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1 params {
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2 workflow_conceived_by = 'Kranti Konganti'
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3 workflow_built_by = 'Kranti Konganti'
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4 workflow_version = '0.2.0'
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5 ref_acc = 'GCF_003516125'
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6 cronology_root_dbdir = '/server/galaxy/tool-data/cronology-db/PDG000000043.213'
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7 upload_microreact = true
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8 microreact_api_key = ("${projectDir}"
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9 + File.separator
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10 + 'assets'
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11 + File.separator
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12 + 'microreact_api.key')
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13 microreact_tree_name = 'cronology_run_tree'
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14 dpubmlstpy_run = true
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15 dpubmlstpy_org = 'cronobacter'
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16 dpubmlstpy_mlsts = 'schemes/1'
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17 dpubmlstpy_profile = false
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18 dpubmlstpy_loci = false
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19 dpubmlstpy_suffix = false
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20 dpubmlstpy_akey = false
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21 dpubmlstpy_id = false
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22 fastp_run = true
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23 fastp_failed_out = false
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24 fastp_merged_out = false
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25 fastp_overlapped_out = false
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26 fastp_6 = false
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27 fastp_reads_to_process = 0
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28 fastp_fix_mgi_id = false
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29 fastp_A = false
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30 fastp_f = 0
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31 fastp_t = 0
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32 fastp_b = 0
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33 fastp_F = 0
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34 fastp_T = 0
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35 fastp_B = 0
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36 fastp_dedup = true
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37 fastp_dup_calc_accuracy = 6
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38 fastp_poly_g_min_len = 10
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39 fastp_G = true
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40 fastp_x = false
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41 fastp_poly_x_min_len = 10
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42 fastp_cut_front = true
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43 fastp_cut_tail = false
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44 fastp_cut_right = true
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45 fastp_W = 20
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46 fastp_M = 30
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47 fastp_q = 30
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48 fastp_u = 40
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49 fastp_n = 5
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50 fastp_e = 0
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51 fastp_l = 35
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52 fastp_max_len = 0
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53 fastp_y = true
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54 fastp_Y = 30
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55 fastp_U = false
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56 fastp_umi_loc = false
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57 fastp_umi_len = false
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58 fastp_umi_prefix = false
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59 fastp_umi_skip = false
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60 fastp_p = true
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61 fastp_P = 20
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62 fastp_use_custom_adapters = false
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63 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
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64 + File.separator
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65 + 'assets'
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66 + File.separator
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67 + 'adaptors.fa' : false)
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68 mashscreen_w = false
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69 mashscreen_i = false
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70 mashscreen_v = false
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71 tuspy_run = true
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72 tuspy_s = false
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73 tuspy_m = false
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74 tuspy_ps = (params.cronology_root_dbdir
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75 + File.separator
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76 + 'index_pdg_metadata'
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77 + File.separator
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78 + 'IDXD_PDG_METAD.pickle')
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79 tuspy_gd = (params.cronology_root_dbdir
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80 + File.separator
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81 + 'scaffold_genomes')
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82 tuspy_gds = '_scaffolded_genomic.fna.gz'
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83 tuspy_n = 5
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84 spades_run = false
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85 spades_isolate = false
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86 spades_sc = false
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87 spades_meta = true
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88 spades_bio = false
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89 spades_corona = false
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90 spades_rna = false
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91 spades_plasmid = false
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92 spades_metaviral = false
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93 spades_metaplasmid = false
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94 spades_rnaviral = false
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95 spades_iontorrent = false
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96 spades_only_assembler = false
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97 spades_careful = false
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98 spades_cov_cutoff = false
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99 spades_k = false
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100 spades_hmm = false
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101 shovill_run = true
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102 shovill_depth = 150
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103 shovill_gsize = false
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104 shovill_minlen = 200
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105 shovill_mincov = 5
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106 shovill_namefmt = false
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107 shovill_keepfiles = false
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108 shovill_assembler = false
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109 shovill_opts = false
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110 shovill_kmers = false
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111 shovill_trim = false
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112 shovill_noreadcorr = false
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113 shovill_nostitch = false
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114 shovill_nocorr = false
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115 polypolish_run = true
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116 polypolish_d = 5
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117 polypolish_i = 0.2
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118 polypolish_m = 10
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119 polypolish_v = 0.5
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120 mashtree_run = true
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121 mashtree_fofn = true
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122 mashtree_trunclength = false
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123 mashtree_mindepth = false
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124 mashtree_kmerlength = false
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125 mashtree_sketchsize = false
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126 mashtree_seed = false
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127 mashtree_genomesize = false
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128 mashtree_sigfigs = false
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129 mashtree_sortorder = false
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130 quast_run = true
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131 quast_min_contig = 200
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132 quast_split_scaffolds = false
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133 quast_euk = false
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134 quast_fungal = false
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135 quast_large = false
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136 quast_k = false
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137 quast_kmer_size = false
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138 quast_circos = true
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139 quast_glimmer = true
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140 quast_gene_thr = '0,300,1500,3000'
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141 quast_rna_finding = true
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142 quast_ref_size = false
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143 quast_ctg_thr = '0,1000,5000,10000,25000,50000'
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144 quast_x_for_nx = 90
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145 quast_use_all_alns = false
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146 quast_min_alignment = 65
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147 quast_min_identity = '95.0'
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148 quast_ambig_usage = 'one'
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149 quast_ambig_score = '0.99'
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150 quast_strict_na = false
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151 quast_x = 1000
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152 quast_local_mis_size = 200
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153 quast_sca_gap_size = 10000
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154 quast_unaln_part_size = 500
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155 quast_skip_unaln_mis_ctgs = false
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156 quast_fragmented = false
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157 quast_frag_max_ident = (params.quast_fragmented ? 200 : false)
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158 quast_plots_format = 'pdf'
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159 prodka_run = true
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160 prodigal_run = (params.prodka_run ?: false)
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161 prodigal_c = false
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162 prodigal_f = 'gbk'
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163 prodigal_g = 11
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164 prodigal_m = true
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165 prodigal_n = false
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166 prodigal_p = 'single'
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167 prodigal_t = true
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168 prokka_run = (params.prodka_run ?: false)
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169 prokka_dbdir = false
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170 prokka_addgenes = true
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171 prokka_addmrna = true
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172 prokka_locustag = false
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173 prokka_increment = false
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174 prokka_gffver = false
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175 prokka_compliant = true
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176 prokka_centre = 'CFSAN-FDA'
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177 prokka_accver = false
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178 prokka_genus = (params.dpubmlstpy_org.capitalize() ?: 'Cronobacter')
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179 prokka_species = false
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180 prokka_strain = false
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181 prokka_plasmid = false
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182 prokka_kingdom = false
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183 prokka_gcode = false
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184 prokka_usegenus = true
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185 prokka_metagenome = false
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186 prokka_rawproduct = false
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187 prokka_cdsrnaolap = false
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188 prokka_evalue = '1e-9'
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189 prokka_coverage = 80
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190 prokka_fast = false
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191 prokka_noanno = false
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192 prokka_mincontiglen = 200
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193 prokka_rfam = false
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194 prokka_norrna = false
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195 prokka_notrna = false
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196 prokka_rnammer = false
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197 pirate_run = false
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198 pirate_steps = false
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199 pirate_features = false
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200 pirate_nucl = false
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201 pirate_pan_opt = "'--diamond'"
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202 pirate_pan_off = false
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203 pirate_min_len = 200
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204 pirate_para_off = false
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205 pirate_para_args = false
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206 pirate_classify_off = false
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207 pirate_align = false
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208 pirate_rplots = false
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209 mashscreen_run = true
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210 mash_sketch = (params.cronology_root_dbdir
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211 + File.separator
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212 + 'mash_paste'
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213 + File.separator
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214 + 'msh.k21.1000h.'
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215 + getPDGRelease(params.cronology_root_dbdir)
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216 + '.msh')
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217 mlst_run = true
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218 mlst_scheme = (params.dpubmlstpy_org ?: 'cronobacter')
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219 mlst_legacy = true
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220 mlst_minid = 95
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221 mlst_mincov = 10
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222 mlst_minscore = 50
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223 mlst_blastdb = false
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224 mlst_datadir = false
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225 mlst_label = true
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226 abricate_run = true
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227 abricate_datadir = ("${projectDir}"
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228 + File.separator
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229 + 'assets'
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230 + File.separator
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231 + 'abricate_dbs')
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232 abricate_minid = 90
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233 abricate_mincov = 80
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234 abricate_summary_run = true
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235 fq_filter_by_len = 0
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236 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
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237 fq2_suffix = '_R2_001.fastq.gz'
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238 }
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239
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240 /*
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241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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242 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
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243 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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244 */
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245
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246 def getPDGRelease(db_path) {
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247 db_path_obj = new File( db_path )
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248 def pdg_release = []
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249
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250 db_path_obj.eachDirRecurse {
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251 it.toString() =~ /PDG/ \
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252 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
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253 : null
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254 }
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255
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256 return pdg_release.unique().join('').toString()
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257 }
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