Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/workflows/conf/centriflaken.config @ 0:082e0091e813 draft default tip

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planemo upload
author galaxytrakr
date Fri, 29 May 2026 13:27:47 +0000
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-1:000000000000 0:082e0091e813
1 params {
2 workflow_built_by = 'Kranti.Konganti@fda.hhs.gov'
3 workflow_version = '0.2.2'
4 centrifuge_x = '/server/galaxy/tool-data/centriflaken-dbs/centrifuge/2022-04-12/ab'
5 centrifuge_extract_bug = 'Escherichia coli'
6 centrifuge_save_aligned = false
7 centrifuge_save_unaligned = false
8 centrifuge_out_fmt_sam = false
9 centrifuge_ignore_quals = false
10 kraken2_db = '/server/galaxy/tool-data/centriflaken-dbs/kraken2/standard-210914'
11 kraken2_confidence = '0.0'
12 kraken2_quick = false
13 kraken2_use_mpa_style = false
14 kraken2_minimum_base_quality = '0'
15 kraken2_report_zero_counts = false
16 kraken2_report_minimizer_data = false
17 kraken2_use_names = true
18 kraken2_extract_bug = params.centrifuge_extract_bug
19 flye_pacbio_raw = false
20 flye_pacbio_corr = false
21 flye_pacbio_hifi = false
22 flye_nano_raw = true
23 flye_nano_corr = false
24 flye_nano_hq = false
25 flye_genome_size = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? '5m' : '5.5m')
26 flye_polish_iter = false
27 flye_min_overlap = false
28 flye_scaffold = false
29 flye_meta = true
30 ectyper_run = false
31 ectyper_perc_opid = 90
32 ectyper_perc_hpid = 95
33 ectyper_perc_opcov = 95
34 ectyper_perc_hpcov = 50
35 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
36 serotypefinder_db = '/server/galaxy/tool-data/centriflaken-dbs/serotypefinder/2.0.2'
37 serotypefinder_min_cov = 0.80
38 serotypefinder_min_threshold = 0.85
39 serotypefinder_x = true
40 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
41 seqsero2_t = 4
42 seqsero2_m = 'k'
43 seqsero2_c = false
44 seqsero2_s = false
45 mlst_run = true
46 mlst_minid = 95
47 mlst_mincov = 10
48 mlst_minscore = 50
49 amrfinderplus_run = false
50 amrfinderplus_db = '/server/galaxy/tool-data/centriflaken-dbs/amrfinderplus/3.10.24/latest'
51 amrfinderplus_genes = true
52 abricate_run = true
53 abricate_datadir = '/server/galaxy/tool-data/centriflaken-dbs/abricate/1.0.1/db'
54 abricate_minid = 90
55 abricate_mincov = 80
56 abricate_summary_run = true
57 seqkit_grep_on = false
58 }