|
kkonganti@0
|
1 params {
|
|
kkonganti@0
|
2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
|
|
kkonganti@0
|
3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
|
|
kkonganti@0
|
4 workflow_version = '0.2.0'
|
|
kkonganti@38
|
5 centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
|
|
kkonganti@0
|
6 centrifuge_extract_bug = 'Escherichia coli'
|
|
kkonganti@0
|
7 centrifuge_save_aligned = false
|
|
kkonganti@0
|
8 centrifuge_save_unaligned = false
|
|
kkonganti@0
|
9 centrifuge_out_fmt_sam = false
|
|
kkonganti@0
|
10 centrifuge_ignore_quals = false
|
|
kkonganti@38
|
11 kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
|
|
kkonganti@0
|
12 kraken2_confidence = '0.0'
|
|
kkonganti@0
|
13 kraken2_quick = false
|
|
kkonganti@0
|
14 kraken2_use_mpa_style = false
|
|
kkonganti@0
|
15 kraken2_minimum_base_quality = '0'
|
|
kkonganti@0
|
16 kraken2_report_zero_counts = false
|
|
kkonganti@0
|
17 kraken2_report_minimizer_data = false
|
|
kkonganti@0
|
18 kraken2_use_names = true
|
|
kkonganti@0
|
19 kraken2_extract_bug = params.centrifuge_extract_bug
|
|
kkonganti@0
|
20 spades_isolate = false
|
|
kkonganti@0
|
21 spades_sc = false
|
|
kkonganti@0
|
22 spades_meta = true
|
|
kkonganti@0
|
23 spades_bio = false
|
|
kkonganti@0
|
24 spades_corona = false
|
|
kkonganti@0
|
25 spades_rna = false
|
|
kkonganti@0
|
26 spades_plasmid = false
|
|
kkonganti@0
|
27 spades_metaviral = false
|
|
kkonganti@0
|
28 spades_metaplasmid = false
|
|
kkonganti@0
|
29 spades_rnaviral = false
|
|
kkonganti@0
|
30 spades_iontorrent = false
|
|
kkonganti@0
|
31 spades_only_assembler = false
|
|
kkonganti@0
|
32 spades_careful = false
|
|
kkonganti@0
|
33 spades_cov_cutoff = false
|
|
kkonganti@0
|
34 spades_k = false
|
|
kkonganti@0
|
35 spades_hmm = false
|
|
kkonganti@0
|
36 ectyper_run = false
|
|
kkonganti@0
|
37 ectyper_perc_opid = 90
|
|
kkonganti@0
|
38 ectyper_perc_hpid = 95
|
|
kkonganti@0
|
39 ectyper_perc_opcov = 95
|
|
kkonganti@0
|
40 ectyper_perc_hpcov = 50
|
|
kkonganti@0
|
41 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
|
|
kkonganti@38
|
42 serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
|
|
kkonganti@0
|
43 serotypefinder_min_cov = 0.80
|
|
kkonganti@0
|
44 serotypefinder_min_threshold = 0.85
|
|
kkonganti@0
|
45 serotypefinder_x = true
|
|
kkonganti@0
|
46 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
|
|
kkonganti@0
|
47 seqsero2_t = 4
|
|
kkonganti@0
|
48 seqsero2_m = 'k'
|
|
kkonganti@0
|
49 seqsero2_c = false
|
|
kkonganti@0
|
50 seqsero2_s = false
|
|
kkonganti@0
|
51 mlst_run = true
|
|
kkonganti@0
|
52 mlst_minid = 95
|
|
kkonganti@0
|
53 mlst_mincov = 10
|
|
kkonganti@0
|
54 mlst_minscore = 50
|
|
kkonganti@0
|
55 amrfinderplus_run = false
|
|
kkonganti@38
|
56 amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
|
|
kkonganti@0
|
57 amrfinderplus_genes = true
|
|
kkonganti@0
|
58 abricate_run = true
|
|
kkonganti@38
|
59 abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
|
|
kkonganti@0
|
60 abricate_minid = 90
|
|
kkonganti@0
|
61 abricate_mincov = 80
|
|
kkonganti@0
|
62 abricate_summary_run = true
|
|
kkonganti@0
|
63 seqkit_grep_on = false
|
|
kkonganti@0
|
64 fq_filter_by_len = 75
|
|
kkonganti@0
|
65 fq_suffix = '_R1_001.fastq.gz'
|
|
kkonganti@0
|
66 fq2_suffix = '_R2_001.fastq.gz'
|
|
kkonganti@0
|
67 } |
