Mercurial > repos > galaxytrakr > hfp_centriflaken_awsbatch

comparison 0.4.2/workflows/conf/centriflaken_hy.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 = '0.4.1'
4 seqkit_rmdup_run = false
5 seqkit_rmdup_n = false
6 seqkit_rmdup_s = true
7 seqkit_rmdup_d = false
8 seqkit_rmdup_D = false
9 seqkit_rmdup_P = false
10 seqkit_rmdup_i = false
11 centrifuge_x = '/server/galaxy/tool-data/centriflaken-dbs/centrifuge/2022-04-12/ab'
12 centrifuge_extract_bug = 'Escherichia coli'
13 centrifuge_save_aligned = false
14 centrifuge_save_unaligned = false
15 centrifuge_out_fmt_sam = false
16 centrifuge_ignore_quals = false
17 kraken2_db = '/server/galaxy/tool-data/centriflaken-dbs/kraken2/standard-210914'
18 kraken2_confidence = '0.0'
19 kraken2_quick = false
20 kraken2_use_mpa_style = false
21 kraken2_minimum_base_quality = '0'
22 kraken2_report_zero_counts = false
23 kraken2_report_minimizer_data = false
24 kraken2_use_names = true
25 kraken2_extract_bug = params.centrifuge_extract_bug
26 megahit_run = true
27 megahit_min_count = false
28 megahit_k_list = false
29 megahit_no_mercy = false
30 megahit_bubble_level = false
31 megahit_merge_level = false
32 megahit_prune_level = false
33 megahit_prune_depth = false
34 megahit_low_local_ratio = false
35 megahit_max_tip_len = false
36 megahit_no_local = false
37 megahit_kmin_1pass = false
38 megahit_preset = 'meta-sensitive'
39 megahit_mem_flag = 2
40 megahit_min_contig_len = false
41 spades_run = false
42 spades_isolate = false
43 spades_sc = false
44 spades_meta = true
45 spades_bio = false
46 spades_corona = false
47 spades_rna = false
48 spades_plasmid = false
49 spades_metaviral = false
50 spades_metaplasmid = false
51 spades_rnaviral = false
52 spades_iontorrent = false
53 spades_only_assembler = false
54 spades_careful = false
55 spades_cov_cutoff = false
56 spades_k = false
57 spades_hmm = false
58 ectyper_run = false
59 ectyper_perc_opid = 90
60 ectyper_perc_hpid = 95
61 ectyper_perc_opcov = 95
62 ectyper_perc_hpcov = 50
63 serotypefinder_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? false : true)
64 serotypefinder_db = '/server/galaxy/tool-data/centriflaken-dbs/serotypefinder/2.0.2'
65 serotypefinder_min_cov = 0.80
66 serotypefinder_min_threshold = 0.85
67 serotypefinder_x = true
68 seqsero2_run = (params.centrifuge_extract_bug ==~ /(?i)Salmonella/ ? true : false)
69 seqsero2_t = 4
70 seqsero2_m = 'k'
71 seqsero2_c = false
72 seqsero2_s = false
73 mlst_run = true
74 mlst_minid = 95
75 mlst_mincov = 10
76 mlst_minscore = 50
77 amrfinderplus_run = false
78 amrfinderplus_db = '/server/galaxy/tool-data/centriflaken-dbs/amrfinderplus/3.10.24/latest'
79 amrfinderplus_genes = true
80 abricate_run = true
81 abricate_datadir = '/server/galaxy/tool-data/centriflaken-dbs/abricate/1.0.1/db'
82 abricate_minid = 90
83 abricate_mincov = 80
84 abricate_summary_run = true
85 seqkit_grep_on = false
86 fq_filter_by_len = 75
87 fq_suffix = '_R1_001.fastq.gz'
88 fq2_suffix = '_R2_001.fastq.gz'
89 }