From 04a580a3c0d7dd733c50765ca0d8659a04a8722f Mon Sep 17 00:00:00 2001
From: Olamide Isreal <olamide@omicmd.com>
Date: Thu, 26 Mar 2026 14:20:32 +0100
Subject: [PATCH] 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 | 55 ++++++++++++++-----------------------------------
 1 file changed, 15 insertions(+), 40 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index ab3a7ab..cb33984 100644
--- a/nextflow.config
+++ b/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 {
-            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
-        }
-    }
+docker {
+    enabled = true
 }
 
 process {
@@ -53,3 +15,16 @@ process {
     cpus = 2
     memory = '8 GB'
 }
+
+profiles {
+    k8s {
+        process {
+            executor = 'k8s'
+        }
+    }
+    k8s_gpu {
+        process {
+            executor = 'k8s'
+        }
+    }
+}