Update Clinvar database for ANNOVAR #2181
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| name: Update Clinvar database for ANNOVAR | |
| on: | |
| schedule: | |
| - cron: "0 3,15 * * *" | |
| workflow_dispatch: | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| matrix: | |
| genome: ["hg19", "hg38"] | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GH_TOKEN }} | |
| submodules: "true" | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirement.txt | |
| - name: Update Clinvar with GRCh37 | |
| if: matrix.genome == 'hg19' | |
| run: | | |
| cd ./update_annovar_db | |
| python3 ./update_resources.py -d clinvar -w -hp ../Clinvar_build/hg19 -a ../ANNOVAR_script -g GRCh37 | |
| - name: Update Clinvar with GRCh38 | |
| if: matrix.genome == 'hg38' | |
| run: | | |
| cd ./update_annovar_db | |
| python3 ./update_resources.py -d clinvar -w -hp ../Clinvar_build/hg38 -a ../ANNOVAR_script -g GRCh38 | |
| - name: Upload artifacts | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ matrix.genome }} | |
| path: ./Clinvar_build/${{ matrix.genome }} | |
| retention-days: 1 | |
| release: | |
| runs-on: ubuntu-latest | |
| needs: build | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| token: ${{ secrets.GH_TOKEN }} | |
| - name: clean previous build | |
| run: | | |
| rm -f Clinvar_build/hg19/* | |
| rm -f Clinvar_build/hg38/* | |
| - name: Download artifacts for GRCh37 | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "hg19" | |
| path: ./Clinvar_build/hg19 | |
| - name: Download artifacts for GRCh38 | |
| uses: actions/download-artifact@v4 | |
| with: | |
| name: "hg38" | |
| path: ./Clinvar_build/hg38 | |
| - name: Commit | |
| id: auto-commit-action | |
| uses: stefanzweifel/git-auto-commit-action@v5 | |
| - name: Push changes | |
| uses: ad-m/github-push-action@master | |
| with: | |
| github_token: ${{ secrets.GH_TOKEN }} | |
| branch: master | |
| - name: Get current date | |
| id: date | |
| run: echo "date=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT | |
| - name: Create Github Release | |
| if: steps.auto-commit-action.outputs.changes_detected == 'true' | |
| uses: actions/create-release@v1 | |
| id: create_release | |
| with: | |
| tag_name: tag-${{ steps.date.outputs.date }} | |
| release_name: release-${{ steps.date.outputs.date }} | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GH_TOKEN }} | |
| - name: Upload assets to Github Release | |
| if: steps.auto-commit-action.outputs.changes_detected == 'true' | |
| uses: csexton/release-asset-action@v3 | |
| with: | |
| pattern: "Clinvar_build/*/*.gz" | |
| github-token: ${{ secrets.GH_TOKEN }} | |
| release-url: ${{ steps.create_release.outputs.upload_url }} |