Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.3.0/workflows/conf/centriflaken_hy.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 = '0.3.0' 4 workflow_version = '0.3.0'
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
53 ectyper_perc_opid = 90 53 ectyper_perc_opid = 90
54 ectyper_perc_hpid = 95 54 ectyper_perc_hpid = 95
55 ectyper_perc_opcov = 95 55 ectyper_perc_opcov = 95
56 ectyper_perc_hpcov = 50 56 ectyper_perc_hpcov = 50
57 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) 57 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
58 serotypefinder_db = '/tool/tool-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' 58 serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
59 serotypefinder_min_cov = 0.80 59 serotypefinder_min_cov = 0.80
60 serotypefinder_min_threshold = 0.85 60 serotypefinder_min_threshold = 0.85
61 serotypefinder_x = true 61 serotypefinder_x = true
62 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) 62 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
63 seqsero2_t = 4 63 seqsero2_t = 4
67 mlst_run = true 67 mlst_run = true
68 mlst_minid = 95 68 mlst_minid = 95
69 mlst_mincov = 10 69 mlst_mincov = 10
70 mlst_minscore = 50 70 mlst_minscore = 50
71 amrfinderplus_run = false 71 amrfinderplus_run = false
72 amrfinderplus_db = '/tool/tool-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' 72 amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
73 amrfinderplus_genes = true 73 amrfinderplus_genes = true
74 abricate_run = true 74 abricate_run = true
75 abricate_datadir = '/tool/tool-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' 75 abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db'
76 abricate_minid = 90 76 abricate_minid = 90
77 abricate_mincov = 80 77 abricate_mincov = 80
78 abricate_summary_run = true 78 abricate_summary_run = true
79 seqkit_grep_on = false 79 seqkit_grep_on = false
80 fq_filter_by_len = 75 80 fq_filter_by_len = 75