nextflow.config

manifest {

    author          = "Eachan O. Johnson"
    homePage        = "https://github.com/scbirlab/nf-inspect"
    description     = "Process demultiplexed Illumina paired-end FASTQ files from INSPECT experiments."
    defaultBranch   = "v0.0.3"
    nextflowVersion = '!>=24.0.0'
    version         = "0.0.3"
    doi             = ''

}

nextflow {
  enable.moduleBinaries = true
}

params {
    
    help = false
    
    // *** Pipeline Input parameters ***

    sample_sheet = null
    fastq = null
    reference = null

    // *** Pipeline processing parameters ***

    // - Adapter trimming
    trim_qual = 10
    min_length = 105

    // - UMI-tools
    umitools_error = 2
}

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 = '7d'
        cpus = 1
        memory = 128.GB
      }

      withLabel: some_mem {
        memory = 16.GB
      }

      withLabel: med_mem {
        memory = 64.GB
      }

      withLabel: big_mem {
        memory = 128.GB
      }
      withLabel: gpu {
        queue = 'gpu'
        time = '24h'
        module = 'cuDNN/8.9.2.26-CUDA-12.1.1'
        clusterOptions = '--gres=gpu:1'
        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.enabled = true
    process {
      executor = 'local'

      withLabel: big_cpu {
        time = '3h'
        cpus = 1
        memory = '12GB'
      }
      withLabel: some_mem {
          cpus = 1
          memory = '12GB'
      }
      withLabel: med_mem {
          cpus = 1
          memory = '12GB'
      }
      withLabel: big_mem {
          cpus = 1
          memory = '12GB'
        }
      withLabel: big_gpu {
        cpus = 1
        memory = '12GB'
      }

    }

  }

}