From 4d2f1c8cd9154fb1eaaf4dc93d03c790f04c86fd Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Fri, 13 Mar 2020 17:32:49 +0100 Subject: [PATCH 1/5] fix typo --- conf/base.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/base.config b/conf/base.config index 929158315c..e06ddedad7 100644 --- a/conf/base.config +++ b/conf/base.config @@ -68,7 +68,7 @@ process { errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } withName:Snpeff { - container = {(params.annotation_cache && params.snpEff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"} + container = {(params.annotation_cache && params.snpeff_cache) ? 'nfcore/sarek:dev' : "nfcore/sareksnpeff:dev.${params.genome}"} errorStrategy = {task.exitStatus == 143 ? 'retry' : 'ignore'} } withLabel:VEP { From 212a7b3910314eb674f4b075f64302468deb91f0 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 17 Mar 2020 16:40:51 +0100 Subject: [PATCH 2/5] add ggplot2 --- environment.yml | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index dc427c9861..07a6fce7dc 100644 --- a/environment.yml +++ b/environment.yml @@ -30,4 +30,5 @@ dependencies: - bioconda::trim-galore=0.6.5 - bioconda::vcfanno=0.3.2 - bioconda::vcftools=0.1.16 - - conda-forge::pigz=2.3.4 \ No newline at end of file + - conda-forge::pigz=2.3.4 + - conda-forge::r-ggplot2=3.0.0 \ No newline at end of file From f2f83add5c8a76b32fde554ad4c5f4fef14fecbc Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 17 Mar 2020 16:54:16 +0100 Subject: [PATCH 3/5] update ggplot2 version --- environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/environment.yml b/environment.yml index 07a6fce7dc..84fd4dc8cb 100644 --- a/environment.yml +++ b/environment.yml @@ -31,4 +31,4 @@ dependencies: - bioconda::vcfanno=0.3.2 - bioconda::vcftools=0.1.16 - conda-forge::pigz=2.3.4 - - conda-forge::r-ggplot2=3.0.0 \ No newline at end of file + - conda-forge::r-ggplot2=3.3.0 \ No newline at end of file From 1900b1e42c2022d021447f0e92eca9bb25df5817 Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 17 Mar 2020 16:54:23 +0100 Subject: [PATCH 4/5] update docs --- docs/containers.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/docs/containers.md b/docs/containers.md index 01ba9476f3..2c55b4015c 100644 --- a/docs/containers.md +++ b/docs/containers.md @@ -23,6 +23,7 @@ For annotation, the main container can be used, but the cache has to be download - Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.3.2 - Contain **[GATK4-spark](https://github.com/broadinstitute/gatk)** 4.1.4.1 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0 +- Contain **[ggplot2](https://github.com/tidyverse/ggplot2)** 3.3.0 - Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9 - Contain **[Manta](https://github.com/Illumina/manta)** 1.6.0 - Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.8 @@ -41,14 +42,14 @@ For annotation, the main container can be used, but the cache has to be download - Based on `nfcore/base:1.9` - Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t -- Contains cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1` +- Contains cache for `GRCh37`, `GRCh38`, `GRCm38`, `CanFam3.1` or `WBcel235` ### sarekvep [![sarekvep-docker status](https://img.shields.io/docker/automated/nfcore/sarekvep.svg)](https://hub.docker.com/r/nfcore/sarekvep) - Based on `nfcore/base:1.9` - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0 - Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 99.2 -- Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1` +- Contain cache for `GRCh37`, `GRCh38`, `GRCm38`, `CanFam3.1` or `WBcel235` ## Building your own From b2cf4b718c2ff9b68662335e3883fbab2793a81e Mon Sep 17 00:00:00 2001 From: MaxUlysse Date: Tue, 17 Mar 2020 17:12:37 +0100 Subject: [PATCH 5/5] update CHANGELOG --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d678bf7abb..5e74d9ec10 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a - [#117](https://github.com/nf-core/sarek/pull/117) - Add `Trim Galore` possibilities to Sarek - [#141](https://github.com/nf-core/sarek/pull/141) - Add containers for `WBcel235` - [#150](https://github.com/nf-core/sarek/pull/150), [#151](https://github.com/nf-core/sarek/pull/151), [#154](https://github.com/nf-core/sarek/pull/154) - Add AWS mega test GitHub Actions +- [#158](https://github.com/nf-core/sarek/pull/158) - Added `ggplot2` v `3.3.0` ### `Changed` @@ -40,7 +41,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a - [#141](https://github.com/nf-core/sarek/pull/141) - Update `VEP` databases to `99` - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `75` for `GRCh37` - [#143](https://github.com/nf-core/sarek/pull/143) - Revert `snpEff` cache version to `86` for `GRCh38` -- [#152](https://github.com/nf-core/sarek/pull/152) - Update docs +- [#152](https://github.com/nf-core/sarek/pull/152), [#158](https://github.com/nf-core/sarek/pull/158) - Update docs ### `Fixed` @@ -60,6 +61,7 @@ The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/) a - [#146](https://github.com/nf-core/sarek/pull/146) - Fix `--no_intervals` for `Mutect2` cf [#135](https://github.com/nf-core/sarek/issues/135) - [#156](https://github.com/nf-core/sarek/pull/156) - Fix typos - [#156](https://github.com/nf-core/sarek/pull/156) - Fix issues with `dbsnp` files while using only `Sention` tools +- [#158](https://github.com/nf-core/sarek/pull/158) - Fix typo with `params.snpeff_cache` to decide containers for `snpEff` ### `Deprecated`