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params.yaml
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# Below is a sample configuration for extracting coverage features
# input_dir: "input_data"
# output_dir: "output_data"
# supplement_dir: "supplement"
# interval_file: "intervals.bins"
# file_format: "bed.gz"
# Finaletoolkit filter-file parameters
# filter_file: True
# filter_file_mapq: 30
# filter_file_min_length: 50
# filter_file_max_length: 350
# filter_file_blacklist_file: "blacklist.bed"
# filter_file_whitelist_file: "whitelist.bed"
# filter_file_intersect_policy: "midpoint"
# filter_file_workers: 1
# Mappability parameters
# mappability_file: "mappability.bw"
# mappability_threshold: 0.00
# Frag-length-bins parameters
# frag_length_bins: True
# frag_length_bins_bin_size: 10
# frag_length_bins_mapq: 30
# frag_length_bins_policy: "midpoint"
# frag_length_bins_min_len: 50
# frag_length_bins_max_len: 350
# frag_length_bins_chrom: "22"
# frag_length_bins_start: 0
# frag_length_bins_end: 41000000
# Frag-length-intervals parameters
# frag_length_intervals: True
# frag_length_intervals_mapq: 30
# frag_length_intervals_policy: "midpoint"
# frag_length_intervals_min_len: 50
# frag_length_intervals_max_len: 350
# frag_length_intervals_workers: 1
# coverage: True
# coverage_mapq: 30
# coverage_intersect_policy: "any"
# coverage_min_len: 50
# coverage_max_len: 350
# coverage_workers: 1
# coverage_normalize: True
# coverage_scale_factor: 1000000
# end_motifs: True
# end_motifs_kmer_length: 5
# end_motifs_min_len: 50
# end_motifs_max_len: 350
# end_motifs_no_both_strands: True
# end_motifs_negative_strand: False
# end_motifs_mapq: 30
# end_motifs_workers: 1
# interval_end_motifs: True
# interval_end_motifs_refseq_file: "ref.2bit"
# interval_end_motifs_kmer_length: 4
# interval_end_motifs_min_len: 50
# interval_end_motifs_max_len: 350
# interval_end_motifs_single_strand: False
# interval_end_motifs_negative_strand: False
# interval_end_motifs_mapq: 30
# interval_end_motifs_workers: 1
# mds: True
# mds_sep: " "
# mds_header: 0
# interval_mds: True
# interval_mds_sep: " "
# interval_mds_header: 0
# wps: True
# wps_chrom_sizes: "ref.chrom.sizes"
# wps_site_bed: "sites.bed"
# wps_interval_size: 5000
# wps_window_size: 120
# wps_min_len: 120
# wps_max_len: 180
# wps_mapq: 30
# wps_workers: 4
# adjust_wps: True
# adjust_wps_interval_file: "sites.bed"
# adjust_wps_chrom_sizes: "ref.chrom.sizes"
# adjust_wps_interval_size: 5000
# adjust_wps_median_window_size: 200
# adjust_wps_savgol_window_size: 21
# adjust_wps_savgol_poly_deg: 2
# adjust_wps_exclude_savgol: True
# adjust_wps_workers: 4
# adjust_wps_mean: False
# adjust_wps_subtract_edges: True
# adjust_wps_edge_size: 500 # Breaks functionality for some reason
# delfi: True
# Only one of the two parameters below need to be given
# delfi_gap_file: "ref.gap.bed"
# delfi_gap_reference_genome: "ref"
# delfi_chrom_sizes: "ref.chrom.sizes"
# delfi_reference_file: "ref.2bit"
# delfi_bins_file: "interval.bins"
# delfi_no_gc_correct: False
# delfi_keep_nocov: False
# delfi_no_merge_bins: True
# delfi_window_size: 5000000
# delfi_mapq: 30
# delfi_workers: 4
# cleavage_profile: True
# cleavage_profile_chrom_sizes: "ref.chrom.sizes"
# cleavage_profile_min_len: 50
# cleavage_profile_max_len: 350
# cleavage_profile_mapq: 30
# cleavage_profile_left: 2000
# cleavage_profile_right: 2000
# cleavage_profile_workers: 8
# agg_bw: True
# agg_bw_median_window_size: 1
# agg_bw_mean: True