digital-patients/k8s/README.md

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