From 97bcf162f758e64d1f323bdfd85d80536b31a610 Mon Sep 17 00:00:00 2001
From: jemten <jemten@users.noreply.github.com>
Date: Tue, 6 Sep 2022 11:41:07 +0200
Subject: [PATCH] updates chromograph to version 1.1.5

---
 CHANGELOG.md                      |  7 +++++++
 containers/chromograph/Dockerfile | 10 +++++-----
 documentation/Setup.md            |  2 +-
 lib/MIP/Constants.pm              |  2 +-
 templates/mip_install_config.yaml |  4 ++--
 5 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index bb261f271..44c533841 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -3,6 +3,13 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [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`.
diff --git a/containers/chromograph/Dockerfile b/containers/chromograph/Dockerfile
index b330eacc8..38144e2f9 100644
--- a/containers/chromograph/Dockerfile
+++ b/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/
diff --git a/documentation/Setup.md b/documentation/Setup.md
index d9ca5f6ad..26d9e9856 100644
--- a/documentation/Setup.md
+++ b/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)
diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
index e6e828afe..0dd91c0d8 100644
--- a/lib/MIP/Constants.pm
+++ b/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;
diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
index 84ad16300..1f91f8841 100644
--- a/templates/mip_install_config.yaml
+++ b/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:
@@ -121,7 +121,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v11.0.1
+    uri: docker.io/clinicalgenomics/mip:v11.0.2
   multiqc:
     executable:
       multiqc: