be organized into a sub-dir
[x] Evaluate the level of chatter in a standard run, and the spelling. Make some cuts if poss
[x] Clean up the outputs folder so that best_ref.* and the other random files go somewhere organized.
[x] maybe change the internal outputs to 'results'
[ ] maybe change combine_and_infer to something more intuitive?

snacktavish commented 3 years ago

Specially "random alignment" statements are sort of mysterious

jtfield commented 2 years ago

3 tasks down. the last 3 will take a little more time.