nextflow.config

// Default  workflow parameters
// Execution specific profile parameters are found in conf/profiles.config
// mads 2024-02-09

params {

    // ID for VCF output files:
    outputId = ""

    // Table containing pool ids and corresponding FastQ files
    pooltable = ""

    // Table linking pool ids to sample ids
    decodetable = ""

    // Reference genome
    reference_genome = ""

    // Target genes bedfile
    bedfile = ""

    // Target regions extraction from truth wgs bam file
    bedfile_bam_extraction = ""

    // Target genes gatk dictfile
    dictfile = ""

    // Downsample to this million reads
    // 150x on the Twist panel is app. 8M.
    downsample = 0

    // Experiment ploidy
    ploidy = 48

    // Run HaplotypeCaller by intervals. Default is by chromosome.
    runHCParallel = true
    intervalList = (1..22).collect { "chr${it}" } + ["chrX"]

    // Minimum alternative support for lofreq variants
    // 0 = no filtering
    minAltSupport = 0

    // ONLY run the following step: 'mapping', 'calling' or 'pinpoint'.
    // If calling - a cramtable is required.
    // If pinpoint - a vcftable is required.
    step = ''
    cramtable = "$projectDir/cramtable.tsv"
    vcftable = "$projectDir/vcftable.tsv"

    // Run full WGS pipeline
    fqtable = ''
    // Subset WGS cram files as input to WGS workflow
    subset_wgs = false
    // Use already subset cram files as input. Define path to input cramtable:
    wgs_subset_input = ""

    // Perform fast duplication removal
    // Does NOT discern between PCR duplicates and optical duplicates, but both are marked.
    fast_markdup = false
    // Perform duplication using spark (beta tool)
    spark_markdup = true

    // UMI processing (opional)
    umi = false

    // Quality control
    fullQC = false
    doFastqc = true

    // Variant calling methods
    lofreq = true
    gatk_joint_calling = false
    crisp = false // Pool only (not available through conda)
    octopus = false // Pool only (linux only)
    deepvariant = false // WGS only (linux only)

    // Variant filtering. Either optimised for sensitivity or balance
    filter = true
    filter_method = 'sensitivity'
    filter_indels = false
    discard_filtered = true

    // Pinpoint method (pilot or new)
    pinpoint_method = 'new'

    // Annotation configurations
    annotate = true
    snpeff_db = 'GRCh38.99'
    snpeff_config = ""
    snpeff_cache = ""
    clinvar_db = ""
    // Add gene annotation based on third column in bedfile
    bedfile_gene_annotation = true

    // Misc (never edit here)
    help = false
    testing = false

}

// Processes should always fail if any pipe element has a non-zero exit code.
process.shell = ['/bin/bash', '-euo', 'pipefail']

// Include execution profiles and reference files

includeConfig 'conf/profiles.config'

// Add additional log and tracing. Trace can be adjusted to specific outputs.

trace {
    enabled = true
    file = 'trace.txt'
    overwrite = true
}

report {
    enabled = true
    file = 'report.html'
    overwrite = true
}

// Set default branch if running directly from github

manifest {
    defaultBranch = 'main'
}