nf-cellbender/nextflow.config at main · cellgeni/nf-cellbender · GitHub

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plugins {
  // Parameter validation, --help and the launch summary, from nextflow_schema.json
  id 'nf-schema@3.0.0'
}

// Nextflow flags
nextflow.enable.configProcessNamesValidation = false
nextflow.enable.moduleBinaries = true

// Unscoped options
workDir = "nf-work"

// Global default params, used in configs. Types, enums and cross-parameter rules live in nextflow_schema.json
params {
  // Input/output options
  samples           = null
  on_irods          = false
  ignore_extensions = null // Only with --on_irods; the default list is in configs/irods_loadcatalog.config
  outdir            = "results"
  publish_mode      = 'copy'

  // CellBender options
  version               = "0.3"
  cells                 = null // Only for version 0.2 when .h5 file or .mtx file is provided
  droplets              = null // Only for version 0.2 when .h5 file or .mtx file is provided
  mapper_preset         = false
  starsolo_mapper       = "GeneFull"
  exclude_features      = null
  epochs                = null
  fpr                   = null
  lr                    = null
  min_umi               = null
  force_empty_umi_prior = null
  estimator             = null // Only for version 0.3; CellBender defaults to "mckp"
  qc_mode               = 3

  // Cluster options
  gpuqueue      = "gpu"
  costcode      = null // Only for (and required by) "cub" and "tiger" queues
  ignore_failed = false

  // Generic options
  help       = false
  helpFull   = false
  showHidden = false
}

// Singularity environment parameters
singularity {
  enabled     = true
  autoMounts  = true
  cacheDir    = '/nfs/cellgeni/singularity/images/'
  runOptions  = '-B /lustre,/nfs'
  pullTimeout = '100m'
}

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

process {
  errorStrategy = 'retry'
  maxRetries    = 5
}

// Published outputs are declared in the output block of main.nf. Set after params so
// the defaults are visible. Copy by default, so the results survive deleting nf-work/
outputDir = params.outdir

workflow {
  output {
    mode = params.publish_mode
  }
}

// Load process configurations
includeConfig 'configs/irods_loadcatalog.config'
includeConfig 'configs/cellbender_removebackground.config'
includeConfig 'configs/cellbender_qc.config'
includeConfig 'configs/multiqc.config'

// 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      = "execution-reports/timeline.html"
  overwrite = true
}

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

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

// Manifest
manifest {
  name            = 'cellgeni/nf-cellbender'
  homePage        = 'https://github.com/cellgeni/nf-cellbender'
  description     = "Nextflow pipeline to run CellBender"
  mainScript      = 'main.nf'
  nextflowVersion = '!>=26.04.0'
  version         = '26-295'
  defaultBranch   = 'main'
  contributors    = [
    [
      name: 'Simon Murray',
      github: 'just-simon-5',
      contribution: ['author'],
    ],
    [
      name: 'Aljes Binkevich',
      email: 'ab76@sanger.ac.uk',
      github: 'claptar',
      contribution: ['maintainer', 'contributor'],
    ],
    [
      name: 'Batuhan Cakir',
      email: 'bc8@sanger.ac.uk',
      github: 'cakirb',
      contribution: ['contributor'],
    ],
    [
      name: 'Pavel Mazin',
      email: 'pm19@sanger.ac.uk',
      github: 'iaaka',
      contribution: ['contributor'],
    ],
    [
      name: 'Martin Prete',
      email: 'martin.prete@sanger.ac.uk',
      github: 'prete',
      contribution: ['contributor'],
    ],
  ]
}