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1 // Help text for bbmerge within CPIPES.
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2
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3 def bbmergeHelp(params) {
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4
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5 Map tool = [:]
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6 Map toolspecs = [:]
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7 tool.text = [:]
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8 tool.helpparams = [:]
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9
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10 toolspecs = [
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11 'bbmerge_run': [
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12 clihelp: 'Run BBMerge tool. Default: ' +
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13 (params.bbmerge_run ?: false),
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14 cliflag: null,
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15 clivalue: null
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16 ],
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17 'bbmerge_reads': [
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18 clihelp: 'Quit after this many read pairs (-1 means all) ' +
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19 "Default: ${params.bbmerge_reads}",
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20 cliflag: 'reads=',
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21 clivalue: (params.bbmerge_reads ?: '')
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22 ],
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23 'bbmerge_adapters': [
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24 clihelp: 'Absolute UNIX path pointing to the adapters file in ' +
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25 "FASTA format. Default: ${params.bbmerge_adapters}",
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26 cliflag: 'adapters=',
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27 clivalue: (params.bbmerge_adapters ?: '')
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28 ],
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29 'bbmerge_ziplevel': [
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30 clihelp: 'Set to 1 (lowest) through 9 (max) to change compression ' +
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31 "level; lower compression is faster. Default: ${params.bbmerge_ziplevel}",
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32 cliflag: 'ziplevel=',
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33 clivalue: (params.bbmerge_ziplevel ?: '')
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34 ],
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35 'bbmerge_ordered': [
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36 clihelp: 'Output reads in the same order as input. ' +
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37 "Default: ${params.bbmerge_ordered}",
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38 cliflag: 'ordered=',
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39 clivalue: (params.bbmerge_ordered ?: '')
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40 ],
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41 'bbmerge_qtrim': [
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42 clihelp: 'Trim read ends to remove bases with quality below --bbmerge_minq. ' +
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43 'Trims BEFORE merging. Values: t (trim both ends), ' +
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44 'f (neither end), r (right end only), l (left end only). ' +
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45 "Default: ${params.bbmerge_qtrim}",
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46 cliflag: 'qtrim=',
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47 clivalue: (params.bbmerge_qtrim ?: '')
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48 ],
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49 'bbmerge_qtrim2': [
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50 clihelp: 'May be specified instead of --bbmerge_qtrim to perform trimming ' +
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51 'only if merging is unsuccesful. then retry merging. ' +
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52 "Default: ${params.bbmerge_qtrim2}",
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53 cliflag: 'qtrim2=',
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54 clivalue: (params.bbmerge_qtrim2 ?: '')
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55 ],
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56 'bbmerge_trimq': [
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57 clihelp: 'Trim quality threshold. This may be comma-delimited list (ascending) ' +
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58 "to try multiple values. Default: ${params.bbmerge_trimq}",
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59 cliflag: 'trimq=',
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60 clivalue: (params.bbmerge_trimq ?: '')
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61 ],
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62 'bbmerge_minlength': [
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63 clihelp: '(ml) Reads shorter than this after trimming, but before ' +
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64 'merging, will be discarded. Pairs will be discarded only' +
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65 "if both are shorter. Default: ${params.bbmerge_minlength}",
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66 cliflag: 'minlength=',
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67 clivalue: (params.bbmerge_minlength ?: '')
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68 ],
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69 'bbmerge_tbo': [
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70 clihelp: '(trimbyoverlap). Trim overlapping reads to remove right ' +
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71 "most (3') non-overlaping portion instead of joining " +
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72 "Default: ${params.bbmerge_tbo}",
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73 cliflag: 'tbo=',
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74 clivalue: (params.bbmerge_tbo ?: '')
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75 ],
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76 'bbmerge_minavgquality': [
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77 clihelp: '(maq). Reads with average quality below this after trimming will ' +
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78 "not be attempted to merge. Default: ${params.bbmerge_minavgquality}",
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79 cliflag: 'minavgquality=',
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80 clivalue: (params.bbmerge_minavgquality ?: '')
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81 ],
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82 'bbmerge_trimpolya': [
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83 clihelp: 'Trim trailing poly-A tail from adapter output. Only affects ' +
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84 'outadapter. This also trims poly-A followed by poly-G, which ' +
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85 "occurs on NextSeq. Default: ${params.bbmerge_trimpolya}",
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86 cliflag: 'trimpolya=',
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87 clivalue: (params.bbmerge_trimpolya ?: '')
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88 ],
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89 'bbmerge_pfilter': [
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90 clihelp: 'Ban improbable overlaps. Higher is more strict. 0 will ' +
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91 'disable the filter; 1 will allow only perfect overlaps. ' +
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92 "Default: ${params.bbmerge_pfilter}",
