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.

test_string_only.nf

@@ -0,0 +1,27 @@
+nextflow.enable.dsl=2
+
+// STRING-only re-run workflow
+// Feeds existing ConPLex significant_interactions files into NETWORK_ENRICHMENT
+//
+// Required params:
+//   interactions  - directory containing *_significant_interactions.tsv files
+//   interaction_ids - comma-separated InChIKey prefixes to select (e.g. "PWKSKIMOESPYIA_SCSAIBSYSA_N,ZETLRLRYANUSAI_SCSAIBSYSA_N")
+//                     if empty/not set, all files in the directory are used
+
+params.protein_network_threshold = 0.65
+
+include { NETWORK_ENRICHMENT } from './main_conplex.nf'
+
+workflow {
+    if (params.interaction_ids) {
+        // Build a channel from the explicit list of IDs
+        ids = params.interaction_ids.tokenize(',')
+        interactions_ch = Channel
+            .fromList(ids)
+            .map { id -> file("${params.interactions}/${id}_patient_0_significant_interactions.tsv") }
+    } else {
+        interactions_ch = Channel.fromPath("${params.interactions}/*_significant_interactions.tsv")
+    }
+
+    NETWORK_ENRICHMENT(interactions_ch)
+}