Configure pipeline for WES execution on k8s cluster

- Add main.nf as WES entry point with PVC-based paths
- Update nextflow.config with k8s/k8s_gpu profiles (eureka-pvc)
- Update params.json defaults to /omic/eureka/digital-patients/ paths
- Remove stageInMode 'copy' from corto and vcf2prot for k8s compat
- Add reassemble.nf for one-time chunk reassembly on PVC

nextflow.config

@@ -1,98 +1,47 @@
 manifest {
-    name                = 'digital patients'
+    name                = 'digital-patients'
     author              = 'omic'
     recurseSubmodules   = true
-    homePage            = 'https://gitlab.com/omic/next/registry/pipelines/digitalpatients'
+    homePage            = 'https://trs-gitea.cluster.omic.ai/omic/digital-patients'
     description         = 'generative digital patients and multi-omics pipeline'
     mainScript          = 'main.nf'
     nextflowVersion     = '!>=21.04.3'
-    defaultBranch       = 'master'
+    defaultBranch       = 'main'
 }
 
-// docker {
-//     enabled = true
-//     temp = 'auto'
-// }
-
-// process {
-//     withLabel: 'gpu_process' {
-//         containerOptions = '--gpus all --rm'
-//     }
-//     
-//     withLabel: 'cpu_process' {
-//         containerOptions = '--rm'
-//     }
-// }
-
-def sharedPod = [
-  [env: 'NXF_DEBUG', value: '0'],
-  [label: 'omic-app', value: 'digitalpatients'],
-  [imagePullSecret: 'gitlab-registry-secret'],
-  [volumeClaim: 'avatar-new', mountPath: '/mnt/Avatar/'],
-]
-
 profiles {
-  docker {
-    docker.enabled = true
-    
-    process {
-      executor = 'local'
-      
-      withLabel: 'gpu_process' {
-        maxForks = 1  // Only one GPU task at a time on single GPU system
-        containerOptions = '--gpus all --rm'
-      }
-      
-      withLabel: 'cpu_process' {
-        containerOptions = '--rm'
-      }
-    }
-  }
-
-  k8s {
-    process {
-     
-      executor = 'k8s'
-      namespace = 'bioinformatics'  
-      debug = true
-      
-      pod = sharedPod
-
-      withLabel: 'gpu_process' {
-       
-        pod = sharedPod + [
-          [nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
-        ]
-      }
+    standard {
+        docker {
+            enabled = true
+            temp = 'auto'
+        }
     }
 
-    workDir = "/mnt/dreamdock-data/digital-patient-data/work"
+    k8s_gpu {
+        process {
+            executor = 'k8s'
+            pod = [[nodeSelector: 'nvidia.com/gpu.present=true']]
+            accelerator = [request: 1, type: 'nvidia.com/gpu']
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
+    }
 
     k8s {
-      serviceAccount = 'nextflow-sa'
-      namespace = 'bioinformatics'
-      storageClaimName = 'dreamdock-data'
-      storageMountPath = '/mnt/dreamdock-data'
-      
-      pullPolicy = 'IfNotPresent'
-      cleanup = true                    // delete pods after Ctrl+C or finished?
-      // cleanup = false                    // delete pods after Ctrl+C or finished?
-      
-
-      // RUN AS DIFFERENT USERS
-      // securityContext = [fsGroup: 1000]
-      // securityContext = [
-      //   runAsUser: 1000,
-      //   fsGroup: 1000,
-      //   runAsNonRoot: true
-      // ]
+        process {
+            executor = 'k8s'
+        }
+        docker {
+            enabled = true
+        }
+        k8s {
+            storageClaimName = 'eureka-pvc'
+            storageMountPath = '/omic/eureka'
+        }
     }
-    
-
-
-    // Use container image
-    // process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
-
-  }
 }
-