Initial commit: digital-patients pipeline (clean, no large files)

Large reference/model files excluded from repo - to be staged to S3 or baked into Docker images.

nextflow.config

@@ -0,0 +1,98 @@
+manifest {
+    name                = 'digital patients'
+    author              = 'omic'
+    recurseSubmodules   = true
+    homePage            = 'https://gitlab.com/omic/next/registry/pipelines/digitalpatients'
+    description         = 'generative digital patients and multi-omics pipeline'
+    mainScript          = 'main.nf'
+    nextflowVersion     = '!>=21.04.3'
+    defaultBranch       = 'master'
+}
+
+// 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']]
+        ]
+      }
+    }
+
+    workDir = "/mnt/dreamdock-data/digital-patient-data/work"
+
+    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
+      // ]
+    }
+    
+
+
+    // Use container image
+    // process.container = 'harbor.cluster.omic.ai/omic/faiss-indexer:latest'
+
+  }
+}
+