pathogen-repo-builders.yaml

- workflow: ./mpox/.github/workflows/fetch-and-ingest-branch.yaml
  jobs:
    fetch-and-ingest:
      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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ vars.TEST_SLACK_CHANNEL }}
          UPLOAD_CONFIG: ${{ needs.set_config_overrides.outputs.upload_config }}
        run: |
          nextstrain build \
            --aws-batch \
            --detach \
            --no-download \
            --cpus 32 \
            --memory 64gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            ingest \
              nextstrain_automation \
                --configfiles build-configs/nextstrain-automation/config.yaml \
                --config trigger_rebuild=False send_slack_notifications=True upload="$UPLOAD_CONFIG"
- workflow: ./mpox/.github/workflows/ci.yaml
  jobs:
    pathogen-ci:
      strategy:
        matrix:
          runtime: [docker, conda]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: ${{ matrix.runtime }}
        run: |
          nextstrain build \
            phylogenetic \
            --configfile profiles/ci/builds.yaml
        artifact-name: output-${{ matrix.runtime }}
        artifact-paths: |
          phylogenetic/auspice/
          phylogenetic/results/
          phylogenetic/benchmarks/
          phylogenetic/logs/
          phylogenetic/.snakemake/log/
- workflow: ./mpox/.github/workflows/fetch-and-ingest.yaml
  jobs:
    fetch-and-ingest:
      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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
        run: |
          nextstrain build \
            --detach \
            --no-download \
            --cpus 32 \
            --memory 64gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \
            ingest \
              nextstrain_automation \
                --configfiles build-configs/nextstrain-automation/config.yaml \
- workflow: ./mpox/.github/workflows/rebuild-hmpxv1-big.yaml
  jobs:
    rebuild_hmpxv1_big:
      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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
          BUILD_DIR: phylogenetic
          BUILD_NAME: hmpxv1_big
        run: |
          nextstrain build \
            --detach \
            --no-download \
            --cpus 8 \
            --memory 68gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            . \
              notify_on_deploy \
                --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
                --config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
- workflow: ./mpox/.github/workflows/rebuild-mpxv.yaml
  jobs:
    rebuild_mpxv:
      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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
          BUILD_DIR: phylogenetic
          BUILD_NAME: mpxv
        run: |
          nextstrain build \
            --detach \
            --no-download \
            --cpus 8 \
            --memory 32gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            . \
              notify_on_deploy \
                --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
                --config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
- workflow: ./mpox/.github/workflows/rebuild-hmpxv1.yaml
  jobs:
    rebuild_hmpxv1:
      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 }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ vars.SLACK_CHANNELS }}
          BUILD_DIR: phylogenetic
          BUILD_NAME: hmpxv1
        run: |
          nextstrain build \
            --detach \
            --no-download \
            --cpus 8 \
            --memory 32gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            . \
              notify_on_deploy \
              --configfiles $BUILD_DIR/config/$BUILD_NAME/config.yaml $BUILD_DIR/config/nextstrain_automation.yaml \
              --config auspice_prefix=$TRIAL_NAME --directory $BUILD_DIR --snakefile $BUILD_DIR/Snakefile
- workflow: ./forecasts-ncov/.github/workflows/run-models.yaml
  jobs:
    run_models:
      needs: [set_config_overrides]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch
        run: |
          nextstrain build \
            --aws-batch \
            --detach \
            --no-download \
            --image nextstrain/base \
            --cpus 8 \
            --memory 16GiB \
            --env AWS_DEFAULT_REGION \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env GITHUB_RUN_ID \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            . \
              --configfile config/config.yaml config/optional.yaml \
              --config s3_dst="$S3_DST" data_provenances="$DATA_PROVENANCES" \
              --keep-going
        env: |
          DATA_PROVENANCES: ${{ needs.set_config_overrides.outputs.data_provenances }}
          GITHUB_RUN_ID: ${{ github.run_id }}
          SLACK_CHANNELS: ${{ github.event.inputs.slack_channel || vars.SLACK_CHANNELS }}
          S3_DST: ${{ needs.set_config_overrides.outputs.s3_dst }}
- workflow: ./forecasts-ncov/.github/workflows/update-ncov-open-clade-counts.yaml
  jobs:
    open_clade_counts:
      needs: [set_s3_dst]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch
        run: |
          nextstrain build \
            --cpus 8 \
            --memory 16gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            --env S3_DST \
            ingest \
            upload_all_sequence_counts \
            --config data_provenances=["open"] s3_dst="$S3_DST"
        env: |
          SLACK_CHANNELS: ${{ inputs.slack_channel || vars.SLACK_CHANNELS }}
          S3_DST: ${{ needs.set_s3_dst.outputs.s3_dst }}
- workflow: ./forecasts-ncov/.github/workflows/update-ncov-gisaid-clade-counts.yaml
  jobs:
