diff --git a/CHANGELOG.md b/CHANGELOG.md index eb7262e651..417b6da2ac 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/containers/vep/Dockerfile b/containers/vep/Dockerfile index 75a8497b3b..ee617f9f98 100644 --- a/containers/vep/Dockerfile +++ b/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 \ diff --git a/containers/vep/environment.yml b/containers/vep/environment.yml index d426f78a68..831df73abd 100644 --- a/containers/vep/environment.yml +++ b/containers/vep/environment.yml @@ -7,5 +7,5 @@ channels: - defaults dependencies: - - ensembl-vep=95.2 + - ensembl-vep=98.2 - genesplicer=1.0 diff --git a/docs/containers.md b/docs/containers.md index 87b7f05b87..b86347db11 100644 --- a/docs/containers.md +++ b/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 diff --git a/environment.yml b/environment.yml index 94ca2d5a19..797ba0c1ae 100644 --- a/environment.yml +++ b/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 \ No newline at end of file