a test like friedman

Hi there,
I have data that includes baseline, 6 weeks, and 12 weeks, group. each group contains control and test bacteria samples.
I wanted to use the Friedman test to check which group or bacteria is different but I have read that the assumption is to have at least 6 samples in each group while I have only 4 samples.
do you know what other statistical tests should be ok for this case? preferably able to run in qiime environment.
thank you