MicroDA and Cor

Hi,

I've made a new branch to perform DA with the microbes and to only use the top portions for correlation. I have done a test run and it did finish running and the results looked okay but if you could double check some of my changes (please see below), I'd appreciate it:

1. I added an option for contrast for microbes ONLY if mapping is not done. This implies that the same comparisons between groups in host and microbes are done most of the time.
2. In line with that, is my use of microbe contrast (see config) correct?
3. I edited edgeR.R to take in either microbes or genes tables, parameters are not changed
4. I edited cor and used the conditions done for genes as template for the microbes
5. There are no benchmarks for the edgeR runs - i can add if needed
6. I noticed that some benchmarks and log files are in directories while some are not. Should I place them all in directories to be uniform and more organized?