apiVersion: batch/v1
kind: Job
metadata:
  name: nf-cbe54e38abeee6255f1828b8ad7820fa-f1229
  namespace: nextflow
  labels: &id001 {nextflow.io/processName: NFCORE_SAREK_SAREK_CRAM_SAMPLE_INTEGRITY_CRAM_QC_RECAL_SAMTOOLS,
    nextflow.io/runName: sarek-somacnv-functional, nextflow.io/sessionId: uuid-b5387d49-72c9-4ff8-aa3c-dbb27a6c7df7,
    pltf/run-name: sarek-somacnv-functional, pltf/run-component: task, nextflow.io/app: nextflow,
    nextflow.io/taskName: NFCORE_SAREK_SAREK_CRAM_SAMPLE_INTEGRITY_CRAM_QC_RECAL_SAMTOOLS,
    pltf/run-id: 7734f803, pltf/run-engine: nextflow, pltf/run-creator: chnobles}
  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":"sarek-somacnv-functional","run_id":"7734f803","run_creator":"chnobles","run_component":"task","task_process":"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS","task_name":"NFCORE_SAREK:SAREK:CRAM_SAMPLE_INTEGRITY:CRAM_QC_RECAL:SAMTOOLS_STATS
      (1029_11H-T1-TDNA-1_B23KFCWLT4_1)"}', karpenter.sh/do-not-disrupt: 'true'}
  ownerReferences:
  - {apiVersion: v1, kind: Pod, name: sarek-somacnv-functional-7734f803-n89dd, uid: 7d99ce7a-1106-4353-b0a2-84acf00bdfe2,
    controller: true, blockOwnerDeletion: true}
spec:
  backoffLimit: 0
  template:
    metadata:
      name: nf-cbe54e38abeee6255f1828b8ad7820fa-f1229
      namespace: nextflow
      labels: *id001
      annotations: *id002
    spec:
      restartPolicy: Never
      containers:
      - name: nextflow
        image: quay.io/biocontainers/samtools:1.21--h50ea8bc_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/cb/e54e38abeee6255f1828b8ad7820fa/.command.log||true;
            exit $ret; }" EXIT; /opt/s5cmd/bin/s5cmd --log error cat s3://natera-rnd-pltf-dev-nextflow-scratch-01/work/cb/e54e38abeee6255f1828b8ad7820fa/.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: 6144Mi, ephemeral-storage: 20480Mi}
          limits: {memory: 6144Mi, ephemeral-storage: 20480Mi}
        volumeMounts:
        - {name: vol-125, mountPath: /app}
        - {name: vol-126, mountPath: /tmp}
        - {name: vol-127, mountPath: /mnt/secrets}
        - {name: vol-128, 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-125
        emptyDir: []
      - name: vol-126
        emptyDir: []
      - name: vol-127
        secret: {secretName: aws-secrets-manager}
      - name: vol-128
        hostPath: {path: /opt/s5cmd}
  ttlSecondsAfterFinished: 28800