Digital Trials pipeline configured for WES

Source-only snapshot of the cluster branch for WES execution. Large
reference files (HPA/MANE/ensemble FASTA, model weights, ~597 MB) are
omitted: they are baked into the container images at build time and
mounted from the dreamdock-data PVC at runtime, and exceed the Gitea
request size limit.

Pipeline entry point is main.nf, which orchestrates the biotransformer,
conplex and tissue modules as a single workflow. Ligand inputs are read
from the eureka workspace; protein_zarr and chembl_db come from the
dreamdock-data PVC.

k8s/README.md

@@ -0,0 +1,15 @@
+# access the current workspace
+kubectl exec -it -n bioinformatics $(kubectl get pod -l app=digital-trials-nextflow -n bioinformatics | grep Run | awk '{ print $1 }') --  bash
+nextflow run main.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-trials.yaml
+
+# [WARNING] destroy the curent nextflow job
+kubectl delete -f k8s/job-nextflow-digital-trials.yaml