example_conf_full.json

{
	"screen" : "",
	"dry_run" : false,
	"type" : "TF",
	"final_stage" : "idr",
	"out_dir" : "out",
	"title" : "",
	"input_endedness" : {
		"se" : false,
		"pe" : false
	},
	"input_files" : {
	},
	"species" : {
		"species" : "",
		"species_file" : "",
		"species_browser" : "",
		"ref_fa" : "",
		"chrsz" : "",
		"blacklist" : "",
		"gensz" : ""
	},
	"cluster" : {
		"system" : "local",
		"nice" : 0,
		"retrial" : 0,
		"q" : ""
	},
	"resource" : {
		"nth" : 8,
		"no_par" : false,
		"wt" : "5h50m",
		"memory" : "7G",
		"unlimited_mem_wt" : false,
		"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",
			"bwa_idx" : ""
		},
		"filter" : {
			"dup_marker" : "picard",
			"anon_filt_bam" : false,
			"mapq_thresh" : 30,
			"rm_chr_from_tag" : "",
			"no_dup_removal" : false
		},
		"subsample" : {
			"subsample_chip" : "0",
			"subsample_ctl" : "0"
		}
	},
	"cross_corr_analysis" : {
		"no_xcor" : false,
		"subsample_xcor" : "15M",
		"speak_xcor" : -1,
		"extra_param_xcor" : ""
	},
	"callpeak" : {
		"peak_caller" : "spp",
		"ctl_depth_ratio" : 1.2,
		"use_pooled_ctl" : false,
		"true_rep" : false,
		"no_pseudo_rep" : false,
		"spp" : {
			"cap_num_peak_spp" : 300000,
			"max_ppsize_spp" : "",
			"speak_spp" : -1,
			"extra_param_spp" : ""
		},
		"macs2" : {
			"pval_thresh_macs2" : 0.01,
			"keep_dup_macs2" : "all",
			"extsize_macs2" : -1,
			"shift_macs2" : 0,
			"extra_param_macs2" : ""
		},
		"idr" : {
			"idr_suffix" : false,
			"idr_rank" : "",
			"idr_thresh" : 0.05
		},
		"naive_overlap" : {
			"nonamecheck" : false
		}
	},
	"signal_track" : {
		"sig_trk_for_pooled_rep_only" : false
	},
	"bds_configuration" : {
		"env" : "$script_dir/default.env"
	},
	"visualization" : {
		"url_base" : ""
	},
	"ENCODE_accession" : {
		"ENCODE_accession" : "",
		"ENCODE_award_rfa" : "",
		"ENCODE_assay_category" : "",
		"ENCODE_assay_title" : "",
		"ENCODE_award" : "",
		"ENCODE_lab" : "",
		"ENCODE_assembly" : "",
		"ENCODE_alias_prefix" : "KLAB_PIPELINE"
	},
	"shell_environment" : {
		"conda" : {
			"conda_env" : "",
			"conda_env_py3" : "",
			"conda_bin_dir" : ""
		},
		"modules" : {
			"mod" : "",
			"shcmd" : "",
			"addpath" : ""
		}
	}
}