apiVersion: batch/v1
kind: Job
metadata:
  name: nf-80e56c456c96c7bbba8532e483b97490-2400b
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: DAQ_SENTIEON_BWAMEM, nextflow.io/runName: gitlab-daq-build2789101-regression-run-63291544,
    nextflow.io/sessionId: uuid-8940394b-f2c0-4e29-8e8b-152155dff1b2, pltf/run-name: gitlab-daq-build2789101-regression-run-63291544,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: DAQ_SENTIEON_BWAMEM_Sig_18_Blood_L004_0001,
    pltf/run-id: 1a5b75c0, pltf/run-engine: nextflow, instanceLocalNvme: 'true', pltf/run-creator: svc-gitlab-ci}
  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":"gitlab-daq-build2789101-regression-run-63291544","run_id":"1a5b75c0","run_creator":"svc-gitlab-ci","run_component":"task","task_process":"DAQ:SENTIEON_BWAMEM","task_name":"DAQ:SENTIEON_BWAMEM
      (Sig_18_Blood;L004;0001)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: gitlab-daq-build2789101-regression-run-63291544-1a5b75c0-xdpmr,
    uid: f397f13a-50ec-4a3c-9c62-d5c5755fb58d, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-80e56c456c96c7bbba8532e483b97490-2400b
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/daq/markduplicates_sentieon:202308.03-1
        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/80/e56c456c96c7bbba8532e483b97490/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/80/e56c456c96c7bbba8532e483b97490/.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: 31, memory: 128000Mi, ephemeral-storage: 192512Mi}
          limits: {memory: 128000Mi, ephemeral-storage: 192512Mi}
        volumeMounts:
        - {name: vol-241, mountPath: /tmp}
        - {name: vol-242, mountPath: /app}
        - {name: vol-243, mountPath: /mnt/secrets}
        - {name: vol-244, 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}
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      volumes:
      - name: vol-241
        emptyDir: []
      - name: vol-242
        emptyDir: []
      - name: vol-243
        secret: {secretName: aws-secrets-manager}
      - name: vol-244
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800