rebuild #345
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| name: Rebuild hmpxv1 | |
| on: | |
| repository_dispatch: | |
| types: | |
| - rebuild | |
| - rebuild_hmpxv1 | |
| workflow_dispatch: | |
| inputs: | |
| trial_name: | |
| description: "If set, result will be at nextstrain.org/staging/trial/${trial_name}/${auspice_name}" | |
| required: false | |
| image: | |
| description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
| required: false | |
| jobs: | |
| set_config_overrides: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - id: config | |
| name: Set config overrides | |
| env: | |
| TRIAL_NAME: ${{ inputs.trial_name }} | |
| run: | | |
| config="" | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+="--config" | |
| config+=" deploy_url='s3://nextstrain-staging/'" | |
| config+=" auspice_prefix='"$TRIAL_NAME"'" | |
| fi | |
| echo "config=$config" >> "$GITHUB_OUTPUT" | |
| outputs: | |
| config_overrides: ${{ steps.config.outputs.config }} | |
| rebuild_hmpxv1: | |
| needs: [set_config_overrides] | |
| 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.image }} | |
| CONFIG_OVERRIDES: ${{ needs.set_config_overrides.outputs.config_overrides }} | |
| GITHUB_RUN_ID: ${{ github.run_id }} | |
| SLACK_CHANNELS: ${{ inputs.trial_name && vars.TEST_SLACK_CHANNEL || vars.SLACK_CHANNELS }} | |
| BUILD_DIR: phylogenetic | |
| BUILD_NAME: hmpxv1 | |
| run: | | |
| nextstrain build \ | |
| --detach \ | |
| --no-download \ | |
| --cpus 8 \ | |
| --memory 32gib \ | |
| --env GITHUB_RUN_ID \ | |
| --env SLACK_TOKEN \ | |
| --env SLACK_CHANNELS \ | |
| . \ | |
| notify_on_deploy \ | |
| --configfiles $BUILD_DIR/defaults/$BUILD_NAME/config.yaml $BUILD_DIR/build-configs/nextstrain-automation/config.yaml \ | |
| $CONFIG_OVERRIDES --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile |