template.config

/**
*       EXECUTION SETTINGS AND GLOBAL DEFAULTS
*       External config files import. DO NOT MODIFY THESE LINES!
*/
includeConfig "${projectDir}/config/default.config"
includeConfig "${projectDir}/nextflow.config"
includeConfig "${projectDir}/config/methods.config"

/**
*       Inputs/parameters of the pipeline.  MODIFY BELOW
*/

params {
    algorithm = [] // 'somaticsniper', 'strelka2', 'mutect2', 'muse'
    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
    output_dir = ''
    dataset_id = ''
    // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2
    // set params.exome to TRUE will add the '-E' option when running MuSE
    exome = false
    save_intermediate_files = false

    // Module specific options
    bgzip_extra_args = ''
    tabix_extra_args = ''

    // Mutect2 options
    split_intervals_extra_args = ''
    mutect2_extra_args = ''
    filter_mutect_calls_extra_args = ''
    gatk_command_mem_diff = 500.MB
    scatter_count = 50
    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'

    // MuSE options
    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'

    // Variant Intersection options
    ncbi_build = 'GRCh38'
    vcf2maf_extra_args = ''

    // 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()