Conflicts:
	public/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/bowtie/Bowtie.scala
	public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala

Fix issue #248

fix issue #248

See merge request !294

Fix indelrealigner

Small fix

See merge request !293

Add bowtie2 to Mapping (and add wrapper for bowtie2)

Adding a bowtie2 wrapper to extensions and add bowtie2 as an aligner to `Mapping`

Closes #241 

Accepts biopet/Biopet-FunctionalTests!17

See merge request !284

Fix for #238

The issue is caused by the Cutadapt summary not being aware of the
clipped sequence names. This merge request extends the existing Cutadapt
wrapper in the Flexiprep module and makes it so that the wrapper is
aware of FastQC.

See merge request !288

Fix wrong metrics addition in BamMetrics

The CollectHsMetrics was incorrectly added as the CollectTargetedPcrMetrics. This commit fixes it.

See merge request !291

The CollectHsMetrics was incorrectly added as the
CollectTargetedPcrMetrics. This commit fixes it.

Fixed args for CollectGcBiasMetrics



See merge request !290

Fix scatter

Fixes scattering in shiva.

This should fix failing tests here:
http://ci.sasc.nl:8080/job/Biopet-Functional-Tests/36/

See merge request !289

Upgrade queue to 3.5

Fixes #244 

See merge request !286

Split variantcalllers in separated files

Fixes #239, #171 and #147 

See merge request !283

The issue is caused by the Cutadapt summary not being aware of the
clipped sequence names. This merge request extends the existing Cutadapt
wrapper in the Flexiprep module and makes it so that the wrapper is
aware of FastQC.