Merge d3ae3eb into 193fbaa

CHANGELOG.md

@@ -6,10 +6,17 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 ## [Develop]
 
 - HmtNote: annotate mitochondrial variants in VCF file
+- Updating to latest and greatest versions
 
 ### Tools
 
 HmtNote: 0.7.2
+htslib: 1.10.2 -> 1.13
+cyrius v1.1 -> v1.1.1
+gatk 4.2.0.0 -> 4.2.2.0
+glnexus v1.3.1 -> v1.4.1
+multiqc 1.10.1 -> v1.11
+vep release_103.1 -> release_104.3
 
 ### References
 

containers/cyrius/Dockerfile

@@ -4,28 +4,28 @@ FROM clinicalgenomics/mip_base:2.1
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="2"
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="3"
 LABEL software="Cyrius"
-LABEL software.version="v1.1"
+LABEL software.version="v1.1.1"
 LABEL extra.binaries="star_caller.py"
 LABEL maintainer="Clinical-Genomics/MIP"
 
 WORKDIR /opt/conda/share
 
 ## Pysam errors when pip installing
-RUN conda install pysam=0.16.0 && \
+RUN conda install pysam=0.16.0.1 && \
     conda clean -ya
 
 ## Download and extract
-RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.zip && \
-    unzip v1.1.zip && \
-    rm v1.1.zip
+RUN wget --no-verbose --no-check-certificate https://github.com/Illumina/Cyrius/archive/v1.1.1.zip && \
+    unzip v1.1.1.zip && \
+    rm v1.1.1.zip
 
 ## Move to directory and install requirements
-RUN cd Cyrius-1.1 && \
-   python -m pip install --no-cache-dir -r requirements.txt
+RUN cd Cyrius-1.1.1 && \
+    python -m pip install --no-cache-dir -r requirements.txt
 
-RUN chmod a+x /opt/conda/share/Cyrius-1.1/star_caller.py
+RUN chmod a+x /opt/conda/share/Cyrius-1.1.1/star_caller.py
 
-ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1
+ENV PATH ${PATH}:/opt/conda/share/Cyrius-1.1.1

containers/htslib/Dockerfile

@@ -1,17 +1,17 @@
 ################## BASE IMAGE ######################
 
-FROM clinicalgenomics/mip_base:2.0
+FROM clinicalgenomics/mip_base:2.1
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip_base:2.0"
-LABEL version="5"
+LABEL base-image="clinicalgenomics/mip_base:2.1"
+LABEL version="6"
 LABEL software="htslib"
-LABEL software.version="1.10.2"
+LABEL software.version="1.13"
 LABEL extra.binaries="bcftools, bgzip, samtools, tabix"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install bcftools=1.10.2=hd2cd319_0 htslib=1.10.2=h78d89cc_0 samtools=1.10=h9402c20_2
+RUN conda install bcftools=1.13=h3a49de5_0 htslib=1.13=h9093b5e_0 samtools=1.13=h8c37831_0
 
 ## Clean up after conda
 RUN /opt/conda/bin/conda clean -ya

documentation/Setup.md

@@ -45,19 +45,19 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Chanjo] (version: 4.6.0)
 - [Chromograph] (version: 1.1)
 - [Cnvnator] (version: 0.4.1)
-- [Cyrius] (version: v1.1)
+- [Cyrius] (version: v1.1.1)
 - [Expansionhunter] (version 4.0.2)
 - [FastQC] (version: 0.11.9)
 - [Deepvariant] (version: 1.1.0)
 - [Delly] (version 0.8.7)
-- [GATK] (version: 3.8.1 and 4.2.0.0)
+- [GATK] (version: 3.8.1 and 4.2.2.0)
 - [GENMOD] (version: 3.7.3)
 - [Gffcompare] (version: 0.11.2)
-- [Glnexus] (version: 1.3.1)
-- [Htslib] (version: 1.10.2)
+- [Glnexus] (version: v1.4.1)
+- [Htslib] (version: 1.13)
 - [Manta] (version: 1.6.0)
 - [Megafusion] (version: 66a3a80)
-- [MultiQC] (version: 1.10.1)
+- [MultiQC] (version: v1.11)
 - [Pdfmerger] (version: 1.0)
 - [Peddy] (version: 0.4.3)
 - [PicardTools] (version: 2.25.0)
@@ -81,7 +81,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Varg] (version: 1.2.0)
 - [Vcf2cytosure] (version: 0.5.1)
 - [Vcfanno] (version: 0.3.2)
-- [VEP] (version: 103.1) with plugin "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI"
+- [VEP] (version: 104.3) with plugin "dbNSFP", "DisGeNET", "ExACpLI", "MaxEntScan, LoFtool", "SpliceAI"
 
 The version number after the software name are tested for compatibility with MIP.
 

templates/mip_install_config.yaml

@@ -52,7 +52,7 @@ container:
   cyrius:
     executable:
       star_caller.py:
-    uri: docker.io/clinicalgenomics/cyrius:v1.1
+    uri: docker.io/clinicalgenomics/cyrius:v1.1.1
   deepvariant:
     executable:
       run_deepvariant: /opt/deepvariant/bin/run_deepvariant
@@ -85,7 +85,7 @@ container:
   gatk4:
     executable:
       gatk:
-    uri: docker.io/broadinstitute/gatk:4.2.0.0
+    uri: docker.io/broadinstitute/gatk:4.2.2.0
   genmod:
     executable:
       genmod:
@@ -97,7 +97,7 @@ container:
   glnexus:
     executable:
       glnexus_cli:
-    uri: quay.io/mlin/glnexus:v1.3.1
+    uri: ghcr.io/dnanexus-rnd/glnexus:v1.4.1
   hmtnote:
     executable:
       hmtnote:
@@ -108,7 +108,7 @@ container:
       bgzip:
       samtools:
       tabix:
-    uri: docker.io/clinicalgenomics/htslib:1.10.2
+    uri: docker.io/clinicalgenomics/htslib:1.13
   manta:
     executable:
       configManta.py:
@@ -125,7 +125,7 @@ container:
   multiqc:
     executable:
       multiqc:
-    uri: docker.io/ewels/multiqc:1.10.1
+    uri: docker.io/ewels/multiqc:v1.11
   perl:
     executable:
       perl:
@@ -248,9 +248,8 @@ container:
   vep:
     executable:
       vep:
-    uri: docker.io/ensemblorg/ensembl-vep:release_103.1
+    uri: docker.io/ensemblorg/ensembl-vep:release_104.3
   vcf2cytosure:
     executable:
       vcf2cytosure:
     uri: docker.io/jemten/vcf2cytosure:0.5.1
-