diff --git a/CHANGELOG.md b/CHANGELOG.md index a70f294e8..1c996d1b8 100644 --- 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 index 98c60b06e..92251fc5b 100644 --- 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 index edb0e7ac9..b275d7891 100644 --- 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 index 08b2907ca..d7f7e9c5c 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{12.0.2}; +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 index 394a70101..f83418d4c 100644 --- 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: @@ -900,13 +900,6 @@ 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 @@ -914,6 +907,13 @@ reference_feature: 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 index 8508e2d9c..909565828 100644 --- 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: