GenBank ingest #279
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| name: GenBank ingest | |
| on: | |
| # Manually triggered using `./vendored/trigger nextstrain/ncov-ingest genbank/ingest` (or `ingest`, which | |
| # includes GISAID) | |
| repository_dispatch: | |
| types: | |
| - genbank/ingest | |
| - ingest | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| jobs: | |
| ingest: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| SLACK_CHANNELS: ncov-genbank-updates | |
| SLACK_TOKEN: ${{ secrets.SLACK_TOKEN }} | |
| 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 \ | |
| SLACK_TOKEN \ | |
| GITHUB_RUN_ID \ | |
| SLACK_CHANNELS | |
| nextstrain build \ | |
| --aws-batch \ | |
| --detach \ | |
| --no-download \ | |
| --image nextstrain/ncov-ingest \ | |
| --cpus 16 \ | |
| --memory 68GiB \ | |
| --exec env \ | |
| . \ | |
| envdir env.d snakemake \ | |
| --configfile config/genbank.yaml \ | |
| --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 }} | |
| - name: notify_pipeline_failed | |
| if: ${{ failure() }} | |
| run: ./vendored/notify-on-job-fail Ingest nextstrain/ncov-ingest |