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.

params/input_to_run.json

@@ -0,0 +1,19 @@
+{
+  "container_biotransformer": "harbor.cluster.omic.ai/omic/digitaltrials/biotransformer@sha256:fb8bdc0b65376bc154b6051ae07079dd9a0e25c3f4c02de73c502002a94d69d5",
+  "container_conplex": "harbor.cluster.omic.ai/omic/digitaltrials/conplex_dig_pat@sha256:7a3523dba6fa01e3adc9cb79af5e1dcbd2a19d9f92e37cd10df462766078ede3",
+  "container_tissue": "harbor.cluster.omic.ai/omic/digitaltrials/tissue:1.0.2",
+  "container_preprocess": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:872c395e21abd4afea4185b269a8218da4737bd7adbb2cbe2bdf9a1b9c70db17",
+  "container_mass_screen": "harbor.cluster.omic.ai/omic/metabolite-screen@sha256:89fe2221ff6c1e67d20294944f97418f2665d95b9fb873eba9e1fcf3dc6d1ea7",
+  "container_chembl": "harbor.cluster.omic.ai/omic/digitaltrials/chembl:1.0.0",
+  "containerOptions": "--rm",
+  "mode": "HUMAN",
+  "keep_enst": false,
+  "threshold": 0.65,
+  "protein_network_threshold": 0.65,
+  "project_name": "input_to_run",
+  "outdir": "/mnt/dreamdock-data/digital_trials/output",
+  "ligands": "/mnt/dreamdock-data/digital_trials/input/input_to_run",
+  "mutated_protein_fasta": "/mnt/dreamdock-data/digital_trials/input/blank",
+  "protein_zarr": "/mnt/dreamdock-data/digital_trials/zarr/protein_seq.zarr",
+  "chembl_db": "/mnt/dreamdock-data/digital_trials/chembl/chembl_36.db"
+}