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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 = '1.0.0'
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5 bcs_root_dbdir = '/server/galaxy/tool-data/bettercallsal-db/PDG000000002.3082'
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6 bcs_db_mode = 'snp'
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7 bcs_db_mode_index = (params.bcs_db_mode ==~ /snp/ ? '_cluster' : '_serotype')
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8 bcs_thresholds = 'strict'
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9 bcs_concat_pe = true
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10 bbmerge_run = (params.bcs_concat_pe ? false : true)
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11 bbmerge_adapters = false
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12 bbmerge_reads = -1
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13 bbmerge_ziplevel = 1
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14 bbmerge_ordered = false
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15 bbmerge_qtrim = true
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16 bbmerge_qtrim2 = false
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17 bbmerge_trimq = 10
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18 bbmerge_minlength = 1
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19 bbmerge_tbo = false
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20 bbmerge_minavgquality = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
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21 bbmerge_trimpolya = true
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22 bbmerge_pfilter = (params.bcs_thresholds ==~ /strict/ ? 1 : false)
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23 bbmerge_ouq = false
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24 bbmerge_owq = true
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25 bbmerge_strict = false
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26 bbmerge_verystrict = false
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27 bbmerge_ultrastrict = (params.bcs_thresholds ==~ /strict/ ? true : false)
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28 bbmerge_maxstrict = false
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29 bbmerge_loose = false
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30 bbmerge_veryloose = false
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31 bbmerge_ultraloose = false
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32 bbmerge_maxloose = false
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33 bbmerge_fast = false
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34 bbmerge_k = 60
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35 bbmerge_prealloc = true
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36 fastp_run = true
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37 fastp_failed_out = false
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38 fastp_merged_out = false
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39 fastp_overlapped_out = false
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40 fastp_6 = false
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41 fastp_reads_to_process = 0
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42 fastp_fix_mgi_id = false
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43 fastp_A = false
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44 fastp_f = 0
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45 fastp_t = 0
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46 fastp_b = 0
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47 fastp_F = 0
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48 fastp_T = 0
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49 fastp_B = 0
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50 fastp_dedup = true
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51 fastp_dup_calc_accuracy = 6
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52 fastp_poly_g_min_len = 10
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53 fastp_G = true
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54 fastp_x = false
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55 fastp_poly_x_min_len = 10
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56 fastp_cut_front = true
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57 fastp_cut_tail = false
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58 fastp_cut_right = true
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59 fastp_W = 20
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60 fastp_M = 30
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61 fastp_q = 30
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62 fastp_u = 40
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63 fastp_n = 5
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64 fastp_e = 0
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65 fastp_l = 35
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66 fastp_max_len = 0
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67 fastp_y = true
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68 fastp_Y = 30
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69 fastp_U = false
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70 fastp_umi_loc = false
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71 fastp_umi_len = false
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72 fastp_umi_prefix = false
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73 fastp_umi_skip = false
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74 fastp_p = true
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75 fastp_P = 20
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76 fastp_use_custom_adapters = false
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77 fastp_adapter_fasta = (params.fastp_use_custom_adapters ? "${projectDir}"
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78 + File.separator
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79 + 'assets'
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80 + File.separator
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81 + 'adaptors.fa' : false)
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82 mashscreen_run = true
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83 mash_sketch = (params.bcs_root_dbdir
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84 + File.separator
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85 + 'mash_sketch'
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86 + File.separator
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87 + 'msh.k21.1000h.'
