From 35087d2e2239b110dc86cd7dfdf03f84ee4070b5 Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 13 Dec 2018 09:56:22 +0100 Subject: [PATCH 1/2] update GATK to 4.0.9.0 --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index c2546d6976..af16a76a37 100644 --- a/environment.yml +++ b/environment.yml @@ -11,7 +11,7 @@ dependencies: - bwa=0.7.17 - fastqc=0.11.7 - 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 From 5c294211c5dfa9a8fdb51303c94e128a2d7a587a Mon Sep 17 00:00:00 2001 From: Maxime Garcia Date: Thu, 13 Dec 2018 10:00:34 +0100 Subject: [PATCH 2/2] update CHANGELOG --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1c69625f20..3702c48964 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,12 +23,14 @@ 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` ### `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 ## [2.2.1] - 2018-10-04