    gisaid_clade_counts:
      needs: [set_s3_dst]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch
        run: |
          nextstrain build \
            --cpus 8 \
            --memory 16gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env SLACK_TOKEN \
            --env SLACK_CHANNELS \
            --env S3_DST \
            ingest \
            upload_all_sequence_counts \
            --config data_provenances=["gisaid"] s3_dst="$S3_DST"
        env: |
          SLACK_CHANNELS: ${{ inputs.slack_channel || vars.SLACK_CHANNELS }}
          S3_DST: ${{ needs.set_s3_dst.outputs.s3_dst }}
- workflow: ./hepatitisB/.github/workflows/run-builds.yaml
  jobs:
    run-build:
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: conda
        run: |
          nextstrain build --cpus 1 . -pf vendor_nextclade3_x86;
          nextstrain build --cpus 1 . -pf deploy;
- workflow: ./zika/.github/workflows/ci.yaml
  jobs:
    pathogen-ci:
      strategy:
        matrix:
          runtime: [docker, conda]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: ${{ matrix.runtime }}
        run: |
          nextstrain build \
            phylogenetic \
            --configfile profiles/ci/profiles_config.yaml
        artifact-name: output-${{ matrix.runtime }}
        artifact-paths: |-
          phylogenetic/auspice/
          phylogenetic/results/
          phylogenetic/benchmarks/
          phylogenetic/logs/
          phylogenetic/.snakemake/log/
- workflow: ./seasonal-flu/.github/workflows/run-nextflu-private-builds.yaml
  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 \
            --env NEXTSTRAIN_USERNAME \
            --env NEXTSTRAIN_PASSWORD \
            . \
            deploy_all \
            all_counts_of_recent_tips_by_clade \
            -p \
            --configfile profiles/nextflu-private.yaml
- workflow: ./seasonal-flu/.github/workflows/run-private-nextflu-builds.yaml
  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 \
            . \
            all_who \
            -p \
            --configfile profiles/private.nextflu.org.yaml
- workflow: ./seasonal-flu/.github/workflows/run-public-builds.yaml
  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 \
            . \
            deploy_all \
            -p \
            --configfile profiles/nextstrain-public.yaml
- workflow: ./seasonal-flu/.github/workflows/upload.yaml
  jobs:
    upload:
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: docker
        run: |
          nextstrain build \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env RETHINK_AUTH_KEY \
            --env RETHINK_HOST \
            . \
            -j 4 \
            upload_all_titers \
            upload_all_raw_sequences \
            upload_all_sequences \
            upload_all_metadata \
            --configfile profiles/upload.yaml
- workflow: ./dengue/.github/workflows/ci.yaml
  jobs:
    pathogen-ci:
      strategy:
        matrix:
          runtime: [docker, conda]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: ${{ matrix.runtime }}
        run: |
          nextstrain build \
            phylogenetic \
            --configfile profiles/ci/profiles_config.yaml
        artifact-name: output-${{ matrix.runtime }}
        artifact-paths: |-
          phylogenetic/auspice/
          phylogenetic/results/
          phylogenetic/benchmarks/
          phylogenetic/logs/
          phylogenetic/.snakemake/log/
- workflow: ./.github/workflow-templates/pathogen-repo-build.yaml
  jobs:
    run-build:
      # The `id-token: write` permission is required for this workflow.
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
- workflow: ./.github/.github/workflows/ci.yaml
  jobs:
    test-pathogen-repo-build:
      permissions:
        id-token: write
      strategy:
        matrix:
          runtime: [docker, conda, aws-batch]
      uses: ./.github/workflows/pathogen-repo-build.yaml
      with:
        repo: nextstrain/zika-tutorial
        runtime: ${{ matrix.runtime }}
        run: nextstrain build --env BOGUS_ENVVAR .
        artifact-name: build-output-${{ matrix.runtime }}
        env: |
          BOGUS_ENVVAR: BOGUS_ENVVAR
      secrets: inherit
- workflow: ./rsv/.github/workflows/fetch-and-ingest.yaml
  jobs:
    fetch-and-ingest:
      needs: [set_config_overrides]
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch
        run: |
          nextstrain build \
            --aws-batch \
            --detach \
            --no-download \
            --cpus 8 \
            --memory 32gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            --env PAT_GITHUB_DISPATCH="$GH_TOKEN_NEXTSTRAIN_BOT_WORKFLOW_DISPATCH" \
            --env S3_DST \
            --env TRIGGER_REBUILD \
            ingest \
              --configfiles config/config.yaml config/optional.yaml \
              --config s3_dst="$S3_DST" trigger_rebuild="$TRIGGER_REBUILD" \
              --printshellcmds
        env: |
          S3_DST: ${{ needs.set_config_overrides.outputs.s3_dst }}
          TRIGGER_REBUILD: ${{ needs.set_config_overrides.outputs.trigger_rebuild }}
- workflow: ./rsv/.github/workflows/rebuild.yaml
  jobs:
    rebuild_rsv:
      permissions:
        id-token: write
      uses: nextstrain/.github/.github/workflows/pathogen-repo-build.yaml@master
      secrets: inherit
      with:
        runtime: aws-batch
        run: |
          nextstrain build \
            --aws-batch \
            --detach \
            --no-download \
            --cpus 16 \
            --memory 64gib \
            --env AWS_ACCESS_KEY_ID \
            --env AWS_SECRET_ACCESS_KEY \
            . \
            deploy \
              --configfiles config/configfile.yaml config/nextstrain_automation.yaml \
              --printshellcmds