nextflow.config

/*
 * -------------------------------------------------
 *  Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

manifest {
  name = '@git_repo_name@'
  description = '@ap_pipeline_description@'
  homePage = '@git_url@'
  author = 'Institut Curie - Bioinformatics core facility'
  version = '@git_commit@'
  mainScript = 'main.nf'
  nextflowVersion = '>=22.10.6'
}


/**********
 * Params *
 **********/

params {
  email = false 
  help = false
  name = false

  // Input data
  fastaPath =  null
  proteinLigandFile = null

  // GPU usage
  useGpu = false

  // parameters for afMassive
  afMassiveOptions = "--dropout --dropout_structure_module"
  multimerVersions = "v1,v2,v3"
  numberOfModels = 5
  predictionsPerModel = 5

  // parameters for alphaFold
  alphaFoldOptions = "--max_template_date=2024-01-01 --random_seed=654321"

  // parameters for alphaFold3
  alphaFold3Options = null

  // parameters for colabFold
  colabFoldOptions = "--random-seed 654321 --model-type alphafold2 --amber --use-gpu-relax"

  // parameters for diffDock
  diffDockArgsYamlFile = "$projectDir/assets/diffdock_default_inference_args.yaml"

  // parameters for dynamicBind
  dynamicBindOptions = "--savings_per_complex 40 --inference_steps 20 --movie --seed 654321"

  // options to select which tool to use to predict protein 3D structure
  launchAlphaFold = false
  launchAlphaFold3 = false
  launchAfMassive = false
  launchColabFold = false
  launchNanoBert = false
  launchOpenFold = false

  // options to generate reports from existing results
  htmlProteinStruct = false
  htmlMetricsMultimer = false
 
  // options to select which tool to use for molecular docking
  launchAlphaFill = false
  launchDiffDock = false
  launchDynamicBind = false

  // option to perform only msas
  onlyMsas = false

  // option to do prediction from existing msas
  fromMsas = null

  // option to use existing predicted structures
  fromPredictions = null

  // help for the different tools
  alphaFillHelp = false
  alphaFold3Help = false
  alphaFoldHelp = false
  colabFoldHelp = false
  dynamicBindHelp = false
  afMassiveHelp = false

  // Output directories
  outDir = "$launchDir/results"
  summaryDir = "${params.outDir}/summary"
}

/************************
 * Configs and profiles *
 ************************/

// Additional configs
includeConfig 'conf/base.config'
includeConfig 'conf/process.config'
includeConfig 'conf/geniac.config'

// Annotation paths
includeConfig 'conf/genomes.config'

// Profiles
profiles {
  test{
    includeConfig 'conf/test.config'
  }
  apptainer {
    includeConfig 'conf/apptainer.config'
  }
  conda {
    includeConfig 'conf/conda.config'
  }
  multiconda {
    includeConfig 'conf/multiconda.config'
  }
  docker {
    includeConfig 'conf/docker.config'
  }
  podman {
    includeConfig 'conf/podman.config'
  }
  singularity {
    includeConfig 'conf/singularity.config'
  }
  path {
    includeConfig 'conf/path.config'
  }
  multipath {
    includeConfig 'conf/multipath.config'
  }
  cluster {
    includeConfig 'conf/cluster.config'
  }
}