Modify user config and preload modules

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": {
-          "adapter": "TruSeq2"
+          "adapter": "TruSeq2",
           "jarfile": "/mnt/nfs/projects/ecosystem_biology/local_tools/Trimmomatic-0.32/trimmomatic-0.32.jar"
-      }
-      "datadir": "TEST_DATA",
-      "raws": {
-          "Metagenomics": "MG.R1.5_percent.fq MG.R2.5_percent.fq",
-          "Metatranscriptomics": "MT.R1.5_percent.fq MT.R2.5_percent.fq"
-      },
-      "sample": "test",
-      "outputdir": "build",
-      "db_path": "db"
-      }
+     }
    },
     "Assembly": {
       "pre": "echo '//LOADING ASSEMBLY MODULE'"

modules_to_preload.sh

@@ -22,6 +22,6 @@ export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/tabix-0.2.6
 export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/gkno_launcher/tools/freebayes/bin
 export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/bin
 export PERL5LIB=$PERL5LIB:/mnt/nfs/projects/ecosystem_biology/local_tools/vcftools/perl
-export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/Platypus_0.7.9.1
+export PATH=$PATH:/mnt/nfs/projects/ecosystem_biology/local_tools/Platypus/Platypus_0.7.9.1
 
 module list