Conflicts:
	pom.xml
	protected/biopet-gatk-extensions/pom.xml
	protected/biopet-gatk-pipelines/pom.xml
	protected/biopet-protected-package/pom.xml
	protected/pom.xml
	public/bam2wig/pom.xml
	public/bammetrics/pom.xml
	public/basty/pom.xml
	public/biopet-framework/pom.xml
	public/biopet-public-package/pom.xml
	public/carp/pom.xml
	public/flexiprep/pom.xml
	public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/Flexiprep.scala
	public/gentrap/pom.xml
	public/kopisu/pom.xml
	public/mapping/pom.xml
	public/pom.xml
	public/sage/pom.xml
	public/shiva/pom.xml
	public/toucan/pom.xml
	public/yamsvp/pom.xml

Feature report

See also issue #102

Things to do:
- [x] implement template library
- [ ] General features
 - [x] Versions template
 - [x] Intro text sections
 - [x] Intro text pages
 - [x] Fix menu
 - [x] fix sidebar, should highlight current section
 - [x] Fix sortable tables, @wyleung
 - [x] Auto scala width on number of samples
- [ ] Report for Flexiprep
 - [x] Files template
- [ ] Report for bammetrics, #127 required
 - [x] Fix insertsize
- [ ] Report for Mapping
 - [x] Files template
- [ ] Report for Shiva
 - [x] Files template
 - [x] Show tables on click
- [ ] Report for Carp
- [ ] Setup a generic layout

See merge request !149

Docs required

Documentation required settings and flags for pipelines. Now includes the new reference module (e.g. `reference_fasta`) and tries to name namespaces correctly. See #161 (and to a lesser extend #163)

See merge request !174

Force logging to a file

see #158

See merge request !175

Change bwa to bwa-mem

part of #129

See merge request !173

Added executables that are missing on a native osx install

Was installing ide on new mac book and did see some issues in the unit tests

See merge request !171

Fix for issue #167

See merge request !172