removed user control over methylkit params until we figure it out, functional...

removed user control over methylkit params until we figure it out, functional with multiple replicates

.test/comparison/comparisons.tsv

 id	control	treatment
-WT_vs_Meth13	.test/data/chr3test_a_thaliana_met13.CX_report	.test/data/chr3test_a_thaliana_wt.CX_report
+WT_vs_Meth13	.test/data/chr3test_a_thaliana_met13.CX_report,.test/data/chr3test_a_thaliana_met13.CX_report	.test/data/chr3test_a_thaliana_wt.CX_report,.test/data/chr3test_a_thaliana_wt.CX_report

.test/comparison/config.yaml

@@ -11,9 +11,9 @@ params:
   windowSize: 1000
   stepSize: 1000
   test: F # default F, Chisq for overdispersion
-  overdispersion: none # default none, NM for overdispersion
+  overdispersion: NM # default none, NM for overdispersion
   qValue: 0.01
   minCov: 4
   minDiff: 0.4
   context: ["CG"]
-  species: ""
+  species: "Gala"

workflow/scripts/methylkit.R

@@ -96,10 +96,10 @@ dev.off()
 pdf(snakemake@output[["pcaPdf"]])
 PCASamples(meth)
 dev.off()
-
+print(meth)
 
 ### calculating differential methylation ###
-methDiff=calculateDiffMeth(meth,overdispersion=overdispersion,test=testOverdispersion,mc.cores=cores)
+methDiff=calculateDiffMeth(meth,mc.cores=cores)
 
 
 ### filtering differential methylation ###