Merge 1371dda into 8a26aeb

CHANGELOG.md

@@ -38,6 +38,14 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 - loqusdb dump: 20210921 -> 20220810
 - vcf2cytosure blacklist: 200520
 
+## [11.0.2]
+
+Updates chromograph
+
+### Tools
+
+chromograph 1.1.4 -> 1.1.5
+
 ## [11.0.1]
 
 - When running Deepvariant, set tmpdir to analysis folder and use `intermediate_results_dir`.

containers/chromograph/Dockerfile

@@ -5,9 +5,9 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="12"
+LABEL version="13"
 LABEL software="chromograph"
-LABEL software.version="1.1.4"
+LABEL software.version="1.1.5"
 LABEL extra.binaries="chromograph"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -22,9 +22,9 @@ RUN conda install pip python=3.9 matplotlib && \
 
 WORKDIR /opt/conda/share
 
-RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.4.zip && \
-    unzip v1.1.4.zip && \
-    cd chromograph-1.1.4 && \
+RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.5.zip && \
+    unzip v1.1.5.zip && \
+    cd chromograph-1.1.5 && \
     python -m pip install --no-cache-dir .
 
 WORKDIR /data/

documentation/Setup.md

@@ -43,7 +43,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [BWAKit] (version: 0.7.17)
 - [CADD] (version: 1.6)
 - [Chanjo] (version: 4.6.0)
-- [Chromograph] (version: 1.1.4)
+- [Chromograph] (version: 1.1.5)
 - [Cnvnator] (version: 0.4.1)
 - [Cyrius] (version: v1.1.1)
 - [Expansionhunter] (version 4.0.2)

lib/MIP/Constants.pm

@@ -81,7 +81,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{11.0.1};
+Readonly our $MIP_VERSION => q{11.0.2};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

templates/mip_install_config.yaml

@@ -48,7 +48,7 @@ container:
   chromograph:
     executable:
       chromograph:
-    uri: docker.io/clinicalgenomics/chromograph:1.1.4
+    uri: docker.io/clinicalgenomics/chromograph:1.1.5
   cyrius:
     executable:
       star_caller.py: