From aa5ac76fc9c8dd69fc489a4aa57e29d311abe126 Mon Sep 17 00:00:00 2001 From: henrikstranneheim Date: Sat, 19 Sep 2020 09:41:29 +0200 Subject: [PATCH 1/2] feat(reference): Update clinvar to latest in archive - Add to mip download --- CHANGELOG.md | 4 ++ lib/MIP/Constants.pm | 2 +- ...rch37_clinvar_reformated_-20200905-.vcf.gz | 0 ...7_clinvar_reformated_-20200905-.vcf.gz.tbi | 0 templates/grch38_mip_rd_dna_config.yaml | 2 +- .../mip_download_rd_dna_config_-1.0-.yaml | 38 +++++++++---------- templates/mip_dragen_rd_dna_config.yaml | 2 +- templates/mip_rd_dna_config.yaml | 2 +- templates/mip_rd_dna_panel_config.yaml | 2 +- templates/mip_rd_dna_vcf_rerun_config.yaml | 2 +- 10 files changed, 29 insertions(+), 25 deletions(-) create mode 100644 t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz create mode 100644 t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz.tbi diff --git a/CHANGELOG.md b/CHANGELOG.md index bc93dcc20..bfa3e5ccb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -2,6 +2,10 @@ All notable changes to this project will be documented in this file. This project adheres to [Semantic Versioning](http://semver.org/). +## [9.0.2] +**References** +- clinvar_20200728 -> clinvar_20200905 + ## [9.0.1] - Use sample_id in smncopynumber caller instead of file_name_prefix diff --git a/lib/MIP/Constants.pm b/lib/MIP/Constants.pm index 2027873a0..5a599d029 100644 --- a/lib/MIP/Constants.pm +++ b/lib/MIP/Constants.pm @@ -80,7 +80,7 @@ Readonly our %ANALYSIS => ( ); ## Set MIP version -Readonly our $MIP_VERSION => q{v9.0.1}; +Readonly our $MIP_VERSION => q{v9.0.2}; ## Cli Readonly our $MOOSEX_APP_SCEEN_WIDTH => 160; diff --git a/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz b/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz new file mode 100644 index 000000000..e69de29bb diff --git a/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz.tbi b/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz.tbi new file mode 100644 index 000000000..e69de29bb diff --git a/templates/grch38_mip_rd_dna_config.yaml b/templates/grch38_mip_rd_dna_config.yaml index d9a08b45a..e02470897 100755 --- a/templates/grch38_mip_rd_dna_config.yaml +++ b/templates/grch38_mip_rd_dna_config.yaml @@ -88,7 +88,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch38_clinvar_reformated_-20200728-.vcf.gz + path: cluster_constant_path!/references/grch38_clinvar_reformated_-20200905-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-99/cache/ vep_plugins_dir_path: cluster_constant_path!/modules/miniconda/envs/test_env/ensembl-tools-99/cache/Plugins diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml index 4f9accf07..d62a3fc78 100644 --- a/templates/mip_download_rd_dna_config_-1.0-.yaml +++ b/templates/mip_download_rd_dna_config_-1.0-.yaml @@ -26,8 +26,8 @@ reference: chromograph_cytoband: - v1.0 clinvar: - - 20191013 - 20200728 + - 20200905 dbnsfp: - 3.5a - 4.0b2a @@ -311,15 +311,6 @@ reference_feature: url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/region/ clinvar: grch37: - 20191013: - file: clinvar_20191013.vcf.gz - file_check: clinvar_20191013.vcf.gz.md5 - file_index: clinvar_20191013.vcf.gz.tbi - outfile: grch37_clinvar_-20191013-.vcf.gz - outfile_check: grch37_clinvar_-20191013-.vcf.gz.md5 - outfile_index: grch37_clinvar_-20191013-.vcf.gz.tbi - outfile_check_method: md5sum - url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2019/ 20200728: file: clinvar_20200728.vcf.gz file_check: clinvar_20200728.vcf.gz.md5 @@ -329,16 +320,16 @@ reference_feature: outfile_index: grch37_clinvar_-20200728-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2020/ + 20200905: + file: clinvar_20200905.vcf.gz + file_check: clinvar_20200905.vcf.gz.md5 + file_index: clinvar_20200905.vcf.gz.tbi + outfile: grch37_clinvar_-20200905-.vcf.gz + outfile_check: grch37_clinvar_-20200905-.vcf.gz.md5 + outfile_index: grch37_clinvar_-20200905-.vcf.gz.tbi + outfile_check_method: md5sum + url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2020/ grch38: - 20191013: - file: clinvar_20191013.vcf.gz - file_check: clinvar_20191013.vcf.gz.md5 - file_index: clinvar_20191013.vcf.gz.tbi - outfile: grch38_clinvar_-20191013-.vcf.gz - outfile_check: grch38_clinvar_-20191013-.vcf.gz.md5 - outfile_index: grch38_clinvar_-20191013-.vcf.gz.tbi - outfile_check_method: md5sum - url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2019/ 20200728: file: clinvar_20200728.vcf.gz file_check: clinvar_20200728.vcf.gz.md5 @@ -348,6 +339,15 @@ reference_feature: outfile_index: grch38_clinvar_-20200728-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2020/ + 20200905: + file: clinvar_20200905.vcf.gz + file_check: clinvar_20200905.vcf.gz.md5 + file_index: clinvar_20200905.vcf.gz.tbi + outfile: grch38_clinvar_-20200905-.vcf.gz + outfile_check: grch38_clinvar_-20200905-.vcf.gz.md5 + outfile_index: grch38_clinvar_-20200905-.vcf.gz.tbi + outfile_check_method: md5sum + url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/archive_2.0/2020/ dbnsfp: grch37: 3.5a: diff --git a/templates/mip_dragen_rd_dna_config.yaml b/templates/mip_dragen_rd_dna_config.yaml index f5921ac96..ba84185ee 100644 --- a/templates/mip_dragen_rd_dna_config.yaml +++ b/templates/mip_dragen_rd_dna_config.yaml @@ -65,7 +65,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200728-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200905-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-100/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-100/cache/Plugins diff --git a/templates/mip_rd_dna_config.yaml b/templates/mip_rd_dna_config.yaml index abbb5f045..0f38ab16b 100755 --- a/templates/mip_rd_dna_config.yaml +++ b/templates/mip_rd_dna_config.yaml @@ -70,7 +70,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200728-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200905-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-100/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-100/cache/Plugins diff --git a/templates/mip_rd_dna_panel_config.yaml b/templates/mip_rd_dna_panel_config.yaml index dc18e0c5c..f75acc8f0 100755 --- a/templates/mip_rd_dna_panel_config.yaml +++ b/templates/mip_rd_dna_panel_config.yaml @@ -49,7 +49,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200728-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200905-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-100/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-100/cache/Plugins diff --git a/templates/mip_rd_dna_vcf_rerun_config.yaml b/templates/mip_rd_dna_vcf_rerun_config.yaml index e0294327b..83a437a63 100644 --- a/templates/mip_rd_dna_vcf_rerun_config.yaml +++ b/templates/mip_rd_dna_vcf_rerun_config.yaml @@ -62,7 +62,7 @@ vep_custom_annotation: force_report_coordinates: 0 key: CLINVAR file_type: vcf - path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200728-.vcf.gz + path: cluster_constant_path!/references/grch37_clinvar_reformated_-20200905-.vcf.gz vcf_fields: CLNSIG,CLNVID,CLNREVSTAT vep_directory_cache: cluster_constant_path!/references/ensembl-tools-data-100/cache/ vep_plugins_dir_path: cluster_constant_path!/references/ensembl-tools-data-100/cache/Plugins From 1b3ef736a4101663a984e7b47574f2af74b14e9f Mon Sep 17 00:00:00 2001 From: henrikstranneheim Date: Sat, 19 Sep 2020 10:13:14 +0200 Subject: [PATCH 2/2] fix(test): --- templates/mip_download_rd_dna_config_-1.0-.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml index d62a3fc78..3e98f6b92 100644 --- a/templates/mip_download_rd_dna_config_-1.0-.yaml +++ b/templates/mip_download_rd_dna_config_-1.0-.yaml @@ -320,7 +320,7 @@ reference_feature: outfile_index: grch37_clinvar_-20200728-.vcf.gz.tbi outfile_check_method: md5sum url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/archive_2.0/2020/ - 20200905: + 20200905: file: clinvar_20200905.vcf.gz file_check: clinvar_20200905.vcf.gz.md5 file_index: clinvar_20200905.vcf.gz.tbi