Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.2/workflows/conf/centriflaken_hy.config @ 111:da35e8151369

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"planemo upload"
author kkonganti
date Fri, 28 Jun 2024 09:43:24 -0400
parents 52045ea4679d
children
comparison
equal deleted inserted replaced
110:345d0a16f026 111:da35e8151369
7 seqkit_rmdup_s = true 7 seqkit_rmdup_s = true
8 seqkit_rmdup_d = false 8 seqkit_rmdup_d = false
9 seqkit_rmdup_D = false 9 seqkit_rmdup_D = false
10 seqkit_rmdup_P = false 10 seqkit_rmdup_P = false
11 seqkit_rmdup_i = false 11 seqkit_rmdup_i = false
12 centrifuge_x = '/tool-local-data/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab' 12 centrifuge_x = '/galaxy/cfsan-centriflaken-db/0/centrifuge/2022-04-12/ab'
13 centrifuge_extract_bug = 'Escherichia coli' 13 centrifuge_extract_bug = 'Escherichia coli'
14 centrifuge_save_aligned = false 14 centrifuge_save_aligned = false
15 centrifuge_save_unaligned = false 15 centrifuge_save_unaligned = false
16 centrifuge_out_fmt_sam = false 16 centrifuge_out_fmt_sam = false
17 centrifuge_ignore_quals = false 17 centrifuge_ignore_quals = false
18 kraken2_db = '/tool-local-data/cfsan-centriflaken-db/0/kraken2/standard-210914' 18 kraken2_db = '/galaxy/cfsan-centriflaken-db/0/kraken2/standard-210914'
19 kraken2_confidence = '0.0' 19 kraken2_confidence = '0.0'
20 kraken2_quick = false 20 kraken2_quick = false
21 kraken2_use_mpa_style = false 21 kraken2_use_mpa_style = false
22 kraken2_minimum_base_quality = '0' 22 kraken2_minimum_base_quality = '0'
23 kraken2_report_zero_counts = false 23 kraken2_report_zero_counts = false
60 ectyper_perc_opid = 90 60 ectyper_perc_opid = 90
61 ectyper_perc_hpid = 95 61 ectyper_perc_hpid = 95
62 ectyper_perc_opcov = 95 62 ectyper_perc_opcov = 95
63 ectyper_perc_hpcov = 50 63 ectyper_perc_hpcov = 50
64 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true) 64 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
65 serotypefinder_db = '/tool-local-data/cfsan-centriflaken-db/0/serotypefinder/2.0.2' 65 serotypefinder_db = '/galaxy/cfsan-centriflaken-db/0/serotypefinder/2.0.2'
66 serotypefinder_min_cov = 0.80 66 serotypefinder_min_cov = 0.80
67 serotypefinder_min_threshold = 0.85 67 serotypefinder_min_threshold = 0.85
68 serotypefinder_x = true 68 serotypefinder_x = true
69 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false) 69 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
70 seqsero2_t = 4 70 seqsero2_t = 4
74 mlst_run = true 74 mlst_run = true
75 mlst_minid = 95 75 mlst_minid = 95
76 mlst_mincov = 10 76 mlst_mincov = 10
77 mlst_minscore = 50 77 mlst_minscore = 50
78 amrfinderplus_run = false 78 amrfinderplus_run = false
79 amrfinderplus_db = '/tool-local-data/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest' 79 amrfinderplus_db = '/galaxy/cfsan-centriflaken-db/0/amrfinderplus/3.10.24/latest'
80 amrfinderplus_genes = true 80 amrfinderplus_genes = true
81 abricate_run = true 81 abricate_run = true
82 abricate_datadir = '/tool-local-data/cfsan-centriflaken-db/0/abricate/1.0.1/db' 82 abricate_datadir = '/galaxy/cfsan-centriflaken-db/0/abricate/1.0.1/db'
83 abricate_minid = 90 83 abricate_minid = 90
84 abricate_mincov = 80 84 abricate_mincov = 80
85 abricate_summary_run = true 85 abricate_summary_run = true
86 seqkit_grep_on = false 86 seqkit_grep_on = false
87 fq_filter_by_len = 75 87 fq_filter_by_len = 75