Merge branch 'docs-0.4.0' into 'release-0.4.0'

Docs 0.4.0

See merge request !202

docs/release_notes_0.3.2.md

+# Release notes Hotfix 0.3.2
+
+* A bug was discovered in our RNA seq pipeline ( Gentrap )
+ * The merged count table missed out on 1 gene consistently. The separate count files per sample where not affected by this bug
+* This bug involved all previous runs from Gentrap of the last 2 months, all customers where informed and if requested a new file is delivered.
+ * We manually checked all the runs and found that the first gene was almost never expressed in our data sets
+ * In case you haven't heard from us, you can assume your data not to have been affected
+ 
\ No newline at end of file

docs/release_notes_0.4.0.md

+# Release notes Biopet version 0.4.0
+
+* A reporting framework has been added for most pipelines
+ * This framework produces a static HTML report which can be viewed in your browser
+ * The framework contains lots of quality control and downstream analyses plots (genome coverage, transcript coverage etc etc.)
+* An issue where a NullPointerException was being thrown when output_dir was not set in the config was fixed. This now gives a nice error message which points to the missing key in the config
+* Pipelines now automatically write a log file if none is specified on command line
+* Tools writing to VCF will no longer fail when the *output* is not a *gzipped* VCF
+* Pipelines now support passing config options directly into the commandline prompt
+* Pipelines now support a more readable config file format [YAML](https://en.wikipedia.org/?title=YAML)
+* Memlimit and vmem memory issues are solved by automatically increasing the amount of available memory when a job fails. ```--retry 5``` should do the trick
+* BamMetrics pipeline is updated to work with newest version of Picard
+* A bug in VcfStats in comparing samples alleles is fixed. Now each allele can only be used once in the comparison.
+* VcfStats is now capable of summarizing stats per bin (bin size is changeable)
+* There is now a module which checks for the present of correct reference files if not it automatically builds the appropriate ref files
+
+Some pipelines were updated as well:
+
+* Gentrap
+* Shiva
\ No newline at end of file