# Submitted by the Argo Events sensor in events.yaml for each "vcf-uploaded" Pub/Sub message.
# The Nextflow driver runs here; its tasks run on Google Batch (see the gcp profile in
# pipeline/nextflow.config). Image names are rewritten by the gcp overlay and bumped by CI.
apiVersion: argoproj.io/v1alpha1
kind: WorkflowTemplate
metadata: { name: annotate-vcf }
spec:
  serviceAccountName: rarelens-pipeline
  entrypoint: nextflow
  onExit: exit-handler
  arguments:
    parameters:
      - { name: job_id }
      - { name: vcf_uri }
      - { name: assembly, value: GRCh38 }
  templates:
    - name: nextflow
      container:
        image: rarelens/pipeline
        args:
          - run
          - /pipeline/main.nf
          - -profile
          - gcp
          - --vcf
          - "{{workflow.parameters.vcf_uri}}"
          - --job_id
          - "{{workflow.parameters.job_id}}"
          - --assembly
          - "{{workflow.parameters.assembly}}"
        # GCP_PROJECT / GCS_BUCKET / GCP_REGION feed params in nextflow.config.
        envFrom: [{ configMapRef: { name: pipeline-config } }]
        resources: { requests: { cpu: "1", memory: 2Gi } }

    # The loader marks success; anything else (Nextflow error, OOM, eviction) is marked here
    # so the UI never polls a dead job forever.
    - name: exit-handler
      steps:
        - - name: mark-failed
            template: mark-failed
            when: "{{workflow.status}} != Succeeded"
    - name: mark-failed
      container:
        image: rarelens/loader
        command: [set_job_status.py]
        args:
          - --job-id
          - "{{workflow.parameters.job_id}}"
          - --status
          - failed
          - --log
          - "Argo workflow {{workflow.name}} ended {{workflow.status}}"
        envFrom: [{ secretRef: { name: pipeline-secrets } }]
        resources: { requests: { cpu: 100m, memory: 256Mi } }