Merge d86a65f into 40abffc

CHANGELOG.md

@@ -31,6 +31,10 @@ vep release_103.1 -> release_104.3
 - [NEW] gnomad mt: r3.1
 - clinvar: 20210415 -> 20210919
 
+## [10.2.3]
+
+- Updates Chromograph to version 1.1.4
+
 ## [10.2.2]
 
 - Adds missing median coverage metrics to metrics deliverable file
@@ -121,8 +125,8 @@ upd: 0.1 -> 0.1.1
 - Adds possibility to rename arriba fusion report from with sample display name
 - Updates documentation
 
-**Tools**  
-expansionhunter 3.1.2 -> 4.0.2  
+**Tools**
+expansionhunter 3.1.2 -> 4.0.2
 stranger 0.5.5 -> 0.7
 
 ## [9.1.2]
@@ -132,7 +136,7 @@ stranger 0.5.5 -> 0.7
 - Use median coverage instead of expected coverage when evaluating whether expected coverage has been reached or not [#1719](https://github.com/Clinical-Genomics/MIP/issues/1719)
 - Fixes infile error in rtg_vcfeval recipe
 
-**Tools**  
+**Tools**
 chromograph 1.0.0 -> 1.0.1
 
 ## [9.1.1]
@@ -142,7 +146,7 @@ chromograph 1.0.0 -> 1.0.1
 - PNGs generated by chromograph are now uniform in dpi and image size
 - Adds chromograph recipe to generate images of rhocall viz output (regions of autozygosity and fraction of homozygous snps)
 
-**Tools**  
+**Tools**
 chromograph 0.3.3 -> 1.0.0
 
 ## [9.0.6]

containers/chromograph/Dockerfile

@@ -5,9 +5,9 @@ FROM clinicalgenomics/mip_base:2.1
 ################## METADATA ######################
 
 LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="11"
+LABEL version="12"
 LABEL software="chromograph"
-LABEL software.version="1.1"
+LABEL software.version="1.1.4"
 LABEL extra.binaries="chromograph"
 LABEL maintainer="Clinical-Genomics/MIP"
 
@@ -17,20 +17,20 @@ RUN apt-get update --fix-missing && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
 
-RUN conda install pip python=3.7 matplotlib
+RUN conda install pip python=3.9 matplotlib
 
 ## Clean up after conda
 RUN /opt/conda/bin/conda clean -ya
 
 ## Download release
-RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.zip -O /opt/conda/share/chromograph-1.1.zip
+RUN wget --no-verbose https://github.com/mikaell/chromograph/archive/refs/tags/v1.1.4.zip -O /opt/conda/share/chromograph-1.1.4.zip
 
 ## Extract
-RUN unzip -o /opt/conda/share/chromograph-1.1.zip -d /opt/conda/share/ && \
-    rm /opt/conda/share/chromograph-1.1.zip
+RUN unzip -o /opt/conda/share/chromograph-1.1.4.zip -d /opt/conda/share/ && \
+    rm /opt/conda/share/chromograph-1.1.4.zip
 
 ## Move to chromograph directory
-RUN cd /opt/conda/share/chromograph-1.1 && \
+RUN cd /opt/conda/share/chromograph-1.1.4 && \
     python -m pip install --no-cache-dir .
 
 WORKDIR /data/

documentation/Setup.md

@@ -27,7 +27,7 @@ MIP comes with an install application, which will install all necessary programs
 You only need to install the dependencies that are required for the recipes that you want to run. If you have not installed a dependency for a module, MIP will tell you what dependencies you need to install and exit.
 
 **Extra CPANM modules**
-You can speed up, for instance, the Readonly module by also installing the companion module Readonly::XS. No change to the code is required and the Readonly module will call the Readonly::XS module if available.  
+You can speed up, for instance, the Readonly module by also installing the companion module Readonly::XS. No change to the code is required and the Readonly module will call the Readonly::XS module if available.
 
 ### **Programs**
 
@@ -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)
+- [Chromograph] (version: 1.1.4)
 - [Cnvnator] (version: 0.4.1)
 - [Cyrius] (version: v1.1.1)
 - [Expansionhunter] (version 4.0.2)
@@ -155,7 +155,7 @@ Corresponding MIP references:
  - grch37_gatk_merged_reference_samples.txt
 
 ## Gene panel for the clinical test
-MIP will split the variants into two sets (clinical a.k.a "selected" and research) based on gene coordinates and hgnc_id, which is recorded in gene_panels.bed file(s) using MIPs own vcfparser. A template for grch37 can be found in MIPs dir under `templates/gene_panels.bed`.  
+MIP will split the variants into two sets (clinical a.k.a "selected" and research) based on gene coordinates and hgnc_id, which is recorded in gene_panels.bed file(s) using MIPs own vcfparser. A template for grch37 can be found in MIPs dir under `templates/gene_panels.bed`.
 
 #### SpliceAI - Splicing predicition
 Annotations for all possible substitutions, 1 base insertions and 1-4 base deletions. Available from https://basespace.illumina.com/s/5u6ThOblecrh
@@ -191,7 +191,7 @@ Corresponding MIP references:
 [MultiQC]: https://github.com/ewels/MultiQC
 [Pdfmerger]: https://github.com/northwestwitch/pdfmerger
 [Peddy]: https://github.com/brentp/peddy
-[Pedigree file]: ../templates/643594-miptest_pedigree.yaml  
+[Pedigree file]: ../templates/643594-miptest_pedigree.yaml
 [PicardTools]: http://broadinstitute.github.io/picard/
 [PLINK]: https://www.cog-genomics.org/plink2
 [Preseq]: http://smithlabresearch.org/software/preseq/
@@ -212,7 +212,7 @@ Corresponding MIP references:
 [Telomerecat]: https://github.com/cancerit/telomerecat
 [Tiddit]: https://github.com/J35P312/TIDDIT
 [Upd]: https://github.com/bjhall/upd
-[Varg]: https://github.com/Clinical-Genomics/varg  
+[Varg]: https://github.com/Clinical-Genomics/varg
 [Vcf2cytosure]: https://github.com/NBISweden/vcf2cytosure
 [Vcfanno]: https://github.com/brentp/vcfanno
 [VEP]: https://github.com/Ensembl/ensembl-vep

lib/MIP/Constants.pm

@@ -81,7 +81,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{10.2.2};
+Readonly our $MIP_VERSION => q{10.2.3};
 
 ## 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
+    uri: docker.io/clinicalgenomics/chromograph:1.1.4
   cyrius:
     executable:
       star_caller.py:
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v10.2.2
+    uri: docker.io/clinicalgenomics/mip:v10.2.3
   multiqc:
     executable:
       multiqc: