example_conf.json

{
	"screen" : "",
	"dry_run" : false,
	"type" : "TF",
	"final_stage" : "idr",
	"out_dir" : "out",
	"title" : "",
	"input_endedness" : {
		"se" : false,
		"pe" : false
	},
	"input_files" : {
	},
	"species" : {
		"species" : ""
	},
	"cluster" : {
		"use_system" : "local",
		"q" : ""
	},
	"resource" : {
		"nth" : 8,
		"no_par" : false,
		"wt" : "5h50m",
		"memory" : "7G",
		"wt_dedup" : "23h",
		"mem_dedup" : "12G",
		"mem_shuf" : "12G",
		"wt_bwa" : "47h",
		"mem_bwa" : "12G",
		"wt_macs2" : "23h",
		"mem_macs2" : "15G",
		"wt_spp" : "47h",
		"mem_spp" : "12G"
	},
	"alignment" : {
		"aligner" : "bwa",
		"bwa" : {
			"param_bwa_aln" : "-q 5 -l 32 -k 2"
		},
		"filter" : {
			"dup_marker" : "picard",
			"anon_filt_bam" : false,
			"mapq_thresh" : 30,
			"no_dup_removal" : false
		},
		"subsample" : {
			"subsample_chip" : "0",
			"subsample_ctl" : "0"
		}
	},
	"cross_corr_analysis" : {
		"no_xcor" : false,
		"subsample_xcor" : "15M",
		"speak_xcor" : -1
	},
	"callpeak" : {
		"peak_caller" : "spp",
		"ctl_depth_ratio" : 1.2,
		"use_pooled_ctl" : false,
		"true_rep" : false,
		"no_pseudo_rep" : false,
		"spp" : {
			"npeak_spp" : 300000
		},
		"macs2" : {
			"pval_thresh_macs2" : 0.01
		},
		"idr" : {
			"idr_thresh" : 0.05
		},
		"naive_overlap" : {
			"nonamecheck" : false
		}
	},
	"visualization" : {
		"url_base" : ""
	}
}