Ingest fauna #2
Workflow file for this run
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| name: Ingest fauna | |
| defaults: | |
| run: | |
| # This is the same as GitHub Action's `bash` keyword as of 20 June 2023: | |
| # https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#jobsjob_idstepsshell | |
| # | |
| # Completely spelling it out here so that GitHub can't change it out from under us | |
| # and we don't have to refer to the docs to know the expected behavior. | |
| shell: bash --noprofile --norc -eo pipefail {0} | |
| on: | |
| workflow_dispatch: | |
| jobs: | |
| ingest: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| # Starting with the default docker runtime | |
| # We can migrate to AWS Batch when/if we need to for more resources or if | |
| # the job runs longer than the GH Action limit of 6 hours. | |
| runtime: docker | |
| run: | | |
| nextstrain build \ | |
| --env RETHINK_HOST \ | |
| --env RETHINK_AUTH_KEY \ | |
| ingest \ | |
| upload_all | |
| # Specifying artifact name to differentiate ingest build outputs from | |
| # the phylogenetic build outputs | |
| artifact-name: ingest-fauna-build-output | |
| # Explicitly excluding `ingest/fauna/results` and `ingest/fauna/data` | |
| # since this is private data and should not available through the public artifacts | |
| artifact-paths: | | |
| !ingest/fauna/results/ | |
| !ingest/fauna/data/ | |
| ingest/.snakemake/log/ | |
| ingest/fauna/benchmarks/ | |
| ingest/fauna/logs/ |