Mercurial > repos > kkonganti > cfsan_cronology

comparison 0.1.0/workflows/conf/cronology_db.config @ 0:c8597e9e1a97

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"planemo upload"
author kkonganti
date Mon, 27 Nov 2023 12:37:44 -0500
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-1:000000000000 0:c8597e9e1a97
1 params {
2 workflow_conceived_by = 'Kranti Konganti'
3 workflow_built_by = 'Kranti Konganti'
4 workflow_version = '0.1.0'
5 pdg_release = 'PDG000000043.204'
6 pdg_org = 'Cronobacter'
7 ncbi_asm_suffix = '_genomic.fna.gz'
8 dpubmlstpy_run = true
9 dpubmlstpy_org = 'cronobacter'
10 dpubmlstpy_mlsts = 'schemes/1'
11 dpubmlstpy_profile = false
12 dpubmlstpy_loci = false
13 dpubmlstpy_suffix = false
14 dpubmlstpy_akey = false
15 dpubmlstpy_id = false
16 genomes_chunk = 50
17 checkm2predict_run = true
18 checkm2predict_quiet = true
19 checkm2predict_lowmem = false
20 checkm2predict_general = false
21 checkm2predict_specific = false
22 checkm2predict_allmodels = true
23 checkm2predict_genes = false
24 checkm2predict_x = '.fna.gz'
25 checkm2predict_tmpdir = '"."'
26 checkm2predict_rminterfiles = false
27 checkm2predict_ttable = false
28 checkm2predict_dbg_cos = false
29 checkm2predict_dbg_vectors = false
30 checkm2predict_dbpath = ("${projectDir}"
31 + File.separator
32 + 'assets'
33 + File.separator
34 + 'databases'
35 + File.separator
36 + 'checkm2_db'
37 + File.separator
38 + 'uniref100.KO.1.dmnd')
39 guncrun_run = true
40 guncrun_in_is_fasta = false
41 guncrun_in_is_fofn = false
42 guncrun_in_is_dir = false
43 guncrun_file_suffix = (params.checkm2predict_x ?: '.fna.gz')
44 guncrun_gene_calls = false
45 guncrun_temp_dir = '"."'
46 guncrun_sensitive = true
47 guncrun_detailed_output = false
48 guncrun_ctg_tax_output = false
49 guncrun_use_species_lvl = false
50 guncrun_min_mapped_genes = 11
51 guncrun_dbpath = ("${projectDir}"
52 + File.separator
53 + 'assets'
54 + File.separator
55 + 'databases'
56 + File.separator
57 + 'gunc_db'
58 + File.separator
59 + 'gunc_db_progenomes2.1.dmnd')
60 fgq_py_cm2_extract = 'Name'
61 fgq_py_cm2_fcn = "'Completeness_General,Contamination,Completeness_Specific'"
62 fgq_py_cm2_fcv = "'97.5,1,99'"
63 fgq_py_cm2_conds = "'>=,<=,>='"
64 fgq_py_gunc_extract = 'genome'
65 fgq_py_gunc_fcn = "'clade_separation_score,contamination_portion'"
66 fgq_py_gunc_fcv = "'0.45,0.05'"
67 fgq_py_gunc_conds = "'<=,<='"
68 mashsketch_run = true
69 mashsketch_l = false
70 mashsketch_I = false
71 mashsketch_C = false
72 mashsketch_k = 21
73 mashsketch_s = 1000
74 mashsketch_i = false
75 mashsketch_S = false
76 mashsketch_w = false
77 mashsketch_r = false
78 mashsketch_b = false
79 mashsketch_m = false
80 mashsketch_c = false
81 mashsketch_g = false
82 mashsketch_n = false
83 mashsketch_a = false
84 mashsketch_z = false
85 mashsketch_Z = false
86 mlst_run = true
87 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
88 mlst_legacy = true
89 mlst_minid = 95
90 mlst_mincov = 10
91 mlst_minscore = 50
92 mlst_blastdb = false
93 mlst_datadir = false
94 mlst_label = false
95 }