kkonganti@0: params {
kkonganti@0:     workflow_conceived_by = 'Kranti Konganti'
kkonganti@0:     workflow_built_by = 'Kranti Konganti'
kkonganti@0:     workflow_version = '0.1.0'
kkonganti@0:     pdg_release = 'PDG000000043.204'
kkonganti@0:     pdg_org = 'Cronobacter'
kkonganti@0:     ncbi_asm_suffix = '_genomic.fna.gz'
kkonganti@0:     dpubmlstpy_run = true
kkonganti@0:     dpubmlstpy_org = 'cronobacter'
kkonganti@0:     dpubmlstpy_mlsts = 'schemes/1'
kkonganti@0:     dpubmlstpy_profile = false
kkonganti@0:     dpubmlstpy_loci = false
kkonganti@0:     dpubmlstpy_suffix = false
kkonganti@0:     dpubmlstpy_akey = false
kkonganti@0:     dpubmlstpy_id = false
kkonganti@0:     genomes_chunk = 50
kkonganti@0:     checkm2predict_run = true
kkonganti@0:     checkm2predict_quiet = true
kkonganti@0:     checkm2predict_lowmem = false
kkonganti@0:     checkm2predict_general = false
kkonganti@0:     checkm2predict_specific = false
kkonganti@0:     checkm2predict_allmodels = true 
kkonganti@0:     checkm2predict_genes = false
kkonganti@0:     checkm2predict_x = '.fna.gz'
kkonganti@0:     checkm2predict_tmpdir = '"."'
kkonganti@0:     checkm2predict_rminterfiles = false
kkonganti@0:     checkm2predict_ttable = false
kkonganti@0:     checkm2predict_dbg_cos = false
kkonganti@0:     checkm2predict_dbg_vectors = false
kkonganti@0:     checkm2predict_dbpath = ("${projectDir}"
kkonganti@0:         + File.separator
kkonganti@0:         + 'assets'
kkonganti@0:         + File.separator
kkonganti@0:         + 'databases'
kkonganti@0:         + File.separator
kkonganti@0:         + 'checkm2_db'
kkonganti@0:         + File.separator
kkonganti@0:         + 'uniref100.KO.1.dmnd')
kkonganti@0:     guncrun_run = true
kkonganti@0:     guncrun_in_is_fasta = false
kkonganti@0:     guncrun_in_is_fofn = false
kkonganti@0:     guncrun_in_is_dir = false
kkonganti@0:     guncrun_file_suffix = (params.checkm2predict_x ?: '.fna.gz')
kkonganti@0:     guncrun_gene_calls = false
kkonganti@0:     guncrun_temp_dir = '"."'
kkonganti@0:     guncrun_sensitive = true
kkonganti@0:     guncrun_detailed_output = false
kkonganti@0:     guncrun_ctg_tax_output = false
kkonganti@0:     guncrun_use_species_lvl = false
kkonganti@0:     guncrun_min_mapped_genes = 11
kkonganti@0:     guncrun_dbpath = ("${projectDir}"
kkonganti@0:         + File.separator
kkonganti@0:         + 'assets'
kkonganti@0:         + File.separator
kkonganti@0:         + 'databases'
kkonganti@0:         + File.separator
kkonganti@0:         + 'gunc_db'
kkonganti@0:         + File.separator
kkonganti@0:         + 'gunc_db_progenomes2.1.dmnd')
kkonganti@0:     fgq_py_cm2_extract = 'Name'
kkonganti@0:     fgq_py_cm2_fcn = "'Completeness_General,Contamination,Completeness_Specific'"
kkonganti@0:     fgq_py_cm2_fcv = "'97.5,1,99'"
kkonganti@0:     fgq_py_cm2_conds = "'>=,<=,>='"
kkonganti@0:     fgq_py_gunc_extract = 'genome'
kkonganti@0:     fgq_py_gunc_fcn = "'clade_separation_score,contamination_portion'"
kkonganti@0:     fgq_py_gunc_fcv = "'0.45,0.05'"
kkonganti@0:     fgq_py_gunc_conds = "'<=,<='"
kkonganti@0:     mashsketch_run = true
kkonganti@0:     mashsketch_l = false
kkonganti@0:     mashsketch_I = false
kkonganti@0:     mashsketch_C = false
kkonganti@0:     mashsketch_k = 21
kkonganti@0:     mashsketch_s = 1000
kkonganti@0:     mashsketch_i = false
kkonganti@0:     mashsketch_S = false
kkonganti@0:     mashsketch_w = false
kkonganti@0:     mashsketch_r = false
kkonganti@0:     mashsketch_b = false
kkonganti@0:     mashsketch_m = false
kkonganti@0:     mashsketch_c = false
kkonganti@0:     mashsketch_g = false
kkonganti@0:     mashsketch_n = false
kkonganti@0:     mashsketch_a = false
kkonganti@0:     mashsketch_z = false
kkonganti@0:     mashsketch_Z = false
kkonganti@0:     mlst_run = true
kkonganti@0:     mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
kkonganti@0:     mlst_legacy = true
kkonganti@0:     mlst_minid = 95
kkonganti@0:     mlst_mincov = 10
kkonganti@0:     mlst_minscore = 50
kkonganti@0:     mlst_blastdb = false
kkonganti@0:     mlst_datadir = false
kkonganti@0:     mlst_label = false
kkonganti@0: }