feat: update annonars to 0.24.1 (#55)

varfish-org · Oct 18, 2023 · 7756e91 · 7756e91
1 parent 93d0396
commit 7756e91
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Showing 2 changed files with 5 additions and 5 deletions.
diff --git a/.github/actions/download-clinvar/run.sh b/.github/actions/download-clinvar/run.sh
@@ -12,16 +12,16 @@ df -h
 
 # Download the pre-digested JSONL files
 
-URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("acmg-class-by-freq") )' | grep -v sha256 | jq -r .url)
+URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("acmg-class-by-freq") )' | grep -v sha256 | jq -r .url | sort -V | tail -n 1)
 wget -O $CLINVAR_JSONL_DIR/clinvar-data-acmg-class-by-freq.tar.gz $URL
 
-URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("extract-vars") )' | grep -v sha256 | jq -r .url)
+URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("extract-vars") )' | grep -v sha256 | jq -r .url | sort -V | tail -n 1)
 wget -O $CLINVAR_JSONL_DIR/clinvar-data-extract-vars.tar.gz $URL
 
-URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("gene-variant-report") )' | grep -v sha256 | jq -r .url)
+URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("gene-variant-report") )' | grep -v sha256 | jq -r .url | sort -V | tail -n 1)
 wget -O $CLINVAR_JSONL_DIR/clinvar-data-gene-variant-report.tar.gz $URL
 
-URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("phenotype-links") )' | grep -v sha256 | jq -r .url)
+URL=$(gh release view -R bihealth/clinvar-data-jsonl --json assets -q '.assets[] | select( .name | contains("phenotype-links") )' | grep -v sha256 | jq -r .url | sort -V | tail -n 1)
 wget -O $CLINVAR_JSONL_DIR/clinvar-data-phenotype-links.tar.gz $URL
 
 for f in $CLINVAR_JSONL_DIR/*.tar.gz; do

diff --git a/.github/workflows/-build-artifacts.yml b/.github/workflows/-build-artifacts.yml
@@ -26,7 +26,7 @@ env:
   # Python version
   PYTHON_VERSION: "3.10"
   # annonars package version
-  ANNONARS_VERSION: "0.18.0"
+  ANNONARS_VERSION: "0.24.1"
   # Helper to get unique cache keys
   CACHE_SEED: 0
   # Maximal number of RCVs to process (0 = no limit).