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

nextflow.config

@@ -1,38 +1,55 @@
-// Manifest for Nextflow metadata
 manifest {
-    name = 'BioEmu-Nextflow'
-    author = 'Generated from BioEmu repository'
-    homePage = 'https://github.com/microsoft/bioemu'
-    description = 'Nextflow pipeline for BioEmu - Biomolecular Emulator for protein structure sampling'
+    name = 'bioemu'
+    author = 'Olamide'
+    description = 'BioEmu - Biomolecular Emulator for protein structure sampling and binding energy analysis'
     mainScript = 'main.nf'
     version = '1.0.0'
 }
 
-// Global default parameters
 params {
-    fasta = "/mnt/OmicNAS/private/old/olamide/bioemu/input/villin_headpiece.fasta"
-    outdir = "/mnt/OmicNAS/private/old/olamide/bioemu/output"
-    cache_dir = "/mnt/OmicNAS/private/old/olamide/bioemu/cache"
+    protein1_fasta = '/omic/eureka/bioemu/input/trp_cage.fasta'
+    protein2_fasta = '/omic/eureka/bioemu/input/villin_headpiece.fasta'
+    complex_name = 'protein_complex'
+    exp_dG = -10.0
+    outdir = '/omic/eureka/bioemu/output'
+    cache_dir = '/tmp/bioemu_cache'
     num_samples = 10
-    batch_size_100 = 10
+    batch_size = 5
+    temperature = 300
+    n_clusters = 5
 }
 
-// Container configurations
-docker {
-    enabled = true
-    runOptions = '--gpus all'
-}
+profiles {
+    standard {
+        docker {
+            enabled = true
+            runOptions = '--gpus all'
+        }
+    }
 
-// Process configurations
-process {
-    cpus = 1
-    memory = '8 GB'
-}
+    k8s {
+        process {
+            executor = 'k8s'
+        }
+        docker {
+            enabled = true
+        }
+    }
 
-// Execution configurations
-executor {
-    $local {
-        cpus = 4
-        memory = '8 GB'
+    k8s_gpu {
+        process {
+            executor = 'k8s'
+            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
+            accelerator = [request: 1, type: 'nvidia.com/gpu']
+        }
+        docker {
+            enabled = true
+        }
     }
 }
+
+process {
+    container = 'harbor.cluster.omic.ai/omic/bioemu:latest'
+    cpus = 2
+    memory = '8 GB'
+}