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Merge pull request #2063 from Clinical-Genomics/release/12.0.3
Release/12.0.3
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‎CHANGELOG.md

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All notable changes to this project will be documented in this file.
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This project adheres to [Semantic Versioning](http://semver.org/).
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## [12.0.3]
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- Updates genmod to version 3.8.2 to introduce normalized rankscore, [#2055](https://github.com/Clinical-Genomics/MIP/issues/2055)
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### Tools
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- Genmod 3.7.3 -> 3.8.2
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### Databases
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clinvar: 20230508 -> 20231203
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loqusdb snapshot: 20230512 -> 20231204
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## [12.0.2]
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- Fixes the relatedness check in mip qccollect

‎containers/genmod/Dockerfile

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################## BASE IMAGE ######################
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FROM clinicalgenomics/mip_base:2.1
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FROM condaforge/mambaforge:23.1.0-4
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################## METADATA ######################
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LABEL base_image="clinicalgenomics/mip_base:2.1"
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LABEL version="1"
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LABEL base_image="condaforge/mambaforge:23.1.0-4"
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LABEL version="2"
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LABEL software="genmod"
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LABEL software.version="3.7.3"
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LABEL software.version="3.8.1"
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LABEL extra.binaries="genmod"
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LABEL maintainer="Clinical-Genomics/MIP"
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RUN conda install pip python=3.7
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## Clean up after conda
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RUN /opt/conda/bin/conda clean -tipsy
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RUN pip install --no-cache-dir genmod==3.7.3
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WORKDIR /data/
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RUN mamba install -y -c conda-forge -c bioconda pip pytabix python=3.8 && \
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/opt/conda/bin/conda clean -ya && \
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pip install --no-cache-dir genmod==3.8.2

‎documentation/Setup.md

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- [Deepvariant] (version: 1.4.0)
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- [Delly] (version 0.8.7)
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- [GATK] (version: 3.8.1 and 4.2.2.0)
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- [GENMOD] (version: 3.7.3)
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- [GENMOD] (version: 3.8.2)
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- [Gffcompare] (version: 0.11.2)
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- [Glnexus] (version: v1.4.1)
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- [Htslib] (version: 1.13)

‎lib/MIP/Constants.pm

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);
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## Set MIP version
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Readonly our $MIP_VERSION => q{12.0.2};
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Readonly our $MIP_VERSION => q{12.0.3};
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## Cli
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Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160;

