Merge remote-tracking branch 'origin/feature-docs-0.5.0' into feature-docs-0.5.0

docs/cluster/oge.md

 # Introduction
-Within the LUMC we have a compute cluster which runs on the Sun Grid Engine (SGE). The cluster has around 600 cores now and multiple terabytes of memory.
-The SGE enables the cluster to schedule all the jobs coming from different users in a fair way. So Resources are shared equally between multiple users. 
+Within the LUMC we have a compute cluster which runs on the Sun Grid Engine (SGE). This cluster currently consists of around 600 
+cores and several terabytes of memory. The Sun Grid Engine (SGE) enables the cluster to schedule all the jobs coming from 
+different users in a fair way. So Resources are shared equally between multiple users.
 
 # Sun Grid Engine
 

docs/developer/code-style.md

 # Developer - Code style
 
 ## General rules
-- Variable names should always be in *CamelCase* and does **not** start with a capital letter
+- Variable names should always be in *camelCase* and does **not** start with a capital letter
 
 ```scala
 // correct: 
@@ -11,7 +11,7 @@ val outputFromProgram: String = "foobar"
 val OutputFromProgram: String = "foobar"
 ```
 
-- Class names should always be in *CamelCase* and does **always** start with a capital letter
+- Class names should always be in *CamelCase* and **always** start with a capital letter
 
 ```scala
 // correct:

docs/developer/getting-started.md

@@ -43,9 +43,10 @@ import nl.lumc.sasc.biopet.utils.config.Configurable
 import nl.lumc.sasc.biopet.extensions.{ Gzip, Cat }
 import org.broadinstitute.gatk.queue.QScript
 
-//TODO: Replace class name, must be the same as the class of the pipeline
+//TODO: Replace class name, must be the same as the name of the pipeline
 class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript {
   // A constructor without arguments is needed if this pipeline is a root pipeline
+  // Root pipeline = the pipeline one wants to start on the commandline
   def this() = this(null)
 
   @Input(required = true)
@@ -69,7 +70,7 @@ class SimplePipeline(val root: Configurable) extends QScript with BiopetQScript
   }
 }
 
-//TODO: Replace object name, must be the same as the class of the pipeline
+
 object SimplePipeline extends PipelineCommand
 ```
 

docs/general/config.md

@@ -57,10 +57,16 @@ Note that there is a tool called [SamplesTsvToJson](../tools/SamplesTsvToJson.md
 
 ### The settings config
 The settings config enables a user to alter the settings for almost all settings available in the tools used for a given pipeline.
-This config file should be written in JSON format.
-It can contain setup settings like references, cut offs, program modes, memory limits (program specific), if chunking should be used and many more, one can even set program executables here, if for some reason the user does not want to use the systems default tools.
-One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer deeper into the JSON file.
-E.g. in the example below the settings for Picard tools are altered only for Picard and not global. 
+This config file should be written in either JSON or YAML format. It can contain setup settings like:
+
+ * references,
+ * cut offs,
+ * program modes and memory limits (program specific),
+ * Whether chunking should be used
+ * set program executables (if for some reason the user does not want to use the systems default tools)
+ * One could set global variables containing settings for all tools used in the pipeline or set tool specific options one layer 
+ deeper into the JSON file. E.g. in the example below the settings for Picard tools are altered only for Picard and not global. 
+
 
 ~~~
 "picard": { "validationstringency": "LENIENT" } 

docs/release_notes_0.5.0.md

+# Release notes Biopet version 0.5.0
+
+* Our QC and mapping pipeline now use piping for the most used aligners and QC tools
+ * This decreases the disk usage and run time
+* 
\ No newline at end of file