Merge pull request #700 from MaxUlysse/GATK

Update GATK

Author: alneberg

CHANGELOG.md

@@ -24,13 +24,15 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 -   [#677](https://github.com/SciLifeLab/Sarek/pull/677) - Update docs
 -   [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Update old awsbatch configuration
 -   [#693](https://github.com/SciLifeLab/Sarek/pull/693) - Qualimap bamQC is now ran after mapping and after recalibration for better QC
+-   [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Update GATK to `4.0.9.0`
 -   [#702](https://github.com/SciLifeLab/Sarek/pull/702) - update FastQC to `0.11.8`
 
 ### `Fixed`
 
 -   [#665](https://github.com/SciLifeLab/Sarek/pull/665) - Input bam file now has always the same name (whether it is from a single fastq pair or multiple) in the MarkDuplicates process, so metrics too
 -   [#672](https://github.com/SciLifeLab/Sarek/pull/672) - process `PullSingularityContainers` from `buildContainers.nf` now expect a file with the correct `.simg` extension for singularity images, and no longer the `.img` one.
 -   [#679](https://github.com/SciLifeLab/Sarek/pull/679) - Add publishDirMode for `germlineVC.nf`
+-   [#700](https://github.com/SciLifeLab/Sarek/pull/700) - Fix [#699](https://github.com/SciLifeLab/Sarek/issues/699) missing DP in the FORMAT column VCFs for MuTect2
 -   [#702](https://github.com/SciLifeLab/Sarek/pull/702) - Fix [#701](https://github.com/SciLifeLab/Sarek/issues/701)
 
 ## [2.2.1] - 2018-10-04

environment.yml

@@ -13,7 +13,7 @@ dependencies:
   - font-ttf-dejavu-sans-mono=2.37 #for FastQC
   - fontconfig=2.12.6 #for FastQC
   - freebayes=1.2.0
-  - gatk4=4.0.6.0
+  - gatk4=4.0.9.0
   - htslib=1.9
   - igvtools=2.3.93
   - manta=1.4.0