nextflow.config

// General
plugins {
  id 'nf-schema@2.0.0'
}

params {
  outdir            = "results"
  withGeneCoverage  = false
  maxCpu            = 8
  maxMemory         = "80GB"
  enable_conda      = false
  filter            = false
  tfkmers_threshold = 0.2
  bambu_threshold   = 0.2
  operation         = "intersection"
  tfkmers_model     = null
  tfkmers_tokenizer = null
  bambu_strand      = true
  bambu_singleexon  = true
  bambu_rec_ndr     = false
  tx_discovery      = "bambu"
  help              = false
}

process {
  memory = '16GB'
}

profiles {
  standard {
    process.executor = 'local'
  }

  slurm {
    process.executor = 'slurm'
  }

  test {
    params {
      input = "$baseDir/examples/samples.txt"
      gtf = "$baseDir/examples/annotation_19.gtf"
      fa = "$baseDir/examples/sequence_19.fa"
      withGeneCoverage = true
      maxCpu = 2
      maxMemory = '8GB'
    }
  }

  conda {
    params.enable_conda = true
  }

  docker {
    docker.enabled = true
    docker.runOptions = '-u \$(id -u):\$(id -g)'
  }

  singularity {
    singularity.enabled = true
    singularity.autoMounts = true
  }
}

manifest {
	name = 'IGDRion/annexa'
	author = 'IGDR'
	homePage = 'https://github.com/igdrion/annexa'
	description = 'Analysis of Nanopore with Nextflow for EXtended Annotation'
	mainScript = 'main.nf'
	nextflowVersion = '>=19.10.0'
	version = '3.2.3'
}