apiVersion: batch/v1
kind: Job
metadata:
  name: nf-c5e09f79fe0a1a21147850e4de21008f-99afe
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_BAM_VARIANT_CALLING_SOMATIC_ALL_SOMATIC_CNV,
    nextflow.io/runName: sarek-regression-somacnv-v2, 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: e8451078, pltf/run-creator: chnobles, nextflow.io/sessionId: uuid-ca0d60b9-6a95-4998-8029-f794bfe5e089,
    pltf/run-name: sarek-regression-somacnv-v2, 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":"sarek-regression-somacnv-v2","run_id":"e8451078","run_creator":"chnobles","run_component":"task","task_process":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_ALLELE_COUNTS","task_name":"NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:SOMATIC_CNV_CALLING:SOMA_CNV_ALLELE_COUNTS
      (Sig_18_tissue)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: sarek-regression-somacnv-v2-e8451078-r7j4c,
    uid: 56645214-d995-4a83-a162-3dd7c8d3227e, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-c5e09f79fe0a1a21147850e4de21008f-99afe
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/soma-cnv:20260604-348e5b5
        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/c5/e09f79fe0a1a21147850e4de21008f/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/c5/e09f79fe0a1a21147850e4de21008f/.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: 4, memory: 16384Mi, ephemeral-storage: 102400Mi}
          limits: {memory: 16384Mi, ephemeral-storage: 102400Mi}
        volumeMounts:
        - {name: vol-65, mountPath: /tmp}
        - {name: vol-66, mountPath: /app}
        - {name: vol-67, mountPath: /mnt/secrets}
        - {name: vol-68, 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-65
        emptyDir: []
      - name: vol-66
        emptyDir: []
      - name: vol-67
        secret: {secretName: aws-secrets-manager}
      - name: vol-68
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800