Merge pull request #1680 from Clinical-Genomics/feature/clinvar_update_2

feat(reference): Update clinvar to latest in archive
Clinical-Genomics · Sep 22, 2020 · b838183 · b838183
2 parents 2a725e1 + 1b3ef73
commit b838183
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Showing 10 changed files with 29 additions and 25 deletions.
diff --git 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
@@ -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
diff --git a/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz.tbi b/t/data/references/grch37_clinvar_reformated_-20200905-.vcf.gz.tbi
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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