apiVersion: batch/v1
kind: Job
metadata:
  name: job-nextflow-digital-patient
  namespace: bioinformatics
spec:
  backoffLimit: 1
  completionMode: NonIndexed
  completions: 1
  manualSelector: false
  parallelism: 1
  podReplacementPolicy: TerminatingOrFailed
  suspend: false
  template:
    spec:
      containers:
      - command:
        - /bin/bash
        - -c
        - cd /mnt/dreamdock-data/digital-patient-data && nextflow run test.nf -profile k8s
        image: nextflow/nextflow:25.04.6
        imagePullPolicy: IfNotPresent
        name: nextflow
        resources:
          limits:
            cpu: "4"
            memory: 8Gi
          requests:
            cpu: "2"
            memory: 4Gi
        terminationMessagePath: /dev/termination-log
        terminationMessagePolicy: File
        volumeMounts:
        - mountPath: /mnt/Avatar
          name: avatar-nas-volume
        - mountPath: /mnt/dreamdock-data/
          name: dreamdock-volume
      dnsPolicy: ClusterFirst
      restartPolicy: Never
      schedulerName: default-scheduler
      securityContext: {}
      serviceAccount: nextflow-sa
      serviceAccountName: nextflow-sa
      terminationGracePeriodSeconds: 30
      volumes:
      - name: avatar-nas-volume
        hostPath:
          path: /mnt/Avatar-NAS
          type: Directory
      - name: dreamdock-volume
        persistentVolumeClaim:
          claimName: dreamdock-data                     # CHANGE ME, RELATE TO nextflow.params.input