Updated config.json from example to avoid confusion with the TF_disabled parameter

example/input/config.json

@@ -2,7 +2,7 @@
   "par_general": {
     "outdir": "../output",
     "maxCoresPerRule": 2,
-    "dir_TFBS_sorted":true,
+    "dir_TFBS_sorted": false,
     "regionExtension": 100,
     "comparisonType": "GMPvsMPP.all",
     "conditionComparison": "GMP,MPP",
@@ -11,8 +11,8 @@
     "nPermutations": 100,
     "nBootstraps": 0,
     "nCGBins": 10,
-    "TFs": "CTCF,CEBPB,SNAI2,CEBPA,UBIP1,CEBPG,CEBPD,ZFX,AP2D,PAX5.S,SNAI1,ZEB1,SP4,MBD2,IRF1,MECP2,PAX5.D,SP3,NFIA.C,SP1.A,IRF7,MYF6, NRF1,DBP,MAZ,NKX28,DLX2,GATA1,P53,ZN143,AIRE,NR2C2,HMGA1,FUBP1,TEAD3,OVOL1,HXD4,KLF1,RXRG,HNF1B,ZIC3,HNF1A,NANOG.S,GFI1,PO3F1,NR2C1,ELF5,TF65.C,NFAC3,TEAD1",
-    "TFs_disabled": "all",
+    "TFs": "all",
+    "TFs": "CTCF,CEBPB,SNAI2,CEBPA,UBIP1,CEBPG,CEBPD,ZFX,AP2D,PAX5.S,SNAI1,ZEB1,SP4,MBD2,IRF1,MECP2,PAX5.D,SP3,NFIA.C,SP1.A,IRF7,MYF6,NRF1,DBP,MAZ,NKX28,DLX2,GATA1,P53,ZN143,AIRE,NR2C2,HMGA1,FUBP1,TEAD3,OVOL1,HXD4,KLF1,RXRG,HNF1B,ZIC3,HNF1A,NANOG.S,GFI1,PO3F1,NR2C1,ELF5,TF65.C,NFAC3,TEAD1",
     "dir_scripts": "../../src/R",
     "RNASeqIntegration": true
   },