starts organization process

.gitmodules

@@ -1,3 +1,6 @@
 [submodule "statMix"]
 	path = statMix
 	url = https://github.com/raywray/statMix.git
+[submodule "evolutionary_history/supercomputer_scripts"]
+	path = evolutionary_history/supercomputer_scripts
+	url = https://github.com/raywray/supercomputer_scripts.git

README.md

@@ -2,20 +2,4 @@
 
 This is the pipeline used in the hops paper (citation). 
 
-First, we created a reusable pipeline that generates several summary statistics (statMix) and fed our *hops* `vcf` data through the pipeline. The summary statistics and analysis results we generated for *hops* are as follows: 
-- Hardy Weinberg Equilibrium
-- Full population structure analysis using admixture 
-- SFS based on the population structure results
-- tajima's D
-- windowed weir Fst
-- weir Fst
-- site pi
-- site pi per population (from population structure analysis)
-- windowed pi
-- windowed pi per population (from population structure analysis)
-- Fit
-- Fis
-- allele frequency
-- SFS(s) compatible for fastsimcoal analyses
-
-Next, the pipeline uses the SFS(s) created for fastsimcoal analyses, as well as a user-generated parameter `yaml` file, to feed into a fastsimcoal wrapper (citation here) that generates thousands of random coalescent models. This was run on a cluster. The wrapper identified the best model and parameters, ran a bootstrap analysis, and generated images. The results of the best model are included here in the `results/fastsimcoal` folder. 
+We have created different folders for the different analyses performed. Each folder has its own README.md.