apiVersion: batch/v1
kind: Job
metadata:
  name: nf-36f6133db8ba2bc86c713e98a863cf4c-d8a0f
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: MUTECT2_TUMOR_ONLY, nextflow.io/runName: tso_500_mutect_recall_3,
    nextflow.io/sessionId: uuid-89d140fb-3032-4049-921a-3bcb062b559d, pltf/run-name: tso_500_mutect_recall_3,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: MUTECT2_TUMOR_ONLY_LS0902,
    pltf/run-id: 2cc95a90, pltf/run-engine: nextflow, pltf/run-creator: aschultz}
  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":"tso_500_mutect_recall_3","run_id":"2cc95a90","run_creator":"aschultz","run_component":"task","task_process":"MUTECT2_TUMOR_ONLY","task_name":"MUTECT2_TUMOR_ONLY
      (LS0902)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: tso-500-mutect-recall-3-2cc95a90-7hqdd, uid: 49b301f3-02b9-416a-abb8-408a33a042b1,
    controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-36f6133db8ba2bc86c713e98a863cf4c-d8a0f
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: broadinstitute/gatk:4.5.0.0
        args: [/bin/bash, -o, pipefail, -c, 'trap "{ ret=$?; /opt/s5cmd/bin/s5cmd
            --log error cp .command.log s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/36/f6133db8ba2bc86c713e98a863cf4c/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/36/f6133db8ba2bc86c713e98a863cf4c/.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: 4, memory: 16384Mi, ephemeral-storage: 102400Mi}
          limits: {memory: 16384Mi, ephemeral-storage: 102400Mi}
        volumeMounts:
        - {name: vol-93, mountPath: /tmp}
        - {name: vol-94, mountPath: /app}
        - {name: vol-95, mountPath: /mnt/secrets}
        - {name: vol-96, 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}
      volumes:
      - name: vol-93
        emptyDir: []
      - name: vol-94
        emptyDir: []
      - name: vol-95
        secret: {secretName: aws-secrets-manager}
      - name: vol-96
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800