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.

nextflow.config.old

@@ -0,0 +1,69 @@
+manifest {
+    name                = 'Dream Dock'
+    author              = 'omic'
+    recurseSubmodules   = true
+    homePage            = 'https://gitlab.com/omic/next/registry/pipelines/dreamdock'
+    description         = 'Small drug creation based on a protein target'
+    mainScript          = 'main.nf'
+    nextflowVersion     = '!>=21.04.3'
+    defaultBranch       = 'master'
+}
+
+docker {
+    enabled = true
+    temp = 'auto'
+}
+
+profiles {
+  k8s {
+    process.executor = 'k8s'
+    process.namespace = 'bioinformatics'  
+    process.debug = true
+
+    workDir = "/mnt/dreamdock-data/work"
+
+    k8s {
+      serviceAccount = 'nextflow-sa'
+      namespace = 'bioinformatics'
+      storageClaimName = 'dreamdock-data'
+      storageMountPath = '/mnt/dreamdock-data'
+      
+      pullPolicy = 'IfNotPresent'
+      cleanup = true                    // delete pods after Ctrl+C or finished?
+      
+
+      // RUN AS DIFFERENT USERS
+      // securityContext = [fsGroup: 1000]
+      // securityContext = [
+      //   runAsUser: 1000,
+      //   fsGroup: 1000,
+      //   runAsNonRoot: true
+      // ]
+    }
+    
+    // Use container image
+    // process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
+
+    // Pod-level customization
+    process.pod = [
+      [env: 'NXF_DEBUG', value: '0'],
+      [label: 'omic-app', value: 'dreamdock'],
+      [imagePullSecret: 'gitlab-registry-secret'],
+      [hostPath: '/mnt/ZINC-22/', mountPath: '/mnt/ZINC-22/'],
+      [nodeSelector: [gpu: 'yes', 'gpu-type': 'rtx-3090']],
+      [volumeClaim: 'conplex-index-builder-data', mountPath: '/mnt/conplex-index/']
+      //[nodeSelector: [gpu: 'yes', 'kubernetes.io/hostname': 'k8s-node25']],
+      // [privileged: true],
+    ]
+
+  }
+
+  docker {
+    // Docker/Singularity configuration
+    docker {
+      enabled = true
+      runOptions = '--rm'
+    }
+  }
+}
+