# Triggered by an Argo Events sensor listening on the Pub/Sub topic "vcf-uploaded".
apiVersion: argoproj.io/v1alpha1
kind: WorkflowTemplate
metadata: { name: annotate-vcf, namespace: rarelens }
spec:
  entrypoint: nextflow
  arguments:
    parameters:
      - { name: job_id }
      - { name: vcf_uri }
  templates:
    - name: nextflow
      inputs:
        parameters: [{ name: job_id }, { name: vcf_uri }]
      serviceAccountName: rarelens-pipeline
      container:
        image: europe-west2-docker.pkg.dev/PROJECT/rarelens/pipeline:latest
        command: [nextflow]
        args:
          - run
          - /pipeline/main.nf
          - -profile
          - gcp
          - --vcf
          - "{{inputs.parameters.vcf_uri}}"
          - --job_id
          - "{{inputs.parameters.job_id}}"
          - --db_url
          - "$(DATABASE_URL)"
        envFrom: [{ secretRef: { name: api-secrets } }]
        resources: { requests: { cpu: "2", memory: 4Gi } }
    - name: score
      # Optional GPU step for the deep-learning baseline; Autopilot schedules on an L4 node.
      nodeSelector: { cloud.google.com/gke-accelerator: nvidia-l4 }
      container:
        image: europe-west2-docker.pkg.dev/PROJECT/rarelens/ml:latest
        resources: { limits: { nvidia.com/gpu: 1 } }