apiVersion: apps/v1
kind: Deployment
metadata:
  name: digital-patient-nextflow
  namespace: bioinformatics
spec:
  progressDeadlineSeconds: 600
  replicas: 1
  revisionHistoryLimit: 10
  selector:
    matchLabels:
      app: digital-patient-nextflow
  strategy:
    rollingUpdate:
      maxSurge: 25%
      maxUnavailable: 25%
    type: RollingUpdate
  template:
    metadata:
      creationTimestamp: null
      labels:
        app: digital-patient-nextflow
    spec:
      containers:
      - command:
        - sleep
        - infinity
        image: nextflow/nextflow:25.04.6
        imagePullPolicy: IfNotPresent
        name: nextflow
        workingDir: /mnt/dreamdock-data/digital-patient-data
        resources:
          limits:
            cpu: "2"
            memory: 4Gi
          requests:
            cpu: "1"
            memory: 2Gi
        terminationMessagePath: /dev/termination-log
        terminationMessagePolicy: File
        volumeMounts:
        - mountPath: /mnt/Avatar
          name: avatar-new-volume
        - mountPath: /mnt/dreamdock-data/
          name: dreamdock-volume
      dnsPolicy: ClusterFirst
      restartPolicy: Always
      schedulerName: default-scheduler
      securityContext: {}
      serviceAccount: nextflow-sa
      serviceAccountName: nextflow-sa
      terminationGracePeriodSeconds: 30
      volumes:
      - name: avatar-new-volume
        persistentVolumeClaim:
          claimName: avatar-new                     # CHANGE ME, RELATE TO nextflow.params.input
      - name: dreamdock-volume
        persistentVolumeClaim:
          claimName: dreamdock-data                     # CHANGE ME, RELATE TO nextflow.params.input
# ---
# apiVersion: v1
# kind: PersistentVolumeClaim
# metadata:
#   name: digital-patient-data
#   namespace: bioinformatics
# spec:
#   accessModes:
#   - ReadWriteMany
#   resources:
#     requests:
#       storage: 6000Gi
#   storageClassName: truenas-nfs