nextflow.config

//This fixes nf-core launch error: project <project-name> is currently stickied on revision: main 
manifest.defaultBranch = "main"


// Global default params, used in configs
params {
  SAMPLEFILE = null
  outdir = "cellbender-results"
  on_irods = false
  is_h5 = true
  qc_mode = 3
  cells = ""
  droplets = ""
  epochs = ""
  fpr = ""
  learn = ""
  HELP = false
}

// Singularity environment parameters
singularity {
  enabled     = true
  autoMounts  = true
  cacheDir = '/nfs/cellgeni/singularity/images/'
  runOptions = '-B /lustre,/nfs --nv' //--nv enables nvidia GPU support
}

// Configuring LSF job submission parameters for each process
executor {
  name = 'lsf'
  perJobMemLimit = true
}

process {

  errorStrategy = 'retry'
  maxRetries = 5

  withName: get_data {
    cpus = { 1 * task.attempt }
    memory = { 2.GB * task.attempt }
    queue = 'transfer'
    maxForks = 5
  }
  withName: run_cellbender {
    container = '/nfs/cellgeni/singularity/images/cellbender0.3.0-pytorch2.3.1-cuda12.1.1-ubuntu22.04.sif'
    cpus = { 2 * task.attempt }
    memory = { 30.GB * task.attempt }
    queue = 'gpu-normal'
    clusterOptions = { ' -gpu "mode=shared:j_exclusive=no:gmem=6000:num=1"' }
    maxForks = 5
  }
  withName: cellbender_qc {
    container = '/nfs/cellgeni/singularity/images/cellbender0.2.2-pytorch1.11-cuda11.3.1-R4.1.3.sif'
    cpus = { 1 * task.attempt }
    memory = { 2.GB * task.attempt }
    queue = 'normal'
  }
}

// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Capturing Nextflow log files into a reports directory
timeline {
   enabled = true
   file = "cellbender-reports/timeline.html"
   overwrite = true
}

report {
   enabled = true
   file = "cellbender-reports/report.html"
   overwrite = true
}

trace {
   enabled = true
   file = "cellbender-reports/trace.txt"
   overwrite = true
}

// Ensures work directories and removed when pipeline completes
cleanup = true