GISAID fetch and ingest (on branch) #551
Workflow file for this run
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| name: GISAID fetch and ingest (on branch) | |
| # Manually triggered using GitHub's UI | |
| on: workflow_dispatch | |
| jobs: | |
| ingest: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: nextstrain/.github/actions/setup-nextstrain-cli@master | |
| - name: run_pipeline | |
| run: | | |
| ./bin/write-envdir env.d \ | |
| AWS_DEFAULT_REGION \ | |
| GISAID_API_ENDPOINT \ | |
| GISAID_USERNAME_AND_PASSWORD \ | |
| GITHUB_RUN_ID \ | |
| GITHUB_BRANCH=${GITHUB_REF#refs/heads/} | |
| declare -a config | |
| config+=( | |
| fetch_from_database=True | |
| s3_dst=s3://nextstrain-ncov-private/branch/"${GITHUB_BRANCH}" | |
| ) | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --image nextstrain/ncov-ingest \ | |
| --cpus 16 \ | |
| --memory 68GiB \ | |
| --exec env \ | |
| . \ | |
| envdir env.d snakemake \ | |
| --configfile config/gisaid.yaml \ | |
| --config "${config[@]}" \ | |
| --cores 16 \ | |
| --resources mem_mb=68000 \ | |
| --printshellcmds | |
| env: | |
| AWS_DEFAULT_REGION: ${{ secrets.AWS_DEFAULT_REGION }} | |
| AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} | |
| AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} | |
| GISAID_API_ENDPOINT: ${{ secrets.GISAID_API_ENDPOINT }} | |
| GISAID_USERNAME_AND_PASSWORD: ${{ secrets.GISAID_USERNAME_AND_PASSWORD }} | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| GITHUB_REF: ${{ github.ref }} |