params.config

// vim: syntax=groovy expandtab
params {
    project = ""  // The project/account name for use with cluster schedulers such as Slurm, etc.
    clusterOptions = false

    output_dir = "BACTpipe_results"

    reads = ""  // Set on command line as e.g.: --reads 'path/to/*_R{1,2}.fastq.gz'

    kraken2_db = ""  // Set on command line as e.g.: --kraken2_db '/db/kraken2/minikraken2_v2_8GB_201904_UPDATE/'
    kraken2_confidence = 0.5
    kraken2_min_proportion = 1.00  // Minimum proportion of reads assigned to species level to classify sample as containing said species

    shovill_depth = "100"
    shovill_kmers = "31,33,55,77,99,127"
    shovill_minlen = "500"

    prokka_evalue = "1e-09"
    prokka_kingdom = "Bacteria"
    prokka_reference = ""
    prokka_signal_peptides = true

    keep_trimmed_fastq = false
    keep_shovill_output = false


}