Merge pull request #41 from MaxUlysse/environmentUpdate

CHANGELOG.md

@@ -7,6 +7,17 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## dev
 
+### `Added`
+
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `control-freec` from `11.4` to `11.5`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `ensembl-vep` from `95.2` to `98.2`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `freebayes` from `1.2.0` to `1.3.1`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `gatk4` from `4.1.2.0` to `4.1.4.0`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `manta` from `1.5.0` to `1.6.0`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `qualimap` from `2.2.2b` to `2.2.2c`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `tiddit` from `2.7.1` to `2.8.0`
+- [#41](https://github.com/nf-core/sarek/pull/41) - Update `vcfanno` from `0.3.1` to `0.3.2`
+
 ### `Fixed`
 
 - [#40](https://github.com/nf-core/sarek/pull/40) - Fix issue with `publishDirMode` within `test` profile

containers/vep/Dockerfile

@@ -12,7 +12,7 @@ ENV PATH /opt/conda/envs/sarek-vep-2.5.1dev/bin:$PATH
 # Setup default ARG variables
 ARG GENOME=GRCh38
 ARG SPECIES=homo_sapiens
-ARG VEP_VERSION=95
+ARG VEP_VERSION=98
 
 # Download Genome
 RUN vep_install \

containers/vep/environment.yml

@@ -7,5 +7,5 @@ channels:
   - defaults
 
 dependencies:
-  - ensembl-vep=95.2
+  - ensembl-vep=98.2
   - genesplicer=1.0

docs/containers.md

@@ -18,22 +18,22 @@ For annotation, the main container can be used, but the cache has to be download
 - Contain **[AlleleCount](https://github.com/cancerit/alleleCount)** 4.0.2
 - Contain **[BCFTools](https://github.com/samtools/bcftools)** 1.9
 - Contain **[BWA](https://github.com/lh3/bwa)** 0.7.17
-- Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.4
+- Contain **[Control-FREEC](https://github.com/BoevaLab/FREEC)** 11.5
 - Contain **[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/)** 0.11.8
-- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.2.0
-- Contain **[GATK4](https://github.com/broadinstitute/gatk)** 4.1.2.0
+- Contain **[FreeBayes](https://github.com/ekg/freebayes)** 1.3.1
+- Contain **[GATK4](https://github.com/broadinstitute/gatk)** 4.1.4.0
 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
 - Contain **[HTSlib](https://github.com/samtools/htslib)** 1.9
-- Contain **[Manta](https://github.com/Illumina/manta)** 1.5.0
+- Contain **[Manta](https://github.com/Illumina/manta)** 1.6.0
 - Contain **[MultiQC](https://github.com/ewels/MultiQC/)** 1.7
-- Contain **[Qualimap](http://qualimap.bioinfo.cipf.es)** 2.2.2b
+- Contain **[Qualimap](http://qualimap.bioinfo.cipf.es)** 2.2.2c
 - Contain **[samtools](https://github.com/samtools/samtools)** 1.9
 - Contain **[snpEff](http://snpeff.sourceforge.net/)** 4.3.1t
 - Contain **[Strelka2](https://github.com/Illumina/strelka)** 2.9.10
-- Contain **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.7.1
-- Contain **[VCFanno](https://github.com/brentp/vcfanno)** 0.3.1
+- Contain **[TIDDIT](https://github.com/SciLifeLab/TIDDIT)** 2.8.0
+- Contain **[VCFanno](https://github.com/brentp/vcfanno)** 0.3.2
 - Contain **[VCFtools](https://vcftools.github.io/index.html)** 0.1.16
-- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2
+- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 98.2
 
 ### sareksnpeff [![sareksnpeff-docker status](https://img.shields.io/docker/automated/nfcore/sareksnpeff.svg)](https://hub.docker.com/r/nfcore/sareksnpeff)
 
@@ -45,7 +45,7 @@ For annotation, the main container can be used, but the cache has to be download
 
 - Based on `nfcore/base:latest`
 - Contain **[GeneSplicer](https://ccb.jhu.edu/software/genesplicer/)** 1.0
-- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 95.2
+- Contain **[VEP](https://github.com/Ensembl/ensembl-vep)** 98.2
 - Contain cache for `GRCh37`, `GRCh38`, `GRCm38` or `CanFam3.1`
 
 ## Using helper script

environment.yml

@@ -10,19 +10,19 @@ dependencies:
   - bcftools=1.9
   - bwa=0.7.17
   - cancerit-allelecount=4.0.2
-  - control-freec=11.4
-  - ensembl-vep=95.2
+  - control-freec=11.5
+  - ensembl-vep=98.2
   - fastqc=0.11.8
-  - freebayes=1.2.0
-  - gatk4=4.1.2.0
+  - freebayes=1.3.1
+  - gatk4=4.1.4.0
   - genesplicer=1.0
   - htslib=1.9
-  - manta=1.5.0
+  - manta=1.6.0
   - multiqc=1.7
-  - qualimap=2.2.2b
+  - qualimap=2.2.2c
   - samtools=1.9
   - snpeff=4.3.1t
   - strelka=2.9.10
-  - tiddit=2.7.1
-  - vcfanno=0.3.1
+  - tiddit=2.8.0
+  - vcfanno=0.3.2
   - vcftools=0.1.16