template.config

// EXECUTION SETTINGS AND GLOBAL DEFAULTS

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

// Inputs/parameters of the pipeline
params {
    dataset_id = "TEST"
    blcds_registered_dataset = false

    variant_type = ["gSV", "gCNV"]

    // The mode of the call-gSV pipeline to run. Discovery will identify SVs using Delly/Manta. Regenotyping will regenotype SVs/CNVs using Delly. Please note that setting
    // `run_regenotyping` to true will supersede `run_delly` below.
    run_discovery = true
    run_regenotyping = false

    //When `run_regenotyping = true`, uncomment `merged_sites_gSV` & `merged_sites_gCNV`
    //merged_sites_gSV = "" // Path to sites.gSV.bcf
    //merged_sites_gCNV = "" // Path to sites.gCNV.bcf

    // run_delly or run_manta (or both) must be set to true
    run_delly = true
    run_manta = true
    run_qc = true

    save_intermediate_files = false

    output_dir = "where/to/save/outputs/"

    reference_fasta = "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"

    exclusion_file = "/hot/ref/tool-specific-input/Delly/GRCh38/human.hg38.excl.tsv"
    mappability_map = "/hot/ref/tool-specific-input/Delly/GRCh38/Homo_sapiens.GRCh38.dna.primary_assembly.fa.r101.s501.blacklist.gz"

    map_qual = 20 // min. paired-end (PE) mapping quality for Delly

    }

methods.setup()