apiVersion: batch/v1
kind: Job
metadata:
  name: nf-6195e3538fa817a822ad478d5faf800c-222ea
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_BAM_VARIANT_CALLING_SOMATIC_ALL_SOMATIC_CNV,
    nextflow.io/runName: somatic_cnv_clinical_2674-0607-0342, capacityType: spot,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_SAREK_SAREK_BAM_VARIANT_CALLING_SOMATIC_ALL_SOMATIC_CNV,
    pltf/run-id: 761e935b, pltf/run-creator: rsrivas, nextflow.io/sessionId: uuid-95307ca4-0aa4-41ca-bbfa-be45c5d0a48e,
    pltf/run-name: somatic_cnv_clinical_2674-0607-0342, instanceMinCpuSpeedMhz: '2200',
    pltf/run-engine: nextflow, instanceLocalNvme: 'true'}
  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":"somatic_cnv_clinical_2674-0607-0342","run_id":"761e935b","run_creator":"rsrivas","run_component":"task","task_process":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY","task_name":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:BGZIP_TABIX_BLOOD_ONLY
      (1029_1CU-T1-TDNA-1_A23KCGYLT4_1_vs_1029_1CU-N1-BDNA-1_B23KGCJLT4_1)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: somatic-cnv-clinical-2674-0607-0342-761e935b-tjjpl,
    uid: 6f5bd409-7238-4ec6-9f60-967e8fc96bea, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-6195e3538fa817a822ad478d5faf800c-222ea
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-3cb5ec5
        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/61/95e3538fa817a822ad478d5faf800c/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/61/95e3538fa817a822ad478d5faf800c/.command.run
            | bash 2>&1 | tee .command.log']
        workingDir: /tmp
        imagePullPolicy: Always
        env:
        - {name: SSL_CERT_FILE, value: /opt/s5cmd/ssl/ca-certificates.crt}
        - {name: SSL_CERT_DIR, value: /opt/s5cmd/ssl/certs}
        resources:
          requests: {cpu: 1, memory: 6144Mi, ephemeral-storage: 51200Mi}
          limits: {memory: 6144Mi, ephemeral-storage: 51200Mi}
        volumeMounts:
        - {name: vol-103477, mountPath: /app}
        - {name: vol-103478, mountPath: /tmp}
        - {name: vol-103479, mountPath: /mnt/secrets}
        - {name: vol-103480, 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}
              - {key: eks.amazonaws.com/instance-local-nvme, operator: Exists}
              - key: eks.amazonaws.com/instance-cpu-sustained-clock-speed-mhz
                operator: Gt
                values: ['2200']
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      activeDeadlineSeconds: 14400
      volumes:
      - name: vol-103477
        emptyDir: []
      - name: vol-103478
        emptyDir: []
      - name: vol-103479
        secret: {secretName: aws-secrets-manager}
      - name: vol-103480
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800