|
kkonganti@0
|
1 params {
|
|
kkonganti@0
|
2 workflow_conceived_by = 'Kranti Konganti'
|
|
kkonganti@0
|
3 workflow_built_by = 'Kranti Konganti'
|
|
kkonganti@0
|
4 workflow_version = '0.1.0'
|
|
kkonganti@0
|
5 pdg_release = 'PDG000000043.204'
|
|
kkonganti@0
|
6 pdg_org = 'Cronobacter'
|
|
kkonganti@0
|
7 ncbi_asm_suffix = '_genomic.fna.gz'
|
|
kkonganti@0
|
8 dpubmlstpy_run = true
|
|
kkonganti@0
|
9 dpubmlstpy_org = 'cronobacter'
|
|
kkonganti@0
|
10 dpubmlstpy_mlsts = 'schemes/1'
|
|
kkonganti@0
|
11 dpubmlstpy_profile = false
|
|
kkonganti@0
|
12 dpubmlstpy_loci = false
|
|
kkonganti@0
|
13 dpubmlstpy_suffix = false
|
|
kkonganti@0
|
14 dpubmlstpy_akey = false
|
|
kkonganti@0
|
15 dpubmlstpy_id = false
|
|
kkonganti@0
|
16 genomes_chunk = 50
|
|
kkonganti@0
|
17 checkm2predict_run = true
|
|
kkonganti@0
|
18 checkm2predict_quiet = true
|
|
kkonganti@0
|
19 checkm2predict_lowmem = false
|
|
kkonganti@0
|
20 checkm2predict_general = false
|
|
kkonganti@0
|
21 checkm2predict_specific = false
|
|
kkonganti@0
|
22 checkm2predict_allmodels = true
|
|
kkonganti@0
|
23 checkm2predict_genes = false
|
|
kkonganti@0
|
24 checkm2predict_x = '.fna.gz'
|
|
kkonganti@0
|
25 checkm2predict_tmpdir = '"."'
|
|
kkonganti@0
|
26 checkm2predict_rminterfiles = false
|
|
kkonganti@0
|
27 checkm2predict_ttable = false
|
|
kkonganti@0
|
28 checkm2predict_dbg_cos = false
|
|
kkonganti@0
|
29 checkm2predict_dbg_vectors = false
|
|
kkonganti@0
|
30 checkm2predict_dbpath = ("${projectDir}"
|
|
kkonganti@0
|
31 + File.separator
|
|
kkonganti@0
|
32 + 'assets'
|
|
kkonganti@0
|
33 + File.separator
|
|
kkonganti@0
|
34 + 'databases'
|
|
kkonganti@0
|
35 + File.separator
|
|
kkonganti@0
|
36 + 'checkm2_db'
|
|
kkonganti@0
|
37 + File.separator
|
|
kkonganti@0
|
38 + 'uniref100.KO.1.dmnd')
|
|
kkonganti@0
|
39 guncrun_run = true
|
|
kkonganti@0
|
40 guncrun_in_is_fasta = false
|
|
kkonganti@0
|
41 guncrun_in_is_fofn = false
|
|
kkonganti@0
|
42 guncrun_in_is_dir = false
|
|
kkonganti@0
|
43 guncrun_file_suffix = (params.checkm2predict_x ?: '.fna.gz')
|
|
kkonganti@0
|
44 guncrun_gene_calls = false
|
|
kkonganti@0
|
45 guncrun_temp_dir = '"."'
|
|
kkonganti@0
|
46 guncrun_sensitive = true
|
|
kkonganti@0
|
47 guncrun_detailed_output = false
|
|
kkonganti@0
|
48 guncrun_ctg_tax_output = false
|
|
kkonganti@0
|
49 guncrun_use_species_lvl = false
|
|
kkonganti@0
|
50 guncrun_min_mapped_genes = 11
|
|
kkonganti@0
|
51 guncrun_dbpath = ("${projectDir}"
|
|
kkonganti@0
|
52 + File.separator
|
|
kkonganti@0
|
53 + 'assets'
|
|
kkonganti@0
|
54 + File.separator
|
|
kkonganti@0
|
55 + 'databases'
|
|
kkonganti@0
|
56 + File.separator
|
|
kkonganti@0
|
57 + 'gunc_db'
|
|
kkonganti@0
|
58 + File.separator
|
|
kkonganti@0
|
59 + 'gunc_db_progenomes2.1.dmnd')
|
|
kkonganti@0
|
60 fgq_py_cm2_extract = 'Name'
|
|
kkonganti@0
|
61 fgq_py_cm2_fcn = "'Completeness_General,Contamination,Completeness_Specific'"
|
|
kkonganti@0
|
62 fgq_py_cm2_fcv = "'97.5,1,99'"
|
|
kkonganti@0
|
63 fgq_py_cm2_conds = "'>=,<=,>='"
|
|
kkonganti@0
|
64 fgq_py_gunc_extract = 'genome'
|
|
kkonganti@0
|
65 fgq_py_gunc_fcn = "'clade_separation_score,contamination_portion'"
|
|
kkonganti@0
|
66 fgq_py_gunc_fcv = "'0.45,0.05'"
|
|
kkonganti@0
|
67 fgq_py_gunc_conds = "'<=,<='"
|
|
kkonganti@0
|
68 mashsketch_run = true
|
|
kkonganti@0
|
69 mashsketch_l = false
|
|
kkonganti@0
|
70 mashsketch_I = false
|
|
kkonganti@0
|
71 mashsketch_C = false
|
|
kkonganti@0
|
72 mashsketch_k = 21
|
|
kkonganti@0
|
73 mashsketch_s = 1000
|
|
kkonganti@0
|
74 mashsketch_i = false
|
|
kkonganti@0
|
75 mashsketch_S = false
|
|
kkonganti@0
|
76 mashsketch_w = false
|
|
kkonganti@0
|
77 mashsketch_r = false
|
|
kkonganti@0
|
78 mashsketch_b = false
|
|
kkonganti@0
|
79 mashsketch_m = false
|
|
kkonganti@0
|
80 mashsketch_c = false
|
|
kkonganti@0
|
81 mashsketch_g = false
|
|
kkonganti@0
|
82 mashsketch_n = false
|
|
kkonganti@0
|
83 mashsketch_a = false
|
|
kkonganti@0
|
84 mashsketch_z = false
|
|
kkonganti@0
|
85 mashsketch_Z = false
|
|
kkonganti@0
|
86 mlst_run = true
|
|
kkonganti@0
|
87 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
|
|
kkonganti@0
|
88 mlst_legacy = true
|
|
kkonganti@0
|
89 mlst_minid = 95
|
|
kkonganti@0
|
90 mlst_mincov = 10
|
|
kkonganti@0
|
91 mlst_minscore = 50
|
|
kkonganti@0
|
92 mlst_blastdb = false
|
|
kkonganti@0
|
93 mlst_datadir = false
|
|
kkonganti@0
|
94 mlst_label = false
|
|
kkonganti@0
|
95 }
|
