nextflow.config

manifest {
  author = 'Eva Aßmann, Martin Hölzer'
  name = 'VLQ-nf'
  description = 'Analysis pipeline to estimate sc2 lineage abundances from wastewater samples'
  mainScript = 'main.nf'
  nextflowVersion = '>=20.01.0'
}

// default parameters
params {
    max_cores = Runtime.runtime.availableProcessors()
    cores = 2
    memory = '2GB'
    help = false
    profile = false

    // input
    gisaid = ''
    query = ''
    reference = false

    // process-specific parameters
    continent = ''
    country = ''
    startdate = ''
    enddate = ''
    min_len = 29500
    k = 1000
    seed = 0
    min_aaf = 0.5
    max_per_lineage = 0
    min_ab = 0
    // kallisto
    single_end = true
    fragment_length = 200
    fragment_length_sd = 20
    kallisto_threads = 20
    bootstrap = 0
    
    // output
    output = 'sc2-sewage-results'
    workdir = "work"
    cachedir = "conda"
    runinfo = "sc2-sewage-runinfo"
    databases = 'sc2-sewage-databases'
}


timeline {
  enabled = true
  file = "${params.runinfo}/execution_timeline.html"
  overwrite = true
}

report {
  enabled = true
  file = "${params.runinfo}/execution_report.html"
  overwrite = true
}

dag {
  enabled = true
  file = "${params.runinfo}/pipeline_dag.html"
  overwrite = true
}

// Use test or test_full profile for automated pipeline CI tests?
profiles {

    standard {
        executor {
                name = "local"
                cpus = params.max_cores
        }
        workDir = params.workdir
        params.cloudProcess = false
        docker { enabled = false }
        includeConfig 'configs/local.config'
    }

// executer
    local {
        executor {
                name = "local"
                cpus = params.max_cores
        }
        workDir = params.workdir
        params.cloudProcess = false
        includeConfig 'configs/local.config'
    }


// engines
    conda {
        docker { enabled = false }
        includeConfig 'configs/conda.config'
    }

}