Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/workflows/conf/centriflaken.config @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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children 17890124001d
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100:9d9537c907bd 101:ce6d9548fe89
1 params {
2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
4 workflow_version = '0.2.0'
5 centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
6 centrifuge_extract_bug = 'Escherichia coli'
7 centrifuge_save_aligned = false
8 centrifuge_save_unaligned = false
9 centrifuge_out_fmt_sam = false
10 centrifuge_ignore_quals = false
11 kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
12 kraken2_confidence = '0.0'
13 kraken2_quick = false
14 kraken2_use_mpa_style = false
15 kraken2_minimum_base_quality = '0'
16 kraken2_report_zero_counts = false
17 kraken2_report_minimizer_data = false
18 kraken2_use_names = true
19 kraken2_extract_bug = params.centrifuge_extract_bug
20 flye_pacbio_raw = false
21 flye_pacbio_corr = false
22 flye_pacbio_hifi = false
23 flye_nano_raw = true
24 flye_nano_corr = false
25 flye_nano_hq = false
26 flye_genome_size = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? '5m' : '5.5m')
27 flye_polish_iter = false
28 flye_min_overlap = false
29 flye_scaffold = false
30 flye_meta = true
31 ectyper_run = false
32 ectyper_perc_opid = 90
33 ectyper_perc_hpid = 95
34 ectyper_perc_opcov = 95
35 ectyper_perc_hpcov = 50
36 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
37 serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
38 serotypefinder_min_cov = 0.80
39 serotypefinder_min_threshold = 0.85
40 serotypefinder_x = true
41 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
42 seqsero2_t = 4
43 seqsero2_m = 'k'
44 seqsero2_c = false
45 seqsero2_s = false
46 mlst_run = true
47 mlst_minid = 95
48 mlst_mincov = 10
49 mlst_minscore = 50
50 amrfinderplus_run = false
51 amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
52 amrfinderplus_genes = true
53 abricate_run = true
54 abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
55 abricate_minid = 90
56 abricate_mincov = 80
57 abricate_summary_run = true
58 seqkit_grep_on = false
59 }