Merge pull request #158 from MaxUlysse/snpEff

More polishing before 2.6 release

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`
 

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 {

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
 

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 
+  - conda-forge::pigz=2.3.4 
+  - conda-forge::r-ggplot2=3.3.0