‎templates/mip_download_rd_dna_config_-1.0-.yaml

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chromograph_cytoband:
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- v1.0
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clinvar:
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- 20220829
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- 20231203
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- 20230508
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dbnsfp:
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- 3.5a
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- gold_standard_indels
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rank_model:
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- v0.2
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- v1.34
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- v1.35
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- v1.36
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reduced_penetrance:
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- 2017
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scout_exons:
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- v1.4
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svrank_model:
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- v0.1
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- v1.9
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- v1.10
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- v1.11
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vcf2cytosure_blacklist_regions:
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- 1.0
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- 200520
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vcfanno_config:
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- v0.2
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- v1.18
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- v1.19
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- v1.20
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vcfanno_functions:
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- v1.0
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reference_feature:
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/
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clinvar:
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grch37:
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20220829:
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file: clinvar_20220829.vcf.gz
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file_check: clinvar_20220829.vcf.gz.md5
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file_index: clinvar_20220829.vcf.gz.tbi
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outfile: grch37_clinvar_-20220829-.vcf.gz
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outfile_check: grch37_clinvar_-20220829-.vcf.gz.md5
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outfile_index: grch37_clinvar_-20220829-.vcf.gz.tbi
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outfile_check_method: md5sum
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url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
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20230508:
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file: clinvar_20230508.vcf.gz
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file_check: clinvar_20230508.vcf.gz.md5
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outfile_index: grch37_clinvar_-20230508-.vcf.gz.tbi
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outfile_check_method: md5sum
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url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
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grch38:
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20220829:
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file: clinvar_20220829.vcf.gz
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file_check: clinvar_20220829.vcf.gz.md5
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file_index: clinvar_20220829.vcf.gz.tbi
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outfile: grch38_clinvar_-20220829-.vcf.gz
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outfile_check: grch38_clinvar_-20220829-.vcf.gz.md5
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outfile_index: grch38_clinvar_-20220829-.vcf.gz.tbi
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20231203:
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file: clinvar_20231203.vcf.gz
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file_check: clinvar_20231203.vcf.gz.md5
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file_index: clinvar_20231203.vcf.gz.tbi
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outfile: grch37_clinvar_-20231203-.vcf.gz
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outfile_check: grch37_clinvar_-20231203-.vcf.gz.md5
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outfile_index: grch37_clinvar_-20231203-.vcf.gz.tbi
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outfile_check_method: md5sum
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url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
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url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
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grch38:
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file: clinvar_20230508.vcf.gz
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file_check: clinvar_20230508.vcf.gz.md5
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outfile_index: grch38_clinvar_-20230508-.vcf.gz.tbi
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url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
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20231203:
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file: clinvar_20231203.vcf.gz
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file_check: clinvar_20231203.vcf.gz.md5
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file_index: clinvar_20231203.vcf.gz.tbi
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outfile: grch38_clinvar_-20231203-.vcf.gz
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outfile_check: grch38_clinvar_-20231203-.vcf.gz.md5
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outfile_index: grch38_clinvar_-20231203-.vcf.gz.tbi
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outfile_check_method: md5sum
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url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
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dbnsfp:
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grch37:
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url_prefix: https://storage.googleapis.com/genomics-public-data/resources/broad/hg38/v0/
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rank_model:
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grch37:
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file: rank_model_-v1.34-.ini
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file_check: rank_model_-v1.34-.ini.md5
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outfile: rank_model_-v1.34-.ini
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outfile_check: rank_model_-v1.34-.ini.md5
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outfile_check_method: md5sum
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
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v1.35:
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file: rank_model_-v1.35-.ini
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file_check: rank_model_-v1.35-.ini.md5
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outfile: rank_model_-v1.35-.ini
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outfile_check: rank_model_-v1.35-.ini.md5
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outfile_check_method: md5sum
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
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v1.36:
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file: rank_model_-v1.36-.ini
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file_check: rank_model_-v1.36-.ini.md5
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outfile: rank_model_-v1.36-.ini
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outfile_check: rank_model_-v1.36-.ini.md5
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outfile_check_method: md5sum
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
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outfile_check: svrank_model_-v1.10-.ini.md5
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
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v1.11:
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file: svrank_model_-v1.11-.ini
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file_check: svrank_model_-v1.11-.ini.md5
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outfile: svrank_model_-v1.11-.ini
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outfile_check: svrank_model_-v1.11-.ini.md5
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outfile_check_method: md5sum
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/
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outfile_check: grch37_vcfanno_config_-v1.19-.toml.md5
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
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v1.20:
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file: grch37_vcfanno_config_-v1.20-.toml
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file_check: grch37_vcfanno_config_-v1.20-.toml.md5
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outfile: grch37_vcfanno_config_-v1.20-.toml
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outfile_check: grch37_vcfanno_config_-v1.20-.toml.md5
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outfile_check_method: md5sum
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url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
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‎templates/mip_install_config.yaml

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genmod:
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uri: docker.io/clinicalgenomics/genmod:3.7.3
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uri: docker.io/clinicalgenomics/genmod:3.8.2
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gens_preproc:
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generate_gens_data.pl:
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mip:
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mip:
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uri: docker.io/clinicalgenomics/mip:v12.0.2
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uri: docker.io/clinicalgenomics/mip:v12.0.3
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multiqc:
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multiqc:

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