From 937013694dd2d4e75bb37f2500c8ab12fe9ea045 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Tue, 30 Oct 2018 00:33:19 +0100 Subject: [PATCH 1/8] increasing VEP version to 92 --- containers/vepgrch38/Dockerfile | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 \ From cabc5e1d58eef8c984a459268462d873712391f4 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Tue, 30 Oct 2018 00:33:55 +0100 Subject: [PATCH 2/8] Sarek-data update --- Sarek-data | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Sarek-data b/Sarek-data index c2da0d2a8a..ba299d76c8 160000 --- a/Sarek-data +++ b/Sarek-data @@ -1 +1 @@ -Subproject commit c2da0d2a8a1c1a8e9b9b0930b84e34073ea43d03 +Subproject commit ba299d76c851dc916c051ef5f77d7a4ab39dcc9f From 5a9ea248a0b556b62f40ec9f8083c90d1db1a450 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 17:27:13 +0100 Subject: [PATCH 3/8] Changing to VEP 92 --- annotate.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/annotate.nf b/annotate.nf index 396c217dd8..f1e6ebd2f2 100644 --- a/annotate.nf +++ b/annotate.nf @@ -221,7 +221,7 @@ process RunVEP { -o ${vcf.simpleName}_VEP.ann.vcf \ --assembly ${genome} \ --cache \ - --cache_version 91 \ + --cache_version 92 \ --database \ --everything \ --filter_common \ From a2c3dde9eb681246a9c4689d912b877092368b56 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 17:33:58 +0100 Subject: [PATCH 4/8] VEP and snpEff mem and cpu adjust --- conf/uppmax-localhost.config | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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? } } From 64a3507ed295cbe2ee7e9c32e411b3ed5ff0d01f Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 17:37:12 +0100 Subject: [PATCH 5/8] VEP cpu adjust --- conf/uppmax-slurm.config | 1 - 1 file changed, 1 deletion(-) 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' } } } From a51a98928391f247787fcd22fcf7d6784dab8cf0 Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 18:06:30 +0100 Subject: [PATCH 6/8] Sarek-data updated to latest --- CHANGELOG.md | 1 + Sarek-data | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) 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/Sarek-data b/Sarek-data index ba299d76c8..c2da0d2a8a 160000 --- a/Sarek-data +++ b/Sarek-data @@ -1 +1 @@ -Subproject commit ba299d76c851dc916c051ef5f77d7a4ab39dcc9f +Subproject commit c2da0d2a8a1c1a8e9b9b0930b84e34073ea43d03 From 2ada70461116517812de43af904250246e3571dc Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 18:27:42 +0100 Subject: [PATCH 7/8] VEP GRCh38 docs updated --- docs/CONTAINERS.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From 2c1f170459a5731074d1a684c4d43d5b6efcfb4a Mon Sep 17 00:00:00 2001 From: Szilveszter Juhos Date: Wed, 31 Oct 2018 19:45:53 +0100 Subject: [PATCH 8/8] nasty hack to accommodate VEP version for GRCh38 --- annotate.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/annotate.nf b/annotate.nf index f1e6ebd2f2..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 92 \ + --cache_version ${cache_version} \ --database \ --everything \ --filter_common \