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