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

Makefile

@@ -0,0 +1,66 @@
+.PHONY: help build run test clean
+
+# Default target
+help:
+	@echo "PocketMiner - Cryptic Pocket Prediction Tool"
+	@echo ""
+	@echo "Available targets:"
+	@echo "  make build       - Build Docker image (conda-based, includes all dependencies)"
+	@echo "  make run         - Run test prediction (requires test.pdb)"
+	@echo "  make test        - Run Nextflow pipeline on test data"
+	@echo "  make clean       - Clean up generated files"
+	@echo "  make shell       - Open shell in Docker container"
+	@echo "  make download-example - Download example PDB file"
+	@echo ""
+
+# Build Docker image (conda-based with all dependencies)
+build:
+	@echo "Building PocketMiner Docker image (conda-based)..."
+	docker build -t pocketminer:latest .
+	@echo "Build complete!"
+
+# Run single test prediction
+run:
+	@if [ ! -f test.pdb ]; then \
+		echo "Error: test.pdb not found. Please provide a test PDB file."; \
+		exit 1; \
+	fi
+	@echo "Running PocketMiner prediction on test.pdb..."
+	docker run --rm \
+		-v $(PWD):/data \
+		pocketminer:latest \
+		python /workspace/entrypoint.py \
+			--pdb /data/test.pdb \
+			--output-folder /data/output \
+			--output-name test
+	@echo "Results saved to output/"
+
+# Run Nextflow pipeline
+test:
+	@echo "Running Nextflow pipeline..."
+	nextflow run main.nf
+	@echo "Pipeline complete!"
+
+# Clean generated files
+clean:
+	@echo "Cleaning up..."
+	rm -rf output/
+	rm -rf .nextflow/
+	rm -f .nextflow.log*
+	rm -rf work/
+	rm -rf results/
+	rm -f *.npy *.txt
+	@echo "Clean complete!"
+
+# Open shell in container
+shell:
+	docker run --rm -it \
+		-v $(PWD):/data \
+		pocketminer:latest \
+		/bin/bash
+
+# Download example PDB (if internet available)
+download-example:
+	@echo "Downloading example PDB (1HSG - HIV protease)..."
+	wget -O test.pdb https://files.rcsb.org/download/1HSG.pdb
+	@echo "Example downloaded as test.pdb"