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kkonganti@11
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1 params {
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kkonganti@11
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2 workflow_conceived_by = 'Kranti Konganti'
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kkonganti@11
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3 workflow_built_by = 'Kranti Konganti'
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kkonganti@11
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4 workflow_version = '0.1.0'
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kkonganti@11
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5 pdg_release = 'PDG000000043.204'
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kkonganti@11
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6 pdg_org = 'Cronobacter'
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kkonganti@11
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7 ncbi_asm_suffix = '_genomic.fna.gz'
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kkonganti@11
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8 dpubmlstpy_run = true
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kkonganti@11
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9 dpubmlstpy_org = 'cronobacter'
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kkonganti@11
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10 dpubmlstpy_mlsts = 'schemes/1'
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kkonganti@11
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11 dpubmlstpy_profile = false
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kkonganti@11
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12 dpubmlstpy_loci = false
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kkonganti@11
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13 dpubmlstpy_suffix = false
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kkonganti@11
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14 dpubmlstpy_akey = false
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kkonganti@11
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15 dpubmlstpy_id = false
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kkonganti@11
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16 genomes_chunk = 50
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kkonganti@11
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17 checkm2predict_run = true
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kkonganti@11
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18 checkm2predict_quiet = true
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kkonganti@11
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19 checkm2predict_lowmem = false
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kkonganti@11
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20 checkm2predict_general = false
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kkonganti@11
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21 checkm2predict_specific = false
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kkonganti@11
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22 checkm2predict_allmodels = true
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kkonganti@11
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23 checkm2predict_genes = false
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kkonganti@11
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24 checkm2predict_x = '.fna.gz'
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kkonganti@11
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25 checkm2predict_tmpdir = '"."'
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kkonganti@11
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26 checkm2predict_rminterfiles = false
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kkonganti@11
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27 checkm2predict_ttable = false
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kkonganti@11
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28 checkm2predict_dbg_cos = false
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kkonganti@11
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29 checkm2predict_dbg_vectors = false
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kkonganti@11
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30 checkm2predict_dbpath = ("${projectDir}"
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kkonganti@11
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31 + File.separator
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kkonganti@11
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32 + 'assets'
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kkonganti@11
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33 + File.separator
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kkonganti@11
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34 + 'databases'
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kkonganti@11
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35 + File.separator
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kkonganti@11
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36 + 'checkm2_db'
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kkonganti@11
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37 + File.separator
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kkonganti@11
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38 + 'uniref100.KO.1.dmnd')
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kkonganti@11
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39 guncrun_run = true
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kkonganti@11
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40 guncrun_in_is_fasta = false
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kkonganti@11
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41 guncrun_in_is_fofn = false
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kkonganti@11
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42 guncrun_in_is_dir = false
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kkonganti@11
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43 guncrun_file_suffix = (params.checkm2predict_x ?: '.fna.gz')
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kkonganti@11
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44 guncrun_gene_calls = false
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kkonganti@11
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45 guncrun_temp_dir = '"."'
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kkonganti@11
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46 guncrun_sensitive = true
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kkonganti@11
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47 guncrun_detailed_output = false
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kkonganti@11
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48 guncrun_ctg_tax_output = false
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kkonganti@11
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49 guncrun_use_species_lvl = false
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kkonganti@11
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50 guncrun_min_mapped_genes = 11
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kkonganti@11
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51 guncrun_dbpath = ("${projectDir}"
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kkonganti@11
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52 + File.separator
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kkonganti@11
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53 + 'assets'
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kkonganti@11
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54 + File.separator
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kkonganti@11
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55 + 'databases'
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kkonganti@11
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56 + File.separator
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kkonganti@11
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57 + 'gunc_db'
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kkonganti@11
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58 + File.separator
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kkonganti@11
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59 + 'gunc_db_progenomes2.1.dmnd')
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kkonganti@11
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60 fgq_py_cm2_extract = 'Name'
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kkonganti@11
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61 fgq_py_cm2_fcn = "'Completeness_General,Contamination,Completeness_Specific'"
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kkonganti@11
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62 fgq_py_cm2_fcv = "'97.5,1,99'"
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kkonganti@11
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63 fgq_py_cm2_conds = "'>=,<=,>='"
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kkonganti@11
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64 fgq_py_gunc_extract = 'genome'
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kkonganti@11
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65 fgq_py_gunc_fcn = "'clade_separation_score,contamination_portion'"
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kkonganti@11
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66 fgq_py_gunc_fcv = "'0.45,0.05'"
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kkonganti@11
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67 fgq_py_gunc_conds = "'<=,<='"
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kkonganti@11
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68 mashsketch_run = true
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kkonganti@11
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69 mashsketch_l = false
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kkonganti@11
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70 mashsketch_I = false
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kkonganti@11
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71 mashsketch_C = false
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kkonganti@11
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72 mashsketch_k = 21
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kkonganti@11
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73 mashsketch_s = 1000
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kkonganti@11
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74 mashsketch_i = false
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kkonganti@11
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75 mashsketch_S = false
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kkonganti@11
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76 mashsketch_w = false
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kkonganti@11
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77 mashsketch_r = false
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kkonganti@11
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78 mashsketch_b = false
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kkonganti@11
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79 mashsketch_m = false
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kkonganti@11
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80 mashsketch_c = false
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kkonganti@11
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81 mashsketch_g = false
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kkonganti@11
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82 mashsketch_n = false
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kkonganti@11
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83 mashsketch_a = false
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kkonganti@11
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84 mashsketch_z = false
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kkonganti@11
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85 mashsketch_Z = false
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kkonganti@11
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86 mlst_run = true
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kkonganti@11
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87 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
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kkonganti@11
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88 mlst_legacy = true
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kkonganti@11
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89 mlst_minid = 95
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kkonganti@11
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90 mlst_mincov = 10
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kkonganti@11
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91 mlst_minscore = 50
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kkonganti@11
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92 mlst_blastdb = false
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kkonganti@11
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93 mlst_datadir = false
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kkonganti@11
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94 mlst_label = false
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kkonganti@11
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95 }
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