apiVersion: batch/v1
kind: Job
metadata:
  name: nf-dbe2e6289440d290432c44af87cc89c3-314e6
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_VCF_QC_BCFTOOLS_VCFTOOLS_BCFTOOLS_STATS,
    nextflow.io/runName: fusion_v2_220samples_90a6e5e8-0605-1411, nextflow.io/sessionId: uuid-965dafb0-390c-4535-9b16-79dbb12732c0,
    pltf/run-name: fusion_v2_220samples_90a6e5e8-0605-1411, capacityType: spot, pltf/run-component: task,
    nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_SAREK_SAREK_VCF_QC_BCFTOOLS_VCFTOOLS_BCFTOOLS_STATS_117,
    pltf/run-id: '20e90645', pltf/run-engine: nextflow, instanceLocalNvme: 'false',
    pltf/run-creator: rsrivas}
  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":"fusion_v2_220samples_90a6e5e8-0605-1411","run_id":"20e90645","run_creator":"rsrivas","run_component":"task","task_process":"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS","task_name":"NFCORE_SAREK:SAREK:VCF_QC_BCFTOOLS_VCFTOOLS:BCFTOOLS_STATS
      (1173_KQG-T1-TDNA-01_A23T3TCLT4_1_vs_1173_KQG-N1-BDNA-01_A23KFG7LT4_1;manta_fusion)"}',
    karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: fusion-v2-220samples-90a6e5e8-0605-1411-20e90645-mmz28,
    uid: 3472e6a6-dbe0-420e-83e2-a36274a0caf2, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-dbe2e6289440d290432c44af87cc89c3-314e6
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/bcftools:1.20--h8b25389_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/db/e2e6289440d290432c44af87cc89c3/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/db/e2e6289440d290432c44af87cc89c3/.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: 1, memory: 2048Mi, ephemeral-storage: 51200Mi}
          limits: {memory: 2048Mi, ephemeral-storage: 51200Mi}
        volumeMounts:
        - {name: vol-3221, mountPath: /app}
        - {name: vol-3222, mountPath: /tmp}
        - {name: vol-3223, mountPath: /mnt/secrets}
        - {name: vol-3224, 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-3221
        emptyDir: []
      - name: vol-3222
        emptyDir: []
      - name: vol-3223
        secret: {secretName: aws-secrets-manager}
      - name: vol-3224
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800