I compared against the matsengrp/cft master running with the test.yaml file I added (was there supposed to be one there already?), which runs on the test files I added here https://github.com/psathyrella/cft/tree/master/tests
I don't understand the ouputs super well yet, but diffing the full output directory, the only differences seemed to be
in the metadata.json files, there were many thousands of lines, but the differences all seemed to be hashes
the pruned_ids.txt was in a different order
aligned_translated_inseqs.fa-.log had some numbers different which I think just had to do with timing, and anyway it's just a log file
so if that seems sufficient, you can probably merge if the changes look ok to you.
I compared against the matsengrp/cft master running with the test.yaml file I added (was there supposed to be one there already?), which runs on the test files I added here https://github.com/psathyrella/cft/tree/master/tests
I don't understand the ouputs super well yet, but diffing the full output directory, the only differences seemed to be
so if that seems sufficient, you can probably merge if the changes look ok to you.