--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.2.0/workflows/conf/cronology_db.config	Mon Jul 15 16:11:44 2024 -0400
@@ -0,0 +1,95 @@
+params {
+    workflow_conceived_by = 'Kranti Konganti'
+    workflow_built_by = 'Kranti Konganti'
+    workflow_version = '0.1.0'
+    pdg_release = 'PDG000000043.204'
+    pdg_org = 'Cronobacter'
+    ncbi_asm_suffix = '_genomic.fna.gz'
+    dpubmlstpy_run = true
+    dpubmlstpy_org = 'cronobacter'
+    dpubmlstpy_mlsts = 'schemes/1'
+    dpubmlstpy_profile = false
+    dpubmlstpy_loci = false
+    dpubmlstpy_suffix = false
+    dpubmlstpy_akey = false
+    dpubmlstpy_id = false
+    genomes_chunk = 50
+    checkm2predict_run = true
+    checkm2predict_quiet = true
+    checkm2predict_lowmem = false
+    checkm2predict_general = false
+    checkm2predict_specific = false
+    checkm2predict_allmodels = true 
+    checkm2predict_genes = false
+    checkm2predict_x = '.fna.gz'
+    checkm2predict_tmpdir = '"."'
+    checkm2predict_rminterfiles = false
+    checkm2predict_ttable = false
+    checkm2predict_dbg_cos = false
+    checkm2predict_dbg_vectors = false
+    checkm2predict_dbpath = ("${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'databases'
+        + File.separator
+        + 'checkm2_db'
+        + File.separator
+        + 'uniref100.KO.1.dmnd')
+    guncrun_run = true
+    guncrun_in_is_fasta = false
+    guncrun_in_is_fofn = false
+    guncrun_in_is_dir = false
+    guncrun_file_suffix = (params.checkm2predict_x ?: '.fna.gz')
+    guncrun_gene_calls = false
+    guncrun_temp_dir = '"."'
+    guncrun_sensitive = true
+    guncrun_detailed_output = false
+    guncrun_ctg_tax_output = false
+    guncrun_use_species_lvl = false
+    guncrun_min_mapped_genes = 11
+    guncrun_dbpath = ("${projectDir}"
+        + File.separator
+        + 'assets'
+        + File.separator
+        + 'databases'
+        + File.separator
+        + 'gunc_db'
+        + File.separator
+        + 'gunc_db_progenomes2.1.dmnd')
+    fgq_py_cm2_extract = 'Name'
+    fgq_py_cm2_fcn = "'Completeness_General,Contamination,Completeness_Specific'"
+    fgq_py_cm2_fcv = "'97.5,1,99'"
+    fgq_py_cm2_conds = "'>=,<=,>='"
+    fgq_py_gunc_extract = 'genome'
+    fgq_py_gunc_fcn = "'clade_separation_score,contamination_portion'"
+    fgq_py_gunc_fcv = "'0.45,0.05'"
+    fgq_py_gunc_conds = "'<=,<='"
+    mashsketch_run = true
+    mashsketch_l = false
+    mashsketch_I = false
+    mashsketch_C = false
+    mashsketch_k = 21
+    mashsketch_s = 1000
+    mashsketch_i = false
+    mashsketch_S = false
+    mashsketch_w = false
+    mashsketch_r = false
+    mashsketch_b = false
+    mashsketch_m = false
+    mashsketch_c = false
+    mashsketch_g = false
+    mashsketch_n = false
+    mashsketch_a = false
+    mashsketch_z = false
+    mashsketch_Z = false
+    mlst_run = true
+    mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
+    mlst_legacy = true
+    mlst_minid = 95
+    mlst_mincov = 10
+    mlst_minscore = 50
+    mlst_blastdb = false
+    mlst_datadir = false
+    mlst_label = false
+}