nextflow.config

params.ref = ""
params.fcid = "MAD"
params.outdir = ""
params.mut_model_vcf = ""
params.error_model_fq_read1 = ""
params.error_model_fq_read2 = ""
params.readsim_model_bam = ""
params.mut_rate = "0.0045"
params.readsim_cov = 100000
params.readsim_downsample_fracs = [[5, 1.0], [6, 0.1], [7, 0.01], [8, 0.001], [9, 0.002], [10, 0.003], [11, 0.005]]
params.readsim_allele_fracs = [0.01, 0.02, 0.03, 0.05, 0.1, 0.2, 0.25, 0.5, 'random']
params.freebayes_configs = [["default", "-p 1 -F 0.01"]]

// DO NOT EDIT THESE
params.grouping_regex = ""
params.read_pair_regex = "_read[12]"
params.do_sim_reads = true
params.reads = "[!*]"
params.bams = "[!*]"
params.pl = "illumina"
params.pm = "nextseq"

// Set the Nextflow Working Directory
// By default this gets set to params.outdir + '/nextflow_work_dir'
workDir = params.outdir + '/nextflow_work_dir'

// Executor settings
process {
    executor = 'slurm'
    cpus = 10
    memory = { '60 GB' }
    time = { '60 min' }
    withName: trim { cpus = '20' } 
    withName: simulate_reads { time = '240 min'; cpus = '20' }
    withName: simulate_snvs { time = '240 min'; cpus = '20' }
    withName: seqErrorModel { time = '240 min' }
}