// Nextflow configuration file

// Execution report
report {
    enabled = true
    file = "execution_report.html"
    overwrite = true}


// Resource usage tracking
trace {
    enabled = true
    file = "execution_trace.txt"
    overwrite = true
}

// Error reporting
timeline {
    enabled = true
    file = "execution_timeline.html"
    overwrite = true
}

// // Max resources
// executor {
//     $local {
//         memory = '80 GB'
//         cpus = 2
//     }
// }

// Default parameters (overridden by test.nf)
params {
    // Set defaults here
    // input = '/mnt/ZINC-22/conplex/total.zarr'
    nshards = 12
    outdir = "$launchDir"
}

profiles {
  k8s {
    process.executor = 'k8s'
    process.namespace = 'bioinformatics'  
    process.debug = true

    workDir = "/workdir/work"

    k8s {
      serviceAccount = 'nextflow-sa'
      namespace = 'bioinformatics'
      storageClaimName = 'conplex-data'
      storageMountPath = '/workdir'
      
      pullPolicy = 'IfNotPresent'
      cleanup = true                    // 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'

    // Pod-level customization
    process.pod = [
      [env: 'NXF_DEBUG', value: '0'],
      [label: 'omic-app', value: 'conplex'],
      [imagePullSecret: 'gitlab-registry-secret'],
      [volumeClaim: 'fingerprint-data', mountPath: '/fingerprint-data']
      //[nodeSelector: [gpu: 'yes', 'kubernetes.io/hostname': 'k8s-node25']],
      // [privileged: true],
    ]

    // process {
    //   withName: 'trainIndex' {
    //     container = 'harbor.cluster.omic.ai/omic/conplex-faiss-train:latest'
    //     accelerator = 1
    //     memory = '75 GB'
    //     cpus = 1
        
    //     // GPU-specific pod settings
    //     pod = [
    //       [nodeSelector: [gpu: 'yes']]
    //     ]
    //   }
      
    //   // Specific settings for addToIndex process (CPU only)
    //   withName: 'addToIndex' {
    //     container = 'harbor.cluster.omic.ai/omic/conplex-faiss-add:latest'
    //     memory = '75 GB'
    //     cpus = 1
        
    //     // Explicitly ensure no GPU requirements
    //     // No accelerator property set, and no GPU nodeSelector
    //   }
    // }
  }

  docker {
    // Docker/Singularity configuration
    docker {
      enabled = true
      runOptions = '--rm'
    }
  }
}