template.config

// EXECUTION SETTINGS AND GLOBAL DEFAULTS

// External config files import. DO NOT MODIFY THESE LINES!
includeConfig "${projectDir}/config/default.config"
includeConfig "${projectDir}/config/methods.config"
includeConfig "${projectDir}/nextflow.config"


// Inputs/parameters of the pipeline
params {
    algorithm = ['samtools_stats', 'collectwgsmetrics'] // 'fastqc', 'samtools_stats', 'collectwgsmetrics', 'mosdepth_quantize', 'mosdepth_coverage', 'qualimap_bamqc'
    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
    output_dir = '/path/to/output/directory'
    blcds_registered_dataset = false // if you want the output to be registered
    save_intermediate_files = true

    // SAMtools stats options
    stats_max_rgs_per_sample = 20
    stats_remove_duplicates = false
    stats_additional_options = ''

    // mosdepth window-base coverage options
    // fast algorithm ignores read pair overlaps and should not be used on libraries with small insert sizes
    mosdepth_use_fast_algorithm = false
    mosdepth_per_base_output = true
    mosdepth_window_size = 500
    mosdepth_additional_options = '--mapq 20'

    // mosdepth quantized coverage (like GATK's Callable Regions)
    mosdepth_quantize_cutoffs = '0:1:5:150'
    mosdepth_quantize_use_fast_algorithm = false
    mosdepth_q0_label = 'NO_COVERAGE'
    mosdepth_q1_label = 'LOW_COVERAGE'
    mosdepth_q2_label = 'CALLABLE'
    mosdepth_q3_label = 'HIGH_COVERAGE'
    mosdepth_quantize_additional_options = '--mapq 20'

    // Picard CollectWgsMetrics options
    cwm_coverage_cap = 1000
    cwm_minimum_mapping_quality = 20
    cwm_minimum_base_quality = 20
    cwm_use_fast_algorithm = false
    cwm_additional_options = ''

    // Qualimap bamqc options
    bamqc_output_format = 'pdf' // 'html' or 'pdf'
    bamqc_additional_options = ''

    // FastQC options
    fastqc_level = 'sample' // 'readgroup', 'library' or 'sample'
    fastqc_additional_options = ''

    // Base resource allocation updater
      // See README for adding parameters to update the base resource allocations
}

// Setup the pipeline config. DO NOT REMOVE THIS LINE!
methods.setup()