Configure bioemu for WES deployment

- Update main.nf: Harbor container image, PVC mount paths, remove containerOptions and stageInMode
- Update nextflow.config: Add k8s/k8s_gpu profiles, minimal config for WES injection
- Update params.json: Correct paths for eureka PVC
- Update Dockerfile.wes: CUDA base image for GPU support

Dockerfile.wes

@@ -1,15 +1,14 @@
-FROM python:3.11-slim
+FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04
+
+ENV DEBIAN_FRONTEND=noninteractive
+
+RUN apt-get update && apt-get install -y \
+    wget git python3 python3-pip build-essential curl \
+    && rm -rf /var/lib/apt/lists/*
 
 WORKDIR /opt/bioemu
 
-# Install minimal system deps
-RUN apt-get update && apt-get install -y --no-install-recommends \
-    gcc g++ && rm -rf /var/lib/apt/lists/*
-
-# Install bioemu with CPU-only PyTorch first (smaller)
-# The k8s GPU nodes will have CUDA drivers available
-RUN pip install --no-cache-dir --upgrade pip && \
-    pip install --no-cache-dir torch --index-url https://download.pytorch.org/whl/cpu && \
+RUN python3 -m pip install --upgrade pip && \
     pip install --no-cache-dir bioemu mdtraj scikit-learn pandas matplotlib seaborn
 
 RUN mkdir -p /opt/bioemu/scripts/ /data /results && chmod -R 777 /data /results