Merge pull request #2067 from Clinical-Genomics/update_clinvar_loqusdb

loqus and clinvar update

CHANGELOG.md

@@ -11,6 +11,11 @@ This project adheres to [Semantic Versioning](http://semver.org/).
 
 - Fastp: 0.23.4
 
+### Databases
+
+clinvar: 20231203 -> 20240215
+loqusdb snapshot: 20231204 -> 20240220
+
 ## [12.0.3]
 
 - Updates genmod to version 3.8.2 to introduce normalized rankscore, [#2055](https://github.com/Clinical-Genomics/MIP/issues/2055)

templates/mip_download_rd_dna_config_-1.0-.yaml

@@ -27,7 +27,7 @@ reference:
  - v1.0
  clinvar:
  - 20231203
- - 20230508
+ - 20240215
  dbnsfp:
  - 3.5a
  - 4.1a
@@ -131,8 +131,8 @@ reference:
  - 200520
  vcfanno_config:
  - v0.2
- - v1.19
  - v1.20
+ - v1.21
  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:
- 20230508:
- file: clinvar_20230508.vcf.gz
- file_check: clinvar_20230508.vcf.gz.md5
- file_index: clinvar_20230508.vcf.gz.tbi
- outfile: grch37_clinvar_-20230508-.vcf.gz
- outfile_check: grch37_clinvar_-20230508-.vcf.gz.md5
- 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/
  20231203:
  file: clinvar_20231203.vcf.gz
  file_check: clinvar_20231203.vcf.gz.md5
@@ -341,16 +332,16 @@ reference_feature:
  outfile_index: grch37_clinvar_-20231203-.vcf.gz.tbi
  outfile_check_method: md5sum
  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
- file_index: clinvar_20230508.vcf.gz.tbi
- outfile: grch38_clinvar_-20230508-.vcf.gz
- outfile_check: grch38_clinvar_-20230508-.vcf.gz.md5
- outfile_index: grch38_clinvar_-20230508-.vcf.gz.tbi
+ 20240215:
+ file: clinvar_20240215.vcf.gz
+ file_check: clinvar_20240215.vcf.gz.md5
+ file_index: clinvar_20240215.vcf.gz.tbi
+ outfile: grch37_clinvar_-20240215-.vcf.gz
+ outfile_check: grch37_clinvar_-20240215-.vcf.gz.md5
+ outfile_index: grch37_clinvar_-20240215-.vcf.gz.tbi
  outfile_check_method: md5sum
- url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
+ url_prefix: ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh37/weekly/
+ grch38:
  20231203:
  file: clinvar_20231203.vcf.gz
  file_check: clinvar_20231203.vcf.gz.md5
@@ -360,6 +351,15 @@ reference_feature:
  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/
+ 20240215:
+ file: clinvar_20240215.vcf.gz
+ file_check: clinvar_20240215.vcf.gz.md5
+ file_index: clinvar_20240215.vcf.gz.tbi
+ outfile: grch38_clinvar_-20240215-.vcf.gz
+ outfile_check: grch38_clinvar_-20240215-.vcf.gz.md5
+ outfile_index: grch38_clinvar_-20240215-.vcf.gz.tbi
+ outfile_check_method: md5sum
+ url_prefix: https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/weekly/
  dbnsfp:
  grch37:
  3.5a:
@@ -1017,27 +1017,20 @@ reference_feature:
  url_prefix: https://www.encodeproject.org/files/ENCFF356LFX/@@download/
  vcfanno_config:
  grch37:
- v1.18:
- file: grch37_vcfanno_config_-v1.18-.toml
- file_check: grch37_vcfanno_config_-v1.18-.toml.md5
- outfile: grch37_vcfanno_config_-v1.18-.toml
- outfile_check: grch37_vcfanno_config_-v1.18-.toml.md5
- outfile_check_method: md5sum
- url_prefix: https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/annotation/
- v1.19:
- file: grch37_vcfanno_config_-v1.19-.toml
- file_check: grch37_vcfanno_config_-v1.19-.toml.md5
- outfile: grch37_vcfanno_config_-v1.19-.toml
- 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/
+ v1.21:
+ file: grch37_vcfanno_config_-v1.21-.toml
+ file_check: grch37_vcfanno_config_-v1.21-.toml.md5
+ outfile: grch37_vcfanno_config_-v1.21-.toml
+ outfile_check: grch37_vcfanno_config_-v1.21-.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