Add BioEmu Nextflow pipeline implementation

setup.sh

@@ -0,0 +1,21 @@
+#!/bin/bash
+
+# Set up directory structure for BioEmu workflow
+BASE_DIR="/mnt/OmicNAS/private/old/olamide/bioemu"
+
+# Create necessary directories
+mkdir -p ${BASE_DIR}/input
+mkdir -p ${BASE_DIR}/output
+mkdir -p ${BASE_DIR}/cache
+mkdir -p ${BASE_DIR}/scripts
+
+# Copy FASTA files
+cp villin_headpiece.fasta ${BASE_DIR}/input/
+cp trp_cage.fasta ${BASE_DIR}/input/
+
+# Copy scripts
+cp calculate_gibbs.py ${BASE_DIR}/scripts/
+chmod +x ${BASE_DIR}/scripts/calculate_gibbs.py
+
+echo "Directory structure set up at ${BASE_DIR}"
+echo "FASTA files and scripts copied"