manifest {
    name                = 'Digital Trial'
    author              = 'omic'
    recurseSubmodules   = true
    homePage            = 'https://gitlab.com/omic/next/registry/tools/digital-trial.git' 
    description         = 'Digital drug protein interactions'
    mainScript          = 'main.nf'
    nextflowVersion     = '!>=21.04.3'
    defaultBranch       = 'master'
}

docker {
    enabled = true
    temp = 'auto'
    remove = true
}

process {
    withLabel: 'gpu_process' {
        containerOptions = '--gpus all --rm'

        pod = [
            [nodeSelector: [gpu: 'yes', 'gpu-type': 'geforce-rtx-3090']]
        ]
    }
    
    withLabel: 'cpu_process' {
        containerOptions = '--rm'
    }
}

profiles {
  // Minimal k8s profile for WES. WES injects its own profile.config via -C, which
  // supplies the executor, namespace, service account and workDir — so those are
  // deliberately left out here to avoid conflicting with it.
  //
  // The storage block is NOT optional. WES's injected profile does not mount any
  // PVC (verified: a full experiment run produced 468 KB of logs with zero
  // references to dreamdock/storageClaimName/volumeClaim). Without it,
  // /mnt/dreamdock-data does not exist inside task pods and every process that
  // reads params.chembl_db or params.protein_zarr fails immediately —
  // GET_FINAL_METABOLITES_STATIC dies with
  //   sqlite3.OperationalError: unable to open database file
  // and exit status 1, on every task, regardless of input.
  k8s {
    process.executor = 'k8s'

    k8s {
      storageClaimName = 'dreamdock-data'
      storageMountPath = '/mnt/dreamdock-data'
    }
  }

  // Full standalone k8s profile for running this pipeline directly (not via WES),
  // e.g. `nextflow run main.nf -profile k8s_standalone` from a pod on the cluster.
  k8s_standalone {
    process.executor = 'k8s'
    process.namespace = 'bioinformatics'
    process.debug = true

    workDir = "/mnt/dreamdock-data/digital_trials/workdir"

    executor {
        queueSize = 0             // Increase to desired concurrency
//        submitRateLimit = '1 sec'  // Recommended to prevent K8s API timeouts
    }

    k8s {
      serviceAccount = 'nextflow-sa'
      namespace = 'bioinformatics'
      storageClaimName = 'dreamdock-data'
      storageMountPath = '/mnt/dreamdock-data'

      pullPolicy = 'IfNotPresent'
      cleanup = true                    // delete pods after Ctrl+C or finished?

      imagePullSecrets = 'omic-registry-secret'

      // RUN AS DIFFERENT USERS
      // securityContext = [fsGroup: 1000]
      // securityContext = [
      //   runAsUser: 1000,
      //   fsGroup: 1000,
      //   runAsNonRoot: true
      // ]
    }

    // Pod-level customization
    process.pod = [
      [env: 'NXF_DEBUG', value: '0'],
      [label: 'omic-app', value: 'dreamdock'],
      [imagePullSecret: 'gitlab-registry-secret'],
      // [nodeSelector: [gpu: 'yes', 'gpu-type': 'rtx-3090']],
      [hostPath: '/mnt/ZINC-22/', mountPath: '/mnt/ZINC-22/']
      // [volumeClaim: 'conplex-index-builder-data', mountPath: '/mnt/conplex-index/']
      // [privileged: true],
    ]

  }
}