Run Nextclade on all sequences #7
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| name: Run Nextclade on all sequences | |
| on: | |
| workflow_dispatch: | |
| inputs: | |
| dockerImage: | |
| description: "Specific container image to use for build (will override the default of `nextstrain build`)" | |
| required: false | |
| type: string | |
| jobs: | |
| run-build: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.dockerImage }} | |
| run: | | |
| nextstrain build \ | |
| --detach \ | |
| --cpus 36 \ | |
| --memory 72gib \ | |
| --env AWS_ACCESS_KEY_ID \ | |
| --env AWS_SECRET_ACCESS_KEY \ | |
| . \ | |
| upload_all_nextclade_files \ | |
| -p \ | |
| --configfile profiles/nextclade.yaml \ | |
| --set-threads run_nextclade=12 |