nextflow.config

// Dependencies docker image
process.container = 'bluemoon222/gbs-typer-sanger-nf:0.0.7'

manifest {
    homePage = 'https://github.com/sanger-pathogens/GBS-Typer-sanger-nf'
    description = "A NextFlow version of Ben Metcalf's GBS Typer pipeline"
    mainScript = 'main.nf'
    nextflowVersion = '>=20.10.0'
}

params {
    queue_size = 100
    reads = ""
    version = ""
    db_version = "0.2.1"
    db_dir = "./db/$db_version"
    sero_gene_db = "./db/GBS-SBG/GBS-SBG.fasta"
    results_dir = ""
    config = "./headers.json"
    contigs = ""
    serotyper_min_read_depth = 0
    gbs_blactam_db = "$db_dir/GBS_bLactam-DB/GBS_bLactam_Ref.fasta"
    gbs_blactam_1A_db = "$db_dir/GBS_bLactam-DB/GBS_bLactam_1A-DB.faa"
    gbs_blactam_2B_db = "$db_dir/GBS_bLactam-DB/GBS_bLactam_2B-DB.faa"
    gbs_blactam_2X_db = "$db_dir/GBS_bLactam-DB/GBS_bLactam_2X-DB.faa"
    gbs_res_typer_db = "$db_dir/GBS_resTyper_Gene-DB/GBS_Res_Gene-DB_Final.fasta"
    gbs_res_targets_db = "$db_dir/GBS_resTyper_Gene-DB/seqs_of_interest.txt"
    gbs_res_min_coverage = 99.9
    gbs_res_max_divergence = 5
    mlst_min_coverage = 99.999
    mlst_min_read_depth = 30
    other_res_db = "$db_dir/ResFinder-DB/ResFinder.fasta"
    other_res_min_coverage = 70
    other_res_max_divergence = 30
    restyper_min_read_depth = 30
    gbs_surface_typer_db = "$db_dir/GBS_Surface_Gene-DB/GBS_Surface_Gene-DB_Final.fasta"
    surfacetyper_min_coverage = 99.0
    surfacetyper_max_divergence = 8
    surfacetyper_min_read_depth = 30
    pbp_frac_align_threshold = 0.5
    pbp_frac_identity_threshold = 0.5
    help = false
    test = false

    // Specify which pipelines to run by default
    // Serotyping and resistance pipelines are enabled by default
    run_sero_res = true
    run_surfacetyper = true
    run_mlst = true
    run_pbptyper = false

}

env {
    PYTHONPATH = "$baseDir"
}

profiles {
    standard {
        docker {
             enabled = true
             autoMounts = true
             cacheDir = "$PWD"
        }
    }

    // Basic configuration for an LSF environment
    lsf {
        process.cpus = 1
        process.memory = "2GB"
        process.queue = "normal"
        process.errorStrategy = {task.attempt <= 1 ? 'retry' : 'ignore'}
        maxRetries = 2
        process.maxRetries = 3
        executor {
            name = "lsf"
            // Maximum number of jobs to spawn at once - adjust as necessary
            queueSize = params.queue_size
            jobName = { "gbstyper - $task.name - $task.hash" }
            pollInterval = "5 sec"
        }
    }

    // Singularity configuration used by the Sanger Institute
    sanger {
        docker {
             enabled = false
        }
        singularity {
             enabled = true
             autoMounts = true
             cacheDir = "$PWD"
            // Prevent mkfifo failure in srst2 with Nextflow 23+ and Singularity
             runOptions = '-B $(mktemp -d):/tmp'
        }
    }
}