apiVersion: batch/v1
kind: Job
metadata:
  name: nf-897a02f3fc65a54117fc5403e69a8477-9c455
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_CRAM_FILTER_LOW_READS_SAMTOOLS_IDXSTATS_COUN,
    nextflow.io/runName: mimsi-low-input-remaining-20260603-225957, capacityType: spot,
    pltf/run-component: task, nextflow.io/app: nextflow, nextflow.io/taskName: NFCORE_SAREK_SAREK_CRAM_FILTER_LOW_READS_SAMTOOLS_IDXSTATS_COUN,
    pltf/run-id: 15e4090d, pltf/run-creator: mbotlaniesfahani, nextflow.io/sessionId: uuid-5e05fe9e-3412-4e7a-bb73-d75a2bcec89a,
    pltf/run-name: mimsi-low-input-remaining-20260603-225957, instanceMinCpuSpeedMhz: '2200',
    pltf/run-engine: nextflow, instanceLocalNvme: 'true'}
  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":"mimsi-low-input-remaining-20260603-225957","run_id":"15e4090d","run_creator":"mbotlaniesfahani","run_component":"task","task_process":"NFCORE_SAREK:SAREK:CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT","task_name":"NFCORE_SAREK:SAREK:CRAM_FILTER_LOW_READS:SAMTOOLS_IDXSTATS_COUNT
      (1029_0NX-N1-BDNA-1_235YY7LT3_1)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: mimsi-low-input-remaining-20260603-225957-15e4090d-dnsl8,
    uid: 6cc1a959-f416-4cda-b278-cdacf01ff383, controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-897a02f3fc65a54117fc5403e69a8477-9c455
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: 292967571998.dkr.ecr.us-west-2.amazonaws.com/quay/biocontainers/multiqc:1.25.1--pyhdfd78af_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/89/7a02f3fc65a54117fc5403e69a8477/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/89/7a02f3fc65a54117fc5403e69a8477/.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: 2048Mi, ephemeral-storage: 5120Mi}
          limits: {memory: 2048Mi, ephemeral-storage: 5120Mi}
        volumeMounts:
        - {name: vol-29, mountPath: /tmp}
        - {name: vol-30, mountPath: /app}
        - {name: vol-31, mountPath: /mnt/secrets}
        - {name: vol-32, 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}
              - key: eks.amazonaws.com/instance-cpu-sustained-clock-speed-mhz
                operator: Gt
                values: ['2200']
      serviceAccountName: sa-nextflow
      securityContext: {runAsUser: 1000}
      tolerations:
      - {key: workload, operator: Equal, value: nextflow-task, effect: NoSchedule}
      activeDeadlineSeconds: 14400
      volumes:
      - name: vol-29
        emptyDir: []
      - name: vol-30
        emptyDir: []
      - name: vol-31
        secret: {secretName: aws-secrets-manager}
      - name: vol-32
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800