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