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93 cliflag: 'pfilter=',
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94 clivalue: (params.bbmerge_pfilter ?: '')
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95 ],
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96 'bbmerge_ouq': [
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97 clihelp: 'Calculate best overlap using quality values. ' +
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98 "Default: ${params.bbmerge_ouq}",
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99 cliflag: 'ouq',
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100 clivalue: (params.bbmerge_ouq ?: '')
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101 ],
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102 'bbmerge_owq': [
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103 clihelp: 'Calculate best overlap without using quality values. ' +
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104 "Default: ${params.bbmerge_owq}",
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105 cliflag: 'owq=',
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106 clivalue: (params.bbmerge_owq ?: '')
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107 ],
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108 'bbmerge_strict': [
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109 clihelp: 'Decrease false positive rate and merging rate. ' +
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110 "Default: ${params.bbmerge_strict}",
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111 cliflag: 'strict=',
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112 clivalue: (params.bbmerge_strict ?: '')
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113 ],
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114 'bbmerge_verystrict': [
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115 clihelp: 'Greatly decrease false positive rate and merging rate. ' +
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116 "Default: ${params.bbmerge_verystrict}",
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117 cliflag: 'verystrict=',
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118 clivalue: (params.bbmerge_verystrict ?: '')
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119 ],
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120 'bbmerge_ultrastrict': [
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121 clihelp: 'Decrease false positive rate and merging rate even more. ' +
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122 "Default: ${params.bbmerge_ultrastrict}",
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123 cliflag: 'ultrastrict=',
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124 clivalue: (params.bbmerge_ultrastrict ?: '')
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125 ],
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126 'bbmerge_maxstrict': [
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127 clihelp: 'Maxiamally decrease false positive rate and merging rate. ' +
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128 "Default: ${params.bbmerge_maxstrict}",
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129 cliflag: 'maxstrict=',
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130 clivalue: (params.bbmerge_maxstrict ?: '')
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131 ],
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132 'bbmerge_loose': [
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133 clihelp: 'Increase false positive rate and merging rate. ' +
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134 "Default: ${params.bbmerge_loose}",
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135 cliflag: 'loose=',
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136 clivalue: (params.bbmerge_loose ?: '')
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137 ],
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138 'bbmerge_veryloose': [
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139 clihelp: 'Greatly increase false positive rate and merging rate. ' +
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140 "Default: ${params.bbmerge_veryloose}",
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141 cliflag: 'veryloose=',
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142 clivalue: (params.bbmerge_veryloose ?: '')
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143 ],
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144 'bbmerge_ultraloose': [
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145 clihelp: 'Increase false positive rate and merging rate even more. ' +
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146 "Default: ${params.bbmerge_ultraloose}",
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147 cliflag: 'ultraloose=',
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148 clivalue: (params.bbmerge_ultraloose ?: '')
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149 ],
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150 'bbmerge_maxloose': [
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151 clihelp: 'Maximally increase false positive rate and merging rate. ' +
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152 "Default: ${params.bbmerge_maxloose}",
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153 cliflag: 'maxloose=',
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154 clivalue: (params.bbmerge_maxloose ?: '')
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155 ],
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156 'bbmerge_fast': [
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157 clihelp: 'Fastest possible preset. ' +
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158 "Default: ${params.bbmerge_fast}",
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159 cliflag: 'fast=',
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160 clivalue: (params.bbmerge_fast ?: '')
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161 ],
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162 'bbmerge_k': [
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163 clihelp: 'Kmer length. 31 (or less) is fastest and uses the least ' +
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164 'memory, but higher values may be more accurate. ' +
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165 '60 tends to work well for 150bp reads. ' +
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166 "Default: ${params.bbmerge_k}",
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167 cliflag: 'k=',
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168 clivalue: (params.bbmerge_k ?: '')
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169 ],
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170 'bbmerge_prealloc': [
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171 clihelp: 'Pre-allocate memory rather than dynamically growing. ' +
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172 'Faster and more memory-efficient for large datasets. ' +
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173 'A float fraction (0-1) may be specified, default 1. ' +
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174 "Default: ${params.bbmerge_prealloc}",
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175 cliflag: 'prealloc=',
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176 clivalue: (params.bbmerge_prealloc ?: '')
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177 ]
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178 ]
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179
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180 toolspecs.each {
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181 k, v -> tool.text['--' + k] = "${v.clihelp}"
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182 tool.helpparams[k] = [ cliflag: "${v.cliflag}", clivalue: v.clivalue ]
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183 }
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184
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185 return tool
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186 } |
