From efa4fe04c6ed86e69851d7bf3685547c08922ede Mon Sep 17 00:00:00 2001 From: jemten Date: Wed, 21 Feb 2024 10:59:14 +0100 Subject: [PATCH 1/3] updating to mip v12.1.0 --- CHANGELOG.md | 2 +- lib/MIP/Constants.pm | 2 +- templates/mip_install_config.yaml | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 0b6f79cad..87ccc785a 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm index d7f7e9c5c..93b0bc2dd 100644 --- 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{12.0.3}; +Readonly our $MIP_VERSION => q{12.1.0}; ## Cli Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160; diff --git a/templates/mip_install_config.yaml b/templates/mip_install_config.yaml index 84f811c9a..20c723f33 100644 --- a/templates/mip_install_config.yaml +++ b/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: From 1eda07fd542e32045ba19ffc7ef602e768232c5e Mon Sep 17 00:00:00 2001 From: jemten Date: Wed, 21 Feb 2024 11:35:24 +0100 Subject: [PATCH 2/3] adding new rankmodel to download --- templates/mip_download_rd_dna_config_-1.0-.yaml | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml index 1bfae80f2..bb1337bd3 100644 --- a/templates/mip_download_rd_dna_config_-1.0-.yaml +++ b/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: @@ -900,13 +900,6 @@ 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 @@ -914,6 +907,13 @@ reference_feature: 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 From 1681e6c9f0aa2a11156eb3c2e414d12cdbb057c6 Mon Sep 17 00:00:00 2001 From: Anders Jemt Date: Fri, 23 Feb 2024 09:34:14 +0100 Subject: [PATCH 3/3] fixing indentation --- lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm b/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm index 730c4600b..7662fdf14 100644 --- a/lib/MIP/Recipes/Pipeline/Analyse_rd_dna.pm +++ b/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,