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88 + params.bcs_db_mode
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89 + '.msh')
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90 mashscreen_w = false
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91 mashscreen_i = false
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92 mashscreen_v = false
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93 tuspy_run = true
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94 tuspy_s = false
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95 tuspy_m = false
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96 tuspy_ps = (params.bcs_root_dbdir
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97 + File.separator
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98 + 'index_metadata'
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99 + File.separator
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100 + 'per_'
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101 + params.bcs_db_mode
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102 + params.bcs_db_mode_index
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103 + '.ACC2SERO.pickle')
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104 tuspy_gd = (params.bcs_root_dbdir
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105 + File.separator
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106 + 'scaffold_genomes')
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107 tuspy_gds = '_scaffolded_genomic.fna.gz'
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108 tuspy_n = 10
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109 tuspy_skip = 'PRJNA766315,PRJNA675435,PRJNA831577,PRJNA855361'
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110 sourmashsketch_run = true
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111 sourmashsketch_mode = 'dna'
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112 sourmashsketch_file = false
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113 sourmashsketch_f = false
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114 sourmashsketch_merge = false
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115 sourmashsketch_name = false
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116 sourmashsketch_p = 'abund,scaled=1000,k=51,k=61,k=71'
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117 sourmashsketch_singleton = true
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118 sourmashsketch_randomize = false
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119 sourmashgather_run = (params.sourmashsketch_run ?: false)
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120 sourmashgather_n = false
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121 sourmashgather_thr_bp = false
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122 sourmashgather_ignoreabn = false
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123 sourmashgather_prefetch = false
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124 sourmashgather_noprefetch = false
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125 sourmashgather_ani_ci = true
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126 sourmashgather_k = 71
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127 sourmashgather_protein = false
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128 sourmashgather_noprotein = false
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129 sourmashgather_dayhoff = false
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130 sourmashgather_nodayhoff = false
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131 sourmashgather_hp = false
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132 sourmashgather_nohp = false
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133 sourmashgather_dna = true
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134 sourmashgather_nodna = false
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135 sourmashgather_scaled = false
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136 sourmashgather_inc_pat = false
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137 sourmashgather_exc_pat = false
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138 sourmashsearch_run = (params.sourmashsketch_run && !params.sourmashgather_run ?: false)
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139 sourmashsearch_n = false
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140 sourmashsearch_thr = '0'
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141 sourmashsearch_contain = false
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142 sourmashsearch_maxcontain = true
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143 sourmashsearch_ignoreabn = true
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144 sourmashsearch_ani_ci = false
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145 sourmashsearch_k = 71
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146 sourmashsearch_protein = false
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147 sourmashsearch_noprotein = false
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148 sourmashsearch_dayhoff = false
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149 sourmashsearch_nodayhoff = false
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150 sourmashsearch_hp = false
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151 sourmashsearch_nohp = false
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152 sourmashsearch_dna = true
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153 sourmashsearch_nodna = false
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154 sourmashsearch_scaled = false
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155 sourmashsearch_inc_pat = false
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156 sourmashsearch_exc_pat = false
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157 sfhpy_run = true
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158 sfhpy_fcn = (params.sourmashsearch_run ? 'similarity' : 'f_match')
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159 sfhpy_fcv = (params.sourmashsearch_run ? 0.9 : 0.1)
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160 sfhpy_gt = true
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161 sfhpy_lt = false
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162 kmaindex_run = true
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163 kmaindex_t_db = false
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164 kmaindex_k = 31
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165 kmaindex_m = false
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166 kmaindex_hc = false
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167 kmaindex_ML = false
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168 kmaindex_ME = false
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169 kmaindex_Sparse = false
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170 kmaindex_ht = false
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171 kmaindex_hq = false
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172 kmaindex_and = false
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173 kmaindex_nbp = false
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174 kmaalign_run = true
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175 kmaalign_ignorequals = false
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176 kmaalign_int = false
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177 kmaalign_ef = false
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178 kmaalign_vcf = false
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179 kmaalign_sam = false
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180 kmaalign_nc = true
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181 kmaalign_na = true
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182 kmaalign_nf = false
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183 kmaalign_a = false
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184 kmaalign_and = true
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185 kmaalign_oa = false
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186 kmaalign_bc = false
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187 kmaalign_bcNano = false
