Merge pull request #2063 from Clinical-Genomics/release/12.0.3

Release/12.0.3
Clinical-Genomics · Dec 5, 2023 · 9e67ba4 · 9e67ba4
2 parents 443391f + 3538861
commit 9e67ba4
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,19 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
+## [12.0.3]
+
+- Updates genmod to version 3.8.2 to introduce normalized rankscore, [#2055](https://github.com/Clinical-Genomics/MIP/issues/2055)
+
+### Tools
+
+- Genmod 3.7.3 -> 3.8.2
+
+### Databases
+
+clinvar: 20230508 -> 20231203
+loqusdb snapshot: 20230512 -> 20231204
+
 ## [12.0.2]
 
 - Fixes the relatedness check in mip qccollect

diff --git a/containers/genmod/Dockerfile b/containers/genmod/Dockerfile
@@ -1,21 +1,16 @@
 ################## BASE IMAGE ######################
 
-FROM clinicalgenomics/mip_base:2.1
+FROM condaforge/mambaforge:23.1.0-4
 
 ################## METADATA ######################
 
-LABEL base_image="clinicalgenomics/mip_base:2.1"
-LABEL version="1"
+LABEL base_image="condaforge/mambaforge:23.1.0-4"
+LABEL version="2"
 LABEL software="genmod"
-LABEL software.version="3.7.3"
+LABEL software.version="3.8.1"
 LABEL extra.binaries="genmod"
 LABEL maintainer="Clinical-Genomics/MIP"
 
-RUN conda install pip python=3.7
-
-## Clean up after conda
-RUN /opt/conda/bin/conda clean -tipsy
-
-RUN pip install --no-cache-dir genmod==3.7.3
-
-WORKDIR /data/
+RUN mamba install -y -c conda-forge -c bioconda pip pytabix python=3.8 && \
+    /opt/conda/bin/conda clean -ya && \
+    pip install --no-cache-dir genmod==3.8.2
diff --git a/documentation/Setup.md b/documentation/Setup.md
@@ -52,7 +52,7 @@ You can speed up, for instance, the Readonly module by also installing the compa
 - [Deepvariant] (version: 1.4.0)
 - [Delly] (version 0.8.7)
 - [GATK] (version: 3.8.1 and 4.2.2.0)
-- [GENMOD] (version: 3.7.3)
+- [GENMOD] (version: 3.8.2)
 - [Gffcompare] (version: 0.11.2)
 - [Glnexus] (version: v1.4.1)
 - [Htslib] (version: 1.13)

diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm
@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{12.0.2};
+Readonly our $MIP_VERSION => q{12.0.3};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -26,7 +26,7 @@ reference:
   chromograph_cytoband:
     - v1.0
   clinvar:
-    - 20220829
+    - 20231203
     - 20230508
   dbnsfp:
     - 3.5a
@@ -111,8 +111,8 @@ reference:
     - gold_standard_indels
   rank_model:
     - v0.2
-    - v1.34
     - v1.35
+    - v1.36
   reduced_penetrance:
     - 2017
   scout_exons:
@@ -124,15 +124,15 @@ reference:
     - v1.4
   svrank_model:
     - v0.1
-    - v1.9
     - v1.10
+    - v1.11
   vcf2cytosure_blacklist_regions:
     - 1.0
     - 200520
   vcfanno_config:
     - v0.2
-    - v1.18
     - v1.19
+    - v1.20
   vcfanno_functions:
     - v1.0
 reference_feature:
@@ -323,15 +323,6 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
   clinvar:
     grch37:
-      20220829:
-        file: clinvar_20220829.vcf.gz
-        file_check: clinvar_20220829.vcf.gz.md5
-        file_index: clinvar_20220829.vcf.gz.tbi
-        outfile: grch37_clinvar_-20220829-.vcf.gz
-        outfile_check: grch37_clinvar_-20220829-.vcf.gz.md5
-        outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi
-        outfile_check_method: md5sum
-        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
       20230508:
         file: clinvar_20230508.vcf.gz
         file_check: clinvar_20230508.vcf.gz.md5
@@ -341,16 +332,16 @@ reference_feature:
         outfile_index: grch37_clinvar_-20230508-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
-    grch38:
-      20220829:
-        file: clinvar_20220829.vcf.gz
-        file_check: clinvar_20220829.vcf.gz.md5
-        file_index: clinvar_20220829.vcf.gz.tbi
-        outfile: grch38_clinvar_-20220829-.vcf.gz
-        outfile_check: grch38_clinvar_-20220829-.vcf.gz.md5
-        outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi
+      20231203:
+        file: clinvar_20231203.vcf.gz
+        file_check: clinvar_20231203.vcf.gz.md5
+        file_index: clinvar_20231203.vcf.gz.tbi
+        outfile: grch37_clinvar_-20231203-.vcf.gz
+        outfile_check: grch37_clinvar_-20231203-.vcf.gz.md5
+        outfile_index: grch37_clinvar_-20231203-.vcf.gz.tbi
         outfile_check_method: md5sum
-        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
+        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
+    grch38:
       20230508:
         file: clinvar_20230508.vcf.gz
         file_check: clinvar_20230508.vcf.gz.md5
@@ -360,6 +351,15 @@ reference_feature:
         outfile_index: grch38_clinvar_-20230508-.vcf.gz.tbi
         outfile_check_method: md5sum
         url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
+      20231203:
+        file: clinvar_20231203.vcf.gz
+        file_check: clinvar_20231203.vcf.gz.md5
+        file_index: clinvar_20231203.vcf.gz.tbi
+        outfile: grch38_clinvar_-20231203-.vcf.gz
+        outfile_check: grch38_clinvar_-20231203-.vcf.gz.md5
+        outfile_index: grch38_clinvar_-20231203-.vcf.gz.tbi
+        outfile_check_method: md5sum
+        url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
   dbnsfp:
     grch37:
       3.5a:
@@ -900,20 +900,20 @@ reference_feature:
         url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
   rank_model:
     grch37:
-      v1.34:
-        file: rank_model_-v1.34-.ini
-        file_check: rank_model_-v1.34-.ini.md5
-        outfile: rank_model_-v1.34-.ini
-        outfile_check: rank_model_-v1.34-.ini.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
       v1.35:
         file: rank_model_-v1.35-.ini
         file_check: rank_model_-v1.35-.ini.md5
         outfile: rank_model_-v1.35-.ini
         outfile_check: rank_model_-v1.35-.ini.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
+      v1.36:
+        file: rank_model_-v1.36-.ini
+        file_check: rank_model_-v1.36-.ini.md5
+        outfile: rank_model_-v1.36-.ini
+        outfile_check: rank_model_-v1.36-.ini.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
     grch38:
       v0.2:
         file: grch38_rank_model_-v0.2-.ini
@@ -985,6 +985,13 @@ reference_feature:
         outfile_check: svrank_model_-v1.10-.ini.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
+      v1.11:
+        file: svrank_model_-v1.11-.ini
+        file_check: svrank_model_-v1.11-.ini.md5
+        outfile: svrank_model_-v1.11-.ini
+        outfile_check: svrank_model_-v1.11-.ini.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
     grch38:
       v0.1:
         file: grch38_sv_rank_model_-v0.1-.ini
@@ -1024,6 +1031,13 @@ reference_feature:
         outfile_check: grch37_vcfanno_config_-v1.19-.toml.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
+      v1.20:
+        file: grch37_vcfanno_config_-v1.20-.toml
+        file_check: grch37_vcfanno_config_-v1.20-.toml.md5
+        outfile: grch37_vcfanno_config_-v1.20-.toml
+        outfile_check: grch37_vcfanno_config_-v1.20-.toml.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
     grch38:
       v0.2:
         file: grch38_vcfanno_config_-v0.2-.toml

diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml
@@ -89,7 +89,7 @@ container:
   genmod:
     executable:
       genmod:
-    uri: docker.io/clinicalgenomics/genmod:3.7.3
+    uri: docker.io/clinicalgenomics/genmod:3.8.2
   gens_preproc:
     executable:
       generate_gens_data.pl:
@@ -125,7 +125,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:v12.0.2
+    uri: docker.io/clinicalgenomics/mip:v12.0.3
   multiqc:
     executable:
       multiqc: