nextflow.config

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  mpieva/quicksand Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
  Default config options
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/

manifest {
    name             = 'mpieva/quicksand'
    author           = 'Merlin Szymanski'
    homePage         = 'https://mpieva.github.io/quicksand/'
    description      = 'quick analysis of sedimentary ancient DNA'
    nextflowVersion  = '>=22.10'
    version          = 'v2.3'
}

cleanup = true
nextflow.enable.moduleBinaries = true

profiles {
    docker {
        docker.enabled         = true
        singularity.enabled    = false
    }
    singularity {
        docker.enabled         = false
        singularity.enabled    = true
        singularity.autoMounts = true
    }
    debug {
        cleanup                = false
    }
}


params {

    //basic_settings
    help           = false // display help-text and exit

    //user input
    bam            = ""   // multiplexed BAM file, containing merged reads
    rg             = ""   // readgroup index information
    split          = ""   // alternative input: folder with already splitted files (BAM, FASTQ)
    genomes        = ""   // folder with reference genomes fasta-files
    db             = ""   // kraken1 db for krakenuniq
    bedfiles       = ""   // bedfiles (dust-masking) for the genomes in --genomes
    fixed          = ""   // Specify the reference genome for assigned families
    rerun          = false //

    //optional input
    taxlvl         = 'f'  // extract reads on the given taxonomic level
    //

    //process settings
    doublestranded            = false // report damage patterns as observed in double-stranded libraries.
    bamfilterflag             = 1     // 1=filter paired, 4=filter unmapped
    bamfilter_length_cutoff   = 35    // filter out reads shorter < 35bp
    mapbwa_quality_cutoff     = 25    // filter out mapped reads with qualityscore < 25
    krakenuniq_min_kmers      = 129   // filter out families with < 129 kmers assined
    krakenuniq_min_reads      = 3     // filter out families with < 3 reads assigned
    reportfilter_percentage   = 0.5   // for the 'filtered_report.tsv', Specify FamPercentage threshold
    reportfilter_breadth      = 0.5   // for the 'filtered_report.tsv', Specify ProportionExpectedBreadth threshold

    compression_level         = 0    // bgzf compression level for intermediate files, 0..9

    // Defaults only, expecting to be overwritten
    max_memory = 128.GB
    max_cpus   = 16
    max_time   = 24.h
}

includeConfig "conf/process.config"
includeConfig "conf/settings.config"