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/README.md

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+# access the current workspace
+kubectl exec -it -n bioinformatics $(kubectl get pod -l app=digital-patient-nextflow -n bioinformatics | grep Run | awk '{ print $1 }') --  bash
+nextflow run test.nf -profile k8s 
+
+# DEPRECATE: cleanup error pods in bioinformatics
+kubectl get pod -n bioinformatics | grep -E "Pending|Error" | awk '{print $1}' | xargs -P 10 -I {} kubectl delete pod -n bioinformatics {}
+
+# sync data (/data/bugra/similarity-search/utility/vec_db/nf_fingerptint) from node to workspace
+kubectl delete -f k8s/job-copy-node-to-pvc.yaml; kubectl apply -f k8s/job-copy-node-to-pvc.yaml
+
+# run the actual nextflow jobs
+kubectl apply -f k8s/job-nextflow-digital-patient.yaml
+
+# [WARNING] destroy the curent nextflow job
+kubectl delete -f k8s/job-nextflow-digital-patient.yaml