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

    reference_fasta = "/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"
    // GRCh37 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh37-EBI-hs37d5/ENCFF001TDO.bed
    // GRCh38 blacklist - /hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed
    gridss_blacklist = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/ENCFF356LFX.bed"
    gridss_reference_fasta = "/hot/resource/tool-specific-input/GRIDSS-2.13.2/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta"

    exclusion_file = "/hot/resource/tool-specific-input/Delly/hg38/human.hg38.excl.tsv"

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

    // select the tool(s) to run
    algorithm = [] // algorithm = ['delly', 'manta', 'gridss2']

    save_intermediate_files = false

    verbose = false

    /**
    * Set up the Delly filtering parameters
    * The below default values are recommended to reduce runtimes.
    * See - https://github.com/dellytools/delly 'Delly is running too slowly what can I do?' for more
    */
    map_qual = 20
    min_clique_size = 5
    mad_cutoff = 15

    /**
    * The filter condition used by the filter_BCF_BCFtools process.
    * See http://samtools.github.io/bcftools/bcftools.html#expressions
    * Note, put single quotes inside double quotes.
    */
    filter_condition = "FILTER=='PASS'"
    }

methods.setup()