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.

nf_metabol_screen_adaptive/test.nf

@@ -0,0 +1,17 @@
+#!/usr/bin/env nextflow
+
+// params.input_tsv = '../sample/in-molecule/test_known_drugs.tsv'   //metabolites.tsv'
+params.input_tsv = '../sample/in-molecule/metabolites-rev.tsv'   //metabolites.tsv'
+params.input_zarr = '../data/protein_seq.zarr' //mane_all.zarr'
+
+// Include the buildFaissIndex workflow from main.nf
+include { METABOLITE_SCREEN } from './main.nf'
+
+workflow {
+    
+    input_tsv = file(params.input_tsv)
+    input_zarr = file(params.input_zarr)
+    
+    // Call the combined workflow with both inputs
+    protein_scores = METABOLITE_SCREEN(input_tsv, input_zarr)
+}