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.

Note.txt

@@ -0,0 +1,5 @@
+Add options for metabolites not existing and process failed
+Remove unnecessary data while process is running, take up too much memory
+
+
+ncbiproteins_seq_exist.csv is replaced with ncbiproteins_seq_exist_reduce.csv so it will be able to fit to gitlab