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.

.gitignore

@@ -0,0 +1,12 @@
+work
+.nextflow
+*.ignored
+ncbiproteins_seq*
+
+/input/
+
+# Large STRING-DB reference files (baked into Docker image, not needed in git)
+app_network/9606.protein.aliases.v12.0.txt
+app_network/9606.protein.enrichment.terms.v12.0.txt
+app_network/9606.protein.links.detailed.v12.0.txt
+app_network/9606.protein.links.v12.0.txt