Mount the dreamdock-data PVC in the k8s profile, and probe for it

The PVC holding chembl_36.db and protein_seq.zarr was never mounted into task
pods: WES's injected profile.config supplies no storage config (verified across
a full run's logs). Without /mnt/dreamdock-data, sqlite3 raises 'unable to open
database file' and every GET_FINAL_METABOLITES_STATIC task exits 1.

Restore storageClaimName/storageMountPath, and add a probe that reports what is
visible before opening sqlite so the failure names its own cause.

main_biotransformer.nf

@@ -302,6 +302,30 @@ process GET_FINAL_METABOLITES_STATIC {
     import numpy as np
     import pandas as pd
     import sqlite3
+    import os, sys
+
+    # --- diagnostic probe -------------------------------------------------
+    # The ChEMBL DB lives on the dreamdock-data PVC. If that PVC is not mounted
+    # into the task pod, sqlite3 fails with a generic "unable to open database
+    # file" that is indistinguishable from a corrupt/locked DB. Report what is
+    # actually visible before touching sqlite, so the failure names its cause.
+    _db = '$chembl_db'
+    print('[probe] chembl_db path : %s' % _db, file=sys.stderr)
+    print('[probe] exists         : %s' % os.path.exists(_db), file=sys.stderr)
+    for _p in ('/mnt/dreamdock-data', os.path.dirname(_db)):
+        print('[probe] dir %-22s exists=%s' % (_p, os.path.isdir(_p)), file=sys.stderr)
+    if os.path.exists(_db):
+        print('[probe] size           : %d bytes' % os.path.getsize(_db), file=sys.stderr)
+        print('[probe] readable       : %s' % os.access(_db, os.R_OK), file=sys.stderr)
+    else:
+        sys.exit(
+            "[probe] FATAL: %s is not visible inside this task container.\n"
+            "[probe] The dreamdock-data PVC is not mounted. Check that the k8s\n"
+            "[probe] profile sets k8s.storageClaimName/storageMountPath and that\n"
+            "[probe] the WES-injected profile.config does not override them."
+            % _db
+        )
+    # --- end probe --------------------------------------------------------
 
     # Connect to ChEMBL database
     conn = sqlite3.connect('file:$chembl_db?mode=ro&immutable=1', uri=True)

nextflow.config

@@ -30,14 +30,25 @@ process {
 }
 
 profiles {
-  // Minimal k8s profile: WES injects its own profile.config via -C, which supplies the
-  // executor, namespace, service account, workDir and PVC mounts. Anything set here that
-  // WES also sets is either overridden or conflicts, so keep this deliberately sparse.
+  // Minimal k8s profile for WES. WES injects its own profile.config via -C, which
+  // supplies the executor, namespace, service account and workDir — so those are
+  // deliberately left out here to avoid conflicting with it.
   //
-  // NOTE: the dreamdock-data PVC must be mounted by the WES-side profile for
-  // params.protein_zarr and params.chembl_db (/mnt/dreamdock-data/...) to resolve.
+  // The storage block is NOT optional. WES's injected profile does not mount any
+  // PVC (verified: a full experiment run produced 468 KB of logs with zero
+  // references to dreamdock/storageClaimName/volumeClaim). Without it,
+  // /mnt/dreamdock-data does not exist inside task pods and every process that
+  // reads params.chembl_db or params.protein_zarr fails immediately —
+  // GET_FINAL_METABOLITES_STATIC dies with
+  //   sqlite3.OperationalError: unable to open database file
+  // and exit status 1, on every task, regardless of input.
   k8s {
     process.executor = 'k8s'
+
+    k8s {
+      storageClaimName = 'dreamdock-data'
+      storageMountPath = '/mnt/dreamdock-data'
+    }
   }
 
   // Full standalone k8s profile for running this pipeline directly (not via WES),