Add BioEmu Nextflow pipeline implementation

Dockerfile

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+FROM nvidia/cuda:12.2.0-runtime-ubuntu22.04
+
+# Set non-interactive installation
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install system dependencies
+RUN apt-get update && apt-get install -y \
+    wget \
+    git \
+    python3 \
+    python3-pip \
+    build-essential \
+    curl \
+    python3-tk \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set working directory
+WORKDIR /opt/bioemu
+
+# Install Python dependencies
+RUN python3 -m pip install --upgrade pip
+
+# Install BioEmu from PyPI
+RUN pip install bioemu
+
+# Install dependencies for free energy calculation
+RUN pip install mdtraj scikit-learn pandas matplotlib seaborn
+
+# Create directory for ColabFold and set environment variable
+ENV COLABFOLD_DIR=/opt/colabfold
+
+# Create cache directories with proper permissions
+RUN mkdir -p ${COLABFOLD_DIR}/embeds_cache /tmp/colabfold_temp && \
+    chmod -R 777 ${COLABFOLD_DIR} /tmp/colabfold_temp
+
+# Pre-setup ColabFold during build to avoid runtime issues
+RUN wget "https://raw.githubusercontent.com/YoshitakaMo/localcolabfold/5fc8775114b637b5672234179c50e694ab057db4/install_colabbatch_linux.sh" -O ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
+    chmod +x ${COLABFOLD_DIR}/install_colabbatch_linux.sh && \
+    bash ${COLABFOLD_DIR}/install_colabbatch_linux.sh
+
+# Create directories for input/output with proper permissions
+RUN mkdir -p /data /results && chmod -R 777 /data /results
+
+RUN mkdir -p /opt/bioemu/scripts/
+COPY calculate_gibbs.py /opt/bioemu/scripts/
+RUN chmod +x /opt/bioemu/scripts/calculate_gibbs.py
+
+CMD ["/bin/bash"]