    //   Subdirectory Settigns:
    log_dir          = 'logs'
    merge_fastqs_dir = 'S0_B_merged_reads'
    fastqc_pre_dir   = 'S0_C_FastQC_pre'
    trim_dir         = 'S1_A_fastq_trimomatic'
    retrim_dir       = 'S1_B_fastq_kseqtest'
    fastqc_post_dir  = 'S1_C_FastQC_post'
    aln_dir_ref      = 'S2_A_aln_ref'
    aln_dir_mod      = 'S2_B_aln_mod'
    aln_dir_bdg      = 'S2_C_aln_bdg'
    aln_dir_spike    = 'S3_A_aln_spikein'
    aln_dir_norm     = 'S3_B_aln_norm'
    aln_bigwig_dir   = 'S4_A_aln_bigWig'
    peaks_dir_macs   = 'S5_A_peaks_macs'
    peaks_dir_seacr  = 'S5_B_peaks_seacr'
    prep_bt2db_suf   = 'bt2_db'

