NeHub/params_template.json at Ne-nextflow · HighlanderLab/NeHub · GitHub

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{
    "input_dir": "/path/to/input",
    "output_dir": "/path/to/output",
    "method": "GONE,SMCpp,stairway,PSMC,Relate,tskit",
    "chromosomes": [1, 2],
    "mutation_rate": 6.3e-9,
    "population_file": "popLabel.txt",
    "sampling": 1,
    "seed": 100,

    "option": {
        "ref_genome": "/path/to/reference.fa",
        "ancestral_genome": "/path/to/ancestral.fa"
    },
    "PSMC": {
        "ref_genome": "/path/to/reference.fa",
        "timeSegmentPattern": "4+50*1+4+6",
        "bin_size": 100
    },
    "MSMC": {
        "sampleSize": 4,
        "timeSegmentPattern": "1*2+25*1+1*2+1*3",
        "rhoOverMu": 0.22,
        "maxIterative": 5
    },
    "tskit": {
        "ancestral_genome": "/path/to/ancestral.fa",
        "timepoint": 64,
        "max_file_size": 2097152000,
        "chunk_size": 2048
    },
    "stairway": {
        "easysfs_path": "/path/to/tools/easySFS/easySFS.py",
        "stairway_path": "/path/to/tools/stairway_plot_es",
        "ancestral_genome": "/path/to/ancestral.fa",
        "fold": 0,
        "ploids": 2,
        "generation_interval": 3.6,
        "pct_training": 0.67,
        "nrand": "7\t15\t22\t28",
        "ninput": 40,
        "xrange": "0.1,10000",
        "yrange": "0,0",
        "xspacing": 2,
        "yspacing": 2,
        "fontsize": 12
    },
    "Relate": {
        "Relate_path": "/path/to/tools/relate",
        "ancestral_genome": "/path/to/ancestral.fa",
        "genMap_dir": "/path/to/genetic_maps",
        "initial_N": 20000,
        "threshold": 0.5,
        "num_iter": 5,
        "num_chunk": 10,
        "bins": "1.8573,6.8573,0.3",
        "seed": 100,
        "years_per_gen": 3.6
    },
    "GONE": {
        "installation_path": "/path/to/tools/GONE",
        "PHASE": 2,
        "cMMb": 1,
        "DIST": 1,
        "NGEN": 2000,
        "NBIN": 200,
        "MAF": 0.0,
        "ZERO": 1,
        "maxNCHROM": -99,
        "maxNSNP": 50000,
        "hc": 0.05,
        "REPS": 40,
        "threads": 8
    },
    "Phlash": {
        "chr_test": 0
    }
}