nextflow.config

// Config inheritance options
params {
    generic_config_base = "https://raw.githubusercontent.com/sanger-pathogens/nextflow-commons/"
    generic_config_version = "master"
    generic_config_url = ""
}

manifest {
    name            = 'long-read-ampliseq'
    author          = 'PAM Informatics'
    homePage        = 'https://gitlab.internal.sanger.ac.uk/sanger-pathogens/pipelines/long-read-ampliseq'
    description     = 'AmpliSeq analysis pipeline for STI and epidemic pathogens from long reads'
    mainScript      = 'main.nf'
    nextflowVersion = '>=21.04.0'
    version         = 'v0.0.1'
}

params {
    // Basecalling
    basecall = "true"
    basecall_model = "dna_r10.4.1_e8.2_400bps_hac@v4.3.0"
    basecall_model_path = ""
    //this is default anyways but allows for changing
    trim_adapters = "all"
    barcode_kit_name = ["SQK-NBD114-24"] //https://github.com/nanoporetech/dorado/issues/625
    read_format = "fastq"
    dorado_local_path = ""

    // Save output files
    // TODO Make all the file retaining names consistent! 
    keep_sorted_bam = true
    keep_bam_files = false
    save_fastqs = true
    save_trimmed = true
    save_too_short = true
    save_too_long = true

    // QC
    qc_reads = true
    min_qscore = 9
    cutadapt_args = "-e 0.15 --no-indels --overlap 18"
    lower_read_length_cutoff = 450
    upper_read_length_cutoff = 800
    coverage_reporting_thresholds = "1,2,8,10,25,30,40,50,100"
    coverage_filtering_threshold = "25"
    multiqc_config = ""

    // Reference files
    reference = "/data/pam/team216/mb29/scratch/Treponema/Treponema_References/NC_021508.1.mask-Ribosomal-Operon2.fasta"
    raw_read_dir = "/lustre/scratch126/pam/teams/team230/sd28/long-read-ampliseq/pod5"
    primers = "/data/pam/team216/mb29/scratch/Treponema/TP_Discriminatory_sites_2021/MinION_Lab_Testing/binding_sites/TP-Discriminatory-primers.20230208_23S-v1.fas"
    target_regions_bed = "/data/pam/team230/wr7/scratch/tmp/ampliseq_pipeline/fixed.bed"
    additional_metadata = "/lustre/scratch126/pam/teams/team230/sd28/long-read-ampliseq/metadata/sample_to_barcode.csv"

    // Variant calling
    clair3_model = "/lustre/scratch126/pam/teams/team230/sd28/long-read-ampliseq/clair3_model/r1041_e82_400bps_hac_v430"
    clair3_min_coverage = "5"
    remove_recombination = false
    raxml_base_model = 'GTR+G4'
    raxml_threads = 2
    masking_quality = 15

    // Consensus curation
    min_ref_gt_qual = 1
    min_alt_gt_qual = 1


    // LSF options
    queue_size = 50
    submit_rate_limit = '50/2min'
    monochrome_logs = false
}

// to add to nextflow.commons

process {
    withLabel:gpu {

        //forms the resource from other labels
        clusterOptions = { "-M " + task.memory.toMega() + " -R 'select[ngpus>0] span[ptile=1]' -gpu 'num=1:mode=shared:gmem=" + task.memory.toMega() * 2 + "'" }
        
        queue = { task.time > 48.h ? 'gpu-basement' : task.time > 12.h ? 'gpu-huge' : 'gpu-normal' }
        
        // need to set --nv to enable GPU's to be used
        containerOptions = {
            workflow.containerEngine == "singularity" ? '--containall --cleanenv --nv':
            ( workflow.containerEngine == "docker" ? '--gpus all': null )
        }
    }
}

profiles {
    standard {
        inherit_generic_config()
    }
    docker {
        inherit_generic_config()
    }
    singularity {
        inherit_generic_config()
    }
    conda {
        inherit_generic_config()
    }
    laptop {
        includeConfig "./config/nextflow-commons/common.config"

        docker.enabled = true
        params.dorado_local_path = "/Users/Shared/ampliseq/dorado-0.7.1-osx-arm64/bin/dorado"
        params.basecall_model_path = "/Users/Shared/ampliseq/dna_r10.4.1_e8.2_400bps_hac@v4.3.0"
        params.clair3_model = "/Users/Shared/ampliseq/r1041_e82_400bps_hac_v430"
    }
}

// Helper functions
def inherit_generic_config() {
    config_url = params.generic_config_url ? params.generic_config_url : "${params.generic_config_base}/${params.generic_config_version}/configs/nextflow.config"
    try {
        includeConfig "${config_url}"
    } catch (Exception e) {
        System.err.println("ERROR: Could not load generic config: ${config_url}")
        System.err.println("Encountered the following exception:")
        throw e
    }
}