New user config

conf/userconfig.imp.json

 {
-    "General": {
-      "threads": 4,
-      "datadir": "TEST_DATA",
-      "sample": "test",
-      "outputdir": "build",
-      "db_path": "db"
-    },
-    "Preprocessing": {
-      "pre": "echo '//LOADING PREPROCESSING MODULE: You can write custom shell commands here' ",
-      "filtering": false,
-      "trimmomatic": {
+    "threads": 4,
+    "datadir": "TEST_DATA",
+    "sample": "test",
+    "outputdir": "build",
+    "db_path": "db",
+    "preprocessing_filtering": false,
+    "trimmomatic": {
           "adapter": "TruSeq2",
           "jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar"
-        }
-    },
-    "Assembly": {
-      "pre": "echo '//LOADING ASSEMBLY MODULE'"
-    },
-    "Analysis": {
-      "pre": "echo '//LOADING ANALYSIS MODULE'"
-    },
-    "Util": {
-      "pre": "echo '//LOADING UTIL MODULE'"
     },
     "human_filtering": {
         "filter": "chr21"