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nextflow.config
executable file
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nextflow.config
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params.reads = "[!*]"
params.bams = "[!*]"
params.ref = "/scratch/work/cgsb/genomes/In_house/Virus/Influenza/fludb/H1N1/H1N1.fa"
params.adapters = ""
params.pl = "illumina"
params.pm = "nextseq"
params.fcid = "H1N1"
params.outdir = "/scratch/$USER/" + params.fcid
params.do_sim_reads = true
params.mut_model_vcf = "/scratch/cgsb/gresham/maf/data/H1N1/H1N1.vcf"
params.error_model_fq_read1 = "/scratch/cgsb/gencore/out/Ghedin/2019-08-23_HNH27AFXY/merged/HNH27AFXY_n01_HBEpC_LOW_2DPI_H1N1_REP1.fastq.gz"
params.error_model_fq_read2 = "/scratch/cgsb/gencore/out/Ghedin/2019-08-23_HNH27AFXY/merged/HNH27AFXY_n02_HBEpC_LOW_2DPI_H1N1_REP1.fastq.gz"
params.readsim_model_bam = "/scratch/cgsb/gresham/maf/data/H1N1/sim_data/HBEpC_LOW_2DPI_H1N1_REP1.bam"
params.mut_rate = "0.009"
params.m_rates = [['m1', 0.0005], ['m2', 0.0005]]
params.seed = 11
params.readsim_cov = 100000
params.readsim_downsample_fracs = [[1, 1.0], [2, 0.1], [3, 0.01], [4, 0.005], [5, 0.003], [6, 0.002], [7, 0.001]]
params.readsim_allele_fracs = [0.01, 0.02, 0.03, 0.05, 0.1, 0.25, 'random']
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"]]
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
workDir = '/scratch/$USER/nextflow_work_dir/' + 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
}