diff --git a/CHANGELOG.md b/CHANGELOG.md index b8256d0027..be1821cb50 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/annotate.nf b/annotate.nf index 396c217dd8..7ae5fb828a 100644 --- a/annotate.nf +++ b/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 \ diff --git a/conf/uppmax-localhost.config b/conf/uppmax-localhost.config index 08052cc188..10c6725ba4 100644 --- a/conf/uppmax-localhost.config +++ b/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? } } diff --git a/conf/uppmax-slurm.config b/conf/uppmax-slurm.config index 2f8f78ad79..8686d7af91 100644 --- a/conf/uppmax-slurm.config +++ b/conf/uppmax-slurm.config @@ -129,7 +129,6 @@ process { time = {params.runTime * task.attempt} } withName:RunVEP { - cpus = 1 errorStrategy = { task.exitStatus == 143 ? 'retry' : 'ignore' } } } diff --git a/containers/vepgrch38/Dockerfile b/containers/vepgrch38/Dockerfile index 04185c8f13..da3a810a78 100644 --- a/containers/vepgrch38/Dockerfile +++ b/containers/vepgrch38/Dockerfile @@ -8,7 +8,7 @@ LABEL \ # Setup ENV variables ENV \ GENOME=GRCh38 \ - VEP_VERSION=91 + VEP_VERSION=92 # Download Genome RUN \ diff --git a/docs/CONTAINERS.md b/docs/CONTAINERS.md index f223972127..19dfe39df2 100644 --- a/docs/CONTAINERS.md +++ b/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