Merge pull request #2070 from Clinical-Genomics/release/12.1.0

Release branch back into dev

CHANGELOG.md

@@ -3,7 +3,7 @@
 All notable changes to this project will be documented in this file.
 This project adheres to [Semantic Versioning](http://semver.org/).
 
-## [develop]
+## [12.1.0]
 
 - Adds optional trimming of reads with Fastp for the DNA workflow, turned on by default
 - Adds automatic fail in analaysisrunstatus for cases where the peddy detects errors in the pedigree

lib/MIP/Constants.pm

@@ -82,7 +82,7 @@ Readonly our %ANALYSIS => (
 );
 
 ## Set MIP version
-Readonly our $MIP_VERSION => q{12.0.3};
+Readonly our $MIP_VERSION => q{12.1.0};
 
 ## Cli
 Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm

@@ -575,7 +575,7 @@ sub pipeline_analyse_rd_dna {
         delly_reformat              => \&analysis_delly_reformat,
         endvariantannotationblock   => \&analysis_endvariantannotationblock,
         expansionhunter             => \&analysis_expansionhunter,
-        fastp_ar => \&analysis_fastp,
+        fastp_ar                    => \&analysis_fastp,
         fastqc_ar                   => \&analysis_fastqc,
         frequency_filter            => \&analysis_frequency_filter,
         gatk_baserecalibration      => \&analysis_gatk_baserecalibration,

templates/mip_download_rd_dna_config_-1.0-.yaml

@@ -111,8 +111,8 @@ reference:
     - gold_standard_indels
   rank_model:
     - v0.2
-    - v1.35
     - v1.36
+    - v1.37
   reduced_penetrance:
     - 2017
   scout_exons:
@@ -900,20 +900,20 @@ reference_feature:
         url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
   rank_model:
     grch37:
-      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/
+      v1.37:
+        file: rank_model_-v1.37-.ini
+        file_check: rank_model_-v1.37-.ini.md5
+        outfile: rank_model_-v1.37-.ini
+        outfile_check: rank_model_-v1.37-.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

templates/mip_install_config.yaml

@@ -129,7 +129,7 @@ container:
   mip:
     executable:
       mip:
-    uri: docker.io/clinicalgenomics/mip:develop
+    uri: docker.io/clinicalgenomics/mip:v12.1.0
   multiqc:
     executable:
       multiqc: