params_default.config

params {
    // input sequence
    inseq = "${ROOTDIR}/example-data/L_donovani.fasta.1"

    // reference data -- paths must be absolute
    ref_dir = "${ROOTDIR}/example-data/references"
    ref_species = "LmjF.1"

    // output directory, if desired
    // dist_dir = "${ROOTDIR}"

    // enable/disable parts of the pipeline
    run_exonerate    = false
    do_contiguation  = true
    do_circos        = true
    make_embl        = true
    use_reference    = true

    // naming patterns
    GENOME_PREFIX = "LDON"
    CHR_PATTERN = "LDON_(%d+)"
    MAX_GENE_LENGTH = 20000
    ABACAS_CHR_PATTERN = 'LmjF.(%d+)'
    ABACAS_CHR_PREFIX = "LDON"
    ABACAS_SEQ_PREFIX = "LDON"
    ABACAS_BIN_CHR = "LDON_0"

    // RATT parameters
    RATT_TRANSFER_TYPE = 'Species'

    // AUGUSTUS parameters
    AUGUSTUS_SPECIES = 'leishmania_major_sampled'
    AUGUSTUS_GENEMODEL = 'intronless'
    AUGUSTUS_HINTS_MAXINTRONLEN = '1'
    AUGUSTUS_SCORE_THRESHOLD = 0.7

    // EMBL file metadata
    EMBL_AUTHORS = "Foo Bar"
    EMBL_TITLE = "Baz"
    EMBL_PUBLICATION = "Quux"
    EMBL_GENOME_TYPE = "XXX"
    EMBL_CLASSIFICATION = "XXXX"
    EMBL_ORGANISM = "Leishmania donovani"
    EMBL_PROJ_ACCESSION = "123456"
    EMBL_DESCRIPTION = "Foo bar"

    // output GAF metadata
    TAXON_ID = 4711
    DB_ID = "GeneDB"
}