apiVersion: batch/v1
kind: Job
metadata:
  name: nf-059bddda1b65da4a9558ce63d09935cc-92ef4
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_HARMONIZE_HARMONIZE_FILTER_HOTSPOT_VCF,
    nextflow.io/runName: hmnz-cgp-dna-exp0035-20260606-022813, nextflow.io/sessionId: uuid-02a7a0a2-75c7-4a9f-81d6-141deaf746e1,
    pltf/run-name: hmnz-cgp-dna-exp0035-20260606-022813, capacityType: spot, pltf/run-component: task,
    nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_HARMONIZE_HARMONIZE_FILTER_HOTSPOT_VCF_FFPE_HD789_01_p2,
    pltf/run-id: d859d467, pltf/run-engine: nextflow, pltf/run-creator: sgreer}
  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":"hmnz-cgp-dna-exp0035-20260606-022813","run_id":"d859d467","run_creator":"sgreer","run_component":"task","task_process":"NFCORE_HARMONIZE:HARMONIZE:FILTER_HOTSPOT_VCF","task_name":"NFCORE_HARMONIZE:HARMONIZE:FILTER_HOTSPOT_VCF
      (FFPE_HD789_01_p2_gDNA_03_A23WJ5GLT4_1_vs_NA12878_c_0002_gDNA_0005_B23KYWJLT4_1)"}',
    karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: hmnz-cgp-dna-exp0035-20260606-022813-d859d467-fvvvr,
    uid: fcf44696-8d1a-4c45-802a-1457bd5ed261, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-059bddda1b65da4a9558ce63d09935cc-92ef4
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/pysam-pandas-python3:1.1.0
        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/05/9bddda1b65da4a9558ce63d09935cc/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/05/9bddda1b65da4a9558ce63d09935cc/.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: 1, memory: 4096Mi, ephemeral-storage: 20480Mi}
          limits: {memory: 4096Mi, ephemeral-storage: 20480Mi}
        volumeMounts:
        - {name: vol-3481, mountPath: /tmp}
        - {name: vol-3482, mountPath: /app}
        - {name: vol-3483, mountPath: /mnt/secrets}
        - {name: vol-3484, 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}
      activeDeadlineSeconds: 14400
      volumes:
      - name: vol-3481
        emptyDir: []
      - name: vol-3482
        emptyDir: []
      - name: vol-3483
        secret: {secretName: aws-secrets-manager}
      - name: vol-3484
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800