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'

  }
}