MAD2/K4LKV.config at main · gencorefacility/MAD2 · GitHub

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params.reads = "/scratch/cgsb/gencore/out/Ghedin/2021-12-22_K4LKV/1/*.fastq.gz"
params.bams = "[!*]"
params.ref = "/scratch/work/cgsb/genomes/In_house/Virus/Influenza/fludb/K4LKV/ref.fa"
params.adapters = "/scratch/cgsb/gresham/LABSHARE/flu/adapters/NexteraPE-PE.fa"
params.pl = "illumina"
params.pm = "nextseq"
params.fcid = "K4LKV"
params.outdir = "/vast/mk5636/two-sims-2/" + params.fcid
params.grouping_regex = ""
params.read_pair_regex = "_n0[12]"

params.do_sim_reads = false
params.mut_model_vcf = "/scratch/cgsb/gresham/maf/data/H3N2/H3N2.vcf"
params.error_model_fq_read1 = "/scratch/cgsb/gencore/out/Ghedin/2019-08-23_HNH27AFXY/merged/HNH27AFXY_n01_A549_LOW_3DPI_H3N2_REP1.fastq.gz"
params.error_model_fq_read2 = "/scratch/cgsb/gencore/out/Ghedin/2019-08-23_HNH27AFXY/merged/HNH27AFXY_n02_A549_LOW_3DPI_H3N2_REP1.fastq.gz"
params.readsim_model_bam = "/scratch/cgsb/gresham/maf/data/H3N2/sim_data/A549_LOW_3DPI_H3N2_REP1.bam"
params.mut_rate = ""
params.m_rates = []
params.seed = 0

params.readsim_cov = 100000
params.readsim_downsample_fracs = []
params.readsim_allele_fracs = []

params.freebayes_configs = [["default", ""], ["standard", "-p 100 -F 0.01 --min-base-quality 20 --min-coverage 1"], ["custom", "-p 1 -F 0.01 --min-base-quality 20 --min-coverage 1"]]
params.m2_configs = [["default", ""], ["standard", "--min-base-quality-score 20 --minimum-allele-fraction 0.01"], ["custom", "--min-base-quality-score 20 --minimum-allele-fraction 0.001 --max-reads-per-alignment-start 0"]]
params.hc_configs = [["default", ""], ["standard", "-ploidy 100 --min-base-quality-score 20"], ["custom", "-ploidy 1 --min-base-quality-score 20"]]
params.lofreq_configs = [["default", ""], ["standard", "-q 20 -Q 20 -C 1"], ["custom", "-q 20 -Q 20 -C 1 --use-orphan"]]
params.vs_configs = [["default", "", ""], ["standard", "", "--min-coverage 1 --min-var-freq 0.01 --min-avg-qual 20"], ["custom", "-A -d 0 -B", "--min-coverage 1 --min-var-freq 0.01 --min-avg-qual 20"], ["custom-1", "", "--min-coverage 1 --min-var-freq 0.001 --min-avg-qual 20"]]
params.ivar_configs = [["default", ""], ["standard", "-t 0.01 -q 20 -m 1"], ["custom", "-t 0.001 -q 20 -m 1"]]
params.timo_configs = [["default", "-F 1284", ""], ["standard", "-F 1284", "-c 0.01 -C 1 -q 20"], ["custom", "-F 1284", "-c 0.001 -C 1 -q 20"]]

// Set the Nextflow Working Directory
// By default this gets set to params.outdir + '/nextflow_work_dir'
workDir = '/vast/mk5636/nextflow_work_dir/K4LKV/' + params.fcid

// Slurm settings
process {
    executor = 'slurm'
    clusterOptions = '--export=NONE'
    cpus = { 6 * task.attempt }
    memory = { 20.GB * task.attempt }
    time = { 1.h * task.attempt }
    errorStrategy = 'retry'
    maxRetries = 5
}