Simplify nextflow.config for WES compatibility

Remove params block (defined in main.nf) and minimize profiles
to avoid StackOverflowError when WES injects profile.config via -C flag.

nextflow.config

@@ -6,46 +6,8 @@ manifest {
     version = '1.0.0'
 }
 
-params {
-    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 = 5
-    temperature = 300
-    n_clusters = 5
-}
-
-profiles {
-    standard {
-        docker {
+docker {
     enabled = true
-            runOptions = '--gpus all'
-        }
-    }
-
-    k8s {
-        process {
-            executor = 'k8s'
-        }
-        docker {
-            enabled = true
-        }
-    }
-
-    k8s_gpu {
-        process {
-            executor = 'k8s'
-            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
-            accelerator = [request: 1, type: 'nvidia.com/gpu']
-        }
-        docker {
-            enabled = true
-        }
-    }
 }
 
 process {
@@ -53,3 +15,16 @@ process {
     cpus = 2
     memory = '8 GB'
 }
+
+profiles {
+    k8s {
+        process {
+            executor = 'k8s'
+        }
+    }
+    k8s_gpu {
+        process {
+            executor = 'k8s'
+        }
+    }
+}