|
kkonganti@130
|
1 params {
|
|
kkonganti@130
|
2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
|
|
kkonganti@130
|
3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
|
|
kkonganti@130
|
4 workflow_version = '0.4.0'
|
|
kkonganti@130
|
5 seqkit_rmdup_run = false
|
|
kkonganti@130
|
6 seqkit_rmdup_n = false
|
|
kkonganti@130
|
7 seqkit_rmdup_s = true
|
|
kkonganti@130
|
8 seqkit_rmdup_d = false
|
|
kkonganti@130
|
9 seqkit_rmdup_D = false
|
|
kkonganti@130
|
10 seqkit_rmdup_P = false
|
|
kkonganti@130
|
11 seqkit_rmdup_i = false
|
|
kkonganti@130
|
12 centrifuge_x = '/galaxy/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
|
|
kkonganti@130
|
13 centrifuge_extract_bug = 'Escherichia coli'
|
|
kkonganti@130
|
14 centrifuge_save_aligned = false
|
|
kkonganti@130
|
15 centrifuge_save_unaligned = false
|
|
kkonganti@130
|
16 centrifuge_out_fmt_sam = false
|
|
kkonganti@130
|
17 centrifuge_ignore_quals = false
|
|
kkonganti@130
|
18 kraken2_db = '/galaxy/cfsan-centriflaken-db/0/kraken2/standard-210914'
|
|
kkonganti@130
|
19 kraken2_confidence = '0.0'
|
|
kkonganti@130
|
20 kraken2_quick = false
|
|
kkonganti@130
|
21 kraken2_use_mpa_style = false
|
|
kkonganti@130
|
22 kraken2_minimum_base_quality = '0'
|
|
kkonganti@130
|
23 kraken2_report_zero_counts = false
|
|
kkonganti@130
|
24 kraken2_report_minimizer_data = false
|
|
kkonganti@130
|
25 kraken2_use_names = true
|
|
kkonganti@130
|
26 kraken2_extract_bug = params.centrifuge_extract_bug
|
|
kkonganti@130
|
27 megahit_run = true
|
|
kkonganti@130
|
28 megahit_min_count = false
|
|
kkonganti@130
|
29 megahit_k_list = false
|
|
kkonganti@130
|
30 megahit_no_mercy = false
|
|
kkonganti@130
|
31 megahit_bubble_level = false
|
|
kkonganti@130
|
32 megahit_merge_level = false
|
|
kkonganti@130
|
33 megahit_prune_level = false
|
|
kkonganti@130
|
34 megahit_prune_depth = false
|
|
kkonganti@130
|
35 megahit_low_local_ratio = false
|
|
kkonganti@130
|
36 megahit_max_tip_len = false
|
|
kkonganti@130
|
37 megahit_no_local = false
|
|
kkonganti@130
|
38 megahit_kmin_1pass = false
|
|
kkonganti@130
|
39 megahit_preset = 'meta-sensitive'
|
|
kkonganti@130
|
40 megahit_mem_flag = 2
|
|
kkonganti@130
|
41 megahit_min_contig_len = false
|
|
kkonganti@130
|
42 spades_run = false
|
|
kkonganti@130
|
43 spades_isolate = false
|
|
kkonganti@130
|
44 spades_sc = false
|
|
kkonganti@130
|
45 spades_meta = true
|
|
kkonganti@130
|
46 spades_bio = false
|
|
kkonganti@130
|
47 spades_corona = false
|
|
kkonganti@130
|
48 spades_rna = false
|
|
kkonganti@130
|
49 spades_plasmid = false
|
|
kkonganti@130
|
50 spades_metaviral = false
|
|
kkonganti@130
|
51 spades_metaplasmid = false
|
|
kkonganti@130
|
52 spades_rnaviral = false
|
|
kkonganti@130
|
53 spades_iontorrent = false
|
|
kkonganti@130
|
54 spades_only_assembler = false
|
|
kkonganti@130
|
55 spades_careful = false
|
|
kkonganti@130
|
56 spades_cov_cutoff = false
|
|
kkonganti@130
|
57 spades_k = false
|
|
kkonganti@130
|
58 spades_hmm = false
|
|
kkonganti@130
|
59 ectyper_run = false
|
|
kkonganti@130
|
60 ectyper_perc_opid = 90
|
|
kkonganti@130
|
61 ectyper_perc_hpid = 95
|
|
kkonganti@130
|
62 ectyper_perc_opcov = 95
|
|
kkonganti@130
|
63 ectyper_perc_hpcov = 50
|
|
kkonganti@130
|
64 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
|
|
kkonganti@130
|
65 serotypefinder_db = '/galaxy/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
|
|
kkonganti@130
|
66 serotypefinder_min_cov = 0.80
|
|
kkonganti@130
|
67 serotypefinder_min_threshold = 0.85
|
|
kkonganti@130
|
68 serotypefinder_x = true
|
|
kkonganti@130
|
69 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
|
|
kkonganti@130
|
70 seqsero2_t = 4
|
|
kkonganti@130
|
71 seqsero2_m = 'k'
|
|
kkonganti@130
|
72 seqsero2_c = false
|
|
kkonganti@130
|
73 seqsero2_s = false
|
|
kkonganti@130
|
74 mlst_run = true
|
|
kkonganti@130
|
75 mlst_minid = 95
|
|
kkonganti@130
|
76 mlst_mincov = 10
|
|
kkonganti@130
|
77 mlst_minscore = 50
|
|
kkonganti@130
|
78 amrfinderplus_run = false
|
|
kkonganti@130
|
79 amrfinderplus_db = '/galaxy/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
|
|
kkonganti@130
|
80 amrfinderplus_genes = true
|
|
kkonganti@130
|
81 abricate_run = true
|
|
kkonganti@130
|
82 abricate_datadir = '/galaxy/cfsan-centriflaken-db/0/abricate/1.0.1/db'
|
|
kkonganti@130
|
83 abricate_minid = 90
|
|
kkonganti@130
|
84 abricate_mincov = 80
|
|
kkonganti@130
|
85 abricate_summary_run = true
|
|
kkonganti@130
|
86 seqkit_grep_on = false
|
|
kkonganti@130
|
87 fq_filter_by_len = 75
|
|
kkonganti@130
|
88 fq_suffix = '_R1_001.fastq.gz'
|
|
kkonganti@130
|
89 fq2_suffix = '_R2_001.fastq.gz'
|
|
kkonganti@130
|
90 } |
