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

main.nf

@@ -1,23 +1,22 @@
 #!/usr/bin/env nextflow
 nextflow.enable.dsl=2
 
-// Define parameters
-params.complex_name = "hgh_mab1"  // Default complex name
-params.protein1_fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/complexes/hgh.fasta"
-params.protein2_fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/complexes/mab1.fasta"
-params.exp_dG = -13.1  // kcal/mol from experimental database
-params.outdir = "/mnt/OmicNAS/private/old/olamide/bioemu/output"
-params.cache_dir = "/mnt/OmicNAS/private/old/olamide/bioemu/cache"
+// Define parameters — PVC mount paths for k8s execution
+params.protein1_fasta = '/omic/eureka/bioemu/input/trp_cage.fasta'
+params.protein2_fasta = '/omic/eureka/bioemu/input/villin_headpiece.fasta'
+params.complex_name = "protein_complex"
+params.exp_dG = -10.0  // kcal/mol (placeholder experimental value)
+params.outdir = '/omic/eureka/bioemu/output'
+params.cache_dir = '/tmp/bioemu_cache'
 
 // Parameters for structure generation and analysis
-params.num_samples = 20
+params.num_samples = 10
 params.batch_size = 5
 params.temperature = 300
 params.n_clusters = 5
 
 process GENERATE_STRUCTURE {
-    container 'bioemu:latest'
-    containerOptions '--rm --gpus all -v /mnt:/mnt'
+    container 'harbor.cluster.omic.ai/omic/bioemu:latest'
     publishDir "${params.outdir}/${params.complex_name}/${protein_id}", mode: 'copy'
 
     input:
@@ -31,6 +30,9 @@ process GENERATE_STRUCTURE {
     # Extract sequence from FASTA
     SEQUENCE=\$(grep -v ">" ${fasta} | tr -d '\\n')
 
+    # Create cache dir
+    mkdir -p ${params.cache_dir}
+
     # Run BioEmu
     python3 -m bioemu.sample \\
         --sequence "\${SEQUENCE}" \\
@@ -46,8 +48,7 @@ process GENERATE_STRUCTURE {
 }
 
 process CALCULATE_BINDING {
-    container 'bioemu:latest'
-    containerOptions '--rm --gpus all -v /mnt:/mnt -v /data:/data'
+    container 'harbor.cluster.omic.ai/omic/bioemu:latest'
     publishDir "${params.outdir}/${params.complex_name}/analysis", mode: 'copy'
 
     input:
@@ -63,8 +64,8 @@ process CALCULATE_BINDING {
 
     script:
     """
-    # Run binding energy calculation with the existing script
-    python3 /data/olamide/fresh-bioemu2/scripts/calculate_binding.py \\
+    # Run binding energy calculation
+    python3 /opt/bioemu/scripts/calculate_binding.py \\
         --protein1_topology ${protein1_topology} \\
         --protein1_samples ${protein1_samples} \\
         --protein2_topology ${protein2_topology} \\
@@ -119,7 +120,7 @@ workflow {
                       .map { it -> tuple(it[1], it[2]) }
                       .first()
 
-    // Calculate binding energy (direct script reference)
+    // Calculate binding energy
     CALCULATE_BINDING(
         protein1_files[0],  // protein1_topology.pdb
         protein1_files[1],  // protein1_samples.xtc