Phylogenetic NCBI #5
Workflow file for this run
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| name: Phylogenetic NCBI | |
| 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_call: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for phylogenetic workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| workflow_dispatch: | |
| inputs: | |
| image: | |
| description: 'Specific container image to use for ingest workflow (will override the default of "nextstrain build")' | |
| required: false | |
| type: string | |
| trial-name: | |
| description: | | |
| Trial name for deploying builds. | |
| If not set, builds will overwrite existing builds at s3://nextstrain-data/avian-flu* | |
| If set, builds will be deployed to s3://nextstrain-staging/avian-flu_trials_<trial_name>_* | |
| required: false | |
| type: string | |
| jobs: | |
| phylogenetic: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: docker | |
| run: | | |
| declare -a config; | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=( | |
| deploy_url="s3://nextstrain-staging/avian-flu_trials_${TRIAL_NAME}_" | |
| ) | |
| fi; | |
| nextstrain build \ | |
| . \ | |
| deploy_all \ | |
| --configfile config/h5n1-cattle-outbreak.yaml \ | |
| --config "${config[@]}" | |
| env: | | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ inputs.image }} | |
| TRIAL_NAME: ${{ inputs.trial-name }} | |
| artifact-name: phylogenetic-full-genome-build-output |