nextflow.config

manifest {

    author          = "Eachan Johnson"
    homePage        = "https://github.com/scbirlab/nf-ggi"
    description     = "Predict gene-gene interactions based on protein-protein interaction predictions and similar metabolites."
    defaultBranch   = "v0.0.1"
    nextflowVersion = '!>=24.0.0'
    version         = "0.0.1"
    doi             = ''

}

params {

    /* Required */
    sample_sheet = null
    bfd = null
    uniclust = null

    /* Optional */
    test = false
    non_self = false
    help = null
    rhea_url = "https://ftp.expasy.org/databases/rhea"
    outputs = "${launchDir}/outputs"
    batch_size = 100

}

process.conda = "${projectDir}/environment.yml"
conda {
  createTimeout = '2h'
  enabled = true
}

profiles {

  standard {

    process {
      executor = 'slurm'
      array = 1000

      withLabel: big_cpu {
        time = '3h'
        cpus = 16
        memory = 32.GB
      }

      withLabel: big_time {
        time = '4d'
        cpus = 1
        memory = 64.GB
      }

      withLabel: some_mem {
        memory = 16.GB
      }

      withLabel: med_mem {
        memory = 64.GB
      }

      withLabel: big_mem {
        memory = 128.GB
      }

      withLabel: gpu_single {
        queue = 'gpu'
        time = '7d'
        module = 'cuDNN/8.9.2.26-CUDA-12.1.1'
        cpus = 4
        clusterOptions = '--gres=gpu:1'
        memory = 128.GB
      }

      withLabel: gpu {
        queue = 'gpu'
        time = '4h'
        module = 'cuDNN/8.9.2.26-CUDA-12.1.1'
        cpus = 2
        clusterOptions = '--gres=gpu:2'
        memory = 128.GB
      }

    }

    dag {
      enabled = true
      overwrite = true
    }

    notification {
      enabled = true
      to = "$USER@crick.ac.uk"
    }

  }

  local {

    process {
      executor = 'local'

      withLabel: big_cpu {
        time = '3h'
        cpus = 16
        memory = 32.GB
      }

      withLabel: some_mem {
        memory = 8.GB
      }

      withLabel: med_mem {
        memory = 16.GB
      }

      withLabel: big_mem {
        memory = 32.GB
      }

      withLabel: gpu {
        memory = 32.GB
      }

    }

  }

  gh {

    conda.useMamba = false

    process {
      executor = 'local'

      withLabel: big_cpu {
        cpus = 1
        memory = 12.GB
      }

      withLabel: some_mem {
        memory = 12.GB
      }

      withLabel: med_mem {
        memory = 12.GB
      }

      withLabel: gpu {
        memory = 12.GB
      }

    }

  }

}