gisaid/rebuild #800
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| name: Rebuild GISAID phylogenetic datasets | |
| on: | |
| # This workflow can be triggered from repository_dispatch events, | |
| # for instance, after the appropriate preprocessing actions have completed | |
| repository_dispatch: | |
| types: | |
| - rebuild | |
| - gisaid/rebuild | |
| # Manually triggered using GitHub's UI | |
| workflow_dispatch: | |
| inputs: | |
| trial_name: | |
| description: "Short name for this trial build, for prefixing the uploaded data and results files. WARNING: without this we will overwrite files in s3://nextstrain-ncov-private and the trees on nextstrain.org/ncov/gisaid..." | |
| required: false | |
| image: | |
| description: 'Specific container image to use for build (will override the default of "nextstrain build")' | |
| required: false | |
| jobs: | |
| gisaid: | |
| permissions: | |
| id-token: write | |
| uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master | |
| secrets: inherit | |
| with: | |
| runtime: aws-batch | |
| env: | | |
| TRIAL_NAME: ${{ github.event.inputs.trial_name }} | |
| NEXTSTRAIN_DOCKER_IMAGE: ${{ github.event.inputs.image }} | |
| run: | | |
| set -x | |
| declare -a config | |
| config+=(build_date=\'$(date +'%Y-%m-%d')\') | |
| if [[ "$TRIAL_NAME" ]]; then | |
| config+=( | |
| S3_DST_BUCKET=nextstrain-ncov-private/trial/"$TRIAL_NAME" | |
| deploy_url=s3://nextstrain-staging/ | |
| auspice_json_prefix=ncov_gisaid_trial_"$TRIAL_NAME" | |
| ) | |
| else | |
| config+=(slack_token=$SLACK_TOKEN) | |
| fi | |
| nextstrain build \ | |
| --detach \ | |
| --cpus 72 \ | |
| --memory 140GiB \ | |
| . \ | |
| deploy \ | |
| upload \ | |
| --config "${config[@]}" \ | |
| --profile nextstrain_profiles/nextstrain-gisaid \ | |
| --set-threads tree=8 |