apiVersion: batch/v1
kind: Job
metadata:
  name: nf-5f32760d3ae333a5a5f189a39f739f49-4345e
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: CNV_PIPE_CalcPanelCoverage, nextflow.io/runName: bding-cnv-pipe-2026-06-08t22-59-41z,
    nextflow.io/sessionId: uuid-00d4e51c-23fc-474d-a342-246088f738ab, pltf/run-name: bding-cnv-pipe-2026-06-08t22-59-41z,
    capacityType: spot, pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: CNV_PIPE_CalcPanelCoverage_FC13_cnv_mosaic_calc_panel_coverage,
    pltf/run-id: f4ae7cc8, pltf/run-engine: nextflow, pltf/run-creator: bding}
  annotations: &id002 {ad.datadoghq.com/nextflow.logs: '[{"source":"nextflow","service":"nextflow-task","log_processing_rules":[{"type":"multi_line","name":"nextflow_task_multiline","pattern":"^\\x00NEVER_MATCH"}]}]',
    ad.datadoghq.com/tags: '{"run_name":"bding-cnv-pipe-2026-06-08t22-59-41z","run_id":"f4ae7cc8","run_creator":"bding","run_component":"task","task_process":"CNV_PIPE:CalcPanelCoverage","task_name":"CNV_PIPE:CalcPanelCoverage
      (FC13_cnv_mosaic_calc_panel_coverage_3619659355_r13)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: bding-cnv-pipe-2026-06-08t22-59-41z-f4ae7cc8-xsffm,
    uid: cb886eb6-f551-416c-b613-9a526444d652, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-5f32760d3ae333a5a5f189a39f739f49-4345e
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/bding/cnv_pipe:bding_1.0.6
        args: [/bin/bash, -o, pipefail, -c, 'trap "{ ret=$?; /opt/s5cmd/bin/s5cmd
            --log error cp .command.log s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/32760d3ae333a5a5f189a39f739f49/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/5f/32760d3ae333a5a5f189a39f739f49/.command.run
            | bash 2>&1 | tee .command.log']
        workingDir: /tmp
        imagePullPolicy: Always
        env:
        - {name: SSL_CERT_DIR, value: /opt/s5cmd/ssl/certs}
        - {name: SSL_CERT_FILE, value: /opt/s5cmd/ssl/ca-certificates.crt}
        resources:
          requests: {cpu: 2, memory: 204800Mi, ephemeral-storage: 204800Mi}
          limits: {memory: 204800Mi, ephemeral-storage: 204800Mi}
        volumeMounts:
        - {name: vol-61, mountPath: /tmp}
        - {name: vol-62, mountPath: /app}
        - {name: vol-63, mountPath: /mnt/secrets}
        - {name: vol-64, mountPath: /opt/s5cmd}
      nodeSelector: {workload: nextflow-task, karpenter.sh/capacity-type: spot}
      affinity:
        nodeAffinity:
          requiredDuringSchedulingIgnoredDuringExecution:
            nodeSelectorTerms:
            - matchExpressions:
              - {key: eks.amazonaws.com/instance-gpu-count, operator: DoesNotExist}
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      activeDeadlineSeconds: 3600
      volumes:
      - name: vol-61
        emptyDir: []
      - name: vol-62
        emptyDir: []
      - name: vol-63
        secret: {secretName: aws-secrets-manager}
      - name: vol-64
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800