nextflow.config.task.nodoc

process {
    //executor = 'slurm'  // for running processes using SLURM (Default: 'local')
    //time = '12h'
    //cpus = 8
    //withLabel: big_mem   { memory = '16 GB' }
    //withLabel: norm_mem  { memory = '4 GB'  }
    //withLabel: small_mem { memory = '2 GB'  }
    //memory = "16 GB"
    ext.ph = null //Placeholder to prevent errors.
}
params {
    ref_mode       = 'fasta'  // Options: ['name', 'fasta', 'manual']
    ref_fasta      = ''       // REQUIRED: Ex: '/path/to/my/reference.fasta[.gz]'
    norm_ref_fasta = "${projectDir}/ref_dbs/GCF_000005845.2_ASM584v2_genomic.fna.gz"
    treat_fastqs   = []    // REQUIRED, Single-group Treatment fastq Pattern
    ctrl_fastqs    = []    //           Single-group Control   fastq pattern
    //fastq_groups = []    
    do_merge_lanes = true  // Merge sample names differing only by lane-ID (Ex: L001, L002)
    do_fastqc      = true  // Perform FastQC Analysis
    do_trim        = true  // Trim tags using Trimmomatic
    do_norm_spike  = true  // Normalize using aligment count to a spike-in reference
    do_norm_cpm    = false // Normalize using millions of reads per sample
    do_make_bigwig = true  // Create UCSC bigWig files from final alignments
    fastqc_flags   = ''
    use_aln_modes  = ["all"]  // Options: ["all", "all_dedup", "less_120", "less_120_dedup"]
    peak_callers   = ['macs', 'seacr']  // Options: ['macs', 'seacr']
    //trimmomatic_adapterpath = "${projectDir}/ref_dbs/trimmomatic_adapters/TruSeq3-PE-2.fa"
    trimmomatic_adapter_mode   = "ILLUMINACLIP:"
    trimmomatic_adapter_params = ":2:15:4:4:true"
    trimmomatic_settings    = "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:25"
    trimmomatic_flags       = "-phred33"
    aln_ref_flags  = "--local --very-sensitive-local --phred33 -I 10 -X 700 --dovetail --no-unal --no-mixed --no-discordant"
    aln_norm_flags = params.aln_ref_flags
    norm_scale     = 1000  // Arbitrary value for scaling of normalized counts.
    norm_mode      = 'adj' // Options: ['adj', 'all']
    norm_cpm_scale = 1000 // Arbitrary value for scaling of normalized counts.
    macs_qval      = '0.01'
    macs_flags     = ''   
    seacr_fdr_threshhold = "0.01"
    seacr_norm_mode      = "auto" // Options: "auto", "norm", "non"
    seacr_call_stringent = true
    seacr_call_relaxed   = true
    publish_files    = 'default' // Options: ["minimal", "default", "all"]
    publish_mode     = 'copy'    // Options: ["symlink", "copy"]
    trim_name_prefix = ''        // Example: ~/^myprefix./ removes "myprefix." prefix.
    trim_name_suffix = ''        // Example: ~/_mysuffix$/ removes "_mysuffix" suffix.   
    out_dir          = "${launchDir}/cnr_output"
    refs_dir         = "${launchDir}/cnr_references"
}