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.

Dockerfile_chembl

@@ -0,0 +1,15 @@
+FROM mambaorg/micromamba:2.1.1
+
+USER root
+
+ARG MAMBA_DOCKERFILE_ACTIVATE=1 
+
+RUN micromamba install -n base -y -c conda-forge --channel-priority flexible \
+        python=3.12 \
+        numpy \
+        pandas \
+        rdkit \
+        procps-ng
+
+# Note: No need for requests or chembl-downloader in the container
+# since we're passing the pre-downloaded database as input