nextflow.config

// import profiles and workflow SHA from core
includeConfig "base.config"

params {

    help = false
    version = false
    store_dir = null

    disable_ping = false
    threads = 4

    aws_image_prefix = null
    aws_queue = null

    out_dir = "output"

    // feature flags
    snp = true
    sv = true
    mod = true
    str = false

    // benchmark feature flags
    sv_benchmark = false
    sv_benchmark_vcf = null
    sv_benchmark_bed = null

    // common
    bam = null
    ref = null
    bed = null
    out_dir = "output"
    bam_min_coverage = 0
    downsample_coverage = false
    downsample_coverage_target = 60
    downsample_coverage_margin = 1.1
    depth_window_size = 25000
    output_gene_summary = true
    haplocheck = false
    sex = null
    mitogenome = null

    /// common
    ubam_map_threads = 8
    ubam_sort_threads = 3
    ubam_bam2fq_threads = 1

    // annotation
    annotation = true

    // snp
    override_basecaller_cfg = null
    clair3_model_path = null // used for overriding the guessed clair3 model
    // workflow options
    use_longphase = false
    // clair3 parameters
    sample_name = "SAMPLE"
    ctg_name = null
    include_all_ctgs = false
    ref_pct_full = 0.1
    var_pct_full = 0.7
    GVCF = false
    base_err = 0.001
    gq_bin_size = 5
    snp_min_af = 0.08
    indel_min_af = 0.15
    vcf_fn = null
    min_contig_size = 0
    min_mq = 5
    min_cov = 2
    min_qual = 2
    refine_snp_with_sv = true

    // sv
    tr_bed= null
    // filterCalls
    min_sv_length = 30
    min_read_support = "auto"
    min_read_support_limit = 2
    // sniffles2 options
    cluster_merge_pos = 150
    sniffles_args = null

    // mod
    modkit_args = null
    force_strand = false
    modkit_threads = 4

    // output
    depth_intervals = false
    phased = true
    output_report = true
    output_xam_fmt = "bam"

    // nfcore
    monochrome_logs = false
    validate_params = true
    show_hidden_params = false
    schema_ignore_params = 'show_hidden_params,validate_params,monochrome_logs,aws_queue,aws_image_prefix,wf,min_read_support,min_read_support_limit,fastq_only'

    wf {
        name = "wf-hereditary-cancer"
        example_cmd = [
            "--bam 'wf-hereditary-cancer-demo/demo.bam'"
        ]
        agent = null
    }
}

manifest {
    name            = 'epi2me-labs/wf-hereditary-cancer'
    author          = 'Oxford Nanopore Technologies'
    homePage        = 'https://github.com/epi2me-labs/wf-hereditary-cancer'
    description     = 'Variant calling in human hereditary cancer samples.'
    mainScript      = 'main.nf'
    nextflowVersion = '>=23.04.2'
    version         = '1.0.3'
}

epi2melabs {
    tags = "human,variant calling,cancer,targeted"
    icon = "faIdCard"
}