Update evidence pack #22
Workflow file for this run
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| name: Update evidence pack | |
| on: | |
| schedule: | |
| - cron: "15 6 1 * *" | |
| workflow_dispatch: | |
| inputs: | |
| force_refresh: | |
| description: 'Force re-download of all cached evidence sources' | |
| type: boolean | |
| default: false | |
| permissions: | |
| contents: write | |
| pull-requests: write | |
| concurrency: | |
| group: update-evidence-pack | |
| cancel-in-progress: false | |
| jobs: | |
| update-evidence-pack: | |
| name: Update evidence pack | |
| runs-on: ubuntu-latest | |
| environment: Evidence Packs | |
| env: | |
| GWAS_ASSOCIATIONS_URL: ${{ vars.GWAS_ASSOCIATIONS_URL }} | |
| steps: | |
| - name: Check out repository | |
| uses: actions/checkout@v4 | |
| - name: Set cache month | |
| run: echo "CACHE_MONTH=$(date +'%Y-%m')" >> "$GITHUB_ENV" | |
| - name: Cache Bun packages | |
| uses: actions/cache@v4 | |
| with: | |
| path: ~/.bun/install/cache | |
| key: bun-install-${{ runner.os }}-${{ hashFiles('bun.lock') }} | |
| restore-keys: | | |
| bun-install-${{ runner.os }}- | |
| - name: Cache evidence sources | |
| uses: actions/cache@v4 | |
| with: | |
| path: | | |
| .evidence-cache/clinvar | |
| .evidence-cache/gwas | |
| .evidence-cache/snpedia | |
| .evidence-cache/pharmgkb | |
| .evidence-cache/clingen | |
| key: evidence-sources-${{ runner.os }}-${{ env.CACHE_MONTH }} | |
| restore-keys: | | |
| evidence-sources-${{ runner.os }}- | |
| - name: Set up Bun | |
| uses: oven-sh/setup-bun@v2 | |
| with: | |
| bun-version: latest | |
| - name: Install variant tools | |
| run: | | |
| sudo apt-get update | |
| sudo apt-get install -y bcftools tabix | |
| - name: Install dependencies | |
| run: bun install --frozen-lockfile | |
| - name: Update evidence pack | |
| run: | | |
| FORCE="${{ inputs.force_refresh && '--force' || '' }}" | |
| bun run scripts/syncEvidenceSources.ts $FORCE | |
| bun run scripts/syncCpic.ts $FORCE | |
| bun run scripts/syncSnpedia.ts $FORCE | |
| bun run scripts/syncDbsnp.ts $FORCE | |
| bun run scripts/syncPharmgkb.ts $FORCE | |
| bun run scripts/importClinGen.ts $FORCE | |
| bun run scripts/buildEvidencePack.ts | |
| - name: Check evidence pack | |
| run: bun run evidence:check | |
| - name: Run tests | |
| run: bun run test | |
| env: | |
| NODE_OPTIONS: --max-old-space-size=6144 | |
| - name: Build | |
| run: bun run build | |
| env: | |
| NODE_OPTIONS: --max-old-space-size=6144 | |
| - name: Open pull request | |
| uses: peter-evans/create-pull-request@v6 | |
| with: | |
| branch: automation/update-evidence-pack | |
| delete-branch: true | |
| title: Update monthly evidence pack | |
| commit-message: Update monthly evidence pack | |
| body: | | |
| ## Summary | |
| - Syncs public evidence source caches. | |
| - Syncs SNPedia-derived supplementary evidence. | |
| - Syncs GRCh37 and GRCh38 dbSNP references for local VCF annotation. | |
| - Rebuilds the sharded static evidence pack. | |
| - Updates evidence-pack manifests, shard and annotation checksums, and app pack-version constants when needed. | |
| GWAS sync uses the repository `GWAS_ASSOCIATIONS_URL` variable when it is configured. If the variable is empty, the GWAS source sync step is skipped by the evidence tooling. | |
| ## Checks | |
| - `bun run evidence:update:monthly` | |
| - `bun run evidence:check` | |
| - `bun run test` | |
| - `bun run build` |