Merge pull request #678 from szilvajuhos/master

Changing VEP to v92 and adjusting CPUs

Author: Szilveszter Juhos

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Changed`
 
+-   [#678](https://github.com/SciLifeLab/Sarek/pull/678) - Changing VEP to v92 and adjusting CPUs for VEP
 -   [#663](https://github.com/SciLifeLab/Sarek/pull/663) - Update `do_release.sh` script
 -   [#671](https://github.com/SciLifeLab/Sarek/pull/671) - publishDir modes are now params
 

annotate.nf

@@ -215,13 +215,14 @@ process RunVEP {
   script:
   finalannotator = annotator == "snpeff" ? 'merge' : 'vep'
   genome = params.genome == 'smallGRCh37' ? 'GRCh37' : params.genome
+  cache_version = params.genome == 'GRCh38' ? 92 : 91
   """
   /opt/vep/src/ensembl-vep/vep --dir /opt/vep/.vep/  \
   -i ${vcf} \
   -o ${vcf.simpleName}_VEP.ann.vcf \
   --assembly ${genome} \
   --cache \
-	--cache_version 91 \
+	--cache_version ${cache_version} \
   --database \
   --everything \
   --filter_common \

conf/uppmax-localhost.config

@@ -128,15 +128,16 @@ process {
     memory = {params.totalMemory}
   }
   withName:RunSnpeff {
+    cpus = 1
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
-    memory = {params.totalMemory} // TODO Does SnpEff really require that much?
+    memory = {params.singleCPUMem * task.attempt}
   }
   withName:RunStrelka {
     cpus = 16
     memory = {params.totalMemory}
   }
   withName:RunVEP {
+    cpus = 16
     errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'}
-    memory = {params.totalMemory} // TODO Does VEP really require that much?
   }
 }

conf/uppmax-slurm.config

@@ -129,7 +129,6 @@ process {
     time = {params.runTime * task.attempt}
   }
   withName:RunVEP {
-    cpus = 1
     errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' }
   }
 }

containers/vepgrch38/Dockerfile

@@ -8,7 +8,7 @@ LABEL \
 # Setup ENV variables
 ENV \
   GENOME=GRCh38 \
-  VEP_VERSION=91
+  VEP_VERSION=92
 
 # Download Genome
 RUN \

docs/CONTAINERS.md

@@ -120,8 +120,8 @@ We provide script to build/push or pull all containers
 
 ### vepgrch38 [![vepgrch38-docker status][vepgrch38-docker-badge]][vepgrch38-docker-link]
 
-- Based on `willmclaren/ensembl-vep:release_90.6`
-- Contain **[VEP][vep-link]** 90.5
+- Based on `willmclaren/ensembl-vep:release_92`
+- Contain **[VEP][vep-link]** 92
 - Contain GRCh38
 
 [allelecount-link]: https://github.com/cancerit/alleleCount