    // ------- Step-Specific Pipeline Paramaters --------
    // Step Settings:
    do_merge_lanes = true  // Merge sample names differing only by lane-ID (Ex: L001, L002)
    do_fastqc      = true  // Perform FastQC Analysis
    do_trim        = true  // Trim tags using Trimmomatic
    do_retrim      = true  // Retrim tags using kseq_test (CUTRUNTools)
    do_norm_spike  = true  // Normalize using aligment count to a spike-in reference
    do_make_bigwig = true  // Create UCSC bigWig files from final alignments


    //FastQC Settings:
    fastqc_flags = ''
    
    // Alignment Mode Options (params.use_aln_modes) :
    //   "all"            : Use all reads
    //   "all_dedup"      : Use all reads, and remove duplicates.
    //   "less_120"       : Use trimmed reads <= 120 bp 
    //   "less_120_dedup" : Use trimmed reads <= 120 bp and remove duplicates.
    //   (Multiple modes can be performed in parallel. Ex: ['all', 'less_120'])

    use_aln_modes  = ["all"]  // Options: ["all", "all_dedup", "less_120", "less_120_dedup"]
                                   
    // Peak Caller Options (params.peak_callers):
    //   "macs2" : Call Peaks with Macs2
    //   "seacr" : Call Peaks with SEACR
    //   (Multiple callers can be used in parallel. Ex: ['macs2', 'seacr'])

    peak_callers   = ['macs', 'seacr']  // Options: ['macs', 'seacr']
    
    //Trimmomatic Trim Settings
    
    //--Trimmomatic Adapter Path, Downloaded after "nextflow CnR-flow --mode initiate"
    trimmomatic_adapterpath = "${projectDir}/ref_dbs/trimmomatic_adapters/TruSeq3-PE-2.fa"
    trimmomatic_settings    = "ILLUMINACLIP:${params.trimmomatic_adapterpath}/Truseq3.PE.fa:2:15:4:4:true LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25"
    trimmomatic_flags       = "-phred33"
    //kseq_test (CUTRUNTools) Retrim Settings
    input_seq_len = 'auto'  // Length of untrimmed sequence reads (Ex: '150') or 'auto'
    
    //Bowtie2 Alignment Settings
    aln_ref_flags  = "--local --very-sensitive-local --phred33 -I 10 -X 700 --dovetail --no-unal --no-mixed --no-discordant"
    
    //Normalization Settings
    aln_norm_flags = params.aln_ref_flags
    norm_scale     = 1000  // Arbitrary value for scaling of normalized counts.
    norm_mode      = 'adj' // Options: ['adj', 'all']
    
    //Macs2 Settings
    macs_qval  = '0.01'
    macs_flags = ''   
 
    //SEACR Settings
    seacr_fdr_threshhold = "0.01"
    seacr_norm_mode      = "auto" // Options: "auto", "norm", "non"
    seacr_call_stringent = true
    seacr_call_relaxed   = true
    
    // ------- General Pipeline Output Paramaters --------
    publish_files    = 'default' // Options: ["minimal", "default", "all"]
    publish_mode     = 'copy'    // Options: ["symlink", "copy"]

    //Name trim guide: ( regex-based )
    //   ~/groovy-slashy-string/  ;  "~" denotes groovy pattern type.
    //   ~/^/ matches beginning   ;   ~/$/ matches end    
    trim_name_prefix = ''        // Example: ~/^myprefix./ removes "myprefix." prefix.
    trim_name_suffix = ''        // Example: ~/_mysuffix$/ removes "_mysuffix" suffix.   

    // Workflow Output Default Naming Scheme:
    //   Absolute paths for output:
    out_dir          = "${launchDir}/cnr_output"
    refs_dir         = "${launchDir}/cnr_references"
