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/job-nextflow-digital-patient.yaml

@@ -0,0 +1,52 @@
+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