Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

k8s/deployment-worksplace.yaml

@@ -0,0 +1,72 @@
+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