Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/workflows/conf/centriflaken.config @ 97:8d7f482c64de

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"planemo upload"
author kkonganti
date Fri, 29 Jul 2022 11:11:07 -0400
parents 3f367a0de778
children
comparison
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96:ef0b422978fd 97:8d7f482c64de
1 params { 1 params {
2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov' 2 workflow_blueprint_by = 'Narjol.Gonzalez-Escalona@fda.hhs.gov'
3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov' 3 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
4 workflow_version = '0.2.0' 4 workflow_version = '0.2.0'
5 centrifuge_x = '/tool/tool-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' 5 centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
6 centrifuge_extract_bug = 'Escherichia coli' 6 centrifuge_extract_bug = 'Escherichia coli'
7 centrifuge_save_aligned = false 7 centrifuge_save_aligned = false
8 centrifuge_save_unaligned = false 8 centrifuge_save_unaligned = false
9 centrifuge_out_fmt_sam = false 9 centrifuge_out_fmt_sam = false
10 centrifuge_ignore_quals = false 10 centrifuge_ignore_quals = false
11 kraken2_db = '/tool/tool-data/cfsan-centriflaken-db/0/kraken2/standard-210914' 11 kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914'
12 kraken2_confidence = '0.0' 12 kraken2_confidence = '0.0'
13 kraken2_quick = false 13 kraken2_quick = false
14 kraken2_use_mpa_style = false 14 kraken2_use_mpa_style = false
15 kraken2_minimum_base_quality = '0' 15 kraken2_minimum_base_quality = '0'
16 kraken2_report_zero_counts = false 16 kraken2_report_zero_counts = false
32 ectyper_perc_opid = 90 32 ectyper_perc_opid = 90
33 ectyper_perc_hpid = 95 33 ectyper_perc_hpid = 95
34 ectyper_perc_opcov = 95 34 ectyper_perc_opcov = 95
35 ectyper_perc_hpcov = 50 35 ectyper_perc_hpcov = 50
36 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) 36 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
37 serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' 37 serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
38 serotypefinder_min_cov = 0.80 38 serotypefinder_min_cov = 0.80
39 serotypefinder_min_threshold = 0.85 39 serotypefinder_min_threshold = 0.85
40 serotypefinder_x = true 40 serotypefinder_x = true
41 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) 41 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
42 seqsero2_t = 4 42 seqsero2_t = 4
46 mlst_run = true 46 mlst_run = true
47 mlst_minid = 95 47 mlst_minid = 95
48 mlst_mincov = 10 48 mlst_mincov = 10
49 mlst_minscore = 50 49 mlst_minscore = 50
50 amrfinderplus_run = false 50 amrfinderplus_run = false
51 amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' 51 amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
52 amrfinderplus_genes = true 52 amrfinderplus_genes = true
53 abricate_run = true 53 abricate_run = true
54 abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' 54 abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
55 abricate_minid = 90 55 abricate_minid = 90
56 abricate_mincov = 80 56 abricate_mincov = 80
57 abricate_summary_run = true 57 abricate_summary_run = true
58 seqkit_grep_on = false 58 seqkit_grep_on = false
59 } 59 }