Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/workflows/conf/centriflaken_hy.config @ 35:dc9258195982

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 16:31:26 -0400
parents 4f9f145d1946
children d7c07f2456b4
comparison
equal deleted inserted replaced
34:4f9f145d1946 35:dc9258195982
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 = '/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 = '/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
37 ectyper_perc_opid = 90 37 ectyper_perc_opid = 90
38 ectyper_perc_hpid = 95 38 ectyper_perc_hpid = 95
39 ectyper_perc_opcov = 95 39 ectyper_perc_opcov = 95
40 ectyper_perc_hpcov = 50 40 ectyper_perc_hpcov = 50
41 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) 41 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
42 serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' 42 serotypefinder_db = '/data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
43 serotypefinder_min_cov = 0.80 43 serotypefinder_min_cov = 0.80
44 serotypefinder_min_threshold = 0.85 44 serotypefinder_min_threshold = 0.85
45 serotypefinder_x = true 45 serotypefinder_x = true
46 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) 46 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
47 seqsero2_t = 4 47 seqsero2_t = 4
51 mlst_run = true 51 mlst_run = true
52 mlst_minid = 95 52 mlst_minid = 95
53 mlst_mincov = 10 53 mlst_mincov = 10
54 mlst_minscore = 50 54 mlst_minscore = 50
55 amrfinderplus_run = false 55 amrfinderplus_run = false
56 amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' 56 amrfinderplus_db = '/data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
57 amrfinderplus_genes = true 57 amrfinderplus_genes = true
58 abricate_run = true 58 abricate_run = true
59 abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' 59 abricate_datadir = '/data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
60 abricate_minid = 90 60 abricate_minid = 90
61 abricate_mincov = 80 61 abricate_mincov = 80
62 abricate_summary_run = true 62 abricate_summary_run = true
63 seqkit_grep_on = false 63 seqkit_grep_on = false
64 fq_filter_by_len = 75 64 fq_filter_by_len = 75