Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/workflows/conf/centriflaken_hy.config @ 92:295c2597a475

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"planemo upload"
author kkonganti
date Tue, 19 Jul 2022 10:07:24 -0400
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children 3f367a0de778
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91:046e57368d3b 92:295c2597a475
1 params {
2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
4 workflow_version = '0.3.0'
5 centrifuge_x = '/hpc/db/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 = '/hpc/db/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 megahit_run = true
21 megahit_min_count = false
22 megahit_k_list = false
23 megahit_no_mercy = false
24 megahit_bubble_level = false
25 megahit_merge_level = false
26 megahit_prune_level = false
27 megahit_prune_depth = false
28 megahit_low_local_ratio = false
29 megahit_max_tip_len = false
30 megahit_no_local = false
31 megahit_kmin_1pass = false
32 megahit_preset = 'meta-sensitive'
33 megahit_mem_flag = 2
34 megahit_min_contig_len = false
35 spades_run = false
36 spades_isolate = false
37 spades_sc = false
38 spades_meta = true
39 spades_bio = false
40 spades_corona = false
41 spades_rna = false
42 spades_plasmid = false
43 spades_metaviral = false
44 spades_metaplasmid = false
45 spades_rnaviral = false
46 spades_iontorrent = false
47 spades_only_assembler = false
48 spades_careful = false
49 spades_cov_cutoff = false
50 spades_k = false
51 spades_hmm = false
52 ectyper_run = false
53 ectyper_perc_opid = 90
54 ectyper_perc_hpid = 95
55 ectyper_perc_opcov = 95
56 ectyper_perc_hpcov = 50
57 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
58 serotypefinder_db = '/hpc/db/serotypefinder/2.0.2'
59 serotypefinder_min_cov = 0.80
60 serotypefinder_min_threshold = 0.85
61 serotypefinder_x = true
62 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
63 seqsero2_t = 4
64 seqsero2_m = 'k'
65 seqsero2_c = false
66 seqsero2_s = false
67 mlst_run = true
68 mlst_minid = 95
69 mlst_mincov = 10
70 mlst_minscore = 50
71 amrfinderplus_run = false
72 amrfinderplus_db = '/hpc/db/amrfinderplus/3.10.24/latest'
73 amrfinderplus_genes = true
74 abricate_run = true
75 abricate_datadir = '/hpc/db/abricate/1.0.1/db'
76 abricate_minid = 90
77 abricate_mincov = 80
78 abricate_summary_run = true
79 seqkit_grep_on = false
80 fq_filter_by_len = 75
81 fq_suffix = '_R1_001.fastq.gz'
82 fq2_suffix = '_R2_001.fastq.gz'
83 }