{
    "software_config": {
        "Rscriptbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "pythonbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "perlbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin",
        "javabin": "/usr/bin",
        "bowtie2bin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "samtoolsbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "macs2bin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "memebin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/meme/bin", 
        "bedopsbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "bedtoolsbin": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "path_deeptools": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin",
        "path_parallel": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin", 
        "path_tabix": "/dartfs-hpc/rc/home/k/f0042dk/miniconda3/envs/cutruntools2/bin",
        "bt2idx": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/genomes/hg38", 
        "genome_sequence": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/genomes/hg38/hg38.fa", 
        "spike_in_bt2idx": "/gcdata/gcproj/fulong/Data/Genomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index", 
        "spike_in_sequence": "/gcdata/gcproj/fulong/Data/Genomes/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa", 
        "extratoolsbin": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install", 
        "extrasettings": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install",
        "kseqbin": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install", 
        "adapterpath": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/adapters", 
        "trimmomaticbin": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install", 
        "picardbin": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/install", 
        "picardjarfile": "picard-2.8.0.jar", 
        "trimmomaticjarfile": "trimmomatic-0.36.jar", 
        "makecutmatrixbin": "/dartfs-hpc/rc/home/k/f0042dk/.local/bin"
    }, 
    "input_output": {
        "fastq_directory": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CUT-RUNTools-2.0/exampleData", 
        "workdir": "/dartfs-hpc/rc/lab/L/LeachLab/HIMANSHU/CutNrun/CutNRun_6-18-21", 
        "fastq_sequence_length": "42", 
        "organism_build": "hg38",
        "spike_in": "FALSE",
        "spike_in_norm": "FALSE",
        "spikein_scale": "10000",
        "frag_120": "TRUE",
        "peak_caller": "macs2",
        "dup_peak_calling": "FALSE",
        "cores": "8",
        "experiment_type": "CUT&RUN"
    }, 
    "motif_finding": {
        "num_bp_from_summit": "100", 
        "num_peaks": "1000", 
        "total_peaks": "2000", 
        "motif_scanning_pval": "0.0005", 
        "num_motifs": "10"
    }
}