Fix some explaination about the output directories in the config

docs/developer/example-pipeline.md

@@ -136,8 +136,23 @@ Setting up the pipeline is done within the pipeline itself, fine-tuning is alway
 
 ### Config setup
 
+For our new pipeline, one should setup the (default) config options.
+
+Since our pipeline is called `HelloPipeline`, the root of the configoptions will called `hellopipeline` (lowercaps).
+
+```json
+{
+    "output_dir": "/home/user/mypipelineoutpt",
+    "hellopipeline": {
+        
+    }
+}
+
+```
+
+
 ### Test pipeline
 
 ### Summary output
 
-### Reporting output (opt)
\ No newline at end of file
+### Reporting output (optional)
\ No newline at end of file

docs/general/config.md

@@ -8,12 +8,14 @@ The sample config should be in [__JSON__](http://www.json.org/) or [__YAML__](ht
 - Second field should contain the __"libraries"__
 - Third field contains __"R1" or "R2"__ or __"bam"__
 - The fastq input files can be provided zipped and unzipped
+- `output_dir` is a required setting that should be set either in a `config.json` or specified on the invocation command via -cv output_dir=<path/to/outputdir\>. The default value is to place the pipeline output in the current working directory.
 
 #### Example sample config
 
 ###### yaml:
 
 ``` yaml
+output_dir: /home/user/myoutputdir
 samples:
   Sample_ID1:
     libraries:
@@ -26,6 +28,7 @@ samples:
 
 ``` json
     {  
+       "output_dir": "/home/user/myoutputdir",
        "samples":{  
           "Sample_ID1":{  
              "libraries":{  

docs/pipelines/basty.md

@@ -52,7 +52,7 @@ Specific configuration options additional to Basty are:
 ```json
 
 {
-    output_dir: </path/to/out_directory>,
+    "output_dir": </path/to/out_directory>,
     "shiva": {
         "variantcallers": ["freeBayes"]
     },