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188 kmaalign_bcd = false
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189 kmaalign_bcg = false
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190 kmaalign_ID = (params.bcs_thresholds ==~ /strict/ ? 10.0 : 5.0)
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191 kmaalign_md = false
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192 kmaalign_dense = false
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193 kmaalign_ref_fsa = false
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194 kmaalign_Mt1 = false
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195 kmaalign_1t1 = false
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196 kmaalign_mrs = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
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197 kmaalign_mrc = (params.bcs_thresholds ==~ /strict/ ? 0.99 : 0.90)
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198 kmaalign_mp = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
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199 kmaalign_eq = (params.bcs_thresholds ==~ /strict/ ? 30 : 20)
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200 kmaalign_mp = (params.kmaalign_ignorequals ? 0 : params.kmaalign_mp)
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201 kmaalign_eq = (params.kmaalign_ignorequals ? 0 : params.kmaalign_eq)
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202 kmaalign_mq = false
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203 kmaalign_5p = false
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204 kmaalign_3p = false
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205 kmaalign_apm = false
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206 kmaalign_cge = false
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207 kmaalign_mrs = (params.sourmashgather_run ? false : params.kmaalign_mrs)
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208 kmaalign_and = (params.sourmashgather_run ? false : true)
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209 kmaalign_ID = (params.sourmashgather_run ? false : params.kmaalign_ID)
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210 megahit_run = true
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211 megahit_min_count = false
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212 megahit_k_list = false
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213 megahit_no_mercy = false
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214 megahit_bubble_level = false
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215 megahit_merge_level = false
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216 megahit_prune_level = false
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217 megahit_prune_depth = false
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218 megahit_low_local_ratio = false
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219 megahit_max_tip_len = false
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220 megahit_no_local = false
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221 megahit_kmin_1pass = false
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222 megahit_preset = 'meta-sensitive'
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223 megahit_mem_flag = 2
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224 megahit_min_contig_len = false
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225 mlst_run = true
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226 mlst_scheme = 'senterica_achtman_2'
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227 mlst_legacy = true
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228 mlst_minid = 95
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229 mlst_mincov = 10
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230 mlst_minscore = 50
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231 abricate_run = true
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232 abricate_datadir = ("${projectDir}"
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233 + File.separator
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234 + 'assets'
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235 + File.separator
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236 + 'abricate_dbs')
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237 abricate_minid = 90
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238 abricate_mincov = 80
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239 abricate_summary_run = true
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240 salmonidx_run = true
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241 salmonidx_k = false
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242 salmonidx_gencode = false
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243 salmonidx_features = false
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244 salmonidx_keepDuplicates = false
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245 salmonidx_keepFixedFasta = false
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246 salmonidx_filterSize = false
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247 salmonidx_sparse = false
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248 salmonidx_n = false
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249 salmonidx_decoys = false
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250 salmonalign_libtype = 'SF'
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251 gsrpy_run = true
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252 gsrpy_url = true
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253 gsrpy_snp_clus_metadata = (params.bcs_root_dbdir
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254 + File.separator
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255 + 'download_pdg_metadata'
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256 + File.separator
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257 + getPDGRelease(params.bcs_root_dbdir)
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258 + File.separator
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259 + getPDGRelease(params.bcs_root_dbdir)
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260 + '.reference_target.cluster_list.tsv')
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261 sourmashcompare_mode = 'ani,containment'
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262 fq_filter_by_len = 0
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263 fq_suffix = (params.fq_single_end ? '.fastq.gz' : '_R1_001.fastq.gz')
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264 fq2_suffix = '_R2_001.fastq.gz'
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265 multiqc_run = true
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266 }
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267
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268 /*
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269 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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270 METHOD TO GET PDG RELEASE AND SET REST OF THE METADATA FILES
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271 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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272 */
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273
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274 def getPDGRelease(db_path) {
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275 db_path_obj = new File( db_path )
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276 def pdg_release = []
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277
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278 db_path_obj.eachDirRecurse {
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279 it.toString() =~ /PDG/ \
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280 ? pdg_release << it.toString().find(/PDG\d+\.\d+/) \
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281 : null
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282 }
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283
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284 return pdg_release.unique().join('').toString()
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285 }
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