Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/workflows/conf/centriflaken_hy.config @ 0:77494b0fa3c7

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"planemo upload"
author kkonganti
date Mon, 27 Jun 2022 15:55:37 -0400
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children 4f9f145d1946
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-1:000000000000 0:77494b0fa3c7
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 = '/nfs/home/galaxy/cfsan-centriflaken-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 = '/nfs/home/galaxy/cfsan-centriflaken-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 spades_isolate = false
21 spades_sc = false
22 spades_meta = true
23 spades_bio = false
24 spades_corona = false
25 spades_rna = false
26 spades_plasmid = false
27 spades_metaviral = false
28 spades_metaplasmid = false
29 spades_rnaviral = false
30 spades_iontorrent = false
31 spades_only_assembler = false
32 spades_careful = false
33 spades_cov_cutoff = false
34 spades_k = false
35 spades_hmm = false
36 ectyper_run = false
37 ectyper_perc_opid = 90
38 ectyper_perc_hpid = 95
39 ectyper_perc_opcov = 95
40 ectyper_perc_hpcov = 50
41 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
42 serotypefinder_db = '/nfs/home/galaxy/cfsan-centriflaken-db/serotypefinder/2.0.2'
43 serotypefinder_min_cov = 0.80
44 serotypefinder_min_threshold = 0.85
45 serotypefinder_x = true
46 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
47 seqsero2_t = 4
48 seqsero2_m = 'k'
49 seqsero2_c = false
50 seqsero2_s = false
51 mlst_run = true
52 mlst_minid = 95
53 mlst_mincov = 10
54 mlst_minscore = 50
55 amrfinderplus_run = false
56 amrfinderplus_db = '/nfs/home/galaxy/cfsan-centriflaken-db/amrfinderplus/3.10.24/latest'
57 amrfinderplus_genes = true
58 abricate_run = true
59 abricate_datadir = '/nfs/home/galaxy/cfsan-centriflaken-db/abricate/1.0.1/db'
60 abricate_minid = 90
61 abricate_mincov = 80
62 abricate_summary_run = true
63 seqkit_grep_on = false
64 fq_filter_by_len = 75
65 fq_suffix = '_R1_001.fastq.gz'
66 fq2_suffix = '_R2_001.fastq.gz'
67 }