apiVersion: batch/v1
kind: Job
metadata:
  name: nf-952190e27992dd2a2ea4578f74349100-df384
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_CRAM_SAMPLE_INTEGRITY_CRAM_QC_RECAL_SAMTOOLS,
    nextflow.io/runName: sarek-somacnv-functional-v2, capacityType: spot, pltf/run-component: task,
    nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_SAREK_SAREK_CRAM_SAMPLE_INTEGRITY_CRAM_QC_RECAL_SAMTOOLS,
    pltf/run-id: 653ee71f, pltf/run-creator: chnobles, nextflow.io/sessionId: uuid-36866653-3a95-4ccf-a4cd-efe5a0fd6643,
    pltf/run-name: sarek-somacnv-functional-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-somacnv-functional-v2","run_id":"653ee71f","run_creator":"chnobles","run_component":"task","task_process":"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS","task_name":"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS
      (1029_0W2-T1-TDNA-1_A23KCGYLT4_1)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: sarek-somacnv-functional-v2-653ee71f-j8npr,
    uid: 09707f78-7619-4dda-a4f5-1dfd27a1594c, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-952190e27992dd2a2ea4578f74349100-df384
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/samtools:1.21--h50ea8bc_0
        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/95/2190e27992dd2a2ea4578f74349100/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/95/2190e27992dd2a2ea4578f74349100/.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: 4096Mi, ephemeral-storage: 204800Mi}
          limits: {memory: 4096Mi, ephemeral-storage: 204800Mi}
        volumeMounts:
        - {name: vol-105, mountPath: /tmp}
        - {name: vol-106, mountPath: /app}
        - {name: vol-107, mountPath: /mnt/secrets}
        - {name: vol-108, 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-105
        emptyDir: []
      - name: vol-106
        emptyDir: []
      - name: vol-107
        secret: {secretName: aws-secrets-manager}
      - name: vol-108
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800