Merge 3ff3f73 into 054f86f

CHANGELOG.md

@@ -16,13 +16,14 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - Added deepvariant as variant caller and glnexus to merge samples to case vcf
 
 **Tools**
-bcftools: 1.10.2-hd2cd319_0 -> 1.11=h7c999a4_0
+bcftools: 1.10.2-hd2cd319_0 -> 1.11-h7c999a4_0
 chanjo: 4.2.0 -> 4.6
 deepvariant: 1.0.0  
 glnexus: v1.2.7
-htslib: 1.10.2=h78d89cc_0 -> 1.11=hd3b49d5_2
+htslib: 1.10.2-h78d89cc_0 -> 1.11-hd3b49d5_2
 picardtools: 2.23.4 -> 2.25.0
-samtools: 1.10=h9402c20_2 -> 1.11=h6270b1f_0
+sambamba: 0.6.8-h682856c_0 -> 0.8.0-h984e79f_0
+samtools: 1.10-h9402c20_2 -> 1.11-h6270b1f_0
 stranger: 0.7 -> 0.7.1
 tiddit: 2.8.1 -> 2.12.1
 

containers/sambamba/Dockerfile

@@ -5,13 +5,13 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="1"
+LABEL version="2"
 LABEL software="sambamba"
-LABEL software.version="0.6.8"
+LABEL software.version="0.8.0"
 LABEL extra.binaries="sambamba"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install sambamba=0.6.8=h682856c_0 ldc=1.11.0=hb2c9046_0
+RUN conda install sambamba=0.8.0=h984e79f_0
 
 ## Clean up after conda
 RUN /opt/conda/bin/conda clean -tipsy

documentation/Setup.md

@@ -57,7 +57,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [PLINK] (version: 1.90b3x35)
 - [Rhocall] (version: 0.5.1)
 - [rtg-tools] (version: 3.10.1)
-- [Sambamba] (version: 0.6.8)
+- [Sambamba] (version: 0.8.0)
 - [Samtools] (version: 1.11)
 - [SMNCopyNumberCaller] (version: 4b2c1ad)
 - [Stranger] (version: 0.7)

t/data/test_data/miptest_install_config.yaml

@@ -166,7 +166,7 @@ container:
   sambamba:
     executable:
       sambamba:
-    uri: docker.io/clinicalgenomics/sambamba:0.6.8
+    uri: docker.io/clinicalgenomics/sambamba:0.8.0
   smncopynumbercaller:
     executable:
       smn_caller.py: