Add WES pipeline configuration for pocketminer

- Add Nextflow pipeline (main.nf) with Harbor container image
- Add nextflow.config with k8s/k8s_gpu/standard profiles
- Add params.json for TRS/WES parameter discovery
- Add Dockerfile, entrypoint.py, meta.yml from original implementation
- Update paths to use /omic/eureka/Pocketminer/ convention
- Update .gitignore to allow params.json

Dockerfile

@@ -0,0 +1,37 @@
+FROM continuumio/miniconda3:latest
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Update and install basic dependencies
+RUN apt-get update -y \
+    && apt-get -y upgrade --fix-missing \
+    && apt-get -y install git procps coreutils wget \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+WORKDIR /workspace
+
+# Clone PocketMiner repository
+RUN git clone https://github.com/Mickdub/gvp.git \
+    && cd gvp \
+    && git checkout pocket_pred
+
+# Create conda environment and install dependencies
+RUN conda create -n pocketminer python=3.9 -y && \
+    conda install -n pocketminer -c conda-forge \
+    numpy scipy pandas tensorflow tqdm mdtraj pyyaml -y && \
+    conda clean -afy
+
+# Activate environment and set up PATH
+ENV PATH=/opt/conda/envs/pocketminer/bin:$PATH
+ENV CONDA_DEFAULT_ENV=pocketminer
+
+# Copy entrypoint script
+COPY entrypoint.py /workspace/entrypoint.py
+RUN chmod +x /workspace/entrypoint.py
+
+# Set Python path to include the gvp/src directory
+ENV PYTHONPATH=/workspace/gvp/src:$PYTHONPATH
+
+# Default command
+CMD ["python", "/workspace/entrypoint.py", "--help"]