concordance.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Nextflow config file for running minimal tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
    Defines input files and everything required to run a fast and simple pipeline test.

    Use as follows:
        nextflow run nf-core/variantbenchmarking -profile concordance,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

process {
    resourceLimits = [
        cpus: 4,
        memory: '15.GB',
        time: '1.h'
    ]

    withName: 'BCFTOOLS_NORM*' {
        cpus   = { 1                   }
        memory = { 6.GB * task.attempt }
        time   = { 4.h  * task.attempt }
    }
    withName: 'BCFTOOLS_FILTER*' {
        cpus   = { 1                   }
        memory = { 6.GB * task.attempt }
        time   = { 4.h  * task.attempt }
    }
    withName: 'BCFTOOLS_SORT*' {
        cpus   = { 1                   }
        memory = { 6.GB * task.attempt }
        time   = { 4.h  * task.attempt }
    }
}

params {
    config_profile_name        = 'Test profile: concordance'
    config_profile_description = 'Minimal test dataset to check pipeline function'

    // Input data
    input                = "${params.test_data_base}/samplesheet/samplesheet_small_germline_hg38.csv"
    outdir               = "results"

    // Genome references
    genome               = 'GRCh38'

    // Processes
    analysis             = 'germline'
    variant_type         = "small"
    preprocess           = "split_multiallelic,normalize,deduplicate"
    method               = 'concordance'
    }