nextflow.config

/*
 * -------------------------------------------------
 *  metagWGS Nextflow config file
 * -------------------------------------------------
 * Default config options for all environments.
 */

params {
    // metagWGS parameters.
    reads = ""
    assemblies = ""
    single_end = false
    adapter1 = "AGATCGGAAGAGC"
    adapter2 = "AGATCGGAAGAGC"
    quality_type = "sanger"
    host_index = ""
    host_fasta = ""
    assembly = "" // short read: metaspades or megahit || HiFi reads : hifiasm-meta or metaflye
    min_contigs_cpm = 1
    diamond_bank = ""
    gtdbtk_bank = ""
    percentage_identity = 0.95
    type = ""

    // Stop after step or skip optional step/sub-step.

    // Optional step
    stop_at_clean = false
    skip_clean = false

    // Sub-steps of clean
    use_sickle = false
    skip_host_filter = false
    skip_kaiju = false

    // Step
    stop_at_assembly = false

    // Optional step
    stop_at_filtering = false
    skip_filtering = false

    // Step
    stop_at_structural_annot = false

    // Optional step
    skip_func_annot = false

    // Optional step
    skip_taxo_affi = false

    // Optional step
    skip_binning = false
    binning_cross_alignment = 'individual'
    drep_threshold = 0.95
    min_completeness = 50
    max_contamination = 10

    // Ressources.
    kaiju_db_dir = false
    kaiju_db_url = "https://kaiju.binf.ku.dk/database/kaiju_db_refseq_2021-02-26.tgz"
    eggnog_mapper_db_dir = ""
    eggnog_mapper_db_download = true
    // Others parameters.
    outdir = "results"
    databases = "databases"
    accession2taxid = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/accession2taxid/prot.accession2taxid.FULL.gz"
    taxdump = "ftp://ftp.ncbi.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz"
    taxonomy_dir = false
    hifi_multiqc_config = "$baseDir/assets/hifi_multiqc_config.yaml"
    sr_multiqc_config = "$baseDir/assets/sr_multiqc_config.yaml"

    help = false

}

// Load base.config by default for all pipelines.
includeConfig 'conf/base.config'

// Define profiles.
profiles {
    debug { includeConfig 'conf/debug.config' }
    genotoul { includeConfig 'conf/genotoul.config' }
    test { includeConfig 'conf/test.config' }
    functional_test { includeConfig 'conf/functional_test.config' }
    local { process.executor = 'local'}
    conda { includeConfig 'conf/conda.config' }
    singularity { includeConfig 'conf/singularity.config' }
}



// Manifest.
manifest {
    name = 'metagWGS'
    homePage = 'https://forgemia.inra.fr/genotoul-bioinfo/metagwgs'
    description = 'Analysis of metagenomics data'
    mainScript = 'main.nf'
    nextflowVersion = '>=20.01.0'
    version = '2.3'
}