nextflow.config

manifest {
    mainScript = 'main.nf'
}

// default parameters
params {
  cores = '2'
  memory = '2'
  help = false
  profile = false

  // input
  nano = 'data/some.fasta'
  illumina = ''
  list = false

  // parameters
  variable1 = 'variable1'
  variable2 = 'variable2'

  // folder structure
  output = 'results'

  // optional profile configurations, only necessary for HPC LSF execution
  workdir = "/tmp/nextflow-work-$USER"
  cloudDatabase = false
  cachedir = false

}

profiles {

    standard { 
        params.cloudProcess = false
        params.cloudDatabase = false
        includeConfig 'configs/local.config' }

    conda { 
        params.cloudProcess = false
        params.cloudDatabase = false
        includeConfig 'configs/conda.config' }

    lsf {
        params.cloudProcess = true
        includeConfig 'configs/lsf.config' }

    ebi {
        params.cloudProcess = true
  	params.workdir = "/hps/nobackup2/production/metagenomics/$USER/nextflow-work-$USER"
  	params.cloudDatabase = "/homes/$USER/data/nextflow-databases/"
  	params.cachedir = "/hps/nobackup2/singularity/$USER"
        includeConfig 'configs/lsf.config' }

}