Mercurial > repos > kkonganti > cfsan_centriflaken

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

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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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 = '0.4.0'
5 seqkit_rmdup_run = false
6 seqkit_rmdup_n = false
7 seqkit_rmdup_s = true
8 seqkit_rmdup_d = false
9 seqkit_rmdup_D = false
10 seqkit_rmdup_P = false
11 seqkit_rmdup_i = false
12 centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
13 centrifuge_extract_bug = 'Escherichia coli'
14 centrifuge_save_aligned = false
15 centrifuge_save_unaligned = false
16 centrifuge_out_fmt_sam = false
17 centrifuge_ignore_quals = false
18 kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
19 kraken2_confidence = '0.0'
20 kraken2_quick = false
21 kraken2_use_mpa_style = false
22 kraken2_minimum_base_quality = '0'
23 kraken2_report_zero_counts = false
24 kraken2_report_minimizer_data = false
25 kraken2_use_names = true
26 kraken2_extract_bug = params.centrifuge_extract_bug
27 megahit_run = true
28 megahit_min_count = false
29 megahit_k_list = false
30 megahit_no_mercy = false
31 megahit_bubble_level = false
32 megahit_merge_level = false
33 megahit_prune_level = false
34 megahit_prune_depth = false
35 megahit_low_local_ratio = false
36 megahit_max_tip_len = false
37 megahit_no_local = false
38 megahit_kmin_1pass = false
39 megahit_preset = 'meta-sensitive'
40 megahit_mem_flag = 2
41 megahit_min_contig_len = false
42 spades_run = false
43 spades_isolate = false
44 spades_sc = false
45 spades_meta = true
46 spades_bio = false
47 spades_corona = false
48 spades_rna = false
49 spades_plasmid = false
50 spades_metaviral = false
51 spades_metaplasmid = false
52 spades_rnaviral = false
53 spades_iontorrent = false
54 spades_only_assembler = false
55 spades_careful = false
56 spades_cov_cutoff = false
57 spades_k = false
58 spades_hmm = false
59 ectyper_run = false
60 ectyper_perc_opid = 90
61 ectyper_perc_hpid = 95
62 ectyper_perc_opcov = 95
63 ectyper_perc_hpcov = 50
64 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
65 serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
66 serotypefinder_min_cov = 0.80
67 serotypefinder_min_threshold = 0.85
68 serotypefinder_x = true
69 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
70 seqsero2_t = 4
71 seqsero2_m = 'k'
72 seqsero2_c = false
73 seqsero2_s = false
74 mlst_run = true
75 mlst_minid = 95
76 mlst_mincov = 10
77 mlst_minscore = 50
78 amrfinderplus_run = false
79 amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
80 amrfinderplus_genes = true
81 abricate_run = true
82 abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
83 abricate_minid = 90
84 abricate_mincov = 80
85 abricate_summary_run = true
86 seqkit_grep_on = false
87 fq_filter_by_len = 75
88 fq_suffix = '_R1_001.fastq.gz'
89 fq2_suffix = '_R2_001.fastq.gz'
90 }