diff --git a/.github/actions/acmg-class-by-freq/action.yml b/.github/actions/acmg-class-by-freq/action.yml index de88cc8..9bc6106 100644 --- a/.github/actions/acmg-class-by-freq/action.yml +++ b/.github/actions/acmg-class-by-freq/action.yml @@ -25,7 +25,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/acmg-class-by-freq - key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output lookup-only: true - name: Create requirements.txt @@ -50,7 +50,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/acmg-class-by-freq - key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: acmg-class-by-freq-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output - name: Retrieve cached ClinVar JSONL file if: | @@ -58,7 +58,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output fail-on-cache-miss: true - name: Run the ACMG class by freq. generation diff --git a/.github/actions/convert-clinvar/action.yml b/.github/actions/convert-clinvar/action.yml index 082df6e..af94121 100644 --- a/.github/actions/convert-clinvar/action.yml +++ b/.github/actions/convert-clinvar/action.yml @@ -25,7 +25,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output lookup-only: true - name: Create requirements.txt @@ -50,7 +50,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output - name: Retrieve cached ClinVar file if: | diff --git a/.github/actions/convert-clinvar/run.sh b/.github/actions/convert-clinvar/run.sh index b3a99dc..d8592b3 100644 --- a/.github/actions/convert-clinvar/run.sh +++ b/.github/actions/convert-clinvar/run.sh @@ -11,8 +11,8 @@ df -h clinvar-this data xml-to-jsonl \ ${CLINVAR_DIR}/ClinVarFullRelease_00-latest_weekly.xml.gz \ ${OUTPUT_DIR}/convert-clinvar/clinvar-full-release.jsonl.gz \ - $(if [[ "$MAX_RCVS" != "" ]] && [[ "$MAX_RCVS" != "0" ]]; then \ - echo --max-records $MAX_RCVS; + $(if [[ "$MAX_RECORDS" != "" ]] && [[ "$MAX_RECORDS" != "0" ]]; then \ + echo --max-records $MAX_RECORDS; fi) diff --git a/.github/actions/download-clinvar/run.sh b/.github/actions/download-clinvar/run.sh index afa565a..9bcb784 100644 --- a/.github/actions/download-clinvar/run.sh +++ b/.github/actions/download-clinvar/run.sh @@ -12,7 +12,7 @@ df -h # Check that the release name corresponds to the date of the current weekly release. -curl https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/RCV_xml_old_format/weekly_release/ \ +curl https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/weekly_release/ \ > /tmp/lst.html grep 'latest_weekly.xml.gz"' /tmp/lst.html \ @@ -32,6 +32,6 @@ fi # Actually download the file wget -O $CLINVAR_DIR/ClinVarFullRelease_00-latest_weekly.xml.gz \ - https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/RCV_xml_old_format/weekly_release/ClinVarFullRelease_00-latest_weekly.xml.gz + https://ftp.ncbi.nlm.nih.gov/pub/clinvar/xml/weekly_release/ClinVarVCVRelease_00-latest_weekly.xml.gz df -h diff --git a/.github/actions/extract-vars/action.yml b/.github/actions/extract-vars/action.yml index f4f9b55..b2ea3d0 100644 --- a/.github/actions/extract-vars/action.yml +++ b/.github/actions/extract-vars/action.yml @@ -25,7 +25,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/extract-vars - key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output lookup-only: true - name: Create requirements.txt @@ -50,7 +50,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/extract-vars - key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: extract-vars-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output - name: Retrieve cached ClinVar JSONL file if: | @@ -58,7 +58,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output fail-on-cache-miss: true - name: Run the variant extraction generation diff --git a/.github/actions/gene-variant-report/action.yml b/.github/actions/gene-variant-report/action.yml index 0e23153..1519fa6 100644 --- a/.github/actions/gene-variant-report/action.yml +++ b/.github/actions/gene-variant-report/action.yml @@ -25,7 +25,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/gene-variant-report - key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output lookup-only: true - name: Create requirements.txt @@ -50,7 +50,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/gene-variant-report - key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: gene-variant-report-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output - name: Retrieve cached ClinVar JSONL file if: | @@ -58,7 +58,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output fail-on-cache-miss: true - name: Run the gene variant report generation diff --git a/.github/actions/phenotype-links/action.yml b/.github/actions/phenotype-links/action.yml index 4038271..bb6308e 100644 --- a/.github/actions/phenotype-links/action.yml +++ b/.github/actions/phenotype-links/action.yml @@ -25,7 +25,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/phenotype-links - key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output lookup-only: true - name: Create requirements.txt @@ -50,7 +50,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/phenotype-links - key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: phenotype-links-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output - name: Retrieve cached ClinVar JSONL file if: | @@ -58,7 +58,7 @@ runs: uses: actions/cache@v3 with: path: ${{ env.OUTPUT_DIR }}/convert-clinvar - key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RCVS }}-output + key: convert-clinvar-${{ env.CACHE_SEED }}-${{ steps.get-clinvar.outputs.release-name }}-${{ env.CLINVAR_THIS_VERSION }}-${{ env.MAX_RECORDS }}-output fail-on-cache-miss: true - name: Run the phenotype links generation diff --git a/.github/workflows/-build-artifacts.yml b/.github/workflows/-build-artifacts.yml index dc3755b..5ca0d3f 100644 --- a/.github/workflows/-build-artifacts.yml +++ b/.github/workflows/-build-artifacts.yml @@ -26,11 +26,11 @@ env: # Python version PYTHON_VERSION: "3.11" # clinvar-this package version - CLINVAR_THIS_VERSION: "0.14.3" + CLINVAR_THIS_VERSION: "0.15.5" # Helper to get unique cache keys CACHE_SEED: "0" - # Maximal number of RCVs to process (0 = no limit). - MAX_RCVS: "0" + # Maximal number of records to process (0 = no limit). + MAX_RECORDS: "0" # Lower verbosity of TQDM progress bar TQDM_MININTERVAL: "5"