Merge 373232f into 4e052e1

Clinical-Genomics · Jan 9, 2023 · 65ccb8f · 65ccb8f
2 parents 4e052e1 + 373232f
commit 65ccb8f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -5,7 +5,9 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 ## Develop
 
+Updates expansionhunter variant catalog
 Changes sv annotation overlap back to 0.8 (from 0.5) with the new tiddit update
+
 ### Tools
 
 Tiddit 3.3.2 -> 3.4.0

diff --git a/definitions/rd_dna_parameters.yaml b/definitions/rd_dna_parameters.yaml
@@ -866,7 +866,7 @@ expansionhunter_variant_catalog_file_path:
   associated_recipe:
     - expansionhunter
   data_type: SCALAR
-  default: grch37_expansionhunter_variant_catalog_-4.0.2-.json
+  default: grch37_expansionhunter_variant_catalog_-5.0.0-.json
   exists_check: file
   is_reference: 1
   reference: reference_dir

diff --git a/...ansionhunter_variant_catalog_-4.0.2-.json → ...ansionhunter_variant_catalog_-5.0.0-.json b/...ansionhunter_variant_catalog_-4.0.2-.json → ...ansionhunter_variant_catalog_-5.0.0-.json
diff --git a/templates/mip_download_rd_dna_config_-1.0-.yaml b/templates/mip_download_rd_dna_config_-1.0-.yaml
@@ -41,9 +41,8 @@ reference:
     - 20150915
     - 20200310
   expansionhunter:
-    - 3.0.1
-    - 3.1.2
     - 4.0.2
+    - 5.0.0
   gatk_mitochondrial_ref:
     - v0_m_amb
     - v0_m_ann
@@ -445,49 +444,35 @@ reference_feature:
         url_prefix: https://raw.githubusercontent.com/dellytools/delly/master/excludeTemplates/
   expansionhunter:
     grch37:
-      3.0.1:
-        file: variant_catalog_grch37.json
-        file_check: variant_catalog_grch37.json.md5
-        outfile: grch37_expansionhunter_variant_catalog_-3.0.1-.json
-        outfile_check: grch37_expansionhunter_variant_catalog_-3.0.1-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.0.1/
-      3.1.2:
-        file: variant_catalog_grch37.json
-        file_check: variant_catalog_grch37.json.md5
-        outfile: grch37_expansionhunter_variant_catalog_-3.1.2-.json
-        outfile_check: grch37_expansionhunter_variant_catalog_-3.1.2-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.1.2/
       4.0.2:
         file: variant_catalog_grch37.json
         file_check: variant_catalog_grch37.json.md5
         outfile: grch37_expansionhunter_variant_catalog_-4.0.2-.json
         outfile_check: grch37_expansionhunter_variant_catalog_-4.0.2-.json.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
-    grch38:
-      3.0.1:
-        file: variant_catalog_grch38.json
-        file_check: variant_catalog_grch38.json.md5
-        outfile: grch38_expansionhunter_variant_catalog_-3.0.1-.json
-        outfile_check: grch38_expansionhunter_variant_catalog_-3.0.1-.json.md5
-        outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.0.1/
-      3.1.2:
-        file: variant_catalog_hg38.json
-        file_check: variant_catalog_hg38.json.md5
-        outfile: grch38_expansionhunter_variant_catalog_-3.1.2-.json
-        outfile_check: grch38_expansionhunter_variant_catalog_-3.1.2-.json.md5
+      5.0.0:
+        file: variant_catalog_grch37.json
+        file_check: variant_catalog_grch37.json.md5
+        outfile: grch37_expansionhunter_variant_catalog_-5.0.0-.json
+        outfile_check: grch37_expansionhunter_variant_catalog_-5.0.0-.json.md5
         outfile_check_method: md5sum
-        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v3.1.2/
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
+    grch38:
       4.0.2:
         file: variant_catalog_hg38.json
         file_check: variant_catalog_hg38.json.md5
         outfile: grch38_expansionhunter_variant_catalog_-4.0.2-.json
         outfile_check: grch38_expansionhunter_variant_catalog_-4.0.2-.json.md5
         outfile_check_method: md5sum
         url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v4.0.2/
+      5.0.0:
+        file: variant_catalog_hg38.json
+        file_check: variant_catalog_hg38.json.md5
+        outfile: grch38_expansionhunter_variant_catalog_-5.0.0-.json
+        outfile_check: grch38_expansionhunter_variant_catalog_-5.0.0-.json.md5
+        outfile_check_method: md5sum
+        url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/disease_loci/ExpansionHunter-v5.0.0/
   gatk_mitochondrial_ref:
     grch38:
       v0_m_amb: