Configexample reordered by likelyhood of change

configExample.json

@@ -1,50 +1,52 @@
 {
   "_comment": "SBATCH configuration",
   "slurm_header": {
-    "project": "prod001",
-    "type": "core",
+    "time": "06:00:00",
     "threads": "8",
-    "time": "00:30:00",
     "qos": "normal",
-    "job_prefix": "MLST"
+    "job_prefix": "MLST",
+    "project": "prod001",
+    "type": "core"
   },
 
   "_comment": "File finding patterns. Only single capture group accepted (for reverse/forward identifier)",
   "regex":  {
-    "file_pattern": "\\w{8,12}_\\w{8,10}(?:-\\d+)*_L\\d_(?:R)*(\\d{1}).fastq.gz",
-    "mail_recipient": "user@examplegroup.com"
-  },
-
-  "_comment": "Thresholds for Displayed results",
-  "threshold":  {
-    "mlst_id": 100,
-    "mlst_novel_id": 99.5,
-    "mlst_span": 0.9,
-    "res_id": 97,
-    "res_span": 0.9
+    "mail_recipient": "user@examplegroup.com",
+    "file_pattern": "\\w{8,12}_\\w{8,10}(?:-\\d+)*_L\\d_(?:R)*(\\d{1}).fastq.gz"
   },
 
   "_comment": "Folders",
   "folders":  {
+    "_comment": "Root folder for ALL output",
+    "results": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/results/",
     "_comment": "Log file position and name",
     "log_file": "~/microsalt.log",
+
     "_comment": "Root folder for fasta sequencing data",
     "seqdata": "/mnt/hds/proj/bioinfo/MICROBIAL/projects/",
     "_comment": "Cutadapt adapters folder",
     "adapters": "/mnt/hds/proj/bioinfo/SERVER/miniconda/envs/microSALT/share/trimmomatic-0.38-1/adapters/",
-    "_comment": "ST references. Each ST profile file under 'profiles' have an identicial namefolder under references. Each references sub-folder contains the .tfa file for each locus",
+    "_comment": "ST references. Each ST profile file under 'profiles' have an identicial namefolder under references.\
+                 Each references sub-folder contains the .tfa file for each locus",
     "profiles": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/references/profiles",
     "references": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/references/definitions_locisplit",
     "resistances": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/references/resistances",
-    "gene_set": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/references/gene_set",
-    "_comment": "Root folder for ALL output",
-    "results": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/results/"
+    "gene_set": "/mnt/hds/proj/bioinfo/MICROBIAL/MLST/references/gene_set"
   },
 
   "_comment": "Database/Flask configuration",
   "database": {
     "SQLALCHEMY_DATABASE_URI": "sqlite:////tmp/microsalt.db",
     "SQLALCHEMY_TRACK_MODIFICATIONS": "False",
     "DEBUG": "True"
+  },
+
+  "_comment": "Thresholds for Displayed results",
+  "threshold":  {
+    "mlst_id": 100,
+    "mlst_novel_id": 99.5,
+    "mlst_span": 0.9,
+    "res_id": 97,
+    "res_span": 0.9
   }
 }