apiVersion: batch/v1
kind: Job
metadata:
  name: nf-a0db03e061b19d4d1f0e81e16fb7610e-027ec
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: TASTER_FREQ__1, nextflow.io/runName: gui-test-9,
    nextflow.io/sessionId: uuid-63615c3f-74c3-46e8-92a1-b58fe6439d91, pltf/run-name: gui-test-9,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: TASTER_FREQ__1_one.deduped.bam,
    pltf/run-id: 4c806f7e, 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":"gui-test-9","run_id":"4c806f7e","run_creator":"aschultz","run_component":"task","task_process":"TASTER_FREQ__1","task_name":"TASTER_FREQ__1
      (one.deduped.bam)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: gui-test-9-4c806f7e-s9qzp, uid: 6cae6581-4946-4014-8e7a-4fc0c58b3af8,
    controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-a0db03e061b19d4d1f0e81e16fb7610e-027ec
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 644019535899.dkr.ecr.us-west-2.amazonaws.com/lcgp/rmdupes:taster-ts500-0.0.0
        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/a0/db03e061b19d4d1f0e81e16fb7610e/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-fsdx-dev-nextflow-scratch-01/work/a0/db03e061b19d4d1f0e81e16fb7610e/.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: 4096Mi, ephemeral-storage: 20480Mi}
          limits: {memory: 4096Mi, ephemeral-storage: 20480Mi}
        volumeMounts:
        - {name: vol-65, mountPath: /app}
        - {name: vol-66, mountPath: /tmp}
        - {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